@article {pmid30373756,
year = {2018},
author = {Peck, RF and Graham, SM and Gregory, AM},
title = {Species widely distributed in halophilic Archaea exhibit opsin-mediated inhibition of bacterioruberin biosynthesis.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {},
doi = {10.1128/JB.00576-18},
pmid = {30373756},
issn = {1098-5530},
abstract = {Halophilic Archaea are a distinctive pink color due to a carotenoid pigment called bacterioruberin. To sense or utilize light, many halophilic Archaea also produce rhodopsins, complexes of opsin proteins with a retinal prosthetic group. Both bacterioruberin and retinal are synthesized from isoprenoid precursors with lycopene as the last shared intermediate. We previously described a regulatory mechanism in which Halobacterium salinarum bacterioopsin and Haloarcula vallismortis cruxopsin, respectively, inhibit bacterioruberin synthesis catalyzed by lycopene elongase. In this work, we found that opsins in all three major Halobacteria clades inhibit bacterioruberin synthesis, suggesting that this regulatory mechanism existed in the common Halobacteria ancestor. Halophilic Archaea, generally heterotrophic and aerobic, likely evolved from an autotrophic, anaerobic methanogen ancestor by acquiring many genes from Bacteria via lateral gene transfer. These Bacteria "imports" include genes encoding opsins and lycopene elongases. To determine if opsins from Bacteria inhibit bacterioruberin synthesis, we tested Bacterial opsins and found that an opsin from Curtobacterium, in the Actinobacteria phylum, inhibits bacterioruberin synthesis catalyzed by its own lycopene elongase as well as several Archaeal enzymes. We also determined that the lycopene elongase from Halococcus salifodinae, a species from a family of Halobacteria lacking opsin homologs, retained the capacity to be inhibited by opsins. Together, our results indicate that opsin-mediated inhibition of bacterioruberin biosynthesis is a widely-distributed mechanism found in both Archaea and Bacteria, possibly predating the divergence of the two domains. Further analysis may provide insight into the acquisition and evolution of the genes and their host species.IMPORTANCE All organisms use a variety of mechanisms to allocate limited resources to match their needs in their current environment. We explore how halophilic microbes use a novel mechanism to allow efficient production of rhodopsin, a complex of an opsin proteins and a retinal prosthetic group. We previously demonstrated that Halobacterium salinarum bacterioopsin directs available resources towards retinal by inhibiting synthesis of bacterioruberin, a molecule that shares precursors with retinal. In this work, we show that this mechanism can be carried out by proteins from halophilic Archaea that are not closely related to H. salinarum and in at least one species of Bacteria. Therefore, opsin-mediated inhibition of bacterioruberin synthesis may be a highly-conserved, ancient regulatory mechanism.},
}
@article {pmid30370585,
year = {2018},
author = {Seth-Pasricha, M and Senn, S and Sanman, LE and Bogyo, M and Nanda, V and Bidle, KA and Bidle, KD},
title = {Catalytic linkage between caspase activity and proteostasis in Archaea.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.14456},
pmid = {30370585},
issn = {1462-2920},
abstract = {The model haloarchaeon, Haloferax volcanii possess an extremely high, and highly specific, basal caspase activity in exponentially growing cells that closely resembles caspase-4, is specifically inhibited by the pan-caspase inhibitor, z-VAD-FMK, has no cross-reactivity with other known protease families. Although it is one of the dominant cellular proteolytic activities in exponentially growing H. volcanii cells, the interactive cellular roles remain unknown and the protein(s) responsible for this activity remain elusive. Here, biochemical purification and in situ trapping with caspase targeted covalent inhibitors combined with genome-enabled proteomics, structural analysis, targeted gene knockouts, and treatment with canavanine demonstrated a catalytic linkage between caspase activity and thermosomes, proteasomes, and cdc48b, a cell division protein and proteasomal degradation facilitating ATPase, as part of an 'interactase' of stress-related protein complexes with an established link to the unfolded protein response (UPR). Our findings provide novel cellular and biochemical context for the observed caspase activity in Archaea and add new insight to understanding the role of this activity, implicating their possible role in the establishment of protein stress and ER associated degradation pathways in Eukarya. This article is protected by copyright. All rights reserved.},
}
@article {pmid30357005,
year = {2018},
author = {Harish, A},
title = {What is an archaeon and are the Archaea really unique?.},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e5770},
doi = {10.7717/peerj.5770},
pmid = {30357005},
issn = {2167-8359},
abstract = {The recognition of the group Archaea as a major branch of the tree of life (ToL) prompted a new view of the evolution of biodiversity. The genomic representation of archaeal biodiversity has since significantly increased. In addition, advances in phylogenetic modeling of multi-locus datasets have resolved many recalcitrant branches of the ToL. Despite the technical advances and an expanded taxonomic representation, two important aspects of the origins and evolution of the Archaea remain controversial, even as we celebrate the 40th anniversary of the monumental discovery. These issues concern (i) the uniqueness (monophyly) of the Archaea, and (ii) the evolutionary relationships of the Archaea to the Bacteria and the Eukarya; both of these are relevant to the deep structure of the ToL. To explore the causes for this persistent ambiguity, I examine multiple datasets and different phylogenetic approaches that support contradicting conclusions. I find that the uncertainty is primarily due to a scarcity of information in standard datasets-universal core-genes datasets-to reliably resolve the conflicts. These conflicts can be resolved efficiently by comparing patterns of variation in the distribution of functional genomic signatures, which are less diffused unlike patterns of primary sequence variation. Relatively lower heterogeneity in distribution patterns minimizes uncertainties and supports statistically robust phylogenetic inferences, especially of the earliest divergences of life. This case study further highlights the limitations of primary sequence data in resolving difficult phylogenetic problems, and raises questions about evolutionary inferences drawn from the analyses of sequence alignments of a small set of core genes. In particular, the findings of this study corroborate the growing consensus that reversible substitution mutations may not be optimal phylogenetic markers for resolving early divergences in the ToL, nor for determining the polarity of evolutionary transitions across the ToL.},
}
@article {pmid30343425,
year = {2018},
author = {Pornkulwat, P and Kurisu, F and Soonglerdsongpha, S and Banjongproo, P and Srithep, P and Limpiyakorn, T},
title = {Incorporation of 13C-HCO3- by ammonia-oxidizing archaea and bacteria during ammonia oxidation of sludge from a municipal wastewater treatment plant.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00253-018-9436-0},
pmid = {30343425},
issn = {1432-0614},
support = {RSA5780036//Thailand Research Fund (TH)/ ; PHD/0103/2558//Thailand Research Fund/ ; },
abstract = {Ammonia-oxidizing archaea (AOA) have recently been proposed as potential players for ammonia removal in wastewater treatment plants (WWTPs). However, there is little evidence directly showing the contribution of AOA to ammonia oxidation in these engineered systems. In this study, DNA-stable isotope probing (DNA-SIP) with labeled 13C-HCO3- was introduced to sludge from a municipal WWTP. Quantitative PCR demonstrated that AOA amoA genes outnumbered AOB amoA genes in this WWTP sludge. AOA amoA gene sequence analysis revealed that AOA present in this WWTP were specific to one subcluster within the group 1.1b Thaumarchaeota. When ammonia was supplied to DNA-SIP incubation, the DNA-SIP profiles demonstrated the incorporation of the 13C into AOA and AOB. However, the 13C was not found to be assimilated into both microorganisms in the incubation without ammonia. Specific primers were designed to target amoA genes of AOA belonging to the subcluster found in this WWTP. Applying the primers to DNA-SIP experiment revealed that AOA of this subcluter most likely utilized inorganic carbon during ammonia oxidation under the studied conditions.},
}
@article {pmid30342933,
year = {2018},
author = {Lemor, M and Kong, Z and Henry, E and Brizard, R and Laurent, S and Bossé, A and Henneke, G},
title = {Differential Activities of DNA Polymerases in Processing Ribonucleotides during DNA Synthesis in Archaea.},
journal = {Journal of molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jmb.2018.10.004},
pmid = {30342933},
issn = {1089-8638},
abstract = {Consistent with the fact that ribonucleotides (rNTPs) are in excess over deoxyribonucleotides (dNTPs) in vivo, recent findings indicate that replicative DNA polymerases (DNA Pols) are able to insert ribonucleotides (rNMPs) during DNA synthesis, raising crucial questions about the fidelity of DNA replication in both Bacteria and Eukarya. Here, we report that the level of rNTPs is 20-fold higher than that of dNTPs in Pyrococcus abyssi cells. Using dNTP and rNTP concentrations present in vivo, we recorded rNMP incorporation in a template-specific manner during in vitro synthesis, with the family-D DNA Pol (PolD) having the highest propensity compared with the family-B DNA Pol and the p41/p46 complex. We also showed that ribonucleotides accumulate at a relatively high frequency in the genome of wild-type Thermococcales cells and this frequency significantly increases upon deletion of RNase HII, the major enzyme responsible for the removal of RNA from DNA. Because ribonucleotides remain in genomic DNA, we then analyzed the effects on polymerization activities by the three DNA Pols. Depending on the identity of the base and the sequence context, all three DNA Pols bypass rNMP-containing DNA templates with variable efficiency and nucleotide (mis)incorporation ability. Unexpectedly, we found that PolD correctly base-paired a single ribonucleotide opposite rNMP-containing DNA templates. An evolutionary scenario is discussed concerning rNMP incorporation into DNA and genome stability.},
}
@article {pmid30327333,
year = {2018},
author = {Huang, L and Ashraf, S and Lilley, DMJ},
title = {The role of RNA structure in translational regulation by L7Ae protein in archaea.},
journal = {RNA (New York, N.Y.)},
volume = {},
number = {},
pages = {},
doi = {10.1261/rna.068510.118},
pmid = {30327333},
issn = {1469-9001},
abstract = {A recent study has shown that archaeal L7Ae binds to a putative k-turn structure in the 5'-leader of the mRNA of its structural gene to regulate translation. To function as a regulator the RNA should be unstructured in the absence of protein, but it should adopt a k-turn-containing stem-loop on binding L7Ae. Sequence analysis of UTR sequences indicates that their k-turn elements will be unable to fold in the absence of L7Ae, and we have demonstrated this experimentally in solution using FRET for the Archeoglobus fulgidus sequence. We have solved the X-ray crystal structure of the complex of the A. fulgidus RNA bound to its cognate L7Ae protein. The RNA adopts a standard k-turn conformation, that is specifically recognized by the L7Ae protein so stabilizing the stem-loop. In-line probing of the natural-sequence UTR shows that the RNA is unstructured in the absence of L7Ae binding, but folds on binding the protein such that the ribosome binding site is occluded. Thus L7Ae regulates its own translation by switching the conformation of the RNA to alter accessibility.},
}
@article {pmid30323263,
year = {2018},
author = {Rinke, C and Rubino, F and Messer, LF and Youssef, N and Parks, DH and Chuvochina, M and Brown, M and Jeffries, T and Tyson, GW and Seymour, JR and Hugenholtz, P},
title = {A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.).},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41396-018-0282-y},
pmid = {30323263},
issn = {1751-7370},
support = {FT170100213//Australian Research Council (ARC)/ ; FL150100038//Australian Research Council (ARC)/ ; FL150100038//Australian Research Council (ARC)/ ; },
abstract = {Marine Group II (MGII) archaea represent the most abundant planktonic archaeal group in ocean surface waters, but our understanding of the group has been limited by a lack of cultured representatives and few sequenced genomes. Here, we conducted a comparative phylogenomic analysis of 270 recently available MGII metagenome-assembled genomes (MAGs) to investigate their evolution and ecology. Based on a rank-normalised genome phylogeny, we propose that MGII is an order-level lineage for which we propose the name Candidatus Poseidoniales (after Gr. n. Poseidon, God of the sea), comprising the families Candidatus Poseidonaceae fam. nov. (formerly subgroup MGIIa) and Candidatus Thalassarchaeaceae fam. nov. (formerly subgroup MGIIb). Within these families, 21 genera could be resolved, many of which had distinct biogeographic ranges and inferred nutrient preferences. Phylogenetic analyses of key metabolic functions suggest that the ancestor of Ca. Poseidoniales was a surface water-dwelling photoheterotroph that evolved to occupy multiple related ecological niches based primarily on spectral tuning of proteorhodopsin genes. Interestingly, this adaptation appears to involve an overwrite mechanism whereby an existing single copy of the proteorhodopsin gene is replaced by a horizontally transferred copy, which in many instances should allow an abrupt change in light absorption capacity. Phototrophy was lost entirely from five Ca. Poseidoniales genera coinciding with their adaptation to deeper aphotic waters. We also report the first instances of nitrate reductase in two genera acquired via horizontal gene transfer (HGT), which was a potential adaptation to oxygen limitation. Additional metabolic traits differentiating families and genera include flagellar-based adhesion, transporters, and sugar, amino acid, and peptide degradation. Our results suggest that HGT has shaped the evolution of Ca. Poseidoniales to occupy a variety of ecological niches and to become the most successful archaeal lineage in ocean surface waters.},
}
@article {pmid30302054,
year = {2018},
author = {Yin, Z and Bi, X and Xu, C},
title = {Ammonia-Oxidizing Archaea (AOA) Play with Ammonia-Oxidizing Bacteria (AOB) in Nitrogen Removal from Wastewater.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2018},
number = {},
pages = {8429145},
doi = {10.1155/2018/8429145},
pmid = {30302054},
issn = {1472-3654},
abstract = {An increase in the number of publications in recent years indicates that besides ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA) may play an important role in nitrogen removal from wastewater, gaining wide attention in the wastewater engineering field. This paper reviews the current knowledge on AOA and AOB involved in wastewater treatment systems and summarises the environmental factors affecting AOA and AOB. Current findings reveal that AOA have stronger environmental adaptability compared with AOB under extreme environmental conditions (such as low temperature and low oxygen level). However, there is still little information on the cooperation and competition relationship between AOA and AOB, and other microbes related to nitrogen removal, which needs further exploration. Furthermore, future studies are proposed to develop novel nitrogen removal processes dominated by AOA by parameter optimization.},
}
@article {pmid30294305,
year = {2018},
author = {Genderjahn, S and Alawi, M and Mangelsdorf, K and Horn, F and Wagner, D},
title = {Desiccation- and Saline-Tolerant Bacteria and Archaea in Kalahari Pan Sediments.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2082},
doi = {10.3389/fmicb.2018.02082},
pmid = {30294305},
issn = {1664-302X},
abstract = {More than 41% of the Earth's land area is covered by permanent or seasonally arid dryland ecosystems. Global development and human activity have led to an increase in aridity, resulting in ecosystem degradation and desertification around the world. The objective of the present work was to investigate and compare the microbial community structure and geochemical characteristics of two geographically distinct saline pan sediments in the Kalahari Desert of southern Africa. Our data suggest that these microbial communities have been shaped by geochemical drivers, including water content, salinity, and the supply of organic matter. Using Illumina 16S rRNA gene sequencing, this study provides new insights into the diversity of bacteria and archaea in semi-arid, saline, and low-carbon environments. Many of the observed taxa are halophilic and adapted to water-limiting conditions. The analysis reveals a high relative abundance of halophilic archaea (primarily Halobacteria), and the bacterial diversity is marked by an abundance of Gemmatimonadetes and spore-forming Firmicutes. In the deeper, anoxic layers, candidate division MSBL1, and acetogenic bacteria (Acetothermia) are abundant. Together, the taxonomic information and geochemical data suggest that acetogenesis could be a prevalent form of metabolism in the deep layers of a saline pan.},
}
@article {pmid30291304,
year = {2018},
author = {Du Toit, A},
title = {Profilin(g) Asgard archaea.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41579-018-0100-6},
pmid = {30291304},
issn = {1740-1534},
}
@article {pmid30283132,
year = {2018},
author = {Akıl, C and Robinson, RC},
title = {Genomes of Asgard archaea encode profilins that regulate actin.},
journal = {Nature},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41586-018-0548-6},
pmid = {30283132},
issn = {1476-4687},
abstract = {The origin of the eukaryotic cell is unresolved1,2. Metagenomics sequencing has recently identified several potential eukaryotic gene homologues in Asgard archaea3,4, consistent with the hypothesis that the eukaryotic cell evolved from within the Archaea domain. However, many of these eukaryotic-like sequences are highly divergent and the organisms have yet to be imaged or cultivated, which brings into question the extent to which these archaeal proteins represent functional equivalents of their eukaryotic counterparts. Here we show that Asgard archaea encode functional profilins and thereby establish that this archaeal superphylum has a regulated actin cytoskeleton, one of the hallmarks of the eukaryotic cell5. Loki profilin-1, Loki profilin-2 and Odin profilin adopt the typical profilin fold and are able to interact with rabbit actin-an interaction that involves proteins from species that diverged more than 1.2 billion years ago6. Biochemical experiments reveal that mammalian actin polymerizes in the presence of Asgard profilins; however, Loki, Odin and Heimdall profilins impede pointed-end elongation. These archaeal profilins also retard the spontaneous nucleation of actin filaments, an effect that is reduced in the presence of phospholipids. Asgard profilins do not interact with polyproline motifs and the profilin-polyproline interaction therefore probably evolved later in the Eukarya lineage. These results suggest that Asgard archaea possess a primordial, polar, profilin-regulated actin system, which may be localized to membranes owing to the sensitivity of Asgard profilins to phospholipids. Because Asgard archaea are also predicted to encode potential eukaryotic-like genes involved in membrane-trafficking and endocytosis3,4, imaging is now necessary to elucidate whether these organisms are capable of generating eukaryotic-like membrane dynamics that are regulated by actin, such as are observed in eukaryotic cell movement, podosomes and endocytosis.},
}
@article {pmid30283097,
year = {2018},
author = {Ramezani, A and Nolin, TD and Barrows, IR and Serrano, MG and Buck, GA and Regunathan-Shenk, R and West, RE and Latham, PS and Amdur, R and Raj, DS},
title = {Gut Colonization with Methanogenic Archaea Lowers Plasma Trimethylamine N-oxide Concentrations in Apolipoprotein e-/- Mice.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {14752},
doi = {10.1038/s41598-018-33018-5},
pmid = {30283097},
issn = {2045-2322},
abstract = {A mechanistic link between trimethylamine N-oxide (TMAO) and atherogenesis has been reported. TMAO is generated enzymatically in the liver by the oxidation of trimethylamine (TMA), which is produced from dietary choline, carnitine and betaine by gut bacteria. It is known that certain members of methanogenic archaea (MA) could use methylated amines such as trimethylamine as growth substrates in culture. Therefore, we investigated the efficacy of gut colonization with MA on lowering plasma TMAO concentrations. Initially, we screened for the colonization potential and TMAO lowering efficacy of five MA species in C57BL/6 mice fed with high choline/TMA supplemented diet, and found out that all five species could colonize and lover plasma TMAO levels, although with different efficacies. The top performing MA, Methanobrevibacter smithii, Methanosarcina mazei, and Methanomicrococcus blatticola, were transplanted into Apoe-/- mice fed with high choline/TMA supplemented diet. Similar to C57BL/6 mice, following initial provision of the MA, there was progressive attrition of MA within fecal microbial communities post-transplantation during the initial 3 weeks of the study. In general, plasma TMAO concentrations decreased significantly in proportion to the level of MA colonization. In a subsequent experiment, use of antibiotics and repeated transplantation of Apoe-/- mice with M. smithii, led to high engraftment levels during the 9 weeks of the study, resulting in a sustained and significantly lower average plasma TMAO concentrations (18.2 ± 19.6 μM) compared to that in mock-transplanted control mice (120.8 ± 13.0 μM, p < 0.001). Compared to control Apoe-/- mice, M. smithii-colonized mice also had a 44% decrease in aortic plaque area (8,570 μm [95% CI 19587-151821] vs. 15,369 μm [95% CI [70058-237321], p = 0.34), and 52% reduction in the fat content in the atherosclerotic plaques (14,283 μm [95% CI 4,957-23,608] vs. 29,870 μm [95% CI 18,074-41,666], p = 0.10), although these differences did not reach significance. Gut colonization with M. smithii leads to a significant reduction in plasma TMAO levels, with a tendency for attenuation of atherosclerosis burden in Apoe-/- mice. The anti-atherogenic potential of MA should be further tested in adequately powered experiments.},
}
@article {pmid30278423,
year = {2018},
author = {Duan, P and Fan, C and Zhang, Q and Xiong, Z},
title = {Overdose fertilization induced ammonia-oxidizing archaea producing nitrous oxide in intensive vegetable fields.},
journal = {The Science of the total environment},
volume = {650},
number = {Pt 2},
pages = {1787-1794},
doi = {10.1016/j.scitotenv.2018.09.341},
pmid = {30278423},
issn = {1879-1026},
abstract = {Little is known about the effects of nitrogen (N) fertilization rates on ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) and their differential contribution to nitrous oxide (N2O) production, particularly in greenhouse based high N input vegetable soils. Six N treatments (N1, N2, N3, N4, N5 and N6 representing 0, 293, 587, 880, 1173 and 1760 kg N ha-1 yr-1, respectively) were continuously managed for three years in a typically intensified vegetable field in China. The aerobic incubation experiment involving these field-treated soils was designed to evaluate the relative contributions of AOA and AOB to N2O production by using acetylene or 1-octyne as inhibitors. The results showed that the soil pH and net nitrification rate gradually declined with increasing the fertilizer N application rates. The AOA were responsible for 44-71% of the N2O production with negligible N2O from AOB in urea unamended control soils. With urea amendment, the AOA were responsible for 48-53% of the N2O production in the excessively fertilized soils, namely the N5-N6 soils, while the AOB were responsible for 42-55% in the conventionally fertilized soils, namely the N1-N4 soils. Results indicated that overdose fertilization induced higher AOA-dependent N2O production than AOB, whereas urea supply led to higher AOB-dependent N2O production than AOA in conventionally fertilized soils. Additionally, a positive relationship existed between N2O production and NO2- accumulation during the incubation. Further mechanisms for NO2--dependent N2O production in intensive vegetable soils therefore deserve urgent attention.},
}
@article {pmid30258074,
year = {2018},
author = {Cheung, MK and Wong, CK and Chu, KH and Kwan, HS},
title = {Community Structure, Dynamics and Interactions of Bacteria, Archaea and Fungi in Subtropical Coastal Wetland Sediments.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {14397},
doi = {10.1038/s41598-018-32529-5},
pmid = {30258074},
issn = {2045-2322},
abstract = {Bacteria, archaea and fungi play crucial roles in wetland biogeochemical processes. However, little is known about their community structure, dynamics and interactions in subtropical coastal wetlands. Here, we examined communities of the three kingdoms in mangrove and mudflat sediments of a subtropical coastal wetland using Ion Torrent amplicon sequencing and co-occurrence network analysis. Bacterial, archaeal and fungal communities comprised mainly of members from the phyla Proteobacteria and Bacteroidetes, Bathyarchaeota and Euryarchaeota, and Ascomycota, respectively. Species richness and Shannon diversity were highest in bacteria, followed by archaea and were lowest in fungi. Distinct spatiotemporal patterns were observed, with bacterial and fungal communities varying, to different extent, between wet and dry seasons and between mangrove and mudflat, and archaeal community remaining relatively stable between seasons and regions. Redundancy analysis revealed temperature as the major driver of the seasonal patterns of bacterial and fungal communities but also highlighted the importance of interkingdom biotic factors in shaping the community structure of all three kingdoms. Potential ecological interactions and putative keystone taxa were identified based on co-occurrence network analysis. These findings facilitate current understanding of the microbial ecology of subtropical coastal wetlands and provide a basis for better modelling of ecological processes in this important ecosystem.},
}
@article {pmid30254509,
year = {2018},
author = {Krzmarzick, MJ and Taylor, DK and Fu, X and McCutchan, AL},
title = {Diversity and Niche of Archaea in Bioremediation.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2018},
number = {},
pages = {3194108},
doi = {10.1155/2018/3194108},
pmid = {30254509},
issn = {1472-3654},
abstract = {Bioremediation is the use of microorganisms for the degradation or removal of contaminants. Most bioremediation research has focused on processes performed by the domain Bacteria; however, Archaea are known to play important roles in many situations. In extreme conditions, such as halophilic or acidophilic environments, Archaea are well suited for bioremediation. In other conditions, Archaea collaboratively work alongside Bacteria during biodegradation. In this review, the various roles that Archaea have in bioremediation is covered, including halophilic hydrocarbon degradation, acidophilic hydrocarbon degradation, hydrocarbon degradation in nonextreme environments such as soils and oceans, metal remediation, acid mine drainage, and dehalogenation. Research needs are addressed in these areas. Beyond bioremediation, these processes are important for wastewater treatment (particularly industrial wastewater treatment) and help in the understanding of the natural microbial ecology of several Archaea genera.},
}
@article {pmid30254323,
year = {2018},
author = {Lambert, S and Tragin, M and Lozano, JC and Ghiglione, JF and Vaulot, D and Bouget, FY and Galand, PE},
title = {Rhythmicity of coastal marine picoeukaryotes, bacteria and archaea despite irregular environmental perturbations.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41396-018-0281-z},
pmid = {30254323},
issn = {1751-7370},
support = {ANR-14-CE02-0004-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-14-CE02-0018//Agence Nationale de la Recherche (French National Research Agency)/ ; },
abstract = {Seasonality in marine microorganisms has been classically observed in phytoplankton blooms, and more recently studied at the community level in prokaryotes, but rarely investigated at the scale of individual microbial taxa. Here we test if specific marine eukaryotic phytoplankton, bacterial and archaeal taxa display yearly rhythms at a coastal site impacted by irregular environmental perturbations. Our seven-year study in the Bay of Banyuls (North Western Mediterranean Sea) shows that despite some fluctuating environmental conditions, many microbial taxa displayed significant yearly rhythms. The robust rhythmicity was found in both autotrophs (picoeukaryotes and cyanobacteria) and heterotrophic prokaryotes. Sporadic meteorological events and irregular nutrient supplies did, however, trigger the appearance of less common non-rhythmic taxa. Among the environmental parameters that were measured, the main drivers of rhythmicity were temperature and day length. Seasonal autotrophs may thus be setting the pace for rhythmic heterotrophs. Similar environmental niches may be driving seasonality as well. The observed strong association between Micromonas and SAR11, which both need thiamine precursors for growth, could be a first indication that shared nutritional niches may explain some rhythmic patterns of co-occurrence.},
}
@article {pmid30254075,
year = {2018},
author = {Michael, AJ},
title = {Polyamine function in archaea and bacteria.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1074/jbc.TM118.005670},
pmid = {30254075},
issn = {1083-351X},
abstract = {Most of the phylogenetic diversity of life is found in bacteria and archaea, and is reflected in the diverse metabolism and functions of bacterial and archaeal polyamines. The polyamine spermidine was probably present in the last universal common ancestor, and polyamines are known to be necessary for critical physiological functions in bacteria, such as growth, biofilm formation, and other surface behaviors, and production of natural products such as siderophores. There is also phylogenetic diversity of function, indicated by the role of polyamines in planktonic growth of different species ranging from absolutely essential to entirely dispensable. However, the cellular molecular mechanisms responsible for polyamine function in bacterial growth are almost entirely unknown. In contrast, the molecular mechanisms of essential polyamine functions in archaea are better understood: covalent modification by polyamines of translation factor aIF5A, and the agmatine modification of tRNAIle. As with bacterial hyperthermophiles, archaeal thermophiles require long chain and branched polyamines for growth at high temperatures. For bacterial species in which polyamines are essential for growth, it is still unknown whether the molecular mechanisms underpinning polyamine function involve covalent or noncovalent interactions. Understanding the cellular molecular mechanisms of polyamine function in bacterial growth and physiology remains one of the great challenges for future polyamine research.},
}
@article {pmid30250155,
year = {2018},
author = {Wolfe, JM and Fournier, GP},
title = {Reply to 'Molecular clocks provide little information to date methanogenic Archaea'.},
journal = {Nature ecology &amp; evolution},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41559-018-0685-1},
pmid = {30250155},
issn = {2397-334X},
}
@article {pmid30250154,
year = {2018},
author = {Roger, AJ and Susko, E},
title = {Molecular clocks provide little information to date methanogenic Archaea.},
journal = {Nature ecology &amp; evolution},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41559-018-0687-z},
pmid = {30250154},
issn = {2397-334X},
}
@article {pmid30245679,
year = {2018},
author = {Zaretsky, M and Roine, E and Eichler, J},
title = {Sialic Acid-Like Sugars in Archaea: Legionaminic Acid Biosynthesis in the Halophile Halorubrum sp. PV6.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2133},
doi = {10.3389/fmicb.2018.02133},
pmid = {30245679},
issn = {1664-302X},
abstract = {N-glycosylation is a post-translational modification that occurs in all three domains. In Archaea, however, N-linked glycans present a degree of compositional diversity not observed in either Eukarya or Bacteria. As such, it is surprising that nonulosonic acids (NulOs), nine-carbon sugars that include sialic acids, pseudaminic acids, and legionaminic acids, are routinely detected as components of protein-linked glycans in Eukarya and Bacteria but not in Archaea. In the following, we report that the N-linked glycan attached to the S-layer glycoprotein of the haloarchaea Halorubrum sp. PV6 includes an N-formylated legionaminic acid. Analysis of the Halorubrum sp. PV6 genome led to the identification of sequences predicted to comprise the legionaminic acid biosynthesis pathway. The transcription of pathway genes was confirmed, as was the co-transcription of several of these genes. In addition, the activities of LegI, which catalyzes the condensation of 2,4-di-N-acetyl-6-deoxymannose and phosphoenolpyruvate to generate legionaminic acid, and LegF, which catalyzes the addition of cytidine monophosphate (CMP) to legionaminic acid, both heterologously expressed in Haloferax volcanii, were demonstrated. Further genome analysis predicts that the genes encoding enzymes of the legionaminic acid biosynthetic pathway are clustered together with sequences seemingly encoding components of the N-glycosylation pathway in this organism. In defining the first example of a legionaminic acid biosynthesis pathway in Archaea, the findings reported here expand our insight into archaeal N-glycosylation, an almost universal post-translational modification in this domain of life.},
}
@article {pmid30241308,
year = {2018},
author = {Maupin-Furlow, JA},
title = {Methionine Sulfoxide Reductases of Archaea.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {7},
number = {10},
pages = {},
doi = {10.3390/antiox7100124},
pmid = {30241308},
issn = {2076-3921},
support = {NSF 1642283//JM-F through the Bilateral NSF/BIO-BBSRC program/ ; DOE DE-FG02-05ER15650//the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences, Physical Biosciences Program/ ; NIH R01 GM57498//National Institutes of Health/ ; },
abstract = {Methionine sulfoxide reductases are found in all domains of life and are important in reversing the oxidative damage of the free and protein forms of methionine, a sulfur containing amino acid particularly sensitive to reactive oxygen species (ROS). Archaea are microbes of a domain of life distinct from bacteria and eukaryotes. Archaea are well known for their ability to withstand harsh environmental conditions that range from habitats of high ROS, such as hypersaline lakes of intense ultraviolet (UV) radiation and desiccation, to hydrothermal vents of low concentrations of dissolved oxygen at high temperature. Recent evidence reveals the methionine sulfoxide reductases of archaea function not only in the reduction of methionine sulfoxide but also in the ubiquitin-like modification of protein targets during oxidative stress, an association that appears evolutionarily conserved in eukaryotes. Here is reviewed methionine sulfoxide reductases and their distribution and function in archaea.},
}
@article {pmid30233557,
year = {2018},
author = {Eger, M and Graz, M and Riede, S and Breves, G},
title = {Application of MootralTM Reduces Methane Production by Altering the Archaea Community in the Rumen Simulation Technique.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2094},
doi = {10.3389/fmicb.2018.02094},
pmid = {30233557},
issn = {1664-302X},
abstract = {The reduction of methane emissions by ruminants is a highly desirable goal to mitigate greenhouse gas emissions. Various feed additives have already been tested for their ability to decrease methane production; however, practical use is often limited due to negative effects on rumen fermentation or high costs. Organosulphur compounds from garlic (Allium sativum) and flavonoids have been identified as promising plant-derived compounds which are able to reduce methane production. Here, we evaluated the effects of a combination of garlic powder and bitter orange (Citrus aurantium) extracts, Mootral, on ruminal methane production, ruminal fermentation and the community of methanogenic Archaea by using the rumen simulation technique as ex vivo model. The experiment consisted of an equilibration period of 7 days, an experimental period of 8 days and a withdrawal period of 4 days. During the experimental period three fermenters each were either treated as controls (CON), received a low dose of Mootral (LD), a high dose of Mootral (HD), or monensin (MON) as positive control. Application of Mootral strongly reduced the proportion of methane in the fermentation gas and the production rate of methane. Moreover, the experimental mixture induced a dose-dependent increase in the production rate of short chain fatty acids and in the molar proportion of butyrate. Some effects persisted during the withdrawal period. Both, single strand conformation polymorphism and Illumina MiSeq 16S rRNA amplicon sequencing indicated an archaeal community distinct from CON and MON samples in the LD and HD samples. Among archaeal families the percentage of Methanobacteriaceae was reduced during application of both doses of Mootral. Moreover, several significant differences were observed on OTU level among treatment groups and after withdrawal of the additives for LD and HD group. At day 14, 4 OTUs were positively correlated with methane production. In conclusion this mixture of garlic and citrus compounds appears to effectively reduce methane production by alteration of the archaeal community without exhibiting negative side effects on rumen fermentation.},
}
@article {pmid30223159,
year = {2018},
author = {Ren, L and Cai, C and Zhang, J and Yang, Y and Wu, G and Luo, L and Huang, H and Zhou, Y and Qin, P and Yu, M},
title = {Key environmental factors to variation of ammonia-oxidizing archaea community and potential ammonia oxidation rate during agricultural waste composting.},
journal = {Bioresource technology},
volume = {270},
number = {},
pages = {278-285},
doi = {10.1016/j.biortech.2018.09.042},
pmid = {30223159},
issn = {1873-2976},
abstract = {In this research, the abundance and structure of AOA amoA gene during agricultural waste composting were determined by quantitative PCR and sequencing techniques, respectively. Pairwise correlations between potential ammonia oxidation (PAO) rate, physicochemical parameters and the AOA abundance were evaluated using Pearson correlation coefficient. Relationships between these parameters, PAO rates and AOA community structure were evaluated by redundancy analysis. Results showed that 22 AOA gene OTUs were divided into the soil/sediment lineage by phylogenetic analyses. Significant positive correlations were obtained between AOA amoA gene abundance and moisture, ammonium, water soluble carbon (WSC) and organic matter (OM), respectively. Redundancy analysis showed OM, pH and nitrate significantly explained the AOA amoA gene structure. Pearson correlation revealed the PAO rate correlated positively to ammonium, AOA amoA gene abundance. These results indicated that AOA communities sense the fluctuations in surrounding environment, and ultimately react and influence the nitrogen transformation during agricultural waste composting.},
}
@article {pmid30212260,
year = {2018},
author = {Santoro, AE and Richter, RA and Dupont, CL},
title = {Planktonic Marine Archaea.},
journal = {Annual review of marine science},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-marine-121916-063141},
pmid = {30212260},
issn = {1941-0611},
abstract = {Archaea are ubiquitous and abundant members of the marine plankton. Once thought of as rare organisms found in exotic extremes of temperature, pressure, or salinity, archaea are now known in nearly every marine environment. Though frequently referred to collectively, the planktonic archaea actually comprise four major phylogenetic groups, each with its own distinct physiology and ecology. Only one group-the marine Thaumarchaeota-has cultivated representatives, making marine archaea an attractive focus point for the latest developments in cultivation-independent molecular methods. Here, we review the ecology, physiology, and biogeochemical impact of the four archaeal groups using recent insights from cultures and large-scale environmental sequencing studies. We highlight key gaps in our knowledge about the ecological roles of marine archaea in carbon flow and food web interactions. We emphasize the incredible uncultivated diversity within each of the four groups, suggesting there is much more to be done. Expected final online publication date for the Annual Review of Marine Science Volume 11 is January 3, 2019. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.},
}
@article {pmid30207323,
year = {2018},
author = {Patching, SG},
title = {Recent developments in nucleobase cation symporter-1 (NCS1) family transport proteins from bacteria, archaea, fungi and plants.},
journal = {Journal of biosciences},
volume = {43},
number = {4},
pages = {797-815},
pmid = {30207323},
issn = {0973-7138},
abstract = {The nucleobase cation symporter-1 (NCS1) family of secondary active transport proteins comprises over 2500 sequenced members from bacteria, archaea, fungi and plants. NCS1 proteins use a proton or sodium gradient to drive inward cellular transport of purine and pyrimidine nucleobases and nucleosides, hydantoins and related compounds. The structural organization, substrate binding residues and molecular mechanism of NCS1 proteins are defined by crystal structures of sodium-coupled hydantoin transporter, Mhp1. Plant proteins are most closely related to bacterial/archaeal proteins and the distinct Fur-type and Fcy-type fungal proteins and plant proteins originated through independent horizontal transfers from prokaryotes. Analyses of 25 experimentally characterized proteins reveal high substrate specificity in bacterial proteins, distinct non-overlapping specificities in Fur-type and Fcy-type fungal proteins and broad specificity in plant proteins. Possible structural explanations are identified for differences in substrate specificity between bacterial proteins, whilst specificities of other proteins cannot be predicted by simple sequence comparisons. Specificity appears to be species specific and determined by combinations of effects dictated by multiple residues in the major substrate binding site and gating domains. This is an exploratory research review of evolutionary relationships, function and structural organization, molecular mechanism and origins of substrate specificity in NCS1 proteins and avenues of future direction.},
}
@article {pmid30199800,
year = {2018},
author = {Pan, KL and Gao, JF and Fan, XY and Li, DC and Dai, HH},
title = {The more important role of archaea than bacteria in nitrification of wastewater treatment plants in cold season despite their numerical relationships.},
journal = {Water research},
volume = {145},
number = {},
pages = {552-561},
doi = {10.1016/j.watres.2018.08.066},
pmid = {30199800},
issn = {1879-2448},
abstract = {Nitrification failure of wastewater treatment plants (WWTPs) in cold season calls into investigations of the functional ammonia-oxidizing microorganisms (AOMs). In this study, we report the abundance of ammonia-oxidizing archaea (AOA), bacteria (AOB) and complete ammonia-oxidizing (comammox) Nitrospira in 23 municipal WWTPs in cold season, and explore the correlations between AOMs abundance and their relative contribution to nitrification. The copy numbers of AOA and AOB amoA gene ranged from 2.42 × 107 to 2.47 × 109 and 5.54 × 106 to 3.31 × 109 copies/g sludge, respectively. The abundance of amoA gene of Candidatus Nitrospira inopinata, an important strain of comammox Nitrospira, was stable with averaged abundance of 8.47 × 106 copies/g sludge. DNA-based stable isotope probing (DNA-SIP) assays were conducted with three typical WWTPs in which the abundance of AOA was lower than, similar to and higher than that of AOB, respectively. The results showed that considerable 13C-assimilation by AOA was detected during active nitrification in all WWTPs, whereas just a much lesser extent of 13C-incorporation by AOB and comammox Nitrospira was found in one WWTP. High-throughput sequencing with 13C-labeled DNA also showed the higher reads abundance of AOA than AOB and comammox Nitrospira. Nitrososphaera viennensis was the dominant active AOA, while Nitrosomonas oligotropha and Nitrosomonas europaea were identified as active AOB. The results obtained suggest that AOA, rather than AOB and comammox Nitrospira, dominate ammonia oxidation in WWTPs in cold season despite the numerical relationships of AOMs.},
}
@article {pmid30194429,
year = {2018},
author = {Beulig, F and Røy, H and McGlynn, SE and Jørgensen, BB},
title = {Cryptic CH4 cycling in the sulfate-methane transition of marine sediments apparently mediated by ANME-1 archaea.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41396-018-0273-z},
pmid = {30194429},
issn = {1751-7370},
support = {DNRF104//Danmarks Grundforskningsfond (Danish National Research Foundation)/ ; Advanced Grant 294200//EC | European Research Council (ERC)/ ; DFF - 7014-00196//Det Frie Forskningsråd (Danish Council for Independent Research)/ ; },
abstract = {Methane in the seabed is mostly oxidized to CO2 with sulfate as the oxidant before it reaches the overlying water column. This microbial oxidation takes place within the sulfate-methane transition (SMT), a sediment horizon where the downward diffusive flux of sulfate encounters an upward flux of methane. Across multiple sites in the Baltic Sea, we identified a systematic discrepancy between the opposing fluxes, such that more sulfate was consumed than expected from the 1:1 stoichiometry of methane oxidation with sulfate. The flux discrepancy was consistent with an oxidation of buried organic matter within the SMT, as corroborated by stable carbon isotope budgets. Detailed radiotracer experiments showed that up to 60% of the organic matter oxidation within the SMT first produced methane, which was concurrently oxidized to CO2 by sulfate reduction. This previously unrecognized &quot;cryptic&quot; methane cycling in the SMT is not discernible from geochemical profiles due to overall net methane consumption. Sedimentary gene pools suggested that nearly all potential methanogens within and beneath the SMT belonged to ANME-1 archaea, which are typically associated with anaerobic methane oxidation. Analysis of a metagenome-assembled genome suggests that predominant ANME-1 do indeed have the enzymatic potential to catalyze both methane production and consumption.},
}
@article {pmid30186275,
year = {2018},
author = {Ghuneim, LJ and Jones, DL and Golyshin, PN and Golyshina, OV},
title = {Nano-Sized and Filterable Bacteria and Archaea: Biodiversity and Function.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {1971},
doi = {10.3389/fmicb.2018.01971},
pmid = {30186275},
issn = {1664-302X},
abstract = {Nano-sized and filterable microorganisms are thought to represent the smallest living organisms on earth and are characterized by their small size (50-400 nm) and their ability to physically pass through <0.45 μm pore size filters. They appear to be ubiquitous in the biosphere and are present at high abundance across a diverse range of habitats including oceans, rivers, soils, and subterranean bedrock. Small-sized organisms are detected by culture-independent and culture-dependent approaches, with most remaining uncultured and uncharacterized at both metabolic and taxonomic levels. Consequently, their significance in ecological roles remain largely unknown. Successful isolation, however, has been achieved for some species (e.g., Nanoarchaeum equitans and &quot;Candidatus Pelagibacter ubique&quot;). In many instances, small-sized organisms exhibit a significant genome reduction and loss of essential metabolic pathways required for a free-living lifestyle, making their survival reliant on other microbial community members. In these cases, the nano-sized prokaryotes can only be co-cultured with their 'hosts.' This paper analyses the recent data on small-sized microorganisms in the context of their taxonomic diversity and potential functions in the environment.},
}
@article {pmid30175688,
year = {2018},
author = {Ten-Caten, F and Vêncio, RZN and Lorenzetti, APR and Zaramela, LS and Santana, AC and Koide, T},
title = {Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea.},
journal = {RNA biology},
volume = {},
number = {},
pages = {},
doi = {10.1080/15476286.2018.1509661},
pmid = {30175688},
issn = {1555-8584},
abstract = {Prokaryotic genomes show a high level of information compaction often with different molecules transcribed from the same locus. Although antisense RNAs have been relatively well studied, RNAs in the same strand, internal RNAs (intraRNAs), are still poorly understood. The question of how common is the translation of overlapping reading frames remains open. We address this question in the model archaeon Halobacterium salinarum. In the present work we used differential RNA-seq (dRNA-seq) in H. salinarum NRC-1 to locate intraRNA signals in subsets of internal transcription start sites (iTSS) and establish the open reading frames associated to them (intraORFs). Using C-terminally flagged proteins, we experimentally observed isoforms accurately predicted by intraRNA translation for kef1, acs3 and orc4 genes. We also recovered from the literature and mass spectrometry databases several instances of protein isoforms consistent with intraRNA translation such as the gas visicle protein gene gvpC1. We found evidence for intraRNAs in horizontally transferred genes such as the chaperone dnaK and the aerobic respiration related cydA in both H. salinarum and Escherichia coli. Also, intraRNA translation evidence in H. salinarum, E. coli and yeast of a universal elongation factor (aEF-2, fusA and eEF-2) suggests that this is an ancient phenomenon present in all domains of life.},
}
@article {pmid30172418,
year = {2018},
author = {Liu, Y and Liu, J and Yao, P and Ge, T and Qiao, Y and Zhao, M and Zhang, XH},
title = {Distribution patterns of ammonia-oxidizing archaea and bacteria in sediments of the eastern China marginal seas.},
journal = {Systematic and applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.syapm.2018.08.008},
pmid = {30172418},
issn = {1618-0984},
abstract = {Ammonia-oxidizing archaea (AOA) and bacteria (AOB) vary in their contribution to nitrification in different environments. The eastern China marginal seas (ECMS) are featured by complex river runoffs and ocean currents, forming different sediment patches. Here, via quantitative PCR and clone library analysis of the amoA genes, we showed that AOB were more abundant than AOA in ECMS sediments. The abundance, diversity and richness of AOA, but not AOB, were higher in the East China Sea (ECS) than in the Yellow Sea (YS) and Bohai Sea (BS). Nitrosopumilus (AOA) and Nitrosospira (AOB) were predominant lineages, but their abundances varied significantly between ECS, and BS and YS. This was mainly attributed to salinity and dissolved oxygen of the bottom water. The discovery of a high abundance of Nitrosophaera at estuarine sites suggested strong terrigenous influence exerted on the AOA community. In contrast, variations in ocean conditions played more important roles in structuring the AOB community, which was separated by bottom water dissolved oxygen into two groups: the south YS, and the north YS and BS. This study provides a comprehensive insight into the spatial distribution pattern of ammonia-oxidizing prokaryotes in ECMS sediments, laying a foundation for understanding their relative roles in nitrification.},
}
@article {pmid30160784,
year = {2018},
author = {Borsodi, AK and Anda, D and Makk, J and Krett, G and Dobosy, P and Büki, G and Erőss, A and Mádl-Szőnyi, J},
title = {Biofilm forming bacteria and archaea in thermal karst springs of Gellért Hill discharge area (Hungary).},
journal = {Journal of basic microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1002/jobm.201800138},
pmid = {30160784},
issn = {1521-4028},
abstract = {The Buda Thermal Karst System (BTKS) is an extensive active hypogenic cave system located beneath the residential area of the Hungarian capital. At the river Danube, several thermal springs discharge forming spring caves. To reveal and compare the morphological structure and prokaryotic diversity of reddish-brown biofilms developed on the carbonate rock surfaces of the springs, scanning electron microscopy (SEM), and molecular cloning were applied. Microbial networks formed by filamentous bacteria and other cells with mineral crystals embedded in extracellular polymeric substances were observed in the SEM images. Biofilms were dominated by prokaryotes belonging to phyla Proteobacteria, Chloroflexi and Nitrospirae (Bacteria) and Thaumarchaeota (Archaea) but their abundance showed differences according to the type of the host rock, geographic distance, and different water exchange. In addition, representatives of phyla Acidobacteria, Actinobacteria, Caldithrix, Cyanobacteria, Firmicutes Gemmatimonadetes, and several candidate divisions of Bacteria as well as Crenarchaeota and Euryarchaeota were detected in sample-dependent higher abundance. The results indicate that thermophilic, anaerobic sulfur-, sulfate-, nitrate-, and iron(III)-reducing chemoorganotrophic as well as sulfur-, ammonia-, and nitrite-oxidizing chemolithotrophic prokaryotes can interact in the studied biofilms adapted to the unique and extreme circumstances (e.g., aphotic and nearly anoxic conditions, oligotrophy, and radionuclide accumulation) in the thermal karst springs.},
}
@article {pmid30158917,
year = {2018},
author = {Fournier, GP and Poole, AM},
title = {A Briefly Argued Case That Asgard Archaea Are Part of the Eukaryote Tree.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {1896},
doi = {10.3389/fmicb.2018.01896},
pmid = {30158917},
issn = {1664-302X},
abstract = {The recent discovery of the Lokiarchaeota and other members of the Asgard superphylum suggests that closer analysis of the cell biology and evolution of these groups may help shed light on the origin of the eukaryote cell. Asgard lineages often appear in molecular phylogenies as closely related to eukaryotes, and possess &quot;Eukaryote Signature Proteins&quot; coded by genes previously thought to be unique to eukaryotes. This phylogenetic affinity to eukaryotes has been widely interpreted as indicating that Asgard lineages are &quot;eukaryote-like archaea,&quot; with eukaryotes evolving from within a paraphyletic Archaea. Guided by the established principles of systematics, we examine the potential implications of the monophyly of Asgard lineages and Eukarya. We show that a helpful parallel case is that of Synapsida, a group that includes modern mammals and their more &quot;reptile-like&quot; ancestors, united by shared derived characters that evolved in their common ancestor. While this group contains extinct members that share many similarities with modern reptiles and their extinct relatives, they are evolutionarily distinct from Sauropsida, the group which includes modern birds, reptiles, and all other amniotes. Similarly, Asgard lineages and eukaryotes are united by shared derived characters to the exclusion of all other groups. Consequently, the Asgard group is not only highly informative for our understanding of eukaryogenesis, but may be better understood as being early diverging members of a broader group including eukaryotes, for which we propose the name &quot;Eukaryomorpha.&quot; Significantly, this means that the relationship between Eukarya and Asgard lineages cannot, on its own, resolve the debate over 2 vs. 3 Domains of life; instead, resolving this debate depends upon identifying the root of Archaea with respect to Bacteria.},
}
@article {pmid30158542,
year = {2018},
author = {Cavazzini, D and Grossi, G and Levati, E and Vallese, F and Montanini, B and Bolchi, A and Zanotti, G and Ottonello, S},
title = {Author Correction: A family of archaea-like carboxylesterases preferentially expressed in the symbiotic phase of the mycorrhizal fungus Tuber melanosporum.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {13173},
doi = {10.1038/s41598-018-29606-0},
pmid = {30158542},
issn = {2045-2322},
abstract = {A correction to this article has been published and is linked from the HTML and the PDF versions of this paper. The error has been fixed in the paper.},
}
@article {pmid30142055,
year = {2018},
author = {Dulmage, KA and Darnell, CL and Vreugdenhil, A and Schmid, AK},
title = {Copy number variation is associated with gene expression change in archaea.},
journal = {Microbial genomics},
volume = {},
number = {},
pages = {},
doi = {10.1099/mgen.0.000210},
pmid = {30142055},
issn = {2057-5858},
abstract = {Genomic instability, although frequently deleterious, is also an important mechanism for microbial adaptation to environmental change. Although widely studied in bacteria, in archaea the effect of genomic instability on organism phenotypes and fitness remains unclear. Here we use DNA segmentation methods to detect and quantify genome-wide copy number variation (CNV) in large compendia of high-throughput datasets in a model archaeal species, Halobacterium salinarum. CNV hotspots were identified throughout the genome. Some hotspots were strongly associated with changes in gene expression, suggesting a mechanism for phenotypic innovation. In contrast, CNV hotspots in other genomic loci left expression unchanged, suggesting buffering of certain phenotypes. The correspondence of CNVs with gene expression was validated with strain- and condition-matched transcriptomics and DNA quantification experiments at specific loci. Significant correlation of CNV hotspot locations with the positions of known insertion sequence (IS) elements suggested a mechanism for generating genomic instability. Given the efficient recombination capabilities in H. salinarum despite stability at the single nucleotide level, these results suggest that genomic plasticity mediated by IS element activity can provide a source of phenotypic innovation in extreme environments.},
}
@article {pmid30137299,
year = {2018},
author = {Pohlschroder, M and Albers, SV},
title = {Editorial: Editorial for thematic issue on Archaea.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuy032},
pmid = {30137299},
issn = {1574-6976},
}
@article {pmid30116037,
year = {2018},
author = {Hoshino, T and Inagaki, F},
title = {Abundance and distribution of Archaea in the subseafloor sedimentary biosphere.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41396-018-0253-3},
pmid = {30116037},
issn = {1751-7370},
abstract = {Subseafloor sedimentary environments harbor a remarkable number of microorganisms that constitute anaerobic and aerobic microbial ecosystems beneath the ocean margins and open-ocean gyres, respectively. Microbial biomass and diversity richness generally decrease with increasing sediment depth and burial time. However, there has been a long-standing debate over the contribution and distribution of Archaea in the subseafloor sedimentary biosphere. Here we show the global quantification of archaeal and bacterial 16S rRNA genes in 221 sediment core samples obtained from diverse oceanographic settings through scientific ocean drilling using microfluidic digital PCR. We estimated that archaeal cells constitute 37.3% of the total microbial cells (40.0% and 12.8% in the ocean margin and open-ocean sites, respectively), corresponding to 1.1 × 1029 cells on Earth. In addition, the relative abundance of archaeal 16S rRNA genes generally decreased with the depth of water in the overlying sedimentary habitat, suggesting that Archaea may be more sensitive to nutrient quality and quantity supplied from the overlying ocean.},
}
@article {pmid30113887,
year = {2018},
author = {Grant, CR and Wan, J and Komeili, A},
title = {Organelle Formation in Bacteria and Archaea.},
journal = {Annual review of cell and developmental biology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-cellbio-100616-060908},
pmid = {30113887},
issn = {1530-8995},
abstract = {Uncovering the mechanisms that underlie the biogenesis and maintenance of eukaryotic organelles is a vibrant and essential area of biological research. In comparison, little attention has been paid to the process of compartmentalization in bacteria and archaea. This lack of attention is in part due to the common misconception that organelles are a unique evolutionary invention of the &quot;complex&quot; eukaryotic cell and are absent from the &quot;primitive&quot; bacterial and archaeal cells. Comparisons across the tree of life are further complicated by the nebulous criteria used to designate subcellular structures as organelles. Here, with the aid of a unified definition of a membrane-bounded organelle, we present some of the recent findings in the study of lipid-bounded organelles in bacteria and archaea. Expected final online publication date for the Annual Review of Cell and Developmental Biology Volume 34 is October 6, 2018. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.},
}
@article {pmid30105504,
year = {2018},
author = {Albright, MBN and Timalsina, B and Martiny, JBH and Dunbar, J},
title = {Comparative Genomics of Nitrogen Cycling Pathways in Bacteria and Archaea.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-018-1239-4},
pmid = {30105504},
issn = {1432-184X},
support = {F260LANL2018//U.S. Department of Energy, Office of Science, Biological and Environmental Research Division/ ; Graduate Student Research (SCGSR) Fellowship//U.S. Department of Energy, Office of Science/ ; },
abstract = {Despite the explosion of metagenomic sequencing data, using -omics data to predict environmental biogeochemistry remains a challenge. One or a few genes (referred to as marker genes) in a metabolic pathway of interest in meta-omic data are typically used to represent the prevalence of a biogeochemical reaction. This approach often fails to demonstrate a consistent relationship between gene abundance and an ecosystem process rate. One reason this may occur is if a marker gene is not a good representative of a complete pathway. Here, we map the presence of 11 nitrogen (N)-cycling pathways in over 6000 complete bacterial and archaeal genomes using the Integrated Microbial Genomes database. Incomplete N-cycling pathways occurred in 39% of surveyed archaeal and bacterial species revealing a weakness in current marker-gene analyses. Furthermore, we found that most organisms have limited ability to utilize inorganic N in multiple oxidation states. This suggests that inter-organism exchange of inorganic N compounds is common, highlighting the importance of both community composition and spatial structure in determining the extent of recycling versus loss in an ecosystem.},
}
@article {pmid30071063,
year = {2018},
author = {Gorlas, A and Jacquemot, P and Guigner, JM and Gill, S and Forterre, P and Guyot, F},
title = {Greigite nanocrystals produced by hyperthermophilic archaea of Thermococcales order.},
journal = {PloS one},
volume = {13},
number = {8},
pages = {e0201549},
doi = {10.1371/journal.pone.0201549},
pmid = {30071063},
issn = {1932-6203},
abstract = {Interactions between hyperthermophilic archaea and minerals occur in hydrothermal deep-sea vents, one of the most extreme environments for life on Earth. These interactions occur in the internal pores and at surfaces of active hydrothermal chimneys. In this study, we show that, at 85°C, Thermococcales, the predominant hyperthermophilic microorganisms inhabiting hot parts of hydrothermal deep-sea vents, produce greigite nanocrystals (Fe3S4) on extracellular polymeric substances, and that an amorphous iron phosphate acts as a precursor phase. Greigite, although a minor component of chimneys, is a recognized catalyst for CO2 reduction thus implying that Thermococcales may influence the balance of CO2 in hydrothermal ecosystems. We propose that observation of greigite nanocrystals on extracellular polymeric substances could provide a signature of hyperthermophilic life in hydrothermal deep-sea vents.},
}
@article {pmid30062501,
year = {2018},
author = {Karray, F and Ben Abdallah, M and Kallel, N and Hamza, M and Fakhfakh, M and Sayadi, S},
title = {Extracellular hydrolytic enzymes produced by halophilic bacteria and archaea isolated from hypersaline lake.},
journal = {Molecular biology reports},
volume = {},
number = {},
pages = {},
doi = {10.1007/s11033-018-4286-5},
pmid = {30062501},
issn = {1573-4978},
abstract = {The screening of bacteria and archaea from Chott El Jerid, a hypersaline lake in the south of Tunisia, led to the isolation of 68 extremely halophilic prokaryotes growing in media with 15-25% of salt. Assessment of 68 partial 16S rRNA analyzed by amplified rDNA restriction analysis (ARDRA) revealed 15 different bacterial and archaeal taxonomic groups. Based on ARDRA results, phenotypic and hydrolytic activity tests, 20 archaeal and 6 bacterial isolates were selected for sequencing. The halophilic isolates were identified as members of the genera: Salicola, Bacillus, Halorubrum, Natrinema and Haloterrigena. Most of these isolates are able to produce hydrolytic enzymes such as amylase, protease, lipase, cellulase, xylanase, pectinase and some of them showed combined activities. Natrinema genus is an excellent candidate for lipase production. These results indicated that the extremely halophilic archaea and bacteria from Chott El Jerid are a potential source of hydrolytic enzymes and may possess commercial value.},
}
@article {pmid30060184,
year = {2018},
author = {Narrowe, AB and Spang, A and Stairs, CW and Caceres, EF and Baker, BJ and Miller, CS and Ettema, TJG},
title = {Complex evolutionary history of translation Elongation Factor 2 and diphthamide biosynthesis in Archaea and parabasalids.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evy154},
pmid = {30060184},
issn = {1759-6653},
abstract = {Diphthamide is a modified histidine residue which is uniquely present in archaeal and eukaryotic elongation factor 2 (EF-2), an essential GTPase responsible for catalyzing the coordinated translocation of tRNA and mRNA through the ribosome. In part due to the role of diphthamide in maintaining translational fidelity, it was previously assumed that diphthamide biosynthesis genes (dph) are conserved across all eukaryotes and archaea. Here, comparative analysis of new and existing genomes reveals that some archaea (i.e., members of the Asgard superphylum, Geoarchaea, and Korarchaeota) and eukaryotes (i.e., parabasalids) lack dph. In addition, while EF-2 was thought to exist as a single copy in archaea, many of these dph-lacking archaeal genomes encode a second EF-2 paralog missing key-residues required for diphthamide modification and for normal translocase function, perhaps suggesting functional divergence linked to loss of diphthamide biosynthesis. Interestingly, some Heimdallarchaeota previously suggested to be most closely related to the eukaryotic ancestor maintain dph genes and a single gene encoding canonical EF-2. Our findings reveal that the ability to produce diphthamide, once thought to be a universal feature in archaea and eukaryotes, has been lost multiple times during evolution, and suggest that anticipated compensatory mechanisms evolved independently.},
}
@article {pmid30054090,
year = {2018},
author = {Ma, M and Du, H and Sun, T and An, S and Yang, G and Wang, D},
title = {Characteristics of archaea and bacteria in rice rhizosphere along a mercury gradient.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.scitotenv.2018.07.175},
pmid = {30054090},
issn = {1879-1026},
abstract = {Several strains of archaea have the ability to methylate or resist mercury (Hg), and the paddy field is regarded to be conducive to Hg methylation. However, our knowledge of Hg-methylating or Hg-resistant archaea in paddy soils is very limited so far. Therefore, the distribution of archaea and bacteria in the rhizosphere (RS) and bulk soil (BS) of the rice growing in Xiushan Hg-mining area of southwest China was investigated. Bacterial and archaeal 16S rRNA gene amplicon sequencing of the rice rhizosphere along the Hg gradient was conducted. THg concentrations in RS were significantly higher than that in BS at site S1 and S2, while MeHg concentrations in RS was always higher than that in BS, except S6. Bacterial species richness estimates were much higher than that in archaea. The bacterial α-diversity in high-Hg sites was significant higher than that in low-Hg sites based on ACE and Shannon indices. At the genus level, Thiobacillus, Xanthomonas, Defluviicoccus and Candidatus Nitrosoarchaeum were significantly more abundant in the rhizosphere of high-Hg sites, which meant that strains in these genera might play important roles in response to Hg stress. Hg-methylating archaea in the paddy field could potentially be affiliated to strains in Methanosarcina, but further evidence need to be found. The results provide reference to understand archaeal rhizosphere community along an Hg gradient paddy soils.},
}
@article {pmid30053578,
year = {2018},
author = {Smith-Moore, CM and Grunden, AM},
title = {Bacteria and archaea as the sources of traits for enhanced plant phenotypes.},
journal = {Biotechnology advances},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.biotechadv.2018.07.007},
pmid = {30053578},
issn = {1873-1899},
abstract = {Rising global demand for food and population increases are driving the need for improved crop productivity over the next 30 years. Plants have inherent metabolic limitations on productivity such as inefficiencies in carbon fixation and sensitivity to environmental conditions. Bacteria and archaea inhabit some of the most inhospitable environments on the planet and possess unique metabolic pathways and genes to cope with these conditions. Microbial genes involved in carbon fixation, abiotic stress tolerance, and nutrient acquisition have been utilized in plants to enhance plant phenotypes by increasing yield, photosynthesis, and abiotic stress tolerance. Transgenic plants expressing bacterial and archaeal genes will be discussed along with emerging strategies and tools to increase plant growth and yield.},
}
@article {pmid30050524,
year = {2018},
author = {Kashyap, S and Sklute, EC and Dyar, MD and Holden, JF},
title = {Reduction and Morphological Transformation of Synthetic Nanophase Iron Oxide Minerals by Hyperthermophilic Archaea.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {1550},
doi = {10.3389/fmicb.2018.01550},
pmid = {30050524},
issn = {1664-302X},
abstract = {Fe(III) (oxyhydr)oxides are electron acceptors for some hyperthermophilic archaea in mildly reducing geothermal environments. However, the kinds of iron oxides that can be used, growth rates, extent of iron reduction, and the morphological changes that occur to minerals are poorly understood. The hyperthermophilic iron-reducing crenarchaea Pyrodictium delaneyi and Pyrobaculum islandicum were grown separately on six different synthetic nanophase Fe(III) (oxyhydr)oxides. For both organisms, growth on ferrihydrite produced the highest growth rates and the largest amounts of Fe(II), although P. delaneyi produced four times more Fe(II) (25 mM) than P. islandicum (6 mM). Both organisms grew on lepidocrocite and akaganéite and produced 2 and 3 mM Fe(II). Modest growth occurred for both organisms on goethite, hematite, and maghemite where ≤1 mM Fe(II) was produced. The diameters of the spherical mineral end-products following P. delaneyi growth increased by 30 nm for ferrihydrite and 50-150 nm for lepidocrocite relative to heated abiotic controls. For akaganéite, spherical particle sizes were the same for P. delaneyi-reacted samples and heated abiotic controls, but the spherical particles were more numerous in the P. delaneyi samples. For P. islandicum, there was no increase in grain size for the mineral end-products following growth on ferrihydrite, lepidocrocite, or akaganéite relative to the heated abiotic controls. High-resolution transmission electron microscopy of lattice fringes and selected-area electron diffraction of the minerals produced by both organisms when grown on ferrihydrite showed that magnetite and/or possibly maghemite were the end-products while the heated abiotic controls only contained ferrihydrite. These results expand the current view of bioavailable Fe(III) (oxyhydr)oxides for reduction by hyperthermophilic archaea when presented as synthetic nanophase minerals. They show that growth and reduction rates are inversely correlated with the iron (oxyhydr)oxide crystallinity and that iron (oxyhydr)oxide mineral transformation takes different forms for these two organisms.},
}
@article {pmid30022612,
year = {2018},
author = {Heal, KR and Qin, W and Amin, SA and Devol, AH and Moffett, JW and Virginia Armbrust, E and Stahl, DA and Ingalls, AE},
title = {Accumulation of NO2 -cobalamin in nutrient-stressed ammonia-oxidizing archaea and in the oxygen deficient zone of the Eastern Tropical North Pacific.},
journal = {Environmental microbiology reports},
volume = {},
number = {},
pages = {},
doi = {10.1111/1758-2229.12664},
pmid = {30022612},
issn = {1758-2229},
abstract = {Cobalamin (vitamin B12) is a precious resource in natural systems that is produced by select prokaryotes and required by a broad range of organisms. In this way, the production of cobalamin reinforces numerous microbial interdependencies. Here we report the accumulation of an unusual form of cobalamin, nitrocobalamin (NO2 -cobalamin), in a marine oxygen deficient zone (ODZ), isolates of ammonia-oxidizing archaea (AOA), and an anaerobic ammonium oxidizing bacteria (anammox) enriched bioreactor. Low oxygen waters were enriched in NO2 -cobalamin, and AOA isolates experiencing ammonia or copper stress produced more NO2 -cobalamin, though there is wide strain-to-strain and batch-to-batch variability. NO2 -cobalamin has no known biochemical role. We hypothesize that AOA and anammox bacteria are a source of marine NO2 -cobalamin in the environment via a reactive nitrogen intermediate. These findings suggest connections between cobalamin forms and nitrogen transformations, physiological stress, and ocean deoxygenation.},
}
@article {pmid30016225,
year = {2018},
author = {Aiewsakun, P and Adriaenssens, EM and Lavigne, R and Kropinski, AM and Simmonds, P},
title = {Evaluation of the genomic diversity of viruses infecting bacteria, archaea and eukaryotes using a common bioinformatic platform: steps towards a unified taxonomy.},
journal = {The Journal of general virology},
volume = {},
number = {},
pages = {},
doi = {10.1099/jgv.0.001110},
pmid = {30016225},
issn = {1465-2099},
abstract = {Genome Relationship Applied to Virus Taxonomy (GRAViTy) is a genetics-based tool that computes sequence relatedness between viruses. Composite generalized Jaccard (CGJ) distances combine measures of homology between encoded viral genes and similarities in genome organizational features (gene orders and orientations). This scoring framework effectively recapitulates the current, largely morphology and phenotypic-based, family-level classification of eukaryotic viruses. Eukaryotic virus families typically formed monophyletic groups with consistent CGJ distance cut-off dividing between and within family divergence ranges. In the current study, a parallel analysis of prokaryotic virus families revealed quite different sequence relationships, particularly those of tailed phage families (Siphoviridae, Myoviridae and Podoviridae), where members of the same family were generally far more divergent and often not detectably homologous to each other. Analysis of the 20 currently classified prokaryotic virus families indeed split them into 70 separate clusters of tailed phages genetically equivalent to family-level assignments of eukaryotic viruses. It further divided several bacterial (Sphaerolipoviridae, Tectiviridae) and archaeal (Lipothrixviridae) families. We also found that the subfamily-level groupings of tailed phages were generally more consistent with the family assignments of eukaryotic viruses, and this supports ongoing reclassifications, including Spounavirinae and Vi1virus taxa as new virus families. The current study applied a common benchmark with which to compare taxonomies of eukaryotic and prokaryotic viruses. The findings support the planned shift away from traditional morphology-based classifications of prokaryotic viruses towards a genome-based taxonomy. They demonstrate the feasibility of a unified taxonomy of viruses into which the vast body of metagenomic viral sequences may be consistently assigned.},
}
@article {pmid30010922,
year = {2018},
author = {van Tran, N and Muller, L and Ross, RL and Lestini, R and Létoquart, J and Ulryck, N and Limbach, PA and de Crécy-Lagard, V and Cianférani, S and Graille, M},
title = {Evolutionary insights into Trm112-methyltransferase holoenzymes involved in translation between archaea and eukaryotes.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gky638},
pmid = {30010922},
issn = {1362-4962},
abstract = {Protein synthesis is a complex and highly coordinated process requiring many different protein factors as well as various types of nucleic acids. All translation machinery components require multiple maturation events to be functional. These include post-transcriptional and post-translational modification steps and methylations are the most frequent among these events. In eukaryotes, Trm112, a small protein (COG2835) conserved in all three domains of life, interacts and activates four methyltransferases (Bud23, Trm9, Trm11 and Mtq2) that target different components of the translation machinery (rRNA, tRNAs, release factors). To clarify the function of Trm112 in archaea, we have characterized functionally and structurally its interaction network using Haloferax volcanii as model system. This led us to unravel that methyltransferases are also privileged Trm112 partners in archaea and that this Trm112 network is much more complex than anticipated from eukaryotic studies. Interestingly, among the identified enzymes, some are functionally orthologous to eukaryotic Trm112 partners, emphasizing again the similarity between eukaryotic and archaeal translation machineries. Other partners display some similarities with bacterial methyltransferases, suggesting that Trm112 is a general partner for methyltransferases in all living organisms.},
}
@article {pmid30003649,
year = {2018},
author = {Aalto, SL and Saarenheimo, J and Mikkonen, A and Rissanen, AJ and Tiirola, M},
title = {Resistant ammonia-oxidizing archaea endure, but adapting ammonia-oxidizing bacteria thrive in boreal lake sediments receiving nutrient-rich effluents.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.14354},
pmid = {30003649},
issn = {1462-2920},
abstract = {Climate change along with anthropogenic activities change biogeochemical conditions in lake ecosystems, modifying the sediment microbial communities. Wastewater effluents introduce nutrients and organic material but also novel microbes to lake ecosystems, simulating forthcoming increases in catchment loadings. In this work, we first used 16s rRNA gene sequencing to study how the overall sediment microbial community responds to wastewater in six boreal lakes. To examine forthcoming changes in the lake biogeochemistry, we focused on the ammonia-oxidizing archaea (AOA) and bacteria (AOB), and examined their functional and compositional community response to wastewater. Although we found the least diverse and least resistant prokaryotic communities from the most wastewater-influenced sediments, the community changed fast towards the natural composition with the diminishing influence of wastewater. Each lake hosted a unique resistant AOA community, while AOB communities were adapting, responding to environmental conditions as well as receiving new members from WWTPs. In general, AOB dominated in numbers in wastewater-influenced sediments, while the ratio between AOA and AOB increased when moving towards pristine conditions. Our results suggest that although future climate-change-driven increases in nutrient loading and microbial migration might significantly disrupt lake sediment microbiomes, they can promote nitrification through adapting and abundant AOB communities. This article is protected by copyright. All rights reserved.},
}
@article {pmid29979671,
year = {2018},
author = {Bowers, RM and Kyrpides, NC and Stepanauskas, R and Harmon-Smith, M and Doud, D and Reddy, TBK and Schulz, F and Jarett, J and Rivers, AR and Eloe-Fadrosh, EA and Tringe, SG and Ivanova, NN and Copeland, A and Clum, A and Becraft, ED and Malmstrom, RR and Birren, B and Podar, M and Bork, P and Weinstock, GM and Garrity, GM and Dodsworth, JA and Yooseph, S and Sutton, G and Glöckner, FO and Gilbert, JA and Nelson, WC and Hallam, SJ and Jungbluth, SP and Ettema, TJG and Tighe, S and Konstantinidis, KT and Liu, WT and Baker, BJ and Rattei, T and Eisen, JA and Hedlund, B and McMahon, KD and Fierer, N and Knight, R and Finn, R and Cochrane, G and Karsch-Mizrachi, I and Tyson, GW and Rinke, C and , and Lapidus, A and Meyer, F and Yilmaz, P and Parks, DH and Eren, AM and Schriml, L and Banfield, JF and Hugenholtz, P and Woyke, T},
title = {Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.},
journal = {Nature biotechnology},
volume = {36},
number = {7},
pages = {660},
doi = {10.1038/nbt0718-660a},
pmid = {29979671},
issn = {1546-1696},
}
@article {pmid29978909,
year = {2018},
author = {Yip, DZ and Veach, AM and Yang, ZK and Cregger, MA and Schadt, CW},
title = {Methanogenic Archaea dominate mature heartwood habitats of Eastern Cottonwood (Populus deltoides).},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.15346},
pmid = {29978909},
issn = {1469-8137},
abstract = {While recent reports demonstrate that the direct emission of methane from living tree trunks may be a significant terrestrial emission source, there has been debate whether tree emissions are due to transport from soils or produced in the wood environment itself. Reports of methanogens from wood of trees were prominent in the literature 40 years ago but have not been revisited with molecular ecology approaches. We examined communities associated with Populus deltoides using rRNA gene sequence analyses and how these vary with tree and wood properties. Our data indicate that wood environments are dominated by anaerobic microbiomes. Methanogens are prominent in heartwood (mean 34% relative abundance) compared to sapwood environments (13%), and dominant operational taxonomic units (OTUs) were classified as the Methanobacterium sp. Members of the Firmicutes phylum comprised 39% of total sequences and were in 42% greater abundance in sapwood over heartwood niches. Tree diameter was the strongest predictor of methanogen abundance, but wood moisture content and pH were also significant predictors of taxon abundance and overall community composition. Unlike microbiomes of the soil, rhizosphere and phyllosphere, wood associated communities are shaped by unique environmental conditions and may be prominent and overlooked sources of methane emissions in temperate forest systems.},
}
@article {pmid29978046,
year = {2018},
author = {Karimi, B and Terrat, S and Dequiedt, S and Saby, NPA and Horrigue, W and Lelièvre, M and Nowak, V and Jolivet, C and Arrouays, D and Wincker, P and Cruaud, C and Bispo, A and Maron, PA and Bouré, NCP and Ranjard, L},
title = {Biogeography of soil bacteria and archaea across France.},
journal = {Science advances},
volume = {4},
number = {7},
pages = {eaat1808},
doi = {10.1126/sciadv.aat1808},
pmid = {29978046},
issn = {2375-2548},
abstract = {Over the last two decades, a considerable effort has been made to decipher the biogeography of soil microbial communities as a whole, from small to broad scales. In contrast, few studies have focused on the taxonomic groups constituting these communities; thus, our knowledge of their ecological attributes and the drivers determining their composition and distribution is limited. We applied a pyrosequencing approach targeting 16S ribosomal RNA (rRNA) genes in soil DNA to a set of 2173 soil samples from France to reach a comprehensive understanding of the spatial distribution of bacteria and archaea and to identify the ecological processes and environmental drivers involved. Taxonomic assignment of the soil 16S rRNA sequences indicated the presence of 32 bacterial phyla or subphyla and 3 archaeal phyla. Twenty of these 35 phyla were cosmopolitan and abundant, with heterogeneous spatial distributions structured in patches ranging from a 43- to 260-km radius. The hierarchy of the main environmental drivers of phyla distribution was soil pH > land management > soil texture > soil nutrients > climate. At a lower taxonomic level, 47 dominant genera belonging to 12 phyla aggregated 62.1% of the sequences. We also showed that the phylum-level distribution can be determined largely by the distribution of the dominant genus or, alternatively, reflect the combined distribution of all of the phylum members. Together, our study demonstrated that soil bacteria and archaea present highly diverse biogeographical patterns on a nationwide scale and that studies based on intensive and systematic sampling on a wide spatial scale provide a promising contribution for elucidating soil biodiversity determinism.},
}
@article {pmid29946801,
year = {2018},
author = {Li, F and Xie, W and Yuan, Q and Luo, H and Li, P and Chen, T and Zhao, X and Wang, Z and Ma, H},
title = {Genome-scale metabolic model analysis indicates low energy production efficiency in marine ammonia-oxidizing archaea.},
journal = {AMB Express},
volume = {8},
number = {1},
pages = {106},
doi = {10.1186/s13568-018-0635-y},
pmid = {29946801},
issn = {2191-0855},
support = {2015CB755704//National Key Basic Research Program of China/ ; 16YFXTsf00460//Major Research Plan of Tianjin/ ; 21390201//National Natural Science Foundation of China/ ; 21621004//National Natural Science Foundation of China/ ; 91428308//National Natural Science Foundation of China/ ; ZDRW-ZS-2016-3//Key Research Program of the Chinese Academy of Sciences/ ; 41306123//National Science Foundation for Young Scholars of China/ ; 2016YFA0601101//the State Key R&amp;D project of China/ ; },
abstract = {Marine ammonia-oxidizing archaea (AOA) play an important role in the global nitrogen cycle by obtaining energy for biomass production from CO2 via oxidation of ammonium. The isolation of Candidatus &quot;Nitrosopumilus maritimus&quot; strain SCM1, which represents the globally distributed AOA in the ocean, provided an opportunity for uncovering the contributions of those AOA to carbon and nitrogen cycles in ocean. Although several ammonia oxidation pathways have been proposed for SCM1, little is known about its ATP production efficiency. Here, based on the published genome of Nitrosopumilus maritimus SCM1, a genome-scale metabolic model named NmrFL413 was reconstructed. Based on the model NmrFL413, the estimated ATP/NH4+ yield (0.149-0.276 ATP/NH4+) is tenfold lower than the calculated theoretical yield of the proposed ammonia oxidation pathways in marine AOA (1.5-1.75 ATP/NH4+), indicating a low energy production efficiency of SCM1. Our model also suggested the minor contribution of marine AOA to carbon cycle comparing with their significant contribution to nitrogen cycle in the ocean.},
}
@article {pmid29945179,
year = {2018},
author = {Straub, CT and Counts, JA and Nguyen, DMN and Wu, CH and Zeldes, BM and Crosby, JR and Conway, JM and Otten, JK and Lipscomb, GL and Schut, GJ and Adams, MWW and Kelly, RM},
title = {Biotechnology of Extremely Thermophilic Archaea.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuy012},
pmid = {29945179},
issn = {1574-6976},
abstract = {Although the extremely thermophilic archaea (Topt ≥ 70°C) may be the most primitive extant forms of life, they have been studied to a limited extent relative to mesophilic microorganisms. Many of these organisms have unique biochemical and physiological characteristics with important biotechnological implications. These include methanogens that generate methane, fermentative anaerobes that produce hydrogen gas with high efficiency, and acidophiles that can mobilize base, precious and strategic metals from mineral ores. Extremely thermophilic archaea also have been a valuable source of thermoactive, thermostable biocatalysts, but their use as cellular systems has been limited because of the general lack of facile genetics tools. This situation has changed recently, however, thereby providing an important avenue for understanding their metabolic and physiological details and also opening up opportunities for metabolic engineering efforts. Along these lines, extreme thermophilic archaea have recently been engineered to produce a variety of alcohols and industrial chemicals, in some cases incorporating CO2 into the final product. There are barriers and challenges to them reaching their full potential as industrial microorganisms but, if these can be overcome, a new dimension for biotechnology will be forthcoming that strategically exploits biology at high temperatures.},
}
@article {pmid29944192,
year = {2018},
author = {Staley, JT and Caetano-Anollés, G},
title = {Archaea-First and the Co-Evolutionary Diversification of Domains of Life.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {},
number = {},
pages = {},
doi = {10.1002/bies.201800036},
pmid = {29944192},
issn = {1521-1878},
abstract = {The origins and evolution of the Archaea, Bacteria, and Eukarya remain controversial. Phylogenomic-wide studies of molecular features that are evolutionarily conserved, such as protein structural domains, suggest Archaea is the first domain of life to diversify from a stem line of descent. This line embodies the last universal common ancestor of cellular life. Here, we propose that ancestors of Euryarchaeota co-evolved with those of Bacteria prior to the diversification of Eukarya. This co-evolutionary scenario is supported by comparative genomic and phylogenomic analyses of the distributions of fold families of domains in the proteomes of free-living organisms, which show horizontal gene recruitments and informational process homologies. It also benefits from the molecular study of cell physiologies responsible for membrane phospholipids, methanogenesis, methane oxidation, cell division, gas vesicles, and the cell wall. Our theory however challenges popular cell fusion and two-domain of life scenarios derived from sequence analysis, demanding phylogenetic reconciliation. Also see the video abstract here: https://youtu.be/9yVWn_Q9faY.},
}
@article {pmid29930548,
year = {2018},
author = {Wu, Y and Wu, P and Wang, B and Shao, ZQ},
title = {Genome-Wide Analysis Reveals Ancestral Lack of Seventeen Different tRNAs and Clade-Specific Loss of tRNA-CNNs in Archaea.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {1245},
doi = {10.3389/fmicb.2018.01245},
pmid = {29930548},
issn = {1664-302X},
abstract = {Transfer RNA (tRNA) is a category of RNAs that specifically decode messenger RNAs (mRNAs) into proteins by recognizing a set of 61 codons commonly adopted by different life domains. The composition and abundance of tRNAs play critical roles in shaping codon usage and pairing bias, which subsequently modulate mRNA translation efficiency and accuracy. Over the past few decades, effort has been concentrated on evaluating the specificity and redundancy of different tRNA families. However, the mechanism and processes underlying tRNA evolution have only rarely been investigated. In this study, by surveying tRNA genes in 167 completely sequenced genomes, we systematically investigated the composition and evolution of tRNAs in Archaea from a phylogenetic perspective. Our data revealed that archaeal genomes are compact in both tRNA types and copy number. Generally, no more than 44 different types of tRNA are present in archaeal genomes to decode the 61 canonical codons, and most of them have only one gene copy per genome. Among them, tRNA-Met was significantly overrepresented, with an average of three copies per genome. In contrast, the tRNA-UAU and 16 tRNAs with A-starting anticodons (tRNA-ANNs) were rarely detected in all archaeal genomes. The conspicuous absence of these tRNAs across the archaeal phylogeny suggests they might have not been evolved in the common ancestor of Archaea, rather than have lost independently from different clades. Furthermore, widespread absence of tRNA-CNNs in the Methanococcales and Methanobacteriales genomes indicates convergent loss of these tRNAs in the two clades. This clade-specific tRNA loss may be attributing to the reductive evolution of their genomes. Our data suggest that the current tRNA profiles in Archaea are contributed not only by the ancestral tRNA composition, but also by differential maintenance and loss of redundant tRNAs.},
}
@article {pmid29916347,
year = {2018},
author = {Höfer, K and Jäschke, A},
title = {Epitranscriptomics: RNA Modifications in Bacteria and Archaea.},
journal = {Microbiology spectrum},
volume = {6},
number = {3},
pages = {},
doi = {10.1128/microbiolspec.RWR-0015-2017},
pmid = {29916347},
issn = {2165-0497},
abstract = {The increasingly complex functionality of RNA is contrasted by its simple chemical composition. RNA is generally built from only four different nucleotides (adenine, guanine, cytosine, and uracil). To date, >160 chemical modifications are known to decorate RNA molecules and thereby alter their function or stability. Many RNA modifications are conserved throughout bacteria, archaea, and eukaryotes, while some are unique to each branch of life. Most known modifications occur at internal positions, while there is limited diversity at the termini. The dynamic nature of RNA modifications and newly discovered regulatory functions of some of these RNA modifications gave birth to a new field, now often referred to as &quot;epitranscriptomics.&quot; This review highlights the major developments in this field and summarizes detection principles for internal as well as 5'-terminal mRNA modifications in prokaryotes and archaea to investigate their biological significance.},
}
@article {pmid29909833,
year = {2018},
author = {Ulrich, EC and Kamat, SS and Hove-Jensen, B and Zechel, DL},
title = {Methylphosphonic Acid Biosynthesis and Catabolism in Pelagic Archaea and Bacteria.},
journal = {Methods in enzymology},
volume = {605},
number = {},
pages = {351-426},
doi = {10.1016/bs.mie.2018.01.039},
pmid = {29909833},
issn = {1557-7988},
abstract = {Inorganic phosphate is essential for all life forms, yet microbes in marine environments are in near constant deprivation of this important nutrient. Organophosphonic acids can serve as an alternative source of inorganic phosphate if microbes possess the appropriate biochemical pathways that allow cleavage of the stable carbon-phosphorus bond that defines this class of molecule. One prominent source of inorganic phosphate is methylphosphonic acid, which is found as a constituent of marine-dissolved organic matter. The cycle of biosynthesis and catabolism of methylphosphonic acid by marine microbes is the likely source of supersaturating levels of methane in shallow ocean waters. This review provides an overview of the rich biochemistry that has evolved to synthesize methylphosphonic acid and catabolize this molecule into Pi and methane, with an emphasis on the reactions catalyzed by methylphosphonic acid synthase MpnS and the carbon-phosphorus lyase system. The protocols and experiments that are described for MpnS and carbon-phosphorus lyase provide a foundation for studying the structures and mechanisms of these and related enzymes.},
}
@article {pmid29905870,
year = {2018},
author = {Rodriguez-R, LM and Gunturu, S and Harvey, WT and Rosselló-Mora, R and Tiedje, JM and Cole, JR and Konstantinidis, KT},
title = {The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level.},
journal = {Nucleic acids research},
volume = {46},
number = {W1},
pages = {W282-W288},
doi = {10.1093/nar/gky467},
pmid = {29905870},
issn = {1362-4962},
abstract = {The small subunit ribosomal RNA gene (16S rRNA) has been successfully used to catalogue and study the diversity of prokaryotic species and communities but it offers limited resolution at the species and finer levels, and cannot represent the whole-genome diversity and fluidity. To overcome these limitations, we introduced the Microbial Genomes Atlas (MiGA), a webserver that allows the classification of an unknown query genomic sequence, complete or partial, against all taxonomically classified taxa with available genome sequences, as well as comparisons to other related genomes including uncultivated ones, based on the genome-aggregate Average Nucleotide and Amino Acid Identity (ANI/AAI) concepts. MiGA integrates best practices in sequence quality trimming and assembly and allows input to be raw reads or assemblies from isolate genomes, single-cell sequences, and metagenome-assembled genomes (MAGs). Further, MiGA can take as input hundreds of closely related genomes of the same or closely related species (a so-called 'Clade Project') to assess their gene content diversity and evolutionary relationships, and calculate important clade properties such as the pangenome and core gene sets. Therefore, MiGA is expected to facilitate a range of genome-based taxonomic and diversity studies, and quality assessment across environmental and clinical settings. MiGA is available at http://microbial-genomes.org/.},
}
@article {pmid29897479,
year = {2018},
author = {Feng, X and Sun, M and Han, W and Liang, YX and She, Q},
title = {A transcriptional factor B paralog functions as an activator to DNA damage-responsive expression in archaea.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gky302},
pmid = {29897479},
issn = {1362-4962},
}
@article {pmid29891388,
year = {2018},
author = {Marshall, A and Phillips, L and Longmore, A and Tang, C and Heidelberg, K and Mele, P},
title = {Primer selection influences abundance estimates of ammonia oxidizing archaea in coastal marine sediments.},
journal = {Marine environmental research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.marenvres.2018.06.001},
pmid = {29891388},
issn = {1879-0291},
abstract = {Quantification of the α-subunit of ammonia monooxygenase (amoA) through PCR is an established technique for estimating the abundance of ammonia oxidizing archaea (AOA) in environmental samples. This study quantified AOA with two established primer sets in 1 cm increments from the sediment surface (0-1 cm) to a depth of 10 cm at two locations within Port Phillip Bay (PPB), Australia. Primer choice had a significant effect on within sample estimates of AOA with copy numbers ranging from 102 to 104 copies per ng DNA. Variation in AOA abundance patterns with increasing sediment depth were site and primer specific. Sequence mismatches between the primer binding region of the isolated amoA sequences from PPB and Nitrosopumilus maritimus SCM1 were identified and may explain the high variation identified between primer estimates. Our results highlight the need for testing multiple primer pairs that target different regions of the AOA amoA sequence prior to large-scale marine sediment environmental studies.},
}
@article {pmid29888297,
year = {2018},
author = {Fu, X and Adams, Z and Maupin-Furlow, JA},
title = {In vitro Analysis of Ubiquitin-like Protein Modification in Archaea.},
journal = {Bio-protocol},
volume = {8},
number = {10},
pages = {},
doi = {10.21769/BioProtoc.2845},
pmid = {29888297},
issn = {2331-8325},
support = {R01 GM057498/GM/NIGMS NIH HHS/United States ; },
abstract = {The ubiquitin-like (Ubl) protein is widely distributed in Archaea and involved in many cellular pathways. A well-established method to reconstitute archaeal Ubl protein conjugation in vitro is important to better understand the process of archaeal Ubl protein modification. This protocol describes the in vitro reconstitution of Ubl protein modification and following analysis of this modification in Haloferax volcanii, a halophilic archaeon serving as the model organism.},
}
@article {pmid29879486,
year = {2018},
author = {McDougall, M and McEleney, K and Francisco, O and Trieu, B and Ogbomo, EK and Tomy, G and Stetefeld, J},
title = {Reductive power of the archaea right-handed coiled coil nanotube (RHCC-NT) and incorporation of mercury clusters inside protein cages.},
journal = {Journal of structural biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jsb.2018.05.013},
pmid = {29879486},
issn = {1095-8657},
abstract = {Coiled coils are well described as powerful oligomerization motifs and exhibit a large diversity of functions, including gene regulation, cell division, membrane fusion and drug extrusion. The archaea S-layer originated right-handed coiled coil -RHCC-NT- is characterized by extreme stability and is free of cysteine and histidine moieties. In the current study, we have followed a multidisciplinary approach to investigate the capacity of RHCC-NT to bind a variety of ionic complex metal ions. At the outside of the RHCC-NT, one mercury ion forms an electrostatic interaction with the S-methyl moiety of the single methionine residue present in each coil. We demonstrate that RHCC-NT is reducing and incorporating metallic mercury in the large-sized interior cavities which are lined up along the tetrameric channel.},
}
@article {pmid29878182,
year = {2018},
author = {Sun, M and Feng, X and Liu, Z and Han, W and Liang, YX and She, Q},
title = {An Orc1/Cdc6 ortholog functions as a key regulator in the DNA damage response in Archaea.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gky487},
pmid = {29878182},
issn = {1362-4962},
abstract = {While bacteria and eukaryotes show distinct mechanisms of DNA damage response (DDR) regulation, investigation of ultraviolet (UV)-responsive expression in a few archaea did not yield any conclusive evidence for an archaeal DDR regulatory network. Nevertheless, expression of Orc1-2, an ortholog of the archaeal origin recognition complex 1/cell division control protein 6 (Orc1/Cdc6) superfamily proteins was strongly activated in Sulfolobus solfataricus and Sulfolobus acidocaldarius upon UV irradiation. Here, a series of experiments were conducted to investigate the possible functions of Orc1-2 in DNA damage repair in Sulfolobus islandicus. Study of DDR in Δorc1-2 revealed that Orc1-2 deficiency abolishes DNA damage-induced differential expression of a large number of genes and the mutant showed hypersensitivity to DNA damage treatment. Reporter gene and DNase I footprinting assays demonstrated that Orc1-2 interacts with a conserved hexanucleotide motif present in several DDR gene promoters and regulates their expression. Manipulation of orc1-2 expression by promoter substitution in this archaeon revealed that a high level of orc1-2 expression is essential but not sufficient to trigger DDR. Together, these results have placed Orc1-2 in the heart of the archaeal DDR regulation, and the resulting Orc1-2-centered regulatory circuit represents the first DDR network identified in Archaea, the third domain of life.},
}
@article {pmid29806626,
year = {2018},
author = {Mihara, T and Koyano, H and Hingamp, P and Grimsley, N and Goto, S and Ogata, H},
title = {Taxon Richness of &quot;Megaviridae&quot; Exceeds those of Bacteria and Archaea in the Ocean.},
journal = {Microbes and environments},
volume = {33},
number = {2},
pages = {162-171},
doi = {10.1264/jsme2.ME17203},
pmid = {29806626},
issn = {1347-4405},
abstract = {Since the discovery of the giant mimivirus, evolutionarily related viruses have been isolated or identified from various environments. Phylogenetic analyses of this group of viruses, tentatively referred to as the family &quot;Megaviridae&quot;, suggest that it has an ancient origin that may predate the emergence of major eukaryotic lineages. Environmental genomics has since revealed that Megaviridae represents one of the most abundant and diverse groups of viruses in the ocean. In the present study, we compared the taxon richness and phylogenetic diversity of Megaviridae, Bacteria, and Archaea using DNA-dependent RNA polymerase as a common marker gene. By leveraging existing microbial metagenomic data, we found higher richness and phylogenetic diversity in this single viral family than in the two prokaryotic domains. We also obtained results showing that the evolutionary rate alone cannot account for the observed high diversity of Megaviridae lineages. These results suggest that the Megaviridae family has a deep co-evolutionary history with diverse marine protists since the early &quot;Big-Bang&quot; radiation of the eukaryotic tree of life.},
}
@article {pmid29797436,
year = {2018},
author = {Ramiro, FS and de Lira, E and Soares, G and Retamal-Valdes, B and Feres, M and Figueiredo, LC and Faveri, M},
title = {Effects of different periodontal treatments in changing the prevalence and levels of Archaea present in the subgingival biofilm of subjects with periodontitis: A secondary analysis from a randomized controlled clinical trial.},
journal = {International journal of dental hygiene},
volume = {},
number = {},
pages = {},
doi = {10.1111/idh.12347},
pmid = {29797436},
issn = {1601-5037},
abstract = {OBJECTIVE: The aim of this randomized double-blind and placebo-controlled study was to assess if periodontal treatment with or without systemic antibiotic would change the mean level of Archaea.<br><br>METHODS: Fifty-nine (59) subjects were randomly assigned to receive scaling and root planing (SRP) alone or combined with metronidazole (MTZ; 400 mg/TID) or either with MTZ and amoxicillin (AMX; 500 mg/TID) for 14 days. Clinical and microbiological examinations were performed at baseline and at 6 months post-SRP. Six subgingival plaque samples per subject were analysed for the presence and levels of Archaea using quantitative polymerase chain reaction.<br><br>RESULTS: Scaling and root planing alone or combined with MTZ or MTZ + AMX significantly reduced the prevalence of subjects colonized by Archaea at 6 months post-therapy, without significant differences among groups (P > .05). Both therapies led to a statistically significant decrease in the mean percentage of sites colonized by Archaea (P < .05). The MTZ and MTZ + AMX group had a significantly lower mean number of sites colonized by Archaea and lower levels of these micro-organisms at sites with probing depth ≥5 mm at 6 months compared with SRP group (P < .05).<br><br>CONCLUSION: Periodontal treatments including adjunctive MTZ or MTZ + AMX are more effective than mechanical treatment alone in reducing the levels and prevalence of sites colonized by Archaea in subjects with chronic periodontitis.},
}
@article {pmid29795539,
year = {2018},
author = {Teske, A},
title = {Aerobic Archaea in iron-rich springs.},
journal = {Nature microbiology},
volume = {3},
number = {6},
pages = {646-647},
doi = {10.1038/s41564-018-0168-9},
pmid = {29795539},
issn = {2058-5276},
}
@article {pmid29789313,
year = {2018},
author = {Pedraza-Pérez, Y and Cuevas-Vede, RA and Canto-Gómez, ÁB and López-Pliego, L and Gutiérrez-Ríos, RM and Hernández-Lucas, I and Rubín-Linares, G and Martínez-Laguna, Y and López-Olguín, JF and Fuentes-Ramírez, LE},
title = {BLAST-XYPlot Viewer: A Tool for Performing BLAST in Whole-Genome Sequenced Bacteria/Archaea and Visualize Whole Results Simultaneously.},
journal = {G3 (Bethesda, Md.)},
volume = {8},
number = {7},
pages = {2167-2172},
doi = {10.1534/g3.118.200220},
pmid = {29789313},
issn = {2160-1836},
abstract = {One of the most commonly used tools to compare protein or DNA sequences against databases is BLAST. We introduce a web tool that allows the performance of BLAST-searches of protein/DNA sequences in whole-genome sequenced bacteria/archaea, and displays a large amount of BLAST-results simultaneously. The circular bacterial replicons are projected as horizontal lines with fixed length of 360, representing the degrees of a circle. A coordinate system is created with length of the replicon along the x-axis and the number of replicon used on the y-axis. When a query sequence matches with a gene/protein of a particular replicon, the BLAST-results are depicted as an &quot;x,y&quot; position in a specially adapted plot. This tool allows the visualization of the results from the whole data to a particular gene/protein in real time with low computational resources.},
}
@article {pmid29788499,
year = {2018},
author = {Nawrocki, EP and Jones, TA and Eddy, SR},
title = {Group I introns are widespread in archaea.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gky414},
pmid = {29788499},
issn = {1362-4962},
abstract = {Group I catalytic introns have been found in bacterial, viral, organellar, and some eukaryotic genomes, but not in archaea. All known archaeal introns are bulge-helix-bulge (BHB) introns, with the exception of a few group II introns. It has been proposed that BHB introns arose from extinct group I intron ancestors, much like eukaryotic spliceosomal introns are thought to have descended from group II introns. However, group I introns have little sequence conservation, making them difficult to detect with standard sequence similarity searches. Taking advantage of recent improvements in a computational homology search method that accounts for both conserved sequence and RNA secondary structure, we have identified 39 group I introns in a wide range of archaeal phyla, including examples of group I introns and BHB introns in the same host gene.},
}
@article {pmid29771354,
year = {2018},
author = {Lui, LM and Uzilov, AV and Bernick, DL and Corredor, A and Lowe, TM and Dennis, PP},
title = {Methylation guide RNA evolution in archaea: structure, function and genomic organization of 110 C/D box sRNA families across six Pyrobaculum species.},
journal = {Nucleic acids research},
volume = {46},
number = {11},
pages = {5678-5691},
doi = {10.1093/nar/gky284},
pmid = {29771354},
issn = {1362-4962},
abstract = {Archaeal homologs of eukaryotic C/D box small nucleolar RNAs (C/D box sRNAs) guide precise 2'-O-methyl modification of ribosomal and transfer RNAs. Although C/D box sRNA genes constitute one of the largest RNA gene families in archaeal thermophiles, most genomes have incomplete sRNA gene annotation because reliable, fully automated detection methods are not available. We expanded and curated a comprehensive gene set across six species of the crenarchaeal genus Pyrobaculum, particularly rich in C/D box sRNA genes. Using high-throughput small RNA sequencing, specialized computational searches and comparative genomics, we analyzed 526 Pyrobaculum C/D box sRNAs, organizing them into 110 families based on synteny and conservation of guide sequences which determine methylation targets. We examined gene duplications and rearrangements, including one family that has expanded in a pattern similar to retrotransposed repetitive elements in eukaryotes. New training data and inclusion of kink-turn secondary structural features enabled creation of an improved search model. Our analyses provide the most comprehensive, dynamic view of C/D box sRNA evolutionary history within a genus, in terms of modification function, feature plasticity, and gene mobility.},
}
@article {pmid29769540,
year = {2018},
author = {Xu, S and Cai, C and Guo, J and Lu, W and Yuan, Z and Hu, S},
title = {Different clusters of Candidatus 'Methanoperedens nitroreducens'-like archaea as revealed by high-throughput sequencing with new primers.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {7695},
doi = {10.1038/s41598-018-24974-z},
pmid = {29769540},
issn = {2045-2322},
abstract = {The newly discovered Candidatus 'Methanoperedens nitroreducens' (M. nitroreducens), mediating nitrate-dependent anaerobic oxidation of methane, is an important microorganism in linking carbon and nitrogen cycles. In order to explore the diversity of M. nitroreducens-like archaea in various environmental niches with advanced high-throughput sequencing, new primers based on alpha subunit of methyl-coenzyme M reductase gene were designed. The PCR results demonstrated that the new primers could effectively detect M. nitroreducens-like archaea from an enrichment culture dominated by M. nitroreducens as well as samples collected from a natural freshwater lake and a full-scale wastewater treatment plant (WWTP). By high-throughput sequencing, more than 30,000 M. nitroreducens-like sequences were obtained. Phylogenetic analysis of these sequences along with published sequences showed that M. nitroreducens-like archaea could be divided into three sub-branches (named as Group A, Group B and Group C in this study). Clear geographical difference was observed, with Group A and Group B dominating samples in Queensland (Australia) and in European ecosystems, respectively. Further quantitative PCR revealed that the M. nitroreducens-like archaea were more abundant in WWTP than the freshwater lake. The study provided a large number of sequences for M. nitroreducens-like archaeal communities, thus expanded our understanding on the ecological diversity of M. nitroreducens-like archaea.},
}
@article {pmid29757234,
year = {2018},
author = {Sinha, N and Kral, TA},
title = {Effect of UVC Radiation on Hydrated and Desiccated Cultures of Slightly Halophilic and Non-Halophilic Methanogenic Archaea: Implications for Life on Mars.},
journal = {Microorganisms},
volume = {6},
number = {2},
pages = {},
doi = {10.3390/microorganisms6020043},
pmid = {29757234},
issn = {2076-2607},
abstract = {Methanogens have been considered models for life on Mars for many years. In order to survive any exposure at the surface of Mars, methanogens would have to endure Martian UVC radiation. In this research, we irradiated hydrated and desiccated cultures of slightly halophilic Methanococcus maripaludis and non-halophilic Methanobacterium formicicum for various time intervals with UVC (254 nm) radiation. The survivability of the methanogens was determined by measuring methane concentrations in the headspace gas samples of culture tubes after re-inoculation of the methanogens into their growth-supporting media following exposure to UVC radiation. Hydrated M. maripaludis survived 24 h of UVC exposure, while in a desiccated condition they endured for 16 h. M. formicicum also survived UVC radiation for 24 h in a liquid state; however, in a desiccated condition, the survivability of M. formicicum was only 12 h. Some of the components of the growth media could have served as shielding agents that protected cells from damage caused by exposure to ultraviolet radiation. Overall, these results suggest that limited exposure (12⁻24 h) to UVC radiation on the surface of Mars would not necessarily be a limiting factor for the survivability of M. maripaludis and M. formicicum.},
}
@article {pmid29753224,
year = {2018},
author = {Liu, X and Pan, J and Liu, Y and Li, M and Gu, JD},
title = {Diversity and distribution of Archaea in global estuarine ecosystems.},
journal = {The Science of the total environment},
volume = {637-638},
number = {},
pages = {349-358},
doi = {10.1016/j.scitotenv.2018.05.016},
pmid = {29753224},
issn = {1879-1026},
abstract = {Estuarine ecosystem is a unique geographical transitional zone between freshwater and seawater, harboring a wide range of microbial communities including Archaea. Although a large number of Archaea have been detected in such ecosystem, the global patterns in archaeal diversity and distribution are extremely scarce. To bridge this gap, we carried out a comprehensive survey of archaeal communities using ca. 4000 publicly available archaeal 16S rRNA gene sequences (>300 bp) collected from 24 estuaries in different latitude regions. These sequences were divided into 1450 operational taxonomic units (OTUs) at 97% identity, suggesting a high biodiversity that increased gradually from the high- to low-latitude estuaries. Phylogenetic analysis showed that estuarine ecosystem was a large biodiversity pool of Archaea that was mainly composed of 12 phyla. Among them, the predominant groups were Bathyarchaeota, Euryarchaeota and Thaumarchaeota. Interestingly, archaeal distribution demonstrated a geographical differentiation in that Thaumarchaeota was dominated in the low-latitude estuaries, Bathyarchaeota in the mid-latitude estuaries, and Euryarchaeota in the high-latitude estuaries, respectively. Furthermore, the majority of the most abundant 20 OTUs demonstrated an overrepresented or underrepresented distribution pattern in some specific estuaries or latitude regions while a few were evenly distributed throughout the estuaries. This pattern indicates a potential selectivity of geographical distribution. In addition, the analysis of environmental parameters suggested that latitude would be one of the major factors driving the distribution of archaeal communities in estuarine ecosystem. This study profiles a clear framework on the diversity and distribution of Archaea in the global estuarine ecosystem and explores the general environmental factors that influence these patterns. Our findings constitute an important part of the exploration of the global ecology of Archaea.},
}
@article {pmid29743201,
year = {2018},
author = {Taffner, J and Erlacher, A and Bragina, A and Berg, C and Moissl-Eichinger, C and Berg, G},
title = {What Is the Role of Archaea in Plants? New Insights from the Vegetation of Alpine Bogs.},
journal = {mSphere},
volume = {3},
number = {3},
pages = {},
doi = {10.1128/mSphere.00122-18},
pmid = {29743201},
issn = {2379-5042},
abstract = {The Archaea represent a significant component of the plant microbiome, whereas their function is still unclear. Different plant species representing the natural vegetation of alpine bogs harbor a substantial archaeal community originating from five phyla, 60 genera, and 334 operational taxonomic units (OTUs). We identified a core archaeome for all bog plants and ecosystem-specific, so far unclassified Archaea In the metagenomic data set, Archaea were found to have the potential to interact with plants by (i) possible plant growth promotion through auxin biosynthesis, (ii) nutrient supply, and (iii) protection against abiotic (especially oxidative and osmotic) stress. The unexpectedly high degree of plant specificity supports plant-archaeon interactions. Moreover, functional signatures of Archaea reveal genetic capacity for the interplay with fungi and an important role in the carbon and nitrogen cycle: e.g., CO2 and N2 fixation. These facts reveal an important, yet unobserved role of the Archaea for plants as well as for the bog ecosystem.IMPORTANCEArchaea are still an underdetected and little-studied part of the plant microbiome. We provide first and novel insights into Archaea as a functional component of the plant microbiome obtained by metagenomic analyses. Archaea were found to have the potential to interact with plants by (i) plant growth promotion through auxin biosynthesis, (ii) nutrient supply, and (iii) protection against abiotic stress.},
}
@article {pmid29741625,
year = {2018},
author = {White, MF and Allers, T},
title = {DNA repair in the archaea-an emerging picture.},
journal = {FEMS microbiology reviews},
volume = {42},
number = {4},
pages = {514-526},
doi = {10.1093/femsre/fuy020},
pmid = {29741625},
issn = {1574-6976},
abstract = {There has long been a fascination in the DNA repair pathways of archaea, for two main reasons. Firstly, many archaea inhabit extreme environments where the rate of physical damage to DNA is accelerated. These archaea might reasonably be expected to have particularly robust or novel DNA repair pathways to cope with this. Secondly, the archaea have long been understood to be a lineage distinct from the bacteria, and to share a close relationship with the eukarya, particularly in their information processing systems. Recent discoveries suggest the eukarya arose from within the archaeal domain, and in particular from lineages related to the TACK superphylum and Lokiarchaea. Thus, archaeal DNA repair proteins and pathways can represent a useful model system. This review focuses on recent advances in our understanding of archaeal DNA repair processes including base excision repair, nucleotide excision repair, mismatch repair and double-strand break repair. These advances are discussed in the context of the emerging picture of the evolution and relationship of the three domains of life.},
}
@article {pmid29733685,
year = {2018},
author = {Rinta-Kanto, JM and Pehkonen, K and Sinkko, H and Tamminen, MV and Timonen, S},
title = {Archaea are prominent members of the prokaryotic communities colonizing common forest mushrooms.},
journal = {Canadian journal of microbiology},
volume = {},
number = {},
pages = {1-11},
doi = {10.1139/cjm-2018-0035},
pmid = {29733685},
issn = {1480-3275},
abstract = {In this study, the abundance and composition of prokaryotic communities associated with the inner tissue of fruiting bodies of Suillus bovinus, Boletus pinophilus, Cantharellus cibarius, Agaricus arvensis, Lycoperdon perlatum, and Piptoporus betulinus were analyzed using culture-independent methods. Our findings indicate that archaea and bacteria colonize the internal tissues of all investigated specimens and that archaea are prominent members of the prokaryotic community. The ratio of archaeal 16S rRNA gene copy numbers to those of bacteria was >1 in the fruiting bodies of four out of six fungal species included in the study. The largest proportion of archaeal 16S rRNA gene sequences belonged to thaumarchaeotal classes Terrestrial group, Miscellaneous Crenarchaeotic Group (MCG), and Thermoplasmata. Bacterial communities showed characteristic compositions in each fungal species. Bacterial classes Gammaproteobacteria, Actinobacteria, Bacilli, and Clostridia were prominent among communities in fruiting body tissues. Bacterial populations in each fungal species had different characteristics. The results of this study imply that fruiting body tissues are an important habitat for abundant and diverse populations of archaea and bacteria.},
}
@article {pmid29720404,
year = {2018},
author = {Prakash, D and Walters, KA and Martinie, RJ and McCarver, AC and Kumar, AK and Lessner, DJ and Krebs, C and Golbeck, JH and Ferry, JG},
title = {Toward a mechanistic and physiological understanding of a ferredoxin:disulfide reductase from the domains Archaea and Bacteria.},
journal = {The Journal of biological chemistry},
volume = {293},
number = {24},
pages = {9198-9209},
doi = {10.1074/jbc.RA118.002473},
pmid = {29720404},
issn = {1083-351X},
abstract = {Disulfide reductases reduce other proteins and are critically important for cellular redox signaling and homeostasis. Methanosarcina acetivorans is a methane-producing microbe from the domain Archaea that produces a ferredoxin:disulfide reductase (FDR) for which the crystal structure has been reported, yet its biochemical mechanism and physiological substrates are unknown. FDR and the extensively characterized plant-type ferredoxin:thioredoxin reductase (FTR) belong to a distinct class of disulfide reductases that contain a unique active-site [4Fe-4S] cluster. The results reported here support a mechanism for FDR similar to that reported for FTR with notable exceptions. Unlike FTR, FDR contains a rubredoxin [1Fe-0S] center postulated to mediate electron transfer from ferredoxin to the active-site [4Fe-4S] cluster. UV-visible, EPR, and Mössbauer spectroscopic data indicated that two-electron reduction of the active-site disulfide in FDR involves a one-electron-reduced [4Fe-4S]1+ intermediate previously hypothesized for FTR. Our results support a role for an active-site tyrosine in FDR that occupies the equivalent position of an essential histidine in the active site of FTR. Of note, one of seven Trxs encoded in the genome (Trx5) and methanoredoxin, a glutaredoxin-like enzyme from M. acetivorans, were reduced by FDR, advancing the physiological understanding of FDR's role in the redox metabolism of methanoarchaea. Finally, bioinformatics analyses show that FDR homologs are widespread in diverse microbes from the domain Bacteria.},
}
@article {pmid29699482,
year = {2018},
author = {Mitić, NS and Malkov, SN and Kovačević, JJ and Pavlović-Lažetić, GM and Beljanski, MV},
title = {Structural disorder of plasmid-encoded proteins in Bacteria and Archaea.},
journal = {BMC bioinformatics},
volume = {19},
number = {1},
pages = {158},
doi = {10.1186/s12859-018-2158-6},
pmid = {29699482},
issn = {1471-2105},
support = {174021//Ministry of Education, Science and Technological Development, Republic of Serbia/ ; },
abstract = {BACKGROUND: In the last decade and a half it has been firmly established that a large number of proteins do not adopt a well-defined (ordered) structure under physiological conditions. Such intrinsically disordered proteins (IDPs) and intrinsically disordered (protein) regions (IDRs) are involved in essential cell processes through two basic mechanisms: the entropic chain mechanism which is responsible for rapid fluctuations among many alternative conformations, and molecular recognition via short recognition elements that bind to other molecules. IDPs possess a high adaptive potential and there is special interest in investigating their involvement in organism evolution.<br><br>RESULTS: We analyzed 2554 Bacterial and 139 Archaeal proteomes, with a total of 8,455,194 proteins for disorder content and its implications for adaptation of organisms, using three disorder predictors and three measures. Along with other findings, we revealed that for all three predictors and all three measures (1) Bacteria exhibit significantly more disorder than Archaea; (2) plasmid-encoded proteins contain considerably more IDRs than proteins encoded on chromosomes (or whole genomes) in both prokaryote superkingdoms; (3) plasmid proteins are significantly more disordered than chromosomal proteins only in the group of proteins with no COG category assigned; (4) antitoxin proteins in comparison to other proteins, are the most disordered (almost double) in both Bacterial and Archaeal proteomes; (5) plasmidal proteins are more disordered than chromosomal proteins in Bacterial antitoxins and toxin-unclassified proteins, but have almost the same disorder content in toxin proteins.<br><br>CONCLUSION: Our results suggest that while disorder content depends on genome and proteome characteristics, it is more influenced by functional engagements than by gene location (on chromosome or plasmid).},
}
@article {pmid29687586,
year = {2018},
author = {Meinhardt, KA and Stopnisek, N and Pannu, MW and Strand, SE and Fransen, SC and Casciotti, KL and Stahl, DA},
title = {Ammonia-oxidizing bacteria are the primary N2 O producers in an ammonia-oxidizing archaea dominated alkaline agricultural soil.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.14246},
pmid = {29687586},
issn = {1462-2920},
abstract = {Most agricultural N2 O emissions are a consequence of microbial transformations of nitrogen (N) fertilizer, and mitigating increases in N2 O emission will depend on identifying microbial sources and variables influencing their activities. Here, using controlled microcosm and field studies, we found that synthetic N addition in any tested amount stimulated the production of N2 O from ammonia-oxidizing bacteria (AOB), but not archaea (AOA), from a bioenergy crop soil. The activities of these two populations were differentiated by N treatments, with abundance and activity of AOB increasing as nitrate and N2 O production increased. Moreover, as N2 O production increased, the isotopic composition of N2 O was consistent with an AOB source. Relative N2 O contributions by both populations were quantified using selective inhibitors and varying N availability. Complementary field analyses confirmed a positive correlation between N2 O flux and AOB abundance with N application. Collectively, our data indicate that AOB are the major N2 O producers, even with low N addition, and that better-metered N application, complemented by selective inhibitors, could reduce projected N2 O emissions from agricultural soils.},
}
@article {pmid29684598,
year = {2018},
author = {Aouad, M and Taib, N and Oudart, A and Lecocq, M and Gouy, M and Brochier-Armanet, C},
title = {Extreme halophilic archaea derive from two distinct methanogen Class II lineages.},
journal = {Molecular phylogenetics and evolution},
volume = {127},
number = {},
pages = {46-54},
doi = {10.1016/j.ympev.2018.04.011},
pmid = {29684598},
issn = {1095-9513},
abstract = {Phylogenetic analyses of conserved core genes have disentangled most of the ancient relationships in Archaea. However, some groups remain debated, like the DPANN, a deep-branching super-phylum composed of nanosized archaea with reduced genomes. Among these, the Nanohaloarchaea require high-salt concentrations for growth. Their discovery in 2012 was significant because they represent, together with Halobacteria (a Class belonging to Euryarchaeota), the only two described lineages of extreme halophilic archaea. The phylogenetic position of Nanohaloarchaea is highly debated, being alternatively proposed as the sister-lineage of Halobacteria or a member of the DPANN super-phylum. Pinpointing the phylogenetic position of extreme halophilic archaea is important to improve our knowledge of the deep evolutionary history of Archaea and the molecular adaptive processes and evolutionary paths that allowed their emergence. Using comparative genomic approaches, we identified 258 markers carrying a reliable phylogenetic signal. By combining strategies limiting the impact of biases on phylogenetic inference, we showed that Nanohaloarchaea and Halobacteria represent two independent lines that derived from two distinct but related methanogen Class II lineages. This implies that adaptation to high salinity emerged twice independently in Archaea and indicates that emergence of Nanohaloarchaea within DPANN in previous studies is likely the consequence of a tree reconstruction artifact, challenging the existence of this super-phylum.},
}
@article {pmid29684129,
year = {2018},
author = {Clouet-d'Orval, B and Batista, M and Bouvier, M and Quentin, Y and Fichant, G and Marchfelder, A and Maier, LK},
title = {Insights into RNA processing pathways and associated-RNA degrading enzymes in Archaea.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuy016},
pmid = {29684129},
issn = {1574-6976},
abstract = {RNA processing pathways are at the center of regulation of gene expression. All RNA transcripts undergo multiple maturation steps in addition to covalent chemical modifications to become functional in the cell. This includes destroying unnecessary or defective cellular RNAs. In Archaea, information on mechanisms by which RNA species reach their mature forms and associated RNA-modifying enzymes is still fragmentary. To date, most archaeal actors and pathways have been proposed in light of information gathered from Bacteria and Eukarya. In this context, this review provides a state of the art overview of archaeal endoribonucleases and exoribonucleases that cleave and trim RNA species and also of the key small archaeal proteins that bind RNAs. Furthermore, synthetic up-to-date views of processing and biogenesis pathways of archaeal transfer and ribosomal RNAs as well as of maturation of stable small non-coding RNAs such as CRISPR RNAs, small C/D and H/ACA box guide RNAs, and other emerging classes of small RNAs are described. Finally prospective post-transcriptional mechanisms to control archaeal messenger RNA quality and quantity are discussed.},
}
@article {pmid29672703,
year = {2018},
author = {Keshri, V and Panda, A and Levasseur, A and Rolain, JM and Pontarotti, P and Raoult, D},
title = {Phylogenomic Analysis of β-Lactamase in Archaea and Bacteria Enables the Identification of Putative New Members.},
journal = {Genome biology and evolution},
volume = {10},
number = {4},
pages = {1106-1114},
doi = {10.1093/gbe/evy028},
pmid = {29672703},
issn = {1759-6653},
abstract = {β-lactamases are enzymes which are commonly produced by bacteria and which degrade the β-lactam ring of β-lactam antibiotics, namely penicillins, cephalosporins, carbapenems, and monobactams, and inactivate these antibiotics. We performed a rational and comprehensive investigation of β-lactamases in different biological databases. In this study, we constructed hidden Markov model profiles as well as the ancestral sequence of four classes of β-lactamases (A, B, C, and D), which were used to identify potential β-lactamases from environmental metagenomic (1206), human microbiome metagenomic (6417), human microbiome reference genome (1310), and NCBI's nonredundant databases (44101). Our analysis revealed the existence of putative β-lactamases in the metagenomic databases, which appeared to be similar to the four different molecular classes (A-D). This is the first report on the large-scale phylogenetic diversity of new members of β-lactamases, and our results revealed that metagenomic database dark-matter contains β-lactamase-like antibiotic resistance genes.},
}
@article {pmid29668953,
year = {2018},
author = {Ausiannikava, D and Mitchell, L and Marriott, H and Smith, V and Hawkins, M and Makarova, KS and Koonin, EV and Nieduszynski, CA and Allers, T},
title = {Evolution of Genome Architecture in Archaea: Spontaneous Generation of a New Chromosome in Haloferax volcanii.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msy075},
pmid = {29668953},
issn = {1537-1719},
abstract = {The common ancestry of archaea and eukaryotes is evident in their genome architecture. All eukaryotic and several archaeal genomes consist of multiple chromosomes, each replicated from multiple origins. Three scenarios have been proposed for the evolution of this genome architecture: (1) mutational diversification of a multi-copy chromosome; (2) capture of a new chromosome by horizontal transfer; (3) acquisition of new origins and splitting into two replication-competent chromosomes. We report an example of the third scenario: the multi-origin chromosome of the archaeon Haloferax volcanii has split into two elements via homologous recombination. The newly-generated elements are bona fide chromosomes, because each bears 'chromosomal' replication origins, rRNA loci and essential genes. The new chromosomes were stable during routine growth but additional genetic manipulation, which involves selective bottlenecks, provoked further rearrangements. To the best of our knowledge, rearrangement of a naturally-evolved prokaryotic genome to generate two new chromosomes has not been described previously.},
}
@article {pmid29668558,
year = {2018},
author = {Brugère, JF and Ben Hania, W and Arnal, ME and Ribière, C and Ballet, N and Vandeckerkove, P and Ollivier, B and O'Toole, PW},
title = {Archaea: Microbial Candidates in Next-generation Probiotics Development.},
journal = {Journal of clinical gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1097/MCG.0000000000001043},
pmid = {29668558},
issn = {1539-2031},
abstract = {Pharmabiotics and probiotics in current use or under development belong to 2 of 3 domains of life, Eukarya (eg, yeasts) and Bacteria (eg, lactobacilli). Archaea constitute a third domain of life, and are currently not used as probiotics, despite several interesting features. This includes the absence of known pathogens in humans, animals, or plants and the existence of some archaea closely associated to humans in various microbiomes. We promote the concept that some specific archaea that naturally thrive in the human gut are potential next-generation probiotics that can be rationally selected on the basis of their metabolic phenotype not being encountered in other human gut microbes, neither Bacteria nor Eukarya. The example of the possible bioremediation of the proatherogenic compound trimethylamine into methane by archaeal microbes is described.},
}
@article {pmid29666365,
year = {2018},
author = {Alves, RJE and Minh, BQ and Urich, T and von Haeseler, A and Schleper, C},
title = {Unifying the global phylogeny and environmental distribution of ammonia-oxidising archaea based on amoA genes.},
journal = {Nature communications},
volume = {9},
number = {1},
pages = {1517},
doi = {10.1038/s41467-018-03861-1},
pmid = {29666365},
issn = {2041-1723},
abstract = {Ammonia-oxidising archaea (AOA) are ubiquitous and abundant in nature and play a major role in nitrogen cycling. AOA have been studied intensively based on the amoA gene (encoding ammonia monooxygenase subunit A), making it the most sequenced functional marker gene. Here, based on extensive phylogenetic and meta-data analyses of 33,378 curated archaeal amoA sequences, we define a highly resolved taxonomy and uncover global environmental patterns that challenge many earlier generalisations. Particularly, we show: (i) the global frequency of AOA is extremely uneven, with few clades dominating AOA diversity in most ecosystems; (ii) characterised AOA do not represent most predominant clades in nature, including soils and oceans; (iii) the functional role of the most prevalent environmental AOA clade remains unclear; and (iv) AOA harbour molecular signatures that possibly reflect phenotypic traits. Our work synthesises information from a decade of research and provides the first integrative framework to study AOA in a global context.},
}
@article {pmid29656122,
year = {2018},
author = {Rother, M and Quitzke, V},
title = {Selenoprotein synthesis and regulation in Archaea.},
journal = {Biochimica et biophysica acta},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bbagen.2018.04.008},
pmid = {29656122},
issn = {0006-3002},
abstract = {BACKGROUND: The major biological form of selenium is that of the co-translationally inserted amino acid selenocysteine (Sec). In Archaea, the majority of proteins containing Sec, selenoproteins, are involved in methanogenesis. However, the function of this residue is often not known because selenium-independent homologs of the selenoproteins can be employed, sometimes even in one organism.<br><br>SCOPE OF REVIEW: This review summarizes current knowledge about the selenoproteins of Archaea, the metabolic pathways where they are involved, and discusses the (potential) function of individual Sec residues. Also, what is known about the &quot;archaeal&quot; way of selenoprotein synthesis, and the regulatory mechanism leading to the replacement of the selenoproteins with selenium-independent homologs, will be presented. Where appropriate, similarities with (and differences to) the respective steps employed in the other two domains, Bacteria and Eukarya, will be emphasized.<br><br>MAJOR CONCLUSIONS: Genetic and biochemical studies guided by analysis of genome sequences of Sec-encoding archaea has revealed that the pathway of Sec synthesis in Archaea and Eukarya are principally identical and that Sec insertion in Eukarya probably evolved from an archaeal mechanism employed prior to the separation of the archaeal and eukaryal lines of decent.<br><br>GENERAL SIGNIFICANCE: In light of the emerging close phylogenetic relationship of Eukarya and Archaea, archaeal models may be highly valuable tools for unraveling &quot;eukaryotic&quot; principles in molecular and cell biology.},
}
@article {pmid29643403,
year = {2018},
author = {Wei, Z and Wang, J and Zhu, L and Wang, J and Zhu, G},
title = {Toxicity of enrofloxacin, copper and their interactions on soil microbial populations and ammonia-oxidizing archaea and bacteria.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {5828},
doi = {10.1038/s41598-018-24016-8},
pmid = {29643403},
issn = {2045-2322},
abstract = {Enrofloxacin (EFX) is one of the most frequently used broad-spectrum veterinary drugs, and copper (Cu) is a heavy metal that could easily bind to certain antibiotic molecules. Hence EFX and Cu were chosen as representatives of antibiotics and heavy metals to explore the abundance and variation of soil microbial populations with a plate-counting technique, as well as the copy numbers of amoA gene in ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) by quantitative PCR methods in Argosols samples. Treatments of applied EFX (0.05, 0.20, 0.80 mmol/kg), Cu (1.60 mmol/kg) and combined EFX and Cu (at molar ratios of 1:32,1:8,1:2) exhibited various effects on different soil microorganisms. The toxicity of combined EFX and Cu was more strongly expressed on both soil microbial populations and amoA gene (AOA and AOB) compared to the EFX treatment alone, in most cases, time and dose effects were observed. With respect to the amoA gene, the AOA-amoA gene was more abundant than the AOB-amoA gene, and the ratio ranged from ~8 to ~11. Moreover, the interaction types of EFX and Cu were more likely to be antagonistic (64.29%) than synergistic (35.71%) on soil abundance and function, which may be related to the incubation time and the ratio of EFX to Cu in the soil.},
}
@article {pmid29636434,
year = {2018},
author = {Gilmour, CC and Bullock, AL and McBurney, A and Podar, M and Elias, DA},
title = {Robust Mercury Methylation across Diverse Methanogenic Archaea.},
journal = {mBio},
volume = {9},
number = {2},
pages = {},
doi = {10.1128/mBio.02403-17},
pmid = {29636434},
issn = {2150-7511},
}
@article {pmid29631688,
year = {2018},
author = {Khallef, S and Lestini, R and Myllykallio, H and Houali, K},
title = {Isolation and identification of two extremely halophilic archaea from sebkhas in the Algerian Sahara.},
journal = {Cellular and molecular biology (Noisy-le-Grand, France)},
volume = {64},
number = {4},
pages = {83-91},
pmid = {29631688},
issn = {1165-158X},
abstract = {In Algeria, many salt lakes are to be found spread from southern Tunisia up to the Atlas Mountains in northern Algeria. Oum Eraneb and Ain El beida sebkhas (salt lakes), are located in the Algerian Sahara. The aim of this study was to explore the diversity of the halobacteria in this type of habitats. The physicochemical properties of these shallow saline environments were examined and compared with other hypersaline and marine ecosystems. Both sites were relatively alkaline with a pH around 8.57- 8.74 and rich in salt at 13% and 16% (w/v) salinity for Oum Eraneb and Ain El beida, respectively, with dominant ions of sodium and chloride. The microbial approach revealed the presence of two halophilic archaea, strains JCM13561 and A33T in both explored sebkhas. Growth occurred between 10 and 25% (w/v) NaCl and the isolates grow optimally at 20% (w/v) NaCl. The pH range for growth was 6 to 9.5 with an optimum at pH 7.5 for the first strain and 7 to 9.5 with an optimum pH at 8.5-9 for the second strain. On the basis of 16S rRNA gene sequence analysis, strains JCM13561 and A33T were most closely related to Halorubrum litoreum and Natronorubrum bangense (99% and 96% similarity, respectively).},
}
@article {pmid29625978,
year = {2018},
author = {McGlynn, SE and Chadwick, GL and O'Neill, A and Mackey, M and Thor, A and Deerinck, TJ and Ellisman, MH and Orphan, VJ},
title = {Subgroup characteristics of marine methane-oxidizing ANME-2 archaea and their syntrophic partners revealed by integrated multimodal analytical microscopy.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.00399-18},
pmid = {29625978},
issn = {1098-5336},
support = {P41 GM103412/GM/NIGMS NIH HHS/United States ; },
abstract = {Phylogenetically diverse environmental ANME archaea and sulfate-reducing bacteria cooperatively catalyze the anaerobic oxidation of methane oxidation (AOM) in multi-celled consortia within methane seep environments. To better understand these cells and their symbiotic associations, we applied a suite of electron microscopy approaches including correlative fluorescence in situhybridization - electron microscopy (FISH-EM), transmission electron microscopy (TEM), and serial block face scanning electron microscopy 3D reconstructions (SBEM). FISH-EM of methane seep derived consortia revealed phylogenetic variability in terms of cell morphology, ultrastructure, and storage granules. Representatives of the ANME-2b clade, but not other ANME-2 groups, contained polyphosphate-like granules, while some bacteria associated with ANME-2a/2c contained two distinct phases of iron mineral chains resembling magnetosomes. 3D segmentation of two ANME-2 consortia types revealed cellular volumes of ANME and their symbiotic partners which were larger than previous estimates based on light microscopy. Phosphorous granule containing ANME (tentatively ANME-2b) were larger than both ANME with no granules and partner bacteria. This cell type was observed with up to 4 granules per cell and the volume of the cell was larger in proportion to the number of granules inside it, but the percent of the cell occupied by these granules did not vary with granule number. These results illuminate distinctions between ANME-2 archaeal lineages and partnering bacterial populations that are apparently unified in their capability of performing anaerobic methane oxidation.Importance Methane oxidation in anaerobic environments can be accomplished by a number of archaeal groups, some of which live in syntrophic relationships with bacteria in structured consortia. Little is known as to the distinguishing characteristics of these groups. Here we applied imaging approaches to better understand the properties of these cells. We found unexpected morphological, structural, and volume variability of these uncultured groups by correlating fluorescence labeling of cells with electron microscopy observables.},
}
@article {pmid29622618,
year = {2018},
author = {Poehlein, A and Heym, D and Quitzke, V and Fersch, J and Daniel, R and Rother, M},
title = {Complete Genome Sequence of the Methanococcus maripaludis Type Strain JJ (DSM 2067), a Model for Selenoprotein Synthesis in Archaea.},
journal = {Genome announcements},
volume = {6},
number = {14},
pages = {},
doi = {10.1128/genomeA.00237-18},
pmid = {29622618},
issn = {2169-8287},
abstract = {Methanococcus maripaludis type strain JJ (DSM 2067) is an important organism because it serves as a model for primary energy metabolism and hydrogenotrophic methanogenesis and is amenable to genetic manipulation. The complete genome (1.7 Mb) harbors 1,815 predicted protein-encoding genes, including 9 encoding selenoproteins.},
}
@article {pmid29618058,
year = {2018},
author = {Feng, X and Sun, M and Han, W and Liang, YX and She, Q},
title = {A transcriptional factor B paralog functions as an activator to DNA damage-responsive expression in archaea.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gky236},
pmid = {29618058},
issn = {1362-4962},
abstract = {Previously it was shown that UV irradiation induces a strong upregulation of tfb3 coding for a paralog of the archaeal transcriptional factor B (TFB) in Sulfolobus solfataricus, a crenarchaea. To investigate the function of this gene in DNA damage response (DDR), tfb3 was inactivated by gene deletion in Sulfolobus islandicus and the resulting Δtfb3 was more sensitive to DNA damage agents than the original strain. Transcriptome analysis revealed that a large set of genes show TFB3-dependent activation, including genes of the ups operon and ced system. Furthermore, the TFB3 protein was found to be associated with DDR gene promoters and functional dissection of TFB3 showed that the conserved Zn-ribbon and coiled-coil motif are essential for the activation. Together, the results indicated that TFB3 activates the expression of DDR genes by interaction with other transcriptional factors at the promoter regions of DDR genes to facilitate the formation of transcription initiation complex. Strikingly, TFB3 and Ced systems are present in a wide range of crenarchaea, suggesting that the Ced system function as a primary DNA damage repair mechanism in Crenarchaeota. Our findings further suggest that TFB3 and the concurrent TFB1 form a TFB3-dependent DNA damage-responsive circuit with their target genes, which is evolutionarily conserved in the major lineage of Archaea.},
}
@article {pmid29596428,
year = {2018},
author = {Da Cunha, V and Gaia, M and Nasir, A and Forterre, P},
title = {Asgard archaea do not close the debate about the universal tree of life topology.},
journal = {PLoS genetics},
volume = {14},
number = {3},
pages = {e1007215},
doi = {10.1371/journal.pgen.1007215},
pmid = {29596428},
issn = {1553-7404},
}
@article {pmid29596421,
year = {2018},
author = {Spang, A and Eme, L and Saw, JH and Caceres, EF and Zaremba-Niedzwiedzka, K and Lombard, J and Guy, L and Ettema, TJG},
title = {Asgard archaea are the closest prokaryotic relatives of eukaryotes.},
journal = {PLoS genetics},
volume = {14},
number = {3},
pages = {e1007080},
doi = {10.1371/journal.pgen.1007080},
pmid = {29596421},
issn = {1553-7404},
}
@article {pmid29595162,
year = {2018},
author = {Kiadehi, MSH and Amoozegar, MA and Asad, S and Siroosi, M},
title = {Exploring the potential of halophilic archaea for the decolorization of azo dyes.},
journal = {Water science and technology : a journal of the International Association on Water Pollution Research},
volume = {77},
number = {5-6},
pages = {1602-1611},
doi = {10.2166/wst.2018.040},
pmid = {29595162},
issn = {0273-1223},
abstract = {Azo dyes are being extensively used in textile industries, so finding a proper solution to decolorize them is of high importance. In order to find azo dye decolorizing strains among haloarchaea, which are well known for their tolerance to harsh environmental conditions, fifteen haloarchaeal strains were screened. Halogeometricum sp. strain A and Haloferax sp. strain B with the highest decolorization ability (95% and 91% for Remazol black B; both about 60% for Acid blue 161, respectively) were selected for further studies. It was shown that both strains were able to grow and decolorize the dye in a medium containing up to 5 M NaCl, with optimum decolorization activity at 2.5-3.4 M, pH 7, and a wide temperature range between 30 to 45 °C. Moreover, both strains were able to tolerate and decolorize up to 1,000 mg l-1 Remazol black B. Also, they were able to survive in 5,000 mg l-1 of the dye after 20 days' incubation. Glucose and yeast extract were found to be the best carbon and nitrogen sources in the decolorization medium for both strains. This is the first report studying decolorization of azo dyes using halophilic archaea.},
}
@article {pmid29573609,
year = {2018},
author = {Pillot, G and Frouin, E and Pasero, E and Godfroy, A and Combet-Blanc, Y and Davidson, S and Liebgott, PP},
title = {Specific enrichment of hyperthermophilic electroactive Archaea from deep-sea hydrothermal vent on electrically conductive support.},
journal = {Bioresource technology},
volume = {259},
number = {},
pages = {304-311},
doi = {10.1016/j.biortech.2018.03.053},
pmid = {29573609},
issn = {1873-2976},
mesh = {*Archaea ; Atlantic Ocean ; Bacteria ; Electrolysis ; *Hydrothermal Vents ; Phylogeny ; RNA, Ribosomal, 16S ; Seawater ; },
abstract = {While more and more investigations are done to study hyperthermophilic exoelectrogenic communities from environments, none have been performed yet on deep-sea hydrothermal vent. Samples of black smoker chimney from Rainbow site on the Atlantic mid-oceanic ridge have been harvested for enriching exoelectrogens in microbial electrolysis cells under hyperthermophilic (80 °C) condition. Two enrichments were performed in a BioElectrochemical System specially designed: one from direct inoculation of crushed chimney and the other one from inoculation of a pre-cultivation on iron (III) oxide. In both experiments, a current production was observed from 2.4 A/m2 to 5.8 A/m2 with a set anode potential of -0.110 V vs Ag/AgCl. Taxonomic affiliation of the exoelectrogen communities obtained on the electrode exhibited a specific enrichment of Archaea belonging to Thermococcales and Archeoglobales orders, even when both inocula were dominated by Bacteria.},
}
@article {pmid29522733,
year = {2018},
author = {},
title = {Extreme Excitement about Archaea.},
journal = {Cell},
volume = {172},
number = {6},
pages = {1153-1154},
doi = {10.1016/j.cell.2018.02.038},
pmid = {29522733},
issn = {1097-4172},
}
@article {pmid29510582,
year = {2018},
author = {Gelsinger, DR and DiRuggiero, J},
title = {The Non-Coding Regulatory RNA Revolution in Archaea.},
journal = {Genes},
volume = {9},
number = {3},
pages = {},
doi = {10.3390/genes9030141},
pmid = {29510582},
issn = {2073-4425},
abstract = {Small non-coding RNAs (sRNAs) are ubiquitously found in the three domains of life playing large-scale roles in gene regulation, transposable element silencing and defense against foreign elements. While a substantial body of experimental work has been done to uncover function of sRNAs in Bacteria and Eukarya, the functional roles of sRNAs in Archaea are still poorly understood. Recently, high throughput studies using RNA-sequencing revealed that sRNAs are broadly expressed in the Archaea, comprising thousands of transcripts within the transcriptome during non-challenged and stressed conditions. Antisense sRNAs, which overlap a portion of a gene on the opposite strand (cis-acting), are the most abundantly expressed non-coding RNAs and they can be classified based on their binding patterns to mRNAs (3' untranslated region (UTR), 5' UTR, CDS-binding). These antisense sRNAs target many genes and pathways, suggesting extensive roles in gene regulation. Intergenic sRNAs are less abundantly expressed and their targets are difficult to find because of a lack of complete overlap between sRNAs and target mRNAs (trans-acting). While many sRNAs have been validated experimentally, a regulatory role has only been reported for very few of them. Further work is needed to elucidate sRNA-RNA binding mechanisms, the molecular determinants of sRNA-mediated regulation, whether protein components are involved and how sRNAs integrate with complex regulatory networks.},
}
@article {pmid29507381,
year = {2018},
author = {Burns, JA and Pittis, AA and Kim, E},
title = {Publisher Correction: Gene-based predictive models of trophic modes suggest Asgard archaea are not phagocytotic.},
journal = {Nature ecology &amp; evolution},
volume = {2},
number = {4},
pages = {751},
doi = {10.1038/s41559-018-0520-8},
pmid = {29507381},
issn = {2397-334X},
abstract = {In the version of this Article originally published, question marks appeared in Table 1; they should have been tick marks. This has now been corrected in all versions of the Article.},
}
@article {pmid29497404,
year = {2018},
author = {Liu, J and Yu, Z and Yao, Q and Sui, Y and Shi, Y and Chu, H and Tang, C and Franks, AE and Jin, J and Liu, X and Wang, G},
title = {Ammonia-Oxidizing Archaea Show More Distinct Biogeographic Distribution Patterns than Ammonia-Oxidizing Bacteria across the Black Soil Zone of Northeast China.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {171},
doi = {10.3389/fmicb.2018.00171},
pmid = {29497404},
issn = {1664-302X},
abstract = {Black soils (Mollisols) of northeast China are highly productive and agriculturally important for food production. Ammonia-oxidizing microbes play an important role in N cycling in the black soils. However, the information related to the composition and distribution of ammonia-oxidizing microbes in the black soils has not yet been addressed. In this study, we used the amoA gene to quantify the abundance and community composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) across the black soil zone. The amoA abundance of AOA was remarkably larger than that of AOB, with ratios of AOA/AOB in the range from 3.1 to 91.0 across all soil samples. The abundance of AOA amoA was positively correlated with total soil C content (p < 0.001) but not with soil pH (p > 0.05). In contrast, the abundance of AOB amoA positively correlated with soil pH (p = 0.009) but not with total soil C. Alpha diversity of AOA did not correlate with any soil parameter, however, alpha diversity of AOB was affected by multiple soil factors, such as soil pH, total P, N, and C, available K content, and soil water content. Canonical correspondence analysis indicated that the AOA community was mainly affected by the sampling latitude, followed by soil pH, total P and C; while the AOB community was mainly determined by soil pH, as well as total P, C and N, water content, and sampling latitude, which highlighted that the AOA community was more geographically distributed in the black soil zone of northeast China than AOB community. In addition, the pairwise analyses showed that the potential nitrification rate (PNR) was not correlated with alpha diversity but weakly positively with the abundance of the AOA community (p = 0.048), whereas PNR significantly correlated positively with the richness (p = 0.003), diversity (p = 0.001) and abundance (p < 0.001) of the AOB community, which suggested that AOB community might make a greater contribution to nitrification than AOA community in the black soils when ammonium is readily available.},
}
@article {pmid29478661,
year = {2018},
author = {Ma, W and Sun, J and Li, Y and Lun, X and Shan, D and Nie, C and Liu, M},
title = {17α-Ethynylestradiol biodegradation in different river-based groundwater recharge modes with reclaimed water and degradation-associated community structure of bacteria and archaea.},
journal = {Journal of environmental sciences (China)},
volume = {64},
number = {},
pages = {51-61},
doi = {10.1016/j.jes.2016.11.022},
pmid = {29478661},
issn = {1001-0742},
mesh = {Archaea/physiology ; Bacteria/metabolism ; Ethinyl Estradiol/analysis/*metabolism ; Groundwater/chemistry/*microbiology ; Rivers/chemistry/*microbiology ; Water Microbiology ; Water Pollutants, Chemical/analysis/*metabolism ; },
abstract = {This study investigated 17α-ethynylestradiol (EE2) biodegradation process and primary metabolic pathways associated with community structures of microorganism during groundwater recharge using reclaimed water. The attenuation rate is 1.58 times higher in wetting and drying alternative recharge (WDAR) than in continual recharge (CR). The primary biotransformation pathways of EE2 in WDAR system began with the oxidation of C-17 on ring D to form a ketone group, and D-ring was subsequently hydroxylated and cleaved. In the CR system, the metabolic pathway changed from the oxidation of C-17 on ring D to hydroxylation of C-4 on ring A, and ring A or B subsequently cleaved; this transition was related to DO, and the microbial community structure. Four hundred fifty four pyrosequencing of 16s rRNA genes indicated that the bacterial communities in the upper layer of the WDAR system were more diverse than those found in the bottom layer of the CR system; this result was reversed for archaea. Unweighted UniFrac and taxonomic analyses were conducted to relate the change in bacterial community structure to the metabolic pathway. Microorganism community diversity and structure were related to the concentrations of dissolved oxygen, EE2 and its intermediates in the system. Five known bacterial classes and one known archaeal class, five major bacterial genera and one major archaeal genus might be involved in EE2 degradation. The findings of this study provide an understanding of EE2 biodegradation in groundwater recharge areas under different recharging modes and can facilitate the prediction of the fate of EE2 in underground aquifers.},
}
@article {pmid29472326,
year = {2018},
author = {Oger, PM},
title = {Complete Genome Sequences of 11 Type Species from the Thermococcus Genus of Hyperthermophilic and Piezophilic Archaea.},
journal = {Genome announcements},
volume = {6},
number = {8},
pages = {},
doi = {10.1128/genomeA.00037-18},
pmid = {29472326},
issn = {2169-8287},
abstract = {We report here the genome sequences of the type strains of the species Thermococcus barossii, T. celer, T. chitonophagus, T. gorgonarius, T. pacificus, T. peptonophilus, T. profundus, T. radiotolerans, T. siculi, and T. thioreducens, as well as the prototype of a possible type strain of a novel Thermococcus species, strain P6.},
}
@article {pmid29465796,
year = {2018},
author = {Abdul Halim, MF and Rodriguez, R and Stoltzfus, JD and Duggin, IG and Pohlschroder, M},
title = {Conserved residues are critical for Haloferax volcanii archaeosortase catalytic activity: Implications for convergent evolution of the catalytic mechanisms of non-homologous sortases from archaea and bacteria.},
journal = {Molecular microbiology},
volume = {108},
number = {3},
pages = {276-287},
doi = {10.1111/mmi.13935},
pmid = {29465796},
issn = {1365-2958},
abstract = {Proper protein anchoring is key to the biogenesis of prokaryotic cell surfaces, dynamic, resilient structures that play crucial roles in various cell processes. A novel surface protein anchoring mechanism in Haloferax volcanii depends upon the peptidase archaeosortase A (ArtA) processing C-termini of substrates containing C-terminal tripartite structures and anchoring mature substrates to the cell membrane via intercalation of lipid-modified C-terminal amino acid residues. While this membrane protein lacks clear homology to soluble sortase transpeptidases of Gram-positive bacteria, which also process C-termini of substrates whose C-terminal tripartite structures resemble those of ArtA substrates, archaeosortases do contain conserved cysteine, arginine and arginine/histidine/asparagine residues, reminiscent of His-Cys-Arg residues of sortase catalytic sites. The study presented here shows that ArtAWT -GFP expressed in trans complements ΔartA growth and motility phenotypes, while alanine substitution mutants, Cys173 (C173A), Arg214 (R214A) or Arg253 (R253A), and the serine substitution mutant for Cys173 (C173S), fail to complement these phenotypes. Consistent with sortase active site replacement mutants, ArtAC173A -GFP, ArtAC173S -GFP and ArtAR214A -GFP cannot process substrates, while replacement of the third residue, ArtAR253A -GFP retains some processing activity. These findings support the view that similarities between certain aspects of the structures and functions of the sortases and archaeosortases are the result of convergent evolution.},
}
@article {pmid29459706,
year = {2018},
author = {Burns, JA and Pittis, AA and Kim, E},
title = {Gene-based predictive models of trophic modes suggest Asgard archaea are not phagocytotic.},
journal = {Nature ecology &amp; evolution},
volume = {2},
number = {4},
pages = {697-704},
doi = {10.1038/s41559-018-0477-7},
pmid = {29459706},
issn = {2397-334X},
abstract = {With the current explosion of genomic data, there is a greater need to draw inference on phenotypic information based on DNA sequence alone. We considered complete genomes from 35 diverse eukaryotic lineages, and discovered sets of proteins predictive of trophic mode, including a set of 485 proteins that are enriched among phagocytotic eukaryotes (organisms that internalize large particles). Our model is also predictive of other aspects of trophic mode, including photosynthesis and the ability to synthesize a set of organic compounds needed for growth (prototrophy for those molecules). We applied our model to the Asgard archaea, a group of uncultured microorganisms that show close affinities to eukaryotes, to test whether the organisms are capable of phagocytosis, a phenotypic trait often considered a prerequisite for mitochondrial acquisition. Our analyses suggest that members of the Asgard archaea-despite having some eukaryote-specific protein families not found in other prokaryotes-do not use phagocytosis. Moreover, our data suggest that the process of phagocytosis arose from a combination of both archaeal and bacterial components, but also required additional eukaryote-specific innovations.},
}
@article {pmid29459337,
year = {2018},
author = {Yan, L and Wang, G and Ai, S and Huo, Z and Wang, Y and Gu, JD and Wang, W},
title = {Abundance of ammonia-oxidizing bacteria and archaea under different ventilation strategies during cattle manure composting.},
journal = {Journal of environmental management},
volume = {212},
number = {},
pages = {375-383},
doi = {10.1016/j.jenvman.2018.02.032},
pmid = {29459337},
issn = {1095-8630},
abstract = {Composting of cattle manure was conducted under four ventilation strategies, i.e., no-aeration (A-00), continuous aeration (B-44), non-aeration for 14 d and then aeration for 42 d (C-04), aeration for 14 d and then no-aeration for 42 d (D-40). Physicochemical parameters and potential ammonia oxidation (PAO) indicated that continuous and intermittent ventilation provide favourable conditions for ammonia-oxidizing bacteria (AOB) and archaea (AOA) to oxidize ammonia. Quantitative PCR (qPCR) analysis showed AOB amoA gene abundance of all treatments on every sampling day ranged from 2.25 × 105 to 2.76 × 109copies/g, was significantly lower than that of archaeal amoA gene from 2.71 × 108 to 9.05 × 1011copies/g. There was also a significantly positive relationship between PAO rates and AOB (r2 ≥ 0.066, p < 0.05) and AOA (r2 ≥ 0.300, p < 0.05) abundance. These data suggested that ammonia oxidation is driven by both AOA and AOB in cattle manure composting.},
}
@article {pmid29459210,
year = {2018},
author = {Araujo, ASF and Mendes, LW and Bezerra, WM and Nunes, LAPL and Lyra, MDCCP and Figueiredo, MDVB and Melo, VMM},
title = {Archaea diversity in vegetation gradients from the Brazilian Cerrado.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bjm.2017.08.010},
pmid = {29459210},
issn = {1678-4405},
abstract = {We used 16S rRNA sequencing to assess the archaeal communities across a gradient of Cerrado. The archaeal communities differed across the gradient. Crenarcheota was the most abundant phyla, with Nitrosphaerales and NRPJ as the predominant classes. Euryachaeota was also found across the Cerrado gradient, including the classes Metanocellales and Methanomassiliicoccaceae.},
}
@article {pmid29458865,
year = {2018},
author = {Menasria, T and Aguilera, M and Hocine, H and Benammar, L and Ayachi, A and Si Bachir, A and Dekak, A and Monteoliva-Sánchez, M},
title = {Diversity and bioprospecting of extremely halophilic archaea isolated from Algerian arid and semi-arid wetland ecosystems for halophilic-active hydrolytic enzymes.},
journal = {Microbiological research},
volume = {207},
number = {},
pages = {289-298},
doi = {10.1016/j.micres.2017.12.011},
pmid = {29458865},
issn = {1618-0623},
abstract = {The diversity of haloarchaea associated with different dry salt lakes in northeastern Algeria was investigated together with their potential of hydrolytic enzyme production. A total of 68 aerobic halophilic archaea were isolated from saline sediments. Based on the 16S rRNA gene sequencing, the isolates were assigned to seven phylotypes within the class Halobacteria, namely Haloarcula, Halococcus, Haloferax, Halogeometricum, Haloterrigena, Natrialba, and Natrinema. The results showed that Haloferax group was found to be dominant in all samples (30 isolates) (44%) with high diversity, followed by Halococcus spp. (13%) (9 isolates). All phylotypes are extreme halophiles and thermotolerant with the ability to grow at temperatures up to 48 °C. In addition, the screening for extracellular halophilic enzymes showed that 89.7% of the isolates were able to produce at least two types of the screened enzymes. The strains producing esterase, gelatinase, inulinase, cellulase and protease activities were the most diverse functional group. These data showed an abundant and diverse haloarchaeal community, detected in Algerian wetland ecosystems, presenting a promising source of molecules with important biotechnological applications.},
}
@article {pmid29456526,
year = {2018},
author = {He, H and Zhen, Y and Mi, T and Fu, L and Yu, Z},
title = {Ammonia-Oxidizing Archaea and Bacteria Differentially Contribute to Ammonia Oxidation in Sediments from Adjacent Waters of Rushan Bay, China.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {116},
doi = {10.3389/fmicb.2018.00116},
pmid = {29456526},
issn = {1664-302X},
abstract = {Ammonia oxidation plays a significant role in the nitrogen cycle in marine sediments. Ammonia-oxidizing archaea (AOA) and bacteria (AOB) are the key contributors to ammonia oxidation, and their relative contribution to this process is one of the most important issues related to the nitrogen cycle in the ocean. In this study, the differential contributions of AOA and AOB to ammonia oxidation in surface sediments from adjacent waters of Rushan Bay were studied based on the ammonia monooxygenase (amoA) gene. Molecular biology techniques were used to analyze ammonia oxidizers' community characteristics, and potential nitrification incubation was applied to understand the ammonia oxidizers' community activity. The objective was to determine the community structure and activity of AOA and AOB in surface sediments from adjacent waters of Rushan Bay and to discuss the different contributions of AOA and AOB to ammonia oxidation during summer and winter seasons in the studied area. Pyrosequencing analysis revealed that the diversity of AOA was higher than that of AOB. The majority of AOA and AOB clustered into Nitrosopumilus and Nitrosospira, respectively, indicating that the Nitrosopumilus group and Nitrosospira groups may be more adaptable in studied sediments. The AOA community was closely correlated to temperature, salinity and ammonium concentration, whereas the AOB community showed a stronger correlation with temperature, chlorophyll-a content (chla) and nitrite concentration. qPCR results showed that both the abundance and the transcript abundance of AOA was consistently greater than that of AOB. AOA and AOB differentially contributed to ammonia oxidation in different seasons. AOB occupied the dominant position in mediating ammonia oxidation during summer, while AOA might play a dominant role in ammonia oxidation during winter.},
}
@article {pmid29446847,
year = {2018},
author = {Řezanka, T and Kolouchová, I and Gharwalová, L and Palyzová, A and Sigler, K},
title = {Lipidomic Analysis: From Archaea to Mammals.},
journal = {Lipids},
volume = {53},
number = {1},
pages = {5-25},
doi = {10.1002/lipd.12001},
pmid = {29446847},
issn = {1558-9307},
abstract = {Lipids are among the most important organic compounds found in all living cells, from primitive archaebacteria to flowering plants or mammalian cells. They form part of cell walls and constitute cell storage material. Their biosynthesis and metabolism play key roles in faraway topics such as biofuel production (third-generation biofuels produced by microorganisms, e.g. algae) and human diseases such as adrenoleukodystrophy, Zellweger syndrome, or Refsum disease. Current lipidomic analysis requires fast and accurate processing of samples and especially their characterization. Because the number of possible lipids and, more specifically, molecular species of lipids is of the order of hundreds to thousands, it is necessary to process huge amounts of data in a short time. There are two basic approaches to lipidomic analysis: shotgun and liquid chromatography-mass spectometry. Both methods have their pros and cons. This review deals with lipidomics not according to the type of ionization or the lipid classes analyzed but according to the types of samples (organisms) under study. Thus, it is divided into lipidomic analysis of archaebacteria, bacteria, yeast, fungi, algae, plants, and animals.},
}
@article {pmid29429071,
year = {2018},
author = {Huang, Z and Jiang, Y and Song, X and Hallerman, E and Peng, L and Dong, D and Ma, T and Zhai, J and Li, W},
title = {Ammonia-oxidizing bacteria and archaea within biofilters of a commercial recirculating marine aquaculture system.},
journal = {AMB Express},
volume = {8},
number = {1},
pages = {17},
doi = {10.1186/s13568-018-0551-1},
pmid = {29429071},
issn = {2191-0855},
support = {31502212//National Natural Science Foundation of China/ ; },
abstract = {While biofilters are widely used to metabolize ammonia and other wastes in marine recirculating aquaculture systems, the ammonia-oxidizing bacterial and archaeal communities have not been characterized across a diversity of production systems. Using a metagenomics approach, we characterized the ammonia-oxidizing microbiological community of biofilters in a commercial recirculating marine aquaculture system producing hybrid grouper (Epinephelus lanceolatus × E. fuscoguttatus). Cloning and sequencing of the amoA gene showed that nitrifying bacteria included Nitrosomonas europea, N. stercoris, N. cryotolerans, N. eutropha, N. estuarii, eight strains of N. marina, and 15 strains not associated with described species. Nitrifying archaea included eight strains of Nitrosopumilus maritimus, N. koreensis, N. piranensis, N. adriaticus, undescribed congeners, and other undescribed archaea. The species composition of the bacterial and especially the archaeal communities was beyond that yet reported for aquaculture biofilters. While ammonia flux through the respective communities has yet to be estimated, the diverse environmental adaptations of the bacterial and archaeal communities suggest resilience of function under a range of environmental conditions.},
}
@article {pmid29406516,
year = {2018},
author = {Bowers, RM and Kyrpides, NC and Stepanauskas, R and Harmon-Smith, M and Doud, D and Reddy, TBK and Schulz, F and Jarett, J and Rivers, AR and Eloe-Fadrosh, EA and Tringe, SG and Ivanova, NN and Copeland, A and Clum, A and Becraft, ED and Malmstrom, RR and Birren, B and Podar, M and Bork, P and Weinstock, GM and Garrity, GM and Dodsworth, JA and Yooseph, S and Sutton, G and Glöckner, FO and Gilbert, JA and Nelson, WC and Hallam, SJ and Jungbluth, SP and Ettema, TJG and Tighe, S and Konstantinidis, KT and Liu, WT and Baker, BJ and Rattei, T and Eisen, JA and Hedlund, B and McMahon, KD and Fierer, N and Knight, R and Finn, R and Cochrane, G and Karsch-Mizrachi, I and Tyson, GW and Rinke, C and , and Lapidus, A and Meyer, F and Yilmaz, P and Parks, DH and Eren, AM and Schriml, L and Banfield, JF and Hugenholtz, P and Woyke, T},
title = {Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.},
journal = {Nature biotechnology},
volume = {36},
number = {2},
pages = {196},
doi = {10.1038/nbt0218-196a},
pmid = {29406516},
issn = {1546-1696},
}
@article {pmid29401401,
year = {2018},
author = {Brzezińska-Błaszczyk, E and Pawłowska, E and Płoszaj, T and Witas, H and Godzik, U and Agier, J},
title = {Presence of archaea and selected bacteria in infected root canal systems.},
journal = {Canadian journal of microbiology},
volume = {64},
number = {5},
pages = {317-326},
doi = {10.1139/cjm-2017-0531},
pmid = {29401401},
issn = {1480-3275},
mesh = {Adult ; Archaea/*genetics ; Bacterial Infections/*microbiology ; Bacteroidaceae/*genetics ; DNA, Bacterial/genetics ; Dental Pulp Cavity/microbiology ; Dental Pulp Necrosis/*microbiology ; Female ; Humans ; Male ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Young Adult ; },
abstract = {Infections of the root canal have polymicrobial etiology. The main group of microflora in the infected pulp is bacteria. There is limited data that archaea may be present in infected pulp tissue. The aim of this study was to check the prevalence of archaea in necrotic root canal samples obtained from patients with primary or post-treatment infection. The prevalence of selected bacteria species (Prevotella intermedia, Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, Synergistes sp.) in necrotic samples was evaluated as well. Sixty-four samples from root canal were collected for DNA and RNA extraction. A PCR assay based on the 16S rRNA gene was used to determine the presence of archaea and selected bacteria. Of the 64 samples, 6 were analyzed by semiquantitative reverse transcription PCR to estimate expression profiles of 16S rRNA, and another 9 were selected for direct sequencing. Archaea were detected in 48.4% samples. Statistical analysis indicated a negative association in coexistence between archaea and Treponema denticola (P < 0.05; Pearson's χ2 test). The main representative of the Archaea domain found in infected pulp tissue was Methanobrevibacter oralis. Archaea 16S rRNA gene expression was significantly lower than Synergistes sp., Porphyromonas gingivalis, and Tannerella forsythia (P < 0.05; Student's t test). Thus, it can be hypothesized that archaea may participate in the endodontic microbial community.},
}
@article {pmid29396546,
year = {2018},
author = {Gonzalez-Martinez, A and Sihvonen, M and Muñoz-Palazon, B and Rodriguez-Sanchez, A and Mikola, A and Vahala, R},
title = {Microbial ecology of full-scale wastewater treatment systems in the Polar Arctic Circle: Archaea, Bacteria and Fungi.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {2208},
doi = {10.1038/s41598-018-20633-5},
pmid = {29396546},
issn = {2045-2322},
abstract = {Seven full-scale biological wastewater treatment systems located in the Polar Arctic Circle region in Finland were investigated to determine their Archaea, Bacteria and Fungi community structure, and their relationship with the operational conditions of the bioreactors by the means of quantitative PCR, massive parallel sequencing and multivariate redundancy analysis. The results showed dominance of Archaea and Bacteria members in the bioreactors. The activated sludge systems showed strong selection of Bacteria but not for Archaea and Fungi, as suggested by diversity analyses. Core OTUs in influent and bioreactors were classified as Methanobrevibacter, Methanosarcina, Terrestrial Group Thaumarchaeota and unclassified Euryarchaeota member for Archaea; Trichococcus, Leptotrichiaceae and Comamonadaceae family, and Methylorosula for Bacteria and Trichosporonaceae family for Fungi. All influents shared core OTUs in all domains, but in bioreactors this did not occur for Bacteria. Oligotype structure of core OTUs showed several ubiquitous Fungi oligotypes as dominant in sewage and bioreactors. Multivariate redundancy analyses showed that the majority of core OTUs were related to organic matter and nutrients removal. Also, there was evidence of competition among Archaea and Fungi core OTUs, while all Bacteria OTUs were positively correlated among them. The results obtained highlighted interesting features of extremely cold temperature bioreactors.},
}
@article {pmid29390107,
year = {2018},
author = {Seyler, LM and McGuinness, LR and Gilbert, JA and Biddle, JF and Gong, D and Kerkhof, LJ},
title = {Discerning autotrophy, mixotrophy and heterotrophy in marine TACK archaea from the North Atlantic.},
journal = {FEMS microbiology ecology},
volume = {94},
number = {3},
pages = {},
doi = {10.1093/femsec/fiy014},
pmid = {29390107},
issn = {1574-6941},
abstract = {DNA stable isotope probing (SIP) was used to track the uptake of organic and inorganic carbon sources for TACK archaea (Thaumarchaeota/Aigarchaeota/Crenarchaeota/Korarchaeota) on a cruise of opportunity in the North Atlantic. Due to water limitations, duplicate samples from the deep photic (60-115 m), the mesopelagic zones (local oxygen minimum; 215-835 m) and the bathypelagic zone (2085-2835 m) were amended with various combinations of 12C- or 13C-acetate/urea/bicarbonate to assess cellular carbon acquisition. The SIP results indicated the majority of TACK archaeal operational taxonomic units (OTUs) incorporated 13C from acetate and/or urea into newly synthesized DNA within 48 h. A small fraction (16%) of the OTUs, often representing the most dominant members of the archaeal community, were able to incorporate bicarbonate in addition to organic substrates. Only two TACK archaeal OTUs were found to incorporate bicarbonate but not urea or acetate. These results further demonstrate the utility of SIP to elucidate the metabolic capability of mesothermal archaea in distinct oceanic settings and suggest that TACK archaea play a role in organic carbon recycling in the mid-depth to deep ocean.},
}
@article {pmid29371667,
year = {2018},
author = {Li, M and Wei, G and Shi, W and Sun, Z and Li, H and Wang, X and Gao, Z},
title = {Distinct distribution patterns of ammonia-oxidizing archaea and bacteria in sediment and water column of the Yellow River estuary.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {1584},
doi = {10.1038/s41598-018-20044-6},
pmid = {29371667},
issn = {2045-2322},
abstract = {Ammonia oxidation is a critical process of estuarine nitrogen cycling involving ammonia-oxidizing archaea (AOA) and bacteria (AOB). However, the distribution patterns of ammonia-oxidizing microorganisms (AOMs) between different habitats in the same area remain unclear. The present study investigated the AOMs' abundance and community compositions in both sediment and water habitats of the Yellow River estuary. Quantitative PCR (qPCR) revealed that AOA showed significant higher abundance than AOB both in sediment and water samples. AOA and AOB abundance distribution trends were consistent in sediment but distinct in water along the sampling sites. Clone library-based analyses showed that AOA sequences were affiliated with Nitrososphaera, Nitrosopumilus and Nitrosotalea clusters. Generally, Nitrososphaera was predominant in sediment, while Nitrosopumilus and Nitrosotalea dominated in water column. AOB sequences were classified into genera Nitrosospira and Nitrosomonas, and Nitrosospira dominated in both habitats. Principal coordinate analysis (PCoA) also indicated AOA community structures exhibited significant differences between two habitats, while AOB were not. Ammonium and carbon contents were the potential key factors to influence AOMs' abundance and compositions in sediment, while no measured variables were determined to have major influences on communities in water habitat. These findings increase the understanding of the AOMs' distribution patterns in estuarine ecosystems.},
}
@article {pmid29357055,
year = {2017},
author = {Bell, SD},
title = {Initiation of DNA Replication in the Archaea.},
journal = {Advances in experimental medicine and biology},
volume = {1042},
number = {},
pages = {99-115},
doi = {10.1007/978-981-10-6955-0_5},
pmid = {29357055},
issn = {0065-2598},
mesh = {Archaea/*genetics/metabolism ; Archaeal Proteins/metabolism/physiology ; Chromosomes/metabolism ; DNA Replication/*physiology ; *Replication Origin/genetics ; },
abstract = {Organisms within the archaeal domain of life possess a simplified version of the eukaryotic DNA replication machinery. While some archaea possess a bacterial-like mode of DNA replication with single origins of replication per chromosome, the majority of species characterized to date possess chromosomes with multiple replication origins. Genetic, structural, and biochemical studies have revealed the nature of archaeal origin specification. Recent work has begun to shed light on the mechanisms of replication initiation in these organisms.},
}
@article {pmid29354356,
year = {2018},
author = {Singh, A and Singh, AK},
title = {Isolation, characterization and exploring biotechnological potential of halophilic archaea from salterns of western India.},
journal = {3 Biotech},
volume = {8},
number = {1},
pages = {45},
doi = {10.1007/s13205-017-1072-3},
pmid = {29354356},
issn = {2190-572X},
abstract = {Thirteen halophilic archaea were isolated from Kandla and Bhayander salt pans. These isolates were grouped into three different genera Halobacterium, Haloferax and Haloarcula based on morphological and biochemical characterization, polar lipid analysis, Amplified 16S rDNA restriction analysis (ARDRA) and 16S rDNA sequence analysis. Biochemical characterization suggested the ability of isolates to produce protease, amylase and poly-hydroxybutyrate (PHB) indicating their biotechnological potential. The isolates were further screened for the amount of extracellular protease produced. Halobacterium sp. SP1(1) showed significant protease production compared to other isolates. Protease producing ability of the isolate was influenced by several factors such as NaCl concentration, type of protein source, metal ions and surfactants, and presence of amino acid supplements in the production medium. Soybean flour, FeCl3 and dicotylsulfosuccinate were found to increase protease production by 2.36, 1.54 and 1.26 folds, respectively compared to production in basal medium. Effect of organic solvents used in paints (n-decane, n-undecane and n-dodecane) was also investigated on protease production by the isolate. Protease production by Halobacterium sp. SP1(1) was enhanced by 1.2 folds in presence of n-decane compared to control. Furthermore, the ability of isolate to hydrolyse fish protein was investigated using three different edible fishes (Pomfret, Flat fish and Seer fish) as sole protein source. Pomfret was found to be a good protein source for protease production by the isolate. These results revealed that Halobacterium sp. SP1(1) may have potential for paint-based antifouling coating preparations and fish sauce preparation by virtue of its extracellular protease.},
}
@article {pmid29335805,
year = {2018},
author = {Oren, A and Hirschberg, J and Mann, V and Jehlička, J},
title = {Effects of nicotine on the biosynthesis of carotenoids in halophilic Archaea (class Halobacteria): an HPLC and Raman spectroscopy study.},
journal = {Extremophiles : life under extreme conditions},
volume = {22},
number = {3},
pages = {359-366},
doi = {10.1007/s00792-018-0995-x},
pmid = {29335805},
issn = {1433-4909},
support = {2221/15//Israel Science Foundation/ ; 850/13//Israel Science Foundation/ ; 17-04270S//Grantová Agentura České Republiky/ ; },
abstract = {Nicotine has a profound influence on the carotenoid metabolism in halophilic Archaea of the class Halobacteria. In a study of Halobacterium salinarum, Haloarcula marismortui and Halorubrum sodomense, using different analytical techniques to monitor the production of different carotenoids as a function of the presence of nicotine, we showed that the formation of α-bacterioruberin was inhibited in all. In Hbt. salinarum, addition of nicotine led to a significant change in the color of the culture due to the accumulation of lycopene, in addition to the formation of bisanhydrobacterioruberin which does not differ in color from α-bacterioruberin. Very little or no lycopene was formed in Har. marismortui and in Hrr. sodomense; instead bisanhydrobacterioruberin was the only major carotenoid found in nicotine-amended cultures. The findings are discussed in the framework of the recently elucidated biochemical pathway for the formation of the different carotenoid pigments encountered in the Halobacteria.},
}
@article {pmid29329319,
year = {2018},
author = {Bader, M and Müller, K and Foerstendorf, H and Schmidt, M and Simmons, K and Swanson, JS and Reed, DT and Stumpf, T and Cherkouk, A},
title = {Comparative analysis of uranium bioassociation with halophilic bacteria and archaea.},
journal = {PloS one},
volume = {13},
number = {1},
pages = {e0190953},
doi = {10.1371/journal.pone.0190953},
pmid = {29329319},
issn = {1932-6203},
mesh = {Bacteria/classification/growth &amp; development/*metabolism ; Halobacterium/classification/growth &amp; development/*metabolism ; Microscopy, Electron, Scanning ; Phylogeny ; Radioactive Waste ; Spectrometry, X-Ray Emission ; Spectroscopy, Fourier Transform Infrared ; Uranium/*metabolism ; },
abstract = {Rock salt represents a potential host rock formation for the final disposal of radioactive waste. The interactions between indigenous microorganisms and radionuclides, e.g. uranium, need to be investigated to better predict the influence of microorganisms on the safety assessment of the repository. Hence, the association process of uranium with two microorganisms isolated from rock salt was comparatively studied. Brachybacterium sp. G1, which was isolated from the German salt dome Gorleben, and Halobacterium noricense DSM15987T, were selected as examples of a moderately halophilic bacterium and an extremely halophilic archaeon, respectively. The microorganisms exhibited completely different association behaviors with uranium. While a pure biosorption process took place with Brachybacterium sp. G1 cells, a multistage association process occurred with the archaeon. In addition to batch experiments, in situ attenuated total reflection Fourier-transform infrared spectroscopy was applied to characterize the U(VI) interaction process. Biosorption was identified as the dominating process for Brachybacterium sp. G1 with this method. Carboxylic functionalities are the dominant interacting groups for the bacterium, whereas phosphoryl groups are also involved in U(VI) association by the archaeon H. noricense.},
}
@article {pmid29322393,
year = {2018},
author = {Srithep, P and Pornkulwat, P and Limpiyakorn, T},
title = {Contribution of ammonia-oxidizing archaea and ammonia-oxidizing bacteria to ammonia oxidation in two nitrifying reactors.},
journal = {Environmental science and pollution research international},
volume = {25},
number = {9},
pages = {8676-8687},
doi = {10.1007/s11356-017-1155-z},
pmid = {29322393},
issn = {1614-7499},
support = {RSA5780036//Thailand Research Fund (TH)/ ; },
abstract = {In this study, two laboratory nitrifying reactors (NRI and NRII), which were seeded by sludge from different sources and operated under different operating conditions, were found to possess distinct dominant ammonia-oxidizing microorganisms. Ammonia-oxidizing archaeal (AOA) amoA genes outnumbered ammonia-oxidizing bacterial (AOB) amoA genes in reactor NRI, while only AOB amoA genes were detectable in reactor NRII. The AOA amoA gene sequences retrieved from NRI were characterized within the Nitrososphaera sister cluster of the group 1.1b Thaumarchaeota. Two inhibitors for ammonia oxidation, allylthiourea (ATU) and 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO), were applied individually and as a mixture to observe the ammonia-oxidizing activity of both microorganisms in the reactors' sludge. The results indicated that AOA and AOB jointly oxidized ammonia in NRI, while AOB played the main role in ammonia oxidation in NRII. DNA-stable isotope probing with labeled 13C-HCO3- was performed on NRI sludge. Incorporation of 13C into AOA and AOB implied that both microorganisms may perform autotrophy during ammonia oxidation. Taken together, the results from this study provide direct evidence demonstrating the contribution of AOA and AOB to ammonia oxidation in the nitrifying reactors.},
}
@article {pmid29268981,
year = {2018},
author = {Kelman, LM and Kelman, Z},
title = {Do Archaea Need an Origin of Replication?.},
journal = {Trends in microbiology},
volume = {26},
number = {3},
pages = {172-174},
doi = {10.1016/j.tim.2017.12.001},
pmid = {29268981},
issn = {1878-4380},
abstract = {Chromosomal DNA replication starts at a specific region called an origin of replication. Until recently, all organisms were thought to require origins to replicate their chromosomes. It was recently discovered that some archaeal species do not utilize origins of replication under laboratory growth conditions.},
}
@article {pmid29235710,
year = {2018},
author = {Xie, W and Luo, H and Murugapiran, SK and Dodsworth, JA and Chen, S and Sun, Y and Hedlund, BP and Wang, P and Fang, H and Deng, M and Zhang, CL},
title = {Localized high abundance of Marine Group II archaea in the subtropical Pearl River Estuary: implications for their niche adaptation.},
journal = {Environmental microbiology},
volume = {20},
number = {2},
pages = {734-754},
doi = {10.1111/1462-2920.14004},
pmid = {29235710},
issn = {1462-2920},
abstract = {Marine Group II archaea are widely distributed in global oceans and dominate the total archaeal community within the upper euphotic zone of temperate waters. However, factors controlling the distribution of MGII are poorly delineated and the physiology and ecological functions of these still-uncultured organisms remain elusive. In this study, we investigated the planktonic MGII associated with particles and in free-living forms in the Pearl River Estuary (PRE) over a 10-month period. We detected high abundance of particle-associated MGII in PRE (up to ∼108 16S rRNA gene copies/l), which was around 10-fold higher than the free-living MGII in the same region, and an order of magnitude higher than previously reported in other marine environments. 10‰ salinity appeared to be a threshold value for these MGII because MGII abundance decreased sharply below it. Above 10‰ salinity, the abundance of MGII on the particles was positively correlated with phototrophs and MGII in the surface water was negatively correlated with irradiance. However, the abundances of those free-living MGII showed positive correlations with salinity and temperature, suggesting the different physiological characteristics between particle-attached and free-living MGIIs. A nearly completely assembled metagenome, MGIIa_P, was recovered using metagenome binning methods. Compared with the other two MGII genomes from surface ocean, MGIIa_P contained higher proportions of glycoside hydrolases, indicating the ability of MGIIa_P to hydrolyse glycosidic bonds in complex sugars in PRE. MGIIa_P is the first assembled MGII metagenome containing a catalase gene, which might be involved in scavenging reactive oxygen species generated by the abundant phototrophs in the eutrophic PRE. Our study presented the widespread and high abundance of MGII in the water columns of PRE, and characterized the determinant abiotic factors affecting their distribution. Their association with heterotrophs, preference for particles and resourceful metabolic traits indicate MGII might play a significant role in metabolising organic matters in the PRE and other temperate estuarine systems.},
}
@article {pmid29222443,
year = {2018},
author = {Chen, LX and Méndez-García, C and Dombrowski, N and Servín-Garcidueñas, LE and Eloe-Fadrosh, EA and Fang, BZ and Luo, ZH and Tan, S and Zhi, XY and Hua, ZS and Martinez-Romero, E and Woyke, T and Huang, LN and Sánchez, J and Peláez, AI and Ferrer, M and Baker, BJ and Shu, WS},
title = {Metabolic versatility of small archaea Micrarchaeota and Parvarchaeota.},
journal = {The ISME journal},
volume = {12},
number = {3},
pages = {756-775},
doi = {10.1038/s41396-017-0002-z},
pmid = {29222443},
issn = {1751-7370},
abstract = {Small acidophilic archaea belonging to Micrarchaeota and Parvarchaeota phyla are known to physically interact with some Thermoplasmatales members in nature. However, due to a lack of cultivation and limited genomes on hand, their biodiversity, metabolisms, and physiologies remain largely unresolved. Here, we obtained 39 genomes from acid mine drainage (AMD) and hot spring environments around the world. 16S rRNA gene based analyses revealed that Parvarchaeota were only detected in AMD and hot spring habitats, while Micrarchaeota were also detected in others including soil, peat, hypersaline mat, and freshwater, suggesting a considerable higher diversity and broader than expected habitat distribution for this phylum. Despite their small genomes (0.64-1.08 Mb), these archaea may contribute to carbon and nitrogen cycling by degrading multiple saccharides and proteins, and produce ATP via aerobic respiration and fermentation. Additionally, we identified several syntenic genes with homology to those involved in iron oxidation in six Parvarchaeota genomes, suggesting their potential role in iron cycling. However, both phyla lack biosynthetic pathways for amino acids and nucleotides, suggesting that they likely scavenge these biomolecules from the environment and/or other community members. Moreover, low-oxygen enrichments in laboratory confirmed our speculation that both phyla are microaerobic/anaerobic, based on several specific genes identified in them. Furthermore, phylogenetic analyses provide insights into the close evolutionary history of energy related functionalities between both phyla with Thermoplasmatales. These results expand our understanding of these elusive archaea by revealing their involvement in carbon, nitrogen, and iron cycling, and suggest their potential interactions with Thermoplasmatales on genomic scale.},
}
@article {pmid29218041,
year = {2017},
author = {Ito, M and Morino, M and Krulwich, TA},
title = {Mrp Antiporters Have Important Roles in Diverse Bacteria and Archaea.},
journal = {Frontiers in microbiology},
volume = {8},
number = {},
pages = {2325},
doi = {10.3389/fmicb.2017.02325},
pmid = {29218041},
issn = {1664-302X},
support = {R01 GM028454/GM/NIGMS NIH HHS/United States ; },
abstract = {Mrp (Multiple resistance and pH) antiporter was identified as a gene complementing an alkaline-sensitive mutant strain of alkaliphilic Bacillus halodurans C-125 in 1990. At that time, there was no example of a multi-subunit type Na+/H+ antiporter comprising six or seven hydrophobic proteins, and it was newly designated as the monovalent cation: proton antiporter-3 (CPA3) family in the classification of transporters. The Mrp antiporter is broadly distributed among bacteria and archaea, not only in alkaliphiles. Generally, all Mrp subunits, mrpA-G, are required for enzymatic activity. Two exceptions are Mrp from the archaea Methanosarcina acetivorans and the eubacteria Natranaerobius thermophilus, which are reported to sustain Na+/H+ antiport activity with the MrpA subunit alone. Two large subunits of the Mrp antiporter, MrpA and MrpD, are homologous to membrane-embedded subunits of the respiratory chain complex I, NuoL, NuoM, and NuoN, and the small subunit MrpC has homology with NuoK. The functions of the Mrp antiporter include sodium tolerance and pH homeostasis in an alkaline environment, nitrogen fixation in Schizolobium meliloti, bile salt tolerance in Bacillus subtilis and Vibrio cholerae, arsenic oxidation in Agrobacterium tumefaciens, pathogenesis in Pseudomonas aeruginosa and Staphylococcus aureus, and the conversion of energy involved in metabolism and hydrogen production in archaea. In addition, some Mrp antiporters transport K+ and Ca2+ instead of Na+, depending on the environmental conditions. Recently, the molecular structure of the respiratory chain complex I has been elucidated by others, and details of the mechanism by which it transports protons are being clarified. Based on this, several hypotheses concerning the substrate transport mechanism in the Mrp antiporter have been proposed. The MrpA and MrpD subunits, which are homologous to the proton transport subunit of complex I, are involved in the transport of protons and their coupling cations. Herein, we outline other recent findings on the Mrp antiporter.},
}
@article {pmid29208997,
year = {2017},
author = {Miot, J and Bernard, S and Bourreau, M and Guyot, F and Kish, A},
title = {Experimental maturation of Archaea encrusted by Fe-phosphates.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {16984},
doi = {10.1038/s41598-017-17111-9},
pmid = {29208997},
issn = {2045-2322},
abstract = {Burial is generally detrimental to the preservation of biological signals. It has often been assumed that (bio)mineral-encrusted microorganisms are more resistant to burial-induced degradation than non-encrusted ones over geological timescales. For the present study, we submitted Sulfolobus acidocaldarius experimentally encrusted by amorphous Fe phosphates to constrained temperature conditions (150 °C) under pressure for 1 to 5 days, thereby simulating burial-induced processes. We document the molecular and mineralogical evolution of these assemblages down to the sub-micrometer scale using X-ray diffraction, scanning and transmission electron microscopies and synchrotron-based X-ray absorption near edge structure spectroscopy at the carbon K-edge. The present results demonstrate that the presence of Fe-phosphates enhances the chemical degradation of microbial organic matter. While Fe-phosphates remained amorphous in abiotic controls, crystalline lipscombite (FeIIxFeIII3-x(PO4)2(OH)3-x) entrapping organic matter formed in the presence of S. acidocaldarius cells. Lipscombite textures (framboidal vs. bipyramidal) appeared only controlled by the initial level of encrustation of the cells, suggesting that the initial organic matter to mineral ratio influences the competition between nucleation and crystal growth. Altogether these results highlight the important interplay between minerals and organic matter during fossilization, which should be taken into account when interpreting the fossil record.},
}
@article {pmid29208747,
year = {2017},
author = {Makarova, KS and Galperin, MY and Koonin, EV},
title = {Proposed Role for KaiC-Like ATPases as Major Signal Transduction Hubs in Archaea.},
journal = {mBio},
volume = {8},
number = {6},
pages = {},
doi = {10.1128/mBio.01959-17},
pmid = {29208747},
issn = {2150-7511},
abstract = {All organisms must adapt to ever-changing environmental conditions and accordingly have evolved diverse signal transduction systems. In bacteria, the most abundant networks are built around the two-component signal transduction systems that include histidine kinases and receiver domains. In contrast, eukaryotic signal transduction is dominated by serine/threonine/tyrosine protein kinases. Both of these systems are also found in archaea, but they are not as common and diversified as their bacterial and eukaryotic counterparts, suggesting the possibility that archaea have evolved other, still uncharacterized signal transduction networks. Here we propose a role for KaiC family ATPases, known to be key components of the circadian clock in cyanobacteria, in archaeal signal transduction. The KaiC family is notably expanded in most archaeal genomes, and although most of these ATPases remain poorly characterized, members of the KaiC family have been shown to control archaellum assembly and have been found to be a stable component of the gas vesicle system in Halobacteria Computational analyses described here suggest that KaiC-like ATPases and their homologues with inactivated ATPase domains are involved in many other archaeal signal transduction pathways and comprise major hubs of complex regulatory networks. We predict numerous input and output domains that are linked to KaiC-like proteins, including putative homologues of eukaryotic DEATH domains that could function as adapters in archaeal signaling networks. We further address the relationships of the archaeal family of KaiC homologues to the bona fide KaiC of cyanobacteria and implications for the existence of a KaiC-based circadian clock apparatus in archaea.IMPORTANCE Little is currently known about signal transduction pathways in Archaea Recent studies indicate that KaiC-like ATPases, known as key components of the circadian clock apparatus in cyanobacteria, are involved in the regulation of archaellum assembly and, likely, type IV pili and the gas vesicle system in Archaea We performed comprehensive comparative genomic analyses of the KaiC family. A vast protein interaction network was revealed, with KaiC family proteins as hubs for numerous input and output components, many of which are shared with two-component signal transduction systems. Putative KaiC-based signal transduction systems are predicted to regulate the activities of membrane-associated complexes and individual proteins, such as signal recognition particle and membrane transporters, and also could be important for oxidative stress response regulation. KaiC-centered signal transduction networks are predicted to play major roles in archaeal physiology, and this work is expected to stimulate their experimental characterization.},
}
@article {pmid29198957,
year = {2018},
author = {Kazlauskas, D and Sezonov, G and Charpin, N and Venclovas, Č and Forterre, P and Krupovic, M},
title = {Novel Families of Archaeo-Eukaryotic Primases Associated with Mobile Genetic Elements of Bacteria and Archaea.},
journal = {Journal of molecular biology},
volume = {430},
number = {5},
pages = {737-750},
doi = {10.1016/j.jmb.2017.11.014},
pmid = {29198957},
issn = {1089-8638},
support = {340440//European Research Council/International ; },
abstract = {Cellular organisms in different domains of life employ structurally unrelated, non-homologous DNA primases for synthesis of a primer for DNA replication. Archaea and eukaryotes encode enzymes of the archaeo-eukaryotic primase (AEP) superfamily, whereas bacteria uniformly use primases of the DnaG family. However, AEP genes are widespread in bacterial genomes raising questions regarding their provenance and function. Here, using an archaeal primase-polymerase PolpTN2 encoded by pTN2 plasmid as a seed for sequence similarity searches, we recovered over 800 AEP homologs from bacteria belonging to 12 highly diverse phyla. These sequences formed a supergroup, PrimPol-PV1, and could be classified into five novel AEP families which are characterized by a conserved motif containing an arginine residue likely to be involved in nucleotide binding. Functional assays confirm the essentiality of this motif for catalytic activity of the PolpTN2 primase-polymerase. Further analyses showed that bacterial AEPs display a range of domain organizations and uncovered several candidates for novel families of helicases. Furthermore, sequence and structure comparisons suggest that PriCT-1 and PriCT-2 domains frequently fused to the AEP domains are related to each other as well as to the non-catalytic, large subunit of archaeal and eukaryotic primases, and to the recently discovered PriX subunit of archaeal primases. Finally, genomic neighborhood analysis indicates that the identified AEPs encoded in bacterial genomes are nearly exclusively associated with highly diverse integrated mobile genetic elements, including integrative conjugative plasmids and prophages.},
}
@article {pmid29194812,
year = {2018},
author = {Chaudhury, P and Quax, TEF and Albers, SV},
title = {Versatile cell surface structures of archaea.},
journal = {Molecular microbiology},
volume = {107},
number = {3},
pages = {298-311},
doi = {10.1111/mmi.13889},
pmid = {29194812},
issn = {1365-2958},
abstract = {Archaea are ubiquitously present in nature and colonize environments with broadly varying growth conditions. Several surface appendages support their colonization of new habitats. A hallmark of archaea seems to be the high abundance of type IV pili (T4P). However, some unique non T4 filaments are present in a number of archaeal species. Archaeal surface structures can mediate different processes such as cellular surface adhesion, DNA exchange, motility and biofilm formation and represent an initial attachment site for infecting viruses. In addition to the functionally characterized archaeal T4P, archaeal genomes encode a large number of T4P components that might form yet undiscovered surface structures with novel functions. In this review, we summarize recent advancement in structural and functional characterizations of known archaeal surface structures and highlight the diverse processes in which they play a role.},
}
@article {pmid29184545,
year = {2017},
author = {Yang, W and Wang, Y and Tago, K and Tokuda, S and Hayatsu, M},
title = {Comparison of the Effects of Phenylhydrazine Hydrochloride and Dicyandiamide on Ammonia-Oxidizing Bacteria and Archaea in Andosols.},
journal = {Frontiers in microbiology},
volume = {8},
number = {},
pages = {2226},
doi = {10.3389/fmicb.2017.02226},
pmid = {29184545},
issn = {1664-302X},
abstract = {Dicyandiamide, a routinely used commercial nitrification inhibitor (NI), inhibits ammonia oxidation catalyzed by ammonia monooxygenase (AMO). Phenylhydrazine hydrochloride has shown considerable potential for the development of next-generation NIs targeting hydroxylamine dehydrogenase (HAO). The effects of the AMO inhibitor and the HAO inhibitor on ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) present in agricultural soils have not been compared thus far. In the present study, the effects of the two inhibitors on soil nitrification and the abundance of AOA and AOB as well as their community structure were investigated in a soil microcosm using quantitative polymerase chain reaction and pyrosequencing. The net nitrification rates and the growth of AOA and AOB in this soil microcosm were inhibited by both NIs. Both NIs had limited effect on the community structure of AOB and no effect on that of AOA in this soil microcosm. The effects of phenylhydrazine hydrochloride were similar to those of dicyandiamide. These results indicated that organohydrazine-based NIs have potential for the development of next-generation NIs targeting HAO in the future.},
}
@article {pmid29178818,
year = {2017},
author = {Martinez-Pastor, M and Tonner, PD and Darnell, CL and Schmid, AK},
title = {Transcriptional Regulation in Archaea: From Individual Genes to Global Regulatory Networks.},
journal = {Annual review of genetics},
volume = {51},
number = {},
pages = {143-170},
doi = {10.1146/annurev-genet-120116-023413},
pmid = {29178818},
issn = {1545-2948},
mesh = {Adaptation, Biological/genetics ; Archaea/*genetics/metabolism ; Archaeal Proteins/*genetics/metabolism ; Chromosome Mapping ; *Gene Expression Regulation, Archaeal ; *Gene Regulatory Networks ; Gene-Environment Interaction ; *Genome, Archaeal ; Metabolic Networks and Pathways/genetics ; Stress, Physiological/genetics ; Systems Biology/methods ; Transcription Factors/*genetics/metabolism ; *Transcription, Genetic ; },
abstract = {Archaea are major contributors to biogeochemical cycles, possess unique metabolic capabilities, and resist extreme stress. To regulate the expression of genes encoding these unique programs, archaeal cells use gene regulatory networks (GRNs) composed of transcription factor proteins and their target genes. Recent developments in genetics, genomics, and computational methods used with archaeal model organisms have enabled the mapping and prediction of global GRN structures. Experimental tests of these predictions have revealed the dynamical function of GRNs in response to environmental variation. Here, we review recent progress made in this area, from investigating the mechanisms of transcriptional regulation of individual genes to small-scale subnetworks and genome-wide global networks. At each level, archaeal GRNs consist of a hybrid of bacterial, eukaryotic, and uniquely archaeal mechanisms. We discuss this theme from the perspective of the role of individual transcription factors in genome-wide regulation, how these proteins interact to compile GRN topological structures, and how these topologies lead to emergent, high-level GRN functions. We conclude by discussing how systems biology approaches are a fruitful avenue for addressing remaining challenges, such as discovering gene function and the evolution of GRNs.},
}
@article {pmid29176585,
year = {2018},
author = {Eme, L and Spang, A and Lombard, J and Stairs, CW and Ettema, TJG},
title = {Archaea and the origin of eukaryotes.},
journal = {Nature reviews. Microbiology},
volume = {16},
number = {2},
pages = {120},
doi = {10.1038/nrmicro.2017.154},
pmid = {29176585},
issn = {1740-1534},
abstract = {This corrects the article DOI: 10.1038/nrmicro.2017.133.},
}
@article {pmid29175107,
year = {2018},
author = {Krupovic, M and Cvirkaite-Krupovic, V and Iranzo, J and Prangishvili, D and Koonin, EV},
title = {Viruses of archaea: Structural, functional, environmental and evolutionary genomics.},
journal = {Virus research},
volume = {244},
number = {},
pages = {181-193},
doi = {10.1016/j.virusres.2017.11.025},
pmid = {29175107},
issn = {1872-7492},
support = {Z01 LM000073-12/NULL/Intramural NIH HHS/United States ; },
abstract = {Viruses of archaea represent one of the most enigmatic parts of the virosphere. Most of the characterized archaeal viruses infect extremophilic hosts and display remarkable diversity of virion morphotypes, many of which have never been observed among viruses of bacteria or eukaryotes. The uniqueness of the virion morphologies is matched by the distinctiveness of the genomes of these viruses, with ∼75% of genes encoding unique proteins, refractory to functional annotation based on sequence analyses. In this review, we summarize the state-of-the-art knowledge on various aspects of archaeal virus genomics. First, we outline how structural and functional genomics efforts provided valuable insights into the functions of viral proteins and revealed intricate details of the archaeal virus-host interactions. We then highlight recent metagenomics studies, which provided a glimpse at the diversity of uncultivated viruses associated with the ubiquitous archaea in the oceans, including Thaumarchaeota, Marine Group II Euryarchaeota, and others. These findings, combined with the recent discovery that archaeal viruses mediate a rapid turnover of thaumarchaea in the deep sea ecosystems, illuminate the prominent role of these viruses in the biosphere. Finally, we discuss the origins and evolution of archaeal viruses and emphasize the evolutionary relationships between viruses and non-viral mobile genetic elements. Further exploration of the archaeal virus diversity as well as functional studies on diverse virus-host systems are bound to uncover novel, unexpected facets of the archaeal virome.},
}
@article {pmid29170214,
year = {2017},
author = {Pennisi, E},
title = {Survey of archaea in the body reveals other microbial guests.},
journal = {Science (New York, N.Y.)},
volume = {358},
number = {6366},
pages = {983},
doi = {10.1126/science.358.6366.983},
pmid = {29170214},
issn = {1095-9203},
mesh = {Constipation/microbiology ; Digestion ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Humans ; Lung/microbiology ; Methane/*biosynthesis ; Methanobrevibacter/*pathogenicity ; Nose/microbiology ; Skin/microbiology ; },
}
@article {pmid29138298,
year = {2017},
author = {Koskinen, K and Pausan, MR and Perras, AK and Beck, M and Bang, C and Mora, M and Schilhabel, A and Schmitz, R and Moissl-Eichinger, C},
title = {First Insights into the Diverse Human Archaeome: Specific Detection of Archaea in the Gastrointestinal Tract, Lung, and Nose and on Skin.},
journal = {mBio},
volume = {8},
number = {6},
pages = {},
doi = {10.1128/mBio.00824-17},
pmid = {29138298},
issn = {2150-7511},
mesh = {Archaea/*classification/genetics/*isolation &amp; purification ; Gastrointestinal Tract/*microbiology ; Humans ; Lung/*microbiology ; Metagenomics/methods ; *Microbiota ; Nose/*microbiology ; Polymerase Chain Reaction/methods ; Skin/*microbiology ; },
abstract = {Human-associated archaea remain understudied in the field of microbiome research, although in particular methanogenic archaea were found to be regular commensals of the human gut, where they represent keystone species in metabolic processes. Knowledge on the abundance and diversity of human-associated archaea is extremely limited, and little is known about their function(s), their overall role in human health, or their association with parts of the human body other than the gastrointestinal tract and oral cavity. Currently, methodological issues impede the full assessment of the human archaeome, as bacteria-targeting protocols are unsuitable for characterization of the full spectrum of Archaea The goal of this study was to establish conservative protocols based on specifically archaea-targeting, PCR-based methods to retrieve first insights into the archaeomes of the human gastrointestinal tract, lung, nose, and skin. Detection of Archaea was highly dependent on primer selection and the sequence processing pipeline used. Our results enabled us to retrieve a novel picture of the human archaeome, as we found for the first time Methanobacterium and Woesearchaeota (DPANN superphylum) to be associated with the human gastrointestinal tract and the human lung, respectively. Similar to bacteria, human-associated archaeal communities were found to group biogeographically, forming (i) the thaumarchaeal skin landscape, (ii) the (methano)euryarchaeal gastrointestinal tract, (iii) a mixed skin-gastrointestinal tract landscape for the nose, and (iv) a woesearchaeal lung landscape. On the basis of the protocols we used, we were able to detect unexpectedly high diversity of archaea associated with different body parts.IMPORTANCE In summary, our study highlights the importance of the primers and data processing pipeline used to study the human archaeome. We were able to establish protocols that revealed the presence of previously undetected Archaea in all of the tissue samples investigated and to detect biogeographic patterns of the human archaeome in the gastrointestinal tract and on the skin and for the first time in the respiratory tract, i.e., the nose and lungs. Our results are a solid basis for further investigation of the human archaeome and, in the long term, discovery of the potential role of archaea in human health and disease.},
}
@article {pmid29138003,
year = {2018},
author = {Stancik, IA and Šestak, MS and Ji, B and Axelson-Fisk, M and Franjevic, D and Jers, C and Domazet-Lošo, T and Mijakovic, I},
title = {Serine/Threonine Protein Kinases from Bacteria, Archaea and Eukarya Share a Common Evolutionary Origin Deeply Rooted in the Tree of Life.},
journal = {Journal of molecular biology},
volume = {430},
number = {1},
pages = {27-32},
doi = {10.1016/j.jmb.2017.11.004},
pmid = {29138003},
issn = {1089-8638},
mesh = {Amino Acid Sequence ; Archaea/*genetics ; Bacteria/*genetics ; Eukaryota/*genetics ; Evolution, Molecular ; Protein-Serine-Threonine Kinases/*genetics ; },
abstract = {The main family of serine/threonine/tyrosine protein kinases present in eukarya was defined and described by Hanks et al. in 1988 (Science, 241, 42-52). It was initially believed that these kinases do not exist in bacteria, but extensive genome sequencing revealed their existence in many bacteria. For historical reasons, the term &quot;eukaryotic-type kinases&quot; propagated in the literature to describe bacterial members of this protein family. Here, we argue that this term should be abandoned as a misnomer, and we provide several lines of evidence to support this claim. Our comprehensive phylostratigraphic analysis suggests that Hanks-type kinases present in eukarya, bacteria and archaea all share a common evolutionary origin in the lineage leading to the last universal common ancestor (LUCA). We found no evidence to suggest substantial horizontal transfer of genes encoding Hanks-type kinases from eukarya to bacteria. Moreover, our systematic structural comparison suggests that bacterial Hanks-type kinases resemble their eukaryal counterparts very closely, while their structures appear to be dissimilar from other kinase families of bacterial origin. This indicates that a convergent evolution scenario, by which bacterial kinases could have evolved a kinase domain similar to that of eukaryal Hanks-type kinases, is not very likely. Overall, our results strongly support a monophyletic origin of all Hanks-type kinases, and we therefore propose that this term should be adopted as a universal name for this protein family.},
}
@article {pmid29123229,
year = {2017},
author = {},
title = {A flourishing field: going back to the roots of the Archaea.},
journal = {Nature reviews. Microbiology},
volume = {15},
number = {12},
pages = {705},
doi = {10.1038/nrmicro.2017.144},
pmid = {29123229},
issn = {1740-1534},
}
@article {pmid29123225,
year = {2017},
author = {Eme, L and Spang, A and Lombard, J and Stairs, CW and Ettema, TJG},
title = {Archaea and the origin of eukaryotes.},
journal = {Nature reviews. Microbiology},
volume = {15},
number = {12},
pages = {711-723},
doi = {10.1038/nrmicro.2017.133},
pmid = {29123225},
issn = {1740-1534},
mesh = {Archaea/*genetics ; *Biological Evolution ; Eukaryota/*genetics ; Pharmacogenomic Variants ; },
abstract = {Woese and Fox's 1977 paper on the discovery of the Archaea triggered a revolution in the field of evolutionary biology by showing that life was divided into not only prokaryotes and eukaryotes. Rather, they revealed that prokaryotes comprise two distinct types of organisms, the Bacteria and the Archaea. In subsequent years, molecular phylogenetic analyses indicated that eukaryotes and the Archaea represent sister groups in the tree of life. During the genomic era, it became evident that eukaryotic cells possess a mixture of archaeal and bacterial features in addition to eukaryotic-specific features. Although it has been generally accepted for some time that mitochondria descend from endosymbiotic alphaproteobacteria, the precise evolutionary relationship between eukaryotes and archaea has continued to be a subject of debate. In this Review, we outline a brief history of the changing shape of the tree of life and examine how the recent discovery of a myriad of diverse archaeal lineages has changed our understanding of the evolutionary relationships between the three domains of life and the origin of eukaryotes. Furthermore, we revisit central questions regarding the process of eukaryogenesis and discuss what can currently be inferred about the evolutionary transition from the first to the last eukaryotic common ancestor.},
}
@article {pmid29118356,
year = {2017},
author = {Nordgård, ASR and Bergland, WH and Vadstein, O and Mironov, V and Bakke, R and Østgaard, K and Bakke, I},
title = {Anaerobic digestion of pig manure supernatant at high ammonia concentrations characterized by high abundances of Methanosaeta and non-euryarchaeotal archaea.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {15077},
doi = {10.1038/s41598-017-14527-1},
pmid = {29118356},
issn = {2045-2322},
abstract = {We examined the effect of ammonium and temperature on methane production in high rate upflow anaerobic sludge bed reactors treating pig manure supernatant. We operated four reactors at two ammonium concentrations ('low' at 1.9, 'high' at 3.7 g L-1, termed LA and HA reactors, respectively) and at variable temperatures over 358 days. Archaeal and bacterial communities were characterized by Illumina sequencing of 16S rRNA amplicons. Ammonium was a major selective factor for bacterial and archaeal community structure. After ~200 days of adaptation to high ammonium levels, acetate and propionate removal and methane production improved substantially in HA reactors. Aceticlastic Methanosaeta was abundant and positively correlated to methane yield in the HA reactors, whereas Methanosarcina was more abundant in LA reactors. Furthermore, a group of monophyletic OTUs that was related to Thaumarchaeota in phylogenetic analysis was highly abundant in the archaeal communities, particularly in the HA reactors. The most abundant bacterial OTU in LA reactors, representing Syntrophomonadaceae, was also positively correlated to methane yield in the HA reactors, indicating its importance in methane production under ammonia stress. In conclusion, efficient methane production, involving aceticlastic methanogenesis by Methanosaeta took place in the reactors at free ammonia concentrations as high as 1 g L-1.},
}
@article {pmid29109713,
year = {2017},
author = {Xia, X and Guo, W and Liu, H},
title = {Basin Scale Variation on the Composition and Diversity of Archaea in the Pacific Ocean.},
journal = {Frontiers in microbiology},
volume = {8},
number = {},
pages = {2057},
doi = {10.3389/fmicb.2017.02057},
pmid = {29109713},
issn = {1664-302X},
abstract = {The Archaea are a widely distributed group of prokaryotes that inhabit and thrive in many different environments. In the sea, they play key roles in various global biogeochemical processes. Here, in order to investigate the vertical profiles of archaeal community across a large geographic distance, the compositions of archaeal communities in seven seawater columns in the Pacific Ocean were investigated using high throughput 454 pyrosequencing of the 16S rRNA gene. The surface archaeal communities showed lower diversity and greater variability than those in the deeper layers. Two of the major archaeal phyla that displayed different depth preferences were Thaumarchaeota and Euryarchaeota. The majority of Thaumarchaeota belonged to Marine Group I (MGI), which had high relative abundance in deep water. In contrast, Euryarchaeota, which mainly consisted of Marine Group II (MGII) and III (MGIII), were dominant in the surface layer. Compared with MGI and MGII, MGIII were less abundant in seawater and generally absent from the surface water of the subarctic Pacific. In addition, niche separation in the MGI, MGII, and MGIII subgroups was also observed. For example, MGI.C and MGII.A (the major subgroups of MGI and MGII, respectively) displayed a strong negative correlation with each other. The highest level of archaeal diversity was found in the core of an oxygen minimum zone (OMZ) located off Costa Rica, which resulted from the co-occurrence of both anaerobic and aerobic archaea. For example, methanotrophic archaea ANME-2, methanogenic archaea and several sediment origin archaea, such as Marine Benthic Group A (MBGA) and Bathyarchaeota, were all detected at relatively high abundance in the OMZ. Together, our findings indicate that vertical heterogeneities along water columns and latitudinal differentiation in the surface waters are ubiquitous features of archaeal communities in the Pacific Ocean, and the OMZ off Costa Rica is an archaeal biodiversity hot-spot.},
}
@article {pmid29107227,
year = {2018},
author = {Wang, L and Li, Y and Niu, L and Zhang, W and Zhang, H and Wang, L and Wang, P},
title = {Response of ammonia oxidizing archaea and bacteria to decabromodiphenyl ether and copper contamination in river sediments.},
journal = {Chemosphere},
volume = {191},
number = {},
pages = {858-867},
doi = {10.1016/j.chemosphere.2017.10.067},
pmid = {29107227},
issn = {1879-1298},
mesh = {Ammonia/*metabolism ; Archaea/*metabolism ; Bacteria/*metabolism ; Copper/*metabolism ; Environmental Pollutants/analysis/*metabolism ; Geologic Sediments/*chemistry ; Halogenated Diphenyl Ethers/*analysis ; Metals, Heavy/metabolism ; Nitrogen Cycle ; Oxidation-Reduction ; Oxidoreductases/metabolism ; Rivers/*microbiology ; },
abstract = {Ammonia oxidation plays a fundamental role in river nitrogen cycling ecosystems, which is normally governed by both ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB). Co-contamination of typical emerging pollutant Polybrominated diphenyl ethers (PBDEs) and heavy metal on AOA and AOB communities in river sediments remains unknown. In this study, multiple analytical tools, including high-throughput pyrosequencing and real-time quantitative PCR (qPCR), were used to reveal the ammonia monooxygenase (AMO) activity, subunit alpha (amoA) gene abundance, and community structures of AOA and AOB in river sediments. It was found that the inhibition of AMO activities was increased with the increase of decabromodiphenyl ether (BDE 209, 1-100 mg kg-1) and copper (Cu, 50-500 mg kg-1) concentrations. Moreover, the synergic effects of BDE 209 and Cu resulted in a higher AMO activity reduction than the individual pollutant BDE 209. The AOA amoA copy number declined by 75.9% and 83.2% and AOB amoA gene abundance declined 82.8% and 90.0% at 20 and 100 mg kg-1 BDE 209 with a 100 mg kg-1 Cu co-contamination, respectively. The pyrosequencing results showed that both AOB and AOA community structures were altered, with a higher change of AOB than that of AOA. The results demonstrated that the AOB microbial community may be better adapted to BDE 209 and Cu pollution, while AOA might possess a greater capacity for stress resistance. Our study provides a better understanding of the ecotoxicological effects of heavy metal and micropollutant combined exposure on AOA and AOB in river sediments.},
}
@article {pmid29098760,
year = {2017},
author = {Herbold, CW and Lehtovirta-Morley, LE and Jung, MY and Jehmlich, N and Hausmann, B and Han, P and Loy, A and Pester, M and Sayavedra-Soto, LA and Rhee, SK and Prosser, JI and Nicol, GW and Wagner, M and Gubry-Rangin, C},
title = {Ammonia-oxidising archaea living at low pH: Insights from comparative genomics.},
journal = {Environmental microbiology},
volume = {19},
number = {12},
pages = {4939-4952},
doi = {10.1111/1462-2920.13971},
pmid = {29098760},
issn = {1462-2920},
support = {294343//European Research Council/International ; },
mesh = {Ammonia/*metabolism ; Base Sequence ; Biological Evolution ; DNA, Archaeal/genetics ; Euryarchaeota/*genetics/*metabolism ; Gene Transfer, Horizontal ; Genome, Archaeal/*genetics ; Genomics ; Nitrification/*physiology ; Oxidation-Reduction ; Phylogeny ; Proteomics ; Sequence Analysis, DNA ; Soil/chemistry ; Soil Microbiology ; },
abstract = {Obligate acidophilic members of the thaumarchaeotal genus Candidatus Nitrosotalea play an important role in nitrification in acidic soils, but their evolutionary and physiological adaptations to acidic environments are still poorly understood, with only a single member of this genus (Ca. N. devanaterra) having its genome sequenced. In this study, we sequenced the genomes of two additional cultured Ca. Nitrosotalea strains, extracted an almost complete Ca. Nitrosotalea metagenome-assembled genome from an acidic fen, and performed comparative genomics of the four Ca. Nitrosotalea genomes with 19 other archaeal ammonia oxidiser genomes. Average nucleotide and amino acid identities revealed that the four Ca. Nitrosotalea strains represent separate species within the genus. The four Ca. Nitrosotalea genomes contained a core set of 103 orthologous gene families absent from all other ammonia-oxidizing archaea and, for most of these gene families, expression could be demonstrated in laboratory culture or the environment via proteomic or metatranscriptomic analyses respectively. Phylogenetic analyses indicated that four of these core gene families were acquired by the Ca. Nitrosotalea common ancestor via horizontal gene transfer from acidophilic representatives of Euryarchaeota. We hypothesize that gene exchange with these acidophiles contributed to the competitive success of the Ca. Nitrosotalea lineage in acidic environments.},
}
@article {pmid29084543,
year = {2017},
author = {Lambrecht, J and Cichocki, N and Hübschmann, T and Koch, C and Harms, H and Müller, S},
title = {Flow cytometric quantification, sorting and sequencing of methanogenic archaea based on F420 autofluorescence.},
journal = {Microbial cell factories},
volume = {16},
number = {1},
pages = {180},
doi = {10.1186/s12934-017-0793-7},
pmid = {29084543},
issn = {1475-2859},
mesh = {Archaea/cytology/genetics/*metabolism ; Archaeal Proteins/genetics/metabolism ; Biofuels ; Biomass ; Flow Cytometry ; Methane/*metabolism ; Microscopy, Fluorescence ; Organic Chemicals/chemistry ; RNA, Ribosomal, 16S/chemistry/isolation &amp; purification/metabolism ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: The widely established production of CH4 from renewable biomass in industrial scale anaerobic reactors may play a major role in the future energy supply. It relies on methanogenic archaea as key organisms which represent the bottleneck in the process. The quantitative analysis of these organisms can help to maximize process performance, uncover disturbances before failure, and may ultimately lead to community-based process control schemes. Existing qPCR and fluorescence microscopy-based methods are very attractive but can be cost-intensive and laborious.<br><br>RESULTS: In this study we present an autofluorescence-based, flow cytometric method for the fast low-cost quantification of methanogenic archaea in complex microbial communities and crude substrates. The method was applied to a methanogenic enrichment culture (MEC) and digester samples (DS). The methanogenic archaea were quantified using the distinct fluorescence of their cofactor F420 in a range from 3.7 × 108 (± 3.3 × 106) cells mL-1 and 1.8 x 109 (± 1.1 × 108) cells mL-1. We evaluated different fixation methods and tested the sample stability. Stable abundance and fluorescence intensity were recorded up to 26 days during aerobic storage in PBS at 6 °C. The discrimination of the whole microbial community from the ubiquitous particle noise was facilitated by SYBR Green I staining and enabled calculation of relative abundances of methanogenic archaea of up to 9.64 ± 0.23% in the MEC and up to 4.43 ± 0.74% in the DS. The metaprofiling of the mcrA gene reinforced the results.<br><br>CONCLUSIONS: The presented method allows for fast and reliable quantification of methanogenic archaea in microbial communities under authentic digester conditions and can thus be useful for process monitoring and control in biogas digesters.},
}
@article {pmid29083035,
year = {2018},
author = {Laskar, F and Das Purkayastha, S and Sen, A and Bhattacharya, MK and Misra, BB},
title = {Diversity of methanogenic archaea in freshwater sediments of lacustrine ecosystems.},
journal = {Journal of basic microbiology},
volume = {58},
number = {2},
pages = {101-119},
doi = {10.1002/jobm.201700341},
pmid = {29083035},
issn = {1521-4028},
abstract = {About half of the global methane (CH4) emission is contributed by the methanogenic archaeal communities leading to a significant increase in global warming. This unprecedented situation has increased the ever growing necessity of evaluating the control measures for limiting CH4 emission to the atmosphere. Unfortunately, research endeavors on the diversity and functional interactions of methanogens are not extensive till date. We anticipate that the study of the diversity of methanogenic community is paramount for understanding the metabolic processes in freshwater lake ecosystems. Although there are several disadvantages of conventional culture-based methods for determining the diversity of methanogenic archaeal communities, in order to understand their ecological roles in natural environments it is required to culture the microbes. Recently different molecular techniques have been developed for determining the structure of methanogenic archaeal communities thriving in freshwater lake ecosystem. The two gene based cloning techniques required for this purpose are 16S rRNA and methyl coenzyme M reductase (mcrA) in addition to the recently developed metagenomics approaches and high throughput next generation sequencing efforts. This review discusses the various methods of culture-dependent and -independent measures of determining the diversity of methanogen communities in lake sediments in lieu of the different molecular approaches and inter-relationships of diversity of methanogenic archaea.},
}
@article {pmid29080506,
year = {2018},
author = {Chaari, M and Theochari, I and Papadimitriou, V and Xenakis, A and Ammar, E},
title = {Encapsulation of carotenoids extracted from halophilic Archaea in oil-in-water (O/W) micro- and nano-emulsions.},
journal = {Colloids and surfaces. B, Biointerfaces},
volume = {161},
number = {},
pages = {219-227},
doi = {10.1016/j.colsurfb.2017.10.042},
pmid = {29080506},
issn = {1873-4367},
abstract = {Carotenoids extracted from halophilc Archaea have potential health benefits. Their poor water-solubility and low bioavailability is a challenge to their incorporation into foods. The aim of this work was the carotenoids encapsulation into two oil-in-water (O/W) dispersions, to increase their use as functional food applications. A nanoemulsion produced by high pressure homogenization and a spontaneously formed microemulsion were conceived. The limonene was the dispersed oil phase, and mixtures of Triton X-100/Tween-80 (3:1) as emulsifiers and of water/glycerol (2:1) as the continuous aqueous phase. The microemulsion monophasic area was determined through the pseudo-ternary phase diagram. Dynamic Light Scattering was used for the structural characterization of the nano- and micro-emulsions in the presence of the carotenoids. Moreover, the radical scavenging activity of the encapsulated carotenoids was examined by Electron Paramagnetic Resonance spectroscopy. The results confirmed the delivery systems design effectiveness to encapsulate and stabilize the carotenoids for food applications.},
}
@article {pmid29064676,
year = {2017},
author = {White, RH},
title = {Identification and Biosynthesis of 1-Mercaptoethanesulfonic Acid (1-MES), an Analogue of Coenzyme M, Found Widely in the Methanogenic Archaea.},
journal = {Biochemistry},
volume = {56},
number = {46},
pages = {6137-6144},
doi = {10.1021/acs.biochem.7b00971},
pmid = {29064676},
issn = {1520-4995},
mesh = {*Biosynthetic Pathways ; Ethylenes/metabolism ; Mesna/*analogs &amp; derivatives/*metabolism ; Methanococcus/enzymology/growth &amp; development/*metabolism ; Sulfides/metabolism ; Sulfonic Acids/metabolism ; },
abstract = {Here I report on the identification of 1-mercaptoethanesulfonic acid (1-MES), an analogue of 2-mercaptoethanesulfonic acid (coenzyme M, HSCoM). 1-MES and HSCoM were both present in the growth media of eight different methanogens at concentrations ranging from ∼1 to 100 μM. In an effort to determine a chemical origin of 1-MES, several plausible chemical routes were examined each assuming that HSCoM was the precursor. In all examined routes, no 1-MES was formed. However, 1-MES was formed when a solution of vinylsulfonic acid and sulfide were exposed to ultraviolet light. On the basis of these results, I conclude 1-MES is formed enzymatically. This was confirmed by growing a culture of Methanococcus maripaludis S2 in the presence of [1,1',2,2'-2H4]HSCoM and measuring the incorporation of deuterium into 1-MES. 1-MES incorporated three of the four deuteriums from the fed HSCoM. This result is consistent with the abstraction of a C-2 deuterium of the HSCoM, likely by a 5'-dAdoCH2• radical, followed by a radical rearrangement in which the sulfonic acid moves to position C-1, followed by abstraction of a H• likely from 5'-dAdoCH2D. At present, the reason for the production of 1-MES is not clear. This is the first report of the occurrence of 1-MES in Nature.},
}
@article {pmid29038844,
year = {2018},
author = {Hou, J and Cui, HL},
title = {In Vitro Antioxidant, Antihemolytic, and Anticancer Activity of the Carotenoids from Halophilic Archaea.},
journal = {Current microbiology},
volume = {75},
number = {3},
pages = {266-271},
doi = {10.1007/s00284-017-1374-z},
pmid = {29038844},
issn = {1432-0991},
support = {31600002//National Natural Science Foundation of China/ ; 31370054//National Natural Science Foundation of China/ ; },
abstract = {Halophilic archaea represent a promising natural source of carotenoids. However, little information is available about the biological effects of carotenoids from halophilic archaea. In this study, the carotenoids produced by seven halophilic archaeal strains Halogeometricum rufum, Halogeometricum limi, Haladaptatus litoreus, Haloplanus vescus, Halopelagius inordinatus, Halogranum rubrum, and Haloferax volcanii were identified by ultraviolet/visible spectroscopy, thin-layer chromatography, and high-performance liquid chromatography-tandem mass spectrometry. The C50 carotenoids bacterioruberin and its derivatives monoanhydrobacterioruberin and bisanhydrobacterioruberin were found to be the predominant carotenoids. The antioxidant capacities of the carotenoids from these strains were significantly higher than β-carotene as determined by 1,1-diphenyl-2-picrylhydrazyl radical scavenging assay. The antihemolytic activities of these carotenoid extracts against H2O2-induced hemolysis in mouse erythrocytes were 3.9-6.3 times higher than β-carotene. A dose-dependent in vitro antiproliferative activity against HepG2 cells was observed for the extract from Hgm. limi, while that from Hpn. vescus exhibited a relatively high activity in a dose-independent manner. These results suggested that halophilic archaea could be considered as an alternative source of natural carotenoids with high antioxidant, antihemolytic, and anticancer activity.},
}
@article {pmid29037137,
year = {2017},
author = {Peng, S and Chu, Z and Lu, J and Li, D and Wang, Y and Yang, S and Zhang, Y},
title = {Heterologous Expression of Chaperones from Hyperthermophilic Archaea Inhibits Aminoglycoside-Induced Protein Misfolding in Escherichia coli.},
journal = {Biochemistry. Biokhimiia},
volume = {82},
number = {10},
pages = {1169-1175},
doi = {10.1134/S0006297917100091},
pmid = {29037137},
issn = {1608-3040},
mesh = {Chaperonin 10/genetics/metabolism ; Chaperonin 60/genetics/*metabolism ; Escherichia coli/*metabolism ; Membrane Potentials/drug effects ; Molecular Chaperones/genetics/metabolism ; Protein Folding/drug effects ; Pyrococcus furiosus/*metabolism ; Recombinant Proteins/biosynthesis/chemistry ; Streptomycin/pharmacology ; },
abstract = {Aminoglycoside antibiotics affect protein translation fidelity and lead to protein aggregation and an increase in intracellular oxidative stress level as well. The overexpression of the chaperonin GroEL/GroES system promotes short-term tolerance to aminoglycosides in Escherichia coli. Here, we demonstrated that the coexpression of prefoldin or Hsp60 originating from the hyperthermophilic archaeon Pyrococcus furiosus in E. coli cells can rescue cell growth and inhibit protein aggregation induced by streptomycin exposure. The results of our study show that hyperthermophilic chaperones endow E. coli with a higher tolerance to streptomycin than the GroEL/GroES system, and that they exert better effects on the reduction of intracellular protein misfolding, indicating that these chaperones have unique features and functions.},
}
@article {pmid29034851,
year = {2017},
author = {Qin, W and Heal, KR and Ramdasi, R and Kobelt, JN and Martens-Habbena, W and Bertagnolli, AD and Amin, SA and Walker, CB and Urakawa, H and Könneke, M and Devol, AH and Moffett, JW and Armbrust, EV and Jensen, GJ and Ingalls, AE and Stahl, DA},
title = {Nitrosopumilus maritimus gen. nov., sp. nov., Nitrosopumilus cobalaminigenes sp. nov., Nitrosopumilus oxyclinae sp. nov., and Nitrosopumilus ureiphilus sp. nov., four marine ammonia-oxidizing archaea of the phylum Thaumarchaeota.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {67},
number = {12},
pages = {5067-5079},
doi = {10.1099/ijsem.0.002416},
pmid = {29034851},
issn = {1466-5034},
mesh = {Ammonia/metabolism ; Archaea/*classification/genetics/isolation &amp; purification ; Base Composition ; DNA, Archaeal/genetics ; Estuaries ; Geologic Sediments/*microbiology ; Glyceryl Ethers/chemistry ; Oxidation-Reduction ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Washington ; },
abstract = {Four mesophilic, neutrophilic, and aerobic marine ammonia-oxidizing archaea, designated strains SCM1T, HCA1T, HCE1T and PS0T, were isolated from a tropical marine fish tank, dimly lit deep coastal waters, the lower euphotic zone of coastal waters, and near-surface sediment in the Puget Sound estuary, respectively. Cells are straight or slightly curved small rods, 0.15-0.26 µm in diameter and 0.50-1.59 µm in length. Motility was not observed, although strain PS0T possesses genes associated with archaeal flagella and chemotaxis, suggesting it may be motile under some conditions. Cell membranes consist of glycerol dibiphytanyl glycerol tetraether (GDGT) lipids, with crenarchaeol as the major component. Strain SCM1T displays a single surface layer (S-layer) with p6 symmetry, distinct from the p3-S-layer reported for the soil ammonia-oxidizing archaeon Nitrososphaera viennensis EN76T. Respiratory quinones consist of fully saturated and monounsaturated menaquinones with 6 isoprenoid units in the side chain. Cells obtain energy from ammonia oxidation and use carbon dioxide as carbon source; addition of an α-keto acid (α-ketoglutaric acid) was necessary to sustain growth of strains HCA1T, HCE1T, and PS0T. Strain PS0T uses urea as a source of ammonia for energy production and growth. All strains synthesize vitamin B1 (thiamine), B2 (riboflavin), B6 (pyridoxine), and B12 (cobalamin). Optimal growth occurs between 25 and 32 °C, between pH 6.8 and 7.3, and between 25 and 37 ‰ salinity. All strains have a low mol% G+C content of 33.0-34.2. Strains are related by 98 % or greater 16S rRNA gene sequence identity, sharing ~85 % 16S rRNA gene sequence identity with Nitrososphaera viennensis EN76T. All four isolates are well separated by phenotypic and genotypic characteristics and are here assigned to distinct species within the genus Nitrosopumilus gen. nov. Isolates SCM1T (=ATCC TSD-97T =NCIMB 15022T), HCA1T (=ATCC TSD-96T), HCE1T (=ATCC TSD-98T), and PS0T (=ATCC TSD-99T) are type strains of the species Nitrosopumilusmaritimus sp. nov., Nitrosopumilus cobalaminigenes sp. nov., Nitrosopumilus oxyclinae sp. nov., and Nitrosopumilus ureiphilus sp. nov., respectively. In addition, we propose the family Nitrosopumilaceae fam. nov. and the order Nitrosopumilales ord. nov. within the class Nitrososphaeria.},
}
@article {pmid29034077,
year = {2017},
author = {Danovaro, R and Rastelli, E and Corinaldesi, C and Tangherlini, M and Dell'Anno, A},
title = {Marine archaea and archaeal viruses under global change.},
journal = {F1000Research},
volume = {6},
number = {},
pages = {1241},
doi = {10.12688/f1000research.11404.1},
pmid = {29034077},
issn = {2046-1402},
abstract = {Global change is altering oceanic temperature, salinity, pH, and oxygen concentration, directly and indirectly influencing marine microbial food web structure and function. As microbes represent >90% of the ocean's biomass and are major drivers of biogeochemical cycles, understanding their responses to such changes is fundamental for predicting the consequences of global change on ecosystem functioning. Recent findings indicate that marine archaea and archaeal viruses are active and relevant components of marine microbial assemblages, far more abundant and diverse than was previously thought. Further research is urgently needed to better understand the impacts of global change on virus-archaea dynamics and how archaea and their viruses can interactively influence the ocean's feedbacks on global change.},
}
@article {pmid29033920,
year = {2017},
author = {Jones, DL and Baxter, BK},
title = {DNA Repair and Photoprotection: Mechanisms of Overcoming Environmental Ultraviolet Radiation Exposure in Halophilic Archaea.},
journal = {Frontiers in microbiology},
volume = {8},
number = {},
pages = {1882},
doi = {10.3389/fmicb.2017.01882},
pmid = {29033920},
issn = {1664-302X},
abstract = {Halophilic archaea push the limits of life at several extremes. In particular, they are noted for their biochemical strategies in dealing with osmotic stress, low water activity and cycles of desiccation in their hypersaline environments. Another feature common to their habitats is intense ultraviolet (UV) radiation, which is a challenge that microorganisms must overcome. The consequences of high UV exposure include DNA lesions arising directly from bond rearrangement of adjacent bipyrimidines, or indirectly from oxidative damage, which may ultimately result in mutation and cell death. As such, these microorganisms have evolved a number of strategies to navigate the threat of DNA damage, which we differentiate into two categories: DNA repair and photoprotection. Photoprotection encompasses damage avoidance strategies that serve as a &quot;first line of defense,&quot; and in halophilic archaea include pigmentation by carotenoids, mechanisms of oxidative damage avoidance, polyploidy, and genomic signatures that make DNA less susceptible to photodamage. Photolesions that do arise are addressed by a number of DNA repair mechanisms that halophilic archaea efficiently utilize, which include photoreactivation, nucleotide excision repair, base excision repair, and homologous recombination. This review seeks to place DNA damage, repair, and photoprotection in the context of halophilic archaea and the solar radiation of their hypersaline environments. We also provide new insight into the breadth of strategies and how they may work together to produce remarkable UV-resistance for these microorganisms.},
}
@article {pmid29033916,
year = {2017},
author = {Wang, S and Giller, K and Kreuzer, M and Ulbrich, SE and Braun, U and Schwarm, A},
title = {Contribution of Ruminal Fungi, Archaea, Protozoa, and Bacteria to the Methane Suppression Caused by Oilseed Supplemented Diets.},
journal = {Frontiers in microbiology},
volume = {8},
number = {},
pages = {1864},
doi = {10.3389/fmicb.2017.01864},
pmid = {29033916},
issn = {1664-302X},
abstract = {Dietary lipids can suppress methane emission from ruminants, but effects are variable. Especially the role of bacteria, archaea, fungi and protozoa in mediating the lipid effects is unclear. In the present in vitro study, archaea, fungi and protozoa were selectively inhibited by specific agents. This was fully or almost fully successful for fungi and protozoa as well as archaeal activity as determined by the methyl-coenzyme M reductase alpha subunit gene. Five different microbial treatments were generated: rumen fluid being intact (I), without archaea (-A), without fungi (-F), without protozoa (-P) and with bacteria only (-AFP). A forage-concentrate diet given alone or supplemented with crushed full-fat oilseeds of either safflower (Carthamus tinctorius) or poppy (Papaver somniferum) or camelina (Camelina sativa) at 70 g oil kg-1 diet dry matter was incubated. This added up to 20 treatments with six incubation runs per treatment. All oilseeds suppressed methane emission compared to the non-supplemented control. Compared to the non-supplemented control, -F decreased organic matter (OM) degradation, and short-chain fatty acid concentration was greater with camelina and safflower seeds. Methane suppression per OM digested in -F was greater with camelina seeds (-12 vs.-7% with I, P = 0.06), but smaller with poppy seeds (-4 vs. -8% with I, P = 0.03), and not affected with safflower seeds. With -P, camelina seeds decreased the acetate-to-propionate ratio and enhanced the methane suppression per gram dry matter (18 vs. 10% with I, P = 0.08). Hydrogen recovery was improved with -P in any oilseeds compared to non-supplemented control. No methane emission was detected with the -A and -AFP treatments. In conclusion, concerning methanogenesis, camelina seeds seem to exert effects only on archaea and bacteria. By contrast, with safflower and poppy seeds methane was obviously reduced mainly through the interaction with protozoa or archaea associated with protozoa. This demonstrated that the microbial groups differ in their contribution to the methane suppressing effect dependent on the source of lipid. These findings help to understand how lipid supplementation and microbial groups interact, and thus may assist in making this methane mitigation tool more efficient, but await confirmation in vivo.},
}
@article {pmid29029047,
year = {2017},
author = {Yang, S and Winkel, M and Wagner, D and Liebner, S},
title = {Community structure of rare methanogenic archaea: insight from a single functional group.},
journal = {FEMS microbiology ecology},
volume = {93},
number = {11},
pages = {},
doi = {10.1093/femsec/fix126},
pmid = {29029047},
issn = {1574-6941},
mesh = {Bacteria/*classification/genetics ; *Biodiversity ; DNA Restriction Enzymes/genetics ; Euryarchaeota/*classification/genetics ; Methane/*biosynthesis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; },
abstract = {The rare biosphere, the low abundant microbial populations, is suggested to be a conserved way of microbial life. Here we conducted a molecular survey of rare methanogenic archaea in the environment targeting the mcrA gene in order to test if general concepts associated with the structure of the rare bacterial biosphere also apply to single functional groups. Similar to what is known about rare bacterial communities, the contribution of rare methanogens to the alpha diversity is much larger than to Bray-Curtis measures. Moreover, a similar core group of methanogens harbored by the abundant and rare communities suggests similar sources and environmental controls of both groups. Among the communities of different levels of rarity, the conditionally rare methanogenic taxa largely account for the overall community dynamics of the rare biosphere and likely enter the dominant community under favorable environmental conditions. In addition, we observed a positive correlation between the alpha diversity and the production of methane when the rare taxa were taken into account. This supports the concept that increasing microbial biodiversity enhances ecological function. The composition and environmental associations of the rare methanogenic biosphere allow us to conclude that rarity is a conserved way also for single functional groups.},
}
@article {pmid28992595,
year = {2018},
author = {Yilmazel, YD and Zhu, X and Kim, KY and Holmes, DE and Logan, BE},
title = {Electrical current generation in microbial electrolysis cells by hyperthermophilic archaea Ferroglobus placidus and Geoglobus ahangari.},
journal = {Bioelectrochemistry (Amsterdam, Netherlands)},
volume = {119},
number = {},
pages = {142-149},
doi = {10.1016/j.bioelechem.2017.09.012},
pmid = {28992595},
issn = {1878-562X},
mesh = {Archaeoglobales/*chemistry/physiology ; Biofilms ; *Electric Conductivity ; *Electrolysis ; *Temperature ; },
abstract = {Few microorganisms have been examined for current generation under thermophilic (40-65°C) or hyperthermophilic temperatures (≥80°C) in microbial electrochemical systems. Two iron-reducing archaea from the family Archaeoglobaceae, Ferroglobus placidus and Geoglobus ahangari, showed electro-active behavior leading to current generation at hyperthermophilic temperatures in single-chamber microbial electrolysis cells (MECs). A current density (j) of 0.68±0.11A/m2 was attained in F. placidus MECs at 85°C, and 0.57±0.10A/m2 in G. ahangari MECs at 80°C, with an applied voltage of 0.7V. Cyclic voltammetry (CV) showed that both strains produced a sigmoidal catalytic wave, with a mid-point potential of -0.39V (vs. Ag/AgCl) for F. placidus and -0.37V for G. ahangari. The comparison of CVs using spent medium and turnover CVs, coupled with the detection of peaks at the same potentials in both turnover and non-turnover conditions, suggested that mediators were not used for electron transfer and that both archaea produced current through direct contact with the electrode. These two archaeal species, and other hyperthermophilic exoelectrogens, have the potential to broaden the applications of microbial electrochemical technologies for producing biofuels and other bioelectrochemical products under extreme environmental conditions.},
}
@article {pmid28992240,
year = {2017},
author = {Nakamura, T and Oshima, M and Yasuda, M and Shimamura, A and Morita, J and Uegaki, K},
title = {Alteration of molecular assembly of peroxiredoxins from hyperthermophilic archaea.},
journal = {Journal of biochemistry},
volume = {162},
number = {6},
pages = {415-422},
doi = {10.1093/jb/mvx045},
pmid = {28992240},
issn = {1756-2651},
mesh = {Aeropyrum/*chemistry ; Hydrogen Peroxide/pharmacology ; Models, Molecular ; Peroxiredoxins/*chemistry/genetics/metabolism ; Point Mutation/genetics ; Protein Conformation ; Pyrococcus horikoshii/chemistry ; },
abstract = {Peroxiredoxin from Pyrococcus horikoshii (PhPrx) is a decameric protein formed by ring-type assembly of five dimers. To engineer the quaternary structure of PhPrx, we created a mutant PhPrx (PhPrx6m) by introducing six point mutations designed to dissociate PhPrx into dimers. Although PhPrx6m was a dimer in solution, the six dimers assembled into a dodecamer following crystallization. In the crystal structure, PhPrx6m was overoxidized, and the peroxidatic cysteine was in sulfonic acid form and two cysteines in the C-terminal region were linked by an intramolecular disulfide bond. Thus, we characterized the wild-type PhPrx overoxidized by hydrogen peroxide (PhPrxPer). Analytical ultracentrifugation showed that PhPrxPer had a higher molecular mass in solution than PhPrx. This was confirmed by analysis of the crystal structure of PhPrxPer, which was found to form a ring-type dodecamer composed of six dimers. The monomeric structures of PhPrx6m and PhPrxPer differed from that of PhPrx in the relative orientation of two domains, reflecting the number of dimers in the ring-type assembly. Unlike PhPrx, homologous peroxiredoxin from Aeropyrum pernix (ApPrx) did not undergo hexameric association. This property can be explained by the stronger connection between the two domains in ApPrx due to its C-terminal extension relative to PhPrx.},
}
@article {pmid28975058,
year = {2017},
author = {Fuchsman, CA and Collins, RE and Rocap, G and Brazelton, WJ},
title = {Effect of the environment on horizontal gene transfer between bacteria and archaea.},
journal = {PeerJ},
volume = {5},
number = {},
pages = {e3865},
doi = {10.7717/peerj.3865},
pmid = {28975058},
issn = {2167-8359},
abstract = {BACKGROUND: Horizontal gene transfer, the transfer and incorporation of genetic material between different species of organisms, has an important but poorly quantified role in the adaptation of microbes to their environment. Previous work has shown that genome size and the number of horizontally transferred genes are strongly correlated. Here we consider how genome size confuses the quantification of horizontal gene transfer because the number of genes an organism accumulates over time depends on its evolutionary history and ecological context (e.g., the nutrient regime for which it is adapted).<br><br>RESULTS: We investigated horizontal gene transfer between archaea and bacteria by first counting reciprocal BLAST hits among 448 bacterial and 57 archaeal genomes to find shared genes. Then we used the DarkHorse algorithm, a probability-based, lineage-weighted method (Podell &amp; Gaasterland, 2007), to identify potential horizontally transferred genes among these shared genes. By removing the effect of genome size in the bacteria, we have identified bacteria with unusually large numbers of shared genes with archaea for their genome size. Interestingly, archaea and bacteria that live in anaerobic and/or high temperature conditions are more likely to share unusually large numbers of genes. However, high salt was not found to significantly affect the numbers of shared genes. Numbers of shared (genome size-corrected, reciprocal BLAST hits) and transferred genes (identified by DarkHorse) were strongly correlated. Thus archaea and bacteria that live in anaerobic and/or high temperature conditions are more likely to share horizontally transferred genes. These horizontally transferred genes are over-represented by genes involved in energy conversion as well as the transport and metabolism of inorganic ions and amino acids.<br><br>CONCLUSIONS: Anaerobic and thermophilic bacteria share unusually large numbers of genes with archaea. This is mainly due to horizontal gene transfer of genes from the archaea to the bacteria. In general, these transfers are from archaea that live in similar oxygen and temperature conditions as the bacteria that receive the genes. Potential hotspots of horizontal gene transfer between archaea and bacteria include hot springs, marine sediments, and oil wells. Cold spots for horizontal transfer included dilute, aerobic, mesophilic environments such as marine and freshwater surface waters.},
}
@article {pmid28974619,
year = {2017},
author = {Skennerton, CT and Chourey, K and Iyer, R and Hettich, RL and Tyson, GW and Orphan, VJ},
title = {Erratum for Skennerton et al., &quot;Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea&quot;.},
journal = {mBio},
volume = {8},
number = {5},
pages = {},
doi = {10.1128/mBio.01561-17},
pmid = {28974619},
issn = {2150-7511},
}
@article {pmid28973467,
year = {2017},
author = {Martinez-Pastor, M and Lancaster, WA and Tonner, PD and Adams, MWW and Schmid, AK},
title = {A transcription network of interlocking positive feedback loops maintains intracellular iron balance in archaea.},
journal = {Nucleic acids research},
volume = {45},
number = {17},
pages = {9990-10001},
doi = {10.1093/nar/gkx662},
pmid = {28973467},
issn = {1362-4962},
mesh = {Archaeal Proteins/*genetics/metabolism ; DNA-Binding Proteins/genetics/metabolism ; *Feedback, Physiological ; *Gene Expression Regulation, Archaeal ; *Gene Regulatory Networks ; Halobacterium salinarum/*genetics/metabolism ; Homeostasis/genetics ; Iron/*metabolism ; Mutation ; Repressor Proteins/genetics/metabolism ; Transcription, Genetic ; },
abstract = {Iron is required for key metabolic processes but is toxic in excess. This circumstance forces organisms across the tree of life to tightly regulate iron homeostasis. In hypersaline lakes dominated by archaeal species, iron levels are extremely low and subject to environmental change; however, mechanisms regulating iron homeostasis in archaea remain unclear. In previous work, we demonstrated that two transcription factors (TFs), Idr1 and Idr2, collaboratively regulate aspects of iron homeostasis in the model species Halobacterium salinarum. Here we show that Idr1 and Idr2 are part of an extended regulatory network of four TFs of the bacterial DtxR family that maintains intracellular iron balance. We demonstrate that each TF directly regulates at least one of the other DtxR TFs at the level of transcription. Dynamical modeling revealed interlocking positive feedback loop architecture, which exhibits bistable or oscillatory network dynamics depending on iron availability. TF knockout mutant phenotypes are consistent with model predictions. Together, our results support that this network regulates iron homeostasis despite variation in extracellular iron levels, consistent with dynamical properties of interlocking feedback architecture in eukaryotes. These results suggest that archaea use bacterial-type TFs in a eukaryotic regulatory network topology to adapt to harsh environments.},
}
@article {pmid28973046,
year = {2017},
author = {Visone, V and Han, W and Perugino, G and Del Monaco, G and She, Q and Rossi, M and Valenti, A and Ciaramella, M},
title = {In vivo and in vitro protein imaging in thermophilic archaea by exploiting a novel protein tag.},
journal = {PloS one},
volume = {12},
number = {10},
pages = {e0185791},
doi = {10.1371/journal.pone.0185791},
pmid = {28973046},
issn = {1932-6203},
mesh = {Archaea/*metabolism ; Archaeal Proteins/*metabolism ; DNA Topoisomerases, Type I/metabolism ; Hot Temperature ; Sulfolobus/*metabolism ; Sulfolobus solfataricus/*metabolism ; },
abstract = {Protein imaging, allowing a wide variety of biological studies both in vitro and in vivo, is of great importance in modern biology. Protein and peptide tags fused to proteins of interest provide the opportunity to elucidate protein location and functions, detect protein-protein interactions, and measure protein activity and kinetics in living cells. Whereas several tags are suitable for protein imaging in mesophilic organisms, the application of this approach to microorganisms living at high temperature has lagged behind. Archaea provide an excellent and unique model for understanding basic cell biology mechanisms. Here, we present the development of a toolkit for protein imaging in the hyperthermophilic archaeon Sulfolobus islandicus. The system relies on a thermostable protein tag (H5) constructed by engineering the alkylguanine-DNA-alkyl-transferase protein of Sulfolobus solfataricus, which can be covalently labeled using a wide range of small molecules. As a suitable host, we constructed, by CRISPR-based genome-editing technology, a S. islandicus mutant strain deleted for the alkylguanine-DNA-alkyl-transferase gene (Δogt). Introduction of a plasmid-borne H5 gene in this strain led to production of a functional H5 protein, which was successfully labeled with appropriate fluorescent molecules and visualized in cell extracts as well as in Δogt live cells. H5 was fused to reverse gyrase, a peculiar thermophile-specific DNA topoisomerase endowed with positive supercoiling activity, and allowed visualization of the enzyme in living cells. To the best of our knowledge, this is the first report of in vivo imaging of any protein of a thermophilic archaeon, filling an important gap in available tools for cell biology studies in these organisms.},
}
@article {pmid28957503,
year = {2017},
author = {Bobay, LM and Ochman, H},
title = {Impact of Recombination on the Base Composition of Bacteria and Archaea.},
journal = {Molecular biology and evolution},
volume = {34},
number = {10},
pages = {2627-2636},
doi = {10.1093/molbev/msx189},
pmid = {28957503},
issn = {1537-1719},
support = {R01 GM108657/GM/NIGMS NIH HHS/United States ; R35 GM118038/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/genetics ; Bacteria/genetics ; Base Composition/*genetics ; Computer Simulation ; Evolution, Molecular ; Gene Conversion ; Genome, Bacterial ; Mutation ; Phylogeny ; Recombination, Genetic/*genetics ; Selection, Genetic ; Sequence Analysis/methods ; },
abstract = {The mutational process in bacteria is biased toward A and T, and most species are GC-rich relative to the mutational input to their genome. It has been proposed that the shift in base composition is an adaptive process-that natural selection operates to increase GC-contents-and there is experimental evidence that bacterial strains with GC-rich versions of genes have higher growth rates than those strains with AT-rich versions expressing identical proteins. Alternatively, a nonadaptive process, GC-biased gene conversion (gBGC), could also increase the GC-content of DNA due to the mechanistic bias of gene conversion events during recombination. To determine what role recombination plays in the base composition of bacterial genomes, we compared the spectrum of nucleotide polymorphisms introduced by recombination in all microbial species represented by large numbers of sequenced strains. We found that recombinant alleles are consistently biased toward A and T, and that the magnitude of AT-bias introduced by recombination is similar to that of mutations. These results indicate that recombination alone, without the intervention of selection, is unlikely to counteract the AT-enrichment of bacterial genomes.},
}
@article {pmid28942710,
year = {2017},
author = {Yamauchi, N and Tanoue, R},
title = {Deuterium incorporation experiments from (3R)- and (3S)-[3-2H]leucine into characteristic isoprenoidal lipid-core of halophilic archaea suggests the involvement of isovaleryl-CoA dehydrogenase.},
journal = {Bioscience, biotechnology, and biochemistry},
volume = {81},
number = {11},
pages = {2062-2070},
doi = {10.1080/09168451.2017.1373588},
pmid = {28942710},
issn = {1347-6947},
mesh = {Deuterium/*chemistry ; Halobacterium salinarum/*metabolism ; Isovaleryl-CoA Dehydrogenase/*metabolism ; Leucine/*chemistry ; Lipid Metabolism ; Lipids/*chemistry ; Terpenes/*chemistry ; },
abstract = {The stereochemical reaction course for the two C-3 hydrogens of leucine to produce a characteristic isoprenoidal lipid in halophilic archaea was observed using incubation experiments with whole cell Halobacterium salinarum. Deuterium-labeled (3R)- and (3S)-[3-2H]leucine were freshly prepared as substrates from 2,3-epoxy-4-methyl-1-pentanol. Incorporation of deuterium from (3S)-[3-2H]leucine and loss of deuterium from (3R)-[3-2H]leucine in the lipid-core of H. salinarum was observed. Taken together with the results of our previous report, involving the incubation of chiral-labeled [5-2H]leucine, these results strongly suggested an involvement of isovaleryl-CoA dehydrogenase in leucine conversion to isoprenoid lipid in halophilic archaea. The stereochemical course of the reaction (anti-elimination) might have been the same as that previously reported for mammalian enzyme reactions. Thus, these results suggested that branched amino acids were metabolized to mevalonate in archaea in a manner similar to other organisms.},
}
@article {pmid28920507,
year = {2018},
author = {Sharma, A and Rani, S and Goel, M},
title = {Navigating the structure-function-evolutionary relationship of CsaA chaperone in archaea.},
journal = {Critical reviews in microbiology},
volume = {44},
number = {3},
pages = {274-289},
doi = {10.1080/1040841X.2017.1357535},
pmid = {28920507},
issn = {1549-7828},
abstract = {CsaA is a protein involved in the post-translational translocation of proteins across the cytoplasmic membrane. It is considered to be a functional homolog of SecB which participates in the Sec-dependent translocation pathway in an analogous manner. CsaA has also been reported to act as a molecular chaperone, preventing aggregation of unfolded proteins. It is essentially a prokaryotic protein which is absent in eukaryotes, but found extensively in bacteria and earlier thought to be widely present in archaea. The study of phylogenetic distribution of CsaA among prokaryotes suggests that it is present only in few archaeal organisms, mainly species of Thermoplasmatales and Halobacteriales. Interestingly, the CsaA protein from these two archaeal orders cluster separately on the phylogenetic tree with CsaA from Gram-positive and Gram-negative bacteria. It, thus, appears that this protein might have been acquired in these archaeal organisms through independent horizontal gene transfer (HGT) events from different bacteria. In this review, we summarize the earlier biochemical, structural, and functional characterization studies of CsaA. We draw new insights into the evolutionary history of this protein through phylogenetic and structural comparison of bacterial CsaA with modelled archaeal CsaA from Picrophilus torridus and Natrialba magadii.},
}
@article {pmid28917104,
year = {2017},
author = {Lee, J and Shin, SG and Han, G and Koo, T and Hwang, S},
title = {Bacteria and archaea communities in full-scale thermophilic and mesophilic anaerobic digesters treating food wastewater: Key process parameters and microbial indicators of process instability.},
journal = {Bioresource technology},
volume = {245},
number = {Pt A},
pages = {689-697},
doi = {10.1016/j.biortech.2017.09.015},
pmid = {28917104},
issn = {1873-2976},
mesh = {Anaerobiosis ; *Archaea ; Bacteria ; Bioreactors ; Methane ; Sewage ; *Waste Water ; },
abstract = {In this study, four different mesophilic and thermophilic full-scale anaerobic digesters treating food wastewater (FWW) were monitored for 1-2years in order to investigate: 1) microbial communities underpinning anaerobic digestion of FWW, 2) significant factors shaping microbial community structures, and 3) potential microbial indicators of process instability. Twenty-seven bacterial genera were identified as abundant bacteria underpinning the anaerobic digestion of FWW. Methanosaeta harundinacea, M. concilii, Methanoculleus bourgensis, M. thermophilus, and Methanobacterium beijingense were revealed as dominant methanogens. Bacterial community structures were clearly differentiated by digesters; archaeal community structures of each digester were dominated by one or two methanogen species. Temperature, ammonia, propionate, Na+, and acetate in the digester were significant factors shaping microbial community structures. The total microbial populations, microbial diversity, and specific bacteria genera showed potential as indicators of process instability in the anaerobic digestion of FWW.},
}
@article {pmid28910647,
year = {2017},
author = {Dai, X and Hu, C and Zhang, D and Dai, L and Duan, N},
title = {Impact of a high ammonia-ammonium-pH system on methane-producing archaea and sulfate-reducing bacteria in mesophilic anaerobic digestion.},
journal = {Bioresource technology},
volume = {245},
number = {Pt A},
pages = {598-605},
doi = {10.1016/j.biortech.2017.08.208},
pmid = {28910647},
issn = {1873-2976},
mesh = {*Ammonia ; Ammonium Compounds ; Anaerobiosis ; *Archaea ; Bacteria, Anaerobic ; Bioreactors ; *Methane ; Sulfates ; },
abstract = {A novel strategy for acclimation to ammonia stress was implemented by stimulating a high ammonia-ammonium-pH environment in a high-solid anaerobic digestion (AD) system in this study. Three semi-continuously stirred anaerobic reactors performed well over the whole study period under mesophilic conditions, especially in experimental group (R-2) when accommodated from acclimation period which the maximum total ammonia nitrogen (TAN) and free ammonia nitrogen (FAN) increased to 4921 and 2996mg/L, respectively. Moreover, when it accommodated the high ammonia-ammonium-pH system, the daily biogas production and methane content were similar to those in R-1 (the blank control to R-2), but the hydrogen sulfide (H2S) content lower than the blank control. Moreover, mechanistic studies showed that high ammonia stress enhanced the activity of coenzyme F420. The results of real-time fluorescent quantitative polymerase chain reaction (PCR) showed that ammonia stress decreased the abundance of sulfate-reducing bacteria and increased the abundance of methane-producing archaea.},
}
@article {pmid28905430,
year = {2017},
author = {McDougall, M and Francisco, O and Harder-Viddal, C and Roshko, R and Meier, M and Stetefeld, J},
title = {Archaea S-layer nanotube from a &quot;black smoker&quot; in complex with cyclo-octasulfur (S8) rings.},
journal = {Proteins},
volume = {85},
number = {12},
pages = {2209-2216},
doi = {10.1002/prot.25385},
pmid = {28905430},
issn = {1097-0134},
mesh = {Amino Acid Motifs ; Archaeal Proteins ; Crystallography, X-Ray ; Desulfurococcaceae/*chemistry/metabolism ; Escherichia coli/genetics/metabolism ; Gene Expression ; Hydrophobic and Hydrophilic Interactions ; Hydrothermal Vents ; Molecular Dynamics Simulation ; Nanotubes/*chemistry/ultrastructure ; Plasmids/chemistry/metabolism ; Protein Interaction Domains and Motifs ; Protein Structure, Secondary ; Recombinant Fusion Proteins/chemistry/genetics/metabolism ; Sulfur/*chemistry/metabolism ; Thermodynamics ; Water/*chemistry/metabolism ; },
abstract = {Elemental sulfur exists primarily as an S80 ring and serves as terminal electron acceptor for a variety of sulfur-fermenting bacteria. Hyperthermophilic archaea from black smoker vents are an exciting research tool to advance our knowledge of sulfur respiration under extreme conditions. Here, we use a hybrid method approach to demonstrate that the proteinaceous cavities of the S-layer nanotube of the hyperthermophilic archaeon Staphylothermus marinus act as a storage reservoir for cyclo-octasulfur S8. Fully atomistic molecular dynamics (MD) simulations were performed and the method of multiconfigurational thermodynamic integration was employed to compute the absolute free energy for transferring a ring of elemental sulfur S8 from an aqueous bath into the largest hydrophobic cavity of a fragment of archaeal tetrabrachion. Comparisons with earlier MD studies of the free energy of hydration as a function of water occupancy in the same cavity of archaeal tetrabrachion show that the sulfur ring is energetically favored over water.},
}
@article {pmid28885627,
year = {2018},
author = {Ino, K and Hernsdorf, AW and Konno, U and Kouduka, M and Yanagawa, K and Kato, S and Sunamura, M and Hirota, A and Togo, YS and Ito, K and Fukuda, A and Iwatsuki, T and Mizuno, T and Komatsu, DD and Tsunogai, U and Ishimura, T and Amano, Y and Thomas, BC and Banfield, JF and Suzuki, Y},
title = {Ecological and genomic profiling of anaerobic methane-oxidizing archaea in a deep granitic environment.},
journal = {The ISME journal},
volume = {12},
number = {1},
pages = {31-47},
doi = {10.1038/ismej.2017.140},
pmid = {28885627},
issn = {1751-7370},
mesh = {Anaerobiosis ; Environment ; Genomics ; Groundwater/chemistry/*microbiology ; Methane/*metabolism ; Methanosarcinales/classification/*genetics/isolation &amp; purification/*metabolism ; Nitrates/metabolism ; Oxidation-Reduction ; Phylogeny ; Silicon Dioxide/*analysis/metabolism ; Sulfates/metabolism ; },
abstract = {Recent single-gene-based surveys of deep continental aquifers demonstrated the widespread occurrence of archaea related to Candidatus Methanoperedens nitroreducens (ANME-2d) known to mediate anaerobic oxidation of methane (AOM). However, it is unclear whether ANME-2d mediates AOM in the deep continental biosphere. In this study, we found the dominance of ANME-2d in groundwater enriched in sulfate and methane from a 300-m deep underground borehole in granitic rock. A near-complete genome of one representative species of the ANME-2d obtained from the underground borehole has most of functional genes required for AOM and assimilatory sulfate reduction. The genome of the subsurface ANME-2d is different from those of other members of ANME-2d by lacking functional genes encoding nitrate and nitrite reductases and multiheme cytochromes. In addition, the subsurface ANME-2d genome contains a membrane-bound NiFe hydrogenase gene putatively involved in respiratory H2 oxidation, which is different from those of other methanotrophic archaea. Short-term incubation of microbial cells collected from the granitic groundwater with 13C-labeled methane also demonstrates that AOM is linked to microbial sulfate reduction. Given the prominence of granitic continental crust and sulfate and methane in terrestrial subsurface fluids, we conclude that AOM may be widespread in the deep continental biosphere.},
}
@article {pmid28880150,
year = {2017},
author = {Nayak, DD and Mahanta, N and Mitchell, DA and Metcalf, WW},
title = {Post-translational thioamidation of methyl-coenzyme M reductase, a key enzyme in methanogenic and methanotrophic Archaea.},
journal = {eLife},
volume = {6},
number = {},
pages = {},
doi = {10.7554/eLife.29218},
pmid = {28880150},
issn = {2050-084X},
support = {R01 GM097142/GM/NIGMS NIH HHS/United States ; },
mesh = {Amides/*chemistry ; Archaea/*enzymology/growth &amp; development ; Binding Sites ; Catalysis ; Methane/*metabolism ; Oxidoreductases/*chemistry/*metabolism ; Phylogeny ; *Protein Processing, Post-Translational ; Sulfhydryl Compounds/*chemistry ; },
abstract = {Methyl-coenzyme M reductase (MCR), found in strictly anaerobic methanogenic and methanotrophic archaea, catalyzes the reversible production and consumption of the potent greenhouse gas methane. The α subunit of MCR (McrA) contains several unusual post-translational modifications, including a rare thioamidation of glycine. Based on the presumed function of homologous genes involved in the biosynthesis of thioviridamide, a thioamide-containing natural product, we hypothesized that the archaeal tfuA and ycaO genes would be responsible for post-translational installation of thioglycine into McrA. Mass spectrometric characterization of McrA from the methanogenic archaeon Methanosarcina acetivorans lacking tfuA and/or ycaO revealed the presence of glycine, rather than thioglycine, supporting this hypothesis. Phenotypic characterization of the ∆ycaO-tfuA mutant revealed a severe growth rate defect on substrates with low free energy yields and at elevated temperatures (39°C - 45°C). Our analyses support a role for thioglycine in stabilizing the protein secondary structure near the active site.},
}
@article {pmid28874471,
year = {2017},
author = {Fu, X and Adams, Z and Liu, R and Hepowit, NL and Wu, Y and Bowmann, CF and Moskovitz, J and Maupin-Furlow, JA},
title = {Methionine Sulfoxide Reductase A (MsrA) and Its Function in Ubiquitin-Like Protein Modification in Archaea.},
journal = {mBio},
volume = {8},
number = {5},
pages = {},
doi = {10.1128/mBio.01169-17},
pmid = {28874471},
issn = {2150-7511},
support = {P20 GM103418/GM/NIGMS NIH HHS/United States ; P30 AG035982/AG/NIA NIH HHS/United States ; R01 GM057498/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/*enzymology ; Chromatography, Liquid ; Dimethyl Sulfoxide/pharmacology ; Methionine/analogs &amp; derivatives/metabolism ; Methionine Sulfoxide Reductases/biosynthesis/*genetics/*metabolism ; Oxidants/pharmacology ; Oxidative Stress ; Protein Processing, Post-Translational ; Proteolysis ; Tandem Mass Spectrometry ; Ubiquitination ; Ubiquitins/chemistry/*metabolism ; },
abstract = {Methionine sulfoxide reductase A (MsrA) is an antioxidant enzyme found in all domains of life that catalyzes the reduction of methionine-S-sulfoxide (MSO) to methionine in proteins and free amino acids. We demonstrate that archaeal MsrA has a ubiquitin-like (Ubl) protein modification activity that is distinct from its stereospecific reduction of MSO residues. MsrA catalyzes this Ubl modification activity, with the Ubl-activating E1 UbaA, in the presence of the mild oxidant dimethyl sulfoxide (DMSO) and in the absence of reductant. In contrast, the MSO reductase activity of MsrA is inhibited by DMSO and requires reductant. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis reveals that MsrA-dependent Ubl conjugates are associated with DNA replication, protein remodeling, and oxidative stress and include the Ubl-modified MsrA, Orc3 (Orc1/Cdc6), and Cdc48d (Cdc48/p97 AAA+ ATPase). Overall, we found archaeal MsrA to have opposing MSO reductase and Ubl modifying activities that are associated with oxidative stress responses and controlled by exposure to mild oxidant.IMPORTANCE Proteins that are damaged by oxidative stress are often targeted for proteolysis by the ubiquitin-proteasome system (UPS). The mechanisms that control this response are poorly understood, especially under conditions of mild oxidative stress when protein damage is modest. Here, we discovered a novel function of archaeal MsrA in guiding the Ubl modification of target proteins in the presence of mild oxidant. This newly reported activity of MsrA is distinct from its stereospecific reduction of methionine-S-sulfoxide to methionine residues. Our results are significant steps forward, first, in elucidating a protein factor that guides Ubl modification in archaea, and second, in providing an insight into oxidative stress responses that can trigger Ubl modification in a cell.},
}
@article {pmid28853770,
year = {2016},
author = {Kozhevnikova, DA and Taranov, EA and Lebedinsky, AV and Bonch-Osmolovskaya, EA and Sokolova, TG},
title = {Hydrogenogenic and Sulfidogenic Growth of Thermococcus Archaea on Carbon Monoxide and Formate.},
journal = {Mikrobiologiia},
volume = {85},
number = {4},
pages = {381-392},
pmid = {28853770},
issn = {0026-3656},
mesh = {Aldehyde Oxidoreductases/genetics/*metabolism ; Atlantic Ocean ; Carbon Monoxide/*metabolism ; Formate Dehydrogenases/genetics/*metabolism ; Formates/*metabolism ; Gene Expression ; *Genome, Archaeal ; Hot Temperature ; Hydrogen/metabolism ; Hydrothermal Vents ; Kinetics ; Multienzyme Complexes/genetics/*metabolism ; Multigene Family ; Oxidation-Reduction ; Phylogeny ; Seawater ; Sulfur/metabolism ; Thermococcus/classification/genetics/*metabolism ; },
abstract = {Enrichment and pure cultures of hyperthermophilic archaea capable of anaerobic growth on one- carbon compounds (CO and/or formate) were obtained from deep-sea sites of hydrothermal activity at the Mid-Atlantic Ridge, Lau Basin, and Guaymas Basin. All isolates belonged to the T barophilus-T paralvi- .nellae group within the genus Thermococcus. In all cases available for analysis, the genomes of Thermococcus strains capable of growth by hydrogenogenic utilization of CO and/or formate contained clusters of genes en- coding energy-converting hydrogenase and either CO dehydrogenase or formate dehydrogenase and formate transporter. Apart from the previously known processes of hydrogenogenic oxidation of CO and formate, the oxidation of these substrates coupled to sulfur reduction was observed, processes previously unknown among archaea. The capacities for hydrogenogenic or sulfidogenic oxidation of CO and formate occurred in the studied strains in all possible combinations, which could only in part be explained by peculiarities of organi- zation of genetic determinants revealed in the genomes. Investigation of CO and formate consumption kinet- ics revealed that T barophilus strain Ch5 was able to grow at concentrations close to the environmental ones. Thus, it was shown that hyperthermophilic archaea from deep-sea hydrothermal vents are able to utilize one- carbon substrates of abiotic origin both in the presence of an electron acceptor (sulfur) and in its absence. These processes were probably of importance under the conditions of the early Earth biosphere.},
}
@article {pmid28841790,
year = {2017},
author = {Roy, D and McEvoy, J and Blonigen, M and Amundson, M and Khan, E},
title = {Seasonal variation and ex-situ nitrification activity of ammonia oxidizing archaea in biofilm based wastewater treatment processes.},
journal = {Bioresource technology},
volume = {244},
number = {Pt 1},
pages = {850-859},
doi = {10.1016/j.biortech.2017.08.060},
pmid = {28841790},
issn = {1873-2976},
mesh = {Ammonia ; *Archaea ; Bacteria ; Biofilms ; *Nitrification ; Oxidation-Reduction ; Phylogeny ; Seasons ; *Waste Water ; },
abstract = {The abundance of ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB) was investigated in full-scale two-stage trickling filters (TF) and moving bed bioreactor (MBBR) treating municipal wastewater. Biofilm samples were collected for 17months from nitrifying TF (NTF), biochemical oxygen demand TF (BTF), and MBBR media. The abundance of AOA and AOB was determined using a quantitative PCR approach targeting the ammonia monooxygenase subunit A gene of archaea and bacteria. AOA were dominant in the NTF and MBBR, while AOB dominated in the BTF. AOA and AOB were more abundant during warmer months, and AOA were detected in the BTF only during warmer months. In laboratory nitrification activity experiments, ammonia oxidation to nitrite decreased when AOA populations from the NTF and MBBR were inhibited, demonstrating that AOA contributed to nitrification. This study has shown that AOA outnumber AOB and contribute to ammonia oxidation in full-scale nitrifying biofilm processes.},
}
@article {pmid28840778,
year = {2017},
author = {Tomita, T},
title = {Structure, function, and regulation of enzymes involved in amino acid metabolism of bacteria and archaea.},
journal = {Bioscience, biotechnology, and biochemistry},
volume = {81},
number = {11},
pages = {2050-2061},
doi = {10.1080/09168451.2017.1365593},
pmid = {28840778},
issn = {1347-6947},
mesh = {Allosteric Regulation ; Amino Acids/*metabolism ; Animals ; Archaea/*enzymology/metabolism ; Bacteria/*enzymology/metabolism ; Glutamate Dehydrogenase/*chemistry/*metabolism ; Humans ; },
abstract = {Amino acids are essential components in all organisms because they are building blocks of proteins. They are also produced industrially and used for various purposes. For example, L-glutamate is used as the component of &quot;umami&quot; taste and lysine has been used as livestock feed. Recently, many kinds of amino acids have attracted attention as biological regulators and are used for a healthy life. Thus, to clarify the mechanism of how amino acids are biosynthesized and how they work as biological regulators will lead to further effective utilization of them. Here, I review the leucine-induced-allosteric activation of glutamate dehydrogenase (GDH) from Thermus thermophilus and the relationship with the allosteric regulation of GDH from mammals. Next, I describe structural insights into the efficient production of L-glutamate by GDH from an excellent L-glutamate producer, Corynebacterium glutamicum. Finally, I review the structural biology of lysine biosynthesis of thermophilic bacterium and archaea.},
}
@article {pmid28837073,
year = {2017},
author = {Yi, GS and Song, Y and Wang, WW and Chen, JN and Deng, W and Cao, W and Wang, FP and Xiao, X and Liu, XP},
title = {Two Archaeal RecJ Nucleases from Methanocaldococcus jannaschii Show Reverse Hydrolysis Polarity: Implication to Their Unique Function in Archaea.},
journal = {Genes},
volume = {8},
number = {9},
pages = {},
doi = {10.3390/genes8090211},
pmid = {28837073},
issn = {2073-4425},
abstract = {Bacterial nuclease RecJ, which exists in almost all bacterial species, specifically degrades single-stranded (ss) DNA in the 5' to 3' direction. Some archaeal phyla, except Crenarchaea, also encode RecJ homologs. Compared with bacterial RecJ, archaeal RecJ exhibits a largely different amino acid sequence and domain organization. Archaeal RecJs from Thermococcus kodakarensis and Pyrococcus furiosus show 5'→3' exonuclease activity on ssDNA. Interestingly, more than one RecJ exists in some Euryarchaeota classes, such as Methanomicrobia, Methanococci, Methanomicrobia, Methanobacteria, and Archaeoglobi. Here we report the biochemical characterization of two RecJs from Methanocaldococcus jannaschii, the long RecJ1 (MJ0977) and short RecJ2 (MJ0831) to understand their enzymatic properties. RecJ1 is a 5'→3' exonuclease with a preference to ssDNA; however, RecJ2 is a 3'→5' exonuclease with a preference to ssRNA. The 5' terminal phosphate promotes RecJ1 activity, but the 3' terminal phosphate inhibits RecJ2 nuclease. Go-Ichi-Ni-San (GINS) complex does not interact with two RecJs and does not promote their nuclease activities. Finally, we discuss the diversity, function, and molecular evolution of RecJ in archaeal taxonomy. Our analyses provide insight into the function and evolution of conserved archaeal RecJ/eukaryotic Cdc45 protein.},
}
@article {pmid28826642,
year = {2018},
author = {Moissl-Eichinger, C and Pausan, M and Taffner, J and Berg, G and Bang, C and Schmitz, RA},
title = {Archaea Are Interactive Components of Complex Microbiomes.},
journal = {Trends in microbiology},
volume = {26},
number = {1},
pages = {70-85},
doi = {10.1016/j.tim.2017.07.004},
pmid = {28826642},
issn = {1878-4380},
abstract = {Recent findings have shaken our picture of the biology of the archaea and revealed novel traits beyond archaeal extremophily and supposed 'primitiveness'. The archaea constitute a considerable fraction of the Earth's ecosystems, and their potential to shape their surroundings by a profound interaction with their biotic and abiotic environment has been recognized. Moreover, archaea have been identified as a substantial component, or even as keystone species, in complex microbiomes - in the environment or accompanying a holobiont. Species of the Euryarchaeota (methanogens, halophiles) and Thaumarchaeota, in particular, have the capacity to coexist in plant, animal, and human microbiomes, where syntrophy allows them to thrive under energy-deficiency stress. Due to methodological limitations, the archaeome remains mysterious, and many questions with respect to potential pathogenicity, function, and structural interactions with their host and other microorganisms remain.},
}
@article {pmid28826405,
year = {2017},
author = {Gilmore, SP and Henske, JK and Sexton, JA and Solomon, KV and Seppälä, S and Yoo, JI and Huyett, LM and Pressman, A and Cogan, JZ and Kivenson, V and Peng, X and Tan, Y and Valentine, DL and O'Malley, MA},
title = {Genomic analysis of methanogenic archaea reveals a shift towards energy conservation.},
journal = {BMC genomics},
volume = {18},
number = {1},
pages = {639},
doi = {10.1186/s12864-017-4036-4},
pmid = {28826405},
issn = {1471-2164},
mesh = {Anaerobiosis ; Archaeal Proteins/metabolism ; Energy Metabolism/*genetics ; *Genomics ; Methane/*biosynthesis ; Methanobacterium/*genetics/*metabolism ; },
abstract = {BACKGROUND: The metabolism of archaeal methanogens drives methane release into the environment and is critical to understanding global carbon cycling. Methanogenesis operates at a very low reducing potential compared to other forms of respiration and is therefore critical to many anaerobic environments. Harnessing or altering methanogen metabolism has the potential to mitigate global warming and even be utilized for energy applications.<br><br>RESULTS: Here, we report draft genome sequences for the isolated methanogens Methanobacterium bryantii, Methanosarcina spelaei, Methanosphaera cuniculi, and Methanocorpusculum parvum. These anaerobic, methane-producing archaea represent a diverse set of isolates, capable of methylotrophic, acetoclastic, and hydrogenotrophic methanogenesis. Assembly and analysis of the genomes allowed for simple and rapid reconstruction of metabolism in the four methanogens. Comparison of the distribution of Clusters of Orthologous Groups (COG) proteins to a sample of genomes from the RefSeq database revealed a trend towards energy conservation in genome composition of all methanogens sequenced. Further analysis of the predicted membrane proteins and transporters distinguished differing energy conservation methods utilized during methanogenesis, such as chemiosmotic coupling in Msar. spelaei and electron bifurcation linked to chemiosmotic coupling in Mbac. bryantii and Msph. cuniculi.<br><br>CONCLUSIONS: Methanogens occupy a unique ecological niche, acting as the terminal electron acceptors in anaerobic environments, and their genomes display a significant shift towards energy conservation. The genome-enabled reconstructed metabolisms reported here have significance to diverse anaerobic communities and have led to proposed substrate utilization not previously reported in isolation, such as formate and methanol metabolism in Mbac. bryantii and CO2 metabolism in Msph. cuniculi. The newly proposed substrates establish an important foundation with which to decipher how methanogens behave in native communities, as CO2 and formate are common electron carriers in microbial communities.},
}
@article {pmid28812261,
year = {2017},
author = {Xuan, J and Yao, H and Feng, Y and Wang, J},
title = {Backbone and side-chain 1H, 15N and 13C resonance assignments of two Sac10b family members Mvo10b and Mth10bTQQA from archaea.},
journal = {Biomolecular NMR assignments},
volume = {11},
number = {2},
pages = {269-273},
doi = {10.1007/s12104-017-9761-8},
pmid = {28812261},
issn = {1874-270X},
support = {31300635//National Natural Science Foundation of China/ ; 31670735//National Natural Science Foundation of China/ ; 30770434//National Natural Science Foundation of China/ ; },
mesh = {Archaeal Proteins/*chemistry ; DNA-Binding Proteins/*chemistry ; *Nuclear Magnetic Resonance, Biomolecular ; },
abstract = {The Sac10b family proteins, also named as Alba, are small, basic, nucleic acid-binding proteins widely distributed in archaea. They possess divergent physiological functions such as binding to both DNA and RNA with a high affinity and involving in genomic DNA compaction, RNA transactions and transcriptional regulations. The structures of many Sac10b family proteins from hyperthermophilic archaea have been reported, while those from thermophilic and mesophilic archaea are largely unknown. As was pointed out, the homologous members from thermophilic and mesophilic archaea may have functions different from the hyperthermophilic members. Therefore, comparison of these homologous members can provide biophysical and structural insight into the functional diversity and thermal adaptation mechanism. The present work mainly focused on the NMR study of two Sac10b family members, Mvo10b and Mth10b, from the mesophilic and thermophilic archaea, respectively. To overcome the difficulties caused by the oligomerization and conformation heterogeneity of Mth10b, a M13T/L17Q/I20Q/P56A mutant Mth10b (Mth10bTQQA) was constructed and used together with Mvo10b for multi-dimensional NMR experiments. The resonance assignments of Mvo10b and Mth10bTQQA are reported for further structural determination which is a basis for understanding the functional diversity and their thermal adaption mechanisms.},
}
@article {pmid28808742,
year = {2017},
author = {Wu, RN and Meng, H and Wang, YF and Lan, W and Gu, JD},
title = {A More Comprehensive Community of Ammonia-Oxidizing Archaea (AOA) Revealed by Genomic DNA and RNA Analyses of amoA Gene in Subtropical Acidic Forest Soils.},
journal = {Microbial ecology},
volume = {74},
number = {4},
pages = {910-922},
doi = {10.1007/s00248-017-1045-4},
pmid = {28808742},
issn = {1432-184X},
mesh = {Ammonia/metabolism ; Archaea/classification/*physiology ; Archaeal Proteins/*analysis ; China ; Cunninghamia/growth &amp; development ; *Forestry ; Forests ; *Microbiota ; Oxidation-Reduction ; Phylogeny ; *Soil Microbiology ; },
abstract = {Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are the main nitrifiers which are well studied in natural environments, and AOA frequently outnumber AOB by orders especially in acidic conditions, making AOA the most promising ammonia oxidizers. The phylogeny of AOA revealed in related studies, however, often varied and hardly reach a consensus on functional phylotypes. The objective of this study was to compare ammonia-oxidizing communities by amoA gene and transcript based on both genomic DNA and RNA in extremely acidic forest soils (pH <4.5). Our results support the numerical and functional dominance of AOA over AOB in acidic soils as bacterial amoA gene and transcript were both under detection limits and archaeal amoA, in contrast, were abundant and responded to the fluctuations of environmental factors. Organic matter from tree residues was proposed as the main source of microbial available nitrogen, and the potential co-precipitation of dissolved organic matter (DOM) with soluble Al3+ species in acidic soil matrix may further restrict the amount of nitrogen sources required by AOB besides NH3/NH4+ equilibrium. Although AOA were better adapted to oligotrophic environments, they were susceptible to the toxicity of exchangeable Al3+. Phylotypes affiliated to Nitrososphaera, Nitrososphaera sister group, and Nitrosotalea were detected by amoA gene and transcript. Nitrosotalea devantaerra and Nitrososphaera sister group were the major AOA. Compared to the genomic DNA data, higher relative abundances of Nitrososphaera and Nitrososphaera sister group were recognized in amoA transcript inferred AOA communities, where Nitrosotalea relative abundance was found lower, implying the functional activities of Nitrososphaera sister group and Nitrososphaera were easily underestimated and Nitrosotalea did not attribute proportionally to nitrification in extremely acidic soils. Further comparison of the different AOA community compositions and relative abundance of each phylotypes revealed by amoA genes and transcripts make it possible to identify the functional AOA species and assess their ecological role in extremely acidic soils.},
}
@article {pmid28798133,
year = {2017},
author = {Mattiroli, F and Bhattacharyya, S and Dyer, PN and White, AE and Sandman, K and Burkhart, BW and Byrne, KR and Lee, T and Ahn, NG and Santangelo, TJ and Reeve, JN and Luger, K},
title = {Structure of histone-based chromatin in Archaea.},
journal = {Science (New York, N.Y.)},
volume = {357},
number = {6351},
pages = {609-612},
doi = {10.1126/science.aaj1849},
pmid = {28798133},
issn = {1095-9203},
support = {R01 GM114594/GM/NIGMS NIH HHS/United States ; R01 GM053185/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; R01 GM067777/GM/NIGMS NIH HHS/United States ; R01 GM100329/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Substitution ; Chromatin/chemistry/*ultrastructure ; Crystallography, X-Ray ; DNA, Archaeal/chemistry/ultrastructure ; Gene Expression Regulation, Archaeal ; Glycine/genetics ; Histones/chemistry/*ultrastructure ; Nucleosomes/chemistry/ultrastructure ; Protein Multimerization ; *Thermococcus/chemistry/genetics/growth &amp; development ; Transcription, Genetic ; },
abstract = {Small basic proteins present in most Archaea share a common ancestor with the eukaryotic core histones. We report the crystal structure of an archaeal histone-DNA complex. DNA wraps around an extended polymer, formed by archaeal histone homodimers, in a quasi-continuous superhelix with the same geometry as DNA in the eukaryotic nucleosome. Substitutions of a conserved glycine at the interface of adjacent protein layers destabilize archaeal chromatin, reduce growth rate, and impair transcription regulation, confirming the biological importance of the polymeric structure. Our data establish that the histone-based mechanism of DNA compaction predates the nucleosome, illuminating the origin of the nucleosome.},
}
@article {pmid28794466,
year = {2017},
author = {Cavazzini, D and Grossi, G and Levati, E and Vallese, F and Montanini, B and Bolchi, A and Zanotti, G and Ottonello, S},
title = {A family of archaea-like carboxylesterases preferentially expressed in the symbiotic phase of the mychorrizal fungus Tuber melanosporum.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {7628},
doi = {10.1038/s41598-017-08007-9},
pmid = {28794466},
issn = {2045-2322},
abstract = {An increasing number of esterases is being revealed by (meta) genomic sequencing projects, but few of them are functionally/structurally characterized, especially enzymes of fungal origin. Starting from a three-member gene family of secreted putative &quot;lipases/esterases&quot; preferentially expressed in the symbiotic phase of the mycorrhizal fungus Tuber melanosporum (&quot;black truffle&quot;), we show here that these enzymes (TmelEST1-3) are dimeric, heat-resistant carboxylesterases capable of hydrolyzing various short/medium chain p-nitrophenyl esters. TmelEST2 was the most active (kcat = 2302 s-1 for p-nitrophenyl-butyrate) and thermally stable (T50 = 68.3 °C), while TmelEST3 was the only one displaying some activity on tertiary alcohol esters. X-ray diffraction analysis of TmelEST2 revealed a classical α/β hydrolase-fold structure, with a network of dimer-stabilizing intermolecular interactions typical of archaea esterases. The predicted structures of TmelEST1 and 3 are overall quite similar to that of TmelEST2 but with some important differences. Most notably, the much smaller volume of the substrate-binding pocket and the more acidic electrostatic surface profile of TmelEST1. This was also the only TmelEST capable of hydrolyzing feruloyl-esters, suggestinng a possible role in root cell-wall deconstruction during symbiosis establishment. In addition to their potential biotechnological interest, TmelESTs raise important questions regarding the evolutionary recruitment of archaea-like enzymes into mesophilic subterranean fungi such as truffles.},
}
@article {pmid28790990,
year = {2017},
author = {Chen, J and Nie, Y and Liu, W and Wang, Z and Shen, W},
title = {Ammonia-Oxidizing Archaea Are More Resistant Than Denitrifiers to Seasonal Precipitation Changes in an Acidic Subtropical Forest Soil.},
journal = {Frontiers in microbiology},
volume = {8},
number = {},
pages = {1384},
doi = {10.3389/fmicb.2017.01384},
pmid = {28790990},
issn = {1664-302X},
abstract = {Seasonal precipitation changes are increasingly severe in subtropical areas. However, the responses of soil nitrogen (N) cycle and its associated functional microorganisms to such precipitation changes remain unclear. In this study, two projected precipitation patterns were manipulated: intensifying the dry-season drought (DD) and extending the dry-season duration (ED) but increasing the wet-season storms following the DD and ED treatment period. The effects of these two contrasting precipitation patterns on soil net N transformation rates and functional gene abundances were quantitatively assessed through a resistance index. Results showed that the resistance index of functional microbial abundance (-0.03 ± 0.08) was much lower than that of the net N transformation rate (0.55 ± 0.02) throughout the experiment, indicating that microbial abundance was more responsive to precipitation changes compared with the N transformation rate. Spring drought under the ED treatment significantly increased the abundances of both nitrifying (amoA) and denitrifying genes (nirK, nirS, and nosZ), while changes in these gene abundances overlapped largely with control treatment during droughts in the dry season. Interestingly, the resistance index of the ammonia-oxidizing archaea (AOA) amoA abundance was significantly higher than that of the denitrifying gene abundances, suggesting that AOA were more resistant to the precipitation changes. This was attributed to the stronger environmental adaptability and higher resource utilization efficiency of the AOA community, as indicated by the lack of correlations between AOA gene abundance and environmental factors [i.e., soil water content, ammonium (NH4+) and dissolved organic carbon concentrations] during the experiment.},
}
@article {pmid28787424,
year = {2017},
author = {Bowers, RM and Kyrpides, NC and Stepanauskas, R and Harmon-Smith, M and Doud, D and Reddy, TBK and Schulz, F and Jarett, J and Rivers, AR and Eloe-Fadrosh, EA and Tringe, SG and Ivanova, NN and Copeland, A and Clum, A and Becraft, ED and Malmstrom, RR and Birren, B and Podar, M and Bork, P and Weinstock, GM and Garrity, GM and Dodsworth, JA and Yooseph, S and Sutton, G and Glöckner, FO and Gilbert, JA and Nelson, WC and Hallam, SJ and Jungbluth, SP and Ettema, TJG and Tighe, S and Konstantinidis, KT and Liu, WT and Baker, BJ and Rattei, T and Eisen, JA and Hedlund, B and McMahon, KD and Fierer, N and Knight, R and Finn, R and Cochrane, G and Karsch-Mizrachi, I and Tyson, GW and Rinke, C and , and Lapidus, A and Meyer, F and Yilmaz, P and Parks, DH and Eren, AM and Schriml, L and Banfield, JF and Hugenholtz, P and Woyke, T},
title = {Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.},
journal = {Nature biotechnology},
volume = {35},
number = {8},
pages = {725-731},
doi = {10.1038/nbt.3893},
pmid = {28787424},
issn = {1546-1696},
support = {R01 AI123037/AI/NIAID NIH HHS/United States ; R01 DE024463/DE/NIDCR NIH HHS/United States ; },
mesh = {Genome, Archaeal/*genetics ; Genome, Bacterial/genetics ; Genomics/*methods/standards ; Metagenomics/*methods/standards ; Sequence Analysis, DNA ; },
abstract = {We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum Information about a Metagenome-Assembled Genome (MIMAG), including, but not limited to, assembly quality, and estimates of genome completeness and contamination. These standards can be used in combination with other GSC checklists, including the Minimum Information about a Genome Sequence (MIGS), Minimum Information about a Metagenomic Sequence (MIMS), and Minimum Information about a Marker Gene Sequence (MIMARKS). Community-wide adoption of MISAG and MIMAG will facilitate more robust comparative genomic analyses of bacterial and archaeal diversity.},
}
@article {pmid28784816,
year = {2017},
author = {Peck, RF and Pleşa, AM and Graham, SM and Angelini, DR and Shaw, EL},
title = {Opsin-Mediated Inhibition of Bacterioruberin Synthesis in Halophilic Archaea.},
journal = {Journal of bacteriology},
volume = {199},
number = {21},
pages = {},
doi = {10.1128/JB.00303-17},
pmid = {28784816},
issn = {1098-5530},
support = {P20 GM103423/GM/NIGMS NIH HHS/United States ; R15 GM094735/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/*metabolism ; Bacteriorhodopsins/genetics/*metabolism ; Carotenoids/*biosynthesis ; Cloning, Molecular ; Colorimetry ; Gene Expression ; Haloarcula/enzymology/genetics ; Haloferax volcanii/genetics/*metabolism ; Recombinant Proteins/genetics/metabolism ; Retinaldehyde/metabolism ; },
abstract = {Halophilic archaea often inhabit environments with limited oxygen, and many produce ion-pumping rhodopsin complexes that allow them to maintain electrochemical gradients when aerobic respiration is inhibited. Rhodopsins require a protein, an opsin, and an organic cofactor, retinal. We previously demonstrated that in Halobacterium salinarum, bacterioopsin (BO), when not bound by retinal, inhibits the production of bacterioruberin, a biochemical pathway that shares intermediates with retinal biosynthesis. In this work, we used heterologous expression in a related halophilic archaeon, Haloferax volcanii, to demonstrate that BO is sufficient to inhibit bacterioruberin synthesis catalyzed by the H. salinarum lycopene elongase (Lye) enzyme. This inhibition was observed both in liquid culture and in a novel colorimetric assay to quantify bacterioruberin abundance based on the colony color. Addition of retinal to convert BO to the bacteriorhodopsin complex resulted in a partial rescue of bacterioruberin production. To explore if this regulatory mechanism occurs in other organisms, we expressed a Lye homolog and an opsin from Haloarcula vallismortis in H. volcaniiH. vallismortis cruxopsin-3 expression inhibited bacterioruberin synthesis catalyzed by H. vallismortis Lye but had no effect when bacterioruberin synthesis was catalyzed by H. salinarum or H. volcanii Lye. Conversely, H. salinarum BO did not inhibit H. vallismortis Lye activity. Together, our data suggest that opsin-mediated inhibition of Lye is potentially widespread and represents an elegant regulatory mechanism that allows organisms to efficiently utilize ion-pumping rhodopsins obtained through lateral gene transfer.IMPORTANCE Many enzymes are complexes of proteins and nonprotein organic molecules called cofactors. To ensure efficient formation of functional complexes, organisms must regulate the production of proteins and cofactors. To study this regulation, we used bacteriorhodopsin from the archaeon Halobacterium salinarum Bacteriorhodopsin consists of the bacterioopsin protein and a retinal cofactor. In this article, we further characterize a novel regulatory mechanism in which bacterioopsin promotes retinal production by inhibiting a reaction that consumes lycopene, a retinal precursor. By expressing H. salinarum genes in a different organism, Haloferax volcanii, we demonstrated that bacterioopsin alone is sufficient for this inhibition. We also found that an opsin from Haloarcula vallismortis has inhibitory activity, suggesting that this regulatory mechanism might be found in other organisms.},
}
@article {pmid28783564,
year = {2017},
author = {Barros, VG and Duda, RM and Vantini, JDS and Omori, WP and Ferro, MIT and Oliveira, RA},
title = {Improved methane production from sugarcane vinasse with filter cake in thermophilic UASB reactors, with predominance of Methanothermobacter and Methanosarcina archaea and Thermotogae bacteria.},
journal = {Bioresource technology},
volume = {244},
number = {Pt 1},
pages = {371-381},
doi = {10.1016/j.biortech.2017.07.106},
pmid = {28783564},
issn = {1873-2976},
mesh = {Anaerobiosis ; *Archaea ; Bacteria ; *Bioreactors ; *Methane ; *Methanobacteriaceae ; *Methanosarcina ; Saccharum ; },
abstract = {Biogas production from sugarcane vinasse has enormous economic, energy, and environmental management potential. However, methane production stability and biodigested vinasse quality remain key issues, requiring better nutrient and alkalinity availability, operational strategies, and knowledge of reactor microbiota. This study demonstrates increased methane production from vinasse through the use of sugarcane filter cake and improved effluent recirculation, with elevated organic loading rates (OLR) and good reactor stability. We used UASB reactors in a two-stage configuration, with OLRs up to 45gCODL-1d-1, and obtained methane production as high as 3LL-1d-1. Quantitative PCR indicated balanced amounts of bacteria and archaea in the sludge (109-1010copiesg-1VS), and of the predominant archaea orders, Methanobacteriales and Methanosarcinales (106-108copiesg-1VS). 16S rDNA sequencing also indicated the thermophilic Thermotogae as the most abundant class of bacteria in the sludge.},
}
@article {pmid28779290,
year = {2017},
author = {Vaksmaa, A and Guerrero-Cruz, S and van Alen, TA and Cremers, G and Ettwig, KF and Lüke, C and Jetten, MSM},
title = {Enrichment of anaerobic nitrate-dependent methanotrophic 'Candidatus Methanoperedens nitroreducens' archaea from an Italian paddy field soil.},
journal = {Applied microbiology and biotechnology},
volume = {101},
number = {18},
pages = {7075-7084},
doi = {10.1007/s00253-017-8416-0},
pmid = {28779290},
issn = {1432-0614},
support = {VENI 863.13.007//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; SIAM 024002002//Gravitation grant SIAM/ ; NESSC 024001001//Gravitation grant NESSC/ ; AG 339880 Eco_MoM//European Research Council/International ; 13178//Stichting voor de Technische Wetenschappen/ ; },
mesh = {Anaerobiosis ; Archaea/genetics/growth &amp; development/*isolation &amp; purification/metabolism ; Bioreactors ; Genome, Archaeal/*genetics ; Methane/*metabolism ; Molecular Sequence Annotation ; Nitrates/*metabolism ; Nitrites/*metabolism ; Oxidation-Reduction ; Phylogeny ; Sequence Analysis, DNA ; Soil ; Wetlands ; },
abstract = {Paddy fields are a significant source of methane and contribute up to 20% of total methane emissions from wetland ecosystems. These inundated, anoxic soils featuring abundant nitrogen compounds and methane are an ideal niche for nitrate-dependent anaerobic methanotrophs. After 2 years of enrichment with a continuous supply of methane and nitrate as the sole electron donor and acceptor, a stable enrichment dominated by 'Candidatus Methanoperedens nitroreducens' archaea and 'Candidatus Methylomirabilis oxyfera' NC10 phylum bacteria was achieved. In this community, the methanotrophic archaea supplied the NC10 phylum bacteria with the necessary nitrite through nitrate reduction coupled to methane oxidation. The results of qPCR quantification of 16S ribosomal RNA (rRNA) gene copies, analysis of metagenomic 16S rRNA reads, and fluorescence in situ hybridization (FISH) correlated well and showed that after 2 years, 'Candidatus Methanoperedens nitroreducens' had the highest abundance of (2.2 ± 0.4 × 108) 16S rRNA copies per milliliter and constituted approximately 22% of the total microbial community. Phylogenetic analysis showed that the 16S rRNA genes of the dominant microorganisms clustered with previously described 'Candidatus Methanoperedens nitroreducens ANME2D' (96% identity) and 'Candidatus Methylomirabilis oxyfera' (99% identity) strains. The pooled metagenomic sequences resulted in a high-quality draft genome assembly of 'Candidatus Methanoperedens nitroreducens Vercelli' that contained all key functional genes for the reverse methanogenesis pathway and nitrate reduction. The diagnostic mcrA gene was 96% similar to 'Candidatus Methanoperedens nitroreducens ANME2D' (WP_048089615.1) at the protein level. The 'Candidatus Methylomirabilis oxyfera' draft genome contained the marker genes pmoCAB, mdh, and nirS and putative NO dismutase genes. Whole-reactor anaerobic activity measurements with methane and nitrate revealed an average methane oxidation rate of 0.012 mmol/h/L, with cell-specific methane oxidation rates up to 0.57 fmol/cell/day for 'Candidatus Methanoperedens nitroreducens'. In summary, this study describes the first enrichment and draft genome of methanotrophic archaea from paddy field soil, where these organisms can contribute significantly to the mitigation of methane emissions.},
}
@article {pmid28777382,
year = {2017},
author = {Adam, PS and Borrel, G and Brochier-Armanet, C and Gribaldo, S},
title = {The growing tree of Archaea: new perspectives on their diversity, evolution and ecology.},
journal = {The ISME journal},
volume = {11},
number = {11},
pages = {2407-2425},
doi = {10.1038/ismej.2017.122},
pmid = {28777382},
issn = {1751-7370},
mesh = {Archaea/*classification/genetics/*isolation &amp; purification ; *Biodiversity ; Ecology ; Genome, Archaeal ; Phylogeny ; },
abstract = {The Archaea occupy a key position in the Tree of Life, and are a major fraction of microbial diversity. Abundant in soils, ocean sediments and the water column, they have crucial roles in processes mediating global carbon and nutrient fluxes. Moreover, they represent an important component of the human microbiome, where their role in health and disease is still unclear. The development of culture-independent sequencing techniques has provided unprecedented access to genomic data from a large number of so far inaccessible archaeal lineages. This is revolutionizing our view of the diversity and metabolic potential of the Archaea in a wide variety of environments, an important step toward understanding their ecological role. The archaeal tree is being rapidly filled up with new branches constituting phyla, classes and orders, generating novel challenges for high-rank systematics, and providing key information for dissecting the origin of this domain, the evolutionary trajectories that have shaped its current diversity, and its relationships with Bacteria and Eukarya. The present picture is that of a huge diversity of the Archaea, which we are only starting to explore.},
}
@article {pmid28777072,
year = {2017},
author = {Rivera-Gómez, N and Martínez-Núñez, MA and Pastor, N and Rodriguez-Vazquez, K and Perez-Rueda, E},
title = {Dissecting the protein architecture of DNA-binding transcription factors in bacteria and archaea.},
journal = {Microbiology (Reading, England)},
volume = {163},
number = {8},
pages = {1167-1178},
doi = {10.1099/mic.0.000504},
pmid = {28777072},
issn = {1465-2080},
mesh = {Archaea/chemistry/classification/genetics/*metabolism ; Archaeal Proteins/chemistry/genetics/*metabolism ; Bacteria/chemistry/classification/genetics/*metabolism ; Bacterial Proteins/chemistry/genetics/*metabolism ; DNA-Binding Proteins/chemistry/genetics/*metabolism ; Dimerization ; Genome, Archaeal ; Genome, Bacterial ; Models, Molecular ; Phylogeny ; Protein Conformation ; Transcription Factors/chemistry/genetics/*metabolism ; },
abstract = {Gene regulation at the transcriptional level is a central process in all organisms where DNA-binding transcription factors play a fundamental role. This class of proteins binds specifically at DNA sequences, activating or repressing gene expression as a function of the cell's metabolic status, operator context and ligand-binding status, among other factors, through the DNA-binding domain (DBD). In addition, TFs may contain partner domains (PaDos), which are involved in ligand binding and protein-protein interactions. In this work, we systematically evaluated the distribution, abundance and domain organization of DNA-binding TFs in 799 non-redundant bacterial and archaeal genomes. We found that the distributions of the DBDs and their corresponding PaDos correlated with the size of the genome. We also identified specific combinations between the DBDs and their corresponding PaDos. Within each class of DBDs there are differences in the actual angle formed at the dimerization interface, responding to the presence/absence of ligands and/or crystallization conditions, setting the orientation of the resulting helices and wings facing the DNA. Our results highlight the importance of PaDos as central elements that enhance the diversity of regulatory functions in all bacterial and archaeal organisms, and our results also demonstrate the role of PaDos in sensing diverse signal compounds. The highly specific interactions between DBDs and PaDos observed in this work, together with our structural analysis highlighting the difficulty in predicting both inter-domain geometry and quaternary structure, suggest that these systems appeared once and evolved with diverse duplication events in all the analysed organisms.},
}
@article {pmid28776097,
year = {2017},
author = {Zhao, K and Kong, W and Khan, A and Liu, J and Guo, G and Muhanmmad, S and Zhang, X and Dong, X},
title = {Elevational diversity and distribution of ammonia-oxidizing archaea community in meadow soils on the Tibetan Plateau.},
journal = {Applied microbiology and biotechnology},
volume = {101},
number = {18},
pages = {7065-7074},
doi = {10.1007/s00253-017-8435-x},
pmid = {28776097},
issn = {1432-0614},
support = {XDB15010203//Chinese Academy of Sciences/ ; KZZD-EW-TZ-14//Chinese Academy of Sciences/ ; 41471054//National Natural Science Foundation of China/ ; 41401287//National Natural Science Foundation of China/ ; },
mesh = {Ammonia/*metabolism ; Archaea/*metabolism ; Grassland ; Nitrification ; Oxidation-Reduction ; Polymorphism, Restriction Fragment Length ; Soil ; Tibet ; },
abstract = {Unraveling elevational diversity patterns of plants and animals has long been attracting scientific interests. However, whether soil microorganisms exhibit similar elevational patterns remains largely less explored, especially for functional microbial communities, such as ammonia oxidizers. Here, we investigated the diversity and distribution pattern of ammonia-oxidizing archaea (AOA) in meadow soils along an elevation gradient from 4400 m to the grassline at 5100 m on the Tibetan Plateau using terminal restriction fragment length polymorphism (T-RFLP) and sequencing methods by targeting amoA gene. Increasing elevations led to lower soil temperature and pH, but higher nutrients and water content. The results showed that AOA diversity and evenness monotonically increased with elevation, while richness was relatively stable. The increase of diversity and evenness was attributed to the growth inhibition of warm-adapted AOA phylotypes by lower temperature and the growth facilitation of cold-adapted AOA phylotypes by richer nutrients at higher elevations. Low temperature thus played an important role in the AOA growth and niche separation. The AOA community variation was explained by the combined effect of all soil properties (32.6%), and 8.1% of the total variation was individually explained by soil pH. The total AOA abundance decreased, whereas soil potential nitrification rate (PNR) increased with increasing elevations. Soil PNR positively correlated with the abundance of cold-adapted AOA phylotypes. Our findings suggest that low temperature plays an important role in AOA elevational diversity pattern and niche separation, rising the negative effects of warming on AOA diversity and soil nitrification process in the Tibetan region.},
}
@article {pmid28769904,
year = {2017},
author = {Wen, X and Yang, S and Horn, F and Winkel, M and Wagner, D and Liebner, S},
title = {Global Biogeographic Analysis of Methanogenic Archaea Identifies Community-Shaping Environmental Factors of Natural Environments.},
journal = {Frontiers in microbiology},
volume = {8},
number = {},
pages = {1339},
doi = {10.3389/fmicb.2017.01339},
pmid = {28769904},
issn = {1664-302X},
abstract = {Methanogenic archaea are important for the global greenhouse gas budget since they produce methane under anoxic conditions in numerous natural environments such as oceans, estuaries, soils, and lakes. Whether and how environmental change will propagate into methanogenic assemblages of natural environments remains largely unknown owing to a poor understanding of global distribution patterns and environmental drivers of this specific group of microorganisms. In this study, we performed a meta-analysis targeting the biogeographic patterns and environmental controls of methanogenic communities using 94 public mcrA gene datasets. We show a global pattern of methanogenic archaea that is more associated with habitat filtering than with geographical dispersal. We identify salinity as the control on methanogenic community composition at global scale whereas pH and temperature are the major controls in non-saline soils and lakes. The importance of salinity for structuring methanogenic community composition is also reflected in the biogeography of methanogenic lineages and the physiological properties of methanogenic isolates. Linking methanogenic alpha-diversity with reported values of methane emission identifies estuaries as the most diverse methanogenic habitats with, however, minor contribution to the global methane budget. With salinity, temperature and pH our study identifies environmental drivers of methanogenic community composition facing drastic changes in many natural environments at the moment. However, consequences of this for the production of methane remain elusive owing to a lack of studies that combine methane production rate with community analysis.},
}
@article {pmid28765217,
year = {2017},
author = {Daume, M and Uhl, M and Backofen, R and Randau, L},
title = {RIP-Seq Suggests Translational Regulation by L7Ae in Archaea.},
journal = {mBio},
volume = {8},
number = {4},
pages = {},
doi = {10.1128/mBio.00730-17},
pmid = {28765217},
issn = {2150-7511},
mesh = {Archaeal Proteins/*genetics/metabolism ; Escherichia coli/genetics ; *Gene Expression Regulation, Archaeal ; Immunoprecipitation ; Protein Binding ; *Protein Biosynthesis ; RNA, Archaeal/chemistry/*genetics ; RNA, Untranslated/genetics ; RNA-Binding Proteins/genetics/metabolism ; Ribosomal Proteins/genetics ; *Sequence Analysis, RNA ; Sulfolobus acidocaldarius/*genetics/metabolism ; },
abstract = {L7Ae is a universal archaeal protein that recognizes and stabilizes kink-turn (k-turn) motifs in RNA substrates. These structural motifs are widespread in nature and are found in many functional RNA species, including ribosomal RNAs. Synthetic biology approaches utilize L7Ae/k-turn interactions to control gene expression in eukaryotes. Here, we present results of comprehensive RNA immunoprecipitation sequencing (RIP-Seq) analysis of genomically tagged L7Ae from the hyperthermophilic archaeon Sulfolobus acidocaldarius A large set of interacting noncoding RNAs was identified. In addition, several mRNAs, including the l7ae transcript, were found to contain k-turn motifs that facilitate L7Ae binding. In vivo studies showed that L7Ae autoregulates the translation of its mRNA by binding to a k-turn motif present in the 5' untranslated region (UTR). A green fluorescent protein (GFP) reporter system was established in Escherichia coli and verified conservation of L7Ae-mediated feedback regulation in Archaea Mobility shift assays confirmed binding to a k-turn in the transcript of nop5-fibrillarin, suggesting that the expression of all C/D box sRNP core proteins is regulated by L7Ae. These studies revealed that L7Ae-mediated gene regulation evolved in archaeal organisms, generating new tools for the modulation of synthetic gene circuits in bacteria.IMPORTANCE L7Ae is an essential archaeal protein that is known to structure ribosomal RNAs and small RNAs (sRNAs) by binding to their kink-turn motifs. Here, we utilized RIP-Seq methodology to achieve a first global analysis of RNA substrates for L7Ae. Several novel interactions with noncoding RNA molecules (e.g., with the universal signal recognition particle RNA) were discovered. In addition, L7Ae was found to bind to mRNAs, including its own transcript's 5' untranslated region. This feedback-loop control is conserved in most archaea and was incorporated into a reporter system that was utilized to control gene expression in bacteria. These results demonstrate that L7Ae-mediated gene regulation evolved originally in archaeal organisms. The feedback-controlled reporter gene system can easily be adapted for synthetic biology approaches that require strict gene expression control.},
}
@article {pmid28765215,
year = {2017},
author = {Skennerton, CT and Chourey, K and Iyer, R and Hettich, RL and Tyson, GW and Orphan, VJ},
title = {Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea.},
journal = {mBio},
volume = {8},
number = {4},
pages = {},
doi = {10.1128/mBio.00530-17},
pmid = {28765215},
issn = {2150-7511},
mesh = {Anaerobiosis ; Archaea/*genetics/*metabolism ; Bacteria/*genetics/*metabolism ; Electron Transport ; Genome, Archaeal ; Genome, Bacterial ; Geologic Sediments/microbiology ; Hydrogen/metabolism ; Metagenomics ; Methane/*metabolism ; Oxidation-Reduction ; Phylogeny ; Sulfates/metabolism ; },
abstract = {The anaerobic oxidation of methane by anaerobic methanotrophic (ANME) archaea in syntrophic partnership with deltaproteobacterial sulfate-reducing bacteria (SRB) is the primary mechanism for methane removal in ocean sediments. The mechanism of their syntrophy has been the subject of much research as traditional intermediate compounds, such as hydrogen and formate, failed to decouple the partners. Recent findings have indicated the potential for extracellular electron transfer from ANME archaea to SRB, though it is unclear how extracellular electrons are integrated into the metabolism of the SRB partner. We used metagenomics to reconstruct eight genomes from the globally distributed SEEP-SRB1 clade of ANME partner bacteria to determine what genomic features are required for syntrophy. The SEEP-SRB1 genomes contain large multiheme cytochromes that were not found in previously described free-living SRB and also lack periplasmic hydrogenases that may prevent an independent lifestyle without an extracellular source of electrons from ANME archaea. Metaproteomics revealed the expression of these cytochromes at in situ methane seep sediments from three sites along the Pacific coast of the United States. Phylogenetic analysis showed that these cytochromes appear to have been horizontally transferred from metal-respiring members of the Deltaproteobacteria such as Geobacter and may allow these syntrophic SRB to accept extracellular electrons in place of other chemical/organic electron donors.IMPORTANCE Some archaea, known as anaerobic methanotrophs, are capable of converting methane into carbon dioxide when they are growing syntopically with sulfate-reducing bacteria. This partnership is the primary mechanism for methane removal in ocean sediments; however, there is still much to learn about how this syntrophy works. Previous studies have failed to identify the metabolic intermediate, such as hydrogen or formate, that is passed between partners. However, recent analysis of methanotrophic archaea has suggested that the syntrophy is formed through direct electron transfer. In this research, we analyzed the genomes of multiple partner bacteria and showed that they also contain the genes necessary to perform extracellular electron transfer, which are absent in related bacteria that do not form syntrophic partnerships with anaerobic methanotrophs. This genomic evidence shows a possible mechanism for direct electron transfer from methanotrophic archaea into the metabolism of the partner bacteria.},
}
@article {pmid28755506,
year = {2017},
author = {Di Maiuta, N and Rüfenacht, A and Küenzi, P},
title = {Assessment of bacteria and archaea in metalworking fluids using massive parallel 16S rRNA gene tag sequencing.},
journal = {Letters in applied microbiology},
volume = {65},
number = {4},
pages = {266-273},
doi = {10.1111/lam.12782},
pmid = {28755506},
issn = {1472-765X},
mesh = {Azides/chemistry ; Disinfectants ; Fungi/*classification/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Manufacturing and Industrial Facilities ; Methanobrevibacter/*classification/genetics/isolation &amp; purification ; Propidium/analogs &amp; derivatives/chemistry ; Pseudomonas/*classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Determination of the bacterial diversity in industry-based liquid in-use water-miscible metalworking fluid (MWF) samples was targeted by massive parallel multiplex DNA sequencing, either directly or upon pretreatment with propidium monoazide (PMA) that allows differentiation between intact and physically damaged cells. As MWFs provide a suitable basis of life for micro-organisms, the majority is preserved by biocides. 'Bio-concept' fluids on the other hand are bactericide free, which intentionally leads to substantial bacterial populations. Samples from both fluid types were chosen: A median of 51 operational taxonomic units at genera level (OTUs) were detected per sample, but only 13 were present at or above 1·0% of the total population in any PMA-treated sample analysed. As both fluid types were mainly dominated by Pseudomonas spp., we resolved this genus on the species level and found the Pseudomonas oleovorans/pseudoalcaligenes group to predominate. We also looked for archaea and detected Methanobrevibacter spp., albeit in <3% of all samples analysed.<br><br>Water-miscible metalworking fluids provide a suitable base of life for micro-organisms, mainly bacteria and fungi. Earlier publications suggested that the diversity is rather low, but these studies were largely based on heterotrophic plate counts. This might have resulted in underestimation of population density and microbial diversity as some organisms might just refuse to grow. This study used high-throughput sequencing in the absence and presence of propidium monoazide to explore bacterial and archaeal presence in metalworking fluids. We established that diversity is low and bacterial populations are dominated by the genus Pseudomonas spp.},
}
@article {pmid28741608,
year = {2017},
author = {Spang, A and Ettema, TJG},
title = {Archaeal evolution: The methanogenic roots of Archaea.},
journal = {Nature microbiology},
volume = {2},
number = {},
pages = {17109},
doi = {10.1038/nmicrobiol.2017.109},
pmid = {28741608},
issn = {2058-5276},
}
@article {pmid28734066,
year = {2017},
author = {Varnava, KG and Ronimus, RS and Sarojini, V},
title = {A review on comparative mechanistic studies of antimicrobial peptides against archaea.},
journal = {Biotechnology and bioengineering},
volume = {114},
number = {11},
pages = {2457-2473},
doi = {10.1002/bit.26387},
pmid = {28734066},
issn = {1097-0290},
mesh = {Antimicrobial Cationic Peptides/*administration &amp; dosage ; Apoptosis/*drug effects/*physiology ; Archaea/cytology/*drug effects/*physiology ; Cell Survival/drug effects/physiology ; Dose-Response Relationship, Drug ; Microbial Sensitivity Tests/*methods ; Species Specificity ; },
abstract = {Archaea was until recently considered as a third domain of life in addition to bacteria and eukarya but recent studies support the existence of only two superphyla (bacteria and archaea). The fundamental differences between archaeal, bacterial, and eukaryal cells are probably the main reasons for the comparatively lower susceptibility of archaeal strains to current antimicrobial agents. The possible emerging pathogenicity of archaea and the role of archaeal methanogens in methane emissions, a potent greenhouse gas, has led many researchers to examine the sensitivity patterns of archaea and make attempts to find agents that have significant anti-archaeal activity. Even though antimicrobial peptides (AMPs) are well known with several published reviews concerning their mode of action against bacteria and eukarya, to our knowledge, to date no reviews are available that focus on the action of these peptides against archaea. Herein, we present a review on all the peptides that have been tested against archaea. In addition, in an attempt to shed more light on possible future work that needs to be performed we have included a brief overview of the chemical characteristics, spectrum of activity, and the known mechanism of action of each of these peptides against bacteria and/or fungi. We also discuss the nature of and key physiological differences between Archaea, Bacteria, and Eukarya that are relevant to the development of anti-archaeal peptides. Despite our relatively limited knowledge about archaea, available data suggest that AMPs have an even broader spectrum of activity than currently recognized.},
}
@article {pmid28713363,
year = {2017},
author = {Jing, H and Cheung, S and Xia, X and Suzuki, K and Nishioka, J and Liu, H},
title = {Geographic Distribution of Ammonia-Oxidizing Archaea along the Kuril Islands in the Western Subarctic Pacific.},
journal = {Frontiers in microbiology},
volume = {8},
number = {},
pages = {1247},
doi = {10.3389/fmicb.2017.01247},
pmid = {28713363},
issn = {1664-302X},
abstract = {Community composition and abundance of ammonia-oxidizing archaea (AOA) in the ocean were affected by different physicochemical conditions, but their responses to physical barriers (such as a chain of islands) were largely unknown. In our study, geographic distribution of the AOA from the surface photic zone to the deep bathypelagic waters in the western subarctic Pacific adjacent to the Kuril Islands was investigated using pyrosequencing based on the ammonia monooxygenase subunit A (amoA) gene. Genotypes of clusters A and B dominated in the upper euphotic zone and the deep waters, respectively. Quantitative PCR assays revealed that the occurrence and ammonia-oxidizing activity of ammonia-oxidizing archaea (AOA) reached their maxima at the depth of 200 m, where a higher diversity and abundance of actively transcribed AOA was observed at the station located in the marginal sea exposed to more terrestrial input. Similar community composition of AOA observed at the two stations adjacent to the Kuril Islands maybe due to water exchange across the Bussol Strait. They distinct from the station located in the western subarctic gyre, where sub-cluster WCAII had a specific distribution in the surface water, and this sub-cluster seemed having a confined distribution in the western Pacific. Habitat-specific groupings of different WCB sub-clusters were observed reflecting the isolated microevolution existed in cluster WCB. The effect of the Kuril Islands on the phylogenetic composition of AOA between the Sea of Okhotsk and the western subarctic Pacific is not obvious, possibly because our sampling stations are near to the Bussol Strait, the main gateway through which water is exchanged between the Sea of Okhotsk and the Pacific. The vertical and horizontal distribution patterns of AOA communities among stations along the Kuril Islands were essentially determined by the in situ prevailing physicochemical gradients along the two dimensions.},
}
@article {pmid28710268,
year = {2017},
author = {Duszenko, N and Buan, NR},
title = {Physiological Evidence for Isopotential Tunneling in the Electron Transport Chain of Methane-Producing Archaea.},
journal = {Applied and environmental microbiology},
volume = {83},
number = {18},
pages = {},
doi = {10.1128/AEM.00950-17},
pmid = {28710268},
issn = {1098-5336},
support = {P20 GM113126/GM/NIGMS NIH HHS/United States ; P20 RR017675/RR/NCRR NIH HHS/United States ; },
mesh = {Benzoquinones/metabolism ; Electron Transport ; Escherichia coli/genetics/growth &amp; development/metabolism ; Hydrogen/metabolism ; Methane/*metabolism ; Methanosarcina/genetics/growth &amp; development/*metabolism ; },
abstract = {Many, but not all, organisms use quinones to conserve energy in their electron transport chains. Fermentative bacteria and methane-producing archaea (methanogens) do not produce quinones but have devised other ways to generate ATP. Methanophenazine (MPh) is a unique membrane electron carrier found in Methanosarcina species that plays the same role as quinones in the electron transport chain. To extend the analogy between quinones and MPh, we compared the MPh pool sizes between two well-studied Methanosarcina species, Methanosarcina acetivorans C2A and Methanosarcina barkeri Fusaro, to the quinone pool size in the bacterium Escherichia coli We found the quantity of MPh per cell increases as cultures transition from exponential growth to stationary phase, and absolute quantities of MPh were 3-fold higher in M. acetivorans than in M. barkeri The concentration of MPh suggests the cell membrane of M. acetivorans, but not of M. barkeri, is electrically quantized as if it were a single conductive metal sheet and near optimal for rate of electron transport. Similarly, stationary (but not exponentially growing) E. coli cells also have electrically quantized membranes on the basis of quinone content. Consistent with our hypothesis, we demonstrated that the exogenous addition of phenazine increases the growth rate of M. barkeri three times that of M. acetivorans Our work suggests electron flux through MPh is naturally higher in M. acetivorans than in M. barkeri and that hydrogen cycling is less efficient at conserving energy than scalar proton translocation using MPh.IMPORTANCE Can we grow more from less? The ability to optimize and manipulate metabolic efficiency in cells is the difference between commercially viable and nonviable renewable technologies. Much can be learned from methane-producing archaea (methanogens) which evolved a successful metabolic lifestyle under extreme thermodynamic constraints. Methanogens use highly efficient electron transport systems and supramolecular complexes to optimize electron and carbon flow to control biomass synthesis and the production of methane. Worldwide, methanogens are used to generate renewable methane for heat, electricity, and transportation. Our observations suggest Methanosarcina acetivorans, but not Methanosarcina barkeri, has electrically quantized membranes. Escherichia coli, a model facultative anaerobe, has optimal electron transport at the stationary phase but not during exponential growth. This study also suggests the metabolic efficiency of bacteria and archaea can be improved using exogenously supplied lipophilic electron carriers. The enhancement of methanogen electron transport through methanophenazine has the potential to increase renewable methane production at an industrial scale.},
}
@article {pmid28681113,
year = {2017},
author = {Sheppard, C and Werner, F},
title = {Structure and mechanisms of viral transcription factors in archaea.},
journal = {Extremophiles : life under extreme conditions},
volume = {21},
number = {5},
pages = {829-838},
doi = {10.1007/s00792-017-0951-1},
pmid = {28681113},
issn = {1433-4909},
mesh = {Archaeal Viruses/*genetics/metabolism ; Gene Expression Regulation, Viral ; Transcription Factors/chemistry/genetics/*metabolism ; Viral Proteins/chemistry/genetics/*metabolism ; },
abstract = {Virus-encoded transcription factors have been pivotal in exploring the molecular mechanisms and regulation of gene expression in bacteria and eukaryotes since the birth of molecular biology, while our understanding of viral transcription in archaea is still in its infancy. Archaeal viruses do not encode their own RNA polymerases (RNAPs) and are consequently entirely dependent on their hosts for gene expression; this is fundamentally different from many bacteriophages and requires alternative regulatory strategies. Archaeal viruses wield a repertoire of proteins to expropriate the host transcription machinery to their own benefit. In this short review we summarise our current understanding of gene-specific and global mechanisms that viruses employ to chiefly downregulate host transcription and enable the efficient and temporal expression of the viral transcriptome. Most of the experimentally characterised archaeo-viral transcription regulators possess either ribbon-helix-helix or Zn-finger motifs that allow them to engage with the DNA in a sequence-specific manner, altering the expression of a specific subset of genes. Recently a novel type of regulator was reported that directly binds to the RNAP and shuts down transcription of both host and viral genes in a global fashion.},
}
@article {pmid28680072,
year = {2017},
author = {Golyshina, OV and Toshchakov, SV and Makarova, KS and Gavrilov, SN and Korzhenkov, AA and La Cono, V and Arcadi, E and Nechitaylo, TY and Ferrer, M and Kublanov, IV and Wolf, YI and Yakimov, MM and Golyshin, PN},
title = {'ARMAN' archaea depend on association with euryarchaeal host in culture and in situ.},
journal = {Nature communications},
volume = {8},
number = {1},
pages = {60},
doi = {10.1038/s41467-017-00104-7},
pmid = {28680072},
issn = {2041-1723},
support = {/ImNIH/Intramural NIH HHS/United States ; },
mesh = {Archaea/*classification/genetics/*physiology ; Gene Expression Regulation, Archaeal ; Genetic Variation ; Genome, Archaeal ; Microscopy, Fluorescence ; Phylogeny ; RNA, Archaeal/genetics ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; },
abstract = {Intriguing, yet uncultured 'ARMAN'-like archaea are metabolically dependent on other members of the microbial community. It remains uncertain though which hosts they rely upon, and, because of the lack of complete genomes, to what extent. Here, we report the co-culturing of ARMAN-2-related organism, Mia14, with Cuniculiplasma divulgatum PM4 during the isolation of this strain from acidic streamer in Parys Mountain (Isle of Anglesey, UK). Mia14 is highly enriched in the binary culture (ca. 10% genomic reads) and its ungapped 0.95 Mbp genome points at severe voids in central metabolic pathways, indicating dependence on the host, C. divulgatum PM4. Analysis of C. divulgatum isolates from different sites and shotgun sequence data of Parys Mountain samples suggests an extensive genetic exchange between Mia14 and hosts in situ. Within the subset of organisms with high-quality genomic assemblies representing the 'DPANN' superphylum, the Mia14 lineage has had the largest gene flux, with dozens of genes gained that are implicated in the host interaction.In the absence of complete genomes, the metabolic capabilities of uncultured ARMAN-like archaea have been uncertain. Here, Golyshina et al. apply an enrichment culture technique and find that the ungapped genome of the ARMAN-like archaeon Mia14 has lost key metabolic pathways, suggesting dependence on the host archaeon Cuniculiplasma divulgatum.},
}
@article {pmid28677304,
year = {2017},
author = {Tolar, BB and Herrmann, J and Bargar, JR and van den Bedem, H and Wakatsuki, S and Francis, CA},
title = {Integrated structural biology and molecular ecology of N-cycling enzymes from ammonia-oxidizing archaea.},
journal = {Environmental microbiology reports},
volume = {9},
number = {5},
pages = {484-491},
doi = {10.1111/1758-2229.12567},
pmid = {28677304},
issn = {1758-2229},
mesh = {Ammonia/*metabolism ; Archaea/classification/enzymology/*genetics/*metabolism ; Enzymes/*chemistry/*metabolism ; Nitrite Reductases/chemistry/genetics/metabolism ; *Oxidation-Reduction ; Oxidoreductases/chemistry/genetics/metabolism ; Phylogeny ; Structure-Activity Relationship ; },
abstract = {Knowledge of the molecular ecology and environmental determinants of ammonia-oxidizing organisms is critical to understanding and predicting the global nitrogen (N) and carbon cycles, but an incomplete biochemical picture hinders in vitro studies of N-cycling enzymes. Although an integrative structural and dynamic characterization at the atomic scale would advance our understanding of function tremendously, structural knowledge of key N-cycling enzymes from ecologically relevant ammonia oxidizers is unfortunately extremely limited. Here, we discuss the challenges and opportunities for examining the ecology of ammonia-oxidizing organisms, particularly uncultivated Thaumarchaeota, through (meta)genome-driven structural biology of the enzymes ammonia monooxygenase (AMO) and nitrite reductase (NirK).},
}
@article {pmid28663746,
year = {2017},
author = {Liu, H and Zhang, CL and Yang, C and Chen, S and Cao, Z and Zhang, Z and Tian, J},
title = {Marine Group II Dominates Planktonic Archaea in Water Column of the Northeastern South China Sea.},
journal = {Frontiers in microbiology},
volume = {8},
number = {},
pages = {1098},
doi = {10.3389/fmicb.2017.01098},
pmid = {28663746},
issn = {1664-302X},
abstract = {Temperature, nutrients, and salinity are among the important factors constraining the distribution and abundance of microorganisms in the ocean. Marine Group II (MGII) belonging to Euryarchaeota commonly dominates the planktonic archaeal community in shallow water and Marine Group I (MGI, now is called Thaumarchaeota) in deeper water in global oceans. Results of quantitative PCR (qPCR) and 454 sequencing in our study, however, showed the dominance of MGII in planktonic archaea throughout the water column of the northeastern South China Sea (SCS) that is characterized by strong water mixing. The abundance of ammonia-oxidizing archaea (AOA) representing the main group of Thaumarchaeota in deeper water in the northeastern SCS was significantly lower than in other oceanic regions. Phylogenetic analysis showed that the top operational taxonomic units (OTUs) of the MGII occurring predominantly below 200 m depth may be unique in the northeastern SCS based on the observation that they are distantly related to known sequences (identity ranging from 90-94%). The abundance of MGII was also significantly correlated with total bacteria in the whole column, which may indicate that MGII and bacteria may have similar physiological or biochemical properties or responses to environmental variation. This study provides valuable information about the dominance of MGII over AOA in both shallow and deep water in the northeastern SCS and highlights the need for comprehensive studies integrating physical, chemical, and microbial oceanography.},
}
@article {pmid28659382,
year = {2017},
author = {Staley, JT},
title = {Domain Cell Theory supports the independent evolution of the Eukarya, Bacteria and Archaea and the Nuclear Compartment Commonality hypothesis.},
journal = {Open biology},
volume = {7},
number = {6},
pages = {},
doi = {10.1098/rsob.170041},
pmid = {28659382},
issn = {2046-2441},
abstract = {In 2015, the Royal Society of London held a meeting to discuss the various hypotheses regarding the origin of the Eukarya. Although not all participants supported a hypothesis, the proposals that did fit into two broad categories: one group favoured 'Prokaryotes First' hypotheses and another addressed 'Eukaryotes First' hypotheses. Those who proposed Prokaryotes First hypotheses advocated either a fusion event between a bacterium and an archaeon that produced the first eukaryote or the direct evolution of the Eukarya from the Archaea. The Eukaryotes First proponents posit that the eukaryotes evolved initially and then, by reductive evolution, produced the Bacteria and Archaea. No mention was made of another previously published hypothesis termed the Nuclear Compartment Commonality (NuCom) hypothesis, which proposed the evolution of the Eukarya and Bacteria from nucleated ancestors (Staley 2013 Astrobiol Outreach1, 105 (doi:10.4172/2332-2519.1000105)). Evidence from two studies indicates that the nucleated Planctomycetes-Verrucomicrobia-Chlamydia superphylum members are the most ancient Bacteria known (Brochier &amp; Philippe 2002 Nature417, 244 (doi:10.1038/417244a); Jun et al. 2010 Proc. Natl Acad. Sci. USA107, 133-138 (doi:10.1073/pnas.0913033107)). This review summarizes the evidence for the NuCom hypothesis and discusses how simple the NuCom hypothesis is in explaining eukaryote evolution relative to the other hypotheses. The philosophical importance of simplicity and its relationship to truth in hypotheses such as NuCom and Domain Cell Theory is presented. Domain Cell Theory is also proposed herein, which contends that each of the three cellular lineages of life, the Archaea, Bacteria and Eukarya domains, evolved independently, in support of the NuCom hypothesis. All other proposed hypotheses violate Domain Cell Theory because they posit the evolution of different cellular descendants from ancestral cellular types.},
}
@article {pmid28657885,
year = {2017},
author = {Koonin, EV and Makarova, KS and Wolf, YI},
title = {Evolutionary Genomics of Defense Systems in Archaea and Bacteria.},
journal = {Annual review of microbiology},
volume = {71},
number = {},
pages = {233-261},
doi = {10.1146/annurev-micro-090816-093830},
pmid = {28657885},
issn = {1545-3251},
support = {Z01 LM000061-15/NULL/Intramural NIH HHS/United States ; Z01 LM000073-12/NULL/Intramural NIH HHS/United States ; },
mesh = {Archaea/*genetics/*virology ; Bacteria/*genetics/*virology ; CRISPR-Cas Systems ; DNA Restriction-Modification Enzymes ; *Evolution, Molecular ; Genome, Archaeal ; Genome, Bacterial ; Genomics ; *Host-Parasite Interactions ; },
abstract = {Evolution of bacteria and archaea involves an incessant arms race against an enormous diversity of genetic parasites. Accordingly, a substantial fraction of the genes in most bacteria and archaea are dedicated to antiparasite defense. The functions of these defense systems follow several distinct strategies, including innate immunity; adaptive immunity; and dormancy induction, or programmed cell death. Recent comparative genomic studies taking advantage of the expanding database of microbial genomes and metagenomes, combined with direct experiments, resulted in the discovery of several previously unknown defense systems, including innate immunity centered on Argonaute proteins, bacteriophage exclusion, and new types of CRISPR-Cas systems of adaptive immunity. Some general principles of function and evolution of defense systems are starting to crystallize, in particular, extensive gain and loss of defense genes during the evolution of prokaryotes; formation of genomic defense islands; evolutionary connections between mobile genetic elements and defense, whereby genes of mobile elements are repeatedly recruited for defense functions; the partially selfish and addictive behavior of the defense systems; and coupling between immunity and dormancy induction/programmed cell death.},
}
@article {pmid28655184,
year = {2017},
author = {Cranford, MT and Chu, AM and Baguley, JK and Bauer, RJ and Trakselis, MA},
title = {Characterization of a coupled DNA replication and translesion synthesis polymerase supraholoenzyme from archaea.},
journal = {Nucleic acids research},
volume = {45},
number = {14},
pages = {8329-8340},
doi = {10.1093/nar/gkx539},
pmid = {28655184},
issn = {1362-4962},
mesh = {Archaeal Proteins/chemistry/genetics/*metabolism ; Blotting, Western ; *DNA Repair ; *DNA Replication ; DNA, Archaeal/chemistry/genetics/metabolism ; DNA-Directed DNA Polymerase/chemistry/genetics/*metabolism ; Holoenzymes/chemistry/genetics/metabolism ; Kinetics ; Models, Molecular ; Nucleic Acid Conformation ; Proliferating Cell Nuclear Antigen/genetics/metabolism ; Protein Binding ; Protein Structure, Tertiary ; Spectrometry, Fluorescence ; Sulfolobus solfataricus/enzymology/genetics/metabolism ; },
abstract = {The ability of the replisome to seamlessly coordinate both high fidelity and translesion DNA synthesis requires a means to regulate recruitment and binding of enzymes from solution. Co-occupancy of multiple DNA polymerases within the replisome has been observed primarily in bacteria and is regulated by posttranslational modifications in eukaryotes, and both cases are coordinated by the processivity clamp. Because of the heterotrimeric nature of the PCNA clamp in some archaea, there is potential to occupy and regulate specific polymerases at defined subunits. In addition to specific PCNA and polymerase interactions (PIP site), we have now identified and characterized a novel protein contact between the Y-family DNA polymerase and the B-family replication polymerase (YB site) bound to PCNA and DNA from Sulfolobus solfataricus. These YB contacts are essential in forming and stabilizing a supraholoenzyme (SHE) complex on DNA, effectively increasing processivity of DNA synthesis. The SHE complex can not only coordinate polymerase exchange within the complex but also provides a mechanism for recruitment of polymerases from solution based on multiequilibrium processes. Our results provide evidence for an archaeal PCNA 'tool-belt' recruitment model of multienzyme function that can facilitate both high fidelity and translesion synthesis within the replisome during DNA replication.},
}
@article {pmid28647121,
year = {2017},
author = {Xu, J and Jia, Z and Lin, X and Feng, Y},
title = {DNA-based stable isotope probing identifies formate-metabolizing methanogenic archaea in paddy soil.},
journal = {Microbiological research},
volume = {202},
number = {},
pages = {36-42},
doi = {10.1016/j.micres.2017.05.004},
pmid = {28647121},
issn = {1618-0623},
mesh = {*Biodegradation, Environmental ; Carbon Isotopes ; China ; Cloning, Molecular ; DNA/chemistry ; *DNA Probes ; DNA, Archaeal ; Denaturing Gradient Gel Electrophoresis ; Euryarchaeota/classification/*genetics/*metabolism ; Formates/*metabolism ; Methane/biosynthesis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Soil ; Soil Microbiology ; },
abstract = {Paddy methane (CH4) production is biologically dominated by methanogenic archaea that metabolize a variety of organic and/or inorganic carbon sources. Though formate is easily dissimilated into H2/CO2, formate-metabolizing methanogenic archaea are distinct from CO2-utilizing methanogen taxa. The identity of formate-metabolizing methanogenic archaea in paddy soil remains elusive. In this investigation, molecular approaches based on stable isotope probing (SIP) technique were conducted to identify the formate-metabolizing methanogenic archaea in paddy soil. CH4 emission monitor, real-time quantitative PCR (qPCR) and Denaturing Gradient Gel Electrophoresis (DGGE) analyses consistently indicated that some methanogenic archaea metabolized 13C-labeled formate in microcosm and accounted for a large portion of formate-metabolizing archaea in anoxic paddy soil. Phylogenetic identification further found that this guild was affiliated to Methanobacteriaceae. Taken together Methanobacteriaceae could be the dominant formate-metabolizing methanogenic archaea and play an important role in the CH4 production in paddy soil. These findings would extend the extant knowledge on paddy methanogenic archaea and microbial-driven paddy CH4 emission.},
}
@article {pmid28642547,
year = {2017},
author = {Moissl-Eichinger, C and Probst, AJ and Birarda, G and Auerbach, A and Koskinen, K and Wolf, P and Holman, HN},
title = {Human age and skin physiology shape diversity and abundance of Archaea on skin.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {4039},
doi = {10.1038/s41598-017-04197-4},
pmid = {28642547},
issn = {2045-2322},
abstract = {The human skin microbiome acts as an important barrier protecting our body from pathogens and other environmental influences. Recent investigations have provided evidence that Archaea are a constant but highly variable component of the human skin microbiome, yet factors that determine their abundance changes are unknown. Here, we tested the hypothesis that the abundance of archaea on human skin is influenced by human age and skin physiology by quantitative PCR of 51 different skin samples taken from human subjects of various age. Our results reveal that archaea are more abundant in human subjects either older than 60 years or younger than 12 years as compared to middle-aged human subjects. These results, together with results obtained from spectroscopy analysis, allowed us gain first insights into a potential link of lower sebum levels and lipid content and thus reduced skin moisture with an increase in archaeal signatures. Amplicon sequencing of selected samples revealed the prevalence of specific eury- and mainly thaumarchaeal taxa, represented by a core archaeome of the human skin.},
}
@article {pmid28628615,
year = {2017},
author = {Cossu, M and Badel, C and Catchpole, R and Gadelle, D and Marguet, E and Barbe, V and Forterre, P and Oberto, J},
title = {Flipping chromosomes in deep-sea archaea.},
journal = {PLoS genetics},
volume = {13},
number = {6},
pages = {e1006847},
doi = {10.1371/journal.pgen.1006847},
pmid = {28628615},
issn = {1553-7404},
mesh = {Chromosome Inversion/*genetics ; *Evolution, Molecular ; Genome, Archaeal ; Integrases/*genetics ; Interspersed Repetitive Sequences/genetics ; Plasmids/genetics ; Recombination, Genetic ; Thermococcales/*genetics ; },
abstract = {One of the major mechanisms driving the evolution of all organisms is genomic rearrangement. In hyperthermophilic Archaea of the order Thermococcales, large chromosomal inversions occur so frequently that even closely related genomes are difficult to align. Clearly not resulting from the native homologous recombination machinery, the causative agent of these inversions has remained elusive. We present a model in which genomic inversions are catalyzed by the integrase enzyme encoded by a family of mobile genetic elements. We characterized the integrase from Thermococcus nautili plasmid pTN3 and showed that besides canonical site-specific reactions, it catalyzes low sequence specificity recombination reactions with the same outcome as homologous recombination events on DNA segments as short as 104bp both in vitro and in vivo, in contrast to other known tyrosine recombinases. Through serial culturing, we showed that the integrase-mediated divergence of T. nautili strains occurs at an astonishing rate, with at least four large-scale genomic inversions appearing within 60 generations. Our results and the ubiquitous distribution of pTN3-like integrated elements suggest that a major mechanism of evolution of an entire order of Archaea results from the activity of a selfish mobile genetic element.},
}
@article {pmid28628315,
year = {2017},
author = {Dokainish, HM and Simard, DJ and Gauld, JW},
title = {A Pseudohypervalent Sulfur Intermediate as an Oxidative Protective Mechanism in the Archaea Peroxiredoxin Enzyme ApTPx.},
journal = {The journal of physical chemistry. B},
volume = {121},
number = {27},
pages = {6570-6579},
doi = {10.1021/acs.jpcb.7b04671},
pmid = {28628315},
issn = {1520-5207},
mesh = {Archaea/*enzymology ; Molecular Dynamics Simulation ; Oxidation-Reduction ; Peroxiredoxins/chemistry/*metabolism ; *Quantum Theory ; Sulfur/chemistry/*metabolism ; },
abstract = {Peroxiredoxins (Prxs) are a ubiquitous class of enzymes that have central roles in a number of important physiological processes. Using a multiscale computational approach, we have investigated the mechanism by which the active-site cysteine (Cys50) in the typical 2-Cys Prx from Archaea (ApTPx) is oxidized by H2O2 to sulfenic acid. In addition, its further oxidation to give a sulfinic acid and its possible alternate intramolecular reaction to form an experimentally proposed hypervalent sulfurane were examined. Oxidation of Cys50 by H2O2 to give the sulfenic acid intermediate occurs in one step with a barrier of 82.1 kJ mol-1. A two-step pathway is proposed with a very low barrier of 16.5 kJ mol-1 by which it can subsequently react with an adjacent histidyl (His42) to form the pseudohypervalent sulfurane. This pathway also involves an adjacent aspartyl (Asp45), which helps alternate the protonation state of His42. The sulfurane's Cys50S···NδHis42 interaction was characterized using QTAIM, NCI, and NBO analyses and found to be a noncovalent interaction. Notably, this bond helps orient the Cys50SOH moiety such that it is less susceptible to oxidation by H2O2 to sulfinic acid. Significantly, sulfurane formation is energetically favored to further H2O2 oxidation of Cys50SOH to a sulfinic acid, providing a mechanism by which the active-site Cys50 is protected against overoxidation.},
}
@article {pmid28625421,
year = {2017},
author = {Gaglione, R and Pirone, L and Farina, B and Fusco, S and Smaldone, G and Aulitto, M and Dell'Olmo, E and Roscetto, E and Del Gatto, A and Fattorusso, R and Notomista, E and Zaccaro, L and Arciello, A and Pedone, E and Contursi, P},
title = {Insights into the anticancer properties of the first antimicrobial peptide from Archaea.},
journal = {Biochimica et biophysica acta},
volume = {1861},
number = {9},
pages = {2155-2164},
doi = {10.1016/j.bbagen.2017.06.009},
pmid = {28625421},
issn = {0006-3002},
mesh = {Animals ; Antimicrobial Cationic Peptides/chemistry/*pharmacology ; Antineoplastic Agents/chemistry/*pharmacology ; BALB 3T3 Cells ; Cell Death/drug effects ; Cell Membrane/drug effects ; Circular Dichroism ; Humans ; Mice ; Nuclear Magnetic Resonance, Biomolecular ; Protein Conformation ; Sulfolobus/*chemistry ; },
abstract = {BACKGROUND: The peptide VLL-28, identified in the sequence of an archaeal protein, the transcription factor Stf76 from Sulfolobus islandicus, was previously identified and characterized as an antimicrobial peptide, possessing a broad-spectrum antibacterial activity.<br><br>METHODS: Through a combined approach of NMR and Circular Dichroism spectroscopy, Dynamic Light Scattering, confocal microscopy and cell viability assays, the interaction of VLL-28 with the membranes of both parental and malignant cell lines has been characterized and peptide mechanism of action has been studied.<br><br>RESULTS: It is here demonstrated that VLL-28 selectively exerts cytotoxic activity against murine and human tumor cells. By means of structural methodologies, VLL-28 interaction with the membranes has been proven and the binding residues have been identified. Confocal microscopy data show that VLL-28 is internalized only into tumor cells. Finally, it is shown that cell death is mainly caused by a time-dependent activation of apoptotic pathways.<br><br>CONCLUSIONS: VLL-28, deriving from the archaeal kingdom, is here found to be endowed with selective cytotoxic activity towards both murine and human cancer cells and consequently can be classified as an ACP.<br><br>GENERAL SIGNIFICANCE: VLL-28 represents the first ACP identified in an archaeal microorganism, exerting a trans-kingdom activity.},
}
@article {pmid28587211,
year = {2017},
author = {Karayanni, H and Meziti, A and Spatharis, S and Genitsaris, S and Courties, C and Kormas, KA},
title = {Changes in Microbial (Bacteria and Archaea) Plankton Community Structure after Artificial Dispersal in Grazer-Free Microcosms.},
journal = {Microorganisms},
volume = {5},
number = {2},
pages = {},
doi = {10.3390/microorganisms5020031},
pmid = {28587211},
issn = {2076-2607},
abstract = {Microbes are considered to have a global distribution due to their high dispersal capabilities. However, our knowledge of the way geographically distant microbial communities assemble after dispersal in a new environment is limited. In this study, we examined whether communities would converge because similar taxa would be selected under the same environmental conditions, or would diverge because of initial community composition, after artificial dispersal. To this aim, a microcosm experiment was performed, in which the temporal changes in the composition and diversity of different prokaryoplankton assemblages from three distant geographic coastal areas (Banyuls-sur-Mer in northwest Mediterranean Sea, Pagasitikos Gulf in northeast Mediterranean and Woods Hole, MA, USA in the northwest Atlantic), were studied. Diversity was investigated using amplicon pyrosequencing of the V1-V3 hypervariable regions of the 16S rRNA. The three assemblages were grown separately in particle free and autoclaved Banyuls-sur-mer seawater at 18 °C in the dark. We found that the variability of prokaryoplankton community diversity (expressed as richness, evenness and dominance) as well as the composition were driven by patterns observed in Bacteria. Regarding community composition, similarities were found between treatments at family level. However, at the OTU level microbial communities from the three different original locations diverge rather than converge during incubation. It is suggested that slight differences in the composition of the initial prokaryoplankton communities, resulted in separate clusters the following days even when growth took place under identical abiotic conditions.},
}
@article {pmid28585938,
year = {2017},
author = {Borrel, G and McCann, A and Deane, J and Neto, MC and Lynch, DB and Brugère, JF and O'Toole, PW},
title = {Genomics and metagenomics of trimethylamine-utilizing Archaea in the human gut microbiome.},
journal = {The ISME journal},
volume = {11},
number = {9},
pages = {2059-2074},
doi = {10.1038/ismej.2017.72},
pmid = {28585938},
issn = {1751-7370},
mesh = {Aged ; Aged, 80 and over ; Animals ; Archaea/classification/*genetics/isolation &amp; purification/*metabolism ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Genomics ; Humans ; Male ; Metagenome ; Metagenomics ; Methylamines/*metabolism ; Microbiota ; Phylogeny ; },
abstract = {The biological significance of Archaea in the human gut microbiota is largely unclear. We recently reported genomic and biochemical analyses of the Methanomassiliicoccales, a novel order of methanogenic Archaea dwelling in soil and the animal digestive tract. We now show that these Methanomassiliicoccales are present in published microbiome data sets from eight countries. They are represented by five Operational Taxonomic Units present in at least four cohorts and phylogenetically distributed into two clades. Genes for utilizing trimethylamine (TMA), a bacterial precursor to an atherosclerogenic human metabolite, were present in four of the six novel Methanomassiliicoccales genomes assembled from ELDERMET metagenomes. In addition to increased microbiota TMA production capacity in long-term residential care subjects, abundance of TMA-utilizing Methanomassiliicoccales correlated positively with bacterial gene count for TMA production and negatively with fecal TMA concentrations. The two large Methanomassiliicoccales clades have opposite correlations with host health status in the ELDERMET cohort and putative distinct genomic signatures for gut adaptation.},
}
@article {pmid28570690,
year = {2017},
author = {Majhi, MC and Behera, AK and Kulshreshtha, NM and Mahmooduzafar, D and Kumar, R and Kumar, A},
title = {Correction: ExtremeDB: A Unified Web Repository of Extremophilic Archaea and Bacteria.},
journal = {PloS one},
volume = {12},
number = {6},
pages = {e0179119},
doi = {10.1371/journal.pone.0179119},
pmid = {28570690},
issn = {1932-6203},
abstract = {[This corrects the article DOI: 10.1371/journal.pone.0063083.].},
}
@article {pmid28546547,
year = {2017},
author = {Chen, X and Andersen, TJ and Morono, Y and Inagaki, F and Jørgensen, BB and Lever, MA},
title = {Bioturbation as a key driver behind the dominance of Bacteria over Archaea in near-surface sediment.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {2400},
doi = {10.1038/s41598-017-02295-x},
pmid = {28546547},
issn = {2045-2322},
abstract = {The factors controlling the relative abundances of Archaea and Bacteria in marine sediments are poorly understood. We determined depth distributions of archaeal and bacterial 16S rRNA genes by quantitative PCR at eight stations in Aarhus Bay, Denmark. Bacterial outnumber archaeal genes 10-60-fold in uppermost sediments that are irrigated and mixed by macrofauna. This bioturbation is indicated by visual observations of sediment color and faunal tracks, by porewater profiles of dissolved inorganic carbon and sulfate, and by distributions of unsupported 210Pb and 137Cs. Below the depth of bioturbation, the relative abundances of archaeal genes increase, accounting for one third of 16S rRNA genes in the sulfate zone, and half of 16S rRNA genes in the sulfate-methane transition zone and methane zone. Phylogenetic analyses reveal a strong shift in bacterial and archaeal community structure from bioturbated sediments to underlying layers. Stable isotopic analyses on organic matter and porewater geochemical gradients suggest that macrofauna mediate bacterial dominance and affect microbial community structure in bioturbated sediment by introducing fresh organic matter and high-energy electron acceptors from overlying seawater. Below the zone of bioturbation, organic matter content and the presence of sulfate exert key influences on bacterial and archaeal abundances and overall microbial community structure.},
}
@article {pmid28523826,
year = {2017},
author = {Zheng, L and Zhao, X and Zhu, G and Yang, W and Xia, C and Xu, T},
title = {Occurrence and abundance of ammonia-oxidizing archaea and bacteria from the surface to below the water table, in deep soil, and their contributions to nitrification.},
journal = {MicrobiologyOpen},
volume = {6},
number = {4},
pages = {},
doi = {10.1002/mbo3.488},
pmid = {28523826},
issn = {2045-8827},
mesh = {Ammonia/*metabolism ; Archaea/*classification/genetics/isolation &amp; purification/metabolism ; Bacteria/*classification/genetics/isolation &amp; purification/metabolism ; Bacterial Load ; *Biodiversity ; China ; Groundwater ; Lakes/*microbiology ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; *Soil Microbiology ; Switzerland ; },
abstract = {Using molecular biology methods (qualitative and quantitative PCR), we determined the occurrence and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) from a dry inland soil in Basel, Switzerland, and from the riparian zone of Baiyangdian Lake, China. We also determined the contributions of these microorganisms to ammonia oxidization at different depths based on the nitrification rate. The number of archaeal amoA genes (the key functional gene in AOA) was larger than the number of bacterial amoA genes in each sample, suggesting a dominant role for the AOA amoA gene in environments with a low ammonium concentration. In Baiyangdian Lake, the number of archaeal amoA genes was highest at 6 m and lowest at 12 m from the land-water interface in the soil (at depths from 40 to 60 cm), close to the groundwater, which suggests that AOA become more competitive in environments with a low dissolved oxygen content and are promoted by low pH. The nitrification rate was significantly negatively correlated with depth in the Baiyangdian Lake soil and significantly positively correlated with the number of AOB amoA genes at this site, 6 m from the water.},
}
@article {pmid28520982,
year = {2017},
author = {Qi, L and Yue, L and Feng, D and Qi, F and Li, J and Dong, X},
title = {Genome-wide mRNA processing in methanogenic archaea reveals post-transcriptional regulation of ribosomal protein synthesis.},
journal = {Nucleic acids research},
volume = {45},
number = {12},
pages = {7285-7298},
doi = {10.1093/nar/gkx454},
pmid = {28520982},
issn = {1362-4962},
support = {R21 DE024235/DE/NIDCR NIH HHS/United States ; },
mesh = {Archaeal Proteins/*genetics/metabolism ; Base Sequence ; Cloning, Molecular ; Escherichia coli/genetics/metabolism ; Gene Expression ; *Genome, Archaeal ; Methanococcus/*genetics/metabolism ; Methanosarcinaceae/*genetics/metabolism ; Nucleic Acid Conformation ; Peptide Chain Initiation, Translational ; Protein Isoforms/genetics/metabolism ; *RNA Processing, Post-Transcriptional ; RNA, Messenger/chemistry/*genetics/metabolism ; Recombinant Proteins/genetics/metabolism ; Ribosomal Proteins/*genetics/metabolism ; },
abstract = {Unlike stable RNAs that require processing for maturation, prokaryotic cellular mRNAs generally follow an 'all-or-none' pattern. Herein, we used a 5΄ monophosphate transcript sequencing (5΄P-seq) that specifically captured the 5΄-end of processed transcripts and mapped the genome-wide RNA processing sites (PSSs) in a methanogenic archaeon. Following statistical analysis and stringent filtration, we identified 1429 PSSs, among which 23.5% and 5.4% were located in 5΄ untranslated region (uPSS) and intergenic region (iPSS), respectively. A predominant uridine downstream PSSs served as a processing signature. Remarkably, 5΄P-seq detected overrepresented uPSS and iPSS in the polycistronic operons encoding ribosomal proteins, and the majority upstream and proximal ribosome binding sites, suggesting a regulatory role of processing on translation initiation. The processed transcripts showed increased stability and translation efficiency. Particularly, processing within the tricistronic transcript of rplA-rplJ-rplL enhanced the translation of rplL, which can provide a driving force for the 1:4 stoichiometry of L10 to L12 in the ribosome. Growth-associated mRNA processing intensities were also correlated with the cellular ribosomal protein levels, thereby suggesting that mRNA processing is involved in tuning growth-dependent ribosome synthesis. In conclusion, our findings suggest that mRNA processing-mediated post-transcriptional regulation is a potential mechanism of ribosomal protein synthesis and stoichiometry.},
}
@article {pmid28515720,
year = {2017},
author = {Rajput, A and Kumar, M},
title = {Computational Exploration of Putative LuxR Solos in Archaea and Their Functional Implications in Quorum Sensing.},
journal = {Frontiers in microbiology},
volume = {8},
number = {},
pages = {798},
doi = {10.3389/fmicb.2017.00798},
pmid = {28515720},
issn = {1664-302X},
abstract = {LuxR solos are unexplored in Archaea, despite their vital role in the bacterial regulatory network. They assist bacteria in perceiving acyl homoserine lactones (AHLs) and/or non-AHLs signaling molecules for establishing intraspecies, interspecies, and interkingdom communication. In this study, we explored the potential LuxR solos of Archaea from InterPro v62.0 meta-database employing taxonomic, probable function, distribution, and evolutionary aspects to decipher their role in quorum sensing (QS). Our bioinformatics analyses showed that putative LuxR solos of Archaea shared few conserved domains with bacterial LuxR despite having less similarity within proteins. Functional characterization revealed their ability to bind various AHLs and/or non-AHLs signaling molecules that involve in QS cascades alike bacteria. Further, the phylogenetic study indicates that Archaeal LuxR solos (with less substitution per site) evolved divergently from bacteria and share distant homology along with instances of horizontal gene transfer. Moreover, Archaea possessing putative LuxR solos, exhibit the correlation between taxonomy and ecological niche despite being the inhabitant of diverse habitats like halophilic, thermophilic, barophilic, methanogenic, and chemolithotrophic. Therefore, this study would shed light in deciphering the role of the putative LuxR solos of Archaea to adapt varied habitats via multilevel communication with other organisms using QS.},
}
@article {pmid28512451,
year = {2017},
author = {Wampach, L and Heintz-Buschart, A and Hogan, A and Muller, EEL and Narayanasamy, S and Laczny, CC and Hugerth, LW and Bindl, L and Bottu, J and Andersson, AF and de Beaufort, C and Wilmes, P},
title = {Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life.},
journal = {Frontiers in microbiology},
volume = {8},
number = {},
pages = {738},
doi = {10.3389/fmicb.2017.00738},
pmid = {28512451},
issn = {1664-302X},
abstract = {Perturbations to the colonization process of the human gastrointestinal tract have been suggested to result in adverse health effects later in life. Although much research has been performed on bacterial colonization and succession, much less is known about the other two domains of life, archaea, and eukaryotes. Here we describe colonization and succession by bacteria, archaea and microeukaryotes during the first year of life (samples collected around days 1, 3, 5, 28, 150, and 365) within the gastrointestinal tract of infants delivered either vaginally or by cesarean section and using a combination of quantitative real-time PCR as well as 16S and 18S rRNA gene amplicon sequencing. Sequences from organisms belonging to all three domains of life were detectable in all of the collected meconium samples. The microeukaryotic community composition fluctuated strongly over time and early diversification was delayed in infants receiving formula milk. Cesarean section-delivered (CSD) infants experienced a delay in colonization and succession, which was observed for all three domains of life. Shifts in prokaryotic succession in CSD infants compared to vaginally delivered (VD) infants were apparent as early as days 3 and 5, which were characterized by increased relative abundances of the genera Streptococcus and Staphylococcus, and a decrease in relative abundance for the genera Bifidobacterium and Bacteroides. Generally, a depletion in Bacteroidetes was detected as early as day 5 postpartum in CSD infants, causing a significantly increased Firmicutes/Bacteroidetes ratio between days 5 and 150 when compared to VD infants. Although the delivery mode appeared to have the strongest influence on differences between the infants, other factors such as a younger gestational age or maternal antibiotics intake likely contributed to the observed patterns as well. Our findings complement previous observations of a delay in colonization and succession of CSD infants, which affects not only bacteria but also archaea and microeukaryotes. This further highlights the need for resolving bacterial, archaeal, and microeukaryotic dynamics in future longitudinal studies of microbial colonization and succession within the neonatal gastrointestinal tract.},
}
@article {pmid28502981,
year = {2017},
author = {Wagner, A and Whitaker, RJ and Krause, DJ and Heilers, JH and van Wolferen, M and van der Does, C and Albers, SV},
title = {Mechanisms of gene flow in archaea.},
journal = {Nature reviews. Microbiology},
volume = {15},
number = {8},
pages = {492-501},
doi = {10.1038/nrmicro.2017.41},
pmid = {28502981},
issn = {1740-1534},
mesh = {Archaea/*genetics ; Evolution, Molecular ; *Gene Flow ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Archaeal ; Genomics ; },
abstract = {Archaea are diverse, ecologically important, single-celled microorganisms. They have unique functions and features, such as methanogenesis and the composition of their cell envelope, although many characteristics are shared with the other domains of life, either through ancestry or through promiscuous horizontal gene transfer. The exchange of genetic material is a major driving force for genome evolution across the tree of life and has a role in archaeal speciation, adaptation and maintenance of diversity. In this Review, we discuss our current knowledge of archaeal mechanisms of DNA transfer and highlight the role of gene transfer in archaeal evolution.},
}
@article {pmid28500534,
year = {2017},
author = {Aylett, CHS and Duggin, IG},
title = {The Tubulin Superfamily in Archaea.},
journal = {Sub-cellular biochemistry},
volume = {84},
number = {},
pages = {393-417},
doi = {10.1007/978-3-319-53047-5_14},
pmid = {28500534},
issn = {0306-0225},
abstract = {In comparison with bacteria and eukaryotes, the large and diverse group of microorganisms known as archaea possess a great diversity of cytoskeletal proteins, including members of the tubulin superfamily. Many species contain FtsZ, CetZ and even possible tubulins; however, some major taxonomic groups do not contain any member of the tubulin superfamily. Studies using the model archaeon, Halferax volcanii have recently been instrumental in defining the fundamental roles of FtsZ and CetZ in archaeal cell division and cell shape regulation. Structural studies of archaeal tubulin superfamily proteins provide a definitive contribution to the cytoskeletal field, showing which protein-types must have developed prior to the divergence of archaea and eukaryotes. Several regions of the globular core domain - the &quot;signature&quot; motifs - combine in the 3D structure of the common molecular fold to form the GTP-binding site. They are the most conserved sequence elements and provide the primary basis for identification of new superfamily members through homology searches. The currently well-characterised proteins also all share a common mechanism of GTP-dependent polymerisation, in which GTP molecules are sandwiched between successive subunits that are arranged in a head-to-tail manner. However, some poorly-characterised archaeal protein families retain only some of the signature motifs and are unlikely to be capable of dynamic polymerisation, since the promotion of depolymerisation by hydrolysis to GDP depends on contributions from both subunits that sandwich the nucleotide in the polymer.},
}
@article {pmid28493148,
year = {2017},
author = {Antranikian, G and Suleiman, M and Schäfers, C and Adams, MWW and Bartolucci, S and Blamey, JM and Birkeland, NK and Bonch-Osmolovskaya, E and da Costa, MS and Cowan, D and Danson, M and Forterre, P and Kelly, R and Ishino, Y and Littlechild, J and Moracci, M and Noll, K and Oshima, T and Robb, F and Rossi, M and Santos, H and Schönheit, P and Sterner, R and Thauer, R and Thomm, M and Wiegel, J and Stetter, KO},
title = {Diversity of bacteria and archaea from two shallow marine hydrothermal vents from Vulcano Island.},
journal = {Extremophiles : life under extreme conditions},
volume = {21},
number = {4},
pages = {733-742},
doi = {10.1007/s00792-017-0938-y},
pmid = {28493148},
issn = {1433-4909},
mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Hydrothermal Vents/*microbiology ; Italy ; *Marine Biology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {To obtain new insights into community compositions of hyperthermophilic microorganisms, defined as having optimal growth temperatures of 80 °C and above, sediment and water samples were taken from two shallow marine hydrothermal vents (I and II) with temperatures of 100 °C at Vulcano Island, Italy. A combinatorial approach of denaturant gradient gel electrophoresis (DGGE) and metagenomic sequencing was used for microbial community analyses of the samples. In addition, enrichment cultures, growing anaerobically on selected polysaccharides such as starch and cellulose, were also analyzed by the combinatorial approach. Our results showed a high abundance of hyperthermophilic archaea, especially in sample II, and a comparable diverse archaeal community composition in both samples. In particular, the strains of the hyperthermophilic anaerobic genera Staphylothermus and Thermococcus, and strains of the aerobic hyperthermophilic genus Aeropyrum, were abundant. Regarding the bacterial community, ε-Proteobacteria, especially the genera Sulfurimonas and Sulfurovum, were highly abundant. The microbial diversity of the enrichment cultures changed significantly by showing a high dominance of archaea, particularly the genera Thermococcus and Palaeococcus, depending on the carbon source and the selected temperature.},
}
@article {pmid28489329,
year = {2017},
author = {Dassen, S and Cortois, R and Martens, H and de Hollander, M and Kowalchuk, GA and van der Putten, WH and De Deyn, GB},
title = {Differential responses of soil bacteria, fungi, archaea and protists to plant species richness and plant functional group identity.},
journal = {Molecular ecology},
volume = {26},
number = {15},
pages = {4085-4098},
doi = {10.1111/mec.14175},
pmid = {28489329},
issn = {1365-294X},
mesh = {Archaea/classification ; Bacteria/classification ; *Biodiversity ; *Ecosystem ; Fungi/classification ; Germany ; Mycorrhizae/classification ; Plants/*classification ; *Soil Microbiology ; },
abstract = {Plants are known to influence belowground microbial community structure along their roots, but the impacts of plant species richness and plant functional group (FG) identity on microbial communities in the bulk soil are still not well understood. Here, we used 454-pyrosequencing to analyse the soil microbial community composition in a long-term biodiversity experiment at Jena, Germany. We examined responses of bacteria, fungi, archaea, and protists to plant species richness (communities varying from 1 to 60 sown species) and plant FG identity (grasses, legumes, small herbs, tall herbs) in bulk soil. We hypothesized that plant species richness and FG identity would alter microbial community composition and have a positive impact on microbial species richness. Plant species richness had a marginal positive effect on the richness of fungi, but we observed no such effect on bacteria, archaea and protists. Plant species richness also did not have a large impact on microbial community composition. Rather, abiotic soil properties partially explained the community composition of bacteria, fungi, arbuscular mycorrhizal fungi (AMF), archaea and protists. Plant FG richness did not impact microbial community composition; however, plant FG identity was more effective. Bacterial richness was highest in legume plots and lowest in small herb plots, and AMF and archaeal community composition in legume plant communities was distinct from that in communities composed of other plant FGs. We conclude that soil microbial community composition in bulk soil is influenced more by changes in plant FG composition and abiotic soil properties, than by changes in plant species richness per se.},
}
@article {pmid28487430,
year = {2017},
author = {Mukai, T and Crnković, A and Umehara, T and Ivanova, NN and Kyrpides, NC and Söll, D},
title = {RNA-Dependent Cysteine Biosynthesis in Bacteria and Archaea.},
journal = {mBio},
volume = {8},
number = {3},
pages = {},
doi = {10.1128/mBio.00561-17},
pmid = {28487430},
issn = {2150-7511},
support = {R01 GM022854/GM/NIGMS NIH HHS/United States ; R35 GM122560/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acyl-tRNA Synthetases/metabolism ; Archaea/*genetics/metabolism ; Archaeal Proteins/genetics/metabolism ; Bacteria/*genetics/metabolism ; Computational Biology ; Crystallography, X-Ray ; Cysteine/*biosynthesis ; Genetic Code ; Genome, Archaeal ; Genome, Bacterial ; Phosphoserine/metabolism ; Protein Binding ; Protein Biosynthesis ; RNA, Archaeal/*metabolism ; RNA, Bacterial/*metabolism ; RNA, Transfer, Amino Acyl/*metabolism ; RNA, Transfer, Cys/*metabolism ; Sulfur/metabolism ; },
abstract = {The diversity of the genetic code systems used by microbes on earth is yet to be elucidated. It is known that certain methanogenic archaea employ an alternative system for cysteine (Cys) biosynthesis and encoding; tRNACys is first acylated with phosphoserine (Sep) by O-phosphoseryl-tRNA synthetase (SepRS) and then converted to Cys-tRNACys by Sep-tRNA:Cys-tRNA synthase (SepCysS). In this study, we searched all genomic and metagenomic protein sequence data in the Integrated Microbial Genomes (IMG) system and at the NCBI to reveal new clades of SepRS and SepCysS proteins belonging to diverse archaea in the four major groups (DPANN, Euryarchaeota, TACK, and Asgard) and two groups of bacteria (&quot;Candidatus Parcubacteria&quot; and Chloroflexi). Bacterial SepRS and SepCysS charged bacterial tRNACys species with cysteine in vitro Homologs of SepCysE, a scaffold protein facilitating SepRS⋅SepCysS complex assembly in Euryarchaeota class I methanogens, are found in a few groups of TACK and Asgard archaea, whereas the C-terminally truncated homologs exist fused or genetically coupled with diverse SepCysS species. Investigation of the selenocysteine (Sec)- and pyrrolysine (Pyl)-utilizing traits in SepRS-utilizing archaea and bacteria revealed that the archaea carrying full-length SepCysE employ Sec and that SepRS is often found in Pyl-utilizing archaea and Chloroflexi bacteria. We discuss possible contributions of the SepRS-SepCysS system for sulfur assimilation, methanogenesis, and other metabolic processes requiring large amounts of iron-sulfur enzymes or Pyl-containing enzymes.IMPORTANCE Comprehensive analyses of all genomic and metagenomic protein sequence data in public databases revealed the distribution and evolution of an alternative cysteine-encoding system in diverse archaea and bacteria. The finding that the SepRS-SepCysS-SepCysE- and the selenocysteine-encoding systems are shared by the Euryarchaeota class I methanogens, the Crenarchaeota AK8/W8A-19 group, and an Asgard archaeon suggests that ancient archaea may have used both systems. In contrast, bacteria may have obtained the SepRS-SepCysS system from archaea. The SepRS-SepCysS system sometimes coexists with a pyrrolysine-encoding system in both archaea and bacteria. Our results provide additional bioinformatic evidence for the contribution of the SepRS-SepCysS system for sulfur assimilation and diverse metabolisms which require vast amounts of iron-sulfur enzymes and proteins. Among these biological activities, methanogenesis, methylamine metabolism, and organohalide respiration may have local and global effects on earth. Taken together, uncultured bacteria and archaea provide an expanded record of the evolution of the genetic code.},
}
@article {pmid28480883,
year = {2017},
author = {Zweerink, S and Kallnik, V and Ninck, S and Nickel, S and Verheyen, J and Blum, M and Wagner, A and Feldmann, I and Sickmann, A and Albers, SV and Bräsen, C and Kaschani, F and Siebers, B and Kaiser, M},
title = {Activity-based protein profiling as a robust method for enzyme identification and screening in extremophilic Archaea.},
journal = {Nature communications},
volume = {8},
number = {},
pages = {15352},
doi = {10.1038/ncomms15352},
pmid = {28480883},
issn = {2041-1723},
abstract = {Archaea are characterized by a unique life style in often environmental extremes but their thorough investigation is currently hampered by a limited set of suitable in vivo research methodologies. Here, we demonstrate that in vivo activity-based protein profiling (ABPP) may be used to sensitively detect either native or heterogeneously expressed active enzymes in living archaea even under these extreme conditions. In combination with the development of a genetically engineered archaeal screening strain, ABPP can furthermore be used in functional enzyme screenings from (meta)genome samples. We anticipate that our ABPP approach may therefore find application in basic archaeal research but also in the discovery of novel enzymes from (meta)genome libraries.},
}
@article {pmid28480138,
year = {2017},
author = {Bolduc, B and Jang, HB and Doulcier, G and You, ZQ and Roux, S and Sullivan, MB},
title = {vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria.},
journal = {PeerJ},
volume = {5},
number = {},
pages = {e3243},
doi = {10.7717/peerj.3243},
pmid = {28480138},
issn = {2167-8359},
abstract = {Taxonomic classification of archaeal and bacterial viruses is challenging, yet also fundamental for developing a predictive understanding of microbial ecosystems. Recent identification of hundreds of thousands of new viral genomes and genome fragments, whose hosts remain unknown, requires a paradigm shift away from traditional classification approaches and towards the use of genomes for taxonomy. Here we revisited the use of genomes and their protein content as a means for developing a viral taxonomy for bacterial and archaeal viruses. A network-based analytic was evaluated and benchmarked against authority-accepted taxonomic assignments and found to be largely concordant. Exceptions were manually examined and found to represent areas of viral genome 'sequence space' that are under-sampled or prone to excessive genetic exchange. While both cases are poorly resolved by genome-based taxonomic approaches, the former will improve as viral sequence space is better sampled and the latter are uncommon. Finally, given the largely robust taxonomic capabilities of this approach, we sought to enable researchers to easily and systematically classify new viruses. Thus, we established a tool, vConTACT, as an app at iVirus, where it operates as a fast, highly scalable, user-friendly app within the free and powerful CyVerse cyberinfrastructure.},
}
@article {pmid28464532,
year = {2017},
author = {Sogin, EM and Putnam, HM and Nelson, CE and Anderson, P and Gates, RD},
title = {Correspondence of coral holobiont metabolome with symbiotic bacteria, archaea and Symbiodinium communities.},
journal = {Environmental microbiology reports},
volume = {9},
number = {3},
pages = {310-315},
doi = {10.1111/1758-2229.12541},
pmid = {28464532},
issn = {1758-2229},
mesh = {Alveolata/*growth &amp; development/metabolism ; Animals ; Anthozoa/*microbiology/*parasitology ; Archaea/classification/*growth &amp; development/metabolism ; Biodiversity ; Coral Reefs ; Gammaproteobacteria/*growth &amp; development/metabolism ; Metabolome/physiology ; Symbiosis/*physiology ; Vibrionaceae/*growth &amp; development/metabolism ; },
abstract = {Microbial symbiotic partners, such as those associated with Scleractinian corals, mediate biochemical transformations that influence host performance and survival. While evidence suggests microbial community composition partly accounts for differences in coral physiology, how these symbionts affect metabolic pathways remains underexplored. We aimed to assess functional implications of variation among coral-associated microbial partners in hospite. To this end, we characterized and compared metabolomic profiles and microbial community composition from nine reef-building coral species. These data demonstrate metabolite profiles and microbial communities are species-specific and are correlated to one another. Using Porites spp. as a case study, we present evidence that the relative abundance of different sub-clades of Symbiodinium and bacterial/archaeal families are linked to positive and negative metabolomic signatures. Our data suggest that while some microbial partners benefit the union, others are more opportunistic with potential detriment to the host. Consequently, coral partner choice likely influences cellular metabolic activities and, therefore, holobiont nutrition.},
}
@article {pmid28446901,
year = {2017},
author = {Weber, HS and Habicht, KS and Thamdrup, B},
title = {Anaerobic Methanotrophic Archaea of the ANME-2d Cluster Are Active in a Low-sulfate, Iron-rich Freshwater Sediment.},
journal = {Frontiers in microbiology},
volume = {8},
number = {},
pages = {619},
doi = {10.3389/fmicb.2017.00619},
pmid = {28446901},
issn = {1664-302X},
abstract = {ANaerobic MEthanotrophic (ANME) archaea remove the greenhouse gas methane from anoxic environments and diminish its flux to the atmosphere. High methane removal efficiencies are well documented in marine environments, whereas anaerobic oxidation of methane (AOM) was only recently indicated as an important methane sink in freshwater systems. Freshwater AOM-mediating microorganisms lack taxonomic identification and only little is known about metabolic adaptions to prevailing biogeochemical conditions. One of the first study sites providing information about AOM activity in freshwater sediment is Lake Ørn, a low-sulfate, iron-rich Danish lake. With the aim to identify freshwater AOM-mediating archaea, we incubated AOM-active anoxic, nitrate-free freshwater sediment from Lake Ørn with 13C-labeled methane (13CCH4) and 13C-labeled bicarbonate (13CDIC) and followed the assimilation of 13C into RNA by stable isotope probing. While AOM was active, 13CCH4 and probably also 13CDIC were incorporated into uncultured archaea of the Methanosarcinales-related cluster ANME-2d, whereas other known ANME lineages were not detected. This finding strongly suggests that ANME-2d archaea perform AOM coupled to sulfate and/or iron reduction and may have the capability of mixed assimilation of CH4 and DIC. ANME-2d archaea may thus play an important role in controlling methane emissions from nitrate-depleted and low-sulfate freshwater systems.},
}
@article {pmid28425930,
year = {2017},
author = {Zhang, Y and Kouril, T and Snoep, JL and Siebers, B and Barberis, M and Westerhoff, HV},
title = {The Peculiar Glycolytic Pathway in Hyperthermophylic Archaea: Understanding Its Whims by Experimentation In Silico.},
journal = {International journal of molecular sciences},
volume = {18},
number = {4},
pages = {},
doi = {10.3390/ijms18040876},
pmid = {28425930},
issn = {1422-0067},
mesh = {Adenosine Triphosphate/metabolism ; Computer Simulation ; Glyceraldehyde 3-Phosphate/metabolism ; Glyceraldehyde-3-Phosphate Dehydrogenases/metabolism ; *Glycolysis ; *Hot Temperature ; Kinetics ; Metabolic Networks and Pathways ; *Models, Biological ; Saccharomyces cerevisiae/metabolism ; Sulfolobus solfataricus/*metabolism ; Systems Biology ; },
abstract = {Mathematical models are key to systems biology where they typically describe the topology and dynamics of biological networks, listing biochemical entities and their relationships with one another. Some (hyper)thermophilic Archaea contain an enzyme, called non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN), which catalyzes the direct oxidation of glyceraldehyde-3-phosphate to 3-phosphoglycerate omitting adenosine 5'-triphosphate (ATP) formation by substrate-level-phosphorylation via phosphoglycerate kinase. In this study we formulate three hypotheses that could explain functionally why GAPN exists in these Archaea, and then construct and use mathematical models to test these three hypotheses. We used kinetic parameters of enzymes of Sulfolobus solfataricus (S. solfataricus) which is a thermo-acidophilic archaeon that grows optimally between 60 and 90 °C and between pH 2 and 4. For comparison, we used a model of Saccharomyces cerevisiae (S. cerevisiae), an organism that can live at moderate temperatures. We find that both the first hypothesis, i.e., that the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) plus phosphoglycerate kinase (PGK) route (the alternative to GAPN) is thermodynamically too much uphill and the third hypothesis, i.e., that GAPDH plus PGK are required to carry the flux in the gluconeogenic direction, are correct. The second hypothesis, i.e., that the GAPDH plus PGK route delivers less than the 1 ATP per pyruvate that is delivered by the GAPN route, is only correct when GAPDH reaction has a high rate and 1,3-bis-phosphoglycerate (BPG) spontaneously degrades to 3PG at a high rate.},
}
@article {pmid28424284,
year = {2017},
author = {Liu, Y and Ishino, S and Ishino, Y and Pehau-Arnaudet, G and Krupovic, M and Prangishvili, D},
title = {A Novel Type of Polyhedral Viruses Infecting Hyperthermophilic Archaea.},
journal = {Journal of virology},
volume = {91},
number = {13},
pages = {},
doi = {10.1128/JVI.00589-17},
pmid = {28424284},
issn = {1098-5514},
mesh = {DNA Viruses/*classification/genetics/*isolation &amp; purification/ultrastructure ; Gene Order ; Genome, Viral ; Microscopy, Electron ; Open Reading Frames ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Sulfolobus/*virology ; Viral Proteins/genetics ; *Viral Structures ; Virion/chemistry/ultrastructure ; },
abstract = {Encapsidation of genetic material into polyhedral particles is one of the most common structural solutions employed by viruses infecting hosts in all three domains of life. Here, we describe a new virus of hyperthermophilic archaea, Sulfolobus polyhedral virus 1 (SPV1), which condenses its circular double-stranded DNA genome in a manner not previously observed for other known viruses. The genome complexed with virion proteins is wound up sinusoidally into a spherical coil which is surrounded by an envelope and further encased by an outer polyhedral capsid apparently composed of the 20-kDa virion protein. Lipids selectively acquired from the pool of host lipids are integral constituents of the virion. None of the major virion proteins of SPV1 show similarity to structural proteins of known viruses. However, minor structural proteins, which are predicted to mediate host recognition, are shared with other hyperthermophilic archaeal viruses infecting members of the order Sulfolobales The SPV1 genome consists of 20,222 bp and contains 45 open reading frames, only one-fifth of which could be functionally annotated.IMPORTANCE Viruses infecting hyperthermophilic archaea display a remarkable morphological diversity, often presenting architectural solutions not employed by known viruses of bacteria and eukaryotes. Here we present the isolation and characterization of Sulfolobus polyhedral virus 1, which condenses its genome into a unique spherical coil. Due to the original genomic and architectural features of SPV1, the virus should be considered a representative of a new viral family, &quot;Portogloboviridae.&quot;},
}
@article {pmid28420220,
year = {2017},
author = {Michel, CJ},
title = {The Maximal C³ Self-Complementary Trinucleotide Circular Code X in Genes of Bacteria, Archaea, Eukaryotes, Plasmids and Viruses.},
journal = {Life (Basel, Switzerland)},
volume = {7},
number = {2},
pages = {},
doi = {10.3390/life7020020},
pmid = {28420220},
issn = {2075-1729},
abstract = {In 1996, a set X of 20 trinucleotides was identified in genes of both prokaryotes and eukaryotes which has on average the highest occurrence in reading frame compared to its two shifted frames. Furthermore, this set X has an interesting mathematical property as X is a maximal C 3 self-complementary trinucleotide circular code. In 2015, by quantifying the inspection approach used in 1996, the circular code X was confirmed in the genes of bacteria and eukaryotes and was also identified in the genes of plasmids and viruses. The method was based on the preferential occurrence of trinucleotides among the three frames at the gene population level. We extend here this definition at the gene level. This new statistical approach considers all the genes, i.e., of large and small lengths, with the same weight for searching the circular code X . As a consequence, the concept of circular code, in particular the reading frame retrieval, is directly associated to each gene. At the gene level, the circular code X is strengthened in the genes of bacteria, eukaryotes, plasmids, and viruses, and is now also identified in the genes of archaea. The genes of mitochondria and chloroplasts contain a subset of the circular code X . Finally, by studying viral genes, the circular code X was found in DNA genomes, RNA genomes, double-stranded genomes, and single-stranded genomes.},
}
@article {pmid28409190,
year = {2017},
author = {Salah Ud-Din, AIM and Roujeinikova, A},
title = {Methyl-accepting chemotaxis proteins: a core sensing element in prokaryotes and archaea.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {74},
number = {18},
pages = {3293-3303},
doi = {10.1007/s00018-017-2514-0},
pmid = {28409190},
issn = {1420-9071},
mesh = {Archaea/classification/*metabolism ; Chemotaxis ; Membrane Proteins/chemistry/metabolism ; Methyl-Accepting Chemotaxis Proteins/chemistry/*metabolism ; Prokaryotic Cells/classification/*metabolism ; Protein Domains ; Signal Transduction ; Structure-Activity Relationship ; },
abstract = {Chemotaxis is the directed motility by means of which microbes sense chemical cues and relocate towards more favorable environments. Methyl-accepting chemotaxis proteins (MCPs) are the most common receptors in bacteria and archaea. They are arranged as trimers of dimers that, in turn, form hexagonal arrays in the cytoplasmic membrane or in the cytoplasm. Several different classes of MCPs have been identified according to their ligand binding region and membrane topology. MCPs have been further classified based on the length and sequence conservation of their cytoplasmic domains. Clusters of membrane-embedded MCPs often localize to the poles of the cell, whereas cytoplasmic MCPs can be targeted to the poles or distributed throughout the cell body. MCPs play an important role in cell survival, pathogenesis, and biodegradation. Bacterial adaptation to diverse environmental conditions promotes diversity among the MCPs. This review summarizes structure, classification, and structure-activity relationship of the known MCP receptors, with a brief overview of the signal transduction mechanisms in bacteria and archaea.},
}
@article {pmid28402397,
year = {2017},
author = {Peay, KG and von Sperber, C and Cardarelli, E and Toju, H and Francis, CA and Chadwick, OA and Vitousek, PM},
title = {Convergence and contrast in the community structure of Bacteria, Fungi and Archaea along a tropical elevation-climate gradient.},
journal = {FEMS microbiology ecology},
volume = {93},
number = {5},
pages = {},
doi = {10.1093/femsec/fix045},
pmid = {28402397},
issn = {1574-6941},
mesh = {Ammonia/analysis ; Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Biodiversity ; Carbon/analysis ; Fungi/*classification/genetics ; High-Throughput Nucleotide Sequencing ; Microbial Consortia/*physiology ; Nitrogen/analysis ; Phosphorus/analysis ; Soil/*chemistry ; Soil Microbiology ; Tropical Climate ; },
abstract = {Changes in species richness along climatological gradients have been instrumental in developing theories about the general drivers of biodiversity. Previous studies on microbial communities along climate gradients on mountainsides have revealed positive, negative and neutral richness trends. We examined changes in richness and composition of Fungi, Bacteria and Archaea in soil along a 50-1000 m elevation, 280-3280 mm/yr precipitation gradient in Hawai'i. Soil properties and their drivers are exceptionally well understood along this gradient. All three microbial groups responded strongly to the gradient, with community ordinations being similar along axes of environmental conditions (pH, rainfall) and resource availability (nitrogen, phosphorus). However, the form of the richness-climate relationship varied between Fungi (positive linear), Bacteria (unimodal) and Archaea (negative linear). These differences were related to resource-ecology and limiting conditions for each group, with fungal richness increasing most strongly with soil carbon, ammonia-oxidizing Archaea increasing with nitrogen mineralization rate, and Bacteria increasing with both carbon and pH. Reponses to the gradient became increasingly variable at finer taxonomic scales and within any taxonomic group most individual OTUs occurred in narrow climate-elevation ranges. These results show that microbial responses to climate gradients are heterogeneous due to complexity of underlying environmental changes and the diverse ecologies of microbial taxa.},
}
@article {pmid28397816,
year = {2017},
author = {Wong, HL and Visscher, PT and White, RA and Smith, DL and Patterson, MM and Burns, BP},
title = {Dynamics of archaea at fine spatial scales in Shark Bay mat microbiomes.},
journal = {Scientific reports},
volume = {7},
number = {},
pages = {46160},
doi = {10.1038/srep46160},
pmid = {28397816},
issn = {2045-2322},
abstract = {The role of archaea in microbial mats is poorly understood. Delineating the spatial distribution of archaea with mat depth will enable resolution of putative niches in these systems. In the present study, high throughput amplicon sequencing was undertaken in conjunction with analysis of key biogeochemical properties of two mats (smooth and pustular) from Shark Bay, Australia. One-way analysis of similarity tests indicated the archaeal community structures of smooth and pustular mats were significantly different (global R = 1, p = 0.1%). Smooth mats possessed higher archaeal diversity, dominated by Parvarchaeota. The methanogenic community in smooth mats was dominated by hydrogenotrophic Methanomicrobiales, as well as methylotrophic Methanosarcinales, Methanococcales, Methanobacteriales and Methanomassiliicoccaceae. Pustular mats were enriched with Halobacteria and Parvarchaeota. Key metabolisms (bacterial and archaeal) were measured, and the rates of oxygen production/consumption and sulfate reduction were up to four times higher in smooth than in pustular mats. Methane production peaked in the oxic layers and was up to seven-fold higher in smooth than pustular mats. The finding of an abundance of anaerobic methanogens enriched at the surface where oxygen levels were highest, coupled with peak methane production in the oxic zone, suggests putative surface anoxic niches in these microbial mats.},
}
@article {pmid28391963,
year = {2017},
author = {Gophna, U and Allers, T and Marchfelder, A},
title = {Finally, Archaea Get Their CRISPR-Cas Toolbox.},
journal = {Trends in microbiology},
volume = {25},
number = {6},
pages = {430-432},
doi = {10.1016/j.tim.2017.03.009},
pmid = {28391963},
issn = {1878-4380},
mesh = {Archaea/*genetics ; Archaeal Proteins/genetics ; Bacterial Proteins/genetics ; CRISPR-Cas Systems/*genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/*genetics ; DNA End-Joining Repair/genetics ; Gene Deletion ; Gene Editing ; Gene Targeting ; Genes, Archaeal ; Homologous Recombination/genetics ; Methanosarcina/genetics ; RNA, Guide ; },
abstract = {The majority of archaea encode CRISPR-Cas systems but only a few CRISPR-Cas-based genetic tools have been developed for organisms from this domain. Nayak and Metcalf have harnessed a bacterial Cas9 protein for genome editing in Methanosarcina acetivorans, enabling efficient gene deletion and replacement.},
}
@article {pmid28388930,
year = {2017},
author = {Wurzbacher, C and Fuchs, A and Attermeyer, K and Frindte, K and Grossart, HP and Hupfer, M and Casper, P and Monaghan, MT},
title = {Shifts among Eukaryota, Bacteria, and Archaea define the vertical organization of a lake sediment.},
journal = {Microbiome},
volume = {5},
number = {1},
pages = {41},
doi = {10.1186/s40168-017-0255-9},
pmid = {28388930},
issn = {2049-2618},
mesh = {Archaea/*classification/genetics/isolation &amp; purification ; Bacteria/*classification/genetics/isolation &amp; purification ; Ecosystem ; Eukaryota/*classification/genetics/isolation &amp; purification ; Geologic Sediments/*microbiology/*parasitology ; Germany ; Lakes/*microbiology/*parasitology ; Microbiota/genetics ; Water Microbiology ; },
abstract = {BACKGROUND: Lake sediments harbor diverse microbial communities that cycle carbon and nutrients while being constantly colonized and potentially buried by organic matter sinking from the water column. The interaction of activity and burial remained largely unexplored in aquatic sediments. We aimed to relate taxonomic composition to sediment biogeochemical parameters, test whether community turnover with depth resulted from taxonomic replacement or from richness effects, and to provide a basic model for the vertical community structure in sediments.<br><br>METHODS: We analyzed four replicate sediment cores taken from 30-m depth in oligo-mesotrophic Lake Stechlin in northern Germany. Each 30-cm core spanned ca. 170 years of sediment accumulation according to 137Cs dating and was sectioned into layers 1-4 cm thick. We examined a full suite of biogeochemical parameters and used DNA metabarcoding to examine community composition of microbial Archaea, Bacteria, and Eukaryota.<br><br>RESULTS: Community β-diversity indicated nearly complete turnover within the uppermost 30 cm. We observed a pronounced shift from Eukaryota- and Bacteria-dominated upper layers (<5 cm) to Bacteria-dominated intermediate layers (5-14 cm) and to deep layers (>14 cm) dominated by enigmatic Archaea that typically occur in deep-sea sediments. Taxonomic replacement was the prevalent mechanism in structuring the community composition and was linked to parameters indicative of microbial activity (e.g., CO2 and CH4 concentration, bacterial protein production). Richness loss played a lesser role but was linked to conservative parameters (e.g., C, N, P) indicative of past conditions.<br><br>CONCLUSIONS: By including all three domains, we were able to directly link the exponential decay of eukaryotes with the active sediment microbial community. The dominance of Archaea in deeper layers confirms earlier findings from marine systems and establishes freshwater sediments as a potential low-energy environment, similar to deep sea sediments. We propose a general model of sediment structure and function based on microbial characteristics and burial processes. An upper &quot;replacement horizon&quot; is dominated by rapid taxonomic turnover with depth, high microbial activity, and biotic interactions. A lower &quot;depauperate horizon&quot; is characterized by low taxonomic richness, more stable &quot;low-energy&quot; conditions, and a dominance of enigmatic Archaea.},
}
@article {pmid28373277,
year = {2017},
author = {Heider, MR and Burkhart, BW and Santangelo, TJ and Gardner, AF},
title = {Defining the RNaseH2 enzyme-initiated ribonucleotide excision repair pathway in Archaea.},
journal = {The Journal of biological chemistry},
volume = {292},
number = {21},
pages = {8835-8845},
doi = {10.1074/jbc.M117.783472},
pmid = {28373277},
issn = {1083-351X},
support = {R01 GM100329/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaeal Proteins/genetics/*metabolism ; *DNA Breaks, Single-Stranded ; DNA Ligases/genetics/metabolism ; DNA Polymerase beta/genetics/metabolism ; DNA Repair/*physiology ; DNA, Archaeal/genetics/*metabolism ; Ribonuclease H/genetics/*metabolism ; Thermococcus/genetics/*metabolism ; },
abstract = {Incorporation of ribonucleotides during DNA replication has severe consequences for genome stability. Although eukaryotes possess a number of redundancies for initiating and completing repair of misincorporated ribonucleotides, archaea such as Thermococcus rely only upon RNaseH2 to initiate the pathway. Because Thermococcus DNA polymerases incorporate as many as 1,000 ribonucleotides per genome, RNaseH2 must be efficient at recognizing and nicking at embedded ribonucleotides to ensure genome integrity. Here, we show that ribonucleotides are incorporated by the hyperthermophilic archaeon Thermococcus kodakarensis both in vitro and in vivo and a robust ribonucleotide excision repair pathway is critical to keeping incorporation levels low in wild-type cells. Using pre-steady-state and steady-state kinetics experiments, we also show that archaeal RNaseH2 rapidly cleaves at embedded ribonucleotides (200-450 s-1), but exhibits an ∼1,000-fold slower turnover rate (0.06-0.17 s-1), suggesting a potential role for RNaseH2 in protecting or marking nicked sites for further processing. We found that following RNaseH2 cleavage, the combined activities of polymerase B (PolB), flap endonuclease (Fen1), and DNA ligase are required to complete ribonucleotide processing. PolB formed a ribonucleotide-containing flap by strand displacement synthesis that was cleaved by Fen1, and DNA ligase sealed the nick for complete repair. Our study reveals conservation of the overall mechanism of ribonucleotide excision repair across domains of life. The lack of redundancies in ribonucleotide repair in archaea perhaps suggests a more ancestral form of ribonucleotide excision repair compared with the eukaryotic pathway.},
}
@article {pmid28368387,
year = {2017},
author = {Paul, BG and Burstein, D and Castelle, CJ and Handa, S and Arambula, D and Czornyj, E and Thomas, BC and Ghosh, P and Miller, JF and Banfield, JF and Valentine, DL},
title = {Retroelement-guided protein diversification abounds in vast lineages of Bacteria and Archaea.},
journal = {Nature microbiology},
volume = {2},
number = {},
pages = {17045},
doi = {10.1038/nmicrobiol.2017.45},
pmid = {28368387},
issn = {2058-5276},
support = {R01 AI096838/AI/NIAID NIH HHS/United States ; },
mesh = {Archaea/classification/*genetics/metabolism ; Archaeal Proteins/*genetics ; Bacteria/classification/*genetics/metabolism ; Bacterial Proteins/*genetics ; *Evolution, Molecular ; Genome, Archaeal ; Genome, Bacterial ; Genomics ; Nanoarchaeota/genetics/metabolism ; Phylogeny ; RNA-Directed DNA Polymerase/genetics ; Retroelements/*genetics ; },
abstract = {Major radiations of enigmatic Bacteria and Archaea with large inventories of uncharacterized proteins are a striking feature of the Tree of Life1-5. The processes that led to functional diversity in these lineages, which may contribute to a host-dependent lifestyle, are poorly understood. Here, we show that diversity-generating retroelements (DGRs), which guide site-specific protein hypervariability6-8, are prominent features of genomically reduced organisms from the bacterial candidate phyla radiation (CPR) and as yet uncultivated phyla belonging to the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaea) archaeal superphylum. From reconstructed genomes we have defined monophyletic bacterial and archaeal DGR lineages that expand the known DGR range by 120% and reveal a history of horizontal retroelement transfer. Retroelement-guided diversification is further shown to be active in current CPR and DPANN populations, with an assortment of protein targets potentially involved in attachment, defence and regulation. Based on observations of DGR abundance, function and evolutionary history, we find that targeted protein diversification is a pronounced trait of CPR and DPANN phyla compared to other bacterial and archaeal phyla. This diversification mechanism may provide CPR and DPANN organisms with a versatile tool that could be used for adaptation to a dynamic, host-dependent existence.},
}
@article {pmid28360898,
year = {2017},
author = {Wang, J and Kan, J and Zhang, X and Xia, Z and Zhang, X and Qian, G and Miao, Y and Leng, X and Sun, J},
title = {Archaea Dominate the Ammonia-Oxidizing Community in Deep-Sea Sediments of the Eastern Indian Ocean-from the Equator to the Bay of Bengal.},
journal = {Frontiers in microbiology},
volume = {8},
number = {},
pages = {415},
doi = {10.3389/fmicb.2017.00415},
pmid = {28360898},
issn = {1664-302X},
abstract = {Ammonia-oxidizing Archaea (AOA) and ammonia-oxidizing Bacteria (AOB) oxidize ammonia to nitrite, and therefore play essential roles in nitrification and global nitrogen cycling. To better understand the population structure and the distribution of AOA and AOB in the deep Eastern Indian Ocean (EIO), nine surface sediment samples (>3,300 m depth) were collected during the inter-monsoon Spring 2013. One sediment sample from the South China Sea (SCS; 2,510 m) was also included for comparison. The community composition, species richness, and diversity were characterized by clone libraries (total 1,238 clones), and higher diversity of archaeal amoA genes than bacterial amoA genes was observed in all analyzed samples. Real time qPCR analysis also demonstrated higher abundances (gene copy numbers) of archaeal amoA genes than bacterial amoA genes, and the ratios of AOA/AOB ranged from 1.42 to 8.49 among sites. In addition, unique and distinct clades were found in both reconstructed AOA and AOB phylogeny, suggesting the presence of niche-specific ammonia-oxidizing microorganisms in the EIO. The distribution pattern of both archaeal and bacterial amoA genes revealed by NMDS (non-metric multidimensional scaling) showed a distinct geographic separation of the sample from the SCS and most of the samples from the EIO following nitrogen gradients. Higher abundance and diversity of archaeal amoA genes indicated that AOA may play a more important role than AOB in the deep Indian Ocean. Environmental parameters shaping the distribution pattern of AOA were different from that of AOB, indicating distinct metabolic characteristics and/or adaptation mechanisms between AOA and AOB in the EIO, especially in deep-sea environments.},
}
@article {pmid28350393,
year = {2017},
author = {Hernsdorf, AW and Amano, Y and Miyakawa, K and Ise, K and Suzuki, Y and Anantharaman, K and Probst, A and Burstein, D and Thomas, BC and Banfield, JF},
title = {Potential for microbial H2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments.},
journal = {The ISME journal},
volume = {11},
number = {8},
pages = {1915-1929},
doi = {10.1038/ismej.2017.39},
pmid = {28350393},
issn = {1751-7370},
mesh = {Archaea/*metabolism ; Bacteria/*metabolism ; Carbon/metabolism ; Hydrogen/chemistry/*metabolism ; Hydrogenase ; Metals/chemistry/*metabolism ; Methane/metabolism ; Nitrogen/metabolism ; Oxidation-Reduction ; Radioactive Waste ; Soil/*chemistry ; Soil Microbiology ; Sulfur/metabolism ; Waste Disposal Facilities ; },
abstract = {Geological sequestration in deep underground repositories is the prevailing proposed route for radioactive waste disposal. After the disposal of radioactive waste in the subsurface, H2 may be produced by corrosion of steel and, ultimately, radionuclides will be exposed to the surrounding environment. To evaluate the potential for microbial activities to impact disposal systems, we explored the microbial community structure and metabolic functions of a sediment-hosted ecosystem at the Horonobe Underground Research Laboratory, Hokkaido, Japan. Overall, we found that the ecosystem hosted organisms from diverse lineages, including many from the phyla that lack isolated representatives. The majority of organisms can metabolize H2, often via oxidative [NiFe] hydrogenases or electron-bifurcating [FeFe] hydrogenases that enable ferredoxin-based pathways, including the ion motive Rnf complex. Many organisms implicated in H2 metabolism are also predicted to catalyze carbon, nitrogen, iron and sulfur transformations. Notably, iron-based metabolism is predicted in a novel lineage of Actinobacteria and in a putative methane-oxidizing ANME-2d archaeon. We infer an ecological model that links microorganisms to sediment-derived resources and predict potential impacts of microbial activity on H2 consumption and retardation of radionuclide migration.},
}
@article {pmid28344572,
year = {2017},
author = {van de Pol, JA and van Best, N and Mbakwa, CA and Thijs, C and Savelkoul, PH and Arts, IC and Hornef, MW and Mommers, M and Penders, J},
title = {Gut Colonization by Methanogenic Archaea Is Associated with Organic Dairy Consumption in Children.},
journal = {Frontiers in microbiology},
volume = {8},
number = {},
pages = {355},
doi = {10.3389/fmicb.2017.00355},
pmid = {28344572},
issn = {1664-302X},
abstract = {The gut microbiota represents a complex and diverse ecosystem with a profound impact on human health, promoting immune maturation, and host metabolism as well as colonization resistance. Important members that have often been disregarded are the methanogenic archaea. Methanogenic archaea reduce hydrogen levels via the production of methane, thereby stimulating food fermentation by saccharolytic bacteria. On the other hand, colonization by archaea has been suggested to promote a number of gastrointestinal and metabolic diseases such as colorectal cancer, inflammatory bowel disease, and obesity. Archaea have been shown to be absent during infancy while omnipresent in school-aged children, suggesting that colonization may result from environmental exposure during childhood. The factors that determine the acquisition of methanogenic archaea, however, have remained undefined. Therefore, we aimed to explore determinants associated with the acquisition of the two main gastrointestinal archaeal species, Methanobrevibacter smithii and Methanosphaera stadtmanae, in children. Within the context of the KOALA Birth Cohort Study, fecal samples from 472 children aged 6-10 years were analyzed for the abundance of M. smithii and M. stadtmanae using qPCR. Environmental factors such as diet, lifestyle, hygiene, child rearing, and medication were recorded by repeated questionnaires. The relationship between these determinants and the presence and abundance of archaea was analyzed by logistic and linear regression respectively. Three hundred and sixty-nine out of the 472 children (78.2%) were colonized by M. smithii, and 39 out of the 472 children (8.3%) by M. stadtmanae. The consumption of organic yogurt (odds ratio: 4.25, CI95: 1.51; 11.95) and the consumption of organic milk (odds ratio: 5.58, CI95: 1.83; 17.01) were positively associated with the presence of M. smithii. We subsequently screened raw milk, processed milk, and yogurt samples for methanogens. We identified milk products as possible source for M. smithii, but not M. stadtmanae. In conclusion, M. smithii seems present in milk products and their consumption may determine archaeal gut colonization in children. For the first time, a large variety of determinants have been explored in association with gut colonization by methanogenic archaea. Although more information is needed to confirm and unravel the mechanisms in detail, it provides new insights on microbial colonization processes in early life.},
}
@article {pmid28340330,
year = {2017},
author = {Blombach, F and Grohmann, D},
title = {Same same but different: The evolution of TBP in archaea and their eukaryotic offspring.},
journal = {Transcription},
volume = {8},
number = {3},
pages = {162-168},
doi = {10.1080/21541264.2017.1289879},
pmid = {28340330},
issn = {2154-1272},
mesh = {*Archaea/genetics/metabolism ; *Archaeal Proteins/genetics/metabolism ; DNA, Archaeal/genetics/metabolism ; DNA-Directed RNA Polymerases/genetics/metabolism ; *Evolution, Molecular ; Promoter Regions, Genetic/physiology ; *Transcription Factor TFIIB/metabolism ; },
abstract = {Transcription factors TBP and TF(II)B assemble with RNA polymerase at the promoter DNA forming the initiation complex. Despite a high degree of conservation, the molecular binding mechanisms of archaeal and eukaryotic TBP and TF(II)B differ significantly. Based on recent biophysical data, we speculate how the mechanisms co-evolved with transcription regulation and TBP multiplicity.},
}
@article {pmid28330764,
year = {2017},
author = {Eichler, J and Guan, Z},
title = {Lipid sugar carriers at the extremes: The phosphodolichols Archaea use in N-glycosylation.},
journal = {Biochimica et biophysica acta},
volume = {1862},
number = {6},
pages = {589-599},
doi = {10.1016/j.bbalip.2017.03.005},
pmid = {28330764},
issn = {0006-3002},
support = {R01 EY023666/EY/NEI NIH HHS/United States ; R01 GM120594/GM/NIGMS NIH HHS/United States ; U54 GM069338/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/genetics/*metabolism ; Carbohydrates/genetics ; Dolichol Phosphates/genetics/*metabolism ; Glycosylation ; },
abstract = {N-glycosylation, a post-translational modification whereby glycans are covalently linked to select Asn residues of target proteins, occurs in all three domains of life. Across evolution, the N-linked glycans are initially assembled on phosphorylated cytoplasmically-oriented polyisoprenoids, with polyprenol (mainly C55 undecaprenol) fulfilling this role in Bacteria and dolichol assuming this function in Eukarya and Archaea. The eukaryal and archaeal versions of dolichol can, however, be distinguished on the basis of their length, degree of saturation and by other traits. As is true for many facets of their biology, Archaea, best known in their capacity as extremophiles, present unique approaches for synthesizing phosphodolichols. At the same time, general insight into the assembly and processing of glycan-bearing phosphodolichols has come from studies of the archaeal enzymes responsible. In this review, these and other aspects of archaeal phosphodolichol biology are addressed.},
}
@article {pmid28321126,
year = {2017},
author = {Lazar, CS and Baker, BJ and Seitz, KW and Teske, AP},
title = {Genomic reconstruction of multiple lineages of uncultured benthic archaea suggests distinct biogeochemical roles and ecological niches.},
journal = {The ISME journal},
volume = {11},
number = {4},
pages = {1058},
doi = {10.1038/ismej.2017.8},
pmid = {28321126},
issn = {1751-7370},
}
@article {pmid28321009,
year = {2017},
author = {McGlynn, SE},
title = {Energy Metabolism during Anaerobic Methane Oxidation in ANME Archaea.},
journal = {Microbes and environments},
volume = {32},
number = {1},
pages = {5-13},
doi = {10.1264/jsme2.ME16166},
pmid = {28321009},
issn = {1347-4405},
mesh = {Anaerobiosis ; Archaea/*metabolism ; *Energy Metabolism ; Metabolic Networks and Pathways ; Methane/*metabolism ; Oxidation-Reduction ; },
abstract = {Anaerobic methane oxidation in archaea is often presented to operate via a pathway of &quot;reverse methanogenesis&quot;. However, if the cumulative reactions of a methanogen are run in reverse there is no apparent way to conserve energy. Recent findings suggest that chemiosmotic coupling enzymes known from their use in methylotrophic and acetoclastic methanogens-in addition to unique terminal reductases-biochemically facilitate energy conservation during complete CH4 oxidation to CO2. The apparent enzyme modularity of these organisms highlights how microbes can arrange their energy metabolisms to accommodate diverse chemical potentials in various ecological niches, even in the extreme case of utilizing &quot;reverse&quot; thermodynamic potentials.},
}
@article {pmid28286499,
year = {2017},
author = {Knüppel, R and Kuttenberger, C and Ferreira-Cerca, S},
title = {Toward Time-Resolved Analysis of RNA Metabolism in Archaea Using 4-Thiouracil.},
journal = {Frontiers in microbiology},
volume = {8},
number = {},
pages = {286},
doi = {10.3389/fmicb.2017.00286},
pmid = {28286499},
issn = {1664-302X},
abstract = {Archaea are widespread organisms colonizing almost every habitat on Earth. However, the molecular biology of archaea still remains relatively uncharacterized. RNA metabolism is a central cellular process, which has been extensively analyzed in both bacteria and eukarya. In contrast, analysis of RNA metabolism dynamic in archaea has been limited to date. To facilitate analysis of the RNA metabolism dynamic at a system-wide scale in archaea, we have established non-radioactive pulse labeling of RNA, using the nucleotide analog 4-thiouracil (4TU) in two commonly used model archaea: the halophile Euryarchaeota Haloferax volcanii, and the thermo-acidophile Crenarchaeota Sulfolobus acidocaldarius. In this work, we show that 4TU pulse labeling can be efficiently performed in these two organisms in a dose- and time-dependent manner. In addition, our results suggest that uracil prototrophy had no critical impact on the overall 4TU incorporation in RNA molecules. Accordingly, our work suggests that 4TU incorporation can be widely performed in archaea, thereby expanding the molecular toolkit to analyze archaeal gene expression network dynamic in unprecedented detail.},
}
@article {pmid28270994,
year = {2017},
author = {Qi, X and Carberry, DM and Cai, C and Hu, S and Yuan, Z and Dunlop, HR and Guo, J},
title = {Optical sorting and cultivation of denitrifying anaerobic methane oxidation archaea.},
journal = {Biomedical optics express},
volume = {8},
number = {2},
pages = {934-942},
doi = {10.1364/BOE.8.000934},
pmid = {28270994},
issn = {2156-7085},
abstract = {Denitrifying anaerobic methane oxidizing (DAMO) microorganisms play an important role in the global carbon and nitrogen cycles as they are able to mediate methane oxidation using nitrite/nitrate under anoxic conditions. However, the physiological properties of DAMO microorganisms remain poorly understood, partially since the organisms are difficult to isolate or cultivate in pure culture and partially because of their long cultivation time. In this study, DAMO cell sorting has been conducted by integrating optical tweezers within enclosed microfluidic chips. This integrated cell sorting method has high purity, low infection rates, and causes no discernable harm to cell viability. The purity of the sorted cells was controlled by the microfluidic chip structure design and operation, while the cell viability was verified by imaging the cultured DAMO archaea after 420 days.},
}
@article {pmid28261173,
year = {2017},
author = {Bhute, SS and Suryavanshi, MV and Joshi, SM and Yajnik, CS and Shouche, YS and Ghaskadbi, SS},
title = {Gut Microbial Diversity Assessment of Indian Type-2-Diabetics Reveals Alterations in Eubacteria, Archaea, and Eukaryotes.},
journal = {Frontiers in microbiology},
volume = {8},
number = {},
pages = {214},
doi = {10.3389/fmicb.2017.00214},
pmid = {28261173},
issn = {1664-302X},
abstract = {Diabetes in India has distinct genetic, nutritional, developmental and socio-economic aspects; owing to the fact that changes in gut microbiota are associated with diabetes, we employed semiconductor-based sequencing to characterize gut microbiota of diabetic subjects from this region. We suggest consolidated dysbiosis of eubacterial, archaeal and eukaryotic components in the gut microbiota of newly diagnosed (New-DMs) and long-standing diabetic subjects (Known-DMs) compared to healthy subjects (NGTs). Increased abundance of phylum Firmicutes (p = 0.010) and Operational Taxonomic Units (OTUs) of Lactobacillus (p < 0.01) were observed in Known-DMs subjects along with the concomitant graded decrease in butyrate-producing bacterial families like Ruminococcaceae and Lachnospiraceae. Eukaryotes and fungi were the least affected components in these subjects but archaea, except Methanobrevibacter were significantly decreased in them. The two dominant archaea viz. Methanobrevibacater and Methanosphaera followed opposite trends in abundance from NGTs to Known-DMs subjects. There was a substantial reduction in eubacteria, with a noticeable decrease in Bacteroidetes phylum (p = 0.098) and an increased abundance of fungi in New-DMs subjects. Likewise, opportunistic fungal pathogens such as Aspergillus, Candida were found to be enriched in New-DMs subjects. Analysis of eubacterial interaction network revealed disease-state specific patterns of ecological interactions, suggesting the distinct behavior of individual components of eubacteria in response to the disease. PERMANOVA test indicated that the eubacterial component was associated with diabetes-related risk factors like high triglyceride (p = 0.05), low HDL (p = 0.03), and waist-to-hip ratio (p = 0.02). Metagenomic imputation of eubacteria depict deficiencies of various essential functions such as carbohydrate metabolism, amino acid metabolism etc. in New-DMs subjects. Results presented here shows that in diabetes, microbial dysbiosis may not be just limited to eubacteria. Due to the inter-linked metabolic interactions among the eubacteria, archaea and eukarya in the gut, it may extend into other two domains leading to trans-domain dysbiosis in microbiota. Our results thus contribute to and expand the identification of biomarkers in diabetes.},
}
@article {pmid28249694,
year = {2017},
author = {Rosselló-Móra, R and Trujillo, ME and Sutcliffe, IC},
title = {Introducing a Digital Protologue: A timely move towards a database-driven systematics of Archaea and Bacteria.},
journal = {Systematic and applied microbiology},
volume = {40},
number = {3},
pages = {121-122},
doi = {10.1016/j.syapm.2017.02.001},
pmid = {28249694},
issn = {1618-0984},
}
@article {pmid28249125,
year = {2017},
author = {He, Y and Hu, W and Ma, D and Lan, H and Yang, Y and Gao, Y},
title = {Abundance and diversity of ammonia-oxidizing archaea and bacteria in the rhizosphere soil of three plants in the Ebinur Lake wetland.},
journal = {Canadian journal of microbiology},
volume = {63},
number = {7},
pages = {573-582},
doi = {10.1139/cjm-2016-0492},
pmid = {28249125},
issn = {1480-3275},
mesh = {Amaranthaceae ; Ammonia/*metabolism ; Archaea/*genetics/isolation &amp; purification/metabolism ; Asteraceae ; Bacteria/*genetics/isolation &amp; purification/metabolism ; Biodiversity ; China ; DNA, Ribosomal/chemistry/genetics ; Ecosystem ; Lakes ; Oxidation-Reduction ; Phylogeny ; Poaceae ; Rhizosphere ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; Wetlands ; },
abstract = {Ammonia oxidation is carried out by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). The Ebinur Lake wetland is the best example of a temperate arid zone wetland ecosystem in China. Soil samples were collected from rhizosphere and non-rhizosphere soil containing Halocnemum strobilaceum (samples H and H'), Phragmites australis (samples R and R'), and Karelinia caspia (samples K and K') to study the relationship between environmental factors and the community structure of AOB and AOA. Phylogenetic analysis showed that the AOA sequences belonged to the Nitrosopumilus and Nitrososphaera clusters. AOB were grouped into Nitrosospira sp. and Nitrosomonas sp. Quantitative polymerase chain reaction results showed that the AOA abundance ranged from 2.09 × 104 to 2.94 × 105 gene copies/g soil. The highest number of AOA was detected in sample K, followed by samples R and H. AOB abundance varied between 2.91 × 105 and 1.05 × 106 gene copies/g soil, which was higher than that of AOA. Redundancy analysis indicated that electrical conductivity, pH, and NH4+-N might influence the community structure of AOA and AOB. AOB might play a more crucial role than AOA in ammonia oxidation based on AOB's higher diversity and abundance in the Ebinur Lake wetland in Xinjiang.},
}
@article {pmid28229970,
year = {2017},
author = {Rani, SB and Balamurugan, R and Ramakrishna, BS},
title = {Molecular analysis of the human faecal archaea in a southern Indian population.},
journal = {Journal of biosciences},
volume = {42},
number = {1},
pages = {113-119},
pmid = {28229970},
issn = {0973-7138},
mesh = {Adolescent ; Adult ; Age Factors ; Aged ; Archaea/classification/*genetics/isolation &amp; purification ; Child ; Child, Preschool ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; India ; Infant ; Infant, Newborn ; Male ; Methanobrevibacter/classification/*genetics/isolation &amp; purification ; Middle Aged ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Archaea are an important constituent of the human gut microbiota, but there is no information on human gut archaea in an Indian population. In this study, faecal samples were obtained from different age groups (neonatal babies, preschool children, school-going children, adolescents, adults and elderly) of a southern Indian population, and from a tribal population also resident in southern India). 16S rRNA gene sequences specific to Archaea were amplified from pooled faecal DNA in each group, sequenced, and aligned against the NCBI database. Of the 806 adequate sequences in the study, most aligned with 22 known sequences. There were 9 novel sequences in the present study. All sequences were deposited in the GenBank nucleotide sequence database with the following accession numbers: KF607113 - KF607918. Methanobrevibacter was the most prevalent genus among all the age groups accounting for 98% in neonates, 96% in post-weaning, and 100% each in preschool, school and adult population. In the elderly, Methanobrevibacter accounted for 96% and in tribal adults, 99% of the clones belonged to Methanobrevibacter genus. Other genera detected included Caldisphaera, Halobaculum, Methanosphaeraand Thermogymnomonas. Methanobrevibacter smithii predominated in all age groups, accounting for 749 (92.9%) of the 806 sequences. Archaea can be found in the faeces of southern Indian residents immediately after birth. Methanobrevibacter smithii was the dominant faecal archeon in all age groups, with other genera being found at the extremes of age.},
}
@article {pmid28221378,
year = {2017},
author = {Leriche, G and Cifelli, JL and Sibucao, KC and Patterson, JP and Koyanagi, T and Gianneschi, NC and Yang, J},
title = {Characterization of drug encapsulation and retention in archaea-inspired tetraether liposomes.},
journal = {Organic &amp; biomolecular chemistry},
volume = {15},
number = {10},
pages = {2157-2162},
doi = {10.1039/c6ob02832b},
pmid = {28221378},
issn = {1477-0539},
mesh = {Antineoplastic Agents/*analysis/*chemistry ; Archaea/*chemistry ; *Drug Compounding ; Humans ; KB Cells ; Lipids/chemistry ; Liposomes/chemical synthesis/*chemistry ; },
abstract = {The passive leakage of small molecules across membranes is a major limitation of liposomal drug formulations. Here, we evaluate the leakage of 3 clinically used chemotherapeutic agents (cytarabine, methotrexate and vincristine) encapsulated in liposomes comprised of a synthetic, archaea-inspired, membrane-spanning tetraether lipid. Liposomes comprised of the pure tetraether lipid exhibited superior retention of both a neutrally and positively charged drug (up to an ∼9-fold decrease in the rate of drug leakage) compared to liposomes formed from a commercial diacyl lipid, while exhibiting a similar retention of a negatively charged drug that did not appreciably leak from either type of liposome. We also demonstrate that liposomes made of the archaea-inspired lipid can be used for the delivery of encapsulated small molecules into living cells.},
}
@article {pmid28211189,
year = {2017},
author = {Qin, W and Meinhardt, KA and Moffett, JW and Devol, AH and Virginia Armbrust, E and Ingalls, AE and Stahl, DA},
title = {Influence of oxygen availability on the activities of ammonia-oxidizing archaea.},
journal = {Environmental microbiology reports},
volume = {9},
number = {3},
pages = {250-256},
doi = {10.1111/1758-2229.12525},
pmid = {28211189},
issn = {1758-2229},
mesh = {Ammonia/*metabolism ; Anaerobiosis/*physiology ; Archaea/growth &amp; development/*metabolism ; Hydrogen Peroxide/pharmacology ; Nitrous Oxide/*metabolism ; Oceans and Seas ; Oxidation-Reduction ; Oxygen/*metabolism ; },
abstract = {Recent studies point to the importance of oxygen (O2) in controlling the distribution and activity of marine ammonia-oxidizing archaea (AOA), one of the most abundant prokaryotes in the ocean. The AOA are associated with regions of low O2 tension in oceanic oxygen minimum zones (OMZs), and O2 availability is suggested to influence their production of the ozone-depleting greenhouse gas nitrous oxide (N2 O). We show that marine AOA available in pure culture sustain high ammonia oxidation activity at low μM O2 concentrations, characteristic of suboxic regions of OMZs (<10 µM O2), and that atmospheric concentrations of O2 may inhibit the growth of some environmental populations. We quantify the increasing N2 O production by marine AOA with decreasing O2 tensions, consistent with the plausibility of an AOA contribution to the accumulation of N2 O at the oxic-anoxic redox boundaries of OMZs. Variable sensitivity to peroxide also suggests that endogenous or exogenous reactive oxygen species are of importance in determining the environmental distribution of some populations.},
}
@article {pmid28194147,
year = {2017},
author = {Bartelme, RP and McLellan, SL and Newton, RJ},
title = {Freshwater Recirculating Aquaculture System Operations Drive Biofilter Bacterial Community Shifts around a Stable Nitrifying Consortium of Ammonia-Oxidizing Archaea and Comammox Nitrospira.},
journal = {Frontiers in microbiology},
volume = {8},
number = {},
pages = {101},
doi = {10.3389/fmicb.2017.00101},
pmid = {28194147},
issn = {1664-302X},
abstract = {Recirculating aquaculture systems (RAS) are unique engineered ecosystems that minimize environmental perturbation by reducing nutrient pollution discharge. RAS typically employ a biofilter to control ammonia levels produced as a byproduct of fish protein catabolism. Nitrosomonas (ammonia-oxidizing), Nitrospira, and Nitrobacter (nitrite-oxidizing) species are thought to be the primary nitrifiers present in RAS biofilters. We explored this assertion by characterizing the biofilter bacterial and archaeal community of a commercial scale freshwater RAS that has been in operation for >15 years. We found the biofilter community harbored a diverse array of bacterial taxa (>1000 genus-level taxon assignments) dominated by Chitinophagaceae (~12%) and Acidobacteria (~9%). The bacterial community exhibited significant composition shifts with changes in biofilter depth and in conjunction with operational changes across a fish rearing cycle. Archaea also were abundant, and were comprised solely of a low diversity assemblage of Thaumarchaeota (>95%), thought to be ammonia-oxidizing archaea (AOA) from the presence of AOA ammonia monooxygenase genes. Nitrosomonas were present at all depths and time points. However, their abundance was >3 orders of magnitude less than AOA and exhibited significant depth-time variability not observed for AOA. Phylogenetic analysis of the nitrite oxidoreductase beta subunit (nxrB) gene indicated two distinct Nitrospira populations were present, while Nitrobacter were not detected. Subsequent identification of Nitrospira ammonia monooxygenase alpha subunit genes in conjunction with the phylogenetic placement and quantification of the nxrB genotypes suggests complete ammonia-oxidizing (comammox) and nitrite-oxidizing Nitrospira populations co-exist with relatively equivalent and stable abundances in this system. It appears RAS biofilters harbor complex microbial communities whose composition can be affected directly by typical system operations while supporting multiple ammonia oxidation lifestyles within the nitrifying consortium.},
}
@article {pmid28191504,
year = {2017},
author = {Ma, B and Dai, Z and Wang, H and Dsouza, M and Liu, X and He, Y and Wu, J and Rodrigues, JL and Gilbert, JA and Brookes, PC and Xu, J},
title = {Distinct Biogeographic Patterns for Archaea, Bacteria, and Fungi along the Vegetation Gradient at the Continental Scale in Eastern China.},
journal = {mSystems},
volume = {2},
number = {1},
pages = {},
doi = {10.1128/mSystems.00174-16},
pmid = {28191504},
issn = {2379-5077},
abstract = {The natural forest ecosystem in Eastern China, from tropical forest to boreal forest, has declined due to cropland development during the last 300 years, yet little is known about the historical biogeographic patterns and driving processes for the major domains of microorganisms along this continental-scale natural vegetation gradient. We predicted the biogeographic patterns of soil archaeal, bacterial, and fungal communities across 110 natural forest sites along a transect across four vegetation zones in Eastern China. The distance decay relationships demonstrated the distinct biogeographic patterns of archaeal, bacterial, and fungal communities. While historical processes mainly influenced bacterial community variations, spatially autocorrelated environmental variables mainly influenced the fungal community. Archaea did not display a distance decay pattern along the vegetation gradient. Bacterial community diversity and structure were correlated with the ratio of acid oxalate-soluble Fe to free Fe oxides (Feo/Fed ratio). Fungal community diversity and structure were influenced by dissolved organic carbon (DOC) and free aluminum (Ald), respectively. The role of these environmental variables was confirmed by the correlations between dominant operational taxonomic units (OTUs) and edaphic variables. However, most of the dominant OTUs were not correlated with the major driving variables for the entire communities. These results demonstrate that soil archaea, bacteria, and fungi have different biogeographic patterns and driving processes along this continental-scale natural vegetation gradient, implying different community assembly mechanisms and ecological functions for archaea, bacteria, and fungi in soil ecosystems. IMPORTANCE Understanding biogeographic patterns is a precursor to improving our knowledge of the function of microbiomes and to predicting ecosystem responses to environmental change. Using natural forest soil samples from 110 locations, this study is one of the largest attempts to comprehensively understand the different patterns of soil archaeal, bacterial, and fungal biogeography at the continental scale in eastern China. These patterns in natural forest sites could ascertain reliable soil microbial biogeographic patterns by eliminating anthropogenic influences. This information provides guidelines for monitoring the belowground ecosystem's decline and restoration. Meanwhile, the deviations in the soil microbial communities from corresponding natural forest states indicate the extent of degradation of the soil ecosystem. Moreover, given the association between vegetation type and the microbial community, this information could be used to predict the long-term response of the underground ecosystem to the vegetation distribution caused by global climate change.},
}
@article {pmid28188879,
year = {2017},
author = {Jin, D and Kang, K and Wang, H and Wang, Z and Xue, B and Wang, L and Xu, F and Peng, Q},
title = {Effects of dietary supplementation of active dried yeast on fecal methanogenic archaea diversity in dairy cows.},
journal = {Anaerobe},
volume = {44},
number = {},
pages = {78-86},
doi = {10.1016/j.anaerobe.2017.02.007},
pmid = {28188879},
issn = {1095-8274},
mesh = {Animals ; Archaea/classification/genetics/*isolation &amp; purification/metabolism ; *Biodiversity ; Cattle ; Diet/*methods ; *Dietary Supplements ; Feces/*microbiology ; High-Throughput Nucleotide Sequencing ; Methane/*metabolism ; Real-Time Polymerase Chain Reaction ; Yeast, Dried/*administration &amp; dosage ; },
abstract = {This study aimed to investigate the effects of dietary supplementation of different dosages of active dried yeast (ADY) on the fecal methanogenic archaea community of dairy cattle. Twelve multiparous, healthy, mid-lactating Holstein dairy cows (body weight: 584 ± 23.2 kg, milk produced: 26.3 ± 1.22 kg/d) were randomly assigned to one of three treatments (control, ADY2, and ADY4) according to body weight with four replicates per treatment. Cows in the control group were fed conventional rations without ADY supplementation, while cows in the ADY2 and ADY4 group were fed rations supplemented with ADY at 2 or 4 g/d/head. Real-time PCR analysis showed the populations of total methanogens in the feces were significantly decreased (P < 0.05) in the ADY4 group compared with control. High-throughput sequencing technology was applied to examine the differences in methanogenic archaea diversity in the feces of the three treatment groups. A total of 155,609 sequences were recovered (a mean of 12,967 sequences per sample) from the twelve fecal samples, which consisted of a number of operational taxonomic units (OTUs) ranging from 1451 to 1,733, were assigned to two phyla, four classes, five orders, five families and six genera. Bioinformatic analyses illustrated that the natural fecal archaeal community of the control group was predominated by Methanobrevibacter (86.9% of the total sequence reads) and Methanocorpusculum (10.4%), while the relative abundance of the remaining four genera were below 1% with Methanosphaera comprising 0.8%, Thermoplasma composing 0.4%, and the relative abundance of Candidatus Nitrososphaera and Halalkalicoccus being close to zero. At the genus level, the relative abundances of Methanocorpusculum and Thermoplasma were increased (P < 0.05) with increasing dosage of ADY. Conversely, the predominant methanogen genus Methanobrevibacter was decreased with ADY dosage (P < 0.05). Dietary supplementation of ADY had no significant effect (P > 0.05) on the abundances of genera unclassified, Candidatus Nitrososphaera, and Halalkalicoccus. In conclusion, supplementation of ADY to the rations of dairy cattle could alter the population sizes and composition of fecal methanogenic archaea in the feces of dairy cattle. The decrease in Methanobrevibacter happened with a commensurate increase in the genera Methanocorpusculum and Thermoplasma.},
}
@article {pmid28177649,
year = {2017},
author = {Thomas, L and Ram, H and Singh, VP},
title = {Evolutionary Relationships and Taxa-Specific Conserved Signature Indels Among Cellulases of Archaea, Bacteria, and Eukarya.},
journal = {Journal of computational biology : a journal of computational molecular cell biology},
volume = {24},
number = {10},
pages = {1029-1042},
doi = {10.1089/cmb.2016.0161},
pmid = {28177649},
issn = {1557-8666},
mesh = {Archaea/classification/*enzymology/genetics ; Bacteria/classification/*enzymology/genetics ; Cellulases/*genetics ; Eukaryota/classification/*enzymology/genetics ; *Evolution, Molecular ; *INDEL Mutation ; Phylogeny ; Substrate Specificity ; },
abstract = {The cellulases from different cellulolytic organisms have evolutionary relationships, which range from single-celled prokaryotes to the complex eukaryotes of the living world. This in silico analysis revealed the presence of a conserved cellulase domain along with evolutionary relationships among cellulases from several species of Archaea, Bacteria, and Eukarya. The amino acid sequences of cellulases from Archaea and Bacteria showed closer identity with their domain or phylum members that provided insights into convergent and divergent evolution of cellulases from other enzymes with different substrate specificities. Evolutionary relatedness was also observed in phylogenetic trees among a number of cellulase sequences of diverse taxa. In cellulases, propensity for alanine, glycine, leucine, serine, and threonine was high, but low for cysteine, histidine, and methionine. Catalytic aspartic acid had a higher propensity than glutamic acid, and both were involved in regular expression patterns. Characteristic group and multigroup-specific conserved signature indels located in the catalytic domains of cellulases were observed that further clarified evolutionary relationships. These indels can be distinctive molecular tools for understanding phylogeny and identification of unknown cellulolytic species of common evolutionary descent in different environments.},
}
@article {pmid28174314,
year = {2017},
author = {Yan, Z and Wang, M and Ferry, JG},
title = {A Ferredoxin- and F420H2-Dependent, Electron-Bifurcating, Heterodisulfide Reductase with Homologs in the Domains Bacteria and Archaea.},
journal = {mBio},
volume = {8},
number = {1},
pages = {},
doi = {10.1128/mBio.02285-16},
pmid = {28174314},
issn = {2150-7511},
mesh = {Anaerobiosis ; Electron Transport ; Escherichia coli/genetics/*metabolism ; Ferredoxins/*metabolism ; Gene Expression ; Methane/metabolism ; Methanosarcina/*enzymology/genetics ; Oxidation-Reduction ; Oxidoreductases/*genetics/*metabolism ; Riboflavin/*analogs &amp; derivatives/metabolism ; Sequence Homology ; },
abstract = {Heterodisulfide reductases (Hdr) of the HdrABC class are ancient enzymes and a component of the anaerobic core belonging to the prokaryotic common ancestor. The ancient origin is consistent with the widespread occurrence of genes encoding putative HdrABC homologs in metabolically diverse prokaryotes predicting diverse physiological functions; however, only one HdrABC has been characterized and that was from a narrow metabolic group of obligate CO2-reducing methanogenic anaerobes (methanogens) from the domain Archaea Here we report the biochemical characterization of an HdrABC homolog (HdrA2B2C2) from the acetate-utilizing methanogen Methanosarcina acetivorans with unusual properties structurally and functionally distinct from the only other HdrABC characterized. Homologs of the HdrA2B2C2 archetype are present in phylogenetically and metabolically diverse species from the domains Bacteria and Archaea The expression of the individual HdrA2, HdrB2, and HdrB2C2 enzymes in Escherichia coli, and reconstitution of an active HdrA2B2C2 complex, revealed an intersubunit electron transport pathway dependent on ferredoxin or coenzyme F420 (F420H2) as an electron donor. Remarkably, HdrA2B2C2 couples the previously unknown endergonic oxidation of F420H2 and reduction of ferredoxin with the exergonic oxidation of F420H2 and reduction of the heterodisulfide of coenzyme M and coenzyme B (CoMS-SCoB). The unique electron bifurcation predicts a role for HdrA2B2C2 in Fe(III)-dependent anaerobic methane oxidation (ANME) by M. acetivorans and uncultured species from ANME environments. HdrA2B2C2, ubiquitous in acetotrophic methanogens, was shown to participate in electron transfer during acetotrophic growth of M. acetivorans and proposed to be essential for growth in the environment when acetate is limiting.<br><br>IMPORTANCE: Discovery of the archetype HdrA2B2C2 heterodisulfide reductase with categorically unique properties extends the understanding of this ancient family beyond CO2-reducing methanogens to include diverse prokaryotes from the domains Bacteria and Archaea The unprecedented coenzyme F420-dependent electron bifurcation, an emerging fundamental principle of energy conservation, predicts a role for HdrA2B2C2 in diverse metabolisms, including anaerobic CH4-oxidizing pathways. The results document an electron transport role for HdrA2B2C2 in acetate-utilizing methanogens responsible for at least two-thirds of the methane produced in Earth's biosphere. The previously unavailable heterologous production of individual subunits and the reconstitution of HdrA2B2C2 with activity have provided an understanding of intersubunit electron transfer in the HdrABC class and a platform for investigating the principles of electron bifurcation.},
}
@article {pmid28168565,
year = {2017},
author = {Rosselló-Móra, R and Trujillo, ME and Sutcliffe, IC},
title = {Introducing a digital protologue: a timely move towards a database-driven systematics of archaea and bacteria.},
journal = {Antonie van Leeuwenhoek},
volume = {110},
number = {4},
pages = {455-456},
doi = {10.1007/s10482-017-0841-7},
pmid = {28168565},
issn = {1572-9699},
}
@article {pmid28154498,
year = {2017},
author = {Timmers, PH and Welte, CU and Koehorst, JJ and Plugge, CM and Jetten, MS and Stams, AJ},
title = {Reverse Methanogenesis and Respiration in Methanotrophic Archaea.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2017},
number = {},
pages = {1654237},
doi = {10.1155/2017/1654237},
pmid = {28154498},
issn = {1472-3654},
mesh = {Anaerobiosis ; Archaea/*metabolism ; Methane/*metabolism ; Oxidation-Reduction ; },
abstract = {Anaerobic oxidation of methane (AOM) is catalyzed by anaerobic methane-oxidizing archaea (ANME) via a reverse and modified methanogenesis pathway. Methanogens can also reverse the methanogenesis pathway to oxidize methane, but only during net methane production (i.e., &quot;trace methane oxidation&quot;). In turn, ANME can produce methane, but only during net methane oxidation (i.e., enzymatic back flux). Net AOM is exergonic when coupled to an external electron acceptor such as sulfate (ANME-1, ANME-2abc, and ANME-3), nitrate (ANME-2d), or metal (oxides). In this review, the reversibility of the methanogenesis pathway and essential differences between ANME and methanogens are described by combining published information with domain based (meta)genome comparison of archaeal methanotrophs and selected archaea. These differences include abundances and special structure of methyl coenzyme M reductase and of multiheme cytochromes and the presence of menaquinones or methanophenazines. ANME-2a and ANME-2d can use electron acceptors other than sulfate or nitrate for AOM, respectively. Environmental studies suggest that ANME-2d are also involved in sulfate-dependent AOM. ANME-1 seem to use a different mechanism for disposal of electrons and possibly are less versatile in electron acceptors use than ANME-2. Future research will shed light on the molecular basis of reversal of the methanogenic pathway and electron transfer in different ANME types.},
}
@article {pmid28146124,
year = {2017},
author = {Ausiannikava, D and Allers, T},
title = {Diversity of DNA Replication in the Archaea.},
journal = {Genes},
volume = {8},
number = {2},
pages = {},
doi = {10.3390/genes8020056},
pmid = {28146124},
issn = {2073-4425},
abstract = {DNA replication is arguably the most fundamental biological process. On account of their shared evolutionary ancestry, the replication machinery found in archaea is similar to that found in eukaryotes. DNA replication is initiated at origins and is highly conserved in eukaryotes, but our limited understanding of archaea has uncovered a wide diversity of replication initiation mechanisms. Archaeal origins are sequence-based, as in bacteria, but are bound by initiator proteins that share homology with the eukaryotic origin recognition complex subunit Orc1 and helicase loader Cdc6). Unlike bacteria, archaea may have multiple origins per chromosome and multiple Orc1/Cdc6 initiator proteins. There is no consensus on how these archaeal origins are recognised- some are bound by a single Orc1/Cdc6 protein while others require a multi- Orc1/Cdc6 complex. Many archaeal genomes consist of multiple parts-the main chromosome plus several megaplasmids-and in polyploid species these parts are present in multiple copies. This poses a challenge to the regulation of DNA replication. However, one archaeal species (Haloferax volcanii) can survive without replication origins; instead, it uses homologous recombination as an alternative mechanism of initiation. This diversity in DNA replication initiation is all the more remarkable for having been discovered in only three groups of archaea where in vivo studies are possible.},
}
@article {pmid28140393,
year = {2017},
author = {Mamet, SD and Lamb, EG and Piper, CL and Winsley, T and Siciliano, SD},
title = {Archaea and bacteria mediate the effects of native species root loss on fungi during plant invasion.},
journal = {The ISME journal},
volume = {11},
number = {5},
pages = {1261-1275},
doi = {10.1038/ismej.2016.205},
pmid = {28140393},
issn = {1751-7370},
mesh = {Archaea/classification/*isolation &amp; purification ; Bacteria/classification/*isolation &amp; purification ; Biodiversity ; Bromus/microbiology ; Fungi/classification/*isolation &amp; purification ; Introduced Species ; Microbial Interactions ; Plant Roots/*microbiology ; *Soil Microbiology ; },
abstract = {Although invasive plants can drive ecosystem change, little is known about the directional nature of belowground interactions between invasive plants, native roots, bacteria, archaea and fungi. We used detailed bioinformatics and a recently developed root assay on soils collected in fescue grassland along a gradient of smooth brome (Bromus inermis Leyss) invasion to examine the links between smooth brome shoot litter and root, archaea, bacteria and fungal communities. We examined (1) aboveground versus belowground influences of smooth brome on soil microbial communities, (2) the importance of direct versus microbe-mediated impacts of plants on soil fungal communities, and (3) the web of roots, shoots, archaea, bacteria and fungi interactions across the A and B soil horizons in invaded and non-invaded sites. Archaea and bacteria influenced fungal composition, but not vice versa, as indicated by redundancy analyses. Co-inertia analyses suggested that bacterial-fungal variance was driven primarily by 12 bacterial operational taxonomic units (OTUs). Brome increased bacterial diversity via smooth brome litter in the A horizon and roots in the B horizon, which then reduced fungal diversity. Archaea increased abundance of several bacterial OTUs, and the key bacterial OTUs mediated changes in the fungi's response to invasion. Overall, native root diversity loss and bacterial mediation were more important drivers of fungal composition than were the direct effects of increases in smooth brome. Critically, native plant species displacement and root loss appeared to be the most important driver of fungal composition during invasion. This causal web likely gives rise to the plant-fungi feedbacks, which are an essential factor determining plant diversity in invaded grassland ecosystems.},
}
@article {pmid28133437,
year = {2017},
author = {Thor, S and Peterson, JR and Luthey-Schulten, Z},
title = {Genome-Scale Metabolic Modeling of Archaea Lends Insight into Diversity of Metabolic Function.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2017},
number = {},
pages = {9763848},
doi = {10.1155/2017/9763848},
pmid = {28133437},
issn = {1472-3654},
mesh = {Computational Biology ; Euryarchaeota/*metabolism ; *Metabolic Networks and Pathways ; *Models, Biological ; },
abstract = {Decades of biochemical, bioinformatic, and sequencing data are currently being systematically compiled into genome-scale metabolic reconstructions (GEMs). Such reconstructions are knowledge-bases useful for engineering, modeling, and comparative analysis. Here we review the fifteen GEMs of archaeal species that have been constructed to date. They represent primarily members of the Euryarchaeota with three-quarters comprising representative of methanogens. Unlike other reviews on GEMs, we specially focus on archaea. We briefly review the GEM construction process and the genealogy of the archaeal models. The major insights gained during the construction of these models are then reviewed with specific focus on novel metabolic pathway predictions and growth characteristics. Metabolic pathway usage is discussed in the context of the composition of each organism's biomass and their specific energy and growth requirements. We show how the metabolic models can be used to study the evolution of metabolism in archaea. Conservation of particular metabolic pathways can be studied by comparing reactions using the genes associated with their enzymes. This demonstrates the utility of GEMs to evolutionary studies, far beyond their original purpose of metabolic modeling; however, much needs to be done before archaeal models are as extensively complete as those for bacteria.},
}
@article {pmid28115203,
year = {2017},
author = {Michel, CJ},
title = {WITHDRAWN: The maximal C3 self-complementary trinucleotide circular code X in genes of bacteria, archaea, eukaryotes, plasmids and viruses.},
journal = {Journal of theoretical biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jtbi.2017.01.028},
pmid = {28115203},
issn = {1095-8541},
}
@article {pmid28104666,
year = {2017},
author = {Buongiorno, J and Turner, S and Webster, G and Asai, M and Shumaker, AK and Roy, T and Weightman, A and Schippers, A and Lloyd, KG},
title = {Interlaboratory quantification of Bacteria and Archaea in deeply buried sediments of the Baltic Sea (IODP Expedition 347).},
journal = {FEMS microbiology ecology},
volume = {93},
number = {3},
pages = {},
doi = {10.1093/femsec/fix007},
pmid = {28104666},
issn = {1574-6941},
mesh = {Archaea/*genetics/growth &amp; development ; Bacteria/*genetics/growth &amp; development ; *Colony Count, Microbial ; DNA Primers ; Expeditions ; Geologic Sediments/*microbiology ; In Situ Hybridization, Fluorescence/methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; *Water Microbiology ; },
abstract = {Two common quantification methods for subseafloor microorganisms are catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) and quantitative PCR (qPCR). Using these methods, we quantified Bacteria and Archaea in Baltic Sea basin sediments (IODP Exp. 347) down to 90 mbsf, testing the following hypotheses in an interlaboratory comparison: (1) proteinase K permeabilization of archaeal cell walls increases CARD-FISH accuracy and (2) qPCR varies by more than an order of magnitude between laboratories using similar protocols. CARD-FISH counts did not differ between permeabilization treatments, demonstrating that proteinase K did not increase accuracy of CARD-FISH counts. However, 91% of these counts were below the quantification limit of 1.3 × 107 cells cm-3. For qPCR, data varied between laboratories, but were largely within the same order of magnitude if the same primers were used, with 88% of samples being above the quantification limit. Copy number values were elevated by preparing a sediment slurry before DNA extraction: 3.88 × 106-2.34 × 109 16S rRNA gene copies cm-3 vs. 1.39 × 107-1.87 × 109 total cells cm-3. By qPCR, Bacteria were more abundant than Archaea, although they usually were within the same order of magnitude. Overall, qPCR is more sensitive than CARD-FISH, but both require optimization to consistently achieve both precision and accuracy.},
}
@article {pmid28085154,
year = {2017},
author = {Lazar, CS and Baker, BJ and Seitz, KW and Teske, AP},
title = {Genomic reconstruction of multiple lineages of uncultured benthic archaea suggests distinct biogeochemical roles and ecological niches.},
journal = {The ISME journal},
volume = {11},
number = {5},
pages = {1118-1129},
doi = {10.1038/ismej.2016.189},
pmid = {28085154},
issn = {1751-7370},
support = {247153//European Research Council/International ; },
mesh = {Acetyl Coenzyme A/metabolism ; Archaea/classification/*genetics/isolation &amp; purification/metabolism ; Carbon Cycle ; Ecosystem ; Estuaries ; *Genome, Archaeal ; Genomics ; Geologic Sediments/*microbiology ; Phylogeny ; Rivers ; },
abstract = {Genomic bins belonging to multiple archaeal lineages were recovered from distinct redox regimes in sediments of the White Oak River estuary. The reconstructed archaeal genomes were identified as belonging to the rice cluster subgroups III and V (RC-III, RC-V), the Marine Benthic Group D (MBG-D), and a newly described archaeal class, the Theionarchaea. The metabolic capabilities of these uncultured archaea were inferred and indicated a common capability for extracellular protein degradation, supplemented by other pathways. The multiple genomic bins within the MBG-D archaea shared a nearly complete reductive acetyl-CoA pathway suggesting acetogenic capabilities. In contrast, the RC-III metabolism appeared centered on the degradation of detrital proteins and production of H2, whereas the RC-V archaea lacked capabilities for protein degradation and uptake, and appeared to be specialized on carbohydrate fermentation. The Theionarchaea appeared as complex metabolic hybrids; encoding a complete tricarboxylic acid cycle permitting carbon (acetyl-CoA) oxidation, together with a complete reductive acetyl-CoA pathway and sulfur reduction by a sulfhydrogenase. The differentiated inferred capabilities of these uncultured archaeal lineages indicated lineage-specific linkages with the nitrogen, carbon and sulfur cycles. The predicted metabolisms of these archaea suggest preferences for distinct geochemical niches within the estuarine sedimentary environment.},
}
@article {pmid28082747,
year = {2017},
author = {Kono, T and Mehrotra, S and Endo, C and Kizu, N and Matusda, M and Kimura, H and Mizohata, E and Inoue, T and Hasunuma, T and Yokota, A and Matsumura, H and Ashida, H},
title = {A RuBisCO-mediated carbon metabolic pathway in methanogenic archaea.},
journal = {Nature communications},
volume = {8},
number = {},
pages = {14007},
doi = {10.1038/ncomms14007},
pmid = {28082747},
issn = {2041-1723},
abstract = {Two enzymes are considered to be unique to the photosynthetic Calvin-Benson cycle: ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), responsible for CO2 fixation, and phosphoribulokinase (PRK). Some archaea possess bona fide RuBisCOs, despite not being photosynthetic organisms, but are thought to lack PRK. Here we demonstrate the existence in methanogenic archaea of a carbon metabolic pathway involving RuBisCO and PRK, which we term 'reductive hexulose-phosphate' (RHP) pathway. These archaea possess both RuBisCO and a catalytically active PRK whose crystal structure resembles that of photosynthetic bacterial PRK. Capillary electrophoresis-mass spectrometric analysis of metabolites reveals that the RHP pathway, which differs from the Calvin-Benson cycle only in a few steps, is active in vivo. Our work highlights evolutionary and functional links between RuBisCO-mediated carbon metabolic pathways in methanogenic archaea and photosynthetic organisms. Whether the RHP pathway allows for autotrophy (that is, growth exclusively with CO2 as carbon source) remains unknown.},
}
@article {pmid28077874,
year = {2017},
author = {Zaremba-Niedzwiedzka, K and Caceres, EF and Saw, JH and Bäckström, D and Juzokaite, L and Vancaester, E and Seitz, KW and Anantharaman, K and Starnawski, P and Kjeldsen, KU and Stott, MB and Nunoura, T and Banfield, JF and Schramm, A and Baker, BJ and Spang, A and Ettema, TJ},
title = {Asgard archaea illuminate the origin of eukaryotic cellular complexity.},
journal = {Nature},
volume = {541},
number = {7637},
pages = {353-358},
doi = {10.1038/nature21031},
pmid = {28077874},
issn = {1476-4687},
mesh = {Archaea/classification/*cytology/*genetics ; Archaeal Proteins/genetics/metabolism ; Biological Transport/genetics ; COP-Coated Vesicles/metabolism ; Eukaryota/classification/*cytology/genetics ; Eukaryotic Cells/classification/*cytology/metabolism ; *Evolution, Molecular ; Genome, Archaeal/*genetics ; Metagenomics ; *Models, Biological ; *Phylogeny ; },
abstract = {The origin and cellular complexity of eukaryotes represent a major enigma in biology. Current data support scenarios in which an archaeal host cell and an alphaproteobacterial (mitochondrial) endosymbiont merged together, resulting in the first eukaryotic cell. The host cell is related to Lokiarchaeota, an archaeal phylum with many eukaryotic features. The emergence of the structural complexity that characterizes eukaryotic cells remains unclear. Here we describe the 'Asgard' superphylum, a group of uncultivated archaea that, as well as Lokiarchaeota, includes Thor-, Odin- and Heimdallarchaeota. Asgard archaea affiliate with eukaryotes in phylogenomic analyses, and their genomes are enriched for proteins formerly considered specific to eukaryotes. Notably, thorarchaeal genomes encode several homologues of eukaryotic membrane-trafficking machinery components, including Sec23/24 and TRAPP domains. Furthermore, we identify thorarchaeal proteins with similar features to eukaryotic coat proteins involved in vesicle biogenesis. Our results expand the known repertoire of 'eukaryote-specific' proteins in Archaea, indicating that the archaeal host cell already contained many key components that govern eukaryotic cellular complexity.},
}
@article {pmid28073944,
year = {2017},
author = {Rodionova, IA and Vetting, MW and Li, X and Almo, SC and Osterman, AL and Rodionov, DA},
title = {A novel bifunctional transcriptional regulator of riboflavin metabolism in Archaea.},
journal = {Nucleic acids research},
volume = {45},
number = {7},
pages = {3785-3799},
doi = {10.1093/nar/gkw1331},
pmid = {28073944},
issn = {1362-4962},
support = {P30 CA030199/CA/NCI NIH HHS/United States ; },
mesh = {Archaea/enzymology/*genetics/metabolism ; Archaeal Proteins/chemistry/*metabolism ; DNA, Archaeal/chemistry/metabolism ; Evolution, Molecular ; Genome, Archaeal ; Operator Regions, Genetic ; Phosphotransferases (Alcohol Group Acceptor)/chemistry/*metabolism ; Protein Domains ; Regulon ; Riboflavin/*metabolism ; Transcription Factors/chemistry/*metabolism ; },
abstract = {Riboflavin (vitamin B2) is the precursor of flavin mononucleotide (FMN) and flavin adenine dinucleotide, which are essential coenzymes in all free-living organisms. Riboflavin biosynthesis in many Bacteria but not in Archaea is controlled by FMN-responsive riboswitches. We identified a novel bifunctional riboflavin kinase/regulator (RbkR), which controls riboflavin biosynthesis and transport genes in major lineages of Crenarchaeota, Euryarchaeota and Thaumarchaeota. RbkR proteins are composed of the riboflavin kinase domain and a DNA-binding winged helix-turn-helix-like domain. Using comparative genomics, we predicted RbkR operator sites and reconstructed RbkR regulons in 94 archaeal genomes. While the identified RbkR operators showed significant variability between archaeal lineages, the conserved core of RbkR regulons includes riboflavin biosynthesis genes, known/predicted vitamin uptake transporters and the rbkR gene. The DNA motifs and CTP-dependent riboflavin kinase activity of two RbkR proteins were experimentally validated in vitro. The DNA binding activity of RbkR was stimulated by CTP and suppressed by FMN, a product of riboflavin kinase. The crystallographic structure of RbkR from Thermoplasma acidophilum was determined in complex with CTP and its DNA operator revealing key residues for operator and ligand recognition. Overall, this study contributes to our understanding of metabolic and regulatory networks for vitamin homeostasis in Archaea.},
}
@article {pmid28070167,
year = {2016},
author = {Ma, Y and Liu, F and Kong, Z and Yin, J and Kou, W and Wu, L and Ge, G},
title = {The Distribution Pattern of Sediment Archaea Community of the Poyang Lake, the Largest Freshwater Lake in China.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2016},
number = {},
pages = {9278929},
doi = {10.1155/2016/9278929},
pmid = {28070167},
issn = {1472-3654},
mesh = {Archaea/*classification/genetics ; *Biota ; China ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Fresh Water/*microbiology ; Geologic Sediments/*microbiology ; Lakes/*microbiology ; Phylogeography ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Spatial Analysis ; },
abstract = {Archaea plays an important role in the global geobiochemical circulation of various environments. However, much less is known about the ecological role of archaea in freshwater lake sediments. Thus, investigating the structure and diversity of archaea community is vital to understand the metabolic processes in freshwater lake ecosystems. In this study, sediment physicochemical properties were combined with the results from 16S rRNA clone library-sequencing to examine the sediment archaea diversity and the environmental factors driving the sediment archaea community structures. Seven sites were chosen from Poyang Lake, including two sites from the main lake body and five sites from the inflow river estuaries. Our results revealed high diverse archaea community in the sediment of Poyang Lake, including Bathyarchaeota (45.5%), Euryarchaeota (43.1%), Woesearchaeota (3.6%), Pacearchaeota (1.7%), Thaumarchaeota (1.4%), suspended Lokiarchaeota (0.7%), Aigarchaeota (0.2%), and Unclassified Archaea (3.8%). The archaea community compositions differed among sites, and sediment property had considerable influence on archaea community structures and distribution, especially total organic carbon (TOC) and metal lead (Pb) (p < 0.05). This study provides primary profile of sediment archaea distribution in freshwater lakes and helps to deepen our understanding of lake sediment microbes.},
}
@article {pmid28053595,
year = {2016},
author = {Prunetti, L and Graf, M and Blaby, IK and Peil, L and Makkay, AM and Starosta, AL and Papke, RT and Oshima, T and Wilson, DN and de Crécy-Lagard, V},
title = {Deciphering the Translation Initiation Factor 5A Modification Pathway in Halophilic Archaea.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2016},
number = {},
pages = {7316725},
doi = {10.1155/2016/7316725},
pmid = {28053595},
issn = {1472-3654},
support = {R01 GM070641/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaeal Proteins/*metabolism ; Chromatography, Liquid ; Haloferax volcanii/*enzymology/*metabolism ; Lysine/*analogs &amp; derivatives/metabolism ; Peptide Initiation Factors/*metabolism ; *Protein Processing, Post-Translational ; Tandem Mass Spectrometry ; },
abstract = {Translation initiation factor 5A (IF5A) is essential and highly conserved in Eukarya (eIF5A) and Archaea (aIF5A). The activity of IF5A requires hypusine, a posttranslational modification synthesized in Eukarya from the polyamine precursor spermidine. Intracellular polyamine analyses revealed that agmatine and cadaverine were the main polyamines produced in Haloferax volcanii in minimal medium, raising the question of how hypusine is synthesized in this halophilic Archaea. Metabolic reconstruction led to a tentative picture of polyamine metabolism and aIF5A modification in Hfx. volcanii that was experimentally tested. Analysis of aIF5A from Hfx. volcanii by LC-MS/MS revealed it was exclusively deoxyhypusinylated. Genetic studies confirmed the role of the predicted arginine decarboxylase gene (HVO_1958) in agmatine synthesis. The agmatinase-like gene (HVO_2299) was found to be essential, consistent with a role in aIF5A modification predicted by physical clustering evidence. Recombinant deoxyhypusine synthase (DHS) from S. cerevisiae was shown to transfer 4-aminobutyl moiety from spermidine to aIF5A from Hfx. volcanii in vitro. However, at least under conditions tested, this transfer was not observed with the Hfx. volcanii DHS. Furthermore, the growth of Hfx. volcanii was not inhibited by the classical DHS inhibitor GC7. We propose a model of deoxyhypusine synthesis in Hfx. volcanii that differs from the canonical eukaryotic pathway, paving the way for further studies.},
}
@article {pmid28029780,
year = {2017},
author = {Srivastava, SS and Jamkhindikar, AA and Raman, R and Jobby, MK and Chadalawada, S and Sankaranarayanan, R and Sharma, Y},
title = {A Transition Metal-Binding, Trimeric βγ-Crystallin from Methane-Producing Thermophilic Archaea, Methanosaeta thermophila.},
journal = {Biochemistry},
volume = {56},
number = {9},
pages = {1299-1310},
doi = {10.1021/acs.biochem.6b00985},
pmid = {28029780},
issn = {1520-4995},
mesh = {Archaea/*metabolism ; Methane/biosynthesis ; Models, Molecular ; *Protein Multimerization ; Protein Structure, Quaternary ; Temperature ; Transition Elements/*metabolism ; beta-Crystallins/*chemistry/*metabolism ; gamma-Crystallins/*chemistry/*metabolism ; },
abstract = {βγ-Crystallins are important constituents of the vertebrate eye lens, whereas in microbes, they are prevalent as Ca2+-binding proteins. In archaea, βγ-crystallins are conspicuously confined to two methanogens, viz., Methanosaeta and Methanosarcina. One of these, i.e., M-crystallin from Methanosarcina acetivorans, has been shown to be a typical Ca2+-binding βγ-crystallin. Here, with the aid of a high-resolution crystal structure and isothermal titration calorimetry, we report that &quot;Methallin&quot;, a βγ-crystallin from Methanosaeta thermophila, is a trimeric, transition metal-binding protein. It binds Fe, Ni, Co, or Zn ion with nanomolar affinity, which is consistent even at 55 °C, the optimal temperature for the methanogen's growth. At the center of the protein trimer, the metal ion is coordinated by six histidines, two from each protomer, leading to an octahedral geometry. Small-angle X-ray scattering analysis confirms that the trimer seen in the crystal lattice is a biological assembly; this assembly dissociates to monomers upon removal of the metal ion. The introduction of two histidines (S17H/S19H) into a homologous βγ-crystallin, Clostrillin, allows it to bind nickel at the introduced site, though with micromolar affinity. However, because of the lack of a compatible interface, nickel binding could not induce trimerization, affirming that Methallin is a naturally occurring trimer for high-affinity transition metal binding. While βγ-crystallins are known to bind Ca2+ and form homodimers and oligomers, the transition metal-binding, trimeric Methallin is a new paradigm for βγ-crystallins. The distinct features of Methallin, such as nickel or iron binding, are also possible imprints of biogeochemical changes during the period of its origin.},
}
@article {pmid28018603,
year = {2017},
author = {Khelaifia, S and Caputo, A and Djossou, F and Raoult, D},
title = {Draft genome sequence of a human-associated isolate of Haloferax alexandrinus strain Arc-hr, an extremely halophilic archaea.},
journal = {New microbes and new infections},
volume = {15},
number = {},
pages = {44-45},
doi = {10.1016/j.nmni.2016.11.012},
pmid = {28018603},
issn = {2052-2975},
abstract = {We report the draft genome sequence of Haloferax alexandrinus strain Arc-hr (CSUR P798), isolated from the human gut of a 10-year-old Amazonian individual. Its 3 893 626 bp genome exhibits a 66.00% GC content. The genome of the strain Arc-hr contains 37 genes identified as ORFans, seven genes associated to halocin and 11 genes associated with polyketide synthases or nonribosomal peptide synthetases.},
}
@article {pmid27998783,
year = {2017},
author = {Ding, J and Lu, YZ and Fu, L and Ding, ZW and Mu, Y and Cheng, SH and Zeng, RJ},
title = {Decoupling of DAMO archaea from DAMO bacteria in a methane-driven microbial fuel cell.},
journal = {Water research},
volume = {110},
number = {},
pages = {112-119},
doi = {10.1016/j.watres.2016.12.006},
pmid = {27998783},
issn = {1879-2448},
mesh = {Anaerobiosis ; Archaea/*genetics ; Bacteria/metabolism ; Bioelectric Energy Sources ; In Situ Hybridization, Fluorescence ; Methane/metabolism ; Methylococcaceae/*metabolism ; Oxidation-Reduction ; },
abstract = {Anaerobic oxidation of methane (AOM) contributes significantly to the global methane sink. Previously, studies of anaerobic methanotrophic (ANME) archaea have been limited as they have not been separable from their bacterial partners during the AOM process because of their dependence on the bacteria. A microbial fuel cell (MFC) is a device capable of directly transforming chemical energy to electrical energy via electrochemical reactions involving biochemical pathways. In this study, decoupling of denitrifying anaerobic methane oxidation (DAMO) archaea and DAMO bacteria was investigated in an microbial fuel cell (MFC) using methane as the fuel. The DAMO fuel cell worked successfully but demonstrated weak electrogenic capability with around 25 mV production. After 45 days' enrichment, the sequencing and fluorescence in situ hybridization results showed the DAMO archaea percentage had increased from 26.96% (inoculum) to 65.77% (electrode biofilm), while the DAMO bacteria percentage decreased from 24.39% to 2.07%. Moreover, the amount of ANME-2d had doubled in the electrode biofilm compared with the inoculum. The sequencing results also showed substantial enrichment of the Ignavibacterium and Geobacter genera. The roles of Ignavibacterium and Geobacter in the MFC system need to be further investigated. Nevertheless, these results illustrate that an MFC device may provide a possible approach to separate DAMO archaea from DAMO bacteria.},
}
@article {pmid27996979,
year = {2017},
author = {Taylor, AE and Giguere, AT and Zoebelein, CM and Myrold, DD and Bottomley, PJ},
title = {Modeling of soil nitrification responses to temperature reveals thermodynamic differences between ammonia-oxidizing activity of archaea and bacteria.},
journal = {The ISME journal},
volume = {11},
number = {4},
pages = {896-908},
doi = {10.1038/ismej.2016.179},
pmid = {27996979},
issn = {1751-7370},
mesh = {Ammonia/chemistry/*metabolism ; Archaea/classification/*metabolism ; Bacteria/classification/*metabolism ; Nitrification ; Oregon ; Oxidation-Reduction ; Soil/*chemistry ; *Soil Microbiology ; Temperature ; },
abstract = {Soil nitrification potential (NP) activities of ammonia-oxidizing archaea and bacteria (AOA and AOB, respectively) were evaluated across a temperature gradient (4-42 °C) imposed upon eight soils from four different sites in Oregon and modeled with both the macromolecular rate theory and the square root growth models to quantify the thermodynamic responses. There were significant differences in response by the dominant AOA and AOB contributing to the NPs. The optimal temperatures (Topt) for AOA- and AOB-supported NPs were significantly different (P<0.001), with AOA having Topt>12 °C greater than AOB. The change in heat capacity associated with the temperature dependence of nitrification (ΔCP‡) was correlated with Topt across the eight soils, and the ΔCP‡ of AOB activity was significantly more negative than that of AOA activity (P<0.01). Model results predicted, and confirmatory experiments showed, a significantly lower minimum temperature (Tmin) and different, albeit very similar, maximum temperature (Tmax) values for AOB than for AOA activity. The results also suggested that there may be different forms of AOA AMO that are active over different temperature ranges with different Tmin, but no evidence of multiple Tmin values within the AOB. Fundamental differences in temperature-influenced properties of nitrification driven by AOA and AOB provides support for the idea that the biochemical processes associated with NH3 oxidation in AOA and AOB differ thermodynamically from each other, and that also might account for the difficulties encountered in attempting to model the response of nitrification to temperature change in soil environments.},
}
@article {pmid27984824,
year = {2017},
author = {Moukhtar, M and Chaar, W and Abdel-Razzak, Z and Khalil, M and Taha, S and Chamieh, H},
title = {ARCPHdb: A comprehensive protein database for SF1 and SF2 helicase from archaea.},
journal = {Computers in biology and medicine},
volume = {80},
number = {},
pages = {185-189},
doi = {10.1016/j.compbiomed.2016.12.004},
pmid = {27984824},
issn = {1879-0534},
mesh = {Archaea ; *Archaeal Proteins ; *Computational Biology ; Database Management Systems ; *Databases, Protein ; *RNA Helicases ; User-Computer Interface ; },
abstract = {PURPOSE: Superfamily 1 and Superfamily 2 helicases, two of the largest helicase protein families, play vital roles in many biological processes including replication, transcription and translation. Study of helicase proteins in the model microorganisms of archaea have largely contributed to the understanding of their function, architecture and assembly. Based on a large phylogenomics approach, we have identified and classified all SF1 and SF2 protein families in ninety five sequenced archaea genomes. Here we developed an online webserver linked to a specialized protein database named ARCPHdb to provide access for SF1 and SF2 helicase families from archaea.<br><br>METHODS: ARCPHdb was implemented using MySQL relational database. Web interfaces were developed using Netbeans. Data were stored according to UniProt accession numbers, NCBI Ref Seq ID, PDB IDs and Entrez Databases.<br><br>RESULTS: A user-friendly interactive web interface has been developed to browse, search and download archaeal helicase protein sequences, their available 3D structure models, and related documentation available in the literature provided by ARCPHdb. The database provides direct links to matching external databases.<br><br>CONCLUSIONS: The ARCPHdb is the first online database to compile all protein information on SF1 and SF2 helicase from archaea in one platform. This database provides essential resource information for all researchers interested in the field.},
}
@article {pmid27976411,
year = {2017},
author = {Paul, SS and Dey, A and Baro, D and Punia, BS},
title = {Comparative community structure of archaea in rumen of buffaloes and cattle.},
journal = {Journal of the science of food and agriculture},
volume = {97},
number = {10},
pages = {3284-3293},
doi = {10.1002/jsfa.8177},
pmid = {27976411},
issn = {1097-0010},
mesh = {Animals ; Archaea/classification/genetics/growth &amp; development/*isolation &amp; purification ; Buffaloes/*microbiology ; Cattle/*microbiology ; *Gastrointestinal Microbiome ; Phylogeny ; Rumen/*microbiology ; },
abstract = {BACKGROUND: Detailed knowledge of the community structure of methanogens is essential for amelioration of methane emission from livestock species. Several studies have indicated that predominant methanogens of buffalo rumen are different from those in cattle. However, predominant genera of methanogens reported by individual studies varied primarily because of limited scope of sampling, sequencing of limited number of sequences and potential PCR bias in individual studies. In this study, the collective comparative diversity of methanogenic archaea in the rumen of cattle and buffaloes was examined by performing a meta-analysis of all the 16S rRNA (rrn) sequences deposited in GenBank.<br><br>RESULTS: Ruminal methanogen sequences of buffalo were clustered into 900 species-level operational taxonomic units (OTUs), and ruminal methanogen sequences of cattle were clustered into 1522 species level OTUs. The number of species-level OTUs shared between cattle and buffaloes was 229 (10.4% of all OTUs), comprising 1746 sequences (27% of the total 6447 sequences). According to taxonomic classification by three different classifiers, Methanobrevibacter was found to be the most predominant genus both in cattle (69-71% of sequences) as well as buffaloes (65.1-68.9% of sequences). Percentage of Methanomicrobium was much higher (P < 0.05) in the case of buffalo (18%) than that of cattle (4.5%). On the other hand, percentages of Methanosphaera- and Methanomassiliicoccus-like methanogens were much higher (P < 0.05) in cattle than in buffaloes.<br><br>CONCLUSION: This study indicated that there is a substantial difference in community structure of ruminal methanogens of cattle and buffaloes. The study has also indicated that the percent of species-level operational taxonomic units shared between cattle and buffalo is very low, and thus host species-specific methane mitigation strategies need to be developed for cattle and buffaloes. © 2016 Society of Chemical Industry.},
}
@article {pmid27966672,
year = {2016},
author = {Golyshina, OV and Kublanov, IV and Tran, H and Korzhenkov, AA and Lünsdorf, H and Nechitaylo, TY and Gavrilov, SN and Toshchakov, SV and Golyshin, PN},
title = {Biology of archaea from a novel family Cuniculiplasmataceae (Thermoplasmata) ubiquitous in hyperacidic environments.},
journal = {Scientific reports},
volume = {6},
number = {},
pages = {39034},
doi = {10.1038/srep39034},
pmid = {27966672},
issn = {2045-2322},
support = {BB/M029085/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Acids/*chemistry ; Archaeal Proteins/genetics/metabolism ; California ; *Ecosystem ; Euryarchaeota/classification/*genetics/metabolism ; Genome, Archaeal/*genetics ; Genomics/methods ; Geography ; Hydrogen-Ion Concentration ; Microscopy, Electron ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Spain ; Thermoplasmales/*genetics/metabolism/ultrastructure ; United Kingdom ; },
abstract = {The order Thermoplasmatales (Euryarchaeota) is represented by the most acidophilic organisms known so far that are poorly amenable to cultivation. Earlier culture-independent studies in Iron Mountain (California) pointed at an abundant archaeal group, dubbed 'G-plasma'. We examined the genomes and physiology of two cultured representatives of a Family Cuniculiplasmataceae, recently isolated from acidic (pH 1-1.5) sites in Spain and UK that are 16S rRNA gene sequence-identical with 'G-plasma'. Organisms had largest genomes among Thermoplasmatales (1.87-1.94 Mbp), that shared 98.7-98.8% average nucleotide identities between themselves and 'G-plasma' and exhibited a high genome conservation even within their genomic islands, despite their remote geographical localisations. Facultatively anaerobic heterotrophs, they possess an ancestral form of A-type terminal oxygen reductase from a distinct parental clade. The lack of complete pathways for biosynthesis of histidine, valine, leucine, isoleucine, lysine and proline pre-determines the reliance on external sources of amino acids and hence the lifestyle of these organisms as scavengers of proteinaceous compounds from surrounding microbial community members. In contrast to earlier metagenomics-based assumptions, isolates were S-layer-deficient, non-motile, non-methylotrophic and devoid of iron-oxidation despite the abundance of methylotrophy substrates and ferrous iron in situ, which underlines the essentiality of experimental validation of bioinformatic predictions.},
}
@article {pmid27920295,
year = {2017},
author = {Rodionov, DA and Leyn, SA and Li, X and Rodionova, IA},
title = {A Novel Transcriptional Regulator Related to Thiamine Phosphate Synthase Controls Thiamine Metabolism Genes in Archaea.},
journal = {Journal of bacteriology},
volume = {199},
number = {4},
pages = {},
doi = {10.1128/JB.00743-16},
pmid = {27920295},
issn = {1098-5530},
mesh = {Alkyl and Aryl Transferases/genetics/*metabolism ; Archaea/*enzymology/genetics/metabolism ; Computational Biology ; Gene Expression Regulation, Archaeal/*physiology ; Gene Expression Regulation, Enzymologic/*physiology ; Genome, Archaeal/genetics ; Genomics ; Thiamine/*metabolism ; Thiamine Pyrophosphate/*metabolism ; },
abstract = {Thiamine (vitamin B1) is a precursor of thiamine pyrophosphate (TPP), an essential coenzyme in the central metabolism of all living organisms. Bacterial thiamine biosynthesis and salvage genes are controlled at the RNA level by TPP-responsive riboswitches. In Archaea, TPP riboswitches are restricted to the Thermoplasmatales order. Mechanisms of transcriptional control of thiamine genes in other archaeal lineages remain unknown. Using the comparative genomics approach, we identified a novel family of transcriptional regulators (named ThiR) controlling thiamine biosynthesis and transport genes in diverse lineages in the Crenarchaeota phylum as well as in the Halobacteria and Thermococci classes of the Euryarchaeota ThiR regulators are composed of an N-terminal DNA-binding domain and a C-terminal ligand-binding domain, which is similar to the archaeal thiamine phosphate synthase ThiN. By using comparative genomics, we predicted ThiR-binding DNA motifs and reconstructed ThiR regulons in 67 genomes representing all above-mentioned lineages. The predicted ThiR-binding motifs are characterized by palindromic symmetry with several distinct lineage-specific consensus sequences. In addition to thiamine biosynthesis genes, the reconstructed ThiR regulons include various transporters for thiamine and its precursors. Bioinformatics predictions were experimentally validated by in vitro DNA-binding assays with the recombinant ThiR protein from the hyperthermophilic archaeon Metallosphaera yellowstonensis MK1. Thiamine phosphate and, to some extent, TPP and hydroxyethylthiazole phosphate were required for the binding of ThiR to its DNA targets, suggesting that ThiR is derepressed by limitation of thiamine phosphates. The thiamine phosphate-binding residues previously identified in ThiN are highly conserved in ThiR regulators, suggesting a conserved mechanism for effector recognition.<br><br>IMPORTANCE: Thiamine pyrophosphate is a cofactor for many essential enzymes for glucose and energy metabolism. Thiamine or vitamin B1 biosynthesis and its transcriptional regulation in Archaea are poorly understood. We applied the comparative genomics approach to identify a novel family of regulators for the transcriptional control of thiamine metabolism genes in Archaea and reconstructed the respective regulons. The predicted ThiR regulons in archaeal genomes control the majority of thiamine biosynthesis genes. The reconstructed regulon content suggests that numerous uptake transporters for thiamine and/or its precursors are encoded in archaeal genomes. The ThiR regulon was experimentally validated by DNA-binding assays with Metallosphaera spp. These discoveries contribute to our understanding of metabolic and regulatory networks involved in vitamin homeostasis in diverse lineages of Archaea.},
}
@article {pmid27919704,
year = {2017},
author = {Kurt-Kızıldoğan, A and Abanoz, B and Okay, S},
title = {Global transcriptome analysis of Halolamina sp. to decipher the salt tolerance in extremely halophilic archaea.},
journal = {Gene},
volume = {601},
number = {},
pages = {56-64},
doi = {10.1016/j.gene.2016.11.042},
pmid = {27919704},
issn = {1879-0038},
mesh = {Archaeal Proteins/genetics/metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Archaeal ; Genome, Archaeal ; Halobacteriales/*genetics/isolation &amp; purification/*metabolism ; RNA, Archaeal/genetics ; Salinity ; Salt-Tolerance/*genetics ; Sequence Analysis, RNA ; Transcriptome ; },
abstract = {Extremely halophilic archaea survive in the hypersaline environments such as salt lakes or salt mines. Therefore, these microorganisms are good sources to investigate the molecular mechanisms underlying the tolerance to high salt concentrations. In this study, a global transcriptome analysis was conducted in an extremely halophilic archaeon, Halolamina sp. YKT1, isolated from a salt mine in Turkey. A comparative RNA-seq analysis was performed using YKT1 isolate grown either at 2.7M NaCl or 5.5M NaCl concentrations. A total of 2149 genes were predicted to be up-regulated and 1638 genes were down-regulated in the presence of 5.5M NaCl. The salt tolerance of Halolamina sp. YKT1 involves the up-regulation of genes related with membrane transporters, CRISPR-Cas systems, osmoprotectant solutes, oxidative stress proteins, and iron metabolism. On the other hand, the genes encoding the proteins involved in DNA replication, transcription, translation, mismatch and nucleotide excision repair were down-regulated. The RNA-seq data were verified for seven up-regulated genes as well as six down-regulated genes via qRT-PCR analysis. This comprehensive transcriptome analysis showed that the halophilic archaeon canalizes its energy towards keeping the intracellular osmotic balance minimizing the production of nucleic acids and peptides.},
}
@article {pmid27879020,
year = {2017},
author = {Kuhn, A and Kiefer, D},
title = {Membrane protein insertase YidC in bacteria and archaea.},
journal = {Molecular microbiology},
volume = {103},
number = {4},
pages = {590-594},
doi = {10.1111/mmi.13586},
pmid = {27879020},
issn = {1365-2958},
mesh = {Cell Membrane/metabolism ; Escherichia coli/genetics/*metabolism ; Escherichia coli Proteins/genetics/*metabolism ; *Hydrophobic and Hydrophilic Interactions ; Membrane Transport Proteins/genetics/*metabolism ; Methanocaldococcus/genetics/*metabolism ; SEC Translocation Channels/genetics ; },
abstract = {The insertion of proteins into the prokaryotic plasma membrane is catalyzed by translocases and insertases. On one hand, the Sec translocase operates as a transmembrane channel that can open laterally to first bind and then release the hydrophobic segments of a substrate protein into the lipid bilayer. On the other hand, YidC insertases interact with their substrates in a groove-like structure at an amphiphilic protein-lipid interface thus allowing the transmembrane segments of the substrate to slide into the lipid bilayer. The recently published high-resolution structures of YidC provide new mechanistic insights of how transmembrane proteins achieve the transition from an aqueous environment in the cytoplasm to the hydrophobic lipid bilayer environment of the membrane.},
}
@article {pmid27864137,
year = {2017},
author = {Bharathi, M and Chellapandi, P},
title = {Intergenomic evolution and metabolic cross-talk between rumen and thermophilic autotrophic methanogenic archaea.},
journal = {Molecular phylogenetics and evolution},
volume = {107},
number = {},
pages = {293-304},
doi = {10.1016/j.ympev.2016.11.008},
pmid = {27864137},
issn = {1095-9513},
mesh = {Animals ; Archaea/*genetics ; *Autotrophic Processes ; DNA Replication/genetics ; *Evolution, Molecular ; Genetic Markers ; Genetic Variation ; *Genome, Archaeal ; Metabolic Networks and Pathways/genetics ; Methane/*metabolism ; Methanobacteriaceae/genetics ; Phylogeny ; Rumen/*microbiology ; Synteny ; },
abstract = {Methanobrevibacter ruminantium M1 (MRU) is a rumen methanogenic archaean that can be able to utilize formate and CO2/H2 as growth substrates. Extensive analysis on the evolutionary genomic contexts considered herein to unravel its intergenomic relationship and metabolic adjustment acquired from the genomic content of Methanothermobacter thermautotrophicus ΔH. We demonstrated its intergenomic distance, genome function, synteny homologs and gene families, origin of replication, and methanogenesis to reveal the evolutionary relationships between Methanobrevibacter and Methanothermobacter. Comparison of the phylogenetic and metabolic markers was suggested for its archaeal metabolic core lineage that might have evolved from Methanothermobacter. Orthologous genes involved in its hydrogenotrophic methanogenesis might be acquired from intergenomic ancestry of Methanothermobacter via Methanobacterium formicicum. Formate dehydrogenase (fdhAB) coding gene cluster and carbon monoxide dehydrogenase (cooF) coding gene might have evolved from duplication events within Methanobrevibacter-Methanothermobacter lineage, and fdhCD gene cluster acquired from bacterial origins. Genome-wide metabolic survey found the existence of four novel pathways viz. l-tyrosine catabolism, mevalonate pathway II, acyl-carrier protein metabolism II and glutathione redox reactions II in MRU. Finding of these pathways suggested that MRU has shown a metabolic potential to tolerate molecular oxygen, antimicrobial metabolite biosynthesis and atypical lipid composition in cell wall, which was acquainted by metabolic cross-talk with mammalian bacterial origins. We conclude that coevolution of genomic contents between Methanobrevibacter and Methanothermobacter provides a clue to understand the metabolic adaptation of MRU in the rumen at different environmental niches.},
}
@article {pmid27852927,
year = {2016},
author = {Urbonavičius, J and Rutkienė, R and Lopato, A and Tauraitė, D and Stankevičiūtė, J and Aučynaitė, A and Kaliniene, L and van Tilbeurgh, H and Meškys, R},
title = {Evolution of tRNAPhe:imG2 methyltransferases involved in the biosynthesis of wyosine derivatives in Archaea.},
journal = {RNA (New York, N.Y.)},
volume = {22},
number = {12},
pages = {1871-1883},
doi = {10.1261/rna.057059.116},
pmid = {27852927},
issn = {1469-9001},
mesh = {Amino Acid Sequence ; Archaea/*metabolism ; Guanosine/*analogs &amp; derivatives/biosynthesis ; Methyltransferases/chemistry/*metabolism ; RNA, Transfer, Phe/chemistry/*metabolism ; Sequence Homology, Amino Acid ; },
abstract = {Tricyclic wyosine derivatives are found at position 37 of eukaryotic and archaeal tRNAPhe In Archaea, the intermediate imG-14 is targeted by three different enzymes that catalyze the formation of yW-86, imG, and imG2. We have suggested previously that a peculiar methyltransferase (aTrm5a/Taw22) likely catalyzes two distinct reactions: N1-methylation of guanosine to yield m1G; and C7-methylation of imG-14 to yield imG2. Here we show that the recombinant aTrm5a/Taw22-like enzymes from both Pyrococcus abyssi and Nanoarchaeum equitans indeed possess such dual specificity. We also show that substitutions of individual conservative amino acids of P. abyssi Taw22 (P260N, E173A, and R174A) have a differential effect on the formation of m1G/imG2, while replacement of R134, F165, E213, and P262 with alanine abolishes the formation of both derivatives of G37. We further demonstrate that aTrm5a-type enzyme SSO2439 from Sulfolobus solfataricus, which has no N1-methyltransferase activity, exhibits C7-methyltransferase activity, thereby producing imG2 from imG-14. We thus suggest renaming such aTrm5a methyltransferases as Taw21 to distinguish between monofunctional and bifunctional aTrm5a enzymes.},
}
@article {pmid27846569,
year = {2016},
author = {Zheng, K and Ngo, PD and Owens, VL and Yang, XP and Mansoorabadi, SO},
title = {The biosynthetic pathway of coenzyme F430 in methanogenic and methanotrophic archaea.},
journal = {Science (New York, N.Y.)},
volume = {354},
number = {6310},
pages = {339-342},
doi = {10.1126/science.aag2947},
pmid = {27846569},
issn = {1095-9203},
mesh = {Amides/metabolism ; Archaeal Proteins/genetics/*metabolism ; Biosynthetic Pathways ; Genes, Archaeal ; Genetic Loci ; Genomics ; Metalloporphyrins/genetics/*metabolism ; Methane/*metabolism ; Methanosarcina/*enzymology/genetics ; Nickel/metabolism ; Oxidoreductases/genetics/*metabolism ; Uroporphyrins/*metabolism ; },
abstract = {Methyl-coenzyme M reductase (MCR) is the key enzyme of methanogenesis and anaerobic methane oxidation. The activity of MCR is dependent on the unique nickel-containing tetrapyrrole known as coenzyme F430. We used comparative genomics to identify the coenzyme F430 biosynthesis (cfb) genes and characterized the encoded enzymes from Methanosarcina acetivorans C2A. The pathway involves nickelochelation by a nickel-specific chelatase, followed by amidation to form Ni-sirohydrochlorin a,c-diamide. Next, a primitive homolog of nitrogenase mediates a six-electron reduction and γ-lactamization reaction before a Mur ligase homolog forms the six-membered carbocyclic ring in the final step of the pathway. These data show that coenzyme F430 can be synthesized from sirohydrochlorin using Cfb enzymes produced heterologously in a nonmethanogen host and identify several targets for inhibitors of biological methane formation.},
}
@article {pmid27829818,
year = {2016},
author = {Rodrigues, T and Belmok, A and Catão, E and Kyaw, CM},
title = {Archaea in Natural and Impacted Brazilian Environments.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2016},
number = {},
pages = {1259608},
doi = {10.1155/2016/1259608},
pmid = {27829818},
issn = {1472-3654},
mesh = {Archaea/*classification/*isolation &amp; purification ; *Biodiversity ; Brazil ; *Environmental Microbiology ; },
abstract = {In recent years, archaeal diversity surveys have received increasing attention. Brazil is a country known for its natural diversity and variety of biomes, which makes it an interesting sampling site for such studies. However, archaeal communities in natural and impacted Brazilian environments have only recently been investigated. In this review, based on a search on the PubMed database on the last week of April 2016, we present and discuss the results obtained in the 51 studies retrieved, focusing on archaeal communities in water, sediments, and soils of different Brazilian environments. We concluded that, in spite of its vast territory and biomes, the number of publications focusing on archaeal detection and/or characterization in Brazil is still incipient, indicating that these environments still represent a great potential to be explored.},
}
@article {pmid27815273,
year = {2017},
author = {Ballen-Segura, M and Felip, M and Catalan, J},
title = {Some Mixotrophic Flagellate Species Selectively Graze on Archaea.},
journal = {Applied and environmental microbiology},
volume = {83},
number = {2},
pages = {},
doi = {10.1128/AEM.02317-16},
pmid = {27815273},
issn = {1098-5336},
mesh = {*Archaea ; *Bacteria ; Chrysophyta/*physiology ; Cryptophyta/*physiology ; *Food Chain ; In Situ Hybridization, Fluorescence ; Lakes/microbiology ; Plankton/*physiology ; Spain ; },
abstract = {Many phototrophic flagellates ingest prokaryotes. This mixotrophic trait becomes a critical aspect of the microbial loop in planktonic food webs because of the typical high abundance of these flagellates. Our knowledge of their selective feeding upon different groups of prokaryotes, particularly under field conditions, is still quite limited. In this study, we investigated the feeding behavior of three species (Rhodomonas sp., Cryptomonas ovata, and Dinobryon cylindricum) via their food vacuole content in field populations of a high mountain lake. We used the catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) protocol with probes specific for the domain Archaea and three groups of Eubacteria: Betaproteobacteria, Actinobacteria, and Cytophaga-Flavobacteria of Bacteroidetes Our results provide field evidence that contrasting selective feeding exists between coexisting mixotrophic flagellates under the same environmental conditions and that some prokaryotic groups may be preferentially impacted by phagotrophic pressure in aquatic microbial food webs. In our study, Archaea were the preferred prey, chiefly in the case of Rhodomonas sp., which rarely fed on any other prokaryotic group. In general, prey selection did not relate to prey size among the grazed groups. However, Actinobacteria, which were clearly avoided, mostly showed a size of <0.5 μm, markedly smaller than cells from the other groups.<br><br>IMPORTANCE: That mixotrophic flagellates are not randomly feeding in the main prokaryotic groups under field conditions is a pioneer finding in species-specific behavior that paves the way for future studies according to this new paradigm. The particular case that Archaea were preferentially affected in the situation studied shows that phagotrophic pressure cannot be disregarded when considering the distribution of this group in freshwater oligotrophic systems.},
}
@article {pmid27810876,
year = {2017},
author = {Miragoli, F and Federici, S and Ferrari, S and Minuti, A and Rebecchi, A and Bruzzese, E and Buccigrossi, V and Guarino, A and Callegari, ML},
title = {Impact of cystic fibrosis disease on archaea and bacteria composition of gut microbiota.},
journal = {FEMS microbiology ecology},
volume = {93},
number = {2},
pages = {},
doi = {10.1093/femsec/fiw230},
pmid = {27810876},
issn = {1574-6941},
mesh = {Adolescent ; Adult ; Archaea/classification/genetics ; Bacteria/classification/genetics ; *Biodiversity ; Child ; Colon ; Cystic Fibrosis/*microbiology ; Euryarchaeota/genetics ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Intestines/*microbiology/physiopathology ; Male ; Microbiota/genetics ; Real-Time Polymerase Chain Reaction ; Young Adult ; },
abstract = {Cystic fibrosis is often associated with intestinal inflammation due to several factors, including altered gut microbiota composition. In this study, we analyzed the fecal microbiota among patients with cystic fibrosis of 10-22 years of age, and compared the findings with age-matched healthy subjects. The participating patients included 14 homozygotes and 14 heterozygotes with the delF508 mutation, and 2 heterozygotes presenting non-delF508 mutations. We used PCR-DGGE and qPCR to analyze the presence of bacteria, archaea and sulfate-reducing bacteria. Overall, our findings confirmed disruption of the cystic fibrosis gut microbiota. Principal component analysis of the qPCR data revealed no differences between homozygotes and heterozygotes, while both groups were distinct from healthy subjects who showed higher biodiversity. Archaea were under the detection limit in all homozygotes subjects, whereas methanogens were detected in 62% of both cystic fibrosis heterozygotes and healthy subjects. Our qPCR results revealed a low frequency of sulfate-reducing bacteria in the homozygote (13%) and heterozygote (13%) patients with cystic fibrosis compared with healthy subjects (87.5%). This is a pioneer study showing that patients with cystic fibrosis exhibit significant reduction of H2-consuming microorganisms, which could increase hydrogen accumulation in the colon and the expulsion of this gas through non-microbial routes.},
}
@article {pmid27795311,
year = {2017},
author = {Rodrigues, MV and Borges, N and Santos, H},
title = {Glycerol Phosphate Cytidylyltransferase Stereospecificity Is Key to Understanding the Distinct Stereochemical Compositions of Glycerophosphoinositol in Bacteria and Archaea.},
journal = {Applied and environmental microbiology},
volume = {83},
number = {1},
pages = {},
doi = {10.1128/AEM.02462-16},
pmid = {27795311},
issn = {1098-5336},
mesh = {Archaeoglobus/*enzymology/genetics/metabolism ; Bacteria/*enzymology/genetics/metabolism ; Cytidine Triphosphate/chemistry/*metabolism ; Glycerol/metabolism ; Inositol Phosphates/*chemistry/metabolism ; Magnetic Resonance Spectroscopy ; Molecular Conformation ; Nucleotidyltransferases/chemistry/*metabolism ; Recombinant Proteins/metabolism ; Stereoisomerism ; Substrate Specificity ; },
abstract = {Glycerophosphoinositol (GPI) is a compatible solute present in a few hyperthermophiles. Interestingly, different GPI stereoisomers accumulate in Bacteria and Archaea, and the basis for this domain-dependent specificity was investigated herein. The archaeon Archaeoglobus fulgidus and the bacterium Aquifex aeolicus were used as model organisms. The synthesis of GPI involves glycerol phosphate cytidylyltransferase (GCT), which catalyzes the production of CDP-glycerol from CTP and glycerol phosphate, and di-myo-inositol phosphate-phosphate synthase (DIPPS), catalyzing the formation of phosphorylated GPI from CDP-glycerol and l-myo-inositol 1-phosphate. DIPPS of A. fulgidus recognized the two CDP-glycerol stereoisomers similarly. This feature and the ability of 31P nuclear magnetic resonance (NMR) to distinguish the GPI diastereomers provided a means to study the stereospecificity of GCTs. The AF1418 gene and genes aq_185 and aq_1368 are annotated as putative GCT genes in the genomes of A. fulgidus and Aq. aeolicus, respectively. The functions of these genes were determined by assaying the activity of the respective recombinant proteins: AQ1368 and AQ185 are GCTs, while AF1418 has flavin adenine dinucleotide (FAD) synthetase activity. AQ185 is absolutely specific for sn-glycerol 3-phosphate, while AQ1368 recognizes the two enantiomers but has a 2:1 preference for sn-glycerol 3-phosphate. In contrast, the partially purified A. fulgidus GCT uses sn-glycerol 1-phosphate preferentially (4:1). Significantly, the predominant GPI stereoforms found in the bacterium and the archaeon reflect the distinct stereospecificities of the respective GCTs: i.e., A. fulgidus accumulates predominantly sn-glycero-1-phospho-3-l-myo-inositol, while Aq. aeolicus accumulates sn-glycero-3-phospho-3-l-myo-inositol.<br><br>IMPORTANCE: Compatible solutes of hyperthermophiles show high efficacy in thermal protection of proteins in comparison with solutes typical of mesophiles; therefore, they are potentially useful in several biotechnological applications. Glycerophosphoinositol (GPI) is synthesized from CDP-glycerol and l-myo-inositol 1-phosphate in a few hyperthermophiles. In this study, the molecular configuration of the GPI stereoisomers accumulated by members of the Bacteria and Archaea was established. The stereospecificity of glycerol phosphate cytidylyltransferase (GCT), the enzyme catalyzing the synthesis of CDP-glycerol, is crucial to the stereochemistry of GPI. However, the stereospecific properties of GCTs have not been investigated thus far. We devised a method to characterize GCT stereospecificity which does not require sn-glycerol 1-phosphate, a commercially unavailable substrate. This led us to understand the biochemical basis for the distinct GPI stereoisomer composition observed in archaea and bacteria.},
}
@article {pmid27749816,
year = {2016},
author = {Laso-Pérez, R and Wegener, G and Knittel, K and Widdel, F and Harding, KJ and Krukenberg, V and Meier, DV and Richter, M and Tegetmeyer, HE and Riedel, D and Richnow, HH and Adrian, L and Reemtsma, T and Lechtenfeld, OJ and Musat, F},
title = {Thermophilic archaea activate butane via alkyl-coenzyme M formation.},
journal = {Nature},
volume = {539},
number = {7629},
pages = {396-401},
doi = {10.1038/nature20152},
pmid = {27749816},
issn = {1476-4687},
mesh = {Alkylation ; Anaerobiosis ; Archaea/genetics/*metabolism ; Archaeal Proteins/chemistry/genetics/metabolism ; Biocatalysis ; Butanes/*metabolism ; Evolution, Molecular ; Mesna/*chemistry/*metabolism ; Oxidation-Reduction ; Sulfates/metabolism ; Temperature ; },
abstract = {The anaerobic formation and oxidation of methane involve unique enzymatic mechanisms and cofactors, all of which are believed to be specific for C1-compounds. Here we show that an anaerobic thermophilic enrichment culture composed of dense consortia of archaea and bacteria apparently uses partly similar pathways to oxidize the C4 hydrocarbon butane. The archaea, proposed genus 'Candidatus Syntrophoarchaeum', show the characteristic autofluorescence of methanogens, and contain highly expressed genes encoding enzymes similar to methyl-coenzyme M reductase. We detect butyl-coenzyme M, indicating archaeal butane activation analogous to the first step in anaerobic methane oxidation. In addition, Ca. Syntrophoarchaeum expresses the genes encoding β-oxidation enzymes, carbon monoxide dehydrogenase and reversible C1 methanogenesis enzymes. This allows for the complete oxidation of butane. Reducing equivalents are seemingly channelled to HotSeep-1, a thermophilic sulfate-reducing partner bacterium known from the anaerobic oxidation of methane. Genes encoding 16S rRNA and methyl-coenzyme M reductase similar to those identifying Ca. Syntrophoarchaeum were repeatedly retrieved from marine subsurface sediments, suggesting that the presented activation mechanism is naturally widespread in the anaerobic oxidation of short-chain hydrocarbons.},
}
@article {pmid27791189,
year = {2016},
author = {Liu, Y and Vinyard, DJ and Reesbeck, ME and Suzuki, T and Manakongtreecheep, K and Holland, PL and Brudvig, GW and Söll, D},
title = {A [3Fe-4S] cluster is required for tRNA thiolation in archaea and eukaryotes.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {},
number = {},
pages = {},
doi = {10.1073/pnas.1615732113},
pmid = {27791189},
issn = {1091-6490},
support = {R01 GM022854/GM/NIGMS NIH HHS/United States ; R01 GM065313/GM/NIGMS NIH HHS/United States ; R37 GM022854/GM/NIGMS NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; },
abstract = {The sulfur-containing nucleosides in transfer RNA (tRNAs) are present in all three domains of life; they have critical functions for accurate and efficient translation, such as tRNA structure stabilization and proper codon recognition. The tRNA modification enzymes ThiI (in bacteria and archaea) and Ncs6 (in archaea and eukaryotic cytosols) catalyze the formation of 4-thiouridine (s4U) and 2-thiouridine (s2U), respectively. The ThiI homologs were proposed to transfer sulfur via cysteine persulfide enzyme adducts, whereas the reaction mechanism of Ncs6 remains unknown. Here we show that ThiI from the archaeon Methanococcus maripaludis contains a [3Fe-4S] cluster that is essential for its tRNA thiolation activity. Furthermore, the archaeal and eukaryotic Ncs6 homologs as well as phosphoseryl-tRNA (Sep-tRNA):Cys-tRNA synthase (SepCysS), which catalyzes the Sep-tRNA to Cys-tRNA conversion in methanogens, also possess a [3Fe-4S] cluster similar to the methanogenic archaeal ThiI. These results suggest that the diverse tRNA thiolation processes in archaea and eukaryotic cytosols share a common mechanism dependent on a [3Fe-4S] cluster for sulfur transfer.},
}
@article {pmid27791118,
year = {2016},
author = {Ettwig, KF and Zhu, B and Speth, D and Keltjens, JT and Jetten, MS and Kartal, B},
title = {Archaea catalyze iron-dependent anaerobic oxidation of methane.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {},
number = {},
pages = {},
doi = {10.1073/pnas.1609534113},
pmid = {27791118},
issn = {1091-6490},
support = {339880//European Research Council/International ; },
abstract = {Anaerobic oxidation of methane (AOM) is crucial for controlling the emission of this potent greenhouse gas to the atmosphere. Nitrite-, nitrate-, and sulfate-dependent methane oxidation is well-documented, but AOM coupled to the reduction of oxidized metals has so far been demonstrated only in environmental samples. Here, using a freshwater enrichment culture, we show that archaea of the order Methanosarcinales, related to &quot;Candidatus Methanoperedens nitroreducens,&quot; couple the reduction of environmentally relevant forms of Fe3+ and Mn4+ to the oxidation of methane. We obtained an enrichment culture of these archaea under anaerobic, nitrate-reducing conditions with a continuous supply of methane. Via batch incubations using [13C]methane, we demonstrated that soluble ferric iron (Fe3+, as Fe-citrate) and nanoparticulate forms of Fe3+ and Mn4+ supported methane-oxidizing activity. CO2 and ferrous iron (Fe2+) were produced in stoichiometric amounts. Our study connects the previous finding of iron-dependent AOM to microorganisms detected in numerous habitats worldwide. Consequently, it enables a better understanding of the interaction between the biogeochemical cycles of iron and methane.},
}
@article {pmid27137126,
year = {2016},
author = {Wrighton, KC and Castelle, CJ and Varaljay, VA and Satagopan, S and Brown, CT and Wilkins, MJ and Thomas, BC and Sharon, I and Williams, KH and Tabita, FR and Banfield, JF},
title = {RubisCO of a nucleoside pathway known from Archaea is found in diverse uncultivated phyla in bacteria.},
journal = {The ISME journal},
volume = {10},
number = {11},
pages = {2702-2714},
doi = {10.1038/ismej.2016.53},
pmid = {27137126},
issn = {1751-7370},
support = {R01 GM095742/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/genetics/growth &amp; development/isolation &amp; purification/*metabolism ; Archaeal Proteins/genetics/*metabolism ; Bacteria/genetics/growth &amp; development/isolation &amp; purification/*metabolism ; Bacterial Proteins/genetics/metabolism ; Fermentation ; Metagenomics ; Molecular Sequence Data ; Nucleosides/*metabolism ; Phylogeny ; Ribulose-Bisphosphate Carboxylase/genetics ; },
abstract = {Metagenomic studies recently uncovered form II/III RubisCO genes, originally thought to only occur in archaea, from uncultivated bacteria of the candidate phyla radiation (CPR). There are no isolated CPR bacteria and these organisms are predicted to have limited metabolic capacities. Here we expand the known diversity of RubisCO from CPR lineages. We report a form of RubisCO, distantly similar to the archaeal form III RubisCO, in some CPR bacteria from the Parcubacteria (OD1), WS6 and Microgenomates (OP11) phyla. In addition, we significantly expand the Peregrinibacteria (PER) II/III RubisCO diversity and report the first II/III RubisCO sequences from the Microgenomates and WS6 phyla. To provide a metabolic context for these RubisCOs, we reconstructed near-complete (>93%) PER genomes and the first closed genome for a WS6 bacterium, for which we propose the phylum name Dojkabacteria. Genomic and bioinformatic analyses suggest that the CPR RubisCOs function in a nucleoside pathway similar to that proposed in Archaea. Detection of form II/III RubisCO and nucleoside metabolism gene transcripts from a PER supports the operation of this pathway in situ. We demonstrate that the PER form II/III RubisCO is catalytically active, fixing CO2 to physiologically complement phototrophic growth in a bacterial photoautotrophic RubisCO deletion strain. We propose that the identification of these RubisCOs across a radiation of obligately fermentative, small-celled organisms hints at a widespread, simple metabolic platform in which ribose may be a prominent currency.},
}
@article {pmid27771364,
year = {2016},
author = {Loder, AJ and Han, Y and Hawkins, AB and Lian, H and Lipscomb, GL and Schut, GJ and Keller, MW and Adams, MWW and Kelly, RM},
title = {Reaction kinetic analysis of the 3-hydroxypropionate/4-hydroxybutyrate CO2 fixation cycle in extremely thermoacidophilic archaea.},
journal = {Metabolic engineering},
volume = {38},
number = {},
pages = {446-463},
doi = {10.1016/j.ymben.2016.10.009},
pmid = {27771364},
issn = {1096-7184},
support = {T32 GM008776/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/metabolism ; Carbon Dioxide/*metabolism ; Extremophiles/metabolism ; Hydroxybutyrates/*metabolism ; Kinetics ; Lactic Acid/*analogs &amp; derivatives/metabolism ; Metabolic Clearance Rate ; Metabolic Flux Analysis/*methods ; Metabolic Networks and Pathways/*physiology ; *Models, Biological ; Signal Transduction/physiology ; Sulfolobaceae/*metabolism ; },
abstract = {The 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle fixes CO2 in extremely thermoacidophilic archaea and holds promise for metabolic engineering because of its thermostability and potentially rapid pathway kinetics. A reaction kinetics model was developed to examine the biological and biotechnological attributes of the 3HP/4HB cycle as it operates in Metallosphaera sedula, based on previous information as well as on kinetic parameters determined here for recombinant versions of five of the cycle enzymes (malonyl-CoA/succinyl-CoA reductase, 3-hydroxypropionyl-CoA synthetase, 3-hydroxypropionyl-CoA dehydratase, acryloyl-CoA reductase, and succinic semialdehyde reductase). The model correctly predicted previously observed features of the cycle: the 35-65% split of carbon flux through the acetyl-CoA and succinate branches, the high abundance and relative ratio of acetyl-CoA/propionyl-CoA carboxylase (ACC) and MCR, and the significance of ACC and hydroxybutyryl-CoA synthetase (HBCS) as regulated control points for the cycle. The model was then used to assess metabolic engineering strategies for incorporating CO2 into chemical intermediates and products of biotechnological importance: acetyl-CoA, succinate, and 3-hydroxypropionate.},
}
@article {pmid27771305,
year = {2016},
author = {Walter, ME and Ortiz, A and Sondgeroth, C and Sindt, NM and Duszenko, N and Catlett, JL and Zhou, Y and Valloppilly, S and Anderson, C and Fernando, S and Buan, NR},
title = {High-throughput mutation, selection, and phenotype screening of mutant methanogenic archaea.},
journal = {Journal of microbiological methods},
volume = {131},
number = {},
pages = {113-121},
doi = {10.1016/j.mimet.2016.10.010},
pmid = {27771305},
issn = {1872-8359},
mesh = {Acetates/metabolism ; Archaea/*genetics/*isolation &amp; purification/metabolism/*radiation effects ; DNA, Archaeal/genetics/radiation effects ; Genes, Archaeal ; High-Throughput Screening Assays/*methods ; Methane/metabolism ; Methanol/metabolism ; Methanosarcina/genetics/growth &amp; development/radiation effects ; Methyltransferases/genetics ; Microbial Viability/radiation effects ; Mutagenesis/radiation effects ; *Phenotype ; Point Mutation/*radiation effects ; *Ultraviolet Rays ; },
abstract = {Bacterial and archaeal genomes can contain 30% or more hypothetical genes with no predicted function. Phylogenetically deep-branching microbes, such as methane-producing archaea (methanogens), contain up to 50% genes with unknown function. In order to formulate hypotheses about the function of hypothetical gene functions in the strict anaerobe, Methanosarcina acetivorans, we have developed high-throughput anaerobic techniques to UV mutagenize, screen, and select for mutant strains in 96-well plates. Using these approaches we have isolated 10 mutant strains that exhibit a variety of physiological changes including increased or decreased growth rate relative to the parent strain when cells use methanol and/or acetate as carbon and energy sources. This method provides an avenue for the first step in identifying new gene functions: associating a genetic mutation with a reproducible phenotype. Mutations in bona fide methanogenesis genes such as corrinoid methyltransferases and proton-translocating F420H2:methanophenazine oxidoreductase (Fpo) were also generated, opening the door to in vivo functional complementation experiments. Irradiation-based mutagenesis such as from ultraviolet (UV) light, combined with modern genome sequencing, is a useful procedure to discern systems-level gene function in prokaryote taxa that can be axenically cultured but which may be resistant to chemical mutagens.},
}
@article {pmid27752237,
year = {2016},
author = {Sarcinelli, C and Fiorentino, G and Pizzo, E and Bartolucci, S and Limauro, D},
title = {Discovering Antioxidant Molecules in the Archaea Domain: Peroxiredoxin Bcp1 from Sulfolobus solfataricus Protects H9c2 Cardiomyoblasts from Oxidative Stress.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2016},
number = {},
pages = {7424870},
doi = {10.1155/2016/7424870},
pmid = {27752237},
issn = {1472-3654},
mesh = {Animals ; Antioxidants/*isolation &amp; purification/*metabolism ; Apoptosis ; Cell Line ; Hydrogen Peroxide/metabolism/toxicity ; Hydrogen-Ion Concentration ; Myocytes, Cardiac/*drug effects/physiology ; Oxidation-Reduction ; *Oxidative Stress ; Peroxiredoxins/genetics/*isolation &amp; purification/*metabolism ; Rats ; Sulfolobus solfataricus/*enzymology/genetics ; Temperature ; },
abstract = {Peroxiredoxins (Prxs) are ubiquitous thiol peroxidases that are involved in the reduction of peroxides. It has been reported that prokaryotic Prxs generally show greater structural robustness than their eukaryotic counterparts, making them less prone to inactivation by overoxidation. This difference has inspired the search for new antioxidants from prokaryotic sources that can be used as possible therapeutic biodrugs. Bacterioferritin comigratory proteins (Bcps) of the hyperthermophilic archaeon Sulfolobus solfataricus that belong to the Prx family have recently been characterized. One of these proteins, Bcp1, was chosen to determine its antioxidant effects in H9c2 rat cardiomyoblast cells. Bcp1 activity was measured in vitro under physiological temperature and pH conditions that are typical of mammalian cells; the yeast thioredoxin reductase (yTrxR)/thioredoxin (yTrx) reducing system was used to evaluate enzyme activity. A TAT-Bcp1 fusion protein was constructed to allow its internalization and verify the effect of Bcp1 on H9c2 rat cardiomyoblasts subjected to oxidative stress. The results reveal that TAT-Bcp1 is not cytotoxic and inhibits H2O2-induced apoptosis in H9c2 cells by reducing the H2O2 content inside these cells.},
}
@article {pmid27729650,
year = {2016},
author = {Du Toit, A},
title = {Archaeal genomics: Divergent methanogenic archaea.},
journal = {Nature reviews. Microbiology},
volume = {14},
number = {11},
pages = {667},
doi = {10.1038/nrmicro.2016.156},
pmid = {27729650},
issn = {1740-1534},
}
@article {pmid27725793,
year = {2016},
author = {Esquivel-Elizondo, S and Parameswaran, P and Delgado, AG and Maldonado, J and Rittmann, BE and Krajmalnik-Brown, R},
title = {Archaea and Bacteria Acclimate to High Total Ammonia in a Methanogenic Reactor Treating Swine Waste.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2016},
number = {},
pages = {4089684},
doi = {10.1155/2016/4089684},
pmid = {27725793},
issn = {1472-3654},
mesh = {Ammonia/*metabolism ; Anaerobiosis ; Animals ; Archaea/*classification/genetics/growth &amp; development/*metabolism ; Bacteria/*classification/genetics/growth &amp; development/*metabolism ; Biological Oxygen Demand Analysis ; Bioreactors/*microbiology ; *Biota ; Culture Media/chemistry ; Manure ; Real-Time Polymerase Chain Reaction ; Swine ; },
abstract = {Inhibition by ammonium at concentrations above 1000 mgN/L is known to harm the methanogenesis phase of anaerobic digestion. We anaerobically digested swine waste and achieved steady state COD-removal efficiency of around 52% with no fatty-acid or H2 accumulation. As the anaerobic microbial community adapted to the gradual increase of total ammonia-N (NH3-N) from 890 ± 295 to 2040 ± 30 mg/L, the Bacterial and Archaeal communities became less diverse. Phylotypes most closely related to hydrogenotrophic Methanoculleus (36.4%) and Methanobrevibacter (11.6%), along with acetoclastic Methanosaeta (29.3%), became the most abundant Archaeal sequences during acclimation. This was accompanied by a sharp increase in the relative abundances of phylotypes most closely related to acetogens and fatty-acid producers (Clostridium, Coprococcus, and Sphaerochaeta) and syntrophic fatty-acid Bacteria (Syntrophomonas, Clostridium, Clostridiaceae species, and Cloacamonaceae species) that have metabolic capabilities for butyrate and propionate fermentation, as well as for reverse acetogenesis. Our results provide evidence countering a prevailing theory that acetoclastic methanogens are selectively inhibited when the total ammonia-N concentration is greater than ~1000 mgN/L. Instead, acetoclastic and hydrogenotrophic methanogens coexisted in the presence of total ammonia-N of ~2000 mgN/L by establishing syntrophic relationships with fatty-acid fermenters, as well as homoacetogens able to carry out forward and reverse acetogenesis.},
}
@article {pmid27720988,
year = {2016},
author = {Ciragan, A and Aranko, AS and Tascon, I and Iwaï, H},
title = {Salt-inducible Protein Splicing in cis and trans by Inteins from Extremely Halophilic Archaea as a Novel Protein-Engineering Tool.},
journal = {Journal of molecular biology},
volume = {428},
number = {23},
pages = {4573-4588},
doi = {10.1016/j.jmb.2016.10.006},
pmid = {27720988},
issn = {1089-8638},
mesh = {Bacterial Proteins/metabolism ; Enzyme Activators/*metabolism ; Halobacteriales/*enzymology/metabolism ; *Inteins ; Isotope Labeling/methods ; Membrane Proteins/metabolism ; Protein Engineering/*methods ; *Protein Splicing ; Salts/*metabolism ; },
abstract = {Intervening protein sequences (inteins) from extremely halophilic haloarchaea can be inactive under low salinity but could be activated by increasing the salt content to a specific concentration for each intein. The halo-obligatory inteins confer high solubility under both low and high salinity conditions. We showed the broad utility of salt-dependent protein splicing in cis and trans by demonstrating backbone cyclization, self-cleavage for purification, and scarless protein ligation for segmental isotopic labeling. Artificially split MCM2 intein derived from Halorhabdus utahensis remained highly soluble and was capable of protein trans-splicing with excellent ligation kinetics by reassembly under high salinity conditions. Importantly, the MCM2 intein has the active site residue of Ser at the +1 position, which remains in the ligated product, instead of Cys as found in many other efficient split inteins. Since Ser is more abundant than Cys in proteins, the novel split intein could widen the applications of segmental labeling in protein NMR spectroscopy and traceless protein ligation by exploiting a Ser residue in the native sequences as the +1 position of the MCM2 intein. The split halo-obligatory intein was successfully used to demonstrate the utility in NMR investigation of intact proteins by producing segmentally isotope-labeled intact TonB protein from Helicobacter pylori.},
}
@article {pmid27687996,
year = {2016},
author = {Cerrillo, M and Morey, L and Viñas, M and Bonmatí, A},
title = {Assessment of active methanogenic archaea in a methanol-fed upflow anaerobic sludge blanket reactor.},
journal = {Applied microbiology and biotechnology},
volume = {100},
number = {23},
pages = {10137-10146},
doi = {10.1007/s00253-016-7862-4},
pmid = {27687996},
issn = {1432-0614},
mesh = {Acetates/metabolism ; Anaerobiosis ; Archaea/*classification/genetics/*metabolism ; Bioreactors/*microbiology ; DNA, Ribosomal/chemistry/genetics ; High-Throughput Nucleotide Sequencing ; Hydrogen/metabolism ; Methane/*metabolism ; Methanol/*metabolism ; Oxidoreductases/genetics ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sewage/*microbiology ; },
abstract = {Methanogenic archaea enrichment of a granular sludge was undertaken in an upflow anaerobic sludge blanket (UASB) reactor fed with methanol in order to enrich methylotrophic and hydrogenotrophic methanogenic populations. A microbial community assessment, in terms of microbial composition and activity-throughout the different stages of the feeding process with methanol and acetate-was performed using specific methanogenic activity (SMA) assays, quantitative real-time polymerase chain reaction (qPCR), and high-throughput sequencing of 16S ribosomal RNA (rRNA) genes from DNA and complementary DNA (cDNA). Distinct methanogenic enrichment was revealed by qPCR of mcrA gene in the methanol-fed community, being two orders of magnitude higher with respect to the initial inoculum, achieving a final mcrA/16S rRNA ratio of 0.25. High-throughput sequencing analysis revealed that the resulting methanogenic population was mainly composed by methylotrophic archaea (Methanomethylovorans and Methanolobus genus), being also highly active according to the RNA-based assessment. SMA confirmed that the methylotrophic pathway, with a direct conversion of methanol to CH4, was the main step of methanol degradation in the UASB. The biomass from the UASB, enriched in methanogenic archaea, may bear great potential as additional inoculum for bioreactors to carry out biogas production and other related processes.},
}
@article {pmid27683365,
year = {2016},
author = {Gulbudak, H and Weitz, JS},
title = {A touch of sleep: biophysical model of contact-mediated dormancy of archaea by viruses.},
journal = {Proceedings. Biological sciences},
volume = {283},
number = {1839},
pages = {},
doi = {10.1098/rspb.2016.1037},
pmid = {27683365},
issn = {1471-2954},
abstract = {The canonical view of the interactions between viruses and their microbial hosts presumes that changes in host and virus fate requires the initiation of infection of a host by a virus. Infection may lead to the death of the host cell and release of viruses, to the elimination of the viral genome through cellular defence mechanisms or the integration of the viral genome with the host as a chromosomal or extrachromosomal element. Here, we revisit this canonical view, inspired by recent experimental findings in which the majority of target host cells can be induced into a dormant state when exposed to either active or deactivated viruses, even when viruses are present at low relative titre. We propose that both the qualitative phenomena and the quantitative timescales of dormancy induction are consistent with the hypothesis that cellular physiology can be altered by contact on the surface of host cells rather than strictly by infection In order to test this hypothesis, we develop and study a biophysical model of contact-mediated dynamics involving virus particles and target cells. We show how virus particles can catalyse cellular transformations among many cells, even if they ultimately infect only one (or none). We also find that population-scale dormancy is robust to variation in the representation of model dynamics, including cell growth, death and recovery.},
}
@article {pmid27681926,
year = {2016},
author = {Lauer, A and Sørensen, KB and Teske, A},
title = {Phylogenetic Characterization of Marine Benthic Archaea in Organic-Poor Sediments of the Eastern Equatorial Pacific Ocean (ODP Site 1225).},
journal = {Microorganisms},
volume = {4},
number = {3},
pages = {},
doi = {10.3390/microorganisms4030032},
pmid = {27681926},
issn = {2076-2607},
abstract = {Sequencing surveys of microbial communities in marine subsurface sediments have focused on organic-rich, continental margins; the database for organic-lean deep-sea sediments from mid-ocean regions is underdeveloped. The archaeal community in subsurface sediments of ODP Site 1225 in the eastern equatorial Pacific (3760 m water depth; 1.1 and 7.8 m sediment depth) was analyzed by PCR, cloning and sequencing, and by denaturant gradient gel electrophoresis (DGGE) of 16S rRNA genes. Three uncultured archaeal lineages with different depth distributions were found: Marine Group I (MG-I) within the Thaumarchaeota, its sister lineage Marine Benthic Group A (MBG-A), the phylum-level archaeal lineage Marine Benthic Group B (also known as Deep-Sea Archaeal Group or Lokiarchaeota), and the Deep-Sea Euryarchaeotal Group 3. The MG-I phylotypes included representatives of sediment clusters that are distinct from the pelagic members of this phylum. On the scale from fully oxidized, extremely organic carbon-depleted sediments (for example, those the South Pacific Gyre) to fully reduced, organic carbon-rich marine subsurface sediments (such as those of the Peru Margin), Ocean Drilling Program (ODP) Site 1225 falls into the non-extreme organic carbon-lean category, and harbors archaeal communities from both ends of the spectrum.},
}
@article {pmid27679621,
year = {2016},
author = {Zu, Q and Zhong, L and Deng, Y and Shi, Y and Wang, B and Jia, Z and Lin, X and Feng, Y},
title = {Geographical Distribution of Methanogenic Archaea in Nine Representative Paddy Soils in China.},
journal = {Frontiers in microbiology},
volume = {7},
number = {},
pages = {1447},
doi = {10.3389/fmicb.2016.01447},
pmid = {27679621},
issn = {1664-302X},
abstract = {Paddy field methanogenic archaea are responsible for methane (CH4) production and contribute significantly to climate change. The information regarding the spatial variations in the abundance, the diversity and the composition of such ecologically important microbes, however, is quite limited at large scale. In this investigation, we studied the abundance, alpha diversity and geographical distribution of methanogenic archaeal communities in nine representative paddy sites, along a large latitudinal gradient in China, using pyrosequencing and real-time quantitative PCR. It is found that all paddy soils harbor constant methanogenic archaeal constituents, which is dominated by family Methanocellaceae (37.3%), Methanobacteriaceae (22.1%), Methanosaetaceae (17.2%), and Methanosarcinaceae (9.8%). Methanogenic archaeal abundance is primarily influenced by soil C (R = 0.612, P = 0.001) and N (R = 0.673, P = 0.001) contents, as well as alpha diversity by soil pH (PD: R = -0.552, P = 0.006; Chao1: R = -0.615, P = 0.002). Further exploration revealed that both spatial distance (R = 0.3469, P = 0.001, partial mental test) and soil chemical variables mainly about soil C and N (R = 0.2847, P = 0.001) are the two major factors affecting methanogenic archaeal community composition distribution in paddy soils. This finding will allow us to develop a better picture of the biogeographic ranges of these ecologically important microbes and get deeper insights into their ecology.},
}
@article {pmid27679616,
year = {2016},
author = {Chistoserdova, L},
title = {Wide Distribution of Genes for Tetrahydromethanopterin/Methanofuran-Linked C1 Transfer Reactions Argues for Their Presence in the Common Ancestor of Bacteria and Archaea.},
journal = {Frontiers in microbiology},
volume = {7},
number = {},
pages = {1425},
doi = {10.3389/fmicb.2016.01425},
pmid = {27679616},
issn = {1664-302X},
}
@article {pmid27679615,
year = {2016},
author = {Thombre, RS and Shinde, V and Thaiparambil, E and Zende, S and Mehta, S},
title = {Antimicrobial Activity and Mechanism of Inhibition of Silver Nanoparticles against Extreme Halophilic Archaea.},
journal = {Frontiers in microbiology},
volume = {7},
number = {},
pages = {1424},
doi = {10.3389/fmicb.2016.01424},
pmid = {27679615},
issn = {1664-302X},
abstract = {Haloarchaea are salt-loving halophilic microorganisms that inhabit marine environments, sea water, salterns, and lakes. The resistance of haloarchaea to physical extremities that challenge organismic survival is ubiquitous. Metal and antibiotic resistance of haloarchaea has been on an upsurge due to the exposure of these organisms to metal sinks and drug resistance genes augmented in their natural habitats due to anthropogenic activities and environmental pollution. The efficacy of silver nanoparticles (SNPs) as a potent and broad spectrum inhibitory agent is known, however, there are no reports on the inhibitory activity of SNPs against haloarchaea. In the present study, we have investigated the antimicrobial potentials of SNPs synthesized using aqueous leaf extract of Cinnamomum tamala against antibiotic resistant haloarchaeal isolates Haloferax prahovense RR8, Haloferax lucentense RR15, Haloarcula argentinensis RR10 and Haloarcula tradensis RR13. The synthesized SNPs were characterized by UV-Vis spectroscopy, scanning electron microscopy, energy dispersive X-ray spectroscopy, dynamic light scattering, X-ray diffraction and Fourier transform infrared spectroscopy. The SNPs demonstrated potent antimicrobial activity against the haloarchaea with a minimum inhibitory concentration of 300-400 μg/ml. Growth kinetics of haloarchaea in the presence of SNPs was studied by employing the Baranyi mathematical model for microbial growth using the DMFit curve fitting program. The C. tamala SNPs also demonstrated cytotoxic activity against human lung adenocarcinoma epithelial cell line (A540) and human breast adenocarcinoma cell line (MCF-7). The mechanism of inhibition of haloarchaea by the SNPs was investigated. The plausible mechanism proposed is the alterations and disruption of haloarchaeal membrane permeability by turbulence, inhibition of respiratory dehydrogenases and lipid peroxidation causing cellular and DNA damage resulting in cell death.},
}
@article {pmid27670118,
year = {2016},
author = {Dar, D and Prasse, D and Schmitz, RA and Sorek, R},
title = {Widespread formation of alternative 3' UTR isoforms via transcription termination in archaea.},
journal = {Nature microbiology},
volume = {1},
number = {10},
pages = {16143},
doi = {10.1038/nmicrobiol.2016.143},
pmid = {27670118},
issn = {2058-5276},
mesh = {*3' Untranslated Regions ; Archaea/*genetics ; Archaeal Proteins/genetics ; Gene Expression Profiling ; *Gene Expression Regulation, Archaeal ; Genes, Archaeal ; RNA Isoforms/*genetics ; RNA, Archaeal/*genetics ; RNA, Untranslated ; *Transcription Termination, Genetic ; },
abstract = {Transcription termination sets the 3' end boundaries of RNAs and plays key roles in gene regulation. Although termination has been well studied in bacteria, the signals that mediate termination in archaea remain poorly understood. Here, we applied term-seq to comprehensively map RNA 3' termini, with single-base precision, in two phylogenetically distant archaea: Methanosarcina mazei and Sulfolobus acidocaldarius. Comparison of RNA 3' ends across hundreds of genes revealed the sequence composition of transcriptional terminators in each organism, highlighting both common and divergent characteristics between the different archaeal phyla. We find that, in contrast to bacteria, a considerable portion of archaeal genes are controlled by multiple consecutive terminators, generating several alternative 3' untranslated region isoforms for >30% of the genes. These alternative isoforms often present marked length differences, implying that archaea can employ regulation via alternative 3' untranslated regions, similar to eukaryotes. Although most of the terminators are intergenic, we discover numerous cases in which termination of one gene occurs within the coding region of a downstream gene, implying that leaky termination may tune inter-transcript stoichiometry in multi-gene operons. These results provide the first high-throughput maps of transcriptional terminators in archaea and point to an evolutionary path linking bacterial and eukaryal non-coding regulatory strategies.},
}
@article {pmid27652169,
year = {2016},
author = {Watanabe, K and Kohzu, A and Suda, W and Yamamura, S and Takamatsu, T and Takenaka, A and Koshikawa, MK and Hayashi, S and Watanabe, M},
title = {Microbial nitrification in throughfall of a Japanese cedar associated with archaea from the tree canopy.},
journal = {SpringerPlus},
volume = {5},
number = {1},
pages = {1596},
doi = {10.1186/s40064-016-3286-y},
pmid = {27652169},
issn = {2193-1801},
abstract = {To investigate the nitrification potential of phyllospheric microbes, we incubated throughfall samples collected under the canopies of Japanese cedar (Cryptomeria japonica) and analyzed the transformation of inorganic nitrogen in the samples. Nitrate concentration increased in the unfiltered throughfall after 4 weeks of incubation, but remained nearly constant in the filtered samples (pore size: 0.2 and 0.4 µm). In the unfiltered samples, δ(18)O and δ(15)N values of nitrate decreased during incubation. In addition, archaeal ammonia monooxygenase subunit A (amoA) genes, which participate in the oxidation of ammonia, were found in the throughfall samples, although betaproteobacterial amoA genes were not detected. The amoA genes recovered from the leaf surface of C. japonica were also from archaea. Conversely, nitrate production, decreased isotope ratios of nitrate, and the presence of amoA genes was not observed in rainfall samples collected from an open area. Thus, the microbial nitrification that occurred in the incubated throughfall is likely due to ammonia-oxidizing archaea that were washed off the tree canopy by precipitation.},
}
@article {pmid27642845,
year = {2016},
author = {Umu, SU and Poole, AM and Dobson, RC and Gardner, PP},
title = {Avoidance of stochastic RNA interactions can be harnessed to control protein expression levels in bacteria and archaea.},
journal = {eLife},
volume = {5},
number = {},
pages = {},
doi = {10.7554/eLife.13479},
pmid = {27642845},
issn = {2050-084X},
mesh = {Archaea/*genetics/*metabolism ; Bacteria/*genetics/*metabolism ; Genes, Reporter ; Green Fluorescent Proteins/analysis/genetics ; *Protein Biosynthesis ; RNA, Messenger/*metabolism ; RNA, Untranslated/*metabolism ; },
abstract = {A critical assumption of gene expression analysis is that mRNA abundances broadly correlate with protein abundance, but these two are often imperfectly correlated. Some of the discrepancy can be accounted for by two important mRNA features: codon usage and mRNA secondary structure. We present a new global factor, called mRNA:ncRNA avoidance, and provide evidence that avoidance increases translational efficiency. We also demonstrate a strong selection for the avoidance of stochastic mRNA:ncRNA interactions across prokaryotes, and that these have a greater impact on protein abundance than mRNA structure or codon usage. By generating synonymously variant green fluorescent protein (GFP) mRNAs with different potential for mRNA:ncRNA interactions, we demonstrate that GFP levels correlate well with interaction avoidance. Therefore, taking stochastic mRNA:ncRNA interactions into account enables precise modulation of protein abundance.},
}
@article {pmid27624130,
year = {2016},
author = {Quemin, ER and Chlanda, P and Sachse, M and Forterre, P and Prangishvili, D and Krupovic, M},
title = {Eukaryotic-Like Virus Budding in Archaea.},
journal = {mBio},
volume = {7},
number = {5},
pages = {},
doi = {10.1128/mBio.01439-16},
pmid = {27624130},
issn = {2150-7511},
mesh = {Archaea/ultrastructure/*virology ; Electron Microscope Tomography ; Fuselloviridae/*physiology/ultrastructure ; *Virus Release ; },
abstract = {UNLABELLED: Similar to many eukaryotic viruses (and unlike bacteriophages), viruses infecting archaea are often encased in lipid-containing envelopes. However, the mechanisms of their morphogenesis and egress remain unexplored. Here, we used dual-axis electron tomography (ET) to characterize the morphogenesis of Sulfolobus spindle-shaped virus 1 (SSV1), the prototype of the family Fuselloviridae and representative of the most abundant archaea-specific group of viruses. Our results show that SSV1 assembly and egress are concomitant and occur at the cellular cytoplasmic membrane via a process highly reminiscent of the budding of enveloped viruses that infect eukaryotes. The viral nucleoprotein complexes are extruded in the form of previously unknown rod-shaped intermediate structures which have an envelope continuous with the host membrane. Further maturation into characteristic spindle-shaped virions takes place while virions remain attached to the cell surface. Our data also revealed the formation of constricted ring-like structures which resemble the budding necks observed prior to the ESCRT machinery-mediated membrane scission during egress of various enveloped viruses of eukaryotes. Collectively, we provide evidence that archaeal spindle-shaped viruses contain a lipid envelope acquired upon budding of the viral nucleoprotein complex through the host cytoplasmic membrane. The proposed model bears a clear resemblance to the egress strategy employed by enveloped eukaryotic viruses and raises important questions as to how the archaeal single-layered membrane composed of tetraether lipids can undergo scission.<br><br>IMPORTANCE: The replication of enveloped viruses has been extensively studied in eukaryotes but has remained unexplored for enveloped viruses infecting Archaea Here, we provide a sequential view on the assembly and egress of SSV1, a prototypic archaeal virus. The observed process is highly similar to the budding of eukaryotic enveloped viruses, including human immunodeficiency virus, influenza virus, and Ebola virus. The present study is the first to characterize such a phenomenon in archeal cells, showing that membrane budding is not an exclusive feature of eukaryotic viruses. Our results provide significant insights into the biogenesis and architecture of unique, spindle-shaped virions that infect archaea. Furthermore, our findings open doors for future inquiries into (i) the evolution of the virus budding process, (ii) mechanistic details of virus-mediated membrane scission in Archaea, and (iii) elucidation of virus- and host-encoded molecular players responsible for archaeal membrane and surface remodeling.},
}
@article {pmid27598206,
year = {2016},
author = {Jones, DL and Baxter, BK},
title = {Bipyrimidine Signatures as a Photoprotective Genome Strategy in G + C-rich Halophilic Archaea.},
journal = {Life (Basel, Switzerland)},
volume = {6},
number = {3},
pages = {},
doi = {10.3390/life6030037},
pmid = {27598206},
issn = {2075-1729},
abstract = {Halophilic archaea experience high levels of ultraviolet (UV) light in their environments and demonstrate resistance to UV irradiation. DNA repair systems and carotenoids provide UV protection but do not account for the high resistance observed. Herein, we consider genomic signatures as an additional photoprotective strategy. The predominant forms of UV-induced DNA damage are cyclobutane pyrimidine dimers, most notoriously thymine dimers (T^Ts), which form at adjacent Ts. We tested whether the high G + C content seen in halophilic archaea serves a photoprotective function through limiting T nucleotides, and thus T^T lesions. However, this speculation overlooks the other bipyrimidine sequences, all of which capable of forming photolesions to varying degrees. Therefore, we designed a program to determine the frequencies of the four bipyrimidine pairs (5' to 3': TT, TC, CT, and CC) within genomes of halophilic archaea and four other randomized sample groups for comparison. The outputs for each sampled genome were weighted by the intrinsic photoreactivities of each dinucleotide pair. Statistical methods were employed to investigate intergroup differences. Our findings indicate that the UV-resistance seen in halophilic archaea can be attributed in part to a genomic strategy: high G + C content and the resulting bipyrimidine signature reduces the genomic photoreactivity.},
}
@article {pmid27596731,
year = {2016},
author = {Zhang, X and Tang, Y and Shi, Y and He, N and Wen, X and Yu, Q and Zheng, C and Sun, X and Qiu, W},
title = {Responses of soil hydrolytic enzymes, ammonia-oxidizing bacteria and archaea to nitrogen applications in a temperate grassland in Inner Mongolia.},
journal = {Scientific reports},
volume = {6},
number = {},
pages = {32791},
doi = {10.1038/srep32791},
pmid = {27596731},
issn = {2045-2322},
mesh = {Ammonia/*metabolism ; Archaea/*metabolism ; Bacteria/*metabolism ; China ; Ecosystem ; Fertilizers/microbiology ; Grassland ; Hydrolysis ; Nitrification/physiology ; Nitrogen/*metabolism ; Oxidation-Reduction ; Soil ; Soil Microbiology ; },
abstract = {We used a seven-year urea gradient applied field experiment to investigate the effects of nitrogen (N) applications on soil N hydrolytic enzyme activity and ammonia-oxidizing microbial abundance in a typical steppe ecosystem in Inner Mongolia. The results showed that N additions inhibited the soil N-related hydrolytic enzyme activities, especially in 392 kg N ha(-1)yr(-1) treatment. As N additions increased, the amoA gene copy ratios of ammonia-oxidizing archaea (AOA) to ammonia-oxidizing bacteria (AOB) decreased from 1.13 to 0.65. Pearson correlation analysis showed that the AOA gene copies were negatively related with NH4(+)-N content. However, the AOB gene copies were positively correlated with NO3(-)-N content. Moderate N application rates (56-224 kg N ha(-1)yr(-1)) accompanied by P additions are beneficial to maintaining the abundance of AOB, as opposed to the inhibition of highest N application rate (392 kg N ha(-1)yr(-1)) on the abundance of AOB. This study suggests that the abundance of AOB and AOA would not decrease unless N applications exceed 224 kg N ha(-1)yr(-1) in temperate grasslands in Inner Mongolia.},
}
@article {pmid27582505,
year = {2016},
author = {Pergolizzi, G and Wagner, GK and Bowater, RP},
title = {Biochemical and Structural Characterisation of DNA Ligases from Bacteria and Archaea.},
journal = {Bioscience reports},
volume = {},
number = {},
pages = {},
doi = {10.1042/BSR20160003},
pmid = {27582505},
issn = {1573-4935},
abstract = {DNA ligases are enzymes that seal breaks in the backbones of DNA, leading to them being essential for the survival of all organisms. DNA ligases have been studied from many different types of cells and organisms and shown to have diverse sizes and sequences, with well conserved specific sequences that are required for enzymatic activity. A significant number of DNA ligases have been isolated or prepared in recombinant forms and, here, we review their biochemical and structural characterisation. All DNA ligases contain an essential lysine that transfers an adenylate group from a co-factor to the 5'-phosphate of the DNA end that will ultimately be joined to the 3'-hydroxyl of the neighbouring DNA strand. The essential DNA ligases in bacteria use nicotinamide adenine dinucleotide (β -NAD+) as their co-factor whereas those that are essential in other cells use adenosine-5'-triphosphate (ATP) as their co-factor. This observation suggests that the essential bacterial enzyme could be targeted by novel antibiotics and the complex molecular structure of β -NAD+ affords multiple opportunities for chemical modification. Several recent studies have synthesised novel derivatives and their biological activity against a range of DNA ligases has been evaluated as inhibitors for drug discovery and/or non-natural substrates for biochemical applications. Here, we review the recent advances that herald new opportunities to alter the biochemical activities of these important enzymes. The recent development of modified derivatives of nucleotides highlights that the continued combination of structural, biochemical and biophysical techniques will be useful in targeting these essential cellular enzymes.},
}
@article {pmid29251473,
year = {2016},
author = {Dong, L and Meng, Y and Wang, J and Sun, G},
title = {Effects of Transgenic Bt+CpTI cotton on the abundance and diversity of rhizosphere ammonia oxidizing bacteria and archaea.},
journal = {Journal of environmental biology},
volume = {37},
number = {5},
pages = {881-888},
pmid = {29251473},
issn = {0254-8704},
mesh = {Ammonia/*metabolism ; Archaea/classification/*metabolism ; Bacteria/classification/*metabolism ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Gossypium/*genetics ; Oxidation-Reduction ; Plant Roots ; Plants, Genetically Modified ; Soil ; *Soil Microbiology ; },
abstract = {Genetically modified crops (GMCs) hold great promise for improving agricultural output, but at the same time present challenges in terms of environmental safety assessment. Ammonia oxidizers, including ammonia oxidizing bacteria (AOB) and archaea (AOA), are very important functional microbial groups in nitrogen cycle. The abundance and diversity of AOA and AOB in the rhizosphere of genetically modified cotton (SGK321) and non-GM cotton (SY321) across growth stages were investigated using real time quantitative PCR (qPCR) and terminal restriction fragment length polymorphism (T-RFLP). Results showed that cotton genotype had a significant effect on the change in abundance of AOA and AOB, as indicated by amoA copy number. Variations in AOB abundance in rhizosphere of SY321 differed from those in SGK321. The number of AOB in the rhizosphere of SY321 fluctuated considerably: It dramatically decreased from 1.2?106 copies g-1 dry soil to 3?105 copies g-1 dry soil during the flowering stage and then increased to 1.1?106 copies g-1 and 1.5?106 copies g-1 at the belling and boll opening stages, respectively. However, abundance of AOB in the rhizosphere of SGK321 was relatively stable during all the stages of growth. The effect of SGK321 and SY321 on AOA number was quite similar to that of AOB: AOA abundance in SGK321 increased smoothly from 1.0 ?105 copies g-1 dry soil to 1.4?106 copies g-1 dry soil during growth, but that in SY321 fluctuated. Correspondence analysis (CA), canonical CA (CCA), and partial CCA (pCCA) of T-RFLP profiles of AOA and AOB showed that AOB community changed across growth stages in both cotton genotypes, and cotton genotype was the most important factor affecting the AOA community. In conclusion, the current findings indicated no adverse effect of GM cotton on functional microorganisms.},
}
@article {pmid27572439,
year = {2016},
author = {Needham, DM and Fuhrman, JA},
title = {Pronounced daily succession of phytoplankton, archaea and bacteria following a spring bloom.},
journal = {Nature microbiology},
volume = {1},
number = {},
pages = {16005},
doi = {10.1038/nmicrobiol.2016.5},
pmid = {27572439},
issn = {2058-5276},
mesh = {Archaea/classification/genetics/*growth &amp; development ; Bacteria/classification/genetics/*growth &amp; development ; California ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; Eukaryota/classification/genetics/*growth &amp; development ; Phylogeny ; Phytoplankton/classification/genetics/*growth &amp; development ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Protozoan/genetics ; RNA, Ribosomal, 16S/genetics ; Seasons ; Seawater/*microbiology ; Sequence Analysis, DNA ; },
abstract = {Marine phytoplankton perform approximately half of global carbon fixation, with their blooms contributing disproportionately to carbon sequestration(1), and most phytoplankton production is ultimately consumed by heterotrophic prokaryotes(2). Therefore, phytoplankton and heterotrophic community dynamics are important in modelling carbon cycling and the impacts of global change(3). In a typical bloom, diatoms dominate initially, transitioning over several weeks to smaller and motile phytoplankton(4). Here, we show unexpected, rapid community variation from daily rRNA analysis of phytoplankton and prokaryotic community members following a bloom off southern California. Analysis of phytoplankton chloroplast 16S rRNA demonstrated ten different dominant phytoplankton over 18 days alone, including four taxa with animal toxin-producing strains. The dominant diatoms, flagellates and picophytoplankton varied dramatically in carbon export potential. Dominant prokaryotes also varied rapidly. Euryarchaea briefly became the most abundant organism, peaking over a few days to account for about 40% of prokaryotes. Phytoplankton and prokaryotic communities correlated better with each other than with environmental parameters. Extending beyond the traditional view of blooms being controlled primarily by physics and inorganic nutrients, these dynamics imply highly heterogeneous, continually changing conditions over time and/or space and suggest that interactions among microorganisms are critical in controlling plankton diversity, dynamics and fates.},
}
@article {pmid27572167,
year = {2016},
author = {Baker, BJ and Saw, JH and Lind, AE and Lazar, CS and Hinrichs, KU and Teske, AP and Ettema, TJ},
title = {Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea.},
journal = {Nature microbiology},
volume = {1},
number = {},
pages = {16002},
doi = {10.1038/nmicrobiol.2016.2},
pmid = {27572167},
issn = {2058-5276},
mesh = {Ammonia/metabolism ; Archaea/classification/*genetics/*metabolism ; Carbon Monoxide/metabolism ; *Environmental Microbiology ; Estuaries ; Hot Springs ; Hydrogen/metabolism ; Metabolic Networks and Pathways/*genetics ; Nitrites/metabolism ; Oxidation-Reduction ; *Phylogeny ; Sequence Analysis, DNA ; },
abstract = {The subsurface biosphere is largely unexplored and contains a broad diversity of uncultured microbes(1). Despite being one of the few prokaryotic lineages that is cosmopolitan in both the terrestrial and marine subsurface(2-4), the physiological and ecological roles of SAGMEG (South-African Gold Mine Miscellaneous Euryarchaeal Group) Archaea are unknown. Here, we report the metabolic capabilities of this enigmatic group as inferred from genomic reconstructions. Four high-quality (63-90% complete) genomes were obtained from White Oak River estuary and Yellowstone National Park hot spring sediment metagenomes. Phylogenomic analyses place SAGMEG Archaea as a deeply rooting sister clade of the Thermococci, leading us to propose the name Hadesarchaea for this new Archaeal class. With an estimated genome size of around 1.5 Mbp, the genomes of Hadesarchaea are distinctly streamlined, yet metabolically versatile. They share several physiological mechanisms with strict anaerobic Euryarchaeota. Several metabolic characteristics make them successful in the subsurface, including genes involved in CO and H2 oxidation (or H2 production), with potential coupling to nitrite reduction to ammonia (DNRA). This first glimpse into the metabolic capabilities of these cosmopolitan Archaea suggests they are mediating key geochemical processes and are specialized for survival in the subsurface biosphere.},
}
@article {pmid27561235,
year = {2017},
author = {Zhu, Y and Sun, Y and Wang, C and Li, F},
title = {Impact of dietary fibre:starch ratio in shaping caecal archaea revealed in rabbits.},
journal = {Journal of animal physiology and animal nutrition},
volume = {101},
number = {4},
pages = {635-640},
doi = {10.1111/jpn.12585},
pmid = {27561235},
issn = {1439-0396},
mesh = {Animal Feed/analysis ; Animal Nutritional Physiological Phenomena ; Animals ; Archaea/genetics/*physiology ; Cecum/*microbiology ; Diet/veterinary ; Dietary Carbohydrates/analysis/*metabolism ; Dietary Fiber/analysis/*metabolism ; *Rabbits ; },
abstract = {In rabbits, many studies have investigated the effect of diet, including the fibre intake, on caecal microbiota; however, there are no direct measurements of the influence of diets with different dietary fibre-to-starch ratios and the archaeal community composition in the caecum. We used 16S rDNA sequencing to investigate the impact of different dietary neutral detergent fibre (NDF)-to-starch ratios (1.0-2.3) on the caecal archaeal community in rabbits. The results revealed that the archaeal community from all experimental rabbits was relatively less complex than intestinal bacterial community. High-throughput 16S rDNA sequencing of the gut archaea indicated that the rabbit caecum was inhabited by Methanobrevibacter and Methanosphaera species, and therefore is possibly dominated by two species of archaea. Here, we compared the effect of different diets on the archaeal community in the rabbit caecum and found no significant differences in the diversity and abundance of caecal archaeal community of rabbits that were fed diets with different dietary fibre-to-starch ratios. Therefore, we suggest that the contribution of host-derived substrates to caecal archaea constitution is insignificant.},
}
@article {pmid27507826,
year = {2016},
author = {Fu, X and Liu, R and Sanchez, I and Silva-Sanchez, C and Hepowit, NL and Cao, S and Chen, S and Maupin-Furlow, J},
title = {Erratum for Fu et al., Ubiquitin-Like Proteasome System Represents a Eukaryotic-Like Pathway for Targeted Proteolysis in Archaea.},
journal = {mBio},
volume = {7},
number = {4},
pages = {},
doi = {10.1128/mBio.01192-16},
pmid = {27507826},
issn = {2150-7511},
}
@article {pmid27459543,
year = {2016},
author = {Hepowit, NL and de Vera, IM and Cao, S and Fu, X and Wu, Y and Uthandi, S and Chavarria, NE and Englert, M and Su, D and Sӧll, D and Kojetin, DJ and Maupin-Furlow, JA},
title = {Mechanistic insight into protein modification and sulfur mobilization activities of noncanonical E1 and associated ubiquitin-like proteins of Archaea.},
journal = {The FEBS journal},
volume = {283},
number = {19},
pages = {3567-3586},
doi = {10.1111/febs.13819},
pmid = {27459543},
issn = {1742-4658},
support = {R01 GM022854/GM/NIGMS NIH HHS/United States ; R01 GM057498/GM/NIGMS NIH HHS/United States ; R37 GM022854/GM/NIGMS NIH HHS/United States ; },
mesh = {Adenosine Triphosphate/metabolism ; Archaeal Proteins/*chemistry/*metabolism ; Cysteine/physiology ; Haloferax volcanii/enzymology ; Ligands ; Models, Molecular ; Protein Binding ; Protein Domains ; Small Ubiquitin-Related Modifier Proteins/chemistry/*metabolism ; Sulfhydryl Compounds/metabolism ; Sulfur/*metabolism ; Thermodynamics ; Ubiquitin-Activating Enzymes/*chemistry/*metabolism ; Ubiquitination ; },
abstract = {Here we provide the first detailed biochemical study of a noncanonical E1-like enzyme with broad specificity for cognate ubiquitin-like (Ubl) proteins that mediates Ubl protein modification and sulfur mobilization to form molybdopterin and thiolated tRNA. Isothermal titration calorimetry and in vivo analyses proved useful in discovering that environmental conditions, ATP binding, and Ubl type controlled the mechanism of association of the Ubl protein with its cognate E1-like enzyme (SAMP and UbaA of the archaeon Haloferax volcanii, respectively). Further analysis revealed that ATP hydrolysis triggered the formation of thioester and peptide bonds within the Ubl:E1-like complex. Importantly, the thioester was an apparent precursor to Ubl protein modification but not sulfur mobilization. Comparative modeling to MoeB/ThiF guided the discovery of key residues within the adenylation domain of UbaA that were needed to bind ATP as well as residues that were specifically needed to catalyze the downstream reactions of sulfur mobilization and/or Ubl protein modification. UbaA was also found to be Ubl-automodified at lysine residues required for early (ATP binding) and late (sulfur mobilization) stages of enzyme activity revealing multiple layers of autoregulation. Cysteine residues, distinct from the canonical E1 'active site' cysteine, were found important in UbaA function supporting a model that this noncanonical E1 is structurally flexible in its active site to allow Ubl~adenylate, Ubl~E1-like thioester and cysteine persulfide(s) intermediates to form.},
}
@article {pmid27450111,
year = {2016},
author = {Barillà, D},
title = {Driving Apart and Segregating Genomes in Archaea.},
journal = {Trends in microbiology},
volume = {24},
number = {12},
pages = {957-967},
doi = {10.1016/j.tim.2016.07.001},
pmid = {27450111},
issn = {1878-4380},
support = {BB/F012004/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
abstract = {Genome segregation is a fundamental biological process in organisms from all domains of life. How this stage of the cell cycle unfolds in Eukarya has been clearly defined and considerable progress has been made to unravel chromosome partition in Bacteria. The picture is still elusive in Archaea. The lineages of this domain exhibit different cell-cycle lifestyles and wide-ranging chromosome copy numbers, fluctuating from 1 up to 55. This plurality of patterns suggests that a variety of mechanisms might underpin disentangling and delivery of DNA molecules to daughter cells. Here I describe recent developments in archaeal genome maintenance, including investigations of novel genome segregation machines that point to unforeseen bacterial and eukaryotic connections.},
}
@article {pmid27408734,
year = {2016},
author = {Khelaifia, S and Raoult, D},
title = {Haloferax massiliensis sp. nov., the first human-associated halophilic archaea.},
journal = {New microbes and new infections},
volume = {12},
number = {},
pages = {96-98},
doi = {10.1016/j.nmni.2016.05.007},
pmid = {27408734},
issn = {2052-2975},
abstract = {We report the main characteristics of Haloferax massiliensis strain Arc-Hr(T) (= CSUR P974) isolated from stool specimen of a 22-year-old Amazonian obese female patient.},
}
@article {pmid27388368,
year = {2016},
author = {Kambura, AK and Mwirichia, RK and Kasili, RW and Karanja, EN and Makonde, HM and Boga, HI},
title = {Bacteria and Archaea diversity within the hot springs of Lake Magadi and Little Magadi in Kenya.},
journal = {BMC microbiology},
volume = {16},
number = {1},
pages = {136},
doi = {10.1186/s12866-016-0748-x},
pmid = {27388368},
issn = {1471-2180},
mesh = {Archaea/*classification/genetics/isolation &amp; purification ; Bacteria/*classification/genetics/isolation &amp; purification ; Biodiversity ; Classification ; DNA, Archaeal/analysis ; DNA, Bacterial/analysis ; Geologic Sediments ; Hot Springs/*microbiology ; Kenya ; Lakes/chemistry/*microbiology ; Phylogeny ; Sequence Analysis, DNA ; *Water Microbiology ; },
abstract = {BACKGROUND: Lake Magadi and little Magadi are hypersaline, alkaline lakes situated in the southern part of Kenyan Rift Valley. Solutes are supplied mainly by a series of alkaline hot springs with temperatures as high as 86 °C. Previous culture-dependent and culture-independent studies have revealed diverse groups of microorganisms thriving under these conditions. Previous culture independent studies were based on the analysis of 16S rDNA but were done on less saline lakes. For the first time, this study combined illumina sequencing and analysis of amplicons of both total community rDNA and 16S rRNA cDNA to determine the diversity and community structure of bacteria and archaea within 3 hot springs of L. Magadi and little Magadi.<br><br>METHODS: Water, wet sediments and microbial mats were collected from springs in the main lake at a temperature of 45.1 °C and from Little Magadi &quot;Nasikie eng'ida&quot; (temperature of 81 °C and 83.6 °C). Total community DNA and RNA were extracted from samples using phenol-chloroform and Trizol RNA extraction protocols respectively. The 16S rRNA gene variable region (V4 - V7) of the extracted DNA and RNA were amplified and library construction performed following Illumina sequencing protocol. Sequences were analyzed done using QIIME while calculation of Bray-Curtis dissimilarities between datasets, hierarchical clustering, Non Metric Dimensional Scaling (NMDS) redundancy analysis (RDA) and diversity indices were carried out using the R programming language and the Vegan package.<br><br>RESULTS: Three thousand four hundred twenty-six and one thousand nine hundred thirteen OTUs were recovered from 16S rDNA and 16S rRNA cDNA respectively. Uncultured diversity accounted for 89.35 % 16S rDNA and 87.61 % 16S rRNA cDNA reads. The most abundant phyla in both the 16S rDNA and 16S rRNA cDNA datasets included: Proteobacteria (8.33-50 %), Firmicutes 3.52-28.92 %, Bacteroidetes (3.45-26.44 %), Actinobacteria (0.98-28.57 %) and Euryarchaeota (3.55-34.48 %) in all samples. NMDS analyses of taxonomic composition clustered the taxa into three groups according to sample types (i.e. wet sediments, mats and water samples) with evident overlap of clusters between wet sediments and microbial mats from the three sample types in both DNA and cDNA datasets. The hot spring (45.1 °C) contained less diverse populations compared to those in Little Magadi (81-83 °C).<br><br>CONCLUSION: There were significant differences in microbial community structure at 95 % level of confidence for both total diversity (P value, 0.009) based on 16S rDNA analysis and active microbial diversity (P value, 0.01) based on 16S rRNA cDNA analysis, within the three hot springs. Differences in microbial composition and structure were observed as a function of sample type and temperature, with wet sediments harboring the highest diversity.},
}
@article {pmid27388200,
year = {2016},
author = {Castro, C and Zhang, R and Liu, J and Bellenberg, S and Neu, TR and Donati, E and Sand, W and Vera, M},
title = {Biofilm formation and interspecies interactions in mixed cultures of thermo-acidophilic archaea Acidianus spp. and Sulfolobus metallicus.},
journal = {Research in microbiology},
volume = {167},
number = {7},
pages = {604-612},
doi = {10.1016/j.resmic.2016.06.005},
pmid = {27388200},
issn = {1769-7123},
mesh = {Acidianus/*physiology ; Bacterial Adhesion ; Biofilms/*growth &amp; development ; *Environmental Microbiology ; Iron/metabolism ; *Microbial Interactions ; Microscopy, Confocal ; Sulfides/metabolism ; Sulfolobus/*physiology ; Sulfur/metabolism ; },
abstract = {The understanding of biofilm formation by bioleaching microorganisms is of great importance for influencing mineral dissolution rates and to prevent acid mine drainage (AMD). Thermo-acidophilic archaea such as Acidianus, Sulfolobus and Metallosphaera are of special interest due to their ability to perform leaching at high temperatures, thereby enhancing leaching rates. In this work, leaching experiments and visualization by microscopy of cell attachment and biofilm formation patterns of the crenarchaeotes Sulfolobus metallicus DSM 6482(T) and the Acidianus isolates DSM 29038 and DSM 29099 in pure and mixed cultures on sulfur or pyrite were studied. Confocal laser scanning microscopy (CLSM) combined with fluorescent dyes as well as fluorescently labeled lectins were used to visualize different components (e.g. DNA, proteins or glycoconjugates) of the aforementioned species. The data indicate that cell attachment and the subsequently formed biofilms were species- and substrate-dependent. Pyrite leaching experiments coupled with pre-colonization and further inoculation with a second species suggest that both species may negatively influence each other during pyrite leaching with respect to initial attachment and pyrite dissolution rates. In addition, the investigation of binary biofilms on pyrite showed that both species were heterogeneously distributed on pyrite surfaces in the form of individual cells or microcolonies. Physical contact between the two species seems to occur, as revealed by specific lectins able to specifically bind single species within mixed cultures.},
}
@article {pmid27386507,
year = {2016},
author = {Danovaro, R and Molari, M and Corinaldesi, C and Dell'Anno, A},
title = {Macroecological drivers of archaea and bacteria in benthic deep-sea ecosystems.},
journal = {Science advances},
volume = {2},
number = {4},
pages = {e1500961},
doi = {10.1126/sciadv.1500961},
pmid = {27386507},
issn = {2375-2548},
mesh = {Archaea/*growth &amp; development ; Bacteria/*growth &amp; development ; Biodiversity ; Biomass ; Climate Change ; *Ecosystem ; Geologic Sediments ; Seawater/microbiology ; Temperature ; },
abstract = {Bacteria and archaea dominate the biomass of benthic deep-sea ecosystems at all latitudes, playing a crucial role in global biogeochemical cycles, but their macroscale patterns and macroecological drivers are still largely unknown. We show the results of the most extensive field study conducted so far to investigate patterns and drivers of the distribution and structure of benthic prokaryote assemblages from 228 samples collected at latitudes comprising 34°N to 79°N, and from ca. 400- to 5570-m depth. We provide evidence that, in deep-sea ecosystems, benthic bacterial and archaeal abundances significantly increase from middle to high latitudes, with patterns more pronounced for archaea, and particularly for Marine Group I Thaumarchaeota. Our results also reveal that different microbial components show varying sensitivities to changes in temperature conditions and food supply. We conclude that climate change will primarily affect deep-sea benthic archaea, with important consequences on global biogeochemical cycles, particularly at high latitudes.},
}
@article {pmid27376057,
year = {2016},
author = {Régnier, M and Chassignet, P},
title = {Accurate Prediction of the Statistics of Repetitions in Random Sequences: A Case Study in Archaea Genomes.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {4},
number = {},
pages = {35},
doi = {10.3389/fbioe.2016.00035},
pmid = {27376057},
issn = {2296-4185},
abstract = {Repetitive patterns in genomic sequences have a great biological significance and also algorithmic implications. Analytic combinatorics allow to derive formula for the expected length of repetitions in a random sequence. Asymptotic results, which generalize previous works on a binary alphabet, are easily computable. Simulations on random sequences show their accuracy. As an application, the sample case of Archaea genomes illustrates how biological sequences may differ from random sequences.},
}
@article {pmid27356769,
year = {2016},
author = {Xue, C and Zhang, X and Zhu, C and Zhao, J and Zhu, P and Peng, C and Ling, N and Shen, Q},
title = {Quantitative and compositional responses of ammonia-oxidizing archaea and bacteria to long-term field fertilization.},
journal = {Scientific reports},
volume = {6},
number = {},
pages = {28981},
doi = {10.1038/srep28981},
pmid = {27356769},
issn = {2045-2322},
mesh = {Agriculture/*methods ; Ammonia/*metabolism ; Archaea/*classification/genetics/isolation &amp; purification/metabolism ; Bacteria/*classification/genetics/isolation &amp; purification/metabolism ; Biota/*drug effects ; Fertilizers/utilization ; Genes, Archaeal ; Genes, Bacterial ; Oxidation-Reduction ; Sequence Analysis, DNA ; *Soil Microbiology ; },
abstract = {Archaeal (AOA) and bacterial (AOB) ammonia-oxidizer responses to long-term field fertilization in a Mollisol soil were assessed through pyrosequencing of amoA genes. Long-term fertilization treatments including chemical fertilizer (NPK), NPK plus manure (NPKM), and no fertilization over 23 years altered soil properties resulting in significant shifts in AOA and AOB community composition and abundance. NPK exhibited a strong influence on AOA and AOB composition while the addition of manure neutralized the community change induced by NPK. NPK also led to significant soil acidification and enrichment of Nitrosotalea. Nitrosospira cluster 9 and 3c were the most abundant AOB populations with opposing responses to fertilization treatments. NPKM had the largest abundance of ammonia-oxidizers and highest potential nitrification activity (PNA), suggesting high N loss potential due to a doubling of nutrient input compared to NPK. PNA was strongly correlated to AOA and AOB community composition indicating that both were important in ammonium oxidization in this Mollisol soil. Total N and organic C were the most important factors driving shifts in AOA and AOB community composition. The AOA community was strongly correlated to the activities of all sugar hydrolysis associated soil enzymes and was more responsive to C and N input than AOB.},
}
@article {pmid27339136,
year = {2016},
author = {Kim, JG and Park, SJ and Sinninghe Damsté, JS and Schouten, S and Rijpstra, WI and Jung, MY and Kim, SJ and Gwak, JH and Hong, H and Si, OJ and Lee, S and Madsen, EL and Rhee, SK},
title = {Hydrogen peroxide detoxification is a key mechanism for growth of ammonia-oxidizing archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {113},
number = {28},
pages = {7888-7893},
doi = {10.1073/pnas.1605501113},
pmid = {27339136},
issn = {1091-6490},
mesh = {Ammonia/*metabolism ; Archaea/isolation &amp; purification/*physiology ; Genome, Bacterial ; Hydrogen Peroxide/*metabolism ; Nitrification ; Oxidation-Reduction ; Peroxidase/metabolism ; },
abstract = {Ammonia-oxidizing archaea (AOA), that is, members of the Thaumarchaeota phylum, occur ubiquitously in the environment and are of major significance for global nitrogen cycling. However, controls on cell growth and organic carbon assimilation by AOA are poorly understood. We isolated an ammonia-oxidizing archaeon (designated strain DDS1) from seawater and used this organism to study the physiology of ammonia oxidation. These findings were confirmed using four additional Thaumarchaeota strains from both marine and terrestrial habitats. Ammonia oxidation by strain DDS1 was enhanced in coculture with other bacteria, as well as in artificial seawater media supplemented with α-keto acids (e.g., pyruvate, oxaloacetate). α-Keto acid-enhanced activity of AOA has previously been interpreted as evidence of mixotrophy. However, assays for heterotrophic growth indicated that incorporation of pyruvate into archaeal membrane lipids was negligible. Lipid carbon atoms were, instead, derived from dissolved inorganic carbon, indicating strict autotrophic growth. α-Keto acids spontaneously detoxify H2O2 via a nonenzymatic decarboxylation reaction, suggesting a role of α-keto acids as H2O2 scavengers. Indeed, agents that also scavenge H2O2, such as dimethylthiourea and catalase, replaced the α-keto acid requirement, enhancing growth of strain DDS1. In fact, in the absence of α-keto acids, strain DDS1 and other AOA isolates were shown to endogenously produce H2O2 (up to ∼4.5 μM), which was inhibitory to growth. Genomic analyses indicated catalase genes are largely absent in the AOA. Our results indicate that AOA broadly feature strict autotrophic nutrition and implicate H2O2 as an important factor determining the activity, evolution, and community ecology of AOA ecotypes.},
}
@article {pmid27290727,
year = {2016},
author = {Shlaifer, I and Turnbull, JL},
title = {Characterization of two key enzymes for aromatic amino acid biosynthesis in symbiotic archaea.},
journal = {Extremophiles : life under extreme conditions},
volume = {20},
number = {4},
pages = {503-514},
doi = {10.1007/s00792-016-0840-z},
pmid = {27290727},
issn = {1433-4909},
mesh = {Amino Acids, Aromatic/biosynthesis ; Archaeal Proteins/chemistry/genetics/*metabolism ; Chorismate Mutase/chemistry/genetics/*metabolism ; Desulfurococcaceae/*enzymology/physiology ; Enzyme Stability ; Hot Temperature ; Nanoarchaeota/*enzymology/physiology ; Nitrosamines/metabolism ; Prephenate Dehydratase/chemistry/genetics/*metabolism ; Prephenate Dehydrogenase/chemistry/genetics/*metabolism ; Substrate Specificity ; Symbiosis ; },
abstract = {Biosynthesis of L-tyrosine (L-Tyr) and L-phenylalanine (L-Phe) is directed by the interplay of three enzymes. Chorismate mutase (CM) catalyzes the rearrangement of chorismate to prephenate, which can be either converted to hydroxyphenylpyruvate by prephenate dehydrogenase (PD) or to phenylpyruvate by prephenate dehydratase (PDT). This work reports the first characterization of a trifunctional PD-CM-PDT from the smallest hyperthermophilic archaeon Nanoarchaeum equitans and a bifunctional CM-PD from its host, the crenarchaeon Ignicoccus hospitalis. Hexa-histidine tagged proteins were expressed in Escherichia coli and purified by affinity chromatography. Specific activities determined for the trifunctional enzyme were 21, 80, and 30 U/mg for CM, PD, and PDT, respectively, and 47 and 21 U/mg for bifunctional CM and PD, respectively. Unlike most PDs, these two archaeal enzymes were insensitive to regulation by L-Tyr and preferred NADP(+) to NAD(+) as a cofactor. Both the enzymes were highly thermally stable and exhibited maximal activity at 90 °C. N. equitans PDT was feedback inhibited by L-Phe (Ki = 0.8 µM) in a non-competitive fashion consistent with L-Phe's combination at a site separate from that of prephenate. Our results suggest that PD from the unique symbiotic archaeal pair encompass a distinct subfamily of prephenate dehydrogenases with regard to their regulation and co-substrate specificity.},
}
@article {pmid27279625,
year = {2016},
author = {Voica, DM and Bartha, L and Banciu, HL and Oren, A},
title = {Heavy metal resistance in halophilic Bacteria and Archaea.},
journal = {FEMS microbiology letters},
volume = {363},
number = {14},
pages = {},
doi = {10.1093/femsle/fnw146},
pmid = {27279625},
issn = {1574-6968},
mesh = {*Adaptation, Biological ; Archaea/classification/*physiology ; Bacteria/classification/drug effects/genetics/*metabolism ; *Bacterial Physiological Phenomena/drug effects ; Biodegradation, Environmental ; Biological Transport ; Cell Membrane/metabolism ; Inactivation, Metabolic ; Metals, Heavy/*metabolism/pharmacology ; Prokaryotic Cells/physiology ; Salinity ; },
abstract = {Heavy metals are dense chemicals with dual biological role as micronutrients and intoxicants. A few hypersaline environmental systems are naturally enriched with heavy metals, while most metal-contaminated sites are a consequence of human activities. Numerous halotolerant and moderately halophilic Bacteria possess metal tolerance, whereas a few archaeal counterparts share similar features. The main mechanisms underlying heavy metal resistance in halophilic Bacteria and Archaea include extracellular metal sequestration by biopolymers, metal efflux mediated by specific transporters and enzymatic detoxification. Biotransformation of metals by halophiles has implications both for trace metal turnover in natural saline ecosystems and for development of novel bioremediation strategies.},
}
@article {pmid27268252,
year = {2016},
author = {Michael, AJ},
title = {Polyamines in Eukaryotes, Bacteria, and Archaea.},
journal = {The Journal of biological chemistry},
volume = {291},
number = {29},
pages = {14896-14903},
doi = {10.1074/jbc.R116.734780},
pmid = {27268252},
issn = {1083-351X},
mesh = {Archaea/*metabolism ; Bacteria/*metabolism ; Biosynthetic Pathways ; Eukaryota/*metabolism ; Gene Transfer, Horizontal/genetics ; Polyamines/*metabolism ; },
abstract = {Polyamines are primordial polycations found in most cells and perform different functions in different organisms. Although polyamines are mainly known for their essential roles in cell growth and proliferation, their functions range from a critical role in cellular translation in eukaryotes and archaea, to bacterial biofilm formation and specialized roles in natural product biosynthesis. At first glance, the diversity of polyamine structures in different organisms appears chaotic; however, biosynthetic flexibility and evolutionary and ecological processes largely explain this heterogeneity. In this review, I discuss the biosynthetic, evolutionary, and physiological processes that constrain or expand polyamine structural and functional diversity.},
}
@article {pmid27242149,
year = {2016},
author = {Quadri, I and Hassani, II and l'Haridon, S and Chalopin, M and Hacène, H and Jebbar, M},
title = {Characterization and antimicrobial potential of extremely halophilic archaea isolated from hypersaline environments of the Algerian Sahara.},
journal = {Microbiological research},
volume = {186-187},
number = {},
pages = {119-131},
doi = {10.1016/j.micres.2016.04.003},
pmid = {27242149},
issn = {1618-0623},
mesh = {Africa, Northern ; Algeria ; Anti-Infective Agents/*metabolism ; Archaea/classification/genetics/*isolation &amp; purification/*metabolism ; Bacterial Typing Techniques ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Environmental Microbiology ; Enzymes/metabolism ; Peptides/genetics/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {Halophilic archaea were isolated from different chotts and sebkha, dry salt lakes and salt flat respectively, of the Algerian Sahara and characterized using phenotypic and phylogenetic approaches. From 102 extremely halophilic strains isolated, forty three were selected and studied. These strains were also screened for their antagonistic potential and the production of hydrolytic enzymes. Sequencing of the 16S rRNA genes and phylogenetic analysis allowed the identification of 10 archaeal genera within the class Halobacteria: Natrinema (13 strains), Natrialba (12 strains), Haloarcula (4 strains), Halopiger (4 strains), Haloterrigena (3 strains), Halorubrum (2 strains), Halostagnicola (2 strains), Natronococcus, Halogeometricum and Haloferax (1 strain each). The most common producers of antimicrobial compounds belong to the genus Natrinema while the most hydrolytic isolates, with combined production of several enzymes, belong to the genus Natrialba. The strain affiliated to Halopiger djelfamassilliensis was found to produce some substances of interest (halocins, anti-Candida, enzymes). After partial purification and characterization of one of the strains Natrinema gari QI1, we found similarities between the antimicrobial compound and the halocin C8. Therefore, the gene encoding halocin C8 was amplified and sequenced.},
}
@article {pmid27234458,
year = {2016},
author = {Mojica, FJ and Rodriguez-Valera, F},
title = {The discovery of CRISPR in archaea and bacteria.},
journal = {The FEBS journal},
volume = {283},
number = {17},
pages = {3162-3169},
doi = {10.1111/febs.13766},
pmid = {27234458},
issn = {1742-4658},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; *CRISPR-Cas Systems ; Genome, Archaeal ; Genome, Bacterial ; Genomics ; },
abstract = {CRISPR-Cas are self-/nonself-discriminating systems found in prokaryotic cells. They represent a remarkable example of molecular memory that is hereditarily transmitted. Their discovery can be considered as one of the first fruits of the systematic exploration of prokaryotic genomes. Although this genomic feature was serendipitously discovered in molecular biology studies, it was the availability of multiple complete genomes that shed light about their role as a genetic immune system. Here we tell the story of how this discovery originated and was slowly and painstakingly advanced to the point of understating the biological role of what initially was just an odd genomic feature.},
}
@article {pmid27199977,
year = {2016},
author = {Makarova, KS and Koonin, EV and Albers, SV},
title = {Diversity and Evolution of Type IV pili Systems in Archaea.},
journal = {Frontiers in microbiology},
volume = {7},
number = {},
pages = {667},
doi = {10.3389/fmicb.2016.00667},
pmid = {27199977},
issn = {1664-302X},
support = {311523//European Research Council/International ; },
abstract = {Many surface structures in archaea including various types of pili and the archaellum (archaeal flagellum) are homologous to bacterial type IV pili systems (T4P). The T4P consist of multiple proteins, often with poorly conserved sequences, complicating their identification in sequenced genomes. Here we report a comprehensive census of T4P encoded in archaeal genomes using sensitive methods for protein sequence comparison. This analysis confidently identifies as T4P components about 5000 archaeal gene products, 56% of which are currently annotated as hypothetical in public databases. Combining results of this analysis with a comprehensive comparison of genomic neighborhoods of the T4P, we present models of organization of 10 most abundant variants of archaeal T4P. In addition to the differentiation between major and minor pilins, these models include extra components, such as S-layer proteins, adhesins and other membrane and intracellular proteins. For most of these systems, dedicated major pilin families are identified including numerous stand alone major pilin genes of the PilA family. Evidence is presented that secretion ATPases of the T4P and cognate TadC proteins can interact with different pilin sets. Modular evolution of T4P results in combinatorial variability of these systems. Potential regulatory or modulating proteins for the T4P are identified including KaiC family ATPases, vWA domain-containing proteins and the associated MoxR/GvpN ATPase, TFIIB homologs and multiple unrelated transcription regulators some of which are associated specific T4P. Phylogenomic analysis suggests that at least one T4P system was present in the last common ancestor of the extant archaea. Multiple cases of horizontal transfer and lineage-specific duplication of T4P loci were detected. Generally, the T4P of the archaeal TACK superphylum are more diverse and evolve notably faster than those of euryarchaea. The abundance and enormous diversity of T4P in hyperthermophilic archaea present a major enigma. Apparently, fundamental aspects of the biology of hyperthermophiles remain to be elucidated.},
}
@article {pmid27194687,
year = {2016},
author = {Garrity, GM},
title = {A New Genomics-Driven Taxonomy of Bacteria and Archaea: Are We There Yet?.},
journal = {Journal of clinical microbiology},
volume = {54},
number = {8},
pages = {1956-1963},
doi = {10.1128/JCM.00200-16},
pmid = {27194687},
issn = {1098-660X},
mesh = {Archaea/*classification/*genetics ; Bacteria/*classification/*genetics ; Classification/*methods ; Genomics/*methods ; Humans ; },
abstract = {Taxonomy is often criticized for being too conservative and too slow and having limited relevance because it has not taken into consideration the latest methods and findings. Yet the cumulative work product of its practitioners underpins contemporary microbiology and serves as a principal means of shaping and referencing knowledge. Using methods drawn from the field of exploratory data analysis, this minireview examines the current state of the field as it transitions from a taxonomy based on 16S rRNA gene sequences to one based on whole-genome sequences and tests the validity of some commonly held beliefs.},
}
@article {pmid27190215,
year = {2016},
author = {Fu, X and Liu, R and Sanchez, I and Silva-Sanchez, C and Hepowit, NL and Cao, S and Chen, S and Maupin-Furlow, J},
title = {Ubiquitin-Like Proteasome System Represents a Eukaryotic-Like Pathway for Targeted Proteolysis in Archaea.},
journal = {mBio},
volume = {7},
number = {3},
pages = {},
doi = {10.1128/mBio.00379-16},
pmid = {27190215},
issn = {2150-7511},
support = {R01 GM057498/GM/NIGMS NIH HHS/United States ; },
mesh = {Adenosine Triphosphatases/metabolism ; Archaea/*genetics/*metabolism ; Archaeal Proteins/chemistry/genetics/*metabolism ; Cytoplasm/chemistry/*metabolism ; Mutation ; Proteasome Endopeptidase Complex/chemistry/genetics/*metabolism ; Proteolysis ; TATA-Box Binding Protein/*metabolism ; Ubiquitin/genetics/*metabolism ; },
abstract = {UNLABELLED: The molecular mechanisms of targeted proteolysis in archaea are poorly understood, yet they may have deep evolutionary roots shared with the ubiquitin-proteasome system of eukaryotic cells. Here, we demonstrate in archaea that TBP2, a TATA-binding protein (TBP) modified by ubiquitin-like isopeptide bonds, is phosphorylated and targeted for degradation by proteasomes. Rapid turnover of TBP2 required the functions of UbaA (the E1/MoeB/ThiF homolog of archaea), AAA ATPases (Cdc48/p97 and Rpt types), a type 2 JAB1/MPN/MOV34 metalloenzyme (JAMM/MPN+) homolog (JAMM2), and 20S proteasomes. The ubiquitin-like protein modifier small archaeal modifier protein 2 (SAMP2) stimulated the degradation of TBP2, but SAMP2 itself was not degraded. Analysis of the TBP2 fractions that were not modified by ubiquitin-like linkages revealed that TBP2 had multiple N termini, including Met1-Ser2, Ser2, and Met1-Ser2(p) [where (p) represents phosphorylation]. The evidence suggested that the Met1-Ser2(p) form accumulated in cells that were unable to degrade TBP2. We propose a model in archaea in which the attachment of ubiquitin-like tags can target proteins for degradation by proteasomes and be controlled by N-terminal degrons. In support of a proteolytic mechanism that is energy dependent and recycles the ubiquitin-like protein tags, we find that a network of AAA ATPases and a JAMM/MPN+ metalloprotease are required, in addition to 20S proteasomes, for controlled intracellular proteolysis.<br><br>IMPORTANCE: This study advances the fundamental knowledge of signal-guided proteolysis in archaea and sheds light on components that are related to the ubiquitin-proteasome system of eukaryotes. In archaea, the ubiquitin-like proteasome system is found to require function of an E1/MoeB/ThiF homolog, a type 2 JAMM/MPN+ metalloprotease, and a network of AAA ATPases for the targeted destruction of proteins. We provide evidence that the attachment of the ubiquitin-like protein is controlled by an N-terminal degron and stimulates proteasome-mediated proteolysis.},
}
@article {pmid27155047,
year = {2016},
author = {Srivastava, A and Gogoi, P and Deka, B and Goswami, S and Kanaujia, SP},
title = {In silico analysis of 5'-UTRs highlights the prevalence of Shine-Dalgarno and leaderless-dependent mechanisms of translation initiation in bacteria and archaea, respectively.},
journal = {Journal of theoretical biology},
volume = {402},
number = {},
pages = {54-61},
doi = {10.1016/j.jtbi.2016.05.005},
pmid = {27155047},
issn = {1095-8541},
mesh = {5' Untranslated Regions/*genetics ; Archaea/*genetics ; Bacteria/*genetics ; Base Composition/genetics ; Base Sequence ; Codon, Initiator/genetics ; *Computer Simulation ; Genes, Archaeal ; Genes, Bacterial ; Genome Size ; Peptide Chain Initiation, Translational/*genetics ; Prokaryotic Cells ; },
abstract = {In prokaryotes, a heterogeneous set of protein translation initiation mechanisms such as Shine-Dalgarno (SD) sequence-dependent, SD sequence-independent or ribosomal protein S1 mediated and leaderless transcript-dependent exists. To estimate the distribution of coding sequences employing a particular translation initiation mechanism, a total of 107 prokaryotic genomes were analysed using in silico approaches. Analysis of 5'-untranslated regions (UTRs) of genes reveals the existence of three types of mRNAs described as transcripts with and without SD motif and leaderless transcripts. Our results indicate that although all the three types of translation initiation mechanisms are widespread among prokaryotes, the number of SD-dependent genes in bacteria is higher than that of archaea. In contrast, archaea contain a significantly higher number of leaderless genes than SD-led genes. The correlation analysis between genome size and SD-led &amp; leaderless genes suggests that the SD-led genes are decreasing (increasing) with genome size in bacteria (archaea). However, the leaderless genes are increasing (decreasing) in bacteria (archaea) with genome size. Moreover, an analysis of the start-codon biasness confirms that among ATG, GTG and TTG codons, ATG is indeed the most preferred codon at the translation initiation site in most of the coding sequences. In leaderless genes, however, the codons GTG and TTG are also observed at the translation initiation site in some species contradicting earlier studies which suggested the usage of only ATG codon. Henceforth, the conventional mechanism of translation initiation cannot be generalized as an exclusive way of initiating the process of protein biosynthesis in prokaryotes.},
}
@article {pmid27142341,
year = {2016},
author = {Koyanagi, T and Leriche, G and Yep, A and Onofrei, D and Holland, GP and Mayer, M and Yang, J},
title = {Effect of Headgroups on Small-Ion Permeability across Archaea-Inspired Tetraether Lipid Membranes.},
journal = {Chemistry (Weinheim an der Bergstrasse, Germany)},
volume = {22},
number = {24},
pages = {8074-8077},
doi = {10.1002/chem.201601326},
pmid = {27142341},
issn = {1521-3765},
mesh = {Archaea/*metabolism ; Diglycerides/chemistry ; Dynamic Light Scattering ; Fluoresceins/chemistry/metabolism ; Ions/chemistry/metabolism ; Liposomes/chemistry/metabolism ; Membrane Lipids/chemical synthesis/chemistry/*metabolism ; Phosphatidylcholines ; Spectroscopy, Fourier Transform Infrared ; X-Ray Diffraction ; },
abstract = {This paper examines the effects of four different polar headgroups on small-ion membrane permeability from liposomes comprised of Archaea-inspired glycerolmonoalkyl glycerol tetraether (GMGT) lipids. We found that the membrane-leakage rate across GMGT lipid membranes varied by a factor of ≤1.6 as a function of headgroup structure. However, the leakage rates of small ions across membranes comprised of commercial bilayer-forming 1-palmitoyl-2-oleoyl-sn-glycerol (PO) lipids varied by as much as 32-fold within the same series of headgroups. These results demonstrate that membrane leakage from GMGT lipids is less influenced by headgroup structure, making it possible to tailor the structure of the polar headgroups on GMGT lipids while retaining predictable leakage properties of membranes comprised of these tethered lipids.},
}
@article {pmid27137495,
year = {2016},
author = {Gehring, AM and Walker, JE and Santangelo, TJ},
title = {Transcription Regulation in Archaea.},
journal = {Journal of bacteriology},
volume = {198},
number = {14},
pages = {1906-1917},
doi = {10.1128/JB.00255-16},
pmid = {27137495},
issn = {1098-5530},
support = {R01 GM100329/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/*genetics/metabolism ; Archaeal Proteins/*genetics/metabolism ; *Gene Expression Regulation, Archaeal ; *Transcription, Genetic ; },
abstract = {The known diversity of metabolic strategies and physiological adaptations of archaeal species to extreme environments is extraordinary. Accurate and responsive mechanisms to ensure that gene expression patterns match the needs of the cell necessitate regulatory strategies that control the activities and output of the archaeal transcription apparatus. Archaea are reliant on a single RNA polymerase for all transcription, and many of the known regulatory mechanisms employed for archaeal transcription mimic strategies also employed for eukaryotic and bacterial species. Novel mechanisms of transcription regulation have become apparent by increasingly sophisticated in vivo and in vitro investigations of archaeal species. This review emphasizes recent progress in understanding archaeal transcription regulatory mechanisms and highlights insights gained from studies of the influence of archaeal chromatin on transcription.},
}
@article {pmid27127195,
year = {2016},
author = {Rinta-Kanto, JM and Sinkko, H and Rajala, T and Al-Soud, WA and Sørensen, SJ and Tamminen, MV and Timonen, S},
title = {Natural decay process affects the abundance and community structure of Bacteria and Archaea in Picea abies logs.},
journal = {FEMS microbiology ecology},
volume = {92},
number = {7},
pages = {},
doi = {10.1093/femsec/fiw087},
pmid = {27127195},
issn = {1574-6941},
mesh = {Archaea/classification/genetics/*isolation &amp; purification ; Bacteria/classification/genetics/*isolation &amp; purification ; Biota ; Finland ; Fungi/classification/genetics/isolation &amp; purification ; Picea/*microbiology ; Wood/*microbiology ; },
abstract = {Prokaryotes colonize decaying wood and contribute to the degradation process, but the dynamics of prokaryotic communities during wood decay is still poorly understood. We studied the abundance and community composition of Bacteria and Archaea inhabiting naturally decaying Picea abies logs and tested the hypothesis that the variations in archaeal and bacterial abundances and community composition are coupled with environmental parameters related to the decay process. The data set comprises >500 logs at different decay stages from five geographical locations in south and central Finland. The results show that Bacteria and Archaea are an integral and dynamic component of decaying wood biota. The abundances of bacterial and archaeal 16S rRNA genes increase as wood decay progresses. Changes in bacterial community composition are clearly linked to the loss of density of wood, while specific fungal-bacterial interactions may also affect the distribution of bacterial taxa in decaying wood. Thaumarchaeota were prominent members of the archaeal populations colonizing decaying wood, providing further evidence of the versatility and cosmopolitan nature of this phylum in the environment. The composition and dynamics of the prokaryotic community suggest that they are an active component of biota that are involved in processing substrates in decaying wood material.},
}
@article {pmid27114874,
year = {2016},
author = {Trembath-Reichert, E and Case, DH and Orphan, VJ},
title = {Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments.},
journal = {PeerJ},
volume = {4},
number = {},
pages = {e1913},
doi = {10.7717/peerj.1913},
pmid = {27114874},
issn = {2167-8359},
abstract = {Methane seep systems along continental margins host diverse and dynamic microbial assemblages, sustained in large part through the microbially mediated process of sulfate-coupled Anaerobic Oxidation of Methane (AOM). This methanotrophic metabolism has been linked to consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). These two groups are the focus of numerous studies; however, less is known about the wide diversity of other seep associated microorganisms. We selected a hierarchical set of FISH probes targeting a range of Deltaproteobacteria diversity. Using the Magneto-FISH enrichment technique, we then magnetically captured CARD-FISH hybridized cells and their physically associated microorganisms from a methane seep sediment incubation. DNA from nested Magneto-FISH experiments was analyzed using Illumina tag 16S rRNA gene sequencing (iTag). Enrichment success and potential bias with iTag was evaluated in the context of full-length 16S rRNA gene clone libraries, CARD-FISH, functional gene clone libraries, and iTag mock communities. We determined commonly used Earth Microbiome Project (EMP) iTAG primers introduced bias in some common methane seep microbial taxa that reduced the ability to directly compare OTU relative abundances within a sample, but comparison of relative abundances between samples (in nearly all cases) and whole community-based analyses were robust. The iTag dataset was subjected to statistical co-occurrence measures of the most abundant OTUs to determine which taxa in this dataset were most correlated across all samples. Many non-canonical microbial partnerships were statistically significant in our co-occurrence network analysis, most of which were not recovered with conventional clone library sequencing, demonstrating the utility of combining Magneto-FISH and iTag sequencing methods for hypothesis generation of associations within complex microbial communities. Network analysis pointed to many co-occurrences containing putatively heterotrophic, candidate phyla such as OD1, Atribacteria, MBG-B, and Hyd24-12 and the potential for complex sulfur cycling involving Epsilon-, Delta-, and Gammaproteobacteria in methane seep ecosystems.},
}
@article {pmid27113140,
year = {2016},
author = {Feng, G and Sun, W and Zhang, F and Karthik, L and Li, Z},
title = {Inhabitancy of active Nitrosopumilus-like ammonia-oxidizing archaea and Nitrospira nitrite-oxidizing bacteria in the sponge Theonella swinhoei.},
journal = {Scientific reports},
volume = {6},
number = {},
pages = {24966},
doi = {10.1038/srep24966},
pmid = {27113140},
issn = {2045-2322},
mesh = {Animals ; Archaea/classification/enzymology/genetics/*metabolism ; Archaeal Proteins/genetics/metabolism ; Bacteria/classification/enzymology/genetics/*metabolism ; Bacterial Proteins/genetics/metabolism ; Gene Expression Profiling/methods ; Nitrite Reductases/*genetics ; Nitrites/*metabolism ; Oxidoreductases/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/analysis ; Sequence Analysis, DNA/methods ; Sequence Analysis, RNA/methods ; Theonella/genetics/*microbiology ; },
abstract = {Nitrification directly contributes to the ammonia removal in sponges, and it plays an indispensable role in sponge-mediated nitrogen cycle. Previous studies have demonstrated genomic evidences of nitrifying lineages in the sponge Theonella swinhoei. However, little is known about the transcriptional activity of nitrifying community in this sponge. In this study, combined DNA- and transcript-based analyses were performed to reveal the composition and transcriptional activity of the nitrifiers in T. swinhoei from the South China Sea. Transcriptional activity of ammonia-oxidizing archaea (AOA) and nitrite-oxidizing bacteria (NOB) in this sponge were confirmed by targeting their nitrifying genes,16S rRNA genes and their transcripts. Phylogenetic analysis coupled with RDP rRNA classification indicated that archaeal 16S rRNA genes, amoA (the subunit of ammonia monooxygenase) genes and their transcripts were closely related to Nitrosopumilus-like AOA; whereas nitrifying bacterial 16S rRNA genes, nxrB (the subunit of nitrite oxidoreductase) genes and their transcripts were closely related to Nitrospira NOB. Quantitative assessment demonstrated relative higher abundances of nitrifying genes and transcripts of Nitrosopumilus-like AOA than those of Nitrospira NOB in this sponge. This study illustrated the transcriptional potentials of Nitrosopumilus-like archaea and Nitrospira bacteria that would predominantly contribute to the nitrification functionality in the South China Sea T. swinhoei.},
}
@article {pmid27112361,
year = {2017},
author = {Villanueva, L and Schouten, S and Damsté, JS},
title = {Phylogenomic analysis of lipid biosynthetic genes of Archaea shed light on the 'lipid divide'.},
journal = {Environmental microbiology},
volume = {19},
number = {1},
pages = {54-69},
doi = {10.1111/1462-2920.13361},
pmid = {27112361},
issn = {1462-2920},
mesh = {Archaea/genetics/*metabolism ; Bacteria/genetics/*metabolism ; Biological Evolution ; Butadienes/*metabolism ; Cell Membrane/*metabolism ; Fatty Acids/*metabolism ; Genome, Archaeal ; Glycerophosphates/*metabolism ; Hemiterpenes/*metabolism ; Membrane Lipids/chemistry/*metabolism ; Pentanes/*metabolism ; Terpenes ; },
abstract = {The lipid membrane is one of the most characteristic traits distinguishing the three domains of life. Membrane lipids of Bacteria and Eukarya are composed of fatty acids linked to glycerol-3-phosphate (G3P) via ester bonds, while those of Archaea possess isoprene-based alkyl chains linked by ether linkages to glycerol-1-phosphate (G1P), resulting in the opposite stereochemistry of the glycerol phosphate backbone. This 'lipid divide' has raised questions on the evolution of microbial life since eukaryotes are thought to have evolved from the Archaea, requiring a radical change in membrane composition. Here, we searched for homologs of enzymes involved in membrane lipid and fatty acid synthesis in a wide variety of archaeal genomes and performed phylogenomic analyses. We found that two uncultured archaeal groups, i.e. marine euryarchaeota group II/III and 'Lokiarchaeota', recently discovered descendants of the archaeal ancestor leading to eukaryotes, lack the gene to synthesize G1P and, consequently, the capacity to synthesize archaeal membrane lipids. However, our analyses reveal their genetic capacity to synthesize G3P-based 'chimeric lipids' with either two ether-bound isoprenoidal chains or with an ester-bound fatty acid instead of an ether-bound isoprenoid. These archaea may reflect the 'archaea-to-eukaryote' membrane transition stage which have led to the current 'lipid divide'.},
}
@article {pmid27109114,
year = {2016},
author = {Yang, Y and Li, N and Zhao, Q and Yang, M and Wu, Z and Xie, S and Liu, Y},
title = {Ammonia-oxidizing archaea and bacteria in water columns and sediments of a highly eutrophic plateau freshwater lake.},
journal = {Environmental science and pollution research international},
volume = {23},
number = {15},
pages = {15358-15369},
doi = {10.1007/s11356-016-6707-0},
pmid = {27109114},
issn = {1614-7499},
mesh = {Ammonia/analysis ; Archaea/enzymology/genetics ; Archaeal Proteins/genetics ; Bacteria/enzymology/genetics ; Bacterial Proteins/genetics ; China ; Eutrophication ; Geologic Sediments/*microbiology ; Lakes/*microbiology ; Nitrogen Cycle ; Oxidation-Reduction ; Oxidoreductases/genetics ; Phylogeny ; Seasons ; *Water Microbiology ; Water Pollutants, Chemical/analysis ; },
abstract = {Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) can play important roles in the microbial oxidation of ammonia nitrogen in freshwater lake, but information on spatiotemporal variation in water column and sediment community structure is still limited. Additionally, the drivers of the differences between sediment and water assemblages are still unclear. The present study investigated the variation of AOA and AOB communities in both water columns and sediments of eutrophic freshwater Dianchi Lake. The abundance, diversity, and structure of both planktonic and sediment ammonia-oxidizing microorganisms in Dianchi Lake showed the evident changes with sampling site and time. In both water columns and sediments, AOB amoA gene generally outnumbered AOA, and the AOB/AOA ratio was much higher in summer than in autumn. The total AOA amoA abundance was relatively great in autumn, while sediment AOB was relatively abundant in summer. Sediment AOA amoA abundance was likely correlated with ammonia nitrogen (rs = 0.963). The AOB/AOA ratio in lake sediment was positively correlated with total phosphorus (rs = 0.835), while pH, dissolved organic carbon, and ammonia nitrogen might be the key driving forces for the AOB/AOA ratio in lake water. Sediment AOA and AOB diversity was correlated with nitrate nitrogen (rs = -0.786) and total organic carbon (rs = 0.769), respectively, while planktonic AOB diversity was correlated with ammonia nitrogen (rs = 0.854). Surface water and sediment in the same location had a distinctively different microbial community structure. In addition, sediment AOB community structure was influenced by total phosphorus, while total phosphorus might be a key determinant of planktonic AOB community structure.},
}
@article {pmid27098176,
year = {2016},
author = {Pakpour, S and Scott, JA and Turvey, SE and Brook, JR and Takaro, TK and Sears, MR and Klironomos, J},
title = {Presence of Archaea in the Indoor Environment and Their Relationships with Housing Characteristics.},
journal = {Microbial ecology},
volume = {72},
number = {2},
pages = {305-312},
doi = {10.1007/s00248-016-0767-z},
pmid = {27098176},
issn = {1432-184X},
mesh = {Archaea/classification/*isolation &amp; purification ; DNA, Archaeal/genetics ; *Environmental Microbiology ; *Housing ; Humans ; Microbiota ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {Archaea are widespread and abundant in soils, oceans, or human and animal gastrointestinal (GI) tracts. However, very little is known about the presence of Archaea in indoor environments and factors that can regulate their abundances. Using a quantitative PCR approach, and targeting the archaeal and bacterial 16S rRNA genes in floor dust samples, we found that Archaea are a common part of the indoor microbiota, 5.01 ± 0.14 (log 16S rRNA gene copies/g dust, mean ± SE) in bedrooms and 5.58 ± 0.13 in common rooms, such as living rooms. Their abundance, however, was lower than bacteria: 9.20 ± 0.32 and 9.17 ± 0.32 in bedrooms and common rooms, respectively. In addition, by measuring a broad array of environmental factors, we obtained preliminary insights into how the abundance of total archaeal 16S rRNA gene copies in indoor environment would be associated with building characteristics and occupants' activities. Based on the results, Archaea are not equally distributed within houses, and the areas with greater input of outdoor microbiome and higher traffic and material heterogeneity tend to have a higher abundance of Archaea. Nevertheless, more research is needed to better understand causes and consequences of this microbial group in indoor environments.},
}
@article {pmid27094186,
year = {2016},
author = {Zhang, FQ and Pan, W and Gu, JD and Xu, B and Zhang, WH and Zhu, BZ and Wang, YX and Wang, YF},
title = {Dominance of ammonia-oxidizing archaea community induced by land use change from Masson pine to eucalypt plantation in subtropical China.},
journal = {Applied microbiology and biotechnology},
volume = {100},
number = {15},
pages = {6859-6869},
doi = {10.1007/s00253-016-7506-8},
pmid = {27094186},
issn = {1432-0614},
mesh = {Agriculture ; Ammonia/*metabolism ; Archaea/genetics/*metabolism ; Biodiversity ; China ; *Eucalyptus ; Forests ; Nitrification ; Oxidation-Reduction ; *Pinus ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {A considerable proportion of Masson pine forests have been converted into eucalypt plantations in the last 30 years in Guangdong Province, subtropical China, for economic reasons, which may affect the ammonia-oxidizing archaea (AOA) community and the process of ammonia transformation. In order to determine the effects of forest conversion on AOA community, AOA communities in a Masson pine (Pinus massoniana) plantation and a eucalypt (Eucalyptus urophylla) plantation, which was converted from the Masson pine, were compared. Results showed that the land use change from the Masson pine to the eucalypt plantation decreased soil nutrient levels. A significant decrease of the potential nitrification rates (PNR) was also observed after the forest conversion (p < 5 %, n = 6). AOA were the only ammonia oxidizers in both plantations (no ammonia-oxidizing bacteria were detected). The detected AOA are affiliated with the genera Nitrosotalea and Nitrososphaera. A decrease of AOA abundance and an increase of the diversity were evident with the plantation conversion in the surface layer. AOA amoA gene diversity was negatively correlated with organic C and total N, respectively (p < 0.05, n = 12). AOA amoA gene abundance was negatively correlated with NH4 (+) and available P, respectively (p < 0.05, n = 12). However, AOA abundance was positively correlated with PNR, but not significantly (p < 0.05, n = 6), indicating AOA community change was only a partial reason for the decrease of PNR.},
}
@article {pmid27088618,
year = {2016},
author = {Stantial, N and Dumpe, J and Pietrosimone, K and Baltazar, F and Crowley, DJ},
title = {Transcription-coupled repair of UV damage in the halophilic archaea.},
journal = {DNA repair},
volume = {41},
number = {},
pages = {63-68},
doi = {10.1016/j.dnarep.2016.03.007},
pmid = {27088618},
issn = {1568-7856},
mesh = {Archaeal Proteins/genetics/metabolism ; *DNA Damage ; DNA Repair/drug effects/genetics/*radiation effects ; Fructose/pharmacology ; Halobacterium/drug effects/*genetics/radiation effects ; Haloferax/drug effects/*genetics/radiation effects ; Operon/genetics ; Transcription, Genetic/drug effects/*radiation effects ; Ultraviolet Rays/*adverse effects ; },
abstract = {Transcription-coupled repair (TCR) is a subpathway of nucleotide excision repair (NER) in which excision repair proteins are targeted to RNA polymerase-arresting lesions located in the transcribed strand of active genes. TCR has been documented in a variety of bacterial and eukaryotic organisms but has yet to be observed in the Archaea. We used Halobacterium sp. NRC-1 and Haloferax volcanii to determine if TCR occurs in the halophilic archaea. Following UV irradiation of exponentially growing cultures, we quantified the rate of repair of cyclobutane pyrimidine dimers in the two strands of the rpoB2B1A1A2 and the trpDFEG operons of Halobacterium sp. NRC-1 and the pts operon of H. volcanii through the use of a Southern blot assay and strand-specific probes. TCR was observed in all three operons and was dependent on the NER gene uvrA in Halobacterium sp. NRC-1, but not in H. volcanii. The halophilic archaea likely employ a novel mechanism for TCR in which an as yet unknown coupling factor recognizes the arrested archaeal RNA polymerase complex and recruits certain NER proteins to complete the process.},
}
@article {pmid27037935,
year = {2016},
author = {Sher, Y and Ronen, Z and Nejidat, A},
title = {Differential response of ammonia-oxidizing archaea and bacteria to the wetting of salty arid soil.},
journal = {Journal of basic microbiology},
volume = {56},
number = {8},
pages = {900-906},
doi = {10.1002/jobm.201600035},
pmid = {27037935},
issn = {1521-4028},
mesh = {Ammonia/*metabolism ; Archaea/genetics/*metabolism ; Bacteria/genetics/*metabolism ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Desert Climate ; Ecosystem ; Nitrification ; Oxidation-Reduction ; Oxidoreductases/genetics/*metabolism ; Soil/chemistry ; *Soil Microbiology ; Water ; },
abstract = {Ammonia-oxidizing archaea and bacteria (AOA, AOB) catalyze the first and rate-limiting step of nitrification. To examine their differential responses to the wetting of dry and salty arid soil, AOA and AOB amoA genes (encoding subunit A of the ammonia monooxygenase) and transcripts were enumerated in dry (summer) and wet (after the first rainfall) soil under the canopy of halophytic shrubs and between the shrubs. AOA and AOB were more abundant under shrub canopies than between shrubs in both the dry and wetted soil. Soil wetting caused a significant decrease in AOB abundance under the canopy and an increase of AOA between the shrubs. The abundance of the archaeal amoA gene transcript was similar for both the wet and dry soil, and the transcript-to-gene ratios were < 1 independent of niche or water content. In contrast, the bacterial amoA transcript-to-gene ratios were between 78 and 514. The lowest ratio was in dry soil under the canopy and the highest in the soil between the shrubs. The results suggest that the AOA are more resilient to stress conditions and maintain a basic activity in arid ecosystems, while the AOB are more responsive to changes in the biotic and abiotic conditions.},
}
@article {pmid27037624,
year = {2016},
author = {Wang, C and Uversky, VN and Kurgan, L},
title = {Disordered nucleiome: Abundance of intrinsic disorder in the DNA- and RNA-binding proteins in 1121 species from Eukaryota, Bacteria and Archaea.},
journal = {Proteomics},
volume = {16},
number = {10},
pages = {1486-1498},
doi = {10.1002/pmic.201500177},
pmid = {27037624},
issn = {1615-9861},
mesh = {Archaeal Proteins/chemistry ; Bacterial Proteins/chemistry ; Binding Sites ; Computational Biology ; DNA-Binding Proteins/*chemistry ; Intrinsically Disordered Proteins/*chemistry ; Molecular Sequence Annotation ; Protein Domains ; Proteome/*chemistry ; },
abstract = {Intrinsically disordered proteins (IDPs) are abundant in various proteomes, where they play numerous important roles and complement biological activities of ordered proteins. Among functions assigned to IDPs are interactions with nucleic acids. However, often, such assignments are made based on the guilty-by-association principle. The validity of the extension of these correlations to all nucleic acid binding proteins has never been analyzed on a large scale across all domains of life. To fill this gap, we perform a comprehensive computational analysis of the abundance of intrinsic disorder and intrinsically disordered domains in nucleiomes (∼548 000 nucleic acid binding proteins) of 1121 species from Archaea, Bacteria and Eukaryota. Nucleiome is a whole complement of proteins involved in interactions with nucleic acids. We show that relative to other proteins in the corresponding proteomes, the DNA-binding proteins have significantly increased disorder content and are significantly enriched in disordered domains in Eukaryotes but not in Archaea and Bacteria. The RNA-binding proteins are significantly enriched in the disordered domains in Bacteria, Archaea and Eukaryota, while the overall abundance of disorder in these proteins is significantly increased in Bacteria, Archaea, animals and fungi. The high abundance of disorder in nucleiomes supports the notion that the nucleic acid binding proteins often require intrinsic disorder for their functions and regulation.},
}
@article {pmid27034425,
year = {2016},
author = {Surkont, J and Pereira-Leal, JB},
title = {Are There Rab GTPases in Archaea?.},
journal = {Molecular biology and evolution},
volume = {33},
number = {7},
pages = {1833-1842},
doi = {10.1093/molbev/msw061},
pmid = {27034425},
issn = {1537-1719},
mesh = {Archaea/*enzymology/genetics/metabolism ; Biological Evolution ; Eukaryotic Cells/metabolism ; Evolution, Molecular ; Guanine Nucleotide Dissociation Inhibitors/genetics/metabolism ; Phylogeny ; Protein Binding ; Protein Transport ; Sequence Analysis, Protein/methods ; rab GTP-Binding Proteins/genetics/*metabolism ; },
abstract = {A complex endomembrane system is one of the hallmarks of Eukaryotes. Vesicle trafficking between compartments is controlled by a diverse protein repertoire, including Rab GTPases. These small GTP-binding proteins contribute identity and specificity to the system, and by working as molecular switches, trigger multiple events in vesicle budding, transport, and fusion. A diverse collection of Rab GTPases already existed in the ancestral Eukaryote, yet, it is unclear how such elaborate repertoire emerged. A novel archaeal phylum, the Lokiarchaeota, revealed that several eukaryotic-like protein systems, including small GTPases, are present in Archaea. Here, we test the hypothesis that the Rab family of small GTPases predates the origin of Eukaryotes. Our bioinformatic pipeline detected multiple putative Rab-like proteins in several archaeal species. Our analyses revealed the presence and strict conservation of sequence features that distinguish eukaryotic Rabs from other small GTPases (Rab family motifs), mapping to the same regions in the structure as in eukaryotic Rabs. These mediate Rab-specific interactions with regulators of the REP/GDI (Rab Escort Protein/GDP dissociation Inhibitor) family. Sensitive structure-based methods further revealed the existence of REP/GDI-like genes in Archaea, involved in isoprenyl metabolism. Our analysis supports a scenario where Rabs differentiated into an independent family in Archaea, interacting with proteins involved in membrane biogenesis. These results further support the archaeal nature of the eukaryotic ancestor and provide a new insight into the intermediate stages and the evolutionary path toward the complex membrane-associated signaling circuits that characterize the Ras superfamily of small GTPases, and specifically Rab proteins.},
}
@article {pmid27022996,
year = {2016},
author = {Hoedt, EC and Cuív, PÓ and Evans, PN and Smith, WJ and McSweeney, CS and Denman, SE and Morrison, M},
title = {Differences down-under: alcohol-fueled methanogenesis by archaea present in Australian macropodids.},
journal = {The ISME journal},
volume = {10},
number = {10},
pages = {2376-2388},
doi = {10.1038/ismej.2016.41},
pmid = {27022996},
issn = {1751-7370},
mesh = {Alcohols/*metabolism ; Animals ; Archaea/classification/genetics/*isolation &amp; purification/*metabolism ; Australia ; Base Composition ; *Gastrointestinal Microbiome ; Hydrogen/metabolism ; Macropodidae/*microbiology ; Methane/*metabolism ; Stomach/microbiology ; },
abstract = {The Australian macropodids (kangaroos and wallabies) possess a distinctive foregut microbiota that contributes to their reduced methane emissions. However, methanogenic archaea are present within the macropodid foregut, although there is scant understanding of these microbes. Here, an isolate taxonomically assigned to the Methanosphaera genus (Methanosphaera sp. WGK6) was recovered from the anterior sacciform forestomach contents of a Western grey kangaroo (Macropus fuliginosus). Like the human gut isolate Methanosphaera stadtmanae DSMZ 3091(T), strain WGK6 is a methylotroph with no capacity for autotrophic growth. In contrast, though with the human isolate, strain WGK6 was found to utilize ethanol to support growth, but principally as a source of reducing power. Both the WGK6 and DSMZ 3091(T) genomes are very similar in terms of their size, synteny and G:C content. However, the WGK6 genome was found to encode contiguous genes encoding putative alcohol and aldehyde dehydrogenases, which are absent from the DSMZ 3091(T) genome. Interestingly, homologs of these genes are present in the genomes for several other members of the Methanobacteriales. In WGK6, these genes are cotranscribed under both growth conditions, and we propose the two genes provide a plausible explanation for the ability of WGK6 to utilize ethanol for methanol reduction to methane. Furthermore, our in vitro studies suggest that ethanol supports a greater cell yield per mol of methane formed compared to hydrogen-dependent growth. Taken together, this expansion in metabolic versatility can explain the persistence of these archaea in the kangaroo foregut, and their abundance in these 'low-methane-emitting' herbivores.},
}
@article {pmid27012006,
year = {2015},
author = {Li, H and Huang, FY and Su, JQ and Hong, YW and Yu, S},
title = {[Distribution and Diversity of Ammonium-oxidizing Archaea and Ammonium-oxidizing Bacteria in Surface Sediments of Oujiang River].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {36},
number = {12},
pages = {4659-4666},
pmid = {27012006},
issn = {0250-3301},
mesh = {Ammonia ; Ammonium Compounds/*metabolism ; Archaea/*classification/metabolism ; Bacteria/*classification/metabolism ; Denaturing Gradient Gel Electrophoresis ; Geologic Sediments/*microbiology ; Oxidation-Reduction ; Phylogeny ; Rivers/*microbiology ; },
abstract = {Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) play important roles in the biogeochemical nitrogen cycle. Rivers are important ecosystems containing a large number of functional microbes in nitrogen cycle. In this study, denaturing gradient gel electrophoresis (DGGE) and real-time quantitative PCR (qPCR) technology were used to analyze the distribution and diversity of AOA and AOB in sediments from Oujiang. The results showed that the AOA community structure was similar among various sites, while the AOB community structure was significantly different, in which all detected AOB sequences were classified into Nitrosospira and Nitrosomonas, and 90% affiliated to Nitrosospira. The community composition of AOA was influenced by NH₄⁺ and TS, in addition, the AOB composition was affected by NH₄⁺, EC, pH, NO₃⁻, TC and TN. Total sulfur (TS) and electrical conductivity (EC) were the major factors influencing the diversity of AOA and AOB, respectively. AOA abundance was significantly higher than that of AOB. EC, NH₄⁺-N and NO₃⁻-N were the main environmental factors affecting the abundance of AOA and AOB. This study indicated that the community composition and diversity of AOA and AOB were significantly influenced by environmental factors, and AOA might be dominant drivers in the ammonia oxidation process in Oujiang surface sediment.},
}
@article {pmid27010920,
year = {2016},
author = {Tanabe, AS and Toju, H},
title = {Correction: Two New Computational Methods for Universal DNA Barcoding: A Benchmark Using Barcode Sequences of Bacteria, Archaea, Animals, Fungi, and Land Plants.},
journal = {PloS one},
volume = {11},
number = {3},
pages = {e0152242},
doi = {10.1371/journal.pone.0152242},
pmid = {27010920},
issn = {1932-6203},
}
@article {pmid27010812,
year = {2016},
author = {Khelaifia, S and Lagier, JC and Nkamga, VD and Guilhot, E and Drancourt, M and Raoult, D},
title = {Aerobic culture of methanogenic archaea without an external source of hydrogen.},
journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {35},
number = {6},
pages = {985-991},
doi = {10.1007/s10096-016-2627-7},
pmid = {27010812},
issn = {1435-4373},
mesh = {Aerobiosis ; Anti-Bacterial Agents/pharmacology ; Antioxidants/metabolism ; Archaea/drug effects/*growth &amp; development/*metabolism ; Carbon/metabolism ; Culture Media ; Humans ; Hydrogen/*metabolism ; Methane/*biosynthesis ; Methanobacteriaceae/metabolism ; },
abstract = {Culturing methanogenic archaea is fastidious, expensive, and requires an external source of hydrogen and carbon dioxide. Until now, these microorganisms have only been cultivated under strictly anaerobic conditions. We previously developed a single versatile culture medium containing sugars and anti-oxydants for cultivating all human known methanogens. Performing aerobic cultures in the presence of Bacteroides thetaiotaomicron, which produces hydrogen, allows for cultivation of Methanobrevibacter smithii which itself produces methane. To obtain colonies, we cultivated M. smithii in an agar plate in the upper part of a double chamber flask with a liquid culture of B. thetaiotaomicron in the lower compartment. We subsequently cultured four other methanogenic species for the first time and successfully isolated 13 strains of M. smithii and nine strains of Methanobrevibacter oralis from 100 stools and 45 oral samples. This procedure allows aerobic isolation and antibiotic susceptibility testing. This changes the ability to routinely study methanogens, which have been neglected in clinical microbiology laboratories and may be useful for biogas production.},
}
@article {pmid27002962,
year = {2016},
author = {Reitschuler, C and Hofmann, K and Illmer, P},
title = {Abundances, diversity and seasonality of (non-extremophilic) Archaea in Alpine freshwaters.},
journal = {Antonie van Leeuwenhoek},
volume = {109},
number = {6},
pages = {855-868},
doi = {10.1007/s10482-016-0685-6},
pmid = {27002962},
issn = {1572-9699},
mesh = {Ammonia/metabolism ; Archaea/*classification/genetics/metabolism/*physiology ; Austria ; Bacteria/classification ; Biodiversity ; DNA, Archaeal/genetics ; Denaturing Gradient Gel Electrophoresis/methods ; Ecology ; Euryarchaeota/classification/genetics ; Extremophiles/*classification/genetics/metabolism/*physiology ; Fresh Water/*microbiology ; Fungi/classification ; Lakes/microbiology ; Real-Time Polymerase Chain Reaction/methods ; Reproducibility of Results ; Rivers/microbiology ; Seasons ; },
abstract = {The objectives of this study were to assess abundances and community compositions of Archaea within a heterogeneous set of freshwater systems in the Austrian Alps. Seasonal changes and geographical differences within Archaea, considering abiotic and biotic factors (e.g. temperature, pH, total organic carbon (TOC), NH4 (+), bacteria, fungi), were analysed in this context. Water samples were collected from 8 lakes, 10 creeks and the river Inn in 2014. Qualitative-quantitative data were derived via a comprehensive set of (quantitative) PCR assays and PCR-DGGE (denaturing gradient gel electrophoresis) based methodology, which was evaluated concerning specificity and reliability either previously or in this study. QPCR-derived archaeal abundances reached values of 10(3) copies mL(-1) on average, with a peak in winter-spring ('Cold Peak'), and covered 0-15 % (average: 1 %) of the microbial populations. This peak correlated with significantly raised TOC and low NH4 (+) levels during the cold seasons. Stagnant waters showed significantly higher archaeal abundances and diversities than flowing ones. Among methanogens, Methanosarcinales were the most common order. PCR-DGGE data showed that the archaeal communities were site-specific and could function as an ecological marker, in contrast to the more heterogeneous and unsteady bacterial and fungal community. This is attributable to the highly heterogeneous community of methanogenic Archaea (MA, Euryarchaeota), while only two species, Nitrosopumilus maritimus and Ca. Nitrososphaera gargensis, were found to be the ubiquitous representatives of ammonia-oxidizing Archaea (AOA, Thaumarchaeota) in Alpine freshwaters. This work emphasises the diversity, distribution and seasonality of non-extremophilic Archaea in Alpine freshwaters, with a first insight into their ecophysiological potential.},
}
@article {pmid27001046,
year = {2016},
author = {Ishino, S and Nishi, Y and Oda, S and Uemori, T and Sagara, T and Takatsu, N and Yamagami, T and Shirai, T and Ishino, Y},
title = {Identification of a mismatch-specific endonuclease in hyperthermophilic Archaea.},
journal = {Nucleic acids research},
volume = {44},
number = {7},
pages = {2977-2986},
doi = {10.1093/nar/gkw153},
pmid = {27001046},
issn = {1362-4962},
mesh = {Archaeal Proteins/genetics/isolation &amp; purification/*metabolism ; *Base Pair Mismatch ; DNA Cleavage ; Endodeoxyribonucleases/genetics/isolation &amp; purification/*metabolism ; Hot Temperature ; Mutation ; Proliferating Cell Nuclear Antigen/metabolism ; Pyrococcus furiosus/enzymology ; Recombinant Proteins/isolation &amp; purification/metabolism ; Substrate Specificity ; Thermococcus/*enzymology ; },
abstract = {The common mismatch repair system processed by MutS and MutL and their homologs was identified in Bacteria and Eukarya. However, no evidence of a functional MutS/L homolog has been reported for archaeal organisms, and it is not known whether the mismatch repair system is conserved in Archaea. Here, we describe an endonuclease that cleaves double-stranded DNA containing a mismatched base pair, from the hyperthermophilic archaeon Pyrococcus furiosus The corresponding gene revealed that the activity originates from PF0012, and we named this enzyme Endonuclease MS (EndoMS) as the mismatch-specific Endonuclease. The sequence similarity suggested that EndoMS is the ortholog of NucS isolated from Pyrococcus abyssi, published previously. Biochemical characterizations of the EndoMS homolog from Thermococcus kodakarensis clearly showed that EndoMS specifically cleaves both strands of double-stranded DNA into 5'-protruding forms, with the mismatched base pair in the central position. EndoMS cleaves G/T, G/G, T/T, T/C and A/G mismatches, with a more preference for G/T, G/G and T/T, but has very little or no effect on C/C, A/C and A/A mismatches. The discovery of this endonuclease suggests the existence of a novel mismatch repair process, initiated by the double-strand break generated by the EndoMS endonuclease, in Archaea and some Bacteria.},
}
@article {pmid26973602,
year = {2016},
author = {Kan, J and Clingenpeel, S and Dow, CL and McDermott, TR and Macur, RE and Inskeep, WP and Nealson, KH},
title = {Geochemistry and Mixing Drive the Spatial Distribution of Free-Living Archaea and Bacteria in Yellowstone Lake.},
journal = {Frontiers in microbiology},
volume = {7},
number = {},
pages = {210},
doi = {10.3389/fmicb.2016.00210},
pmid = {26973602},
issn = {1664-302X},
abstract = {Yellowstone Lake, the largest subalpine lake in the United States, harbors great novelty and diversity of Bacteria and Archaea. Size-fractionated water samples (0.1-0.8, 0.8-3.0, and 3.0-20 μm) were collected from surface photic zone, deep mixing zone, and vent fluids at different locations in the lake by using a remotely operated vehicle (ROV). Quantification with real-time PCR indicated that Bacteria dominated free-living microorganisms with Bacteria/Archaea ratios ranging from 4037:1 (surface water) to 25:1 (vent water). Microbial population structures (both Bacteria and Archaea) were assessed using 454-FLX sequencing with a total of 662,302 pyrosequencing reads for V1 and V2 regions of 16S rRNA genes. Non-metric multidimensional scaling (NMDS) analyses indicated that strong spatial distribution patterns existed from surface to deep vents for free-living Archaea and Bacteria in the lake. Along with pH, major vent-associated geochemical constituents including CH4, CO2, H2, DIC (dissolved inorganic carbon), DOC (dissolved organic carbon), SO4 (2-), O2 and metals were likely the major drivers for microbial population structures, however, mixing events occurring in the lake also impacted the distribution patterns. Distinct Bacteria and Archaea were present among size fractions, and bigger size fractions included particle-associated microbes (> 3 μm) and contained higher predicted operational taxonomic unit richness and microbial diversities (genus level) than free-living ones (<0.8 μm). Our study represents the first attempt at addressing the spatial distribution of Bacteria and Archaea in Yellowstone Lake, and our results highlight the variable contribution of Archaea and Bacteria to the hydrogeochemical-relevant metabolism of hydrogen, carbon, nitrogen, and sulfur.},
}
@article {pmid26971439,
year = {2017},
author = {Hink, L and Nicol, GW and Prosser, JI},
title = {Archaea produce lower yields of N2 O than bacteria during aerobic ammonia oxidation in soil.},
journal = {Environmental microbiology},
volume = {19},
number = {12},
pages = {4829-4837},
doi = {10.1111/1462-2920.13282},
pmid = {26971439},
issn = {1462-2920},
mesh = {Agriculture ; Alkynes/pharmacology ; Ammonia/*metabolism ; Archaea/growth &amp; development/*metabolism ; Bacteria/growth &amp; development/*metabolism ; Denitrification ; Fertilizers/analysis ; Global Warming ; Nitrification ; Nitrogen Cycle ; Nitrous Oxide/*metabolism ; Oxidation-Reduction ; Soil ; Soil Microbiology ; },
abstract = {Nitrogen fertilisation of agricultural soil contributes significantly to emissions of the potent greenhouse gas nitrous oxide (N2 O), which is generated during denitrification and, in oxic soils, mainly by ammonia oxidisers. Although laboratory cultures of ammonia oxidising bacteria (AOB) and archaea (AOA) produce N2 O, their relative activities in soil are unknown. This work tested the hypothesis that AOB dominate ammonia oxidation and N2 O production under conditions of high inorganic ammonia (NH3) input, but result mainly from the activity of AOA when NH3 is derived from mineralisation. 1-octyne, a recently discovered inhibitor of AOB, was used to distinguish N2 O production resulting from archaeal and bacterial ammonia oxidation in soil microcosms, and specifically inhibited AOB growth, activity and N2 O production. In unamended soils, ammonia oxidation and N2 O production were lower and resulted mainly from ammonia oxidation by AOA. The AOA N2 O yield relative to nitrite produced was half that of AOB, likely due to additional enzymatic mechanisms in the latter, but ammonia oxidation and N2 O production were directly linked in all treatments. Relative contributions of AOA and AOB to N2 O production, therefore, reflect their respective contributions to ammonia oxidation. These results suggest potential mitigation strategies for N2 O emissions from fertilised agricultural soils.},
}
@article {pmid26961528,
year = {2016},
author = {Song, H and Che, Z and Cao, W and Huang, T and Wang, J and Dong, Z},
title = {Changing roles of ammonia-oxidizing bacteria and archaea in a continuously acidifying soil caused by over-fertilization with nitrogen.},
journal = {Environmental science and pollution research international},
volume = {23},
number = {12},
pages = {11964-11974},
doi = {10.1007/s11356-016-6396-8},
pmid = {26961528},
issn = {1614-7499},
mesh = {Ammonia/chemistry ; Archaea/genetics ; Bacteria/genetics ; Betaproteobacteria/genetics ; Fertilizers ; Hydrogen-Ion Concentration ; Microbial Consortia/*drug effects ; *Nitrification ; Nitrogen/chemistry/*pharmacology ; Oxidation-Reduction ; Phylogeny ; Real-Time Polymerase Chain Reaction ; Soil/*chemistry ; *Soil Microbiology ; },
abstract = {Nitrification coupled with nitrate leaching contributes to soil acidification. However, little is known about the effect of soil acidification on nitrification, especially on ammonia oxidation that is the rate-limiting step of nitrification and performed by ammonia-oxidizing bacteria (AOB) and archaea (AOA). Serious soil acidification occurs in Chinese greenhouses due to the overuse of N-fertilizer. In the present study, greenhouse soils with 1, 3, 5, 7, and 9 years of vegetable cultivation showed a consistent pH decline (i.e., 7.0, 6.3, 5.6, 4.9, and 4.3). Across the pH gradient, we analyzed the community structure and abundance of AOB and AOA by pyrosequencing and real-time PCR techniques, respectively. The recovered nitrification potential (RNP) method was used to determine relative contributions of AOA and AOB to nitrification potential. The results revealed that soil acidification shaped the community structures of AOA and AOB. In acidifying soil, soil pH, NH3 concentration, and DOC content were critical factors shaping ammonia oxidizer community structure. AOB abundance, but not AOA, was strongly influenced by soil acidification. When soil pH was below 5.0, AOA rather than AOB were responsible for almost all of the RNP. However, when soil pH ranged from 5.6 to 7.0, AOB were the major contributors to RNP. The group I.1a-associatied AOA had more relative abundance in low pH (pH<6.3), whereas group I.1b tended to prefer neutral pH. Clusters 2, 10, and 12 in AOB were more abundant in acidic soil (pH <5.6), while Nitrosomonas-like lineage and unclassified lineage 3 were prevailing in neutral soil and slightly acidic soil (pH, 6.0-6.5), respectively. These results suggested that soil acidification had a profound impact on ammonia oxidation and more specific lineages in AOB occupying different pH-associated niches required further investigation.},
}
@article {pmid26960319,
year = {2016},
author = {Zhang, Y and Chen, L and Sun, R and Dai, T and Tian, J and Zheng, W and Wen, D},
title = {Population and diversity of ammonia-oxidizing archaea and bacteria in a pollutants' receiving area in Hangzhou Bay.},
journal = {Applied microbiology and biotechnology},
volume = {100},
number = {13},
pages = {6035-6045},
doi = {10.1007/s00253-016-7421-z},
pmid = {26960319},
issn = {1432-0614},
mesh = {Ammonia/*metabolism ; Archaea/classification/genetics/*isolation &amp; purification/metabolism ; Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Bays/analysis/*microbiology ; *Biodiversity ; China ; Geologic Sediments/chemistry/microbiology ; Oxidation-Reduction ; Phylogeny ; Water Pollution, Chemical/analysis ; },
abstract = {The community structure of ammonia-oxidizing microorganisms is sensitive to various environmental factors, including pollutions. In this study, real-time PCR and 454 pyrosequencing were adopted to investigate the population and diversity of ammonia-oxidizing archaea (AOA) and bacteria (AOB) temporally and spatially in the sediments of an industrial effluent receiving area in the Qiantang River's estuary, Hangzhou Bay. The abundances of AOA and AOB amoA genes fluctuated in 10(5)-10(7) gene copies per gram of sediment; the ratio of AOA amoA/AOB amoA ranged in 0.39-5.52. The AOA amoA/archaeal 16S rRNA, AOB amoA/bacterial 16S rRNA, and AOA amoA/AOB amoA were found to positively correlate with NH4 (+)-N concentration of the seawater. Nitrosopumilus cluster and Nitrosomonas-like cluster were the dominant AOA and AOB, respectively. The community structures of both AOA and AOB in the sediments exhibited significant seasonal differences rather than spatial changes in the effluent receiving area. The phylogenetic distribution of AOB in this area was consistent with the wastewater treatment plants (WWTPs) discharging the effluent but differed from the Qiantang River and other estuaries, which might be an outcome of long-term effluent discharge.},
}
@article {pmid26953597,
year = {2016},
author = {Orsi, WD and Smith, JM and Liu, S and Liu, Z and Sakamoto, CM and Wilken, S and Poirier, C and Richards, TA and Keeling, PJ and Worden, AZ and Santoro, AE},
title = {Diverse, uncultivated bacteria and archaea underlying the cycling of dissolved protein in the ocean.},
journal = {The ISME journal},
volume = {10},
number = {9},
pages = {2158-2173},
doi = {10.1038/ismej.2016.20},
pmid = {26953597},
issn = {1751-7370},
mesh = {Archaea/genetics/*metabolism ; Bacteria/genetics/*metabolism ; California ; Carbon/*metabolism ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Nitrogen/*metabolism ; Oceans and Seas ; Phytoplankton/genetics/*metabolism ; Proteins/*metabolism ; },
abstract = {Dissolved organic nitrogen (DON) supports a significant amount of heterotrophic production in the ocean. Yet, to date, the identity and diversity of microbial groups that transform DON are not well understood. To better understand the organisms responsible for transforming high molecular weight (HMW)-DON in the upper ocean, isotopically labeled protein extract from Micromonas pusilla, a eukaryotic member of the resident phytoplankton community, was added as substrate to euphotic zone water from the central California Current system. Carbon and nitrogen remineralization rates from the added proteins ranged from 0.002 to 0.35 μmol C l(-1) per day and 0.03 to 0.27 nmol N l(-1) per day. DNA stable-isotope probing (DNA-SIP) coupled with high-throughput sequencing of 16S rRNA genes linked the activity of 77 uncultivated free-living and particle-associated bacterial and archaeal taxa to the utilization of Micromonas protein extract. The high-throughput DNA-SIP method was sensitive in detecting isotopic assimilation by individual operational taxonomic units (OTUs), as substrate assimilation was observed after only 24 h. Many uncultivated free-living microbial taxa are newly implicated in the cycling of dissolved proteins affiliated with the Verrucomicrobia, Planctomycetes, Actinobacteria and Marine Group II (MGII) Euryarchaeota. In addition, a particle-associated community actively cycling DON was discovered, dominated by uncultivated organisms affiliated with MGII, Flavobacteria, Planctomycetes, Verrucomicrobia and Bdellovibrionaceae. The number of taxa assimilating protein correlated with genomic representation of TonB-dependent receptor (TBDR)-encoding genes, suggesting a possible role of TBDR in utilization of dissolved proteins by marine microbes. Our results significantly expand the known microbial diversity mediating the cycling of dissolved proteins in the ocean.},
}
@article {pmid26950522,
year = {2016},
author = {Zhu, C and Wakeham, SG and Elling, FJ and Basse, A and Mollenhauer, G and Versteegh, GJ and Könneke, M and Hinrichs, KU},
title = {Stratification of archaeal membrane lipids in the ocean and implications for adaptation and chemotaxonomy of planktonic archaea.},
journal = {Environmental microbiology},
volume = {18},
number = {12},
pages = {4324-4336},
doi = {10.1111/1462-2920.13289},
pmid = {26950522},
issn = {1462-2920},
mesh = {Adaptation, Physiological ; Archaea/classification/isolation &amp; purification/*metabolism ; Cell Membrane/chemistry/metabolism ; Ecology ; *Lipid Metabolism ; Lipids/chemistry ; Membrane Lipids/chemistry/*metabolism ; Oceans and Seas ; Oxygen/metabolism ; Plankton/classification/isolation &amp; purification/*metabolism ; Seawater/chemistry/*microbiology ; },
abstract = {Membrane lipids of marine planktonic archaea have provided unique insights into archaeal ecology and paleoceanography. However, past studies of archaeal lipids in suspended particulate matter (SPM) and sediments mainly focused on a small class of fully saturated glycerol dibiphytanyl glycerol tetraether (GDGT) homologues identified decades ago. The apparent low structural diversity of GDGTs is in strong contrast to the high diversity of metabolism and taxonomy among planktonic archaea. Furthermore, adaptation of archaeal lipids in the deep ocean remains poorly constrained. We report the archaeal lipidome in SPM from diverse oceanic regimes. We extend the known inventory of planktonic archaeal lipids to include numerous unsaturated archaeal ether lipids (uns-AELs). We further reveal (i) different thermal regulations and polar headgroup compositions of membrane lipids between the epipelagic (≤ 100 m) and deep (>100 m) populations of archaea, (ii) stratification of unsaturated GDGTs with varying redox conditions, and (iii) enrichment of tetra-unsaturated archaeol and fully saturated GDGTs in epipelagic and deep oxygenated waters, respectively. Such stratified lipid patterns are consistent with the typical distribution of archaeal phylotypes in marine environments. We, thus, provide an ecological context for GDGT-based paleoclimatology and bring about the potential use of uns-AELs as biomarkers for planktonic Euryarchaeota.},
}
@article {pmid26950321,
year = {2016},
author = {Utturkar, SM and Huber, H and Leptihn, S and Loh, B and Brown, SD and Stetter, KO and Podar, M},
title = {Draft Genome Sequence of Pyrodictium occultum PL19T, a Marine Hyperthermophilic Species of Archaea That Grows Optimally at 105°C.},
journal = {Genome announcements},
volume = {4},
number = {1},
pages = {},
doi = {10.1128/genomeA.00016-16},
pmid = {26950321},
issn = {2169-8287},
abstract = {We report here the draft genome sequence of Pyrodictium occultum PL19(T), a marine hyperthermophilic archaeon. The genome provides insights into molecular and cellular adaptation mechanisms to life in extreme environments and the evolution of early organisms on Earth.},
}
@article {pmid26946536,
year = {2016},
author = {Sauder, LA and Ross, AA and Neufeld, JD},
title = {Nitric oxide scavengers differentially inhibit ammonia oxidation in ammonia-oxidizing archaea and bacteria.},
journal = {FEMS microbiology letters},
volume = {363},
number = {7},
pages = {},
doi = {10.1093/femsle/fnw052},
pmid = {26946536},
issn = {1574-6968},
mesh = {Ammonia/antagonists &amp; inhibitors/*metabolism ; Archaea/*drug effects/*metabolism ; Bacteria/*drug effects/*metabolism ; Benzenesulfonates/pharmacology ; Benzoates/pharmacology ; Betaproteobacteria/drug effects/metabolism ; Caffeic Acids/pharmacology ; Chromans/pharmacology ; Curcumin/pharmacology ; Imidazoles/pharmacology ; Nitric Oxide/*metabolism ; Nitrification ; Nitrosomonas europaea/drug effects/metabolism ; Oxidation-Reduction/drug effects ; Phylogeny ; *Soil Microbiology ; },
abstract = {Differential inhibitors are important for measuring the relative contributions of microbial groups, such as ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), to biogeochemical processes in environmental samples. In particular, 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO) represents a nitric oxide scavenger used for the specific inhibition of AOA, implicating nitric oxide as an intermediate of thaumarchaeotal ammonia oxidation. This study investigated four alternative nitric oxide scavengers for their ability to differentially inhibit AOA and AOB in comparison to PTIO. Caffeic acid, curcumin, methylene blue hydrate and trolox were tested onNitrosopumilus maritimus, two unpublished AOA representatives (AOA-6f and AOA-G6) as well as the AOB representative Nitrosomonas europaea All four scavengers inhibited ammonia oxidation by AOA at lower concentrations than for AOB. In particular, differential inhibition of AOA and AOB by caffeic acid (100 μM) and methylene blue hydrate (3 μM) was comparable to carboxy-PTIO (100 μM) in pure and enrichment culture incubations. However, when added to aquarium sponge biofilm microcosms, both scavengers were unable to inhibit ammonia oxidation consistently, likely due to degradation of the inhibitors themselves. This study provides evidence that a variety of nitric oxide scavengers result in differential inhibition of ammonia oxidation in AOA and AOB, and provides support to the proposed role of nitric oxide as a key intermediate in the thaumarchaeotal ammonia oxidation pathway.},
}
@article {pmid26925607,
year = {2016},
author = {Graziadei, A and Masiewicz, P and Lapinaite, A and Carlomagno, T},
title = {Archaea box C/D enzymes methylate two distinct substrate rRNA sequences with different efficiency.},
journal = {RNA (New York, N.Y.)},
volume = {22},
number = {5},
pages = {764-772},
doi = {10.1261/rna.054320.115},
pmid = {26925607},
issn = {1469-9001},
mesh = {Archaea/*enzymology ; Enzymes/*metabolism ; Methylation ; Mutation ; Nucleic Acid Conformation ; RNA, Ribosomal/chemistry/*genetics ; },
abstract = {RNA modifications confer complexity to the 4-nucleotide polymer; nevertheless, their exact function is mostly unknown. rRNA 2'-O-ribose methylation concentrates to ribosome functional sites and is important for ribosome biogenesis. The methyl group is transferred to rRNA by the box C/D RNPs: The rRNA sequence to be methylated is recognized by a complementary sequence on the guide RNA, which is part of the enzyme. In contrast to their eukaryotic homologs, archaeal box C/D enzymes can be assembled in vitro and are used to study the mechanism of 2'-O-ribose methylation. In Archaea, each guide RNA directs methylation to two distinct rRNA sequences, posing the question whether this dual architecture of the enzyme has a regulatory role. Here we use methylation assays and low-resolution structural analysis with small-angle X-ray scattering to study the methylation reaction guided by the sR26 guide RNA fromPyrococcus furiosus We find that the methylation efficacy at sites D and D' differ substantially, with substrate D' turning over more efficiently than substrate D. This observation correlates well with structural data: The scattering profile of the box C/D RNP half-loaded with substrate D' is similar to that of the holo complex, which has the highest activity. Unexpectedly, the guide RNA secondary structure is not responsible for the functional difference at the D and D' sites. Instead, this difference is recapitulated by the nature of the first base pair of the guide-substrate duplex. We suggest that substrate turnover may occur through a zip mechanism that initiates at the 5'-end of the product.},
}
@article {pmid26914534,
year = {2016},
author = {Crits-Christoph, A and Gelsinger, DR and Ma, B and Wierzchos, J and Ravel, J and Davila, A and Casero, MC and DiRuggiero, J},
title = {Functional interactions of archaea, bacteria and viruses in a hypersaline endolithic community.},
journal = {Environmental microbiology},
volume = {18},
number = {6},
pages = {2064-2077},
doi = {10.1111/1462-2920.13259},
pmid = {26914534},
issn = {1462-2920},
mesh = {Archaea/genetics ; Archaeal Proteins/chemistry ; Bacteria/genetics/*isolation &amp; purification ; Cyanobacteria/genetics/isolation &amp; purification/virology ; *Desert Climate ; Ecosystem ; Euryarchaeota/genetics/*isolation &amp; purification/virology ; Genome, Viral ; Isoelectric Point ; Metagenome ; Microbial Consortia ; Microbial Interactions ; Phylogeny ; *Salinity ; Viruses/genetics/*isolation &amp; purification ; },
abstract = {Halite endoliths in the Atacama Desert represent one of the most extreme ecosystems on Earth. Cultivation-independent methods were used to examine the functional adaptations of the microbial consortia inhabiting halite nodules. The community was dominated by haloarchaea and functional analysis attributed most of the autotrophic CO2 fixation to one unique cyanobacterium. The assembled 1.1 Mbp genome of a novel nanohaloarchaeon, Candidatus Nanopetramus SG9, revealed a photoheterotrophic life style and a low median isoelectric point (pI) for all predicted proteins, suggesting a 'salt-in' strategy for osmotic balance. Predicted proteins of the algae identified in the community also had pI distributions similar to 'salt-in' strategists. The Nanopetramus genome contained a unique CRISPR/Cas system with a spacer that matched a partial viral genome from the metagenome. A combination of reference-independent methods identified over 30 complete or near complete viral or proviral genomes with diverse genome structure, genome size, gene content and hosts. Putative hosts included Halobacteriaceae, Nanohaloarchaea and Cyanobacteria. Despite the dependence of the halite community on deliquescence for liquid water availability, this study exposed an ecosystem spanning three phylogenetic domains, containing a large diversity of viruses and predominance of a 'salt-in' strategy to balance the high osmotic pressure of the environment.},
}
@article {pmid26886233,
year = {2016},
author = {MacNeill, SA},
title = {PCNA-binding proteins in the archaea: novel functionality beyond the conserved core.},
journal = {Current genetics},
volume = {62},
number = {3},
pages = {527-532},
doi = {10.1007/s00294-016-0577-3},
pmid = {26886233},
issn = {1432-0983},
mesh = {Archaea/genetics/*metabolism ; Carrier Proteins/chemistry/*metabolism ; DNA Repair ; DNA Replication ; Proliferating Cell Nuclear Antigen/chemistry/*metabolism ; Protein Binding ; Protein Interaction Domains and Motifs ; Protein Interaction Mapping ; Protein Multimerization ; },
abstract = {Sliding clamps play an essential role in coordinating protein activity in DNA metabolism in all three domains of life. In eukaryotes and archaea, the sliding clamp is PCNA (proliferating cell nuclear antigen). Across the diversity of the archaea PCNA interacts with a highly conserved set of proteins with key roles in DNA replication and repair, including DNA polymerases B and D, replication factor C, the Fen1 nuclease and RNAseH2, but this core set of factors is likely to represent a fraction of the PCNA interactome only. Here, I review three recently characterised non-core archaeal PCNA-binding proteins NusS, NreA/NreB and TIP, highlighting what is known of their interactions with PCNA and their functions in vivo and in vitro. Gaining a detailed understanding of the non-core PCNA interactome will provide significant insights into key aspects of chromosome biology in divergent archaeal lineages.},
}
@article {pmid26884161,
year = {2016},
author = {Rensen, EI and Mochizuki, T and Quemin, E and Schouten, S and Krupovic, M and Prangishvili, D},
title = {A virus of hyperthermophilic archaea with a unique architecture among DNA viruses.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {113},
number = {9},
pages = {2478-2483},
doi = {10.1073/pnas.1518929113},
pmid = {26884161},
issn = {1091-6490},
mesh = {Archaea/*virology ; DNA Viruses/*classification/genetics/ultrastructure ; Genome, Viral ; Host-Pathogen Interactions ; Microscopy, Electron, Transmission ; },
abstract = {Viruses package their genetic material in diverse ways. Most known strategies include encapsulation of nucleic acids into spherical or filamentous virions with icosahedral or helical symmetry, respectively. Filamentous viruses with dsDNA genomes are currently associated exclusively with Archaea. Here, we describe a filamentous hyperthermophilic archaeal virus, Pyrobaculum filamentous virus 1 (PFV1), with a type of virion organization not previously observed in DNA viruses. The PFV1 virion, 400 ± 20 × 32 ± 3 nm, contains an envelope and an inner core consisting of two structural units: a rod-shaped helical nucleocapsid formed of two 14-kDa major virion proteins and a nucleocapsid-encompassing protein sheath composed of a single major virion protein of 18 kDa. The virion organization of PFV1 is superficially similar to that of negative-sense RNA viruses of the family Filoviridae, including Ebola virus and Marburg virus. The linear dsDNA of PFV1 carries 17,714 bp, including 60-bp-long terminal inverted repeats, and contains 39 predicted ORFs, most of which do not show similarities to sequences in public databases. PFV1 is a lytic virus that completely disrupts the host cell membrane at the end of the infection cycle.},
}
@article {pmid26879980,
year = {2016},
author = {Gerrity, S and Clifford, E and Kennelly, C and Collins, G},
title = {Ammonia oxidizing bacteria and archaea in horizontal flow biofilm reactors treating ammonia-contaminated air at 10 °C.},
journal = {Journal of industrial microbiology &amp; biotechnology},
volume = {43},
number = {5},
pages = {651-661},
doi = {10.1007/s10295-016-1740-z},
pmid = {26879980},
issn = {1476-5535},
mesh = {Air/*analysis ; Ammonia/*isolation &amp; purification/*metabolism ; Archaea/*metabolism ; Bacteria/*metabolism ; *Biofilms ; *Bioreactors ; Feasibility Studies ; Nitrates/metabolism ; *Nitrification ; Nitrites/metabolism ; Oxidation-Reduction ; *Temperature ; },
abstract = {The objective of this study was to demonstrate the feasibility of novel, Horizontal Flow Biofilm Reactor (HFBR) technology for the treatment of ammonia (NH3)-contaminated airstreams. Three laboratory-scale HFBRs were used for remediation of an NH3-containing airstream at 10 °C during a 90-d trial to test the efficacy of low-temperature treatment. Average ammonia removal efficiencies of 99.7 % were achieved at maximum loading rates of 4.8 g NH3 m(3) h(-1). Biological nitrification of ammonia to nitrite (NO2 (-)) and nitrate (NO3 (-)) was mediated by nitrifying bacterial and archaeal biofilm populations. Ammonia-oxidising bacteria (AOB) were significantly more abundant than ammonia-oxidising archaea (AOA) vertically at each of seven sampling zones along the vertical HFBRs. Nitrosomonas and Nitrosospira, were the two most dominant bacterial genera detected in the HFBRs, while an uncultured archaeal clone dominated the AOA community. The bacterial community composition across the three HFBRs was highly conserved, although variations occurred between HFBR zones and were driven by physicochemical variables. The study demonstrates the feasibility of HFBRs for the treatment of ammonia-contaminated airstreams at low temperatures; identifies key nitrifying microorganisms driving the removal process; and provides insights for process optimisation and control. The findings are significant for industrial applications of gas oxidation technology in temperate climates.},
}
@article {pmid26834709,
year = {2015},
author = {Lu, S and Liu, X and Ma, Z and Liu, Q and Wu, Z and Zeng, X and Shi, X and Gu, Z},
title = {Vertical Segregation and Phylogenetic Characterization of Ammonia-Oxidizing Bacteria and Archaea in the Sediment of a Freshwater Aquaculture Pond.},
journal = {Frontiers in microbiology},
volume = {6},
number = {},
pages = {1539},
doi = {10.3389/fmicb.2015.01539},
pmid = {26834709},
issn = {1664-302X},
abstract = {Pond aquaculture is the major freshwater aquaculture method in China. Ammonia-oxidizing communities inhabiting pond sediments play an important role in controlling culture water quality. However, the distribution and activities of ammonia-oxidizing microbial communities along sediment profiles are poorly understood in this specific environment. Vertical variations in the abundance, transcription, potential ammonia oxidizing rate, and community composition of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in sediment samples (0-50 cm depth) collected from a freshwater aquaculture pond were investigated. The concentrations of the AOA amoA gene were higher than those of the AOB by an order of magnitude, which suggested that AOA, as opposed to AOB, were the numerically predominant ammonia-oxidizing organisms in the surface sediment. This could be attributed to the fact that AOA are more resistant to low levels of dissolved oxygen. However, the concentrations of the AOB amoA mRNA were higher than those of the AOA by 2.5- to 39.9-fold in surface sediments (0-10 cm depth), which suggests that the oxidation of ammonia was mainly performed by AOB in the surface sediments, and by AOA in the deeper sediments, where only AOA could be detected. Clone libraries of AOA and AOB amoA sequences indicated that the diversity of AOA and AOB decreased with increasing depth. The AOB community consisted of two groups: the Nitrosospira and Nitrosomonas clusters, and Nitrosomonas were predominant in the freshwater pond sediment. All AOA amoA gene sequences in the 0-2 cm deep sediment were grouped into the Nitrososphaera cluster, while other AOA sequences in deeper sediments (10-15 and 20-25 cm depths) were grouped into the Nitrosopumilus cluster.},
}
@article {pmid26769275,
year = {2016},
author = {Taha, and Siddiqui, KS and Campanaro, S and Najnin, T and Deshpande, N and Williams, TJ and Aldrich-Wright, J and Wilkins, M and Curmi, PM and Cavicchioli, R},
title = {Single TRAM domain RNA-binding proteins in Archaea: functional insight from Ctr3 from the Antarctic methanogen Methanococcoides burtonii.},
journal = {Environmental microbiology},
volume = {18},
number = {9},
pages = {2810-2824},
doi = {10.1111/1462-2920.13229},
pmid = {26769275},
issn = {1462-2920},
mesh = {Antarctic Regions ; Archaeal Proteins/*chemistry/genetics/metabolism ; Cold Temperature ; Methanosarcinaceae/*genetics ; RNA, Archaeal/*chemistry/metabolism ; RNA, Ribosomal, 5S/chemistry/metabolism ; RNA, Transfer/chemistry/metabolism ; RNA-Binding Proteins/*chemistry/genetics/metabolism ; },
abstract = {TRAM domain proteins present in Archaea and Bacteria have a β-barrel shape with anti-parallel β-sheets that form a nucleic acid binding surface; a structure also present in cold shock proteins (Csps). Aside from protein structures, experimental data defining the function of TRAM domains is lacking. Here, we explore the possible functional properties of a single TRAM domain protein, Ctr3 (cold-responsive TRAM domain protein 3) from the Antarctic archaeon Methanococcoides burtonii that has increased abundance during low temperature growth. Ribonucleic acid (RNA) bound by Ctr3 in vitro was determined using RNA-seq. Ctr3-bound M. burtonii RNA with a preference for transfer (t)RNA and 5S ribosomal RNA, and a potential binding motif was identified. In tRNA, the motif represented the C loop; a region that is conserved in tRNA from all domains of life and appears to be solvent exposed, potentially providing access for Ctr3 to bind. Ctr3 and Csps are structurally similar and are both inferred to function in low temperature translation. The broad representation of single TRAM domain proteins within Archaea compared with their apparent absence in Bacteria, and scarcity of Csps in Archaea but prevalence in Bacteria, suggests they represent distinct evolutionary lineages of functionally equivalent RNA-binding proteins.},
}
@article {pmid26750123,
year = {2016},
author = {Calegari-Santos, R and Diogo, RA and Fontana, JD and Bonfim, TM},
title = {Carotenoid Production by Halophilic Archaea Under Different Culture Conditions.},
journal = {Current microbiology},
volume = {72},
number = {5},
pages = {641-651},
doi = {10.1007/s00284-015-0974-8},
pmid = {26750123},
issn = {1432-0991},
mesh = {Archaea/genetics/*metabolism ; Carotenoids/*biosynthesis ; Culture Media/chemistry/*metabolism ; Sodium Chloride/metabolism ; },
abstract = {Carotenoids are pigments that may be used as colorants and antioxidants in food, pharmaceutical, and cosmetic industries. Since they also benefit human health, great efforts have been undertaken to search for natural sources of carotenoids, including microbial ones. The optimization of culture conditions to increase carotenoid yield is one of the strategies used to minimize the high cost of carotenoid production by microorganisms. Halophilic archaea are capable of producing carotenoids according to culture conditions. Their main carotenoid is bacterioruberin with 50 carbon atoms. In fact, the carotenoid has important biological functions since it acts as cell membrane reinforcement and it protects the microorganism against DNA damaging agents. Moreover, carotenoid extracts from halophilic archaea have shown high antioxidant capacity. Therefore, current review summarizes the effect of different culture conditions such as salt and carbon source concentrations in the medium, light incidence, and oxygen tension on carotenoid production by halophilic archaea and the strategies such as optimization methodology and two-stage cultivation already used to increase the carotenoid yield of these microorganisms.},
}
@article {pmid26745984,
year = {2016},
author = {Yan, S and Wu, G},
title = {Analysis on evolutionary relationship of amylases from archaea, bacteria and eukaryota.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {32},
number = {2},
pages = {24},
doi = {10.1007/s11274-015-1979-y},
pmid = {26745984},
issn = {1573-0972},
mesh = {Amino Acid Sequence ; Amylases/classification/*genetics/metabolism ; Archaea/*enzymology/genetics ; Bacteria/*enzymology/genetics ; Data Interpretation, Statistical ; Eukaryota/*enzymology/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Engineering ; Genetic Variation ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; },
abstract = {Amylase is one of the earliest characterized enzymes and has many applications in clinical and industrial settings. In biotechnological industries, the amylase activity is enhanced through modifying amylase structure and through cloning and expressing targeted amylases in different species. It is important to understand how engineered amylases can survive from generation to generation. This study used phylogenetic and statistical approaches to explore general patterns of amylases evolution, including 3118 α-amylases and 280 β-amylases from archaea, eukaryota and bacteria with fully documented taxonomic lineage. First, the phylogenetic tree was created to analyze the evolution of amylases with focus on individual amylases used in biofuel industry. Second, the average pairwise p-distance was computed for each kingdom, phylum, class, order, family and genus, and its diversity implies multi-time and multi-clan evolution. Finally, the variance was further partitioned into inter-clan variance and intra-clan variance for each taxonomic group, and they represent horizontal and vertical gene transfer. Theoretically, the results show a full picture on the evolution of amylases in manners of vertical and horizontal gene transfer, and multi-time and multi-clan evolution as well. Practically, this study provides the information on the surviving chance of desired amylase in a given taxonomic group, which may potentially enhance the successful rate of cloning and expression of amylase gene in different species.},
}
@article {pmid26733968,
year = {2015},
author = {Arshad, A and Speth, DR and de Graaf, RM and Op den Camp, HJ and Jetten, MS and Welte, CU},
title = {A Metagenomics-Based Metabolic Model of Nitrate-Dependent Anaerobic Oxidation of Methane by Methanoperedens-Like Archaea.},
journal = {Frontiers in microbiology},
volume = {6},
number = {},
pages = {1423},
doi = {10.3389/fmicb.2015.01423},
pmid = {26733968},
issn = {1664-302X},
abstract = {Methane oxidation is an important process to mitigate the emission of the greenhouse gas methane and further exacerbating of climate forcing. Both aerobic and anaerobic microorganisms have been reported to catalyze methane oxidation with only a few possible electron acceptors. Recently, new microorganisms were identified that could couple the oxidation of methane to nitrate or nitrite reduction. Here we investigated such an enrichment culture at the (meta) genomic level to establish a metabolic model of nitrate-driven anaerobic oxidation of methane (nitrate-AOM). Nitrate-AOM is catalyzed by an archaeon closely related to (reverse) methanogens that belongs to the ANME-2d clade, tentatively named Methanoperedens nitroreducens. Methane may be activated by methyl-CoM reductase and subsequently undergo full oxidation to carbon dioxide via reverse methanogenesis. All enzymes of this pathway were present and expressed in the investigated culture. The genome of the archaeal enrichment culture encoded a variety of enzymes involved in an electron transport chain similar to those found in Methanosarcina species with additional features not previously found in methane-converting archaea. Nitrate reduction to nitrite seems to be located in the pseudoperiplasm and may be catalyzed by an unusual Nar-like protein complex. A small part of the resulting nitrite is reduced to ammonium which may be catalyzed by a Nrf-type nitrite reductase. One of the key questions is how electrons from cytoplasmically located reverse methanogenesis reach the nitrate reductase in the pseudoperiplasm. Electron transport in M. nitroreducens probably involves cofactor F420 in the cytoplasm, quinones in the cytoplasmic membrane and cytochrome c in the pseudoperiplasm. The membrane-bound electron transport chain includes F420H2 dehydrogenase and an unusual Rieske/cytochrome b complex. Based on genome and transcriptome studies a tentative model of how central energy metabolism of nitrate-AOM could work is presented and discussed.},
}
@article {pmid28330329,
year = {2016},
author = {Dubey, G and Kollah, B and Gour, VK and Shukla, AK and Mohanty, SR},
title = {Diversity of bacteria and archaea in the rhizosphere of bioenergy crop Jatropha curcas.},
journal = {3 Biotech},
volume = {6},
number = {2},
pages = {257},
doi = {10.1007/s13205-016-0546-z},
pmid = {28330329},
issn = {2190-572X},
abstract = {Plant-microbial interaction in rhizosphere plays vital role in shaping plant's growth and ecosystem function. Most of the rhizospheric microbial diversity studies are restricted to bacteria. In natural ecosystem, archaea also constitutes a major component of the microbial population. However, their diversity is less known compared to bacteria. Experiments were carried out to examine diversity of bacteria and archaea in the rhizosphere of bioenergy crop Jatropha curcas (J. curcas). Samples were collected from three locations varying widely in the soil physico-chemical properties. Diversity was estimated by terminal restriction fragment length polymorphism (TRFLP) targeting 16S rRNA gene of bacteria and archaea. Fifteen bacterial and 17 archaeal terminal restriction fragments (TRFs) were retrieved from J. curcas rhizosphere. Bacterial indicative TRFs were Actinobacteria, Firmicutes, Acidobacteria, Verrumicrobiaceae, and Chlroflexi. Major archaeal TRFs were crenarchaeota, and euryarchaeota. In case of bacteria, relative fluorescence was low for TRF160 and high for TRF51, TRF 420. Similarly, for archaea relative fluorescence of TRF 218, and TRF 282 was low and high for TRF 278, TRF468 and TRF93. Principal component analysis (PCA) of bacterial TRFs designated PC 1 with 46.83% of variation and PC2 with 31.07% variation. Archaeal TRFs designated 90.94% of variation by PC1 and 9.05% by PC2. Simpson index varied from 0.530 to 0.880 and Shannon index from 1.462 to 3.139 for bacteria. For archaea, Simpson index varied from 0.855 to 0.897 and Shannon index varied from 3.027 to 3.155. Study concluded that rhizosphere of J. curcas constituted of diverse set of both bacteria and archaea, which might have promising plant growth promoting activities.},
}
@article {pmid26711582,
year = {2016},
author = {Ortiz-Alvarez, R and Casamayor, EO},
title = {High occurrence of Pacearchaeota and Woesearchaeota (Archaea superphylum DPANN) in the surface waters of oligotrophic high-altitude lakes.},
journal = {Environmental microbiology reports},
volume = {8},
number = {2},
pages = {210-217},
doi = {10.1111/1758-2229.12370},
pmid = {26711582},
issn = {1758-2229},
mesh = {Bacteria/classification/genetics/isolation &amp; purification ; *Biota ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Euryarchaeota/*classification/genetics/*isolation &amp; purification ; Lakes/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Spain ; },
abstract = {We carried out a regional survey on the archaea composition from surface waters of > 300 high-altitude Pyrenean lakes (average altitude 2300 m, pH range 4.4-10.1) by 16S rRNA gene tag sequencing. Relative Archaea abundances ranged between 0% and 6.3% of total prokaryotes amplicons in the polymerase chain reaction (PCR) mixture, and we detected 769 operational taxonomic units (OTUs; grouped at 97% identity) that split into 13 different lineages, with altitude and pH having a significant effect on the community composition. Woesearchaeota and Pacearchaeota (formerly Euryarchaeota DHVEG-6 cluster) dominated the data set (83% of total OTUS), showed a high occurrence (presence in c. 75% of the lakes) and had relative abundances significantly and positively correlated with the phylogenetic diversity of bacterial communities. Micrarchaeota-Diapherotrites (formerly Euryarchaeota MEG cluster), Methanomicrobia, Thermoplasmata and ammonia-oxidizing thaumarchaeota (AOA) showed relative abundances between 1% and 3% and occurrences between 14% and 26%. Minor lineages were SM1K20, Aenigmarchaeota (formerly Euryarchaeota DSEG cluster), Methanobacteria, Bathyarchaeota and SCG. Environmental preferences substantially differed among lineages, with Aenigmarchaeota and Methanomicrobia having the largest habitat breadth, and Thermoplasmata, AOA and Micrarchaeota having the smallest. Pacearchaeota and Woesearchaeota had been mostly reported from saline habitats and sediments, but surface waters of oligotrophic alpine lakes are suitable environments for such ecologically spread and genetically diverse archaeal lineages.},
}
@article {pmid26695717,
year = {2016},
author = {Koyanagi, T and Leriche, G and Onofrei, D and Holland, GP and Mayer, M and Yang, J},
title = {Cyclohexane Rings Reduce Membrane Permeability to Small Ions in Archaea-Inspired Tetraether Lipids.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {55},
number = {5},
pages = {1890-1893},
doi = {10.1002/anie.201510445},
pmid = {26695717},
issn = {1521-3773},
mesh = {Archaea/*chemistry ; *Cell Membrane Permeability ; Cyclohexanes/*chemistry ; Ions ; Lipids/*chemistry ; },
abstract = {Extremophile archaeal organisms overcome problems of membrane permeability by producing lipids with structural elements that putatively improve membrane integrity compared to lipids from other life forms. Herein, we describe a series of lipids that mimic some key structural features of archaeal lipids, such as: 1) single tethering of lipid tails to create fully transmembrane tetraether lipids and 2) the incorporation of small rings into these tethered segments. We found that membranes formed from pure tetraether lipids leaked small ions at a rate that was about two orders of magnitude slower than common bilayer-forming lipids. Incorporation of cyclopentane rings into the tetraether lipids did not affect membrane leakage, whereas a cyclohexane ring reduced leakage by an additional 40 %. These results show that mimicking certain structural features of natural archaeal lipids results in improved membrane integrity, which may help overcome limitations of many current lipid-based technologies.},
}
@article {pmid26661751,
year = {2016},
author = {Sipos, AJ and Urakawa, H},
title = {Differential responses of nitrifying archaea and bacteria to methylene blue toxicity.},
journal = {Letters in applied microbiology},
volume = {62},
number = {2},
pages = {199-206},
doi = {10.1111/lam.12534},
pmid = {26661751},
issn = {1472-765X},
mesh = {Ammonia/metabolism ; Animals ; Aquaculture ; Archaea/*drug effects/metabolism ; Bacteria/*drug effects/metabolism ; Methylene Blue/*pharmacology ; Microbial Sensitivity Tests ; Nitrification/*drug effects ; Oxidation-Reduction ; },
abstract = {UNLABELLED: Methylene blue, a heterocyclic aromatic chemical compound used to treat fish diseases in the ornamental fish aquaculture industry, is believed to impair nitrification as a side effect. However, very little is known about the toxicity of methylene blue to nitrifying micro-organisms. Here, we report the susceptibility of six bacterial and one archaeal ammonia-oxidizing micro-organisms to methylene blue within the range of 10 ppb to 10 ppm. Remarkably high susceptibility was observed in the archaeal species Nitrosopumilus maritimus compared to the bacterial species. Ammonia oxidation by Nitrosopumilus maritimus was inhibited 65% by 10 ppb of methylene blue. Of the bacterial species examined, Nitrosococcus oceani was the most resistant to methylene blue toxicity. For similar inhibition of Nitrosococcus oceani (75% inhibition), one thousand times more methylene blue (10 ppm) was needed. The examination of single cell viability on Nitrosomonas marina demonstrated that methylene blue is lethal to the cells rather than reducing their single cell ammonia oxidation activity. The level of susceptibility to methylene blue was related to the cell volume, intracytoplasmic membrane arrangement and the evolutionary lineage of nitrifying micro-organisms. Our findings are relevant for effectively using methylene blue in various aquaculture settings by helping minimize its impact on nitrifiers during the treatment of fish diseases. In the future, resistant nitrifiers such as Nitrosococcus oceani may be purposely added to aquaculture systems to maintain nitrification activity during treatments with methylene blue.<br><br>The susceptibility of six bacterial and one archaeal nitrifying micro-organisms to methylene blue was tested. Remarkably high susceptibility was observed in the archaeal species compared to the bacterial species. The level of resistance to methylene blue was related to the cell volume, cytomembrane system and the taxonomic position of the nitrifying micro-organisms. This may be significant in the design and management of engineered nitrification systems and the stability of the nitrification process in various ecosystems if these systems are exposed to harmful chemicals or toxins.},
}
@article {pmid26634977,
year = {2015},
author = {Knappy, C and Barillà, D and Chong, J and Hodgson, D and Morgan, H and Suleman, M and Tan, C and Yao, P and Keely, B},
title = {Mono-, di- and trimethylated homologues of isoprenoid tetraether lipid cores in archaea and environmental samples: mass spectrometric identification and significance.},
journal = {Journal of mass spectrometry : JMS},
volume = {50},
number = {12},
pages = {1420-1432},
doi = {10.1002/jms.3709},
pmid = {26634977},
issn = {1096-9888},
support = {BB/F003099/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Archaea/*chemistry ; Chromatography, Liquid ; Diglycerides/*chemistry ; Methylation ; Tandem Mass Spectrometry ; Terpenes/*chemistry ; },
abstract = {Higher homologues of widely reported C(86) isoprenoid diglycerol tetraether lipid cores, containing 0-6 cyclopentyl rings, have been identified in (hyper)thermophilic archaea, representing up to 21% of total tetraether lipids in the cells. Liquid chromatography-tandem mass spectrometry confirms that the additional carbon atoms in the C(87-88) homologues are located in the etherified chains. Structures identified include dialkyl and monoalkyl ('H-shaped') tetraethers containing C(40-42) or C(81-82) hydrocarbons, respectively, many representing novel compounds. Gas chromatography-mass spectrometric analysis of hydrocarbons released from the lipid cores by ether cleavage suggests that the C(40) chains are biphytanes and the C(41) chains 13-methylbiphytanes. Multiple isomers, having different chain combinations, were recognised among the dialkyl lipids. Methylated tetraethers are produced by Methanothermobacter thermautotrophicus in varying proportions depending on growth conditions, suggesting that methylation may be an adaptive mechanism to regulate cellular function. The detection of methylated lipids in Pyrobaculum sp. AQ1.S2 and Sulfolobus acidocaldarius represents the first reported occurrences in Crenarchaeota. Soils and aquatic sediments from geographically distinct mesotemperate environments that were screened for homologues contained monomethylated tetraethers, with di- and trimethylated structures being detected occasionally. The structural diversity and range of occurrences of the C(87-89) tetraethers highlight their potential as complementary biomarkers for archaea in natural environments.},
}
@article {pmid26626057,
year = {2016},
author = {Gan, XH and Zhang, FQ and Gu, JD and Guo, YD and Li, ZQ and Zhang, WQ and Xu, XY and Zhou, Y and Wen, XY and Xie, GG and Wang, YF},
title = {Differential distribution patterns of ammonia-oxidizing archaea and bacteria in acidic soils of Nanling National Nature Reserve forests in subtropical China.},
journal = {Antonie van Leeuwenhoek},
volume = {109},
number = {2},
pages = {237-251},
doi = {10.1007/s10482-015-0627-8},
pmid = {26626057},
issn = {1572-9699},
mesh = {Ammonia/*metabolism ; Archaea/classification/genetics/*isolation &amp; purification/*metabolism ; Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; China ; Conservation of Natural Resources ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {In addition to ammonia-oxidizing bacteria (AOB) the more recently discovered ammonia-oxidizing archaea (AOA) can also oxidize ammonia, but little is known about AOA community structure and abundance in subtropical forest soils. In this study, both AOA and AOB were investigated with molecular techniques in eight types of forests at surface soils (0-2 cm) and deep layers (18-20 cm) in Nanling National Nature Reserve in subtropical China. The results showed that the forest soils, all acidic (pH 4.24-5.10), harbored a wide range of AOA phylotypes, including the genera Nitrosotalea, Nitrososphaera, and another 6 clusters, one of which was reported for the first time. For AOB, only members of Nitrosospira were retrieved. Moreover, the abundance of the ammonia monooxygenase gene (amoA) from AOA dominated over AOB in most soil samples (13/16). Soil depth, rather than forest type, was an important factor shaping the community structure of AOA and AOB. The distribution patterns of AOA and AOB in soil layers were reversed: AOA diversity and abundances in the deep layers were higher than those in the surface layers; on the contrary, AOB diversity and abundances in the deep layers were lower than those in the surface layers. Interestingly, the diversity of AOA was positively correlated with pH, but negatively correlated with organic carbon, total nitrogen and total phosphorus, and the abundance of AOA was negatively correlated with available phosphorus. Our results demonstrated that AOA and AOB were differentially distributed in acidic soils in subtropical forests and affected differently by soil characteristics.},
}
@article {pmid26602691,
year = {2016},
author = {Peabody, MA and Laird, MR and Vlasschaert, C and Lo, R and Brinkman, FS},
title = {PSORTdb: expanding the bacteria and archaea protein subcellular localization database to better reflect diversity in cell envelope structures.},
journal = {Nucleic acids research},
volume = {44},
number = {D1},
pages = {D663-8},
doi = {10.1093/nar/gkv1271},
pmid = {26602691},
issn = {1362-4962},
mesh = {Archaeal Proteins/analysis/*genetics ; Bacterial Proteins/analysis/*genetics ; Cell Membrane/chemistry ; Cell Wall/chemistry ; *Databases, Protein ; Genome, Archaeal ; Genome, Bacterial ; Membrane Proteins/analysis/*genetics ; },
abstract = {Protein subcellular localization (SCL) is important for understanding protein function, genome annotation, and has practical applications such as identification of potential vaccine components or diagnostic/drug targets. PSORTdb (http://db.psort.org) comprises manually curated SCLs for proteins which have been experimentally verified (ePSORTdb), as well as pre-computed SCL predictions for deduced proteomes from bacterial and archaeal complete genomes available from NCBI (cPSORTdb). We now report PSORTdb 3.0. It features improvements increasing user-friendliness, and further expands both ePSORTdb and cPSORTdb with a focus on improving protein SCL data in cases where it is most difficult-proteins associated with non-classical Gram-positive/Gram-negative/Gram-variable cell envelopes. ePSORTdb data curation was expanded, including adding in additional cell envelope localizations, and incorporating markers for cPSORTdb to automatically computationally identify if new genomes to be analysed fall into certain atypical cell envelope categories (i.e. Deinococcus-Thermus, Thermotogae, Corynebacteriales/Corynebacterineae, including Mycobacteria). The number of predicted proteins in cPSORTdb has increased from 3,700,000 when PSORTdb 2.0 was released to over 13,000,000 currently. PSORTdb 3.0 will be of wider use to researchers studying a greater diversity of monoderm or diderm microbes, including medically, agriculturally and industrially important species that have non-classical outer membranes or other cell envelope features.},
}
@article {pmid26592025,
year = {2015},
author = {Gao, JF and Li, T and Zhang, SJ and Fan, XY and Pan, KL and Ma, Q and Yuan, YL},
title = {[Abundance and Community Composition of Ammonia-Oxidizing Archaea in Two Completely Autotrophic Nitrogen Removal over Nitrite Systems].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {36},
number = {8},
pages = {2939-2946},
pmid = {26592025},
issn = {0250-3301},
mesh = {Ammonia/analysis ; Archaea/*classification ; *Denitrification ; Nitrification ; Nitrites/*analysis ; Nitrogen/*analysis ; Oxidation-Reduction ; Sewage ; Waste Disposal, Fluid ; *Waste Water ; },
abstract = {Ammonia oxidation is the first and rate-limiting step of nitrification, which was thought to be only performed by ammonia-oxidizing bacteria (AOB). In recent years, ammonia-oxidizing archaea (AOA) was also confirmed to take part in ammonia oxidation. The diversity and abundance of AOA have been investigated in various environments, however, little is known regarding the AOA in the completely autotrophic nitrogen removal over nitrite (CANON) wastewater treatment process. In this study, the abundance and diversity of AOA were investigated in the biofilm and flocculent activated sludge collected in a lab-scale (L) CANON system and a pilot-scale (P) CANON systems, respectively. The quantitative real time PCR (qPCR) was applied to investigate the abundance of AOA and the diversity of AOA was determined by polymerase chain reaction (PCR), cloning and sequencing. The qPCR results showed that the average abundance of AOA amoA gene of L and P was 2.42 x 10(6) copies x g(-1) dry sludge and 6.51 x 10(6) copies x g(-1) dry sludge, respectively. The abundance of AOA in biofilm was 10.1-14.1 times higher than that in flocculent activated sludge. For P system, the abundance of AOA in flocculent activated sludge was 1.8 times higher than that in biofilm. The results indicated that the abundance of AOA might be affected by different sludge morphology. The diversity of AOA in P system was extremely limited, only one OTU was observed, which was classified into Nitrosopumilus subcluster 5.2. The diversity of AOA in L system was higher, eight OTUs were observed, which were classified into five genera: Nitrososphaera subcluster 9, subcluster 8.1, subcluster 4.1, subcluster 1.1 and Nitrosopumilus subcluster 5.2. The diversity and abundance of AOA were different in CANON systems with different sludge morphology. AOA may play an important role in ammonia oxidation in CANON system.},
}
@article {pmid26585514,
year = {2015},
author = {Palecek, JJ and Gruber, S},
title = {Kite Proteins: a Superfamily of SMC/Kleisin Partners Conserved Across Bacteria, Archaea, and Eukaryotes.},
journal = {Structure (London, England : 1993)},
volume = {23},
number = {12},
pages = {2183-2190},
doi = {10.1016/j.str.2015.10.004},
pmid = {26585514},
issn = {1878-4186},
mesh = {Amino Acid Sequence ; Archaeal Proteins/*chemistry/genetics/metabolism ; Bacterial Proteins/*chemistry/genetics/metabolism ; Cell Cycle Proteins/*chemistry/genetics/metabolism ; Conserved Sequence ; Kinesin/chemistry/metabolism ; Molecular Sequence Data ; },
abstract = {SMC/kleisin complexes form elongated annular structures, which are critical for chromosome segregation, genome maintenance, and the regulation of gene expression. We describe marked structural similarities between bacterial and eukaryotic SMC/kleisin partner proteins (designated here as &quot;kite&quot; proteins for kleisin interacting tandem winged-helix (WH) elements of SMC complexes). Kite proteins are integral parts of all prokaryotic SMC complexes and Smc5/6 but not cohesin and condensin. They are made up of tandem WH domains, form homo- or heterodimers via their amino-terminal WH domain, and they associate with the central part of a kleisin subunit. In placental mammals, the kite subunit NSE3 gave rise to several (>60) kite-related proteins, named MAGE, many of which encode tumor- and testis-specific antigens. Based on architectural rather than sequence similarity, we propose an adapted model for the evolution of the SMC protein complexes and discuss potential functional similarities between bacterial Smc/ScpAB and eukaryotic Smc5/6.},
}
@article {pmid26573375,
year = {2015},
author = {Li, M and Baker, BJ and Anantharaman, K and Jain, S and Breier, JA and Dick, GJ},
title = {Genomic and transcriptomic evidence for scavenging of diverse organic compounds by widespread deep-sea archaea.},
journal = {Nature communications},
volume = {6},
number = {},
pages = {8933},
doi = {10.1038/ncomms9933},
pmid = {26573375},
issn = {2041-1723},
mesh = {Archaea/*genetics/metabolism ; Carbohydrate Metabolism/*genetics ; Carbohydrates ; Carbon/*metabolism ; Carbon Cycle/*genetics ; Caribbean Region ; Fatty Acids/*metabolism ; Gene Expression Profiling ; Genomics ; Hydrothermal Vents/*microbiology ; Lipid Metabolism/*genetics ; Lipids ; Oceans and Seas ; Proteins/*metabolism ; Seawater/microbiology ; },
abstract = {Microbial activity is one of the most important processes to mediate the flux of organic carbon from the ocean surface to the seafloor. However, little is known about the microorganisms that underpin this key step of the global carbon cycle in the deep oceans. Here we present genomic and transcriptomic evidence that five ubiquitous archaeal groups actively use proteins, carbohydrates, fatty acids and lipids as sources of carbon and energy at depths ranging from 800 to 4,950 m in hydrothermal vent plumes and pelagic background seawater across three different ocean basins. Genome-enabled metabolic reconstructions and gene expression patterns show that these marine archaea are motile heterotrophs with extensive mechanisms for scavenging organic matter. Our results shed light on the ecological and physiological properties of ubiquitous marine archaea and highlight their versatile metabolic strategies in deep oceans that might play a critical role in global carbon cycling.},
}
@article {pmid26565069,
year = {2015},
author = {Chen, J and Zhang, H and Liu, W and Lian, J and Ye, W and Shen, W},
title = {Spatial distribution patterns of ammonia-oxidizing archaea abundance in subtropical forests at early and late successional stages.},
journal = {Scientific reports},
volume = {5},
number = {},
pages = {16587},
doi = {10.1038/srep16587},
pmid = {26565069},
issn = {2045-2322},
mesh = {Ammonia/*metabolism ; Archaea/*physiology ; Bacteria/growth &amp; development/metabolism ; Ecosystem ; Forests ; Oxidation-Reduction ; Oxides/*metabolism ; Phylogeny ; Soil ; Soil Microbiology ; },
abstract = {Characterizing the spatial distribution patterns of soil microorganisms is helpful in understanding the biogeochemical processes they perform, but has been less studied relative to those of macroorganisms. In this study, we investigated and compared the spatially explicit distribution patterns of ammonia-oxidizing archaea (AOA) abundance and the influential factors between an early (ES) and a late successional (LS) subtropical forest stand. The average AOA abundance, vegetational attributes, and soil nutrient contents were mostly greater in the LS than the ES stand (P = 0.085 or smaller), but their spatial variations were more pronounced in the ES than the LS stand. The spatial distribution patches of AOA abundance were smaller and more irregular in the ES stand (patch size <50 m) than in the LS stand (patch size about 120 m). Edaphic and vegetational variables contributed more to the spatial variations of AOA abundance for the ES (9.3%) stand than for LS stand, whereas spatial variables (MEMs) were the main contributors (62%) for the LS stand. These results suggest that environmental filtering likely influence the spatial distribution of AOA abundance at early successional stage more than that at late successional stage, while spatial dispersal is dominant at late successional stage.},
}
@article {pmid26559904,
year = {2016},
author = {Gottlieb, K and Wacher, V and Sliman, J and Pimentel, M},
title = {Review article: inhibition of methanogenic archaea by statins as a targeted management strategy for constipation and related disorders.},
journal = {Alimentary pharmacology &amp; therapeutics},
volume = {43},
number = {2},
pages = {197-212},
doi = {10.1111/apt.13469},
pmid = {26559904},
issn = {1365-2036},
mesh = {Archaea/metabolism ; Constipation/*drug therapy/microbiology ; Humans ; Hydroxymethylglutaryl-CoA Reductase Inhibitors/*pharmacology ; Irritable Bowel Syndrome/drug therapy/microbiology ; Male ; Methane/*metabolism ; },
abstract = {BACKGROUND: Observational studies show a strong association between delayed intestinal transit and the production of methane. Experimental data suggest a direct inhibitory activity of methane on the colonic and ileal smooth muscle and a possible role for methane as a gasotransmitter. Archaea are the only confirmed biological sources of methane in nature and Methanobrevibacter smithii is the predominant methanogen in the human intestine.<br><br>AIM: To review the biosynthesis and composition of archaeal cell membranes, archaeal methanogenesis and the mechanism of action of statins in this context.<br><br>METHODS: Narrative review of the literature.<br><br>RESULTS: Statins can inhibit archaeal cell membrane biosynthesis without affecting bacterial numbers as demonstrated in livestock and humans. This opens the possibility of a therapeutic intervention that targets a specific aetiological factor of constipation while protecting the intestinal microbiome. While it is generally believed that statins inhibit methane production via their effect on cell membrane biosynthesis, mediated by inhibition of the HMG-CoA reductase, there is accumulating evidence for an alternative or additional mechanism of action where statins inhibit methanogenesis directly. It appears that this other mechanism may predominate when the lactone form of statins, particularly lovastatin lactone, is administered.<br><br>CONCLUSIONS: Clinical development appears promising. A phase 2 clinical trial is currently in progress that evaluates the effect of lovastatin lactone on methanogenesis and symptoms in patients with irritable bowel syndrome with constipation. The review concludes with an outlook for the future and subsequent work that needs to be done.},
}
@article {pmid26557034,
year = {2015},
author = {Efenberger, M and Agier, J and Pawłowska, E and Brzezińska-Błaszczyk, E},
title = {Archaea prevalence in inflamed pulp tissues.},
journal = {Central-European journal of immunology},
volume = {40},
number = {2},
pages = {194-200},
doi = {10.5114/ceji.2015.51358},
pmid = {26557034},
issn = {1426-3912},
abstract = {Archaea have been detected in several ecological niches of the human body such as the large intestine, skin, vagina as well as the oral cavity. At present, archaea are recognized as nonpathogenic microorganisms. However, some data indicate that they may be involved in the etiopathogenesis of several diseases, including intestinal diseases as well as oral diseases: periodontitis, peri-implantitis and endodontitis. In this study, on the basis of 16S rRNA gene sequence analysis, we examined whether archaea might be present in inflamed pulp tissues and contribute to the development of endodontic infection. In comparison, we also determined selected bacterial species associated with endodontitis. We detected archaea in 85% of infected endodontic samples. In addition, Prevotella intermedia, Porphyromonas gingivalis, Tannerella forsythia and Treponema denticola were present in inflamed pulp tissue samples and Treponema denticola occurred with the highest frequency (70%). Further analysis revealed the presence of methanogenic archaea in analyzed samples. Direct sequencing of archaeal 16S rRNA gene PCR products indicated the occurrence of methanogenic archaea in inflamed pulp tissues; phylogenetically most similar were Methanobrevibacter oralis and Methanobrevibacter smithii. Therefore, our results show that methanogenic archaea are present in inflamed pulp tissues and may participate in the development of endodontic infection.},
}
@article {pmid26554846,
year = {2015},
author = {Kristensen, DM and Saeed, U and Frishman, D and Koonin, EV},
title = {A census of α-helical membrane proteins in double-stranded DNA viruses infecting bacteria and archaea.},
journal = {BMC bioinformatics},
volume = {16},
number = {},
pages = {380},
doi = {10.1186/s12859-015-0817-4},
pmid = {26554846},
issn = {1471-2105},
support = {//Intramural NIH HHS/United States ; },
mesh = {Archaea/*metabolism/virology ; Archaeal Viruses/isolation &amp; purification/*metabolism ; Bacteria/*metabolism/virology ; DNA Viruses/isolation &amp; purification/*metabolism ; Host-Pathogen Interactions ; Membrane Proteins/chemistry/*metabolism ; Viral Proteins/*metabolism ; Virion/*physiology ; Virus Integration ; },
abstract = {BACKGROUND: Viruses are the most abundant and genetically diverse biological entities on earth, yet the repertoire of viral proteins remains poorly explored. As the number of sequenced virus genomes grows into the thousands, and the number of viral proteins into the hundreds of thousands, we report a systematic computational analysis of the point of first-contact between viruses and their hosts, namely viral transmembrane (TM) proteins.<br><br>RESULTS: The complement of α-helical TM proteins in double-stranded DNA viruses infecting bacteria and archaea reveals large-scale trends that differ from those of their hosts. Viruses typically encode a substantially lower fraction of TM proteins than archaea or bacteria, with the notable exception of viruses with virions containing a lipid component such as a lipid envelope, internal lipid core, or inner membrane vesicle. Compared to bacteriophages, archaeal viruses are substantially enriched in membrane proteins. However, this feature is not always stable throughout the evolution of a viral lineage; for example, TM proteins are not part of the common heritage shared between Lipothrixviridae and Rudiviridae. In contrast to bacteria and archaea, viruses almost completely lack proteins with complicated membrane topologies composed of more than 4 TM segments, with the few detected exceptions being obvious cases of relatively recent horizontal transfer from the host.<br><br>CONCLUSIONS: The dramatic differences between the membrane proteomes of cells and viruses stem from the fact that viruses do not depend on essential membranes for energy transformation, ion homeostasis, nutrient transport and signaling.},
}
@article {pmid26543273,
year = {2015},
author = {Chu, YJ and Lee, JY and Shin, SR and Kim, GJ},
title = {A Method for Cell Culture and Maintenance of Ammonia-Oxidizing Archaea in Agar Stab.},
journal = {Indian journal of microbiology},
volume = {55},
number = {4},
pages = {460-463},
doi = {10.1007/s12088-015-0536-6},
pmid = {26543273},
issn = {0046-8991},
abstract = {Ammonia oxidizing archaea (AOA) are predominantly found and closely linked with geochemical cycling of nitrogen in non-extreme habitats. However, these strains have mainly been investigated using liquid cultures of enriched cells. Here, we provide an agar stab as a simple and reliable means of cultivating and maintaining AOA.},
}
@article {pmid26528260,
year = {2015},
author = {Zhang, CL and Xie, W and Martin-Cuadrado, AB and Rodriguez-Valera, F},
title = {Marine Group II Archaea, potentially important players in the global ocean carbon cycle.},
journal = {Frontiers in microbiology},
volume = {6},
number = {},
pages = {1108},
doi = {10.3389/fmicb.2015.01108},
pmid = {26528260},
issn = {1664-302X},
abstract = {Marine Group (MG) I (currently known as Thaumarchaeota) and MG II Archaea were first reported over two decades ago. While significant progress has been made on MG I microbiology and ecology, the progress on MG II has been noticeably slower. The common understanding is that while MG I mainly function as chemolithoautotrophs and occur predominantly in the deep ocean, MG II reside mostly in the photic zone and live heterotrophically. Studies to date have shown that MG II are abundant in the marine aquatic environment and display great seasonal and spatial variation and phylogenetic diversity. They also show unique patterns of organic carbon degradation and their energy requirements may be augmented by light in the photic zone. However, no pure culture of MG II has been obtained and thus their precise ecological role remains elusive.},
}
@article {pmid26522086,
year = {2015},
author = {Zhou, L and Wang, S and Zou, Y and Xia, C and Zhu, G},
title = {Species, Abundance and Function of Ammonia-oxidizing Archaea in Inland Waters across China.},
journal = {Scientific reports},
volume = {5},
number = {},
pages = {15969},
doi = {10.1038/srep15969},
pmid = {26522086},
issn = {2045-2322},
mesh = {Ammonia ; Archaea/*genetics/*physiology ; Bacteria/genetics ; China ; Ecosystem ; Nitrification/genetics/physiology ; Nitrogen Cycle/genetics/physiology ; Oxidation-Reduction ; Phylogeny ; Soil Microbiology ; Temperature ; Water/metabolism ; },
abstract = {Ammonia oxidation is the first step in nitrification and was thought to be performed solely by specialized bacteria. The discovery of ammonia-oxidizing archaea (AOA) changed this view. We examined the large scale and spatio-temporal occurrence, abundance and role of AOA throughout Chinese inland waters (n = 28). Molecular survey showed that AOA was ubiquitous in inland waters. The existence of AOA in extreme acidic, alkaline, hot, cold, eutrophic and oligotrophic environments expanded the tolerance limits of AOA, especially their known temperature tolerance to -25 °C, and substrate load to 42.04 mM. There were spatio-temporal divergences of AOA community structure in inland waters, and the diversity of AOA in inland water ecosystems was high with 34 observed species-level operational taxonomic units (OTUs; based on a 15% cutoff) distributed widely in group I.1b, I.1a, and I.1a-associated. The abundance of AOA was quite high (8.5 × 10(4) to 8.5 × 10(9) copies g(-1)), and AOA outnumbered ammonia-oxidizing bacteria (AOB) in the inland waters where little human activities were involved. On the whole AOB predominate the ammonia oxidation rate over AOA in inland water ecosystems, and AOA play an indispensable role in global nitrogen cycle considering that AOA occupy a broader habitat range than AOB, especially in extreme environments.},
}
@article {pmid26504428,
year = {2015},
author = {Charlesworth, JC and Burns, BP},
title = {Untapped Resources: Biotechnological Potential of Peptides and Secondary Metabolites in Archaea.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2015},
number = {},
pages = {282035},
doi = {10.1155/2015/282035},
pmid = {26504428},
issn = {1472-3654},
mesh = {Archaea/*chemistry/metabolism ; Biological Products/*isolation &amp; purification/*metabolism ; Biotechnology/methods ; Food-Processing Industry/methods ; Peptides/isolation &amp; purification/metabolism ; Technology, Pharmaceutical/methods ; },
abstract = {Archaea are an understudied domain of life often found in &quot;extreme&quot; environments in terms of temperature, salinity, and a range of other factors. Archaeal proteins, such as a wide range of enzymes, have adapted to function under these extreme conditions, providing biotechnology with interesting activities to exploit. In addition to producing structural and enzymatic proteins, archaea also produce a range of small peptide molecules (such as archaeocins) and other novel secondary metabolites such as those putatively involved in cell communication (acyl homoserine lactones), which can be exploited for biotechnological purposes. Due to the wide array of metabolites produced there is a great deal of biotechnological potential from antimicrobials such as diketopiperazines and archaeocins, as well as roles in the cosmetics and food industry. In this review we will discuss the diversity of small molecules, both peptide and nonpeptide, produced by archaea and their potential biotechnological applications.},
}
@article {pmid26499486,
year = {2015},
author = {Serrano, P and Hermelink, A and Lasch, P and de Vera, JP and König, N and Burckhardt, O and Wagner, D},
title = {Confocal Raman microspectroscopy reveals a convergence of the chemical composition in methanogenic archaea from a Siberian permafrost-affected soil.},
journal = {FEMS microbiology ecology},
volume = {91},
number = {12},
pages = {},
doi = {10.1093/femsec/fiv126},
pmid = {26499486},
issn = {1574-6941},
mesh = {Cold Temperature ; DNA Restriction Enzymes/*genetics ; Desiccation ; Euryarchaeota/*chemistry/genetics/*isolation &amp; purification ; Methane/*biosynthesis ; Microscopy, Confocal ; Molecular Typing ; Osmotic Pressure/physiology ; Permafrost/chemistry/*microbiology ; Phylogeny ; Radiation Tolerance/physiology ; Siberia ; Soil Microbiology ; Spectrum Analysis, Raman ; },
abstract = {Methanogenic archaea are widespread anaerobic microorganisms responsible for the production of biogenic methane. Several new species of psychrotolerant methanogenic archaea were recently isolated from a permafrost-affected soil in the Lena Delta (Siberia, Russia), showing an exceptional resistance against desiccation, osmotic stress, low temperatures, starvation, UV and ionizing radiation when compared to methanogens from non-permafrost environments. To gain a deeper insight into the differences observed in their resistance, we described the chemical composition of methanogenic strains from permafrost and non-permafrost environments using confocal Raman microspectroscopy (CRM). CRM is a powerful tool for microbial identification and provides fingerprint-like information about the chemical composition of the cells. Our results show that the chemical composition of methanogens from permafrost-affected soils presents a high homology and is remarkably different from strains inhabiting non-permafrost environments. In addition, we performed a phylogenetic reconstruction of the studied strains based on the functional gene mcrA to prove the different evolutionary relationship of the permafrost strains. We conclude that the permafrost methanogenic strains show a convergent chemical composition regardless of their genotype. This fact is likely to be the consequence of a complex adaptive process to the Siberian permafrost environment and might be the reason underlying their resistant nature.},
}
@article {pmid26490622,
year = {2015},
author = {Wegener, G and Krukenberg, V and Riedel, D and Tegetmeyer, HE and Boetius, A},
title = {Intercellular wiring enables electron transfer between methanotrophic archaea and bacteria.},
journal = {Nature},
volume = {526},
number = {7574},
pages = {587-590},
doi = {10.1038/nature15733},
pmid = {26490622},
issn = {1476-4687},
mesh = {Anaerobiosis ; Archaea/*metabolism ; Bacteria/*metabolism ; Cytochromes/metabolism ; Electron Transport ; Fimbriae, Bacterial/metabolism ; Geologic Sediments/microbiology ; Heme/metabolism ; Hydrogen/metabolism ; Hydrothermal Vents/microbiology ; Methane/*metabolism ; Microbiota/physiology ; Molecular Sequence Data ; Oceans and Seas ; Sulfates/metabolism ; Symbiosis ; Temperature ; },
abstract = {The anaerobic oxidation of methane (AOM) with sulfate controls the emission of the greenhouse gas methane from the ocean floor. In marine sediments, AOM is performed by dual-species consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB) inhabiting the methane-sulfate transition zone. The biochemical pathways and biological adaptations enabling this globally relevant process are not fully understood. Here we study the syntrophic interaction in thermophilic AOM (TAOM) between ANME-1 archaea and their consortium partner SRB HotSeep-1 (ref. 6) at 60 °C to test the hypothesis of a direct interspecies exchange of electrons. The activity of TAOM consortia was compared to the first ANME-free culture of an AOM partner bacterium that grows using hydrogen as the sole electron donor. The thermophilic ANME-1 do not produce sufficient hydrogen to sustain the observed growth of the HotSeep-1 partner. Enhancing the growth of the HotSeep-1 partner by hydrogen addition represses methane oxidation and the metabolic activity of ANME-1. Further supporting the hypothesis of direct electron transfer between the partners, we observe that under TAOM conditions, both ANME and the HotSeep-1 bacteria overexpress genes for extracellular cytochrome production and form cell-to-cell connections that resemble the nanowire structures responsible for interspecies electron transfer between syntrophic consortia of Geobacter. HotSeep-1 highly expresses genes for pili production only during consortial growth using methane, and the nanowire-like structures are absent in HotSeep-1 cells isolated with hydrogen. These observations suggest that direct electron transfer is a principal mechanism in TAOM, which may also explain the enigmatic functioning and specificity of other methanotrophic ANME-SRB consortia.},
}
@article {pmid26477689,
year = {2016},
author = {Cacciapuoti, G and Bagarolo, ML and Martino, E and Scafuri, B and Marabotti, A and Porcelli, M},
title = {Efficient Fludarabine-Activating PNP From Archaea as a Guidance for Redesign the Active Site of E. Coli PNP.},
journal = {Journal of cellular biochemistry},
volume = {117},
number = {5},
pages = {1126-1135},
doi = {10.1002/jcb.25396},
pmid = {26477689},
issn = {1097-4644},
mesh = {Adenosine/chemistry/metabolism ; Arabinonucleosides/chemistry/metabolism ; Archaeal Proteins/chemistry/*metabolism ; Binding, Competitive ; Biocatalysis ; Catalytic Domain ; Crystallography, X-Ray ; Escherichia coli Proteins/chemistry/*metabolism ; Isoenzymes/chemistry/metabolism ; Kinetics ; Models, Molecular ; Molecular Structure ; Protein Binding ; Protein Domains ; Purine-Nucleoside Phosphorylase/chemistry/*metabolism ; Substrate Specificity ; Sulfolobus solfataricus/*enzymology ; Vidarabine/*analogs &amp; derivatives/chemistry/metabolism ; },
abstract = {The combination of the gene of purine nucleoside phosphorylase (PNP) from Escherichia coli and fludarabine represents one of the most promising systems in the gene therapy of solid tumors. The use of fludarabine in gene therapy is limited by the lack of an enzyme that is able to efficiently activate this prodrug which, consequently, has to be administered in high doses that cause serious side effects. In an attempt to identify enzymes with a better catalytic efficiency than E. coli PNP towards fludarabine to be used as a guidance on how to improve the activity of the bacterial enzyme, we have selected 5'-deoxy-5'-methylthioadenosine phosphorylase (SsMTAP) and 5'-deoxy-5'-methylthioadenosine phosphorylase II (SsMTAPII), two PNPs isolated from the hyperthermophilic archaeon Sulfolobus solfataricus. Substrate specificity and catalytic efficiency of SsMTAP and SsMTAPII for fludarabine were analyzed by kinetic studies and compared with E. coli PNP. SsMTAP and SsMTAPII share with E. coli PNP a comparable low affinity for the arabinonucleoside but are better catalysts of fludarabine cleavage with k(cat)/K(m) values that are 12.8-fold and 6-fold higher, respectively, than those reported for the bacterial enzyme. A computational analysis of the interactions of fludarabine in the active sites of E. coli PNP, SsMTAP, and SsMTAPII allowed to identify the crucial residues involved in the binding with this substrate, and provided structural information to improve the catalytic efficiency of E. coli PNP by enzyme redesign.},
}
@article {pmid26472620,
year = {2016},
author = {Elling, FJ and Becker, KW and Könneke, M and Schröder, JM and Kellermann, MY and Thomm, M and Hinrichs, KU},
title = {Respiratory quinones in Archaea: phylogenetic distribution and application as biomarkers in the marine environment.},
journal = {Environmental microbiology},
volume = {18},
number = {2},
pages = {692-707},
doi = {10.1111/1462-2920.13086},
pmid = {26472620},
issn = {1462-2920},
mesh = {Archaea/*classification/genetics/*metabolism ; Bacteria/metabolism ; Biomarkers/metabolism ; Biomass ; Black Sea ; Ecology ; Gene Transfer, Horizontal ; Membrane Lipids/metabolism ; Oxidation-Reduction ; Phylogeny ; Quinones/*chemistry ; Terpenes/*chemistry ; },
abstract = {The distribution of respiratory quinone electron carriers among cultivated organisms provides clues on both the taxonomy of their producers and the redox processes these are mediating. Our study of the quinone inventories of 25 archaeal species belonging to the phyla Eury-, Cren- and Thaumarchaeota facilitates their use as chemotaxonomic markers for ecologically important archaeal clades. Saturated and monounsaturated menaquinones with six isoprenoid units forming the alkyl chain may serve as chemotaxonomic markers for Thaumarchaeota. Other diagnostic biomarkers are thiophene-bearing quinones for Sulfolobales and methanophenazines as functional quinone analogues of the Methanosarcinales. The ubiquity of saturated menaquinones in the Archaea in comparison to Bacteria suggests that these compounds may represent an ancestral and diagnostic feature of the Archaea. Overlap between quinone compositions of distinct thermophilic and halophilic archaea and bacteria may indicate lateral gene transfer. The biomarker potential of thaumarchaeal quinones was exemplarily demonstrated on a water column profile of the Black Sea. Both, thaumarchaeal quinones and membrane lipids showed similar distributions with maxima at the chemocline. Quinone distributions indicate that Thaumarchaeota dominate respiratory activity at a narrow interval in the chemocline, while they contribute only 9% to the microbial biomass at this depth, as determined by membrane lipid analysis.},
}
@article {pmid26463999,
year = {2016},
author = {Niu, J and Kasuga, I and Kurisu, F and Furumai, H and Shigeeda, T and Takahashi, K},
title = {Abundance and diversity of ammonia-oxidizing archaea and bacteria on granular activated carbon and their fates during drinking water purification process.},
journal = {Applied microbiology and biotechnology},
volume = {100},
number = {2},
pages = {729-742},
doi = {10.1007/s00253-015-6969-3},
pmid = {26463999},
issn = {1432-0614},
mesh = {Ammonia/*metabolism ; Archaea/classification/*genetics/isolation &amp; purification/*metabolism ; Bacteria/classification/*genetics/isolation &amp; purification/*metabolism ; Charcoal ; Drinking Water/analysis/*microbiology ; Genetic Variation ; Microbial Consortia/genetics/physiology ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Seasons ; Tokyo ; Water Purification ; },
abstract = {Ammonia is a precursor to trichloramine, which causes an undesirable chlorinous odor. Granular activated carbon (GAC) filtration is used to biologically oxidize ammonia during drinking water purification; however, little information is available regarding the abundance and diversity of ammonia-oxidizing archaea (AOA) and bacteria (AOB) associated with GAC. In addition, their sources and fates in water purification process remain unknown. In this study, six GAC samples were collected from five full-scale drinking water purification plants in Tokyo during summer and winter, and the abundance and community structure of AOA and AOB associated with GAC were studied in these two seasons. In summer, archaeal and bacterial amoA genes on GACs were present at 3.7 × 10(5)-3.9 × 10(8) gene copies/g-dry and 4.5 × 10(6)-4.2 × 10(8) gene copies/g-dry, respectively. In winter, archaeal amoA genes remained at the same level, while bacterial amoA genes decreased significantly for all GACs. No differences were observed in the community diversity of AOA and AOB from summer to winter. Phylogenetic analysis revealed high AOA diversity in group I.1a and group I.1b in raw water. Terminal-restriction fragment length polymorphism analysis of processed water samples revealed that AOA diversity decreased dramatically to only two OTUs in group I.1a after ozonation, which were identical to those detected on GAC. It suggests that ozonation plays an important role in determining AOA diversity on GAC. Further study on the cell-specific activity of AOA and AOB is necessary to understand their contributions to in situ nitrification performance.},
}
@article {pmid26456193,
year = {2016},
author = {Chamieh, H and Ibrahim, H and Kozah, J},
title = {Genome-wide identification of SF1 and SF2 helicases from archaea.},
journal = {Gene},
volume = {576},
number = {1 Pt 2},
pages = {214-228},
doi = {10.1016/j.gene.2015.10.007},
pmid = {26456193},
issn = {1879-0038},
mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Archaeal Proteins/*chemistry/*genetics/metabolism ; Conserved Sequence ; DNA Helicases/*chemistry/*genetics/metabolism ; DNA Repair/physiology ; DNA-Binding Proteins/chemistry/genetics ; Escherichia coli Proteins/chemistry/genetics ; Genome, Archaeal ; Humans ; *Phylogeny ; Protein Structure, Tertiary ; RNA Splicing Factors ; Transcription Factors/chemistry/genetics ; },
abstract = {Archaea microorganisms have long been used as model organisms for the study of protein molecular machines. Archaeal proteins are particularly appealing to study since archaea, even though prokaryotic, possess eukaryotic-like cellular processes. Super Family I (SF1) and Super Family II (SF2) helicase families have been studied in many model organisms, little is known about their presence and distribution in archaea. We performed an exhaustive search of homologs of SF1 and SF2 helicase proteins in 95 complete archaeal genomes. In the present study, we identified the complete sets of SF1 and SF2 helicases in archaea. Comparative analysis between archaea, human and the bacteria E. coli SF1 and SF2 helicases, resulted in the identification of seven helicase families conserved among representatives of the domains of life. This analysis suggests that these helicase families are highly conserved throughout evolution. We highlight the conserved motifs of each family and characteristic domains of the detected families. Distribution of SF1/SF2 families show that Ski2-like, Lhr, Sfth and Rad3-like helicases are ubiquitous among archaeal genomes while the other families are specific to certain archaeal groups. We also report the presence of a novel SF2 helicase specific to archaea domain named Archaea Specific Helicase (ASH). Phylogenetic analysis indicated that ASH has evolved in Euryarchaeota and is evolutionary related to the Ski2-like family with specific characteristic domains. Our study provides the first exhaustive analysis of SF1 and SF2 helicases from archaea. It expands the variety of SF1 and SF2 archaeal helicases known to exist to date and provides a starting point for new biochemical and genetic studies needed to validate their biological functions.},
}
@article {pmid26450358,
year = {2015},
author = {Dong, J and Ding, L and Wang, X and Chi, Z and Lei, J},
title = {Erratum to: Vertical Profiles of Community Abundance and Diversity of Anaerobic Methanotrophic Archaea (ANME) and Bacteria in a Simple Waste Landfill in North China.},
journal = {Applied biochemistry and biotechnology},
volume = {177},
number = {6},
pages = {1394},
doi = {10.1007/s12010-015-1885-7},
pmid = {26450358},
issn = {1559-0291},
}
@article {pmid26441877,
year = {2015},
author = {Sorokin, DY and Toshchakov, SV and Kolganova, TV and Kublanov, IV},
title = {Halo(natrono)archaea isolated from hypersaline lakes utilize cellulose and chitin as growth substrates.},
journal = {Frontiers in microbiology},
volume = {6},
number = {},
pages = {942},
doi = {10.3389/fmicb.2015.00942},
pmid = {26441877},
issn = {1664-302X},
abstract = {Until recently, extremely halophilic euryarchaeota were considered mostly as aerobic heterotrophs utilizing simple organic compounds as growth substrates. Almost nothing is known on the ability of these prokaryotes to utilize complex polysaccharides, such as cellulose, xylan, and chitin. Although few haloarchaeal cellulases and chitinases were recently characterized, the analysis of currently available haloarchaeal genomes deciphered numerous genes-encoding glycosidases of various families including endoglucanases and chitinases. However, all these haloarchaea were isolated and cultivated on simple substrates and their ability to grow on polysaccharides in situ or in vitro is unknown. This study examines several halo(natrono)archaeal strains from geographically distant hypersaline lakes for the ability to grow on insoluble polymers as a sole growth substrate in salt-saturated mineral media. Some of them belonged to known taxa, while other represented novel phylogenetic lineages within the class Halobacteria. All isolates produced extracellular extremely salt-tolerant cellulases or chitinases, either cell-free or cell-bound. Obtained results demonstrate a presence of diverse populations of haloarchaeal cellulo/chitinotrophs in hypersaline habitats indicating that euryarchaea participate in aerobic mineralization of recalcitrant organic polymers in salt-saturated environments.},
}
@article {pmid26441844,
year = {2015},
author = {Borgonie, G and Linage-Alvarez, B and Ojo, A and Shivambu, S and Kuloyo, O and Cason, ED and Maphanga, S and Vermeulen, JG and Litthauer, D and Ralston, CD and Onstott, TC and Sherwood-Lollar, B and Van Heerden, E},
title = {Deep subsurface mine stalactites trap endemic fissure fluid Archaea, Bacteria, and Nematoda possibly originating from ancient seas.},
journal = {Frontiers in microbiology},
volume = {6},
number = {},
pages = {833},
doi = {10.3389/fmicb.2015.00833},
pmid = {26441844},
issn = {1664-302X},
abstract = {Stalactites (CaCO3 and salt) from water seeps are frequently encountered in ceilings of mine tunnels whenever they intersect water-bearing faults or fractures. To determine whether stalactites could be mineralized traps for indigenous fracture water microorganisms, we analyzed stalactites collected from three different mines ranging in depth from 1.3 to 3.1 km. During sampling in Beatrix gold mine (1.4 km beneath the surface), central South Africa, CaCO3 stalactites growing on the mine tunnel ceiling were collected and observed, in two cases, to contain a living obligate brackish water/marine nematode species, Monhystrella parvella. After sterilization of the outer surface, mineral layers were physically removed from the outside to the interior, and DNA extracted. Based upon 16S and 18S rRNA gene sequencing, Archaea, Bacteria, and Eukarya in different combinations were detected for each layer. Using CT scan and electron microscopy the inner structure of CaCO3 and salt stalactites were analyzed. CaCO3 stalactites show a complex pattern of lamellae carrying bacterially precipitated mineral structures. Nematoda were clearly identified between these layers confirming that bacteria and nematodes live inside the stalactites and not only in the central straw. Salt stalactites exhibit a more uniform internal structure. Surprisingly, several Bacteria showing highest sequence identities to marine species were identified. This, together with the observation that the nematode M. parvella recovered from Beatrix gold mine stalactite can only survive in a salty environment makes the origin of the deep subsurface colonization enigmatic. The possibility of a Permian origin of fracture fluids is discussed. Our results indicate stalactites are suitable for biodiversity recovery and act as natural traps for microorganisms in the fissure water long after the water that formed the stalactite stopped flowing.},
}
@article {pmid26439345,
year = {2015},
author = {Eme, L and Doolittle, WF},
title = {Archaea.},
journal = {Current biology : CB},
volume = {25},
number = {19},
pages = {R851-5},
doi = {10.1016/j.cub.2015.05.025},
pmid = {26439345},
issn = {1879-0445},
mesh = {Adaptation, Biological ; Archaea/*classification/genetics/physiology ; Bacteria/*classification/genetics ; Bacterial Physiological Phenomena ; *Biological Evolution ; Eukaryota/*classification/genetics/physiology ; History, 20th Century ; History, 21st Century ; Microbiology/*history ; Phylogeny ; },
abstract = {A headline on the front page of the New York Times for November 3, 1977, read &quot;Scientists Discover a Way of Life That Predates Higher Organisms&quot;. The accompanying article described a spectacular claim by Carl Woese and George Fox to have discovered a third form of life, a new 'domain' that we now call Archaea. It's not that these microbes were unknown before, nor was it the case that their peculiarities had gone completely unnoticed. Indeed, Ralph Wolfe, in the same department at the University of Illinois as Woese, had already discovered how it was that methanogens (uniquely on the planet) make methane, and the bizarre adaptations that allow extremely halophilic archaea (then called halobacteria) and thermoacidophiles to live in the extreme environments where they do were already under investigation in many labs. But what Woese and Fox had found was that these organisms were related to each other not just in their 'extremophily' but also phylogenetically. And, most surprisingly, they were only remotely related to the rest of the prokaryotes, which we now call the domain Bacteria (Figure 1).},
}
@article {pmid26411976,
year = {2015},
author = {Bai, L and Xie, T and Hu, Q and Deng, C and Zheng, R and Chen, W},
title = {Genome-wide comparison of ferritin family from Archaea, Bacteria, Eukarya, and Viruses: its distribution, characteristic motif, and phylogenetic relationship.},
journal = {Die Naturwissenschaften},
volume = {102},
number = {9-10},
pages = {64},
doi = {10.1007/s00114-015-1314-3},
pmid = {26411976},
issn = {1432-1904},
mesh = {Amino Acid Motifs ; Animals ; *Archaea/classification/genetics ; *Bacteria/classification/genetics ; *Eukaryota/classification/genetics ; Evolution, Molecular ; Ferritins/*genetics ; Genome/*genetics ; *Phylogeny ; *Viruses/classification/genetics ; },
abstract = {Ferritins are highly conserved proteins that are widely distributed in various species from archaea to humans. The ubiquitous characteristic of these proteins reflects the pivotal contribution of ferritins to the safe storage and timely delivery of iron to achieve iron homeostasis. This study investigated the ferritin genes in 248 genomes from various species, including viruses, archaea, bacteria, and eukarya. The distribution comparison suggests that mammals and eudicots possess abundant ferritin genes, whereas fungi contain very few ferritin genes. Archaea and bacteria show considerable numbers of ferritin genes. Generally, prokaryotes possess three types of ferritin (the typical ferritin, bacterioferritin, and DNA-binding protein from starved cell), whereas eukaryotes have various subunit types of ferritin, thereby indicating the individuation of the ferritin family during evolution. The characteristic motif analysis of ferritins suggested that all key residues specifying the unique structural motifs of ferritin are highly conserved across three domains of life. Meanwhile, the characteristic motifs were also distinguishable between ferritin groups, especially phytoferritins, which show a plant-specific motif. The phylogenetic analyses show that ferritins within the same subfamily or subunits are generally clustered together. The phylogenetic relationships among ferritin members suggest that both gene duplication and horizontal transfer contribute to the wide variety of ferritins, and their possible evolutionary scenario was also proposed. The results contribute to a better understanding of the distribution, characteristic motif, and evolutionary relationship of the ferritin family.},
}
@article {pmid26403496,
year = {2015},
author = {Prangishvili, D and Gribaldo, S and Franzetti, B and Forterre, P},
title = {Special section on Molecular biology of Archaea.},
journal = {Biochimie},
volume = {118},
number = {},
pages = {253},
doi = {10.1016/j.biochi.2015.09.020},
pmid = {26403496},
issn = {1638-6183},
mesh = {Archaea/*genetics ; Phylogeny ; },
}
@article {pmid26394860,
year = {2016},
author = {Ding, J and Fu, L and Ding, ZW and Lu, YZ and Cheng, SH and Zeng, RJ},
title = {Environmental evaluation of coexistence of denitrifying anaerobic methane-oxidizing archaea and bacteria in a paddy field.},
journal = {Applied microbiology and biotechnology},
volume = {100},
number = {1},
pages = {439-446},
doi = {10.1007/s00253-015-6986-2},
pmid = {26394860},
issn = {1432-0614},
mesh = {Anaerobiosis ; Archaea/classification/*growth &amp; development/isolation &amp; purification/*metabolism ; Bacteria/classification/*growth &amp; development/isolation &amp; purification/*metabolism ; Biota ; Denitrification ; High-Throughput Nucleotide Sequencing ; Methane/*metabolism ; Nitrates/*metabolism ; Oxidation-Reduction ; Sequence Analysis, DNA ; *Soil Microbiology ; },
abstract = {The nitrate-dependent denitrifying anaerobic methane oxidation (DAMO) process, which is metabolized together by anaerobic methanotrophic archaea and NC10 phylum bacteria, is expected to be important for the global carbon and nitrogen cycles. However, there are little studies about the existence of this process and the functional microbes in environments. Therefore, the coexistence of DAMO archaea and bacteria in a paddy field was evaluated in this study. Next-generation sequencing showed that the two orders, Methanosarcinales and Nitrospirales, to which DAMO archaea and DAMO bacteria belong, were detected in the four soil samples. Then the in vitro experiments demonstrated both of nitrite- and nitrate-dependent DAMO activities, which confirmed the coexistence of DAMO archaea and DAMO bacteria. It was the first report about the coexistence of DAMO archaea and bacteria in a paddy field. Furthermore, anammox bacteria were detected in two of the four samples. The in vitro experiments did not show anammox activity in the initial period but showed low anammox activity after 20 days' enrichment. These results implicated that anammox bacteria may coexist with DAMO microorganisms in this field, but at a very low percentage.},
}
@article {pmid26369647,
year = {2015},
author = {Martin del Campo, M and Camacho, RM and Mateos-Díaz, JC and Müller-Santos, M and Córdova, J and Rodríguez, JA},
title = {Solid-state fermentation as a potential technique for esterase/lipase production by halophilic archaea.},
journal = {Extremophiles : life under extreme conditions},
volume = {19},
number = {6},
pages = {1121-1132},
doi = {10.1007/s00792-015-0784-8},
pmid = {26369647},
issn = {1433-4909},
mesh = {Archaeal Proteins/genetics/*metabolism ; Biomass ; Esterases/genetics/*metabolism ; *Fermentation ; Halobacteriaceae/*enzymology/growth &amp; development/metabolism ; Industrial Microbiology/*methods ; Lipase/genetics/*metabolism ; },
abstract = {Halophilic archaea are extremophiles, adapted to high-salt environments, showing a big biotechnological potential as enzyme, lipids and pigments producers. Four inert supports (perlite, vermiculite, polyurethane foam and glass fiber) were employed for solid-state fermentation (SSF) of the halophilic archaeon Natronococcus sp. TC6 to investigate biomass and esterase production. A very low esterase activity and high water activity were observed when perlite, vermiculite and polyurethane were used as supports. When glass fiber was employed, an important moisture loss was observed (8.6%). Moreover, moisture retention was improved by mixing polyurethane and glass fiber, resulting in maximal biomass and esterase production. Three halophilic archaea: Natronococcus sp. TC6, Halobacterium sp. NRC-1 and Haloarcula marismortui were cultured by submerged fermentation (SmF) and by SSF; an improvement of 1.3- to 6.2-fold was observed in the biomass and esterase production when SSF was used. Growth was not homogeneous in the mixture, but was predominant in the glass fiber thus was probably because the glass fiber provides a holder to the cells, while the polyurethane acts as an impregnation medium reservoir. To the best of our knowledge, this work is the first report on haloarchaea cultivation by SSF aiming biomass and esterase/lipase activity production.},
}
@article {pmid26346219,
year = {2015},
author = {Bhattacharyya, A and Majumder, NS and Basak, P and Mukherji, S and Roy, D and Nag, S and Haldar, A and Chattopadhyay, D and Mitra, S and Bhattacharyya, M and Ghosh, A},
title = {Diversity and Distribution of Archaea in the Mangrove Sediment of Sundarbans.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2015},
number = {},
pages = {968582},
doi = {10.1155/2015/968582},
pmid = {26346219},
issn = {1472-3654},
mesh = {Archaea/*classification/genetics/*isolation &amp; purification ; *Biodiversity ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Environmental Microbiology ; India ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Tropical Climate ; *Wetlands ; },
abstract = {Mangroves are among the most diverse and productive coastal ecosystems in the tropical and subtropical regions. Environmental conditions particular to this biome make mangroves hotspots for microbial diversity, and the resident microbial communities play essential roles in maintenance of the ecosystem. Recently, there has been increasing interest to understand the composition and contribution of microorganisms in mangroves. In the present study, we have analyzed the diversity and distribution of archaea in the tropical mangrove sediments of Sundarbans using 16S rRNA gene amplicon sequencing. The extraction of DNA from sediment samples and the direct application of 16S rRNA gene amplicon sequencing resulted in approximately 142 Mb of data from three distinct mangrove areas (Godkhali, Bonnie camp, and Dhulibhashani). The taxonomic analysis revealed the dominance of phyla Euryarchaeota and Thaumarchaeota (Marine Group I) within our dataset. The distribution of different archaeal taxa and respective statistical analysis (SIMPER, NMDS) revealed a clear community shift along the sampling stations. The sampling stations (Godkhali and Bonnie camp) with history of higher hydrocarbon/oil pollution showed different archaeal community pattern (dominated by haloarchaea) compared to station (Dhulibhashani) with nearly pristine environment (dominated by methanogens). It is indicated that sediment archaeal community patterns were influenced by environmental conditions.},
}
@article {pmid26339125,
year = {2015},
author = {Wagner, AO and Praeg, N and Reitschuler, C and Illmer, P},
title = {Effect of DNA extraction procedure, repeated extraction and ethidium monoazide (EMA)/propidium monoazide (PMA) treatment on overall DNA yield and impact on microbial fingerprints for bacteria, fungi and archaea in a reference soil.},
journal = {Applied soil ecology : a section of Agriculture, Ecosystems &amp; Environment},
volume = {93},
number = {},
pages = {56-64},
doi = {10.1016/j.apsoil.2015.04.005},
pmid = {26339125},
issn = {0929-1393},
support = {P 22815//Austrian Science Fund FWF/Austria ; },
abstract = {Different DNA extraction protocols were evaluated on a reference soil. A wide difference was found in the total extractable DNA as derived from different extraction protocols. Concerning the DNA yield phenol-chloroform-isomyl alcohol extraction resulted in high DNA yield but also in a remarkable co-extraction of contaminants making PCR from undiluted DNA extracts impossible. By comparison of two different extraction kits, the Macherey&amp;Nagel SoilExtract II kit resulted in the highest DNA yields when buffer SL1 and the enhancer solution were applied. The enhancer solution not only significantly increased the DNA yield but also the amount of co-extracted contaminates, whereas additional disintegration strategies did not. Although a three times repeated DNA extraction increased the total amount of extracted DNA, microbial fingerprints were merely affected. However, with the 5th extraction this changed. A reduction of total DGGE band numbers was observed for archaea and fungi, whereas for bacteria the diversity increased. The application of ethidium monoazide (EMA) or propidium monoazide (PMA) treatment aiming on the selective removal of soil DNA derived from cells lacking cell wall integrity resulted in a significant reduction of total extracted DNA, however, the hypothesized effect on microbial fingerprints failed to appear indicating the need for further investigations.},
}
@article {pmid26323767,
year = {2015},
author = {Akanni, WA and Siu-Ting, K and Creevey, CJ and McInerney, JO and Wilkinson, M and Foster, PG and Pisani, D},
title = {Horizontal gene flow from Eubacteria to Archaebacteria and what it means for our understanding of eukaryogenesis.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {370},
number = {1678},
pages = {20140337},
doi = {10.1098/rstb.2014.0337},
pmid = {26323767},
issn = {1471-2970},
support = {BB/G024707/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/K007440///Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Bacteria/*genetics ; *Biological Evolution ; *Gene Flow ; Genome, Bacterial ; Models, Genetic ; },
abstract = {The origin of the eukaryotic cell is considered one of the major evolutionary transitions in the history of life. Current evidence strongly supports a scenario of eukaryotic origin in which two prokaryotes, an archaebacterial host and an α-proteobacterium (the free-living ancestor of the mitochondrion), entered a stable symbiotic relationship. The establishment of this relationship was associated with a process of chimerization, whereby a large number of genes from the α-proteobacterial symbiont were transferred to the host nucleus. A general framework allowing the conceptualization of eukaryogenesis from a genomic perspective has long been lacking. Recent studies suggest that the origins of several archaebacterial phyla were coincident with massive imports of eubacterial genes. Although this does not indicate that these phyla originated through the same process that led to the origin of Eukaryota, it suggests that Archaebacteria might have had a general propensity to integrate into their genomes large amounts of eubacterial DNA. We suggest that this propensity provides a framework in which eukaryogenesis can be understood and studied in the light of archaebacterial ecology. We applied a recently developed supertree method to a genomic dataset composed of 392 eubacterial and 51 archaebacterial genera to test whether large numbers of genes flowing from Eubacteria are indeed coincident with the origin of major archaebacterial clades. In addition, we identified two potential large-scale transfers of uncertain directionality at the base of the archaebacterial tree. Our results are consistent with previous findings and seem to indicate that eubacterial gene imports (particularly from δ-Proteobacteria, Clostridia and Actinobacteria) were an important factor in archaebacterial history. Archaebacteria seem to have long relied on Eubacteria as a source of genetic diversity, and while the precise mechanism that allowed these imports is unknown, we suggest that our results support the view that processes comparable to those through which eukaryotes emerged might have been common in archaebacterial history.},
}
@article {pmid26323764,
year = {2015},
author = {Koonin, EV},
title = {Origin of eukaryotes from within archaea, archaeal eukaryome and bursts of gene gain: eukaryogenesis just made easier?.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {370},
number = {1678},
pages = {20140333},
doi = {10.1098/rstb.2014.0333},
pmid = {26323764},
issn = {1471-2970},
mesh = {Archaea/*genetics ; *Biological Evolution ; Eukaryota/genetics ; *Eukaryotic Cells ; *Genome, Archaeal ; },
abstract = {The origin of eukaryotes is a fundamental, forbidding evolutionary puzzle. Comparative genomic analysis clearly shows that the last eukaryotic common ancestor (LECA) possessed most of the signature complex features of modern eukaryotic cells, in particular the mitochondria, the endomembrane system including the nucleus, an advanced cytoskeleton and the ubiquitin network. Numerous duplications of ancestral genes, e.g. DNA polymerases, RNA polymerases and proteasome subunits, also can be traced back to the LECA. Thus, the LECA was not a primitive organism and its emergence must have resulted from extensive evolution towards cellular complexity. However, the scenario of eukaryogenesis, and in particular the relationship between endosymbiosis and the origin of eukaryotes, is far from being clear. Four recent developments provide new clues to the likely routes of eukaryogenesis. First, evolutionary reconstructions suggest complex ancestors for most of the major groups of archaea, with the subsequent evolution dominated by gene loss. Second, homologues of signature eukaryotic proteins, such as actin and tubulin that form the core of the cytoskeleton or the ubiquitin system, have been detected in diverse archaea. The discovery of this 'dispersed eukaryome' implies that the archaeal ancestor of eukaryotes was a complex cell that might have been capable of a primitive form of phagocytosis and thus conducive to endosymbiont capture. Third, phylogenomic analyses converge on the origin of most eukaryotic genes of archaeal descent from within the archaeal evolutionary tree, specifically, the TACK superphylum. Fourth, evidence has been presented that the origin of the major archaeal phyla involved massive acquisition of bacterial genes. Taken together, these findings make the symbiogenetic scenario for the origin of eukaryotes considerably more plausible and the origin of the organizational complexity of eukaryotic cells more readily explainable than they appeared until recently.},
}
@article {pmid26320243,
year = {2015},
author = {Acosta, S and Carela, M and Garcia-Gonzalez, A and Gines, M and Vicens, L and Cruet, R and Massey, SE},
title = {DNA Repair Is Associated with Information Content in Bacteria, Archaea, and DNA Viruses.},
journal = {The Journal of heredity},
volume = {106},
number = {5},
pages = {644-659},
doi = {10.1093/jhered/esv055},
pmid = {26320243},
issn = {1465-7333},
mesh = {Archaea/genetics ; Bacteria/*genetics ; Base Composition ; Cluster Analysis ; *DNA Repair ; DNA Viruses/genetics ; *Evolution, Molecular ; Genes, Archaeal ; *Genes, Bacterial ; Genes, Viral ; Genome, Bacterial ; Mutation Rate ; Phylogeny ; Proteome ; },
abstract = {The concept of a &quot;proteomic constraint&quot; proposes that DNA repair capacity is positively correlated with the information content of a genome, which can be approximated to the size of the proteome (P). This in turn implies that DNA repair genes are more likely to be present in genomes with larger values of P. This stands in contrast to the common assumption that informational genes have a core function and so are evenly distributed across organisms. We examined the presence/absence of 18 DNA repair genes in bacterial genomes. A positive relationship between gene presence and P was observed for 17 genes in the total dataset, and 16 genes when only nonintracellular bacteria were examined. A marked reduction of DNA repair genes was observed in intracellular bacteria, consistent with their reduced value of P. We also examined archaeal and DNA virus genomes, and show that the presence of DNA repair genes is likewise related to a larger value of P. In addition, the products of the bacterial genes mutY, vsr, and ndk, involved in the correction of GC/AT mutations, are strongly associated with reduced genome GC content. We therefore propose that a reduction in information content leads to a loss of DNA repair genes and indirectly to a reduction in genome GC content in bacteria by exposure to the underlying AT mutation bias. The reduction in P may also indirectly lead to the increase in substitution rates observed in intracellular bacteria via loss of DNA repair genes.},
}
@article {pmid26300291,
year = {2015},
author = {Ding, J and Ding, ZW and Fu, L and Lu, YZ and Cheng, SH and Zeng, RJ},
title = {New primers for detecting and quantifying denitrifying anaerobic methane oxidation archaea in different ecological niches.},
journal = {Applied microbiology and biotechnology},
volume = {99},
number = {22},
pages = {9805-9812},
doi = {10.1007/s00253-015-6893-6},
pmid = {26300291},
issn = {1432-0614},
mesh = {Anaerobiosis ; Archaea/classification/*genetics/*isolation &amp; purification ; DNA Primers/*genetics ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Methane/*metabolism ; Oxidation-Reduction ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction/methods ; Sensitivity and Specificity ; *Water Microbiology ; },
abstract = {The significance of ANME-2d in methane sink in the environment has been overlooked, and there was no any study evaluating the distribution of ANME-2d in the environment. New primers were thus needed to be designed for following research. In this paper, a pair of primers (DP397F and DP569R) was designed to quantify ANME-2d. The specificity and amplification efficiency of this primer pair were acceptable. PCR amplification of another pair of primers (DP142F and DP779R) generated a single, bright targeted band from the enrichment sample, but yielded faint, multiple bands from the environmental samples. Nested PCR was conducted using the primers DP142F/DP779R in the first round and DP142F/DP569R in the second round, which generated a bright targeted band. Further phylogenetic analysis showed that these targeted bands were ANME-2d-related sequences. Real-time PCR showed that the copies of the 16s ribosomal RNA gene of ANME-2d in these samples ranged from 3.72 × 10(4) to 2.30 × 10(5) copies μg(-1) DNA, indicating that the percentage of ANME-2d was greatest in a polluted river sample and least in a rice paddy sample. These results demonstrate that the newly developed real-time PCR primers could sufficiently quantify ANME-2d and that nested PCR with an appropriate combination of the new primers could successfully detect ANME-2d in environmental samples; the latter finding suggests that ANME-2d may spread in environments.},
}
@article {pmid26296935,
year = {2015},
author = {Wagner, EG and Romby, P},
title = {Small RNAs in bacteria and archaea: who they are, what they do, and how they do it.},
journal = {Advances in genetics},
volume = {90},
number = {},
pages = {133-208},
doi = {10.1016/bs.adgen.2015.05.001},
pmid = {26296935},
issn = {0065-2660},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; Gene Expression Regulation ; Host Factor 1 Protein/metabolism ; RNA, Archaeal/metabolism ; RNA, Bacterial/metabolism ; RNA, Small Untranslated/*metabolism ; },
abstract = {Small RNAs are ubiquitously present regulators in all kingdoms of life. Most bacterial and archaeal small RNAs (sRNAs) act by antisense mechanisms on multiple target mRNAs, thereby globally affecting essentially any conceivable trait-stress responses, adaptive metabolic changes, virulence etc. The sRNAs display many distinct mechanisms of action, most of them through effects on target mRNA translation and/or stability, and helper proteins like Hfq often play key roles. Recent data highlight the interplay between posttranscriptional control by sRNAs and transcription factor-mediated transcriptional control, and cross talk through mutual regulation of regulators. Based on the properties that distinguish sRNA-type from transcription factors-type control, we begin to glimpse why sRNAs have evolved as a second, essential layer of gene regulation. This review will discuss the prevalence of sRNAs, who they are, what biological roles they play, and how they carry out their functions.},
}
@article {pmid26284058,
year = {2015},
author = {Kumar, S and Indugu, N and Vecchiarelli, B and Pitta, DW},
title = {Associative patterns among anaerobic fungi, methanogenic archaea, and bacterial communities in response to changes in diet and age in the rumen of dairy cows.},
journal = {Frontiers in microbiology},
volume = {6},
number = {},
pages = {781},
doi = {10.3389/fmicb.2015.00781},
pmid = {26284058},
issn = {1664-302X},
abstract = {The rumen microbiome represents a complex microbial genetic web where bacteria, anaerobic rumen fungi (ARF), protozoa and archaea work in harmony contributing to the health and productivity of ruminants. We hypothesized that the rumen microbiome shifts as the dairy cow advances in lactations and these microbial changes may contribute to differences in productivity between primiparous (first lactation) and multiparous (≥second lactation) cows. To this end, we investigated shifts in the ruminal ARF and methanogenic communities in both primiparous (n = 5) and multiparous (n = 5) cows as they transitioned from a high forage to a high grain diet upon initiation of lactation. A total of 20 rumen samples were extracted for genomic DNA, amplified using archaeal and fungal specific primers, sequenced on a 454 platform and analyzed using QIIME. Community comparisons (Bray-Curtis index) revealed the effect of diet (P < 0.01) on ARF composition, while archaeal communities differed between primiparous and multiparous cows (P < 0.05). Among ARF, several lineages were unclassified, however, phylum Neocallimastigomycota showed the presence of three known genera. Abundance of Cyllamyces and Caecomyces shifted with diet, whereas Orpinomyces was influenced by both diet and age. Methanobrevibacter constituted the most dominant archaeal genus across all samples. Co-occurrence analysis incorporating taxa from bacteria, ARF and archaea revealed syntrophic interactions both within and between microbial domains in response to change in diet as well as age of dairy cows. Notably, these interactions were numerous and complex in multiparous cows, supporting our hypothesis that the rumen microbiome also matures with age to sustain the growing metabolic needs of the host. This study provides a broader picture of the ARF and methanogenic populations in the rumen of dairy cows and their co-occurrence implicates specific relationships between different microbial domains in response to diet and age.},
}
@article {pmid26284036,
year = {2015},
author = {Spaans, SK and Weusthuis, RA and van der Oost, J and Kengen, SW},
title = {NADPH-generating systems in bacteria and archaea.},
journal = {Frontiers in microbiology},
volume = {6},
number = {},
pages = {742},
doi = {10.3389/fmicb.2015.00742},
pmid = {26284036},
issn = {1664-302X},
abstract = {Reduced nicotinamide adenine dinucleotide phosphate (NADPH) is an essential electron donor in all organisms. It provides the reducing power that drives numerous anabolic reactions, including those responsible for the biosynthesis of all major cell components and many products in biotechnology. The efficient synthesis of many of these products, however, is limited by the rate of NADPH regeneration. Hence, a thorough understanding of the reactions involved in the generation of NADPH is required to increase its turnover through rational strain improvement. Traditionally, the main engineering targets for increasing NADPH availability have included the dehydrogenase reactions of the oxidative pentose phosphate pathway and the isocitrate dehydrogenase step of the tricarboxylic acid (TCA) cycle. However, the importance of alternative NADPH-generating reactions has recently become evident. In the current review, the major canonical and non-canonical reactions involved in the production and regeneration of NADPH in prokaryotes are described, and their key enzymes are discussed. In addition, an overview of how different enzymes have been applied to increase NADPH availability and thereby enhance productivity is provided.},
}
@article {pmid26248160,
year = {2015},
author = {Scharko, NK and Schütte, UM and Berke, AE and Banina, L and Peel, HR and Donaldson, MA and Hemmerich, C and White, JR and Raff, JD},
title = {Combined Flux Chamber and Genomics Approach Links Nitrous Acid Emissions to Ammonia Oxidizing Bacteria and Archaea in Urban and Agricultural Soil.},
journal = {Environmental science &amp; technology},
volume = {49},
number = {23},
pages = {13825-13834},
doi = {10.1021/acs.est.5b00838},
pmid = {26248160},
issn = {1520-5851},
mesh = {Agriculture ; Ammonia/*metabolism ; Archaea/genetics/*metabolism ; Atmosphere/chemistry ; Betaproteobacteria/genetics/metabolism ; Genomics/methods ; Indiana ; Microbial Consortia/*genetics/physiology ; Nitrification ; Nitrogen Isotopes/analysis ; *Nitrous Acid/metabolism ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; Urbanization ; },
abstract = {Nitrous acid (HONO) is a photochemical source of hydroxyl radical and nitric oxide in the atmosphere that stems from abiotic and biogenic processes, including the activity of ammonia-oxidizing soil microbes. HONO fluxes were measured from agricultural and urban soil in mesocosm studies aimed at characterizing biogenic sources and linking them to indigenous microbial consortia. Fluxes of HONO from agricultural and urban soil were suppressed by addition of a nitrification inhibitor and enhanced by amendment with ammonium (NH4(+)), with peaks at 19 and 8 ng m(-2) s(-1), respectively. In addition, both agricultural and urban soils were observed to convert (15)NH4(+) to HO(15)NO. Genomic surveys of soil samples revealed that 1.5-6% of total expressed 16S rRNA sequences detected belonged to known ammonia oxidizing bacteria and archaea. Peak fluxes of HONO were directly related to the abundance of ammonia-oxidizer sequences, which in turn depended on soil pH. Peak HONO fluxes under fertilized conditions are comparable in magnitude to fluxes reported during field campaigns. The results suggest that biogenic HONO emissions will be important in soil environments that exhibit high nitrification rates (e.g., agricultural soil) although the widespread occurrence of ammonia oxidizers implies that biogenic HONO emissions are also possible in the urban and remote environment.},
}
@article {pmid26235787,
year = {2015},
author = {Barnhart, EP and McClure, MA and Johnson, K and Cleveland, S and Hunt, KA and Fields, MW},
title = {Potential Role of Acetyl-CoA Synthetase (acs) and Malate Dehydrogenase (mae) in the Evolution of the Acetate Switch in Bacteria and Archaea.},
journal = {Scientific reports},
volume = {5},
number = {},
pages = {12498},
doi = {10.1038/srep12498},
pmid = {26235787},
issn = {2045-2322},
mesh = {Acetate Kinase/chemistry/metabolism ; Acetate-CoA Ligase/chemistry/genetics/*metabolism ; Acetates/*metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Archaeal Proteins/*chemistry/genetics/metabolism ; Bacterial Proteins/*chemistry/genetics/metabolism ; *Biological Evolution ; Conserved Sequence ; Evolution, Molecular ; Halobacteriales/enzymology/genetics ; Malate Dehydrogenase/chemistry/genetics/*metabolism ; Methanosarcina/genetics/metabolism ; Phosphate Acetyltransferase/chemistry/metabolism ; Phylogeny ; Substrate Specificity ; },
abstract = {Although many Archaea have AMP-Acs (acetyl-coenzyme A synthetase) and ADP-Acs, the extant methanogenic genus Methanosarcina is the only identified Archaeal genus that can utilize acetate via acetate kinase (Ack) and phosphotransacetylase (Pta). Despite the importance of ack as the potential urkinase in the ASKHA phosphotransferase superfamily, an origin hypothesis does not exist for the acetate kinase in Bacteria, Archaea, or Eukarya. Here we demonstrate that Archaeal AMP-Acs and ADP-Acs contain paralogous ATPase motifs previously identified in Ack, which demonstrate a novel relation between these proteins in Archaea. The identification of ATPase motif conservation and resulting structural features in AMP- and ADP-acetyl-CoA synthetase proteins in this study expand the ASKHA superfamily to include acetyl-CoA synthetase. Additional phylogenetic analysis showed that Pta and MaeB sequences had a common ancestor, and that the Pta lineage within the halophilc archaea was an ancestral lineage. These results suggested that divergence of a duplicated maeB within an ancient halophilic, archaeal lineage formed a putative pta ancestor. These results provide a potential scenario for the establishment of the Ack/Pta pathway and provide novel insight into the evolution of acetate metabolism for all three domains of life.},
}
@article {pmid26226005,
year = {2015},
author = {Stan-Lotter, H and Fendrihan, S},
title = {Halophilic Archaea: Life with Desiccation, Radiation and Oligotrophy over Geological Times.},
journal = {Life (Basel, Switzerland)},
volume = {5},
number = {3},
pages = {1487-1496},
doi = {10.3390/life5031487},
pmid = {26226005},
issn = {2075-1729},
abstract = {Halophilic archaebacteria (Haloarchaea) can survive extreme desiccation, starvation and radiation, sometimes apparently for millions of years. Several of the strategies that are involved appear specific for Haloarchaea (for example, the formation of halomucin, survival in fluid inclusions of halite), and some are known from other prokaryotes (dwarfing of cells, reduction of ATP). Several newly-discovered haloarchaeal strategies that were inferred to possibly promote long-term survival-halomucin, polyploidy, usage of DNA as a phosphate storage polymer, production of spherical dormant stages-remain to be characterized in detail. More information on potential strategies is desirable, since evidence for the presence of halite on Mars and on several moons in the solar system increased interest in halophiles with respect to the search for extraterrestrial life. This review deals in particular with novel findings and hypotheses on haloarchaeal long-term survival.},
}
@article {pmid26217762,
year = {2015},
author = {Cerletti, M and Paggi, RA and Ramallo Guevara, C and Poetsch, A and De Castro, RE},
title = {Data in support of global role of the membrane protease LonB in Archaea: Potential protease targets revealed by quantitative proteome analysis of a lonB mutant in Haloferax volcanii.},
journal = {Data in brief},
volume = {4},
number = {},
pages = {50-53},
doi = {10.1016/j.dib.2015.04.013},
pmid = {26217762},
issn = {2352-3409},
abstract = {This data article provides information in support of the research article &quot;Global role of the membrane protease LonB in Archaea: Potential protease targets revealed by quantitative proteome analysis of a lonB mutant in Haloferax volcanii&quot; [1]. The proteome composition of a wt and a LonB protease mutant strain (suboptimal expression) in the archaeon Haloferax volcanii was assessed by a quantitative shotgun proteomic approach. Membrane and cytosol fractions of H. volcanii strains were examined at two different growth stages (exponential and stationary phase). Data is supplied in the present article. This study represents the first proteome examination of a Lon-deficient cell of the Archaea Domain.},
}
@article {pmid26211960,
year = {2015},
author = {Anupama, VN and Prajeesh, PV and Anju, S and Priya, P and Krishnakumar, B},
title = {Diversity of bacteria, archaea and protozoa in a perchlorate treating bioreactor.},
journal = {Microbiological research},
volume = {177},
number = {},
pages = {8-14},
doi = {10.1016/j.micres.2015.04.011},
pmid = {26211960},
issn = {1618-0623},
mesh = {Acetates/metabolism ; Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Bioreactors/*microbiology ; *Biota ; Biotransformation ; Denaturing Gradient Gel Electrophoresis ; In Situ Hybridization, Fluorescence ; Microscopy ; Molecular Sequence Data ; Oxidation-Reduction ; Perchlorates/*metabolism ; Phylogeny ; Sequence Analysis, DNA ; Volvocida/*classification/genetics ; },
abstract = {A microbial consortium reducing high level of perchlorate was developed and in a fed batch bioreactor using acetate as substrate perchlorate was reduced at 0.25 g/g vss. day. Under stable performance, the microbial community structure of the reactor was analyzed through molecular and phenotypic methods. The diversity of bacteria and archaea were analyzed through whole cell Fluorescence In-Situ Hybridization (FISH) and PCR-Denaturing Gradient Gel Electrophoresis (DGGE), whereas higher trophic community was analyzed phenotypically. FISH analysis revealed the presence of alpha, beta, gamma and delta proteobacteria in the sludge, dominated by beta proteobacteria (68.7%). DGGE analysis of bacteria revealed the presence of a single known perchlorate reducing bacterium-Dechloromonas, nitrate reducers like Thaeura and Azoarcus and a number of other genera so far not reported as perchlorate or nitrate reducing. The archaea community was represented by an acetoclastic methanogen, Methanosaeta harundinacea. We have also observed the presence of an acetate consuming flagellate, Polytomella sp. in significant number in the reactor. Archaea and protozoa community in perchlorate treating bioreactor is reported first time in this study and point out further the significance of non perchlorate reducing but acetate scavenging microbial groups in acetate fed perchlorate treating reactors.},
}
@article {pmid26194817,
year = {2016},
author = {Huynh, HT and Verneau, J and Levasseur, A and Drancourt, M and Aboudharam, G},
title = {Bacteria and archaea paleomicrobiology of the dental calculus: a review.},
journal = {Molecular oral microbiology},
volume = {31},
number = {3},
pages = {234-242},
doi = {10.1111/omi.12118},
pmid = {26194817},
issn = {2041-1014},
mesh = {Adult ; Archaea/genetics/*isolation &amp; purification ; Bacteria/genetics/*isolation &amp; purification ; Bacteroidetes/genetics/isolation &amp; purification ; Dental Calculus/*history/microbiology/virology ; Diet/history ; Fusobacterium/genetics/isolation &amp; purification ; History, Ancient ; Humans ; Immunohistochemistry ; Isotope Labeling ; Microbiota ; Paleodontology ; Phylogeny ; Proteobacteria/genetics/isolation &amp; purification ; Streptococcus mutans/genetics ; },
abstract = {Dental calculus, a material observed in the majority of adults worldwide, emerged as a source for correlating paleomicrobiology with human health and diet. This mini review of 48 articles on the paleomicrobiology of dental calculus over 7550 years discloses a secular core microbiota comprising nine bacterial phyla - Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes, TM7, Synergistetes, Chloroflexi, Fusobacteria, Spirochetes - and one archaeal phylum Euryarchaeota; and some accessory microbiota that appear and disappear according to time frame. The diet residues and oral microbes, including bacteria, archaea, viruses and fungi, consisting of harmless organisms and pathogens associated with local and systemic infections have been found trapped in ancient dental calculus by morphological approaches, immunolabeling techniques, isotope analyses, fluorescent in situ hybridization, DNA-based approaches, and protein-based approaches. These observations led to correlation of paleomicrobiology, particularly Streptococcus mutans and archaea, with past human health and diet.},
}
@article {pmid26174392,
year = {2015},
author = {Oger, PM},
title = {Homeoviscous Adaptation of Membranes in Archaea.},
journal = {Sub-cellular biochemistry},
volume = {72},
number = {},
pages = {383-403},
doi = {10.1007/978-94-017-9918-8_19},
pmid = {26174392},
issn = {0306-0225},
mesh = {*Adaptation, Physiological ; Archaea/*physiology ; Cell Membrane/chemistry ; Membrane Lipids/chemistry ; Molecular Structure ; *Viscosity ; },
abstract = {Because membranes play a central role in regulating fluxes inward and outward from the cells, maintaining the appropriate structure of the membrane is crucial to maintain cellular integrity and functions. Microbes often face contrasted and fluctuating environmental conditions, to which they need to adapt or die. Membrane adaptation is achieved by a modification of the membrane lipid composition, a strategy termed homeoviscous adaptation. Homeoviscous adaptation in archaea involves strategies similar to that observed in bacteria and eucarya, such as the regulation of lipid chain length or saturation levels, as well as strategies specific to archaea, such as the regulation of the number of cycles along the isoprenoid chains or the regulation of the ratio between mono and bipolar lipids. Although not described yet described in hyperthermophilic bacteria, it is possible that these two strategies also apply to these latter organisms.},
}
@article {pmid26172994,
year = {2015},
author = {Chen, Z and Wu, W and Shao, X and Li, L and Guo, Y and Ding, G},
title = {Shifts in Abundance and Diversity of Soil Ammonia-Oxidizing Bacteria and Archaea Associated with Land Restoration in a Semi-Arid Ecosystem.},
journal = {PloS one},
volume = {10},
number = {7},
pages = {e0132879},
doi = {10.1371/journal.pone.0132879},
pmid = {26172994},
issn = {1932-6203},
mesh = {Agriculture ; Ammonia/*metabolism ; Archaea/*genetics ; Bacteria/*genetics ; Biodiversity ; Caragana/growth &amp; development ; China ; Droughts ; Ecosystem ; Environmental Restoration and Remediation/*methods ; Lolium/growth &amp; development ; Nitrification/genetics ; Nitrogen/metabolism ; Nitrogen Cycle/genetics ; Oxidation-Reduction ; Polymorphism, Restriction Fragment Length/genetics ; Soil ; Soil Microbiology ; },
abstract = {The Grain to Green Project (GGP) is an unprecedented land restoration action in China. The project converted large areas (ca 10 million ha) of steep-sloped/degraded farmland and barren land into forest and grassland resulting in ecological benefits such as a reduction in severe soil erosion. It may also affect soil microorganisms involved in ammonia oxidization, which is a key step in the global nitrogen cycle. The methods for restoration that are typically adopted in semi-arid regions include abandoning farmland and growing drought tolerant grass (Lolium perenne L.) or shrubs (Caragana korshinskii Kom.). In the present study, the effects of these methods on the abundance and diversity of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) were evaluated via quantitative real-time PCR, terminal restriction fragment length polymorphism and clone library analysis of amoA genes. Comparisons were made between soil samples from three restored lands and the adjacent farmland in Inner Mongolia. Both the abundance and community composition of AOB were significantly different between the restored lands and the adjacent control. Significantly lower nitrification activity was observed for the restored land. Clone library analysis revealed that all AOB amoA gene sequences were affiliated with Nitrosospira. Abundance of the populations that were associated with Nitrosospira sp. Nv6 which had possibly adapted to high concentrations of inorganic nitrogen, decreased on the restored land. Only a slight difference in the AOB communities was observed between the restored land with and without the shrub (Caragana korshinskii Kom.). A minor effect of land restoration on AOA was observed. In summary, land restoration negatively affected the abundance of AOB and soil nitrification activities, suggesting the potential role of GGP in the leaching of nitrates, and in the emission of N2O in related terrestrial ecosystems.},
}
@article {pmid26161079,
year = {2015},
author = {Lee, HJ and Jeong, SE and Kim, PJ and Madsen, EL and Jeon, CO},
title = {High resolution depth distribution of Bacteria, Archaea, methanotrophs, and methanogens in the bulk and rhizosphere soils of a flooded rice paddy.},
journal = {Frontiers in microbiology},
volume = {6},
number = {},
pages = {639},
doi = {10.3389/fmicb.2015.00639},
pmid = {26161079},
issn = {1664-302X},
abstract = {The communities and abundances of methanotrophs and methanogens, along with the oxygen, methane, and total organic carbon (TOC) concentrations, were investigated along a depth gradient in a flooded rice paddy. Broad patterns in vertical profiles of oxygen, methane, TOC, and microbial abundances were similar in the bulk and rhizosphere soils, though methane and TOC concentrations and 16S rRNA gene copies were clearly higher in the rhizosphere soil than in the bulk soil. Oxygen concentrations decreased sharply to below detection limits at 8 mm depth. Pyrosequencing of 16S rRNA genes showed that bacterial and archaeal communities varied according to the oxic, oxic-anoxic, and anoxic zones, indicating that oxygen is a determining factor for the distribution of bacterial and archaeal communities. Aerobic methanotrophs were maximally observed near the oxic-anoxic interface, while methane, TOC, and methanogens were highest in the rhizosphere soil at 30-200 mm depth, suggesting that methane is produced mainly from organic carbon derived from rice plants and is metabolized aerobically. The relative abundances of type I methanotrophs such as Methylococcus, Methylomonas, and Methylocaldum decreased more drastically than those of type II methanotrophs (such as Methylocystis and Methylosinus) with increasing depth. Methanosaeta and Methanoregula were predominant methanogens at all depths, and the relative abundances of Methanosaeta, Methanoregula, and Methanosphaerula, and GOM_Arc_I increased with increasing depth. Based on contrasts between absolute abundances of methanogens and methanotrophs at depths sampled across rhizosphere and bulk soils (especially millimeter-scale slices at the surface), we have identified populations of methanogens (Methanosaeta, Methanoregula, Methanocella, Methanobacterium, and Methanosphaerula), and methanotrophs (Methylosarcina, Methylococcus, Methylosinus, and unclassified Methylocystaceae) that are likely physiologically active in situ.},
}
@article {pmid26146487,
year = {2015},
author = {Grogan, DW},
title = {Understanding DNA Repair in Hyperthermophilic Archaea: Persistent Gaps and Other Reasons to Focus on the Fork.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2015},
number = {},
pages = {942605},
doi = {10.1155/2015/942605},
pmid = {26146487},
issn = {1472-3654},
mesh = {Archaea/genetics/*physiology/*radiation effects ; DNA Damage ; *DNA Repair ; DNA Repair Enzymes/genetics/metabolism ; DNA, Archaeal/radiation effects ; Hot Temperature ; },
abstract = {Although hyperthermophilic archaea arguably have a great need for efficient DNA repair, they lack members of several DNA repair protein families broadly conserved among bacteria and eukaryotes. Conversely, the putative DNA repair genes that do occur in these archaea often do not generate the expected phenotype when deleted. The prospect that hyperthermophilic archaea have some unique strategies for coping with DNA damage and replication errors has intellectual and technological appeal, but resolving this question will require alternative coping mechanisms to be proposed and tested experimentally. This review evaluates a combination of four enigmatic properties that distinguishes the hyperthermophilic archaea from all other organisms: DNA polymerase stalling at dU, apparent lack of conventional NER, lack of MutSL homologs, and apparent essentiality of homologous recombination proteins. Hypothetical damage-coping strategies that could explain this set of properties may provide new starting points for efforts to define how archaea differ from conventional models of DNA repair and replication fidelity.},
}
@article {pmid26125682,
year = {2015},
author = {Tschitschko, B and Williams, TJ and Allen, MA and Páez-Espino, D and Kyrpides, N and Zhong, L and Raftery, MJ and Cavicchioli, R},
title = {Antarctic archaea-virus interactions: metaproteome-led analysis of invasion, evasion and adaptation.},
journal = {The ISME journal},
volume = {9},
number = {9},
pages = {2094-2107},
doi = {10.1038/ismej.2015.110},
pmid = {26125682},
issn = {1751-7370},
mesh = {Acclimatization ; Antarctic Regions ; Archaea/genetics/virology ; Archaeal Viruses/*genetics ; CRISPR-Cas Systems ; Capsid Proteins/physiology ; Cell Membrane/metabolism ; Ecosystem ; Genetic Variation ; Lakes/*microbiology/*virology ; Metagenome ; Metagenomics ; Phenotype ; Proteomics ; Viruses/genetics ; *Water Microbiology ; },
abstract = {Despite knowledge that viruses are abundant in natural ecosystems, there is limited understanding of which viruses infect which hosts, and how both hosts and viruses respond to those interactions-interactions that ultimately shape community structure and dynamics. In Deep Lake, Antarctica, intergenera gene exchange occurs rampantly within the low complexity, haloarchaea-dominated community, strongly balanced by distinctions in niche adaptation which maintain sympatric speciation. By performing metaproteomics for the first time on haloarchaea, genomic variation of S-layer, archaella and other cell surface proteins was linked to mechanisms of infection evasion. CRISPR defense systems were found to be active, with haloarchaea responding to at least eight distinct types of viruses, including those infecting between genera. The role of BREX systems in defending against viruses was also examined. Although evasion and defense were evident, both hosts and viruses also may benefit from viruses carrying and expressing host genes, thereby potentially enhancing genetic variation and phenotypic differences within populations. The data point to a complex inter-play leading to a dynamic optimization of host-virus interactions. This comprehensive overview was achieved only through the integration of results from metaproteomics, genomics and metagenomics.},
}
@article {pmid26125322,
year = {2015},
author = {Zhang, Y and Tian, Z and Liu, M and Shi, ZJ and Hale, L and Zhou, J and Yang, M},
title = {High Concentrations of the Antibiotic Spiramycin in Wastewater Lead to High Abundance of Ammonia-Oxidizing Archaea in Nitrifying Populations.},
journal = {Environmental science &amp; technology},
volume = {49},
number = {15},
pages = {9124-9132},
doi = {10.1021/acs.est.5b01293},
pmid = {26125322},
issn = {1520-5851},
mesh = {Ammonia/*metabolism ; Anti-Bacterial Agents/*analysis ; Archaea/genetics/*metabolism ; Bacteria/genetics/metabolism ; Genes, Archaeal ; Genetic Variation ; *Nitrification ; Nitrogen Cycle ; Oxidation-Reduction ; Phylogeny ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sewage/microbiology ; Spiramycin/*analysis ; Waste Water/*chemistry/microbiology ; Water Pollutants, Chemical/*analysis ; Water Quality ; },
abstract = {To evaluate the potential effects of antibiotics on ammonia-oxidizing microbes, multiple tools including quantitative PCR (qPCR), 454-pyrosequencing, and a high-throughput functional gene array (GeoChip) were used to reveal the distribution of ammonia-oxidizing archaea (AOA) and archaeal amoA (Arch-amoA) genes in three wastewater treatment systems receiving spiramycin or oxytetracycline production wastewaters. The qPCR results revealed that the copy number ratios of Arch-amoA to ammonia-oxidizing bacteria (AOB) amoA genes were the highest in the spiramycin full-scale (5.30) and pilot-scale systems (1.49 × 10(-1)), followed by the oxytetracycline system (4.90 × 10(-4)), with no Arch-amoA genes detected in the control systems treating sewage or inosine production wastewater. The pyrosequencing result showed that the relative abundance of AOA affiliated with Thaumarchaeota accounted for 78.5-99.6% of total archaea in the two spiramycin systems, which was in accordance with the qPCR results. Mantel test based on GeoChip data showed that Arch-amoA gene signal intensity correlated with the presence of spiramycin (P < 0.05). Antibiotics explained 25.8% of variations in amoA functional gene structures by variance partitioning analysis. This study revealed the selection of AOA in the presence of high concentrations of spiramycin in activated sludge systems.},
}
@article {pmid26103451,
year = {2015},
author = {Paul, SS and Deb, SM and Dey, A and Somvanshi, SP and Singh, D and Rathore, R and Stiverson, J},
title = {16S rDNA analysis of archaea indicates dominance of Methanobacterium and high abundance of Methanomassiliicoccaceae in rumen of Nili-Ravi buffalo.},
journal = {Anaerobe},
volume = {35},
number = {Pt B},
pages = {3-10},
doi = {10.1016/j.anaerobe.2015.06.002},
pmid = {26103451},
issn = {1095-8274},
mesh = {Animals ; Archaea/*classification/genetics/*isolation &amp; purification ; *Biota ; Buffaloes/*microbiology ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Male ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; Sequence Analysis, DNA ; },
abstract = {The molecular diversity of rumen methanogens was investigated using 16S rDNA gene library prepared from the rumen contents of Nili-Ravi buffaloes. Microbial genomic DNA was isolated from four adult male fistulated buffaloes and PCR conditions were set up using specific primers. Amplified product was cloned into a suitable vector, and the inserts of positive clones were sequenced. A total of 142 clones were examined, and the analysis revealed 46 species level (0.01 distance) operational taxonomic units (OTUs). Twenty six OTUs comprising 89 clones (63% of the total clones) were taxonomically assigned to Methanobacterium genus and the majority of them had highest percent identity with Methanobacterium flexile among cultured methanogens. Five OTUs comprising 27 clones (19% of total clones) were taxonomically assigned to Methanomicrobium genus and these clones showed highest sequence identity with Methanomicrobium mobile. Only two OTUs comprising 6 clones (4% of total clones) were assigned to Methanobrevibacter genus. A total of 17 clones belonging to 10 species level OTUs showed highest percent identity (ranging from 85 to 95%) with Methanomassilicoccus luminyensis and were taxonomically classified as Methanomassiliicocaceae. Out of the 142 rDNA clones, 112 clones, which constitute 79% of the total clones representing 42 OTUs, had less than 98.5% sequence identity with any of the cultured strains of methanogens and represent novel species of methanogens. This study has revealed the largest assortment of hydrogenotrophic methanogen phylotypes ever identified from the rumen of Nili-Ravi buffaloes. The study indicates that Methanobacterium is the most dominant methanogen in the rumen of Nili-Ravi buffalo. This is also the first report on the presence of methanogens phylogenetically close to M. luminyensis, an H2 dependent methylotrophic methanogen, in the rumen of buffaloes at such a high level of abundance.},
}
@article {pmid26099334,
year = {2015},
author = {Liu, S and Hu, B and He, Z and Zhang, B and Tian, G and Zheng, P and Fang, F},
title = {Ammonia-oxidizing archaea have better adaptability in oxygenated/hypoxic alternant conditions compared to ammonia-oxidizing bacteria.},
journal = {Applied microbiology and biotechnology},
volume = {99},
number = {20},
pages = {8587-8596},
doi = {10.1007/s00253-015-6750-7},
pmid = {26099334},
issn = {1432-0614},
mesh = {Adaptation, Biological ; Aerobiosis ; Ammonia/*metabolism ; Anaerobiosis ; Archaea/*classification/*genetics/metabolism ; Bacteria/*classification/*genetics/metabolism ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; *Genetic Variation ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; *Soil Microbiology ; },
abstract = {Ammonia oxidation is performed by both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Few studies compared the adaptability of AOA and AOB for oxygenated/hypoxic alternant conditions in water-level-fluctuating zones. Here, using qPCR and 454 high-throughput sequencing of functional amoA genes of AOA and AOB, we examined the changes of abundances, diversities, and community structures of AOA and AOB in periodically flooded soils compared to the non-flooded soils in Three Gorges Reservoir. The increased AOA operational taxonomic unit (OTU) numbers and the higher ratios of abundance (AOA:AOB) in the periodically flooded soils suggested AOA have better adaptability for oxygenated/hypoxic alternant conditions in the water-level-fluctuating zones in the Three Gorges Reservoir and probably responsible for the ammonia oxidation there. Canonical correspondence analysis (CCA) showed that oxidation-reduction potential (ORP) had the most significant effect on the community distribution of AOA (p < 0.01). Pearson analysis also indicated that ORP was the most important factor influencing the abundances and diversities of ammonia-oxidizing microbes. ORP was significantly negatively correlated with AOA OTU numbers (p < 0.05), ratio of OTU numbers (AOA:AOB) (p < 0.01), and ratio of amoA gene abundances (AOA:AOB) (p < 0.05). ORP was also significantly positively correlated with AOB abundance (p < 0.05).},
}
@article {pmid26098850,
year = {2015},
author = {Chang, MM and Imperiali, B and Eichler, J and Guan, Z},
title = {N-Linked Glycans Are Assembled on Highly Reduced Dolichol Phosphate Carriers in the Hyperthermophilic Archaea Pyrococcus furiosus.},
journal = {PloS one},
volume = {10},
number = {6},
pages = {e0130482},
doi = {10.1371/journal.pone.0130482},
pmid = {26098850},
issn = {1932-6203},
support = {GM-039334/GM/NIGMS NIH HHS/United States ; GM-069338/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/*metabolism ; Butadienes/metabolism ; Dolichol/*metabolism ; Dolichol Phosphates/*metabolism ; Glycosylation ; Hemiterpenes/metabolism ; Oligosaccharides/metabolism ; Pentanes/metabolism ; Phosphate Transport Proteins/*metabolism ; Polysaccharides/*metabolism ; Pyrococcus furiosus/*metabolism ; },
abstract = {In all three domains of life, N-glycosylation begins with the assembly of glycans on phosphorylated polyisoprenoid carriers. Like eukaryotes, archaea also utilize phosphorylated dolichol for this role, yet whereas the assembled oligosaccharide is transferred to target proteins from dolichol pyrophosphate in eukaryotes, archaeal N-linked glycans characterized to date are derived from a dolichol monophosphate carrier, apart from a single example. In this study, glycan-charged dolichol phosphate from the hyperthermophile Pyrococcus furiosus was identified and structurally characterized. Normal and reverse phase liquid chromatography-electrospray ionization mass spectrometry revealed the existence of dolichol phosphate charged with the heptasaccharide recently described in in vitro studies of N-glycosylation on this species. As with other described archaeal dolichol phosphates, the α- and ω-terminal isoprene subunits of the P. furiosus lipid are saturated, in contrast to eukaryal phosphodolichols that present only a saturated α-position isoprene subunit. Interestingly, an additional 1-4 of the 12-14 isoprene subunits comprising P. furiosus dolichol phosphate are saturated, making this lipid not only the longest archaeal dolichol phosphate described to date but also the most highly saturated.},
}
@article {pmid26097504,
year = {2015},
author = {Abendroth, C and Vilanova, C and Günther, T and Luschnig, O and Porcar, M},
title = {Eubacteria and archaea communities in seven mesophile anaerobic digester plants in Germany.},
journal = {Biotechnology for biofuels},
volume = {8},
number = {},
pages = {87},
doi = {10.1186/s13068-015-0271-6},
pmid = {26097504},
issn = {1754-6834},
abstract = {BACKGROUND: Only a fraction of the microbial species used for anaerobic digestion in biogas production plants are methanogenic archaea. We have analyzed the taxonomic profiles of eubacteria and archaea, a set of chemical key parameters, and biogas production in samples from nine production plants in seven facilities in Thuringia, Germany, including co-digesters, leach-bed, and sewage sludge treatment plants. Reactors were sampled twice, at a 1-week interval, and three biological replicates were taken in each case.<br><br>RESULTS: A complex taxonomic composition was found for both eubacteria and archaea, both of which strongly correlated with digester type. Plant-degrading Firmicutes as well as Bacteroidetes dominated eubacteria profiles in high biogas-producing co-digesters; whereas Bacteroidetes and Spirochaetes were the major phyla in leach-bed and sewage sludge digesters. Methanoculleus was the dominant archaea genus in co-digesters, whereas Methanosarcina and Methanosaeta were the most abundant methanogens in leachate from leach-bed and sewage sludge digesters, respectively.<br><br>CONCLUSIONS: This is one of the most comprehensive characterizations of the microbial communities of biogas-producing facilities. Bacterial profiles exhibited very low variation within replicates, including those of semi-solid samples; and, in general, low variation in time. However, facility type correlated closely with the bacterial profile: each of the three reactor types exhibited a characteristic eubacteria and archaea profile. Digesters operated with solid feedstock, and high biogas production correlated with abundance of plant degraders (Firmicutes) and biofilm-forming methanogens (Methanoculleus spp.). By contrast, low biogas-producing sewage sludge treatment digesters correlated with high titers of volatile fatty acid-adapted Methanosaeta spp.},
}
@article {pmid26085149,
year = {2015},
author = {Hochstein, R and Bollschweiler, D and Engelhardt, H and Lawrence, CM and Young, M},
title = {Large Tailed Spindle Viruses of Archaea: a New Way of Doing Viral Business.},
journal = {Journal of virology},
volume = {89},
number = {18},
pages = {9146-9149},
doi = {10.1128/JVI.00612-15},
pmid = {26085149},
issn = {1098-5514},
mesh = {Archaea/*virology ; Archaeal Viruses/chemistry/*physiology ; Capsid Proteins/chemistry/*physiology ; Genes, Viral/*physiology ; },
abstract = {Viruses of Archaea continue to surprise us. Archaeal viruses have revealed new morphologies, protein folds, and gene content. This is especially true for large spindle viruses, which infect only Archaea. We present a comparison of particle morphologies, major coat protein structures, and gene content among the five characterized large spindle viruses to elucidate defining characteristics. Structural similarities and a core set of genes support the grouping of the large spindle viruses into a new superfamily.},
}
@article {pmid26084810,
year = {2015},
author = {Grazziotin, AL and Vidal, NM and Venancio, TM},
title = {Uncovering major genomic features of essential genes in Bacteria and a methanogenic Archaea.},
journal = {The FEBS journal},
volume = {282},
number = {17},
pages = {3395-3411},
doi = {10.1111/febs.13350},
pmid = {26084810},
issn = {1742-4658},
support = {ZIA LM594244-08/NULL/Intramural NIH HHS/United States ; },
mesh = {Archaea/genetics ; Biological Evolution ; Burkholderia pseudomallei/genetics ; Escherichia coli/genetics ; *Gene Expression Regulation, Archaeal ; *Gene Expression Regulation, Bacterial ; Gene Regulatory Networks ; *Genes, Essential ; *Genome, Archaeal ; *Genome, Bacterial ; Molecular Sequence Annotation ; Mycobacterium tuberculosis/genetics ; Streptococcus/genetics ; },
abstract = {Identification of essential genes is critical to understanding the physiology of a species, proposing novel drug targets and uncovering minimal gene sets required for life. Although essential gene sets of several organisms have been determined using large-scale mutagenesis techniques, systematic studies addressing their conservation, genomic context and functions remain scant. Here we integrate 17 essential gene sets from genome-wide in vitro screenings and three gene collections required for growth in vivo, encompassing 15 Bacteria and one Archaea. We refine and generalize important theories proposed using Escherichia coli. Essential genes are typically monogenic and more conserved than nonessential genes. Genes required in vivo are less conserved than those essential in vitro, suggesting that more divergent strategies are deployed when the organism is stressed by the host immune system and unstable nutrient availability. We identified essential analogous pathways that would probably be missed by orthology-based essentiality prediction strategies. For example, Streptococcus sanguinis carries horizontally transferred isoprenoid biosynthesis genes that are widespread in Archaea. Genes specifically essential in Mycobacterium tuberculosis and Burkholderia pseudomallei are reported as potential drug targets. Moreover, essential genes are not only preferentially located in operons, but also occupy the first position therein, supporting the influence of their regulatory regions in driving transcription of whole operons. Finally, these important genomic features are shared between Bacteria and at least one Archaea, suggesting that high order properties of gene essentiality and genome architecture were probably present in the last universal common ancestor or evolved independently in the prokaryotic domains.},
}
@article {pmid26075362,
year = {2015},
author = {López-García, P and Zivanovic, Y and Deschamps, P and Moreira, D},
title = {Bacterial gene import and mesophilic adaptation in archaea.},
journal = {Nature reviews. Microbiology},
volume = {13},
number = {7},
pages = {447-456},
doi = {10.1038/nrmicro3485},
pmid = {26075362},
issn = {1740-1534},
support = {322669//European Research Council/International ; },
mesh = {Adaptation, Biological ; Archaea/*classification/*genetics/physiology ; *Evolution, Molecular ; Phylogeny ; Temperature ; },
abstract = {It is widely believed that the archaeal ancestor was hyperthermophilic, but during archaeal evolution, several lineages - including haloarchaea and their sister methanogens, the Thaumarchaeota, and the uncultured Marine Group II and Marine Group III Euryarchaeota (MGII/III) - independently adapted to lower temperatures. Recent phylogenomic studies suggest that the ancestors of these lineages were recipients of massive horizontal gene transfer from bacteria. Many of the acquired genes, which are often involved in metabolism and cell envelope biogenesis, were convergently acquired by distant mesophilic archaea. In this Opinion article, we explore the intriguing hypothesis that the import of these bacterial genes was crucial for the adaptation of archaea to mesophilic lifestyles.},
}
@article {pmid26074892,
year = {2015},
author = {Ozuolmez, D and Na, H and Lever, MA and Kjeldsen, KU and Jørgensen, BB and Plugge, CM},
title = {Methanogenic archaea and sulfate reducing bacteria co-cultured on acetate: teamwork or coexistence?.},
journal = {Frontiers in microbiology},
volume = {6},
number = {},
pages = {492},
doi = {10.3389/fmicb.2015.00492},
pmid = {26074892},
issn = {1664-302X},
abstract = {Acetate is a major product of fermentation processes and an important substrate for sulfate reducing bacteria and methanogenic archaea. Most studies on acetate catabolism by sulfate reducers and methanogens have used pure cultures. Less is known about acetate conversion by mixed pure cultures and the interactions between both groups. We tested interspecies hydrogen transfer and coexistence between marine methanogens and sulfate reducers using mixed pure cultures of two types of microorganisms. First, Desulfovibrio vulgaris subsp. vulgaris (DSM 1744), a hydrogenotrophic sulfate reducer, was cocultured together with the obligate aceticlastic methanogen Methanosaeta concilii using acetate as carbon and energy source. Next, Methanococcus maripaludis S2, an obligate H2- and formate-utilizing methanogen, was used as a partner organism to M. concilii in the presence of acetate. Finally, we performed a coexistence experiment between M. concilii and an acetotrophic sulfate reducer Desulfobacter latus AcSR2. Our results showed that D. vulgaris was able to reduce sulfate and grow from hydrogen leaked by M. concilii. In the other coculture, M. maripaludis was sustained by hydrogen leaked by M. concilii as revealed by qPCR. The growth of the two aceticlastic microbes indicated co-existence rather than competition. Altogether, our results indicate that H2 leaking from M. concilii could be used by efficient H2-scavengers. This metabolic trait, revealed from coculture studies, brings new insight to the metabolic flexibility of methanogens and sulfate reducers residing in marine environments in response to changing environmental conditions and community compositions. Using dedicated physiological studies we were able to unravel the occurrence of less obvious interactions between marine methanogens and sulfate-reducing bacteria.},
}
@article {pmid26068860,
year = {2015},
author = {Ferry, JG},
title = {Acetate Metabolism in Anaerobes from the Domain Archaea.},
journal = {Life (Basel, Switzerland)},
volume = {5},
number = {2},
pages = {1454-1471},
doi = {10.3390/life5021454},
pmid = {26068860},
issn = {2075-1729},
support = {R01 GM044661/GM/NIGMS NIH HHS/United States ; },
abstract = {Acetate and acetyl-CoA play fundamental roles in all of biology, including anaerobic prokaryotes from the domains Bacteria and Archaea, which compose an estimated quarter of all living protoplasm in Earth's biosphere. Anaerobes from the domain Archaea contribute to the global carbon cycle by metabolizing acetate as a growth substrate or product. They are components of anaerobic microbial food chains converting complex organic matter to methane, and many fix CO2 into cell material via synthesis of acetyl-CoA. They are found in a diversity of ecological habitats ranging from the digestive tracts of insects to deep-sea hydrothermal vents, and synthesize a plethora of novel enzymes with biotechnological potential. Ecological investigations suggest that still more acetate-metabolizing species with novel properties await discovery.},
}
@article {pmid26066650,
year = {2015},
author = {Lurie-Weinberger, MN and Gophna, U},
title = {Archaea in and on the Human Body: Health Implications and Future Directions.},
journal = {PLoS pathogens},
volume = {11},
number = {6},
pages = {e1004833},
doi = {10.1371/journal.ppat.1004833},
pmid = {26066650},
issn = {1553-7374},
mesh = {*Archaea ; Humans ; *Microbiota ; },
}
@article {pmid26054421,
year = {2015},
author = {Clouet-d'Orval, B and Phung, DK and Langendijk-Genevaux, PS and Quentin, Y},
title = {Universal RNA-degrading enzymes in Archaea: Prevalence, activities and functions of β-CASP ribonucleases.},
journal = {Biochimie},
volume = {118},
number = {},
pages = {278-285},
doi = {10.1016/j.biochi.2015.05.021},
pmid = {26054421},
issn = {1638-6183},
mesh = {Archaea/*enzymology/*genetics ; Archaeal Proteins/*metabolism ; RNA Stability/*physiology ; Ribonucleases/*metabolism ; },
abstract = {β-CASP ribonucleases are widespread in all three domains of life. They catalyse both 5'-3' exoribonucleolytic RNA trimming and/or endoribonucleolytic RNA cleavage using a unique active site coordinated by two zinc ions. These fascinating enzymes have a key role in 3' end processing in Eukarya and in RNA decay and ribosomal RNA maturation in Bacteria. The recent recognition of β-CASP ribonucleases as major players in Archaea is an important contribution towards identifying RNA-degrading enzymes in the third domain of life. Three β-CASP orthologous groups, aCPSF1, aCPSF2, aCPSF1b, are closely related to the eukaryal CPSF73 termination factor and one, aRNase J, is ortholog of the bacterial RNase J. The endo- and 5'-3' exoribonucleolytic activities carried by archaeal β-CASP enzymes are strictly conserved throughout archaeal phylogeny suggesting essential roles in maturation and/or degradation of RNA. The recent progress in understanding the prevalence, activities and functions of archaeal β-CASP ribonucleases is the focus of this review. The current status of our understanding of RNA processing pathways in Archaea is covered in light of this new knowledge on β-CASP ribonucleases.},
}
@article {pmid26053257,
year = {2015},
author = {Banning, NC and Maccarone, LD and Fisk, LM and Murphy, DV},
title = {Ammonia-oxidising bacteria not archaea dominate nitrification activity in semi-arid agricultural soil.},
journal = {Scientific reports},
volume = {5},
number = {},
pages = {11146},
doi = {10.1038/srep11146},
pmid = {26053257},
issn = {2045-2322},
mesh = {Agriculture ; Ammonia/*metabolism ; Archaea/enzymology/genetics/*metabolism ; Bacteria/enzymology/genetics/*metabolism ; Ecosystem ; Nitrification/*physiology ; Nitrogen/metabolism ; Nitrogen Cycle ; Oxidation-Reduction ; Oxidoreductases/genetics/*metabolism ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; Soil Microbiology ; },
abstract = {Ammonia-oxidising archaea (AOA) and bacteria (AOB) are responsible for the rate limiting step in nitrification; a key nitrogen (N) loss pathway in agricultural systems. Dominance of AOA relative to AOB in the amoA gene pool has been reported in many ecosystems, although their relative contributions to nitrification activity are less clear. Here we examined the distribution of AOA and AOB with depth in semi-arid agricultural soils in which soil organic matter content or pH had been altered, and related their distribution to gross nitrification rates. Soil depth had a significant effect on gene abundances, irrespective of management history. Contrary to reports of AOA dominance in soils elsewhere, AOA gene copy numbers were four-fold lower than AOB in the surface (0-10 cm). AOA gene abundance increased with depth while AOB decreased, and sub-soil abundances were approximately equal (10-90 cm). The depth profile of total archaea did not mirror that of AOA, indicating the likely presence of archaea without nitrification capacity in the surface. Gross nitrification rates declined significantly with depth and were positively correlated to AOB but negatively correlated to AOA gene abundances. We conclude that AOB are most likely responsible for regulating nitrification in these semi-arid soils.},
}
@article {pmid26029183,
year = {2015},
author = {Kletzin, A and Heimerl, T and Flechsler, J and van Niftrik, L and Rachel, R and Klingl, A},
title = {Cytochromes c in Archaea: distribution, maturation, cell architecture, and the special case of Ignicoccus hospitalis.},
journal = {Frontiers in microbiology},
volume = {6},
number = {},
pages = {439},
doi = {10.3389/fmicb.2015.00439},
pmid = {26029183},
issn = {1664-302X},
abstract = {Cytochromes c (Cytc) are widespread electron transfer proteins and important enzymes in the global nitrogen and sulfur cycles. The distribution of Cytc in more than 300 archaeal proteomes deduced from sequence was analyzed with computational methods including pattern and similarity searches, secondary and tertiary structure prediction. Two hundred and fifty-eight predicted Cytc (with single, double, or multiple heme c attachment sites) were found in some but not all species of the Desulfurococcales, Thermoproteales, Archaeoglobales, Methanosarcinales, Halobacteriales, and in two single-cell genome sequences of the Thermoplasmatales, all of them Cren- or Euryarchaeota. Other archaeal phyla including the Thaumarchaeota are so far free of these proteins. The archaeal Cytc sequences were bundled into 54 clusters of mutual similarity, some of which were specific for Archaea while others had homologs in the Bacteria. The cytochrome c maturation system I (CCM) was the only one found. The highest number and variability of Cytc were present in those species with known or predicted metal oxidation and/or reduction capabilities. Paradoxical findings were made in the haloarchaea: several Cytc had been purified biochemically but corresponding proteins were not found in the proteomes. The results are discussed with emphasis on cell morphologies and envelopes and especially for double-membraned Archaea-like Ignicoccus hospitalis. A comparison is made with compartmentalized bacteria such as the Planctomycetes of the Anammox group with a focus on the putative localization and roles of the Cytc and other electron transport proteins.},
}
@article {pmid26014885,
year = {2015},
author = {Guillén-Navarro, K and Herrera-López, D and López-Chávez, MY and Cancino-Gómez, M and Reyes-Reyes, AL},
title = {Assessment of methods to recover DNA from bacteria, fungi and archaea in complex environmental samples.},
journal = {Folia microbiologica},
volume = {60},
number = {6},
pages = {551-558},
doi = {10.1007/s12223-015-0403-1},
pmid = {26014885},
issn = {1874-9356},
mesh = {Archaea/genetics/*isolation &amp; purification ; Bacteria/genetics/*isolation &amp; purification ; Chemistry Techniques, Analytical/*methods ; DNA, Archaeal/genetics/*isolation &amp; purification ; DNA, Bacterial/genetics/*isolation &amp; purification ; DNA, Fungal/genetics/*isolation &amp; purification ; Environmental Microbiology ; Fungi/genetics/*isolation &amp; purification ; Polymerase Chain Reaction ; },
abstract = {DNA extraction from environmental samples is a critical step for metagenomic analysis to study microbial communities, including those considered uncultivable. Nevertheless, obtaining good quality DNA in sufficient quantities for downstream methodologies is not always possible, and it depends on the complexity and stability of each ecosystem, which could be more problematic for samples from tropical regions because those ecosystems are less stable and more complex. Three laboratory methods for the extraction of nucleic acids from samples representing unstable (decaying coffee pulp and mangrove sediments) and relatively stable (compost and soil) environments were tested. The results were compared with those obtained using two commercial DNA extraction kits. The quality of the extracted DNA was evaluated by PCR amplification to verify the recovery of bacterial, archaeal, and fungal genetic material. The laboratory method that gave the best results used a lysis procedure combining physical, chemical, and enzymatic steps.},
}
@article {pmid26013483,
year = {2015},
author = {Gao, L and Imanaka, T and Fujiwara, S},
title = {A Mutant Chaperonin That Is Functional at Lower Temperatures Enables Hyperthermophilic Archaea To Grow under Cold-Stress Conditions.},
journal = {Journal of bacteriology},
volume = {197},
number = {16},
pages = {2642-2652},
doi = {10.1128/JB.00279-15},
pmid = {26013483},
issn = {1098-5530},
mesh = {Adenosine Triphosphatases/metabolism ; Archaeal Proteins/genetics/*metabolism ; *Cold Temperature ; DNA, Archaeal/genetics ; *Gene Expression Regulation, Archaeal ; Hot Temperature ; Molecular Chaperones/genetics/*metabolism ; Mutation ; Plasmids/genetics ; Sequence Alignment ; Thermococcus/*genetics/metabolism ; },
abstract = {UNLABELLED: Thermococcus kodakarensis grows optimally at 85°C and possesses two chaperonins, cold-inducible CpkA and heat-inducible CpkB, which are involved in adaptation to low and high temperatures, respectively. The two chaperonins share a high sequence identity (77%), except in their C-terminal regions. CpkA, which contains tandem repeats of a GGM motif, shows its highest ATPase activity at 60°C to 70°C, whereas CpkB shows its highest activity at temperatures higher than 90°C. To clarify the effects of changes in ATPase activity on chaperonin function at lower temperatures, various CpkA variants were constructed by introducing single point mutations into the C-terminal region. A CpkA variant in which Glu530 was replaced with Gly (CpkA-E530G) showed increased ATPase activity, with its highest activity at 50°C. The efficacy of the CpkA variants against denatured indole-3-glycerol-phosphate synthase of T. kodakarensis (TrpCTk), which is a CpkA target, was then examined in vitro. CpkA-E530G was more effective than wild-type CpkA at facilitating the refolding of chemically unfolded TrpCTk at 50°C. The effect of cpkA-E530G on cell growth was then examined by introducing cpkA-E530G into the genome of T. kodakarensis KU216 (pyrF). The mutant strain, DA4 (pyrF cpkA-E530G), grew as well as the parental KU216 strain at 60°C. In contrast, DA4 grew more vigorously than KU216 at 50°C. These results suggested that the CpkA-E530G mutation prevented cold denaturation of proteins under cold-stress conditions, thereby enabling cells to grow in cooler environments. Thus, a single base pair substitution in a chaperonin gene allows cells to grow vigorously in a new environment.<br><br>IMPORTANCE: Thermococcus kodakarensis possesses two group II chaperonins, cold-inducible CpkA and heat-inducible CpkB, which are involved in adaptation to low and high temperatures, respectively. CpkA might act as an &quot;adaptive allele&quot; to adapt to cooler environments. In this study, we compared the last 20 amino acids within the C termini of the chaperonins and found a clear correlation between the CpkA-type chaperonin gene copy number and growth temperature. Furthermore, we introduced single mutations into the CpkA C-terminal region to clarify its role in cold adaptation, and we showed that a single base substitution allowed the organism to adapt to a lower temperature. The present data suggest that hyperthermophiles have evolved by obtaining mutations in chaperonins that allow them to adapt to a colder environment.},
}
@article {pmid26010867,
year = {2015},
author = {Cao, S and Hepowit, N and Maupin-Furlow, JA},
title = {Ubiquitin-Like Protein SAMP1 and JAMM/MPN+ Metalloprotease HvJAMM1 Constitute a System for Reversible Regulation of Metabolic Enzyme Activity in Archaea.},
journal = {PloS one},
volume = {10},
number = {5},
pages = {e0128399},
doi = {10.1371/journal.pone.0128399},
pmid = {26010867},
issn = {1932-6203},
support = {R01 GM057498/GM/NIGMS NIH HHS/United States ; R01 GM57498/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaeal Proteins/metabolism ; Catalytic Domain ; Enzyme Activation ; Haloferax volcanii/chemistry/*metabolism ; Metalloproteases/*metabolism ; Models, Molecular ; Protein Processing, Post-Translational ; Proteolysis ; Sulfurtransferases/*metabolism ; Ubiquitins/chemistry/*metabolism ; },
abstract = {Ubiquitin/ubiquitin-like (Ub/Ubl) proteins are involved in diverse cellular processes by their covalent linkage to protein substrates. Here, we provide evidence for a post-translational modification system that regulates enzyme activity which is composed of an archaeal Ubl protein (SAMP1) and a JAMM/MPN+ metalloprotease (HvJAMM1). Molybdopterin (MPT) synthase activity was found to be inhibited by covalent linkage of SAMP1 to the large subunit (MoaE) of MPT synthase. HvJAMM1 was shown to cleave the covalently linked inactive form of SAMP1-MoaE to the free functional individual SAMP1 and MoaE subunits of MPT synthase, suggesting reactivation of MPT synthase by this metalloprotease. Overall, this study provides new insight into the broad idea that Ub/Ubl modification is a post-translational process that can directly and reversibly regulate the activity of metabolic enzymes. In particular, we show that Ub/Ubl linkages on the active site residues of an enzyme (MPT synthase) can inhibit its catalytic activity and that the enzyme can be reactivated through cleavage by a JAMM/MPN+ metalloprotease.},
}
@article {pmid25997109,
year = {2015},
author = {French, E and Bollmann, A},
title = {Freshwater Ammonia-Oxidizing Archaea Retain amoA mRNA and 16S rRNA during Ammonia Starvation.},
journal = {Life (Basel, Switzerland)},
volume = {5},
number = {2},
pages = {1396-1404},
doi = {10.3390/life5021396},
pmid = {25997109},
issn = {2075-1729},
abstract = {In their natural habitats, microorganisms are often exposed to periods of starvation if their substrates for energy generation or other nutrients are limiting. Many microorganisms have developed strategies to adapt to fluctuating nutrients and long-term starvation. In the environment, ammonia oxidizers have to compete with many different organisms for ammonium and are often exposed to long periods of ammonium starvation. We investigated the effect of ammonium starvation on ammonia-oxidizing archaea (AOA) and bacteria (AOB) enriched from freshwater lake sediments. Both AOA and AOB were able to recover even after almost two months of starvation; however, the recovery time differed. AOA and AOB retained their 16S rRNA (ribosomes) throughout the complete starvation period. The AOA retained also a small portion of the mRNA of the ammonia monooxygenase subunit A (amoA) for the complete starvation period. However, after 10 days, no amoA mRNA was detected anymore in the AOB. These results indicate that AOA and AOB are able to survive longer periods of starvation, but might utilize different strategies.},
}
@article {pmid25984733,
year = {2015},
author = {Probst, AJ and Moissl-Eichinger, C},
title = {&quot;Altiarchaeales&quot;: uncultivated archaea from the subsurface.},
journal = {Life (Basel, Switzerland)},
volume = {5},
number = {2},
pages = {1381-1395},
doi = {10.3390/life5021381},
pmid = {25984733},
issn = {2075-1729},
abstract = {Due to the limited cultivability of the vast majority of microorganisms, researchers have applied environmental genomics and other state-of-the-art technologies to gain insights into the biology of uncultivated Archaea and bacteria in their natural biotope. In this review, we summarize the scientific findings on a recently proposed order-level lineage of uncultivated Archaea called Altiarchaeales, which includes &quot;Candidatus Altiarchaeum hamiconexum&quot; as the most well-described representative. Ca. A. hamiconexum possesses a complex biology: thriving strictly anaerobically, this microorganism is capable of forming highly-pure biofilms, connecting the cells by extraordinary cell surface appendages (the &quot;hami&quot;) and has other highly unusual traits, such as a double-membrane-based cell wall. Indicated by genomic information from different biotopes, the Altiarchaeales seem to proliferate in deep, anoxic groundwater of Earth's crust bearing a potentially very important function: carbon fixation. Although their net carbon fixation rate has not yet been determined, they appear as highly abundant organisms in their biotopes and may thus represent an important primary producer in the subsurface. In sum, the research over more than a decade on Ca. A. hamiconexum has revealed many interesting features of its lifestyle, its genomic information, metabolism and ultrastructure, making this archaeon one of the best-studied uncultivated Archaea in the literature.},
}
@article {pmid25976837,
year = {2015},
author = {Darnell, CL and Schmid, AK},
title = {Systems biology approaches to defining transcription regulatory networks in halophilic archaea.},
journal = {Methods (San Diego, Calif.)},
volume = {86},
number = {},
pages = {102-114},
doi = {10.1016/j.ymeth.2015.04.034},
pmid = {25976837},
issn = {1095-9130},
mesh = {Archaea/*genetics ; Computational Biology/methods ; Gene Regulatory Networks ; Genome, Archaeal ; Halobacterium salinarum ; *Systems Biology ; Transcription Factors/*genetics ; *Transcription, Genetic ; },
abstract = {To survive complex and changing environmental conditions, microorganisms use gene regulatory networks (GRNs) composed of interacting regulatory transcription factors (TFs) to control the timing and magnitude of gene expression. Genome-wide datasets; such as transcriptomics and protein-DNA interactions; and experiments such as high throughput growth curves; facilitate the construction of GRNs and provide insight into TF interactions occurring under stress. Systems biology approaches integrate these datasets into models of GRN architecture as well as statistical and/or dynamical models to understand the function of networks occurring in cells. Previously, these types of studies have focused on traditional model organisms (e.g. Escherichia coli, yeast). However, recent advances in archaeal genetics and other tools have enabled a systems approach to understanding GRNs in these relatively less studied archaeal model organisms. In this report, we outline a systems biology workflow for generating and integrating data focusing on the TF regulator. We discuss experimental design, outline the process of data collection, and provide the tools required to produce high confidence regulons for the TFs of interest. We provide a case study as an example of this workflow, describing the construction of a GRN centered on multi-TF coordinate control of gene expression governing the oxidative stress response in the hypersaline-adapted archaeon Halobacterium salinarum.},
}
@article {pmid25964353,
year = {2015},
author = {Raymann, K and Brochier-Armanet, C and Gribaldo, S},
title = {The two-domain tree of life is linked to a new root for the Archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {112},
number = {21},
pages = {6670-6675},
doi = {10.1073/pnas.1420858112},
pmid = {25964353},
issn = {1091-6490},
mesh = {Archaea/*classification/*genetics ; Bacteria/classification/genetics ; Bayes Theorem ; *Biological Evolution ; Databases, Genetic ; Eukaryota/classification/genetics ; Euryarchaeota/classification/genetics ; Evolution, Molecular ; Genetic Markers ; Genetic Speciation ; Genome, Archaeal ; Genome, Bacterial ; Models, Biological ; Phylogeny ; },
abstract = {One of the most fundamental questions in evolutionary biology is the origin of the lineage leading to eukaryotes. Recent phylogenomic analyses have indicated an emergence of eukaryotes from within the radiation of modern Archaea and specifically from a group comprising Thaumarchaeota/&quot;Aigarchaeota&quot; (candidate phylum)/Crenarchaeota/Korarchaeota (TACK). Despite their major implications, these studies were all based on the reconstruction of universal trees and left the exact placement of eukaryotes with respect to the TACK lineage unclear. Here we have applied an original two-step approach that involves the separate analysis of markers shared between Archaea and eukaryotes and between Archaea and Bacteria. This strategy allowed us to use a larger number of markers and greater taxonomic coverage, obtain high-quality alignments, and alleviate tree reconstruction artifacts potentially introduced when analyzing the three domains simultaneously. Our results robustly indicate a sister relationship of eukaryotes with the TACK superphylum that is strongly associated with a distinct root of the Archaea that lies within the Euryarchaeota, challenging the traditional topology of the archaeal tree. Therefore, if we are to embrace an archaeal origin for eukaryotes, our view of the evolution of the third domain of life will have to be profoundly reconsidered, as will many areas of investigation aimed at inferring ancestral characteristics of early life and Earth.},
}
@article {pmid25947248,
year = {2015},
author = {Zhang, J and Dai, Y and Wang, Y and Wu, Z and Xie, S and Liu, Y},
title = {Distribution of ammonia-oxidizing archaea and bacteria in plateau soils across different land use types.},
journal = {Applied microbiology and biotechnology},
volume = {99},
number = {16},
pages = {6899-6909},
doi = {10.1007/s00253-015-6625-y},
pmid = {25947248},
issn = {1432-0614},
mesh = {Ammonia/*metabolism ; Archaea/*classification/*metabolism ; Bacteria/*classification/*metabolism ; *Biota ; Carbon/analysis ; Chemical Phenomena ; China ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; Molecular Sequence Data ; Nitrates/analysis ; Nitrification ; Nitrogen/analysis ; Oxidation-Reduction ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {Ammonia oxidation is known to be performed by both ammonia-oxidizing archaea (AOA) and bacteria (AOB), although their relative significance to nitrification process in soil ecosystems remains controversial. The distribution of AOA and AOB in plateau soils with different land use types and the influential factors remains unclear. The present study investigated the abundance and structure of AOA and AOB communities in upland soils adjacent to Erhai Lake in the Yunnan Plateau (China). Quantitative PCR assays indicated a large variation in the community size of AOA and AOB communities, with the numerical dominance of AOA over AOB in most of soils. Clone library analysis illustrated a marked shift in the structure of soil AOA and AOB communities. A high abundance of Nitrososphaera- and Nitrosotalea-like AOA was observed, while Nitrosospira-like species predominated in AOB. AOA and AOB abundance was positively influenced by total nitrogen and moisture content, respectively. Moreover, moisture content might be a key determinant of AOA community composition, while C/N and nitrate nitrogen played an important role in shaping AOB community composition. However, further efforts will be necessary in order to elucidate the links between soil AOA and AOB and land use.},
}
@article {pmid25945739,
year = {2015},
author = {Spang, A and Saw, JH and Jørgensen, SL and Zaremba-Niedzwiedzka, K and Martijn, J and Lind, AE and van Eijk, R and Schleper, C and Guy, L and Ettema, TJG},
title = {Complex archaea that bridge the gap between prokaryotes and eukaryotes.},
journal = {Nature},
volume = {521},
number = {7551},
pages = {173-179},
doi = {10.1038/nature14447},
pmid = {25945739},
issn = {1476-4687},
support = {310039//European Research Council/International ; },
mesh = {Actin Cytoskeleton/metabolism ; Actins/genetics/metabolism ; Archaea/*classification/genetics/metabolism ; Arctic Regions ; Endosomal Sorting Complexes Required for Transport/genetics/metabolism ; Eukaryota/*classification/genetics/metabolism ; Eukaryotic Cells/classification/metabolism ; *Evolution, Molecular ; Hydrothermal Vents/*microbiology ; Metagenome/genetics ; Molecular Sequence Data ; Monomeric GTP-Binding Proteins/genetics/metabolism ; *Phylogeny ; Prokaryotic Cells/*classification ; Proteome/genetics/isolation &amp; purification/metabolism ; },
abstract = {The origin of the eukaryotic cell remains one of the most contentious puzzles in modern biology. Recent studies have provided support for the emergence of the eukaryotic host cell from within the archaeal domain of life, but the identity and nature of the putative archaeal ancestor remain a subject of debate. Here we describe the discovery of 'Lokiarchaeota', a novel candidate archaeal phylum, which forms a monophyletic group with eukaryotes in phylogenomic analyses, and whose genomes encode an expanded repertoire of eukaryotic signature proteins that are suggestive of sophisticated membrane remodelling capabilities. Our results provide strong support for hypotheses in which the eukaryotic host evolved from a bona fide archaeon, and demonstrate that many components that underpin eukaryote-specific features were already present in that ancestor. This provided the host with a rich genomic 'starter-kit' to support the increase in the cellular and genomic complexity that is characteristic of eukaryotes.},
}
@article {pmid25938369,
year = {2015},
author = {Allen, KD and Miller, DV and Rauch, BJ and Perona, JJ and White, RH},
title = {Homocysteine is biosynthesized from aspartate semialdehyde and hydrogen sulfide in methanogenic archaea.},
journal = {Biochemistry},
volume = {54},
number = {20},
pages = {3129-3132},
doi = {10.1021/acs.biochem.5b00118},
pmid = {25938369},
issn = {1520-4995},
mesh = {Aspartic Acid/*analogs &amp; derivatives/metabolism ; Biosynthetic Pathways ; Genes, Archaeal ; Homocysteine/*biosynthesis ; Hydrogen Sulfide/*metabolism ; Methanococcus/genetics/*metabolism ; },
abstract = {The biosynthetic route for homocysteine, intermediate in methionine biosynthesis, is unknown in some methanogenic archaea because homologues of the canonical required genes cannot be identified. Here we demonstrate that Methanocaldococcus jannaschii can biosynthesize homocysteine from aspartate semialdehyde and hydrogen sulfide. Additionally, we confirm the genes involved in this new pathway in Methanosarcina acetivorans. A possible series of reactions in which a thioaldehyde is formed and then reduced to a thiol are proposed. This represents a novel route for the biosynthesis of homocysteine and exemplifies unique aspects of sulfur chemistry occurring in prebiotic environments and in early life forms.},
}
@article {pmid25932531,
year = {2015},
author = {Atanasova, NS and Oksanen, HM and Bamford, DH},
title = {Haloviruses of archaea, bacteria, and eukaryotes.},
journal = {Current opinion in microbiology},
volume = {25},
number = {},
pages = {40-48},
doi = {10.1016/j.mib.2015.04.001},
pmid = {25932531},
issn = {1879-0364},
mesh = {Archaea/*virology ; Archaeal Viruses/*genetics/physiology ; Bacteria/*virology ; Capsid Proteins/genetics ; DNA, Viral/genetics ; Eukaryota/*virology ; Genome, Viral ; *Salinity ; Virion/physiology ; },
abstract = {Hypersaline environments up to near saturation are rich reservoirs of extremophilic viruses. One milliliter of salt water may contain up to 10(9) viruses which can also be trapped inside salt crystals. To date, most of the ∼100 known halovirus isolates infect extremely halophilic archaea, although a few bacterial and eukaryotic viruses have also been described. These isolates comprise tailed and tailless icosahedral, pleomorphic, and lemon-shaped viruses which have been classified according to features such as host range, genome type, and replication. Recent studies have revealed that viruses can be grouped into a few structure-based viral lineages derived from a common ancestor based on conserved virion architectural principles and the major capsid protein fold.},
}
@article {pmid25928466,
year = {2015},
author = {Takeuchi, N and Cordero, OX and Koonin, EV and Kaneko, K},
title = {Gene-specific selective sweeps in bacteria and archaea caused by negative frequency-dependent selection.},
journal = {BMC biology},
volume = {13},
number = {},
pages = {20},
doi = {10.1186/s12915-015-0131-7},
pmid = {25928466},
issn = {1741-7007},
support = {//Intramural NIH HHS/United States ; },
mesh = {Archaea/*genetics ; Bacteria/*genetics ; Clone Cells ; Computer Simulation ; *Genes, Archaeal ; *Genes, Bacterial ; Host-Parasite Interactions/genetics ; Models, Genetic ; Recombination, Genetic ; *Selection, Genetic ; },
abstract = {BACKGROUND: Fixation of beneficial genes in bacteria and archaea (collectively, prokaryotes) is often believed to erase pre-existing genomic diversity through the hitchhiking effect, a phenomenon known as genome-wide selective sweep. Recent studies, however, indicate that beneficial genes spread through a prokaryotic population via recombination without causing genome-wide selective sweeps. These gene-specific selective sweeps seem to be at odds with the existing estimates of recombination rates in prokaryotes, which appear far too low to explain such phenomena.<br><br>RESULTS: We use mathematical modeling to investigate potential solutions to this apparent paradox. Most microbes in nature evolve in heterogeneous, dynamic communities, in which ecological interactions can substantially impact evolution. Here, we focus on the effect of negative frequency-dependent selection (NFDS) such as caused by viral predation (kill-the-winner dynamics). The NFDS maintains multiple genotypes within a population, so that a gene beneficial to every individual would have to spread via recombination, hence a gene-specific selective sweep. However, gene loci affected by NFDS often are located in variable regions of microbial genomes that contain genes involved in the mobility of selfish genetic elements, such as integrases or transposases. Thus, the NFDS-affected loci are likely to experience elevated rates of recombination compared with the other loci. Consequently, these loci might be effectively unlinked from the rest of the genome, so that NFDS would be unable to prevent genome-wide selective sweeps. To address this problem, we analyzed population genetic models of selective sweeps in prokaryotes under NFDS. The results indicate that NFDS can cause gene-specific selective sweeps despite the effect of locally elevated recombination rates, provided NFDS affects more than one locus and the basal rate of recombination is sufficiently low. Although these conditions might seem to contradict the intuition that gene-specific selective sweeps require high recombination rates, they actually decrease the effective rate of recombination at loci affected by NFDS relative to the per-locus basal level, so that NFDS can cause gene-specific selective sweeps.<br><br>CONCLUSION: Because many free-living prokaryotes are likely to evolve under NFDS caused by ubiquitous viruses, gene-specific selective sweeps driven by NFDS are expected to be a major, general phenomenon in prokaryotic populations.},
}
@article {pmid25924080,
year = {2015},
author = {Tucker, YT and Kotcon, J and Mroz, T},
title = {Methanogenic archaea in marcellus shale: a possible mechanism for enhanced gas recovery in unconventional shale resources.},
journal = {Environmental science &amp; technology},
volume = {49},
number = {11},
pages = {7048-7055},
doi = {10.1021/acs.est.5b00765},
pmid = {25924080},
issn = {1520-5851},
mesh = {Archaea/genetics/growth &amp; development/*metabolism ; Geologic Sediments/*microbiology ; Metagenomics ; Methane/*metabolism ; Natural Gas/*analysis ; *Oil and Gas Fields ; Quality Control ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {Marcellus Shale occurs at depths of 1.5-2.5 km (5000 to 8000 feet) where most geologists generally assume that thermogenic processes are the only source of natural gas. However, methanogens in produced fluids and isotopic signatures of biogenic methane in this deep shale have recently been discovered. This study explores whether those methanogens are indigenous to the shale or are introduced during drilling and hydraulic fracturing. DNA was extracted from Marcellus Shale core samples, preinjected fluids, and produced fluids and was analyzed using Miseq sequencing of 16s rRNA genes. Methanogens present in shale cores were similar to methanogens in produced fluids. No methanogens were detected in injected fluids, suggesting that this is an unlikely source and that they may be native to the shale itself. Bench-top methane production tests of shale core and produced fluids suggest that these organisms are alive and active under simulated reservoir conditions. Growth conditions designed to simulate the hydrofracture processes indicated somewhat increased methane production; however, fluids alone produced relatively little methane. Together, these results suggest that some biogenic methane may be produced in these wells and that hydrofracture fluids currently used to stimulate gas recovery could stimulate methanogens and their rate of producing methane.},
}
@article {pmid25923659,
year = {2015},
author = {Dawson, KS and Osburn, MR and Sessions, AL and Orphan, VJ},
title = {Metabolic associations with archaea drive shifts in hydrogen isotope fractionation in sulfate-reducing bacterial lipids in cocultures and methane seeps.},
journal = {Geobiology},
volume = {13},
number = {5},
pages = {462-477},
doi = {10.1111/gbi.12140},
pmid = {25923659},
issn = {1472-4669},
mesh = {Deltaproteobacteria/growth &amp; development/*metabolism ; Deuterium/*analysis ; Hydrogen/*analysis ; *Lipid Metabolism ; Lipids/*chemistry ; Methanosarcina/growth &amp; development/*metabolism ; *Microbial Consortia ; Oregon ; Seawater/microbiology ; },
abstract = {Correlation between hydrogen isotope fractionation in fatty acids and carbon metabolism in pure cultures of bacteria indicates the potential of biomarker D/H analysis as a tool for diagnosing carbon substrate usage in environmental samples. However, most environments, in particular anaerobic habitats, are built from metabolic networks of micro-organisms rather than a single organism. The effect of these networks on D/H of lipids has not been explored and may complicate the interpretation of these analyses. Syntrophy represents an extreme example of metabolic interdependence. Here, we analyzed the effect of metabolic interactions on the D/H biosignatures of sulfate-reducing bacteria (SRB) using both laboratory maintained cocultures of the methanogen Methanosarcina acetivorans and the SRB Desulfococcus multivorans in addition to environmental samples harboring uncultured syntrophic consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing Deltaproteobacteria (SRB) recovered from deep-sea methane seeps. Consistent with previously reported trends, we observed a ~80‰ range in hydrogen isotope fractionation (ε(lipid-water)) for D. multivorans grown under different carbon assimilation conditions, with more D-enriched values associated with heterotrophic growth. In contrast, for cocultures of D. multivorans with M. acetivorans, we observed a reduced range of ε(lipid-water) values (~36‰) across substrates with shifts of up to 61‰ compared to monocultures. Sediment cores from methane seep settings in Hydrate Ridge (offshore Oregon, USA) showed similar D-enrichment in diagnostic SRB fatty acids coinciding with peaks in ANME/SRB consortia concentration suggesting that metabolic associations are connected to the observed shifts in ε(lipid-water) values.},
}
@article {pmid25918386,
year = {2015},
author = {Bhattacharya, A and Köhrer, C and Mandal, D and RajBhandary, UL},
title = {Nonsense suppression in archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {112},
number = {19},
pages = {6015-6020},
doi = {10.1073/pnas.1501558112},
pmid = {25918386},
issn = {1091-6490},
support = {R56 GM017151/GM/NIGMS NIH HHS/United States ; GM17151/GM/NIGMS NIH HHS/United States ; R01 GM017151/GM/NIGMS NIH HHS/United States ; F32 GM017151/GM/NIGMS NIH HHS/United States ; R37 GM017151/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/*genetics/metabolism ; Base Sequence ; Codon, Nonsense ; *Codon, Terminator ; Escherichia coli/metabolism ; Genes, Suppressor ; Haloferax volcanii/*genetics/metabolism ; Molecular Sequence Data ; Novobiocin/chemistry ; Plasmids/metabolism ; Promoter Regions, Genetic ; RNA, Transfer/*metabolism ; Serine/chemistry ; *Suppression, Genetic ; Thymidine/chemistry ; Tryptophan/chemistry ; Uracil/chemistry ; beta-Galactosidase/metabolism ; },
abstract = {Bacterial strains carrying nonsense suppressor tRNA genes played a crucial role in early work on bacterial and bacterial viral genetics. In eukaryotes as well, suppressor tRNAs have played important roles in the genetic analysis of yeast and worms. Surprisingly, little is known about genetic suppression in archaea, and there has been no characterization of suppressor tRNAs or identification of nonsense mutations in any of the archaeal genes. Here, we show, using the β-gal gene as a reporter, that amber, ochre, and opal suppressors derived from the serine and tyrosine tRNAs of the archaeon Haloferax volcanii are active in suppression of their corresponding stop codons. Using a promoter for tRNA expression regulated by tryptophan, we also show inducible and regulatable suppression of all three stop codons in H. volcanii. Additionally, transformation of a ΔpyrE2 H. volcanii strain with plasmids carrying the genes for a pyrE2 amber mutant and the serine amber suppressor tRNA yielded transformants that grow on agar plates lacking uracil. Thus, an auxotrophic amber mutation in the pyrE2 gene can be complemented by expression of the amber suppressor tRNA. These results pave the way for generating archaeal strains carrying inducible suppressor tRNA genes on the chromosome and their use in archaeal and archaeviral genetics. We also provide possible explanations for why suppressor tRNAs have not been identified in archaea.},
}
@article {pmid25911472,
year = {2015},
author = {Najjari, A and Elshahed, MS and Cherif, A and Youssef, NH},
title = {Patterns and determinants of halophilic archaea (class halobacteria) diversity in tunisian endorheic salt lakes and sebkhet systems.},
journal = {Applied and environmental microbiology},
volume = {81},
number = {13},
pages = {4432-4441},
doi = {10.1128/AEM.01097-15},
pmid = {25911472},
issn = {1098-5336},
mesh = {*Biodiversity ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Halobacteriales/*classification/genetics/*isolation &amp; purification ; Lakes/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Tunisia ; },
abstract = {We examined the diversity and community structure of members of the halophilic Archaea (class Halobacteria) in samples from central and southern Tunisian endorheic salt lakes and sebkhet (also known as sebkha) systems using targeted 16S rRNA gene diversity survey and quantitative PCR (qPCR) approaches. Twenty-three different samples from four distinct locations exhibiting a wide range of salinities (2% to 37%) and physical characteristics (water, salt crust, sediment, and biofilm) were examined. A total of 4,759 operational taxonomic units at the 0.03 (species-level) cutoff (OTU0.03s) belonging to 45 currently recognized genera were identified, with 8 to 43 genera (average, 30) identified per sample. In spite of the large number of genera detected per sample, only a limited number (i.e., 2 to 16) usually constituted the majority (≥80%) of encountered sequences. Halobacteria diversity showed a strong negative correlation to salinity (Pearson correlation coefficient = -0.92), and community structure analysis identified salinity, rather than the location or physical characteristics of the sample, as the most important factor shaping the Halobacteria community structure. The relative abundance of genera capable of biosynthesis of the compatible solute(s) trehalose or 2-sulfotrehalose decreased with increasing salinities (Pearson correlation coefficient = -0.80). Indeed, qPCR analysis demonstrated that the Halobacteria otsB (trehalose-6-phosphatase)/16S rRNA gene ratio decreases with increasing salinities (Pearson correlation coefficient = -0.87). The results highlight patterns and determinants of Halobacteria diversity at a previously unexplored ecosystem and indicate that genera lacking trehalose biosynthetic capabilities are more adapted to growth in and colonization of hypersaline (>25% salt) ecosystems than trehalose producers.},
}
@article {pmid25907112,
year = {2015},
author = {Bang, C and Schmitz, RA},
title = {Archaea associated with human surfaces: not to be underestimated.},
journal = {FEMS microbiology reviews},
volume = {39},
number = {5},
pages = {631-648},
doi = {10.1093/femsre/fuv010},
pmid = {25907112},
issn = {1574-6976},
mesh = {Archaea/classification/immunology/*physiology ; Humans ; Immune System/immunology/*microbiology ; Intestines/microbiology ; *Microbiota ; },
abstract = {Over 40 years ago, Carl Woese and his colleagues discovered the existence of two distinctly different groups of prokaryotes-Bacteria and Archaea. In the meantime, extensive research revealed that several hundred of bacterial species are intensely associated with humans' health and disease. Archaea, originally identified and described to occur mainly in extreme environments, have been shown to be ubiquitous and to appear frequently and in high numbers as part of human microbiota in recent years. Despite the improvement in methodologies leading to increased detection, archaea are often still not considered in many studies focusing on the interdependency between members of the microbiota and components of the human immune system. As a consequence, the knowledge on functional role(s) of archaeal species within the human body is mainly limited to their contribution to nutrient degradation in the intestine, and evidence for immunogenic properties of archaea as part of the human microbiota is generally rare. In this review, the current knowledge of human mucosa-associated archaeal species, their interaction with the human immune system and their potential contribution to humans' health and disease will be discussed.},
}
@article {pmid25884952,
year = {2015},
author = {Xiao, D and Peng, SP and Wang, EY},
title = {Fermentation enhancement of methanogenic archaea consortia from an Illinois basin coalbed via DOL emulsion nutrition.},
journal = {PloS one},
volume = {10},
number = {4},
pages = {e0124386},
doi = {10.1371/journal.pone.0124386},
pmid = {25884952},
issn = {1932-6203},
mesh = {Archaea/*metabolism ; *Coal ; Culture Media ; Emulsions ; *Fermentation ; Hydrogen-Ion Concentration ; Illinois ; Methane/*metabolism ; },
abstract = {Microbially enhanced coalbed methane technology must be used to increase the methane content in mining and generate secondary biogenic gas. In this technology, the metabolic processes of methanogenic consortia are the basis for the production of biomethane from some of the organic compounds in coal. Thus, culture nutrition plays an important role in remediating the nutritional deficiency of a coal seam. To enhance the methane production rates for microorganism consortia, different types of nutrition solutions were examined in this study. Emulsion nutrition solutions containing a novel nutritional supplement, called dystrophy optional modification latex, increased the methane yield for methanogenic consortia. This new nutritional supplement can help methanogenic consortia form an enhanced anaerobic environment, optimize the microbial balance in the consortia, and improve the methane biosynthesis rate.},
}
@article {pmid25881705,
year = {2015},
author = {Xiaoli, W and Chuang, J and Jianhua, L and Xipeng, L},
title = {[An efficient genetic knockout system based on linear DNA fragment homologous recombination for halophilic archaea].},
journal = {Yi chuan = Hereditas},
volume = {37},
number = {4},
pages = {388-395},
doi = {10.16288/j.yczz.14-366},
pmid = {25881705},
issn = {0253-9772},
mesh = {DNA, Archaeal/*genetics ; Gene Deletion ; Gene Knockout Techniques/*methods ; Haloferax volcanii/*genetics ; *Homologous Recombination ; Plasmids/genetics ; },
abstract = {With the development of functional genomics, gene-knockout is becoming an important tool to elucidate gene functions in vivo. As a good model strain for archaeal genetics, Haloferax volcanii has received more attention. Although several genetic manipulation systems have been developed for some halophilic archaea, it is time-consuming because of the low percentage of positive clones during the second-recombination selection. These classical gene knockout methods are based on DNA recombination between the genomic homologous sequence and the circular suicide plasmid, which carries a pyrE selection marker and two DNA fragments homologous to the upstream and downstream fragments of the target gene. Many wild-type clones are obtained through a reverse recombination between the plasmid and genome in the classic gene knockout method. Therefore, it is necessary to develop an efficient gene knockout system to increase the positive clone percentage. Here we report an improved gene knockout method using a linear DNA cassette consisting of upstream and downstream homologous fragments, and the pyrE marker. Gene deletions were subsequently detected by colony PCR analysis. We determined the efficiency of our knockout method by deleting the xpb2 gene from the H. volcanii genome, with the percentage of positive clones higher than 50%. Our method provides an efficient gene knockout strategy for halophilic archaea.},
}
@article {pmid25862354,
year = {2015},
author = {Shi, Y and TaPa, M and Li, C and Yang, H and Zhang, T and Gao, Y and Sun, J and Zeng, J and Lin, Q and Cao, Z and OuTi, K and Li, Y and Lou, K},
title = {Diversity and space-time dynamics of endophytic archaea from sugar beet in the north slope of Tianshan Mountain revealed by 454 pyrosequencing and T-RFLP.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {31},
number = {7},
pages = {1031-1039},
doi = {10.1007/s11274-015-1853-y},
pmid = {25862354},
issn = {1573-0972},
mesh = {Archaea/*classification/genetics ; Beta vulgaris/*growth &amp; development/microbiology ; China ; Cluster Analysis ; DNA, Ribosomal/analysis ; Endophytes/*classification/genetics ; Genes, Archaeal ; High-Throughput Nucleotide Sequencing/methods ; *Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/analysis ; Sequence Analysis, DNA/methods ; },
abstract = {Plants harbor complex and variable microbial communities. Using molecular-based techniques targeting the 16S rRNA gene, we studied the developmental stages and geographical location diversity of endophytic archaea in two locations (Shihezi and Changji) and four periods (the seedling growth, rosette formation, tuber growth and sucrose accumulation sampling periods) in the north slope of Tianshan Mountain, China. Community structure of mixed sample from 60 sugar beet plants was examined using PCR-based 454 pyrosequencing and terminal restriction fragment length polymorphism (T-RFLP). In total, 5290 archaea 16S rRNA sequences were obtained from all sugar beet samples. The most abundant archaea groups in all sugar beet were Methanococci, the miscellaneous Crenarchaeotic Group and Thermoplasmata. There was a marked difference in diversity of endophytic archaea in sugar beet for different growth periods. The greatest number of Operational T-RFLP Units (OTUs) was detected during sucrose accumulation (298) and rosette formation (282). Endophytic archaea diversity was reduced during seedling growth (128 OTUs) and tuber growth (55 OTUs). Nine OTUs were common to all four periods of growth. There were more OTUs in Shihezi than in Changji. Clustering analysis and principal component analysis of T-RFLP data revealed distinct shifts in endophytic archaea community profiles that corresponded to plant growth stage rather than geographical location. The dynamics of endophytic archaea communities were influenced by plant growth stage. To our knowledge, this is the first report that archaea has been identified as endophytes associated with sugar beet by the culture-independent approach. The results suggest that the diversity of endophytic archaea is abundant in sugar beet.},
}
@article {pmid25856307,
year = {2015},
author = {Gutiérrez, MH and Galand, PE and Moffat, C and Pantoja, S},
title = {Melting glacier impacts community structure of Bacteria, Archaea and Fungi in a Chilean Patagonia fjord.},
journal = {Environmental microbiology},
volume = {17},
number = {10},
pages = {3882-3897},
doi = {10.1111/1462-2920.12872},
pmid = {25856307},
issn = {1462-2920},
mesh = {Archaea/*classification ; Bacteria/*classification ; Base Sequence ; Chile ; Climate Change ; Ecosystem ; Estuaries ; Fresh Water/*microbiology ; Fungi/*classification ; Ice Cover/*microbiology ; Microbiota/*genetics ; Molecular Sequence Data ; Proteobacteria ; RNA, Ribosomal, 16S/genetics ; Seasons ; Sequence Analysis, DNA ; },
abstract = {Jorge Montt glacier, located in the Patagonian Ice Fields, has undergone an unprecedented retreat during the past century. To study the impact of the meltwater discharge on the microbial community of the downstream fjord, we targeted Bacteria, Archaea and Fungi communities during austral autumn and winter. Our results showed a singular microbial community present in cold and low salinity surface waters during autumn, when a thicker meltwater layer was observed. Meltwater bacterial sequences were related to Cyanobacteria, Proteobacteria, Actinobacteria and Bacteriodetes previously identified in freshwater and cold ecosystems, suggesting the occurrence of microorganisms adapted to live in the extreme conditions of meltwater. For Fungi, representative sequences related to terrestrial and airborne fungal taxa indicated transport of allochthonous Fungi by the meltwater discharge. In contrast, bottom fjord waters from autumn and winter showed representative Operational Taxonomic Units (OTUs) related to sequences of marine microorganisms, which is consistent with current models of fjord circulation. We conclude that meltwater can significantly modify the structure of microbial communities and support the development of a major fraction of microorganisms in surface waters of Patagonian fjords.},
}
@article {pmid25852668,
year = {2015},
author = {Schirmack, J and Alawi, M and Wagner, D},
title = {Influence of Martian regolith analogs on the activity and growth of methanogenic archaea, with special regard to long-term desiccation.},
journal = {Frontiers in microbiology},
volume = {6},
number = {},
pages = {210},
doi = {10.3389/fmicb.2015.00210},
pmid = {25852668},
issn = {1664-302X},
abstract = {Methanogenic archaea have been studied as model organisms for possible life on Mars for several reasons: they can grow lithoautotrophically by using hydrogen and carbon dioxide as energy and carbon sources, respectively; they are anaerobes; and they evolved at a time when conditions on early Earth are believed to have looked similar to those of early Mars. As Mars is currently dry and cold and as water might be available only at certain time intervals, any organism living on this planet would need to cope with desiccation. On Earth there are several regions with low water availability as well, e.g., permafrost environments, desert soils, and salt pans. Here, we present the results of a set of experiments investigating the influence of different Martian regolith analogs (MRAs) on the metabolic activity and growth of three methanogenic strains exposed to culture conditions as well as long-term desiccation. In most cases, concentrations below 1 wt% of regolith in the media resulted in an increase of methane production rates, whereas higher concentrations decreased the rates, thus prolonging the lag phase. Further experiments showed that methanogenic archaea are capable of producing methane when incubated on a water-saturated sedimentary matrix of regolith lacking nutrients. Survival of methanogens under these conditions was analyzed with a 400 day desiccation experiment in the presence of regolith analogs. All tested strains of methanogens survived the desiccation period as it was determined through reincubation on fresh medium and via qPCR following propidium monoazide treatment to identify viable cells. The survival of long-term desiccation and the ability of active metabolism on water-saturated MRAs strengthens the possibility of methanogenic archaea or physiologically similar organisms to exist in environmental niches on Mars. The best results were achieved in presence of a phyllosilicate, which provides insights of possible positive effects in habitats on Earth as well.},
}
@article {pmid25830311,
year = {2015},
author = {Huynh, HT and Pignoly, M and Nkamga, VD and Drancourt, M and Aboudharam, G},
title = {The repertoire of archaea cultivated from severe periodontitis.},
journal = {PloS one},
volume = {10},
number = {4},
pages = {e0121565},
doi = {10.1371/journal.pone.0121565},
pmid = {25830311},
issn = {1932-6203},
mesh = {Adult ; Aged ; Case-Control Studies ; DNA, Archaeal/genetics ; Dental Plaque/microbiology ; Female ; Humans ; Male ; Methanobrevibacter/*genetics/isolation &amp; purification ; Middle Aged ; Molecular Sequence Data ; Molecular Typing ; Periodontitis/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Young Adult ; },
abstract = {In previous studies, the abundance and diversity of methanogenic archaea in the dental microbiota have been analysed by the detection of specific DNA sequences by PCR-based investigations and metagenomic studies. Few data issued regarding methanogens actually living in dental plaque. We collected dental plaque specimens in 15 control individuals and 65 periodontitis patients. Dental plaque specimens were cultured in an anoxic liquid medium for methanogens in the presence of negative control tubes. Dental plaque methanogens were cultured from 1/15 (6.67%) control and 36/65 (55.38%) periodontitis patient samples (p<0.001). The cultures yielded Methanobrevibacter oralis in one control and thirty-one patients, Methanobrevibacter smithii in two patients and a potential new species named Methanobrevibacter sp. strain N13 in three patients with severe periodontitis. Our observations of living methanogens, strengthen previous observations made on DNA-based studies regarding the role of methanogens, in periodontitis.},
}
@article {pmid25829260,
year = {2015},
author = {Cerletti, M and Paggi, RA and Guevara, CR and Poetsch, A and De Castro, RE},
title = {Global role of the membrane protease LonB in Archaea: Potential protease targets revealed by quantitative proteome analysis of a lonB mutant in Haloferax volcanii.},
journal = {Journal of proteomics},
volume = {121},
number = {},
pages = {1-14},
doi = {10.1016/j.jprot.2015.03.016},
pmid = {25829260},
issn = {1876-7737},
mesh = {Amino Acids/chemistry ; Archaeal Proteins/*metabolism ; Carotenoids/chemistry ; Cell Membrane/metabolism ; Cytoplasm/metabolism ; Electrophoresis, Polyacrylamide Gel ; Haloferax volcanii/*enzymology ; Lipid Metabolism ; Membrane Proteins/*metabolism ; Mutation ; Peptide Hydrolases/*metabolism ; Proteome/*metabolism ; Proteomics ; Spectrometry, Mass, Electrospray Ionization ; },
abstract = {UNLABELLED: The membrane-associated LonB protease is essential for viability in Haloferax volcanii, however, the cellular processes affected by this protease in archaea are unknown. In this study, the impact of a lon conditional mutation (down-regulation) on H. volcanii physiology was examined by comparing proteomes of parental and mutant cells using shotgun proteomics. A total of 1778 proteins were identified (44% of H. volcanii predicted proteome) and 142 changed significantly in amount (≥2 fold). Of these, 66 were augmented in response to Lon deficiency suggesting they could be Lon substrates. The &quot;Lon subproteome&quot; included soluble and predicted membrane proteins expected to participate in diverse cellular processes. The dramatic stabilization of phytoene synthase (57 fold) in concert with overpigmentation of lon mutant cells suggests that Lon controls carotenogenesis in H. volcanii. Several hypothetical proteins, which may reveal novel functions and/or be involved in adaptation to extreme environments, were notably increased (300 fold). This study, which represents the first proteome examination of a Lon deficient archaeal cell, shows that Lon has a strong impact on H. volcanii physiology evidencing the cellular processes controlled by this protease in Archaea. Additionally, this work provides a platform for the discovery of novel targets of Lon proteases.<br><br>BIOLOGICAL SIGNIFICANCE: The proteome of a Lon-deficient archaeal cell was examined for the first time showing that Lon has a strong impact on H. volcanii physiology and evidencing the proteins and cellular processes controlled by this protease in Archaea. This work will facilitate future investigations aiming to address Lon function in archaea and provides a platform for the discovery of endogenous targets of the archaeal-type Lon as well as novel targets/processes regulated by Lon proteases. This knowledge will advance the understanding on archaeal physiology and the biological function of membrane proteases in microorganisms.},
}
@article {pmid25822915,
year = {2015},
author = {Aono, R and Sato, T and Imanaka, T and Atomi, H},
title = {A pentose bisphosphate pathway for nucleoside degradation in Archaea.},
journal = {Nature chemical biology},
volume = {11},
number = {5},
pages = {355-360},
doi = {10.1038/nchembio.1786},
pmid = {25822915},
issn = {1552-4469},
mesh = {Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/metabolism ; Aldose-Ketose Isomerases/drug effects/metabolism ; Archaea/*metabolism ; Archaeal Proteins/drug effects/metabolism ; Escherichia coli/genetics ; Genetic Vectors ; Nucleosides/*metabolism ; Pentose Phosphate Pathway/genetics/*physiology ; Pentosephosphates/metabolism ; Plasmids/genetics ; Thermococcus/genetics/*metabolism ; Uridine Kinase/metabolism ; },
abstract = {Owing to the absence of the pentose phosphate pathway, the degradation pathway for the ribose moieties of nucleosides is unknown in Archaea. Here, in the archaeon Thermococcus kodakarensis, we identified a metabolic network that links the pentose moieties of nucleosides or nucleotides to central carbon metabolism. The network consists of three nucleoside phosphorylases, an ADP-dependent ribose-1-phosphate kinase and two enzymes of a previously identified NMP degradation pathway, ribose-1,5-bisphosphate isomerase and type III ribulose-1,5-bisphosphate carboxylase/oxygenase. Ribose 1,5-bisphosphate and ribulose 1,5-bisphosphate are intermediates of this pathway, which is thus designated the pentose bisphosphate pathway.},
}
@article {pmid25820379,
year = {2015},
author = {Boyd, ES},
title = {Archaea on the move.},
journal = {Environmental microbiology reports},
volume = {7},
number = {3},
pages = {385-387},
doi = {10.1111/1758-2229.12281},
pmid = {25820379},
issn = {1758-2229},
mesh = {Archaea/genetics/*physiology ; Gene Regulatory Networks ; *Locomotion ; },
}
@article {pmid25806405,
year = {2015},
author = {Gomes-Filho, JV and Zaramela, LS and Italiani, VC and Baliga, NS and Vêncio, RZ and Koide, T},
title = {Sense overlapping transcripts in IS1341-type transposase genes are functional non-coding RNAs in archaea.},
journal = {RNA biology},
volume = {12},
number = {5},
pages = {490-500},
doi = {10.1080/15476286.2015.1019998},
pmid = {25806405},
issn = {1555-8584},
mesh = {Base Sequence ; Gene Expression Profiling ; *Genes, Archaeal ; Halobacterium salinarum/*genetics/growth &amp; development ; Molecular Sequence Data ; Nucleotide Motifs/genetics ; RNA, Messenger/genetics/metabolism ; RNA, Untranslated/*genetics ; Retroelements/genetics ; Transposases/*genetics ; },
abstract = {The existence of sense overlapping transcripts that share regulatory and coding information in the same genomic sequence shows an additional level of prokaryotic gene expression complexity. Here we report the discovery of ncRNAs associated with IS1341-type transposase (tnpB) genes, at the 3'-end of such elements, with examples in archaea and bacteria. Focusing on the model haloarchaeon Halobacterium salinarum NRC-1, we show the existence of sense overlapping transcripts (sotRNAs) for all its IS1341-type transposases. Publicly available transcriptome compendium show condition-dependent differential regulation between sotRNAs and their cognate genes. These sotRNAs allowed us to find a UUCA tetraloop motif that is present in other archaea (ncRNA family HgcC) and in a H. salinarum intergenic ncRNA derived from a palindrome associated transposable elements (PATE). Overexpression of one sotRNA and the PATE-derived RNA harboring the tetraloop motif improved H. salinarum growth, indicating that these ncRNAs are functional.},
}
@article {pmid25798780,
year = {2015},
author = {Paul, BG and Bagby, SC and Czornyj, E and Arambula, D and Handa, S and Sczyrba, A and Ghosh, P and Miller, JF and Valentine, DL},
title = {Targeted diversity generation by intraterrestrial archaea and archaeal viruses.},
journal = {Nature communications},
volume = {6},
number = {},
pages = {6585},
doi = {10.1038/ncomms7585},
pmid = {25798780},
issn = {2041-1723},
support = {R01 AI096838/AI/NIAID NIH HHS/United States ; R01 AI069838/AI/NIAID NIH HHS/United States ; },
mesh = {Archaea/virology ; Archaeal Proteins/*genetics ; Archaeal Viruses/*genetics ; Base Sequence ; *Genetic Variation ; Metagenome/*genetics ; Molecular Sequence Data ; Mutation Rate ; Nanoarchaeota/*genetics/virology ; Retroelements ; },
abstract = {In the evolutionary arms race between microbes, their parasites, and their neighbours, the capacity for rapid protein diversification is a potent weapon. Diversity-generating retroelements (DGRs) use mutagenic reverse transcription and retrohoming to generate myriad variants of a target gene. Originally discovered in pathogens, these retroelements have been identified in bacteria and their viruses, but never in archaea. Here we report the discovery of intact DGRs in two distinct intraterrestrial archaeal systems: a novel virus that appears to infect archaea in the marine subsurface, and, separately, two uncultivated nanoarchaea from the terrestrial subsurface. The viral DGR system targets putative tail fibre ligand-binding domains, potentially generating >10(18) protein variants. The two single-cell nanoarchaeal genomes each possess ≥4 distinct DGRs. Against an expected background of low genome-wide mutation rates, these results demonstrate a previously unsuspected potential for rapid, targeted sequence diversification in intraterrestrial archaea and their viruses.},
}
@article {pmid25797330,
year = {2015},
author = {Zhang, Y and Chen, L and Dai, T and Sun, R and Wen, D},
title = {Ammonia manipulates the ammonia-oxidizing archaea and bacteria in the coastal sediment-water microcosms.},
journal = {Applied microbiology and biotechnology},
volume = {99},
number = {15},
pages = {6481-6491},
doi = {10.1007/s00253-015-6524-2},
pmid = {25797330},
issn = {1432-0614},
mesh = {Ammonia/*metabolism ; Archaea/*growth &amp; development/metabolism ; Bacteria/*growth &amp; development/metabolism ; *Biota ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; Geologic Sediments/*microbiology ; Isotope Labeling ; Models, Theoretical ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/genetics ; Phylogeny ; Seawater/*chemistry ; Sequence Analysis, DNA ; },
abstract = {Ammonia was observed as a potential significant factor to manipulate the abundance and activity of ammonia-oxidizing microorganisms (AOMs) in water environments. For the first time, this study confirmed this phenomenon by laboratory cultivation. In a series of estuarine sediment-coastal water microcosms, we investigated the AOM's phylogenetic composition and activity change in response to ammonia concentration. Increase of ammonia concentration promoted bacterial amoA gene abundance in a linear pattern. The ratio of transcribed ammonia-oxidizing bacteria (AOB) amoA gene/ammonia-oxidizing archaea (AOA) amoA gene increased from 0.1 to 43 as NH4 (+)-N increased from less than 0.1 to 12 mg L(-1), and AOA amoA transcription was undetected under 20 mg NH4 (+)-N L(-1). The incubation of stable isotope probing (SIP) microcosms revealed a faster (13)C-NaHCO3 incorporation rate of AOA amoA gene under 0.1 mg NH4 (+)-N L(-1) and a sole (13)C-NaHCO3 utilization of the AOB amoA gene under 20 mg NH4 (+)-N L(-1). Our results indicate that ammonia concentration manipulates the structure of AOM. AOA prefers to live and perform higher amoA transcription activity than AOB in ammonia-limited water environments, and AOB tends to take the first contributor place in ammonia-rich ones.},
}
@article {pmid25797107,
year = {2015},
author = {Horz, HP and Robertz, N and Vianna, ME and Henne, K and Conrads, G},
title = {Relationship between methanogenic archaea and subgingival microbial complexes in human periodontitis.},
journal = {Anaerobe},
volume = {35},
number = {Pt A},
pages = {10-12},
doi = {10.1016/j.anaerobe.2015.02.008},
pmid = {25797107},
issn = {1095-8274},
mesh = {Adult ; Aged ; Aged, 80 and over ; Archaea/classification/genetics/isolation &amp; purification/*metabolism ; Bacterial Infections/*microbiology ; Biodiversity ; Female ; Humans ; Male ; Methane/*metabolism ; Middle Aged ; Periodontitis/*microbiology ; Prevotella intermedia/isolation &amp; purification/physiology ; },
abstract = {We compared the amounts of methanogenic archaea with ten of the most important periodontal pathogens in 125 clinical samples. Correlation analysis suggests that the support of the periodontitis-associated bacterial consortium by methanogenic archaea may be driven through direct or indirect interactions with Prevotella intermedia.},
}
@article {pmid25797103,
year = {2015},
author = {Wu, H and Meng, Q and Yu, Z},
title = {Effect of pH buffering capacity and sources of dietary sulfur on rumen fermentation, sulfide production, methane production, sulfate reducing bacteria, and total Archaea in in vitro rumen cultures.},
journal = {Bioresource technology},
volume = {186},
number = {},
pages = {25-33},
doi = {10.1016/j.biortech.2015.02.110},
pmid = {25797103},
issn = {1873-2976},
mesh = {Ammonia/metabolism ; Animals ; Archaea/*metabolism ; Buffers ; Diet/methods ; Fermentation/*physiology ; Hydrogen-Ion Concentration ; Methane/*metabolism ; Rumen/*metabolism/microbiology ; Sulfates/*metabolism ; Sulfides/*metabolism ; Sulfur/*metabolism ; },
abstract = {The effects of three types of dietary sulfur on in vitro fermentation characteristics, sulfide production, methane production, and microbial populations at two different buffer capacities were examined using in vitro rumen cultures. Addition of dry distilled grain with soluble (DDGS) generally decreased total gas production, degradation of dry matter and neutral detergent fiber, and concentration of total volatile fatty acids, while increasing ammonia concentration. High buffering capacity alleviated these adverse effects on fermentation. Increased sulfur content resulted in decreased methane emission, but total Archaea population was not changed significantly. The population of sulfate reducing bacteria was increased in a sulfur type-dependent manner. These results suggest that types of dietary sulfur and buffering capacity can affect rumen fermentation and sulfide production. Diet buffering capacity, and probably alkalinity, may be increased to alleviate some of the adverse effects associated with feeding DDGS at high levels.},
}
@article {pmid25794363,
year = {2015},
author = {, },
title = {Correction: a bioenergetic basis for membrane divergence in archaea and bacteria.},
journal = {PLoS biology},
volume = {13},
number = {3},
pages = {e1002102},
doi = {10.1371/journal.pbio.1002102},
pmid = {25794363},
issn = {1545-7885},
}
@article {pmid25792437,
year = {2015},
author = {Aydin, S and Ince, B and Ince, O},
title = {Application of real-time PCR to determination of combined effect of antibiotics on Bacteria, Methanogenic Archaea, Archaea in anaerobic sequencing batch reactors.},
journal = {Water research},
volume = {76},
number = {},
pages = {88-98},
doi = {10.1016/j.watres.2015.02.043},
pmid = {25792437},
issn = {1879-2448},
mesh = {Anaerobiosis ; Anti-Bacterial Agents/*pharmacology ; Archaea/*drug effects/genetics ; Bacteria/*drug effects/genetics ; Bioreactors/*microbiology ; Erythromycin/pharmacology ; Euryarchaeota/drug effects/genetics ; Methane/metabolism ; Real-Time Polymerase Chain Reaction ; Sulfamethoxazole/pharmacology ; Tetracycline/pharmacology ; Waste Disposal, Fluid/*methods ; },
abstract = {This study evaluated the long-term effects of erythromycin-tetracycline-sulfamethoxazole (ETS) and sulfamethoxazole-tetracycline (ST) antibiotic combinations on the microbial community and examined the ways in which these antimicrobials impact the performance of anaerobic reactors. Quantitative real-time PCR was used to determine the effect that different antibiotic combinations had on the total and active Bacteria, Archae and Methanogenic Archae. Three primer sets that targeted metabolic genes encoding formylterahydrofolate synthetase, methyl-coenzyme M reductase and acetyl-coA synthetase were also used to determine the inhibition level on the mRNA expression of the homoacetogens, methanogens and specifically acetoclastic methanogens, respectively. These microorganisms play a vital role in the anaerobic degradation of organic waste and targeting these gene expressions offers operators or someone at a treatment plant the potential to control and the improve the anaerobic system. The results of the investigation revealed that acetogens have a competitive advantage over Archaea in the presence of ETS and ST combinations. Although the efficiency with which methane production takes place and the quantification of microbial populations in both the ETS and ST reactors decreased as antibiotic concentrations increased, the ETS batch reactor performed better than the ST batch reactor. According to the expression of genes results, the syntrophic interaction of acetogens and methanogens is critical to the performance of the ETS and ST reactors. Failure to maintain the stability of these microorganisms resulted in a decrease in the performance and stability of the anaerobic reactors.},
}
@article {pmid25789552,
year = {2015},
author = {Zuo, G and Xu, Z and Hao, B},
title = {Phylogeny and Taxonomy of Archaea: A Comparison of the Whole-Genome-Based CVTree Approach with 16S rRNA Sequence Analysis.},
journal = {Life (Basel, Switzerland)},
volume = {5},
number = {1},
pages = {949-968},
doi = {10.3390/life5010949},
pmid = {25789552},
issn = {2075-1729},
abstract = {A tripartite comparison of Archaea phylogeny and taxonomy at and above the rank order is reported: (1) the whole-genome-based and alignment-free CVTree using 179 genomes; (2) the 16S rRNA analysis exemplified by the All-Species Living Tree with 366 archaeal sequences; and (3) the Second Edition of Bergey's Manual of Systematic Bacteriology complemented by some current literature. A high degree of agreement is reached at these ranks. From the newly proposed archaeal phyla, Korarchaeota, Thaumarchaeota, Nanoarchaeota and Aigarchaeota, to the recent suggestion to divide the class Halobacteria into three orders, all gain substantial support from CVTree. In addition, the CVTree helped to determine the taxonomic position of some newly sequenced genomes without proper lineage information. A few discrepancies between the CVTree and the 16S rRNA approaches call for further investigation.},
}
@article {pmid25786142,
year = {2015},
author = {Watanabe, S and Tanimoto, Y and Nishiwaki, H and Watanabe, Y},
title = {Identification and characterization of bifunctional proline racemase/hydroxyproline epimerase from archaea: discrimination of substrates and molecular evolution.},
journal = {PloS one},
volume = {10},
number = {3},
pages = {e0120349},
doi = {10.1371/journal.pone.0120349},
pmid = {25786142},
issn = {1932-6203},
mesh = {Amino Acid Isomerases/genetics/*metabolism ; Amino Acid Sequence ; Amino Acid Substitution ; Archaeal Proteins/genetics/*metabolism ; Biocatalysis ; Escherichia coli/genetics/metabolism ; Evolution, Molecular ; Gene Expression ; Hydroxyproline/*metabolism ; Kinetics ; Molecular Sequence Data ; Mutation ; Phylogeny ; Proline/*metabolism ; Recombinant Proteins/genetics/metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; Stereoisomerism ; Substrate Specificity ; Thermococcus/classification/*enzymology/genetics ; },
abstract = {Proline racemase (ProR) is a member of the pyridoxal 5'-phosphate-independent racemase family, and is involved in the Stickland reaction (fermentation) in certain clostridia as well as the mechanisms underlying the escape of parasites from host immunity in eukaryotic Trypanosoma. Hydroxyproline epimerase (HypE), which is in the same protein family as ProR, catalyzes the first step of the trans-4-hydroxy-L-proline metabolism of bacteria. Their substrate specificities were previously considered to be very strict, in spite of similarities in their structures and catalytic mechanisms, and no racemase/epimerase from the ProR superfamily has been found in archaea. We here characterized the ProR-like protein (OCC_00372) from the hyperthermophilic archaeon, Thermococcus litoralis (TlProR). This protein could reversibly catalyze not only the racemization of proline, but also the epimerization of 4-hydroxyproline and 3-hydroxyproline with similar kinetic constants. Among the four (putative) ligand binding sites, one amino acid substitution was detected between TlProR (tryptophan at the position of 241) and natural ProR (phenylalanine). The W241F mutant showed a significant preference for proline over hydroxyproline, suggesting that this (hydrophobic and bulky) tryptophan residue played an importance role in the recognition of hydroxyproline (more hydrophilic and bulky than proline), and substrate specificity for hydroxyproline was evolutionarily acquired separately between natural HypE and ProR. A phylogenetic analysis indicated that such unique broad substrate specificity was derived from an ancestral enzyme of this superfamily.},
}
@article {pmid25772805,
year = {2015},
author = {Rodriguez-Corona, U and Sobol, M and Rodriguez-Zapata, LC and Hozak, P and Castano, E},
title = {Fibrillarin from Archaea to human.},
journal = {Biology of the cell},
volume = {107},
number = {6},
pages = {159-174},
doi = {10.1111/boc.201400077},
pmid = {25772805},
issn = {1768-322X},
mesh = {Animals ; Archaea/*genetics/*metabolism ; Chromosomal Proteins, Non-Histone/*genetics/*metabolism ; Humans ; Methylation ; Neoplasms/genetics/metabolism ; },
abstract = {Fibrillarin is an essential protein that is well known as a molecular marker of transcriptionally active RNA polymerase I. Fibrillarin methyltransferase activity is the primary known source of methylation for more than 100 methylated sites involved in the first steps of preribosomal processing and required for structural ribosome stability. High expression levels of fibrillarin have been observed in several types of cancer cells, particularly when p53 levels are reduced, because p53 is a direct negative regulator of fibrillarin transcription. Here, we show fibrillarin domain conservation, structure and interacting molecules in different cellular processes as well as with several viral proteins during virus infection.},
}
@article {pmid25764551,
year = {2015},
author = {Marusenko, Y and Garcia-Pichel, F and Hall, SJ},
title = {Ammonia-oxidizing archaea respond positively to inorganic nitrogen addition in desert soils.},
journal = {FEMS microbiology ecology},
volume = {91},
number = {2},
pages = {1-11},
doi = {10.1093/femsec/fiu023},
pmid = {25764551},
issn = {1574-6941},
mesh = {Ammonia/*metabolism ; Archaea/genetics/*metabolism ; Desert Climate ; Ecosystem ; Nitrogen/*metabolism ; Nitrosomonas/genetics/metabolism ; Oxidation-Reduction ; Soil ; *Soil Microbiology ; },
abstract = {In soils, nitrogen (N) addition typically enhances ammonia oxidation (AO) rates and increases the population density of ammonia-oxidizing bacteria (AOB), but not that of ammonia-oxidizing archaea (AOA). We asked if long-term inorganic N addition also has similar consequences in arid land soils, an understudied yet spatially ubiquitous ecosystem type. Using Sonoran Desert top soils from between and under shrubs within a long-term N-enrichment experiment, we determined community concentration-response kinetics of AO and measured the total and relative abundance of AOA and AOB based on amoA gene abundance. As expected, N addition increased maximum AO rates and the abundance of bacterial amoA genes compared to the controls. Surprisingly, N addition also increased the abundance of archaeal amoA genes. We did not detect any major effects of N addition on ammonia-oxidizing community composition. The ammonia-oxidizing communities in these desert soils were dominated by AOA as expected (78% of amoA gene copies were related to Nitrososphaera), but contained unusually high contributions of Nitrosomonas (18%) and unusually low numbers of Nitrosospira (2%). This study highlights unique traits of ammonia oxidizers in arid lands, which should be considered globally in predictions of AO responses to changes in N availability.},
}
@article {pmid25764468,
year = {2015},
author = {Fillol, M and Sànchez-Melsió, A and Gich, F and Borrego, CM},
title = {Diversity of Miscellaneous Crenarchaeotic Group archaea in freshwater karstic lakes and their segregation between planktonic and sediment habitats.},
journal = {FEMS microbiology ecology},
volume = {91},
number = {4},
pages = {},
doi = {10.1093/femsec/fiv020},
pmid = {25764468},
issn = {1574-6941},
mesh = {Base Sequence ; Crenarchaeota/*genetics/growth &amp; development/isolation &amp; purification ; DNA, Archaeal/genetics ; Euryarchaeota/*genetics/growth &amp; development/isolation &amp; purification ; Gene Library ; Geologic Sediments/*microbiology ; Lakes/*microbiology ; Molecular Sequence Data ; Phylogeny ; Plankton/microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {The Miscellaneous Crenarchaeotic Group (MCG) is an archaeal lineage whose members are widespread and abundant in marine sediments. MCG archaea have also been consistently found in stratified euxinic lakes. In this work, we have studied archaeal communities in three karstic lakes to reveal potential habitat segregation of MCG subgroups between planktonic and sediment compartments. In the studied lakes, archaeal assemblages were strikingly similar to those of the marine subsurface with predominance of uncultured Halobacteria in the plankton and Thermoplasmata and MCG in anoxic, organic-rich sediments. Multivariate analyses identified sulphide and dissolved organic carbon as predictor variables of archaeal community composition. Quantification of MCG using a newly designed qPCR primer pair that improves coverage for MCG subgroups prevalent in the studied lakes revealed conspicuous populations in both the plankton and the sediment. Subgroups MCG-5a and -5b appear as planktonic specialists thriving in euxinic bottom waters, while subgroup MCG-6 emerges as a generalist group able to cope with varying reducing conditions. Besides, comparison of DNA- and cDNA-based pyrotag libraries revealed that rare subgroups in DNA libraries, i.e. MCG-15, were prevalent in cDNA-based datasets, suggesting that euxinic, organic-rich sediments of karstic lakes provide optimal niches for the activity of some specialized MCG subgroups.},
}
@article {pmid25749160,
year = {2014},
author = {Syutkin, AS and Pyatibratov, MG and Fedorov, OV},
title = {Flagella of halophilic archaea: differences in supramolecular organization.},
journal = {Biochemistry. Biokhimiia},
volume = {79},
number = {13},
pages = {1470-1482},
doi = {10.1134/S0006297914130033},
pmid = {25749160},
issn = {1608-3040},
mesh = {Archaea/physiology/*ultrastructure ; Archaeal Proteins/*chemistry/genetics/metabolism ; Flagella/physiology/*ultrastructure ; Flagellin/*chemistry/genetics/metabolism ; },
abstract = {Archaeal flagella are similar functionally to bacterial flagella, but structurally they are completely different. Helical archaeal flagellar filaments are formed of protein subunits called flagellins (archaellins). Notwithstanding progress in studies of archaeal flagella achieved in recent years, many problems in this area are still unsolved. In this review, we analyze the formation of these supramolecular structures by the example of flagellar filaments of halophilic archaea. Recent data on the structure of the flagellar filaments demonstrate that their supramolecular organization differs considerably in different haloarchaeal species.},
}
@article {pmid25747618,
year = {2015},
author = {Rosselló-Móra, R and Amann, R},
title = {Past and future species definitions for Bacteria and Archaea.},
journal = {Systematic and applied microbiology},
volume = {38},
number = {4},
pages = {209-216},
doi = {10.1016/j.syapm.2015.02.001},
pmid = {25747618},
issn = {1618-0984},
mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Genome, Archaeal/genetics ; Genome, Bacterial/genetics ; *Genomics ; *Sequence Analysis, DNA ; },
abstract = {Species is the basic unit of biological diversity. However, among the different microbiological disciplines there is an important degree of disagreement as to what this unit may be. In this minireview, we argue that the main point of disagreement is the definition (i.e. the way species are circumscribed by means of observable characters) rather than the concept (i.e. the idea of what a species may be as a unit of biodiversity, the meaning of the patterns of recurrence observed in nature, and the why of their existence). Taxonomists have defined species by means of genetic and expressed characters that ensure the members of the unit are monophyletic, and exhibit a large degree of genomic and phenotypic coherence. The new technologies allowing high-throughput data acquisition are expected to improve future classifications significantly and will lead to database-based taxonomy centered on portable and interactive data. Future species descriptions of Bacteria and Archaea should include a high quality genome sequence of at least the type strain as an obligatory requirement, just as today an almost full-length 16S rRNA gene sequence must be provided. Serious efforts are needed in order to re-evaluate the major guidelines for standard descriptions.},
}
@article {pmid25744648,
year = {2015},
author = {Li, H and Weng, BS and Huang, FY and Su, JQ and Yang, XR},
title = {pH regulates ammonia-oxidizing bacteria and archaea in paddy soils in Southern China.},
journal = {Applied microbiology and biotechnology},
volume = {99},
number = {14},
pages = {6113-6123},
doi = {10.1007/s00253-015-6488-2},
pmid = {25744648},
issn = {1432-0614},
mesh = {Ammonia/*metabolism ; Archaea/*classification/enzymology/genetics/metabolism ; Betaproteobacteria/*classification/enzymology/genetics/metabolism ; Biota/*drug effects ; China ; Cloning, Molecular ; Cluster Analysis ; Genetic Variation ; Hydrogen-Ion Concentration ; Molecular Sequence Data ; Nitrification ; Oxidation-Reduction ; Oxidoreductases/genetics ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Soil/*chemistry ; *Soil Microbiology ; },
abstract = {Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play important roles in nitrogen cycling. However, the effects of environmental factors on the activity, abundance, and diversity of AOA and AOB and the relative contributions of these two groups to nitrification in paddy soils are not well explained. In this study, potential nitrification activity (PNA), abundance, and diversity of amoA genes from 12 paddy soils in Southern China were determined by potential nitrification assay, quantitative PCR, and cloning. The results showed that PNA was highly variable between paddy soils, ranging from 4.05 ± 0.21 to 9.81 ± 1.09 mg NOx-N kg(-1) dry soil day(-1), and no significant correlation with soil parameters was found. The abundance of AOA was predominant over AOB, indicating that AOA may be the major members in aerobic ammonia oxidation in these paddy soils. Community compositions of AOA and AOB were highly variable among samples, but the variations were best explained by pH. AOA sequences were affiliated to the Nitrosopumilus cluster and Nitrososphaera cluster, and AOB were classified into the lineages of Nitrosospira and Nitrosomonas, with Nitrosospira being predominant over Nitrosomonas, accounting for 83.6 % of the AOB community. Moreover, the majority of Nitrosomonas was determined in neutral soils. Canonical correspondence analysis (CCA) analysis further demonstrated that AOA and AOB community structures were significantly affected by pH, soil total organic carbon, total nitrogen, and C/N ratio, suggesting that these factors exert strong effects on the distribution of AOB and AOA in paddy soils in Southern China. In conclusion, our results imply that soil pH was a key explanatory variable for both AOA and AOB community structure and nitrification activity.},
}
@article {pmid25736866,
year = {2015},
author = {Tago, K and Okubo, T and Shimomura, Y and Kikuchi, Y and Hori, T and Nagayama, A and Hayatsu, M},
title = {Environmental factors shaping the community structure of ammonia-oxidizing bacteria and archaea in sugarcane field soil.},
journal = {Microbes and environments},
volume = {30},
number = {1},
pages = {21-28},
doi = {10.1264/jsme2.ME14137},
pmid = {25736866},
issn = {1347-4405},
mesh = {Ammonia/*metabolism ; Archaea/*classification/metabolism ; Bacteria/*classification/metabolism ; *Biota ; Cluster Analysis ; Hydrogen-Ion Concentration ; Oxidation-Reduction ; Oxidoreductases/genetics ; Phylogeny ; Polymerase Chain Reaction ; Saccharum/growth &amp; development ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {The effects of environmental factors such as pH and nutrient content on the ecology of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in soil has been extensively studied using experimental fields. However, how these environmental factors intricately influence the community structure of AOB and AOA in soil from farmers' fields is unclear. In the present study, the abundance and diversity of AOB and AOA in soils collected from farmers' sugarcane fields were investigated using quantitative PCR and barcoded pyrosequencing targeting the ammonia monooxygenase alpha subunit (amoA) gene. The abundances of AOB and AOA amoA genes were estimated to be in the range of 1.8 × 10(5)-9.2 × 10(6) and 1.7 × 10(6)-5.3 × 10(7) gene copies g dry soil(-1), respectively. The abundance of both AOB and AOA positively correlated with the potential nitrification rate. The dominant sequence reads of AOB and AOA were placed in Nitrosospira-related and Nitrososphaera-related clusters in all soils, respectively, which varied at the level of their sub-clusters in each soil. The relationship between these ammonia-oxidizing community structures and soil pH was shown to be significant by the Mantel test. The relative abundances of the OTU1 of Nitrosospira cluster 3 and Nitrososphaera subcluster 7.1 negatively correlated with soil pH. These results indicated that soil pH was the most important factor shaping the AOB and AOA community structures, and that certain subclusters of AOB and AOA adapted to and dominated the acidic soil of agricultural sugarcane fields.},
}
@article {pmid25727367,
year = {2016},
author = {Emerson, JB and Thomas, BC and Alvarez, W and Banfield, JF},
title = {Metagenomic analysis of a high carbon dioxide subsurface microbial community populated by chemolithoautotrophs and bacteria and archaea from candidate phyla.},
journal = {Environmental microbiology},
volume = {18},
number = {6},
pages = {1686-1703},
doi = {10.1111/1462-2920.12817},
pmid = {25727367},
issn = {1462-2920},
mesh = {Archaea/classification/*genetics/isolation &amp; purification/metabolism ; Bacteria/classification/*genetics/isolation &amp; purification/metabolism ; Biodiversity ; Carbon Cycle ; Carbon Dioxide/*metabolism ; Chemoautotrophic Growth ; Metagenome ; Metagenomics ; Phylogeny ; Sulfur/metabolism ; },
abstract = {Research on geologic carbon sequestration raises questions about potential impacts of subsurface microbiota on carbon cycling and biogeochemistry. Subsurface, high-CO2 systems are poorly biologically characterized, partly because of difficulty accessing high-volume, uncontaminated samples. CO2 -driven Crystal Geyser (CG, Utah, USA), an established geologic carbon sequestration analogue, provides high volumes of deep (∼ 200-500 m) subsurface fluids. We explored microbial diversity and metabolic potential in this high-CO2 environment by assembly and analysis of metagenomes recovered from geyser water filtrate. The system is dominated by neutrophilic, iron-oxidizing bacteria, including 'marine' Mariprofundus (Zetaproteobacteria) and 'freshwater' Gallionellales, sulfur-oxidizing Thiomicrospira crunogena and Thiobacillus-like Hydrogenophilales. Near-complete genomes were reconstructed for these bacteria. CG is notably populated by a wide diversity of bacteria and archaea from phyla lacking isolated representatives (candidate phyla) and from as-yet undefined lineages. Many bacteria affiliate with OD1, OP3, OP9, PER, ACD58, WWE3, BD1-5, OP11, TM7 and ZB2. The recovery of nearly 100 genes encoding ribulose-1,5 bisphosphate carboxylase-oxygenase subunit proteins of the Calvin cycle and AMP salvage pathways suggests a strong biological role in high-CO2 subsurface carbon cycling. Overall, we predict microbial impacts on subsurface biogeochemistry via iron, sulfur, and complex carbon oxidation, carbon and nitrogen fixation, fermentation, hydrogen metabolism, and aerobic and anaerobic respiration.},
}
@article {pmid25725631,
year = {2015},
author = {Chi, XQ and Liu, K and Zhou, NY},
title = {Effects of bioaugmentation in para-nitrophenol-contaminated soil on the abundance and community structure of ammonia-oxidizing bacteria and archaea.},
journal = {Applied microbiology and biotechnology},
volume = {99},
number = {14},
pages = {6069-6082},
doi = {10.1007/s00253-015-6462-z},
pmid = {25725631},
issn = {1432-0614},
mesh = {Ammonia/*metabolism ; Archaea/*classification/metabolism ; Bacteria/*classification/metabolism ; *Biota ; Denaturing Gradient Gel Electrophoresis ; Nitrophenols/*metabolism ; Oxidation-Reduction ; Real-Time Polymerase Chain Reaction ; *Soil Microbiology ; Soil Pollutants/*metabolism ; },
abstract = {Pseudomonas sp. strain WBC-3 mineralizes the priority pollutant para-nitrophenol (PNP) and releases nitrite (NO2 (-)), which is probably involved in the nitrification. In this study, the rate of PNP removal in soil bioaugmented with strain WBC-3 was more accelerated with more NO2 (-) accumulation than in uninoculated soils. Strain WBC-3 survived well and remained stable throughout the entire period. Real-time polymerase chain reaction (real-time PCR) indicated a higher abundance of ammonia-oxidizing bacteria (AOB) than ammonia-oxidizing archaea (AOA), suggesting that AOB played a greater role in nitrification in the original sampled soil. Real-time PCR and multivariate analysis based on the denaturing gradient gel electrophoresis showed that PNP contamination did not significantly alter the abundance and community structure of ammonia oxidizers except for inhibiting the AOB abundance. Bioaugmentation of PNP-contaminated soil showed a significant effect on AOB populations and community structure as well as AOA populations. In addition, ammonium (NH4 (+)) variation was found to be the primary factor affecting the AOB community structure, as determined by the correlation between the community structures of ammonia oxidizers and environmental factors. It is here proposed that the balance between archaeal and bacterial ammonia oxidation could be influenced significantly by the variation in NH4 (+) levels as caused by bioaugmentation of contaminated soil by a pollutant containing nitrogen.},
}
@article {pmid25709053,
year = {2015},
author = {Shi, Y and Huang, Z and Han, S and Fan, S and Yang, H},
title = {Phylogenetic diversity of Archaea in the intestinal tract of termites from different lineages.},
journal = {Journal of basic microbiology},
volume = {55},
number = {8},
pages = {1021-1028},
doi = {10.1002/jobm.201400678},
pmid = {25709053},
issn = {1521-4028},
mesh = {Animals ; Archaea/*classification/*genetics ; Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Genes, rRNA ; Genetic Variation ; Isoptera/anatomy &amp; histology/classification/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; },
abstract = {Termites are among the few arthropods that emit methane to the atmosphere, which is a significant source of global greenhouse gas due to their huge biomass on earth. In this study, phylogenetic diversity of Archaea of five termite species from different lineages were analyzed based on 16S rRNA genes. Archaea associated with wood-feeding lower termite, R. chinensis were exclusively Methanobrevibacter in the order Methanobacteriales. This type of methanogens was also found in Nasutitermes sp. and Microcerotermes sp. but not in the fungus-cultivating termites, Odontotermes formosanus and Macrotermes barneyi, which harbor Archaea of the order Methanoplasmatales and Methanosarcinales in their guts. Archaeal diversity of wood-feeding higher termites was higher than wood-feeding lower termites. The highest archaeal diversity was found in Nasutitermes sp. In addition to methanogens affiliated with the orders Methanobacteriales, Methanomicrobiales, and Methanoplasmatales, 37% of archaeal clones were affiliated with non-methanogenic Thaumarchaeota. The results of this study will be significant for further understanding of symbiotic relationship between intestinal microbiota and termites.},
}
@article {pmid25705674,
year = {2015},
author = {Cycoń, M and Piotrowska-Seget, Z},
title = {Community structure of ammonia-oxidizing archaea and ammonia-oxidizing bacteria in soil treated with the insecticide imidacloprid.},
journal = {BioMed research international},
volume = {2015},
number = {},
pages = {582938},
doi = {10.1155/2015/582938},
pmid = {25705674},
issn = {2314-6141},
mesh = {Ammonia/chemistry/*metabolism ; Archaea/*drug effects/metabolism ; Bacteria/*drug effects/metabolism ; Imidazoles/toxicity ; Insecticides/toxicity ; Neonicotinoids ; Nitrification/drug effects ; Nitro Compounds/toxicity ; Oxidation-Reduction ; *Soil Microbiology ; },
abstract = {The purpose of this experiment was to assess the effect of imidacloprid on the community structure of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in soil using the denaturing gradient gel electrophoresis (DGGE) approach. Analysis showed that AOA and AOB community members were affected by the insecticide treatment. However, the calculation of the richness (S) and the Shannon-Wiener index (H) values for soil treated with the field rate (FR) dosage of imidacloprid (1 mg/kg soil) showed no changes in measured indices for the AOA and AOB community members. In turn, the 10∗FR dosage of insecticide (10 mg/kg soil) negatively affected the AOA community, which was confirmed by the decrease of the S and H values in comparison with the values obtained for the control soil. In the case of AOB community, an initial decline followed by the increase of the S and H values was obtained. Imidacloprid decreased the nitrification rate while the ammonification process was stimulated by the addition of imidacloprid. Changes in the community structure of AOA and AOB could be due to an increase in the concentration of N-NH4 (+), known as the most important factor which determines the contribution of these microorganisms to soil nitrification.},
}
@article {pmid25702576,
year = {2015},
author = {Castelle, CJ and Wrighton, KC and Thomas, BC and Hug, LA and Brown, CT and Wilkins, MJ and Frischkorn, KR and Tringe, SG and Singh, A and Markillie, LM and Taylor, RC and Williams, KH and Banfield, JF},
title = {Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling.},
journal = {Current biology : CB},
volume = {25},
number = {6},
pages = {690-701},
doi = {10.1016/j.cub.2015.01.014},
pmid = {25702576},
issn = {1879-0445},
mesh = {Anaerobiosis/genetics ; Archaea/classification/*genetics/*metabolism ; Biodiversity ; Carbon Cycle/*genetics ; *Genome, Archaeal ; Metagenomics ; Models, Biological ; Models, Genetic ; Phylogeny ; },
abstract = {BACKGROUND: Archaea represent a significant fraction of Earth's biodiversity, yet they remain much less well understood than Bacteria. Gene surveys, a few metagenomic studies, and some single-cell sequencing projects have revealed numerous little-studied archaeal phyla. Certain lineages appear to branch deeply and may be part of a major phylum radiation. The structure of this radiation and the physiology of the organisms remain almost unknown.<br><br>RESULTS: We used genome-resolved metagenomic analyses to investigate the diversity, genomes sizes, metabolic capacities, and potential roles of Archaea in terrestrial subsurface biogeochemical cycles. We sequenced DNA from complex sediment and planktonic consortia from an aquifer adjacent to the Colorado River (USA) and reconstructed the first complete genomes for Archaea using cultivation-independent methods. To provide taxonomic context, we analyzed an additional 151 newly sampled archaeal sequences. We resolved two new phyla within a major, apparently deep-branching group of phyla (a superphylum). The organisms have small genomes, and metabolic predictions indicate that their primary contributions to Earth's biogeochemical cycles involve carbon and hydrogen metabolism, probably associated with symbiotic and/or fermentation-based lifestyles.<br><br>CONCLUSIONS: The results dramatically expand genomic sampling of the domain Archaea and clarify taxonomic designations within a major superphylum. This study, in combination with recently published work on bacterial phyla lacking cultivated representatives, reveals a fascinating phenomenon of major radiations of organisms with small genomes, novel proteome composition, and strong interdependence in both domains.},
}
@article {pmid25699024,
year = {2015},
author = {Albers, SV and Jarrell, KF},
title = {The archaellum: how Archaea swim.},
journal = {Frontiers in microbiology},
volume = {6},
number = {},
pages = {23},
doi = {10.3389/fmicb.2015.00023},
pmid = {25699024},
issn = {1664-302X},
support = {311523//European Research Council/International ; },
abstract = {Recent studies on archaeal motility have shown that the archaeal motility structure is unique in several aspects. Although it fulfills the same swimming function as the bacterial flagellum, it is evolutionarily and structurally related to the type IV pilus. This was the basis for the recent proposal to term the archaeal motility structure the &quot;archaellum.&quot; This review illustrates the key findings that led to the realization that the archaellum was a novel motility structure and presents the current knowledge about the structural composition, mechanism of assembly and regulation, and the posttranslational modifications of archaella.},
}
@article {pmid25682761,
year = {2015},
author = {La Cono, V and Smedile, F and La Spada, G and Arcadi, E and Genovese, M and Ruggeri, G and Genovese, L and Giuliano, L and Yakimov, MM},
title = {Shifts in the meso- and bathypelagic archaea communities composition during recovery and short-term handling of decompressed deep-sea samples.},
journal = {Environmental microbiology reports},
volume = {7},
number = {3},
pages = {450-459},
doi = {10.1111/1758-2229.12272},
pmid = {25682761},
issn = {1758-2229},
mesh = {Adaptation, Biological ; Archaea/*classification/*isolation &amp; purification/physiology ; *Biota ; *Decompression ; Seawater/*microbiology ; },
abstract = {Dark ocean microbial communities are actively involved in chemoautotrophic and anaplerotic fixation of bicarbonate. Thus, aphotic pelagic realm of the ocean might represent a significant sink of CO2 and source of primary production. However, the estimated metabolic activities in the dark ocean are fraught with uncertainties. Typically, deep-sea samples are recovered to the sea surface for downstream processing on deck. Shifts in ambient settings, associated with such treatments, can likely change the metabolic activity and community structure of deep-sea adapted autochthonous microbial populations. To estimate influence of recovery and short-term handling of deep-sea samples, we monitored the succession of bathypelagic microbial community during its 3 days long on deck incubation. We demonstrated that at the end of exposition, the deep-sea archaeal population decreased threefold, whereas the bacterial fraction doubled in size. As revealed by phylogenetic analyses of amoA gene transcripts, dominance of the active ammonium-oxidizing bathypelagic Thaumarchaeota groups shifted over time very fast. These findings demonstrated the simultaneous existence of various 'deep-sea ecotypes', differentially reacting to the sampling and downstream handling. Our study supports the hypothesis that metabolically active members of meso- and bathypelagic Thaumarchaeota possess the habitat-specific distribution, metabolic complexity and genetic divergence at subpopulation level.},
}
@article {pmid25680859,
year = {2015},
author = {Baricz, A and Cristea, A and Muntean, V and Teodosiu, G and Andrei, AŞ and Molnár, I and Alexe, M and Rakosy-Tican, E and Banciu, HL},
title = {Culturable diversity of aerobic halophilic archaea (Fam. Halobacteriaceae) from hypersaline, meromictic Transylvanian lakes.},
journal = {Extremophiles : life under extreme conditions},
volume = {19},
number = {2},
pages = {525-537},
doi = {10.1007/s00792-015-0738-1},
pmid = {25680859},
issn = {1433-4909},
mesh = {Halobacteriaceae/classification/*genetics/isolation &amp; purification ; Lakes/chemistry/*microbiology ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Salinity ; *Salt-Tolerance ; },
abstract = {Perennially stratified salt lakes situated in the Transylvanian Basin (Central Romania) were surveyed for the diversity of culturable halophilic archaea (Fam. Halobacteriaceae). The physical and chemical characteristics of the waters indicated that all the investigated lakes were meromictic and neutral hypersaline. Samples collected from upper, intermediate, and deeper water layers and sediments were used for the isolation of halophilic strains followed by 16S rRNA gene-based identification and phenotypic characterization. The phylogenetic analysis of the 16S rRNA gene sequences revealed that all 191 isolates reported in this study and 43 strains previously isolated were affiliated with the family Halobacteriaceae and classified to 18 genera. Haloferax was the most frequently isolated genus (~47 %), followed by Halobacterium spp. (~12 %), and Halorubrum spp. (~11 %). Highest culturable diversity was detected in Brâncoveanu Lake, the oldest and saltiest of all studied lakes, while the opposite was observed in the most stable and least human-impacted Fără Fund Lake. One strain from Ursu Lake might possibly constitute a novel Halorubrum species as shown by phylogenetic analysis. Several haloarchaeal taxa recently described in Asian (i.e., Iran, China) saline systems were also identified as inhabiting the Transylvanian salt lakes thus expanding our knowledege on the geographic distribution of Halobacteriaceae.},
}
@article {pmid25665572,
year = {2015},
author = {Smollett, K and Blombach, F and Werner, F},
title = {Transcription in Archaea: in vitro transcription assays for mjRNAP.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1276},
number = {},
pages = {305-314},
doi = {10.1007/978-1-4939-2392-2_18},
pmid = {25665572},
issn = {1940-6029},
mesh = {DNA-Directed RNA Polymerases/*metabolism ; In Vitro Techniques/*methods ; Methanocaldococcus/*enzymology/*physiology ; Protein Subunits/metabolism ; Recombinant Proteins/*metabolism ; Temperature ; Transcription, Genetic/genetics/*physiology ; },
abstract = {The fully recombinant Methanocaldococcus jannaschii RNA polymerase allows for a detailed dissection of the different stages of the transcription. In the previous chapter, we discussed how to purify the different components of the M. jannaschii transcription system, the RNA polymerase subunits, and general transcription factors and how to assemble a functional M. jannaschii enzyme. Standard in vitro transcription assays can be used to examine the different stages of transcription. In this chapter, we describe how some of these assays have been optimized for M. jannaschii RNA polymerase, which transcribes at much higher temperatures than many other transcription complexes.},
}
@article {pmid25665571,
year = {2015},
author = {Smollett, K and Blombach, F and Werner, F},
title = {Transcription in Archaea: preparation of Methanocaldococcus jannaschii transcription machinery.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1276},
number = {},
pages = {291-303},
doi = {10.1007/978-1-4939-2392-2_17},
pmid = {25665571},
issn = {1940-6029},
mesh = {*Biological Evolution ; DNA-Directed RNA Polymerases/genetics/*metabolism ; Methanocaldococcus/*enzymology/*physiology ; Molecular Biology/*methods ; Silver Staining ; Transcription, Genetic/*physiology ; },
abstract = {Archaeal RNA polymerase and general transcription factors are more closely related to those of eukaryotes than of bacteria. As such the study of transcription of archaea is important both in terms of examination of the evolution of the transcriptional machinery and as a simplified tool for eukaryotic transcription. In particular, the hyperthermophilic Methanocaldococcus jannaschii provides us with a fully recombinant RNA polymerase system allowing for much more detailed in vitro examination of the roles of different components during the transcription cycle than otherwise possible. The individual subunits of M. jannaschii enzyme are easily expressed and purified from heterologous expression systems. Forming functional RNA polymerase involves simply combining the different subunits under denaturing conditions and slowly removing the denaturant.},
}
@article {pmid25663452,
year = {2015},
author = {Danis, O and Ogan, A and Tatlican, P and Attar, A and Cakmakci, E and Mertoglu, B and Birbir, M},
title = {Preparation of poly(3-hydroxybutyrate-co-hydroxyvalerate) films from halophilic archaea and their potential use in drug delivery.},
journal = {Extremophiles : life under extreme conditions},
volume = {19},
number = {2},
pages = {515-524},
doi = {10.1007/s00792-015-0735-4},
pmid = {25663452},
issn = {1433-4909},
mesh = {Archaea/genetics/*metabolism/ultrastructure ; Polyesters/*metabolism ; Starch/metabolism ; },
abstract = {Halophilic archaea offer a potential source for production of polyhydroxyalkanoates (PHAs). Hence, the experiments were carried out with five extremely halophilic archaeal isolates to determine the highest PHA-producing strain. PHA production of each isolates was separately examined in cheap carbon sources such as corn starch, sucrose, whey, apple, melon and tomato wastes. Corn starch was found to be a fairly effective substrate for PHA production. Among the strains studied here, the strain with the highest capability for PHA biosynthesis was found to be 1KYS1. Phylogenetic analysis based on 16S rRNA gene sequence comparison showed that 1KYS1 closely related to species of the genus Natrinema. The closest phylogenetic similarity was with the strain of Natrinema pallidum JCM 8980 (99 %). PHA content of 1KYS1 was about 53.14 % of the cell dry weight when starch was used as a carbon source. The formation of large and uniform PHA granules was confirmed by transmission electron microscopy and the biopolymer was identified as poly(3-hydroxybutyrate-co-hydroxyvalerate) (PHBV). PHBV produced by 1KYS1 was blended with low molar mass polyethylene glycol (PEG 300) to prepare biocompatible films for drug delivery. Rifampicin was used as a model drug and its release from PHBV films was investigated at pH 7.4, 37 °C. It was found that PHBV films obtained from 1KYS1 were very effective for drug delivery. In conclusion, PHBV of 1KYS1 may have a potential usage in drug delivery applications.},
}
@article {pmid25660375,
year = {2015},
author = {Petitjean, C and Deschamps, P and López-García, P and Moreira, D and Brochier-Armanet, C},
title = {Extending the conserved phylogenetic core of archaea disentangles the evolution of the third domain of life.},
journal = {Molecular biology and evolution},
volume = {32},
number = {5},
pages = {1242-1254},
doi = {10.1093/molbev/msv015},
pmid = {25660375},
issn = {1537-1719},
mesh = {Archaea/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Archaeal ; *Phylogeny ; RNA, Ribosomal/*genetics ; Ribosomal Proteins/genetics ; Ribosome Subunits, Small/*genetics ; Ribosomes/genetics ; },
abstract = {Initial studies of the archaeal phylogeny relied mainly on the analysis of the RNA component of the small subunit of the ribosome (SSU rRNA). The resulting phylogenies have provided interesting but partial information on the evolutionary history of the third domain of life because SSU rRNA sequences do not contain enough phylogenetic signal to resolve all nodes of the archaeal tree. Thus, many relationships, and especially the most ancient ones, remained elusive. Moreover, SSU rRNA phylogenies can be heavily biased by tree reconstruction artifacts. The sequencing of complete genomes allows using a variety of protein markers as an alternative to SSU rRNA. Taking advantage of the recent burst of archaeal complete genome sequences, we have carried out an in-depth phylogenomic analysis of this domain. We have identified 200 new protein families that, in addition to the ribosomal proteins and the subunits of the RNA polymerase, form a conserved phylogenetic core of archaeal genes. The accurate analysis of these markers combined with desaturation approaches shed new light on the evolutionary history of Archaea and reveals that several relationships recovered in recent analyses are likely the consequence of tree reconstruction artifacts. Among others, we resolve a number of important relationships, such as those among methanogens Class I, and we propose the definition of two new superclasses within the Euryarchaeota: Methanomada and Diaforarchaea.},
}
@article {pmid25629511,
year = {2014},
author = {Suzuki, T and Numata, T},
title = {Convergent evolution of AUA decoding in bacteria and archaea.},
journal = {RNA biology},
volume = {11},
number = {12},
pages = {1586-1596},
doi = {10.4161/15476286.2014.992281},
pmid = {25629511},
issn = {1555-8584},
mesh = {Anticodon/chemistry/*metabolism ; Archaea/classification/genetics/metabolism ; Bacteria/classification/genetics/metabolism ; Biological Evolution ; Codon/chemistry/*metabolism ; Cytidine/*analogs &amp; derivatives/chemistry/genetics/metabolism ; *Genetic Code ; Isoleucine/chemistry/genetics/metabolism ; Lysine/*analogs &amp; derivatives/chemistry/genetics/metabolism ; Methionine/chemistry/genetics/metabolism ; Models, Molecular ; Phylogeny ; Protein Biosynthesis ; Pyrimidine Nucleosides/chemistry/genetics/*metabolism ; RNA, Transfer/chemistry/genetics/*metabolism ; Ribosomes/metabolism ; },
abstract = {Deciphering AUA codons is a difficult task for organisms, because AUA and AUG specify isoleucine (Ile) and methionine (Met), separately. Each of the other purine-ending sense co-don sets (NNR) specifies a single amino acid in the universal genetic code. In bacteria and archaea, the cytidine derivatives, 2-lysylcytidine (L or lysidine) and 2-agmatinylcytidine (agm(2)C or agmatidine), respectively, are found at the first letter of the anticodon of tRNA(Ile) responsible for AUA codons. These modifications prevent base pairing with G of the third letter of AUG codon, and enable tRNA(Ile) to decipher AUA codon specifically. In addition, these modifications confer a charging ability of tRNA(Ile) with Ile. Despite their similar chemical structures, L and agm(2)C are synthesized by distinctive mechanisms and catalyzed by different classes of enzymes, implying that the analogous decoding systems for AUA codons were established by convergent evolution after the phylogenic split between bacteria and archaea-eukaryotes lineages following divergence from the last universal common ancestor (LUCA).},
}
@article {pmid25617114,
year = {2015},
author = {Bae, J and Kim, SM and Lee, SB},
title = {Identification and characterization of 2-keto-3-deoxy-L-rhamnonate dehydrogenase belonging to the MDR superfamily from the thermoacidophilic bacterium Sulfobacillus thermosulfidooxidans: implications to L-rhamnose metabolism in archaea.},
journal = {Extremophiles : life under extreme conditions},
volume = {19},
number = {2},
pages = {469-478},
doi = {10.1007/s00792-015-0731-8},
pmid = {25617114},
issn = {1433-4909},
mesh = {Archaea/enzymology/*metabolism ; Archaeal Proteins/chemistry/genetics/metabolism ; Bacillales/*enzymology/metabolism ; Bacterial Proteins/chemistry/genetics/*metabolism ; Carbohydrate Dehydrogenases/chemistry/genetics/*metabolism ; Phylogeny ; Protein Binding ; Rhamnose/*metabolism ; },
abstract = {We identified the non-phosphorylated L-rhamnose metabolic pathway (Rha_NMP) genes that are homologous to those in the thermoacidophilic archaeon Thermoplasma acidophilum in the genome of the thermoacidophilic bacterium Sulfobacillus thermosulfidooxidans. However, unlike previously known 2-keto-3-deoxy-L-rhamnonate (L-KDR) dehydrogenase (KDRDH) which belongs to the short chain dehydrogenase/reductase superfamily, the putative KDRDHs in S. thermosulfidooxidans (Sulth_3557) and T. acidophilum (Ta0749) belong to the medium chain dehydrogenase/reductase (MDR) superfamily. We demonstrated that Sulth_3559 and Sulth_3557 proteins from S. thermosulfidooxidans function as L-rhamnose dehydrogenase and KDRDH, respectively. Sulth_3557 protein is an NAD(+)-specific KDRDH with optimal temperature and pH of 50 °C and 9.5, respectively. The K m and V max values for L-KDR were 2.0 mM and 12.8 U/mg, respectively. Sulth_3557 also showed weak 2,3-butanediol dehydrogenase activity. Phylogenetic analysis suggests that Sulth_3557 and its homologs form a new subfamily in the MDR superfamily. The results shown in this study imply that thermoacidophilic archaea metabolize L-rhamnose to pyruvate and L-lactate by using the MDR-family KDRDH similarly to that of the thermoacidophilic bacterium S. thermosulfidooxidans.},
}
@article {pmid25605423,
year = {2015},
author = {Lee, SH and Kim, SY and Ding, W and Kang, H},
title = {Impact of elevated CO₂ and N addition on bacteria, fungi, and archaea in a marsh ecosystem with various types of plants.},
journal = {Applied microbiology and biotechnology},
volume = {99},
number = {12},
pages = {5295-5305},
doi = {10.1007/s00253-015-6385-8},
pmid = {25605423},
issn = {1432-0614},
mesh = {Archaea/classification/genetics/isolation &amp; purification/*metabolism ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Biodiversity ; Carbon Dioxide/*metabolism ; Ecosystem ; Fungi/classification/genetics/isolation &amp; purification/*metabolism ; Nitrogen/*metabolism ; Plants/classification/*metabolism ; Soil Microbiology ; Wetlands ; },
abstract = {The individual effects of either elevated CO2 or N deposition on soil microbial communities have been widely studied, but limited information is available regarding the responses of the bacteria, fungi, and archaea communities to both elevated CO2 and N in wetland ecosystems with different types of plants. Using a terminal restriction fragment length polymorphism (T-RFLP) analysis and real-time quantitative PCR (RT-Q-PCR), we compared communities of bacteria, fungi, and archaea in a marsh microcosm with one of seven macrophytes, Typha latifolia, Phragmites japonica, Miscanthus sacchariflorus, Scirpus lacustris, Juncus effusus, Phragmites australis, or Zizania latifolia, after exposing them to eCO2 and/or amended N for 110 days. Overall, our results showed that the elevated CO2 and N may affect the bacterial and archaeal communities, while they may not affect the fungal community in terms of both diversity and abundance. The effects of elevated CO2 and N on microbial community vary depending on the plant types, and each microbial community shows different responses to the elevated CO2 and N. In particular, elevated CO2 might force a shift in the archaeal community irrespective of the plant type, and the effect of elevated CO2 was enhanced when combined with the N effect. This study indicates that elevated CO2 and N addition could lead to changes in the community structures of bacteria and archaea. Our results also suggest that the fungal group is less sensitive to external changes, while the bacterial and archaeal groups are more sensitive to them. Finally, the characteristics of the plant type and relevant physicochemical factors induced by the elevated CO2 and N may be important key factors structuring the microbial community's response to environmental change, which implies the need for a more comprehensive approach to understanding the pattern of the wetland response to climate change.},
}
@article {pmid25604335,
year = {2015},
author = {Jabłoński, S and Rodowicz, P and Łukaszewicz, M},
title = {Methanogenic archaea database containing physiological and biochemical characteristics.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {65},
number = {Pt 4},
pages = {1360-1368},
doi = {10.1099/ijs.0.000065},
pmid = {25604335},
issn = {1466-5034},
mesh = {Anaerobiosis ; Archaea/*classification/growth &amp; development/metabolism ; Base Composition ; Carbon Cycle ; *Databases, Factual ; Ecosystem ; Methane/biosynthesis ; Methanosarcina/metabolism ; RNA, Ribosomal, 16S/genetics ; Temperature ; },
abstract = {The methanogenic archaea are a group of micro-organisms that have developed a unique metabolic pathway for obtaining energy. There are 150 characterized species in this group; however, novel species continue to be discovered. Since methanogens are considered a crucial part of the carbon cycle in the anaerobic ecosystem, characterization of these micro-organisms is important for understanding anaerobic ecology. A methanogens database (MDB; http://metanogen.biotech.uni.wroc.pl/), including physiological and biochemical characteristics of methanogens, was constructed based on the descriptions of isolated type strains. Analysis of the data revealed that methanogens are able to grow from 0 to 122 °C. Methanogens growing at the same temperature may have very different growth rates. There is no clear correlation between the optimal growth temperature and the DNA G+C content. The following substrate preferences are observed in the database: 74.5% of archaea species utilize H2+CO2, 33% utilize methyl compounds and 8.5% utilize acetate. Utilization of methyl compounds (mainly micro-organisms belonging to the genera Methanosarcina and Methanolobus) is seldom accompanied by an ability to utilize H2+CO2. Very often, data for described species are incomplete, especially substrate preferences. Additional research leading to completion of missing information and development of standards, especially for substrate utilization, would be very helpful.},
}
@article {pmid25586577,
year = {2015},
author = {Zhang, Y and Chen, L and Sun, R and Dai, T and Tian, J and Wen, D},
title = {Ammonia-oxidizing bacteria and archaea in wastewater treatment plant sludge and nearby coastal sediment in an industrial area in China.},
journal = {Applied microbiology and biotechnology},
volume = {99},
number = {10},
pages = {4495-4507},
doi = {10.1007/s00253-014-6352-9},
pmid = {25586577},
issn = {1432-0614},
mesh = {Ammonia/*metabolism ; Archaea/classification/genetics/isolation &amp; purification/*metabolism ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Biodiversity ; China ; Geologic Sediments/*microbiology ; Industrial Waste/analysis ; Molecular Sequence Data ; Phylogeny ; Sewage/*microbiology ; Waste Water/chemistry ; Water Purification/instrumentation ; },
abstract = {Under the increasing pressure of human activities, Hangzhou Bay has become one of the most seriously polluted waters along China's coast. Considering the excessive inorganic nitrogen detected in the bay, in this study, the impact of an effluent from a coastal industrial park on ammonia-oxidizing microorganisms (AOMs) of the receiving area was interpreted for the first time by molecular technologies. Revealed by real-time PCR, the ratio of archaeal amoA/bacterial amoA ranged from 5.68 × 10(-6) to 4.79 × 10(-5) in the activated sludge from two wastewater treatment plants (WWTPs) and 0.54-3.44 in the sediments from the effluent receiving coastal area. Analyzed by clone and pyrosequencing libraries, genus Nitrosomonas was the predominant ammonia-oxidizing bacteria (AOB), but no ammonia-oxidizing archaea (AOA) was abundant enough for sequencing in the activated sludge from the WWTPs; genus Nitrosomonas and Nitrosopumilus were the dominant AOB and AOA, respectively, in the coastal sediments. The different abundance of AOA but similar structure of AOB between the WWTPs and nearby coastal area probably indicated an anthropogenic impact on the microbial ecology in Hangzhou Bay.},
}
@article {pmid25585508,
year = {2015},
author = {Randau, L},
title = {Evolution of small guide RNA genes in hyperthermophilic archaea.},
journal = {Annals of the New York Academy of Sciences},
volume = {1341},
number = {},
pages = {188-193},
doi = {10.1111/nyas.12643},
pmid = {25585508},
issn = {1749-6632},
mesh = {Archaea/*genetics ; Base Sequence ; *Evolution, Molecular ; Gene Expression Regulation, Archaeal ; Genome, Archaeal/genetics ; Hot Temperature ; Models, Genetic ; RNA, Archaeal/*genetics/metabolism ; RNA, Guide/*genetics/metabolism ; },
abstract = {Profiling the RNA production in hyperthermophilic archaea revealed an abundance of small RNA-guided processes near the upper temperature limit of life. Archaea utilize the base-pairing ability of RNA guide sequences to target ribosomal RNAs, transfer RNAs, messenger RNAs, and viral genomes. Cellular processes that are guided by small RNAs include the modification of RNA molecules, trans-splicing, gene regulation, and RNA and DNA degradation. Here, a brief overview of our knowledge on small guide RNA genes in archaeal genomes is provided and examples of their putative roles in genome evolution are described.},
}
@article {pmid25583072,
year = {2015},
author = {Makarova, KS and Galperin, MY and Koonin, EV},
title = {Comparative genomic analysis of evolutionarily conserved but functionally uncharacterized membrane proteins in archaea: Prediction of novel components of secretion, membrane remodeling and glycosylation systems.},
journal = {Biochimie},
volume = {118},
number = {},
pages = {302-312},
doi = {10.1016/j.biochi.2015.01.004},
pmid = {25583072},
issn = {1638-6183},
support = {Z01 LM000061-15/NULL/Intramural NIH HHS/United States ; //Intramural NIH HHS/United States ; },
mesh = {Archaea/*physiology ; Archaeal Proteins/*metabolism ; *Biological Evolution ; Comparative Genomic Hybridization ; Computer Simulation ; Conserved Sequence ; Evolution, Molecular ; Genes, Archaeal/*genetics ; Glycosylation ; Membrane Proteins/*metabolism ; Phylogeny ; Protein Conformation ; },
abstract = {A systematic comparative genomic analysis of all archaeal membrane proteins that have been projected to the last archaeal common ancestor gene set led to the identification of several novel components of predicted secretion, membrane remodeling, and protein glycosylation systems. Among other findings, most crenarchaea have been shown to encode highly diverged orthologs of the membrane insertase YidC, which is nearly universal in bacteria, eukaryotes, and euryarchaea. We also identified a vast family of archaeal proteins, including the C-terminal domain of N-glycosylation protein AglD, as membrane flippases homologous to the flippase domain of bacterial multipeptide resistance factor MprF, a bifunctional lysylphosphatidylglycerol synthase and flippase. Additionally, several proteins were predicted to function as membrane transporters. The results of this work, combined with our previous analyses, reveal an unexpected diversity of putative archaeal membrane-associated functional systems that remain to be functionally characterized. A more general conclusion from this work is that the currently available collection of archaeal (and bacterial) genomes could be sufficient to identify (almost) all widespread functional modules and develop experimentally testable predictions of their functions.},
}
@article {pmid25581459,
year = {2015},
author = {Briegel, A and Ortega, DR and Huang, AN and Oikonomou, CM and Gunsalus, RP and Jensen, GJ},
title = {Structural conservation of chemotaxis machinery across Archaea and Bacteria.},
journal = {Environmental microbiology reports},
volume = {7},
number = {3},
pages = {414-419},
doi = {10.1111/1758-2229.12265},
pmid = {25581459},
issn = {1758-2229},
support = {R01 GM101425/GM/NIGMS NIH HHS/United States ; GM101425/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/*genetics/*physiology ; Bacteria/*genetics ; *Bacterial Physiological Phenomena ; *Chemotaxis ; Conserved Sequence ; Evolution, Molecular ; *Gene Regulatory Networks ; },
abstract = {Chemotaxis allows cells to sense and respond to their environment. In Bacteria, stimuli are detected by arrays of chemoreceptors that relay the signal to a two-component regulatory system. These arrays take the form of highly stereotyped super-lattices comprising hexagonally packed trimers-of-receptor-dimers networked by rings of histidine kinase and coupling proteins. This structure is conserved across chemotactic Bacteria, and between membrane-bound and cytoplasmic arrays, and gives rise to the highly cooperative, dynamic nature of the signalling system. The chemotaxis system, absent in eukaryotes, is also found in Archaea, where its structural details remain uncharacterized. Here we provide evidence that the chemotaxis machinery was not present in the last archaeal common ancestor, but rather was introduced in one of the waves of lateral gene transfer that occurred after the branching of Eukaryota but before the diversification of Euryarchaeota. Unlike in Bacteria, the chemotaxis system then evolved largely vertically in Archaea, with very few subsequent successful lateral gene transfer events. By electron cryotomography, we find that the structure of both membrane-bound and cytoplasmic chemoreceptor arrays is conserved between Bacteria and Archaea, suggesting the fundamental importance of this signalling architecture across diverse prokaryotic lifestyles.},
}
@article {pmid25581373,
year = {2015},
author = {Lagostina, L and Goldhammer, T and Røy, H and Evans, TW and Lever, MA and Jørgensen, BB and Petersen, DG and Schramm, A and Schreiber, L},
title = {Ammonia-oxidizing Bacteria of the Nitrosospira cluster 1 dominate over ammonia-oxidizing Archaea in oligotrophic surface sediments near the South Atlantic Gyre.},
journal = {Environmental microbiology reports},
volume = {7},
number = {3},
pages = {404-413},
doi = {10.1111/1758-2229.12264},
pmid = {25581373},
issn = {1758-2229},
support = {294200//European Research Council/International ; },
mesh = {Ammonia/*metabolism ; Archaea/*isolation &amp; purification/*metabolism ; Atlantic Ocean ; Bacteria/*isolation &amp; purification/*metabolism ; *Biodiversity ; Cluster Analysis ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/genetics ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology ; },
abstract = {Sediments across the Namibian continental margin feature a strong microbial activity gradient at their surface. This is reflected in ammonium concentrations of < 10 μM in oligotrophic abyssal plain sediments near the South Atlantic Gyre compared with ammonium concentrations of > 700 μM in upwelling areas near the coast. Here we address changes in apparent abundance and structure of ammonia-oxidizing archaeal and bacterial communities (AOA and AOB) along a transect of seven sediment stations across the Namibian shelf by analysing their respective ammonia monooxygenase genes (amoA). The relative abundance of archaeal and bacterial amoA (g(-1) DNA) decreased with increasing ammonium concentrations, and bacterial amoA frequently outnumbered archaeal amoA at the sediment-water interface [0-1 cm below seafloor (cmbsf)]. In contrast, AOA were apparently as abundant as AOB or dominated in several deeper (> 10 cmbsf), anoxic sediment layers. Phylogenetic analyses showed a change within the AOA community along the transect, from two clusters without cultured representatives at the gyre to Nitrososphaera and Nitrosopumilus clusters in the upwelling region. AOB almost exclusively belonged to the Nitrosospira cluster 1. Our results suggest that this predominantly marine AOB lineage without cultured representatives can thrive at low ammonium concentrations and is active in the marine nitrogen cycle.},
}
@article {pmid25569531,
year = {2015},
author = {Tonner, PD and Pittman, AM and Gulli, JG and Sharma, K and Schmid, AK},
title = {A regulatory hierarchy controls the dynamic transcriptional response to extreme oxidative stress in archaea.},
journal = {PLoS genetics},
volume = {11},
number = {1},
pages = {e1004912},
doi = {10.1371/journal.pgen.1004912},
pmid = {25569531},
issn = {1553-7404},
mesh = {Archaea/genetics/physiology ; DNA-Binding Proteins/*genetics ; Gene Expression Regulation, Bacterial ; *Gene Regulatory Networks ; Nucleotide Motifs/genetics ; Oxidative Stress/*genetics ; Transcription Factor TFIIB/*genetics ; },
abstract = {Networks of interacting transcription factors are central to the regulation of cellular responses to abiotic stress. Although the architecture of many such networks has been mapped, their dynamic function remains unclear. Here we address this challenge in archaea, microorganisms possessing transcription factors that resemble those of both eukaryotes and bacteria. Using genome-wide DNA binding location analysis integrated with gene expression and cell physiological data, we demonstrate that a bacterial-type transcription factor (TF), called RosR, and five TFIIB proteins, homologs of eukaryotic TFs, combinatorially regulate over 100 target genes important for the response to extremely high levels of peroxide. These genes include 20 other transcription factors and oxidative damage repair genes. RosR promoter occupancy is surprisingly dynamic, with the pattern of target gene expression during the transition from rapid growth to stress correlating strongly with the pattern of dynamic binding. We conclude that a hierarchical regulatory network orchestrated by TFs of hybrid lineage enables dynamic response and survival under extreme stress in archaea. This raises questions regarding the evolutionary trajectory of gene networks in response to stress.},
}
@article {pmid25561057,
year = {2015},
author = {Dong, J and Ding, L and Wang, X and Chi, Z and Lei, J},
title = {Vertical profiles of community abundance and diversity of anaerobic methanotrophic archaea (ANME) and bacteria in a simple waste landfill in north China.},
journal = {Applied biochemistry and biotechnology},
volume = {175},
number = {5},
pages = {2729-2740},
doi = {10.1007/s12010-014-1456-3},
pmid = {25561057},
issn = {1559-0291},
mesh = {Archaea/classification/genetics/*isolation &amp; purification/*metabolism ; Autotrophic Processes ; Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; *Biodiversity ; China ; Geologic Sediments/*microbiology ; Methane/*metabolism ; Molecular Sequence Data ; Phylogeny ; Soil Microbiology ; Waste Disposal Facilities ; },
abstract = {Anaerobic methane oxidation (AMO) is considered to be an important sink of CH4 in habitats as marine sediments. But, few studies focused on AMO in landfills which may be an important sink of CH4 derived from waste fermentation. To show evidence of AMO and to uncover function anaerobic methanotroph (ANME) community in landfill, different age waste samples were collected in Jinqianpu landfill located in north China. Through high-throughput sequencing, Methanomicrobiales and Methanosarcinales archaea associated with ANME and reverse methanogenic archaea of Methanosarcina and Methanobacterium were detected. Sulfate-reducing bacteria (SRB) (Desulfobulbus and Desulfococcus) which could couple with ANME-conducting AMO were also found. But, the community structure of ANME had no significant difference with depths. From the results of investigation, we can come to a conclusion that sulfate-dependent anaerobic methane oxidation (SR-DAMO) would be the dominant AMO process in the landfill, while iron-dependent anaerobic methane oxidation (M/IR-DAMO) process was weak though concentration of ferric iron was large in the landfill. Denitrification-dependent anaerobic methane oxidation (NR-DAMO) was negative because of lack of nitrate and relevant function microorganisms in the landfill. Results also indicate that CH4 mitigation would have higher potential by increasing electron acceptor contents and promoting the growth of relevant function microorganisms.},
}
@article {pmid25560263,
year = {2015},
author = {Sinthusith, N and Terada, A and Hahn, M and Noophan, PL and Munakata-Marr, J and Figueroa, LA},
title = {Identification and quantification of bacteria and archaea responsible for ammonia oxidation in different activated sludge of full-scale wastewater treatment plants.},
journal = {Journal of environmental science and health. Part A, Toxic/hazardous substances &amp; environmental engineering},
volume = {50},
number = {2},
pages = {169-175},
doi = {10.1080/10934529.2014.975535},
pmid = {25560263},
issn = {1532-4117},
mesh = {Ammonia/*metabolism ; Archaea/classification/*isolation &amp; purification/*metabolism ; Bacteria/classification/isolation &amp; purification/*metabolism ; Bacterial Load ; Biota ; Japan ; Oxidation-Reduction ; Sewage/*microbiology ; Thailand ; United States ; Waste Disposal, Fluid/*methods ; },
abstract = {In this study, the abundance and sequences of the amoA gene in ammonia oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA) were defined in three wastewater treatment plants using activated sludge with biological nitrogen removal in different countries: Thailand, United States of America (USA), and Japan. Quantitative real-time polymerase chain reaction (PCR) and PCR coupled with denaturing gradient gel electrophoresis were used to find the comparative abundance and identity of AOB and AOA. The conditions at the Phuket WWTP in Thailand promoted the dominance of AOA amoA genes over AOB amoA genes, while conditions at the WWTPs in Japan and USA promoted growth of AOB. Three parameters that may have contributed to the AOA dominance in Phuket were longer SRT, higher temperature, and higher pH. The Phuket WWTP is a unique system that can be used to better understand the conditions that promote AOA growth and dominance over AOB. In addition, analysis of operational data in conjunction with AOA and AOB community structure from the Phuket WWTP may elucidate advantages of AOA in meeting stricter treatment standards.},
}
@article {pmid25534249,
year = {2015},
author = {Meinhardt, KA and Bertagnolli, A and Pannu, MW and Strand, SE and Brown, SL and Stahl, DA},
title = {Evaluation of revised polymerase chain reaction primers for more inclusive quantification of ammonia-oxidizing archaea and bacteria.},
journal = {Environmental microbiology reports},
volume = {7},
number = {2},
pages = {354-363},
doi = {10.1111/1758-2229.12259},
pmid = {25534249},
issn = {1758-2229},
mesh = {Ammonia/*metabolism ; Archaea/*classification/enzymology/*isolation &amp; purification/metabolism ; Bacteria/*classification/enzymology/*isolation &amp; purification/metabolism ; DNA Primers/genetics ; Microbiological Techniques/methods ; Oxidation-Reduction ; Oxidoreductases/*genetics ; Real-Time Polymerase Chain Reaction/*methods ; },
abstract = {Ammonia-oxidizing archaea (AOA) and bacteria (AOB) fill key roles in the nitrogen cycle. Thus, well-vetted methods for characterizing their distribution are essential for framing studies of their significance in natural and managed systems. Quantification of the gene coding for one subunit of the ammonia monooxygenase (amoA) by polymerase chain reaction is frequently employed to enumerate the two groups. However, variable amplification of sequence variants comprising this conserved genetic marker for ammonia oxidizers potentially compromises within- and between-system comparisons. We compared the performance of newly designed non-degenerate quantitative polymerase chain reaction primer sets to existing primer sets commonly used to quantify the amoA of AOA and AOB using a collection of plasmids and soil DNA samples. The new AOA primer set provided improved quantification of model mixtures of different amoA sequence variants and increased detection of amoA in DNA recovered from soils. Although both primer sets for the AOB provided similar results for many comparisons, the new primers demonstrated increased detection in environmental application. Thus, the new primer sets should provide a useful complement to primers now commonly used to characterize the environmental distribution of AOA and AOB.},
}
@article {pmid25527841,
year = {2014},
author = {Petitjean, C and Deschamps, P and López-García, P and Moreira, D},
title = {Rooting the domain archaea by phylogenomic analysis supports the foundation of the new kingdom Proteoarchaeota.},
journal = {Genome biology and evolution},
volume = {7},
number = {1},
pages = {191-204},
doi = {10.1093/gbe/evu274},
pmid = {25527841},
issn = {1759-6653},
mesh = {Archaea/*genetics ; Archaeal Proteins/genetics ; *Evolution, Molecular ; Genome, Archaeal ; *Genomics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The first 16S rRNA-based phylogenies of the Archaea showed a deep division between two groups, the kingdoms Euryarchaeota and Crenarchaeota. This bipartite classification has been challenged by the recent discovery of new deeply branching lineages (e.g., Thaumarchaeota, Aigarchaeota, Nanoarchaeota, Korarchaeota, Parvarchaeota, Aenigmarchaeota, Diapherotrites, and Nanohaloarchaeota) which have also been given the same taxonomic status of kingdoms. However, the phylogenetic position of some of these lineages is controversial. In addition, phylogenetic analyses of the Archaea have often been carried out without outgroup sequences, making it difficult to determine if these taxa actually define lineages at the same level as the Euryarchaeota and Crenarchaeota. We have addressed the question of the position of the root of the Archaea by reconstructing rooted archaeal phylogenetic trees using bacterial sequences as outgroup. These trees were based on commonly used conserved protein markers (32 ribosomal proteins) as well as on 38 new markers identified through phylogenomic analysis. We thus gathered a total of 70 conserved markers that we analyzed as a concatenated data set. In contrast with previous analyses, our trees consistently placed the root of the archaeal tree between the Euryarchaeota (including the Nanoarchaeota and other fast-evolving lineages) and the rest of archaeal species, which we propose to class within the new kingdom Proteoarchaeota. This implies the relegation of several groups previously classified as kingdoms (e.g., Crenarchaeota, Thaumarchaeota, Aigarchaeota, and Korarchaeota) to a lower taxonomic rank. In addition to taxonomic implications, this profound reorganization of the archaeal phylogeny has also consequences on our appraisal of the nature of the last archaeal ancestor, which most likely was a complex organism with a gene-rich genome.},
}
@article {pmid25527539,
year = {2015},
author = {Lever, MA and Teske, AP},
title = {Diversity of methane-cycling archaea in hydrothermal sediment investigated by general and group-specific PCR primers.},
journal = {Applied and environmental microbiology},
volume = {81},
number = {4},
pages = {1426-1441},
doi = {10.1128/AEM.03588-14},
pmid = {25527539},
issn = {1098-5336},
mesh = {Archaea/classification/genetics/*isolation &amp; purification/*metabolism ; Biodiversity ; DNA Primers/genetics ; Geologic Sediments/chemistry/*microbiology ; Methane/*metabolism ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Species Specificity ; },
abstract = {The zonation of anaerobic methane-cycling Archaea in hydrothermal sediment of Guaymas Basin was studied by general primerpairs (mcrI, ME1/ME2, mcrIRD) targeting the alpha subunit of methyl coenzyme M reductase gene (mcrA) and by new group specific mcrA and 16S rRNA gene primer pairs. The mcrIRD primer pair outperformed the other general mcrA primer pairs indetection sensitivity and phylogenetic coverage. Methanotrophic ANME-1 Archaea were the only group detected with group specific primers only. The detection of 14 mcrA lineages surpasses the diversity previously found in this location. Most phylotypes have high sequence similarities to hydrogenotrophs, methylotrophs, and anaerobic methanotrophs previously detected at Guaymas Basin or at hydrothermal vents, cold seeps, and oil reservoirs worldwide. Additionally, five mcrA phylotypes belonging to newly defined lineages are detected. Two of these belong to deeply branching new orders, while the others are new species or genera of Methanopyraceae and Methermicoccaceae. Downcore diversity decreases from all groups detected in the upper 6 cm(2 to 40 °C, sulfate measurable to 4 cm) to only two groups below 6 cm (>40 °C). Despite the presence of hyperthermophilic genera (Methanopyrus, Methanocaldococcus) in cooler surface strata, no genes were detected below 10 cm (>60 °C). While mcrAbased and 16S rRNA gene-based community compositions are generally congruent, the deeply branching mcrA cannot be assigned to specific 16S rRNA gene lineages. Our study indicates that even among well-studied metabolic groups and in previously characterized model environments, major evolutionary branches are overlooked. Detecting these groups by improved molecular biological methods is a crucial first step toward understanding their roles in nature.},
}
@article {pmid25525409,
year = {2014},
author = {Wei, S and Cui, H and He, H and Hu, F and Su, X and Zhu, Y},
title = {Diversity and distribution of archaea community along a stratigraphic permafrost profile from Qinghai-Tibetan Plateau, China.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2014},
number = {},
pages = {240817},
doi = {10.1155/2014/240817},
pmid = {25525409},
issn = {1472-3654},
mesh = {*Biota ; Cluster Analysis ; Crenarchaeota/*classification/genetics/*isolation &amp; purification ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Denaturing Gradient Gel Electrophoresis ; Euryarchaeota/*classification/genetics/*isolation &amp; purification ; Molecular Sequence Data ; Permafrost/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Tibet ; },
abstract = {Accompanying the thawing permafrost expected to result from the climate change, microbial decomposition of the massive amounts of frozen organic carbon stored in permafrost is a potential emission source of greenhouse gases, possibly leading to positive feedbacks to the greenhouse effect. In this study, the community composition of archaea in stratigraphic soils from an alpine permafrost of Qinghai-Tibetan Plateau was investigated. Phylogenic analysis of 16S rRNA sequences revealed that the community was predominantly constituted by Crenarchaeota and Euryarchaeota. The active layer contained a proportion of Crenarchaeota at 51.2%, with the proportion of Euryarchaeota at 48.8%, whereas the permafrost contained 41.2% Crenarchaeota and 58.8% Euryarchaeota, based on 16S rRNA gene sequence analysis. OTU1 and OTU11, affiliated to Group 1.3b/MCG-A within Crenarchaeota and the unclassified group within Euryarchaeota, respectively, were widely distributed in all sediment layers. However, OTU5 affiliated to Group 1.3b/MCG-A was primarily distributed in the active layers. Sequence analysis of the DGGE bands from the 16S rRNAs of methanogenic archaea showed that the majority of methanogens belonged to Methanosarcinales and Methanomicrobiales affiliated to Euryarchaeota and the uncultured ZC-I cluster affiliated to Methanosarcinales distributed in all the depths along the permafrost profile, which indicated a dominant group of methanogens occurring in the cold ecosystems.},
}
@article {pmid25522598,
year = {2014},
author = {Zheng, Y and Wang, X and Gu, Y and Zhang, X},
title = {[Diversity of ammonia-oxidizing archaea in Tibetan Zoige plateau wetland ].},
journal = {Wei sheng wu xue bao = Acta microbiologica Sinica},
volume = {54},
number = {9},
pages = {1090-1096},
pmid = {25522598},
issn = {0001-6209},
mesh = {Ammonia/*metabolism ; Archaea/classification/genetics/*isolation &amp; purification/*metabolism ; *Biodiversity ; Ecosystem ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; Soil/chemistry ; *Soil Microbiology ; Tibet ; },
abstract = {[ OBJECTIVE ] Investigation of ammonia-oxidizing archaea (AOA) in nature environments is important to understand the global nitrogen cycling. However, little is known about the AOA community in plateau wetland. Therefore, we studied the composition and diversity of AOA in Zoige plateau wetland swamp soil. [METHODS] Total DNA was extracted from the swamp soil of three typical wetlands including A'xi pastoral area, Maixi pastoral area and Fenqu pastoral area locate in Zoige plateau wetland, and amoA gene was amplified with universally AOA amoA gene primers and then cloned. Then 80 positive clones for each clone library were chosen for further restriction fragment length polymorphism (RFLP) analysis, and the typical RFLP types were selected for sequencing and clustered into operational taxonomic units (OTUs) at 98% cutoff using the Mothur software. The MEGA 5. 0 software was used for the amoA gene phylogeny analysis. [RESULTS] A total of 240 positive clones for all 3 libraries were used for RFLP analysis, and 15 specific amoA sequences were sequenced and clustered into 7 OTUs at 98% cutoff. Among them, OTU6 was detected in all of the 3 libraries and included 27% of the total specific clones. The phylogeny analysis showed that the 15 amoA sequences were grouped into 3 subgroups consisted of Zoige Wetland Clade 1 (4 OTUs), Zoige Wetland Clade 2 (2 OTUs) and Zoige Wetland Clade 3 (1 OTU). BLAST analysis showed that all OTUs were affiliated with the phylum Crenarchaeota. Correlation analysis showed that the Shannon diversity index (H') was significantly correlated with ammonia, nitrate/nitrite (P <0. 05). [ CONCLUSION] AOA in the Zoige plateau wetland swamp soil are all belonged to the Crenarchaeota, and their diversity is significantly correlated with soil ammonia, nitrate/nitrite content.},
}
@article {pmid25522589,
year = {2014},
author = {Wul, J and Cai, S and Liu, H and Hou, J and Han, J and Zhou, J and Hua, X},
title = {[Development of PhaP-tagged protein expression and purification systems for extremely halophilic archaea ].},
journal = {Wei sheng wu xue bao = Acta microbiologica Sinica},
volume = {54},
number = {9},
pages = {998-1009},
pmid = {25522589},
issn = {0001-6209},
mesh = {Amino Acid Sequence ; Archaeal Proteins/*genetics/isolation &amp; purification/metabolism ; Bacterial Proteins/*genetics/isolation &amp; purification/metabolism ; Chromatography, Affinity ; Cloning, Molecular ; DNA-Binding Proteins/*genetics/isolation &amp; purification/metabolism ; Genetic Vectors/genetics/metabolism ; Haloferax mediterranei/genetics/*metabolism ; Mutagenesis, Site-Directed ; Polyhydroxyalkanoates/biosynthesis ; Recombinant Fusion Proteins/chemistry/*genetics/*isolation &amp; purification ; Sodium Chloride/*metabolism ; },
abstract = {[ OBJECTIVE] To establish a convenient halophilic protein expression and purification system based on the haloarchaeal-type PhaP and polyhydroxyalkanoate (PHA) granule. [METHODS] We cloned a strong haloarchaeal promoter and the phaP-tag into the haloarchaea- Escherichia coli shuttle vector pWL502, and then used the constructed vector to express the PhaP-tagged haloarchaeal proteins in the phaP-deleted strain Haloferax mediterranei AphaP. We purified the PhaP-fusion proteins, which were associated with PHA granules, by sucrose density gradient centrifugation. We also inserted a haloarchaeal intein-containing fragment between phaP and multiple cloning sites, and modulated the intein splicing activity by site-directed mutagenesis. [RESULTS] We successfully constructed two expression vectors, pPM and pIP, in which PhaP was used as N-terminal and C-terminal fusion tag, respectively. The haloarchaeal proteins were effectively expressed by both vectors. The PhaP-tagged proteins were easily purified through the strategy of PHA granulemediated protein purification. In addition, we found that the intein-containing fragment Hbt21 from Halobacterium sp. NRC-1 had maintained splicing activity in H. mediterranei, and its C-terminal cleavage could be blocked or attenuated by mutating the conserved asparagine (N182) or serine (S183) , respectively. [ CONCLUSION] We have established a convenient and economical halophilic protein expression and purification system. We have also identified the splicing active sites of a haloarchaeal intein, which showed potential for removing the PhaP-tag from the purified proteins.},
}
@article {pmid25514401,
year = {2015},
author = {Zhang, J and Zhang, Y and Quan, X and Chen, S},
title = {Enhancement of anaerobic acidogenesis by integrating an electrochemical system into an acidogenic reactor: effect of hydraulic retention times (HRT) and role of bacteria and acidophilic methanogenic Archaea.},
journal = {Bioresource technology},
volume = {179},
number = {},
pages = {43-49},
doi = {10.1016/j.biortech.2014.11.102},
pmid = {25514401},
issn = {1873-2976},
mesh = {Acids/chemistry ; Anaerobiosis ; Archaea/*metabolism ; Bacteria/*metabolism ; Biological Oxygen Demand Analysis ; Bioreactors/*microbiology ; Cluster Analysis ; Electrochemistry/*methods ; Electrodes ; Fatty Acids, Volatile/analysis ; Hydrogen-Ion Concentration ; Iron/analysis ; Methane/*metabolism ; Polysaccharides/analysis ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sewage/microbiology ; Time Factors ; Waste Disposal, Fluid ; },
abstract = {In this study, an acidogenic reactor packed with a pair of Fe-carbon electrodes (R1) was developed to enhance anaerobic acidogenesis of organic wastewater at short hydraulic retention times. The results indicated that the acidogenic efficiency was improved by settling a bio-electrochemical system. When hydraulic retention times decreased from 12 to 3h, R1 showed 18.9% more chemical oxygen demand removal and 13.8% more acidification efficiency. After cutting off the voltage of R1, the COD removal decreased by about 5%. Coupling of Fe(2+) leaching and electric field accelerated the hydrolysis of polysaccharide, relieving its accumulation in the sludge phase. Several acidophilic methanogenic Archaea such as Methanosarcina sp. were enriched in R1, which was favorable for consuming organic acids and preventing excessive pH decline. Thus, the developed acidogenic reactor with Fe-carbon electrodes is expected to be potentially effective and useful for wastewater treatment.},
}
@article {pmid25501889,
year = {2015},
author = {Stempfhuber, B and Engel, M and Fischer, D and Neskovic-Prit, G and Wubet, T and Schöning, I and Gubry-Rangin, C and Kublik, S and Schloter-Hai, B and Rattei, T and Welzl, G and Nicol, GW and Schrumpf, M and Buscot, F and Prosser, JI and Schloter, M},
title = {pH as a Driver for Ammonia-Oxidizing Archaea in Forest Soils.},
journal = {Microbial ecology},
volume = {69},
number = {4},
pages = {879-883},
doi = {10.1007/s00248-014-0548-5},
pmid = {25501889},
issn = {1432-184X},
mesh = {Ammonia/*metabolism ; Archaea/*physiology ; *Forests ; Germany ; Hydrogen-Ion Concentration ; *Microbiota ; Oxidation-Reduction ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {In this study, we investigated the impact of soil pH on the diversity and abundance of archaeal ammonia oxidizers in 27 different forest soils across Germany. DNA was extracted from topsoil samples, the amoA gene, encoding ammonia monooxygenase, was amplified; and the amplicons were sequenced using a 454-based pyrosequencing approach. As expected, the ratio of archaeal (AOA) to bacterial (AOB) ammonia oxidizers' amoA genes increased sharply with decreasing soil pH. The diversity of AOA differed significantly between sites with ultra-acidic soil pH (<3.5) and sites with higher pH values. The major OTUs from soil samples with low pH could be detected at each site with a soil pH <3.5 but not at sites with pH >4.5, regardless of geographic position and vegetation. These OTUs could be related to the Nitrosotalea group 1.1 and the Nitrososphaera subcluster 7.2, respectively, and showed significant similarities to OTUs described from other acidic environments. Conversely, none of the major OTUs typical of sites with a soil pH >4.6 could be found in the ultra- and extreme acidic soils. Based on a comparison with the amoA gene sequence data from a previous study performed on agricultural soils, we could clearly show that the development of AOA communities in soils with ultra-acidic pH (<3.5) is mainly triggered by soil pH and is not influenced significantly by the type of land use, the soil type, or the geographic position of the site, which was observed for sites with acido-neutral soil pH.},
}
@article {pmid25501484,
year = {2015},
author = {Timmers, PH and Gieteling, J and Widjaja-Greefkes, HC and Plugge, CM and Stams, AJ and Lens, PN and Meulepas, RJ},
title = {Growth of anaerobic methane-oxidizing archaea and sulfate-reducing bacteria in a high-pressure membrane capsule bioreactor.},
journal = {Applied and environmental microbiology},
volume = {81},
number = {4},
pages = {1286-1296},
doi = {10.1128/AEM.03255-14},
pmid = {25501484},
issn = {1098-5336},
support = {323009//European Research Council/International ; },
mesh = {Archaea/classification/*growth &amp; development/isolation &amp; purification/metabolism ; Bioreactors/*microbiology ; Ecosystem ; Geologic Sediments/microbiology ; Methane/chemistry/*metabolism ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; Pressure ; Sulfates/analysis/metabolism ; Sulfur-Reducing Bacteria/classification/*growth &amp; development/isolation &amp; purification/metabolism ; },
abstract = {Communities of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB) grow slowly, which limits the ability to perform physiological studies. High methane partial pressure was previously successfully applied to stimulate growth, but it is not clear how different ANME subtypes and associated SRB are affected by it. Here, we report on the growth of ANME-SRB in a membrane capsule bioreactor inoculated with Eckernförde Bay sediment that combines high-pressure incubation (10.1 MPa methane) and thorough mixing (100 rpm) with complete cell retention by a 0.2-m-pore-size membrane. The results were compared to previously obtained data from an ambient-pressure (0.101 MPa methane) bioreactor inoculated with the same sediment. The rates of oxidation of labeled methane were not higher at 10.1 MPa, likely because measurements were done at ambient pressure. The subtype ANME-2a/b was abundant in both reactors, but subtype ANME-2c was enriched only at 10.1 MPa. SRB at 10.1 MPa mainly belonged to the SEEP-SRB2 and Eel-1 groups and the Desulfuromonadales and not to the typically found SEEP-SRB1 group. The increase of ANME-2a/b occurred in parallel with the increase of SEEP-SRB2, which was previously found to be associated only with ANME-2c. Our results imply that the syntrophic association is flexible and that methane pressure and sulfide concentration influence the growth of different ANME-SRB consortia. We also studied the effect of elevated methane pressure on methane production and oxidation by a mixture of methanogenic and sulfate-reducing sludge. Here, methane oxidation rates decreased and were not coupled to sulfide production, indicating trace methane oxidation during net methanogenesis and not anaerobic methane oxidation, even at a high methane partial pressure.},
}
@article {pmid25479061,
year = {2014},
author = {Bagchi, S and Vlaeminck, SE and Sauder, LA and Mosquera, M and Neufeld, JD and Boon, N},
title = {Temporal and spatial stability of ammonia-oxidizing archaea and bacteria in aquarium biofilters.},
journal = {PloS one},
volume = {9},
number = {12},
pages = {e113515},
doi = {10.1371/journal.pone.0113515},
pmid = {25479061},
issn = {1932-6203},
mesh = {Ammonia/metabolism ; Archaea/genetics/*metabolism ; Bacteria/metabolism ; Filtration ; Fresh Water/chemistry/*microbiology ; *Oxidation-Reduction ; Oxidoreductases ; RNA, Ribosomal, 16S/*genetics ; Soil Microbiology ; },
abstract = {Nitrifying biofilters are used in aquaria and aquaculture systems to prevent accumulation of ammonia by promoting rapid conversion to nitrate via nitrite. Ammonia-oxidizing archaea (AOA), as opposed to ammonia-oxidizing bacteria (AOB), were recently identified as the dominant ammonia oxidizers in most freshwater aquaria. This study investigated biofilms from fixed-bed aquarium biofilters to assess the temporal and spatial dynamics of AOA and AOB abundance and diversity. Over a period of four months, ammonia-oxidizing microorganisms from six freshwater and one marine aquarium were investigated at 4-5 time points. Nitrogen balances for three freshwater aquaria showed that active nitrification by aquarium biofilters accounted for ≥ 81-86% of total nitrogen conversion in the aquaria. Quantitative PCR (qPCR) for bacterial and thaumarchaeal ammonia monooxygenase (amoA) genes demonstrated that AOA were numerically dominant over AOB in all six freshwater aquaria tested, and contributed all detectable amoA genes in three aquarium biofilters. In the marine aquarium, however, AOB outnumbered AOA by three to five orders of magnitude based on amoA gene abundances. A comparison of AOA abundance in three carrier materials (fine sponge, rough sponge and sintered glass or ceramic rings) of two three-media freshwater biofilters revealed preferential growth of AOA on fine sponge. Denaturing gel gradient electrophoresis (DGGE) of thaumarchaeal 16S rRNA genes indicated that community composition within a given biofilter was stable across media types. In addition, DGGE of all aquarium biofilters revealed low AOA diversity, with few bands, which were stable over time. Nonmetric multidimensional scaling (NMDS) based on denaturing gradient gel electrophoresis (DGGE) fingerprints of thaumarchaeal 16S rRNA genes placed freshwater and marine aquaria communities in separate clusters. These results indicate that AOA are the dominant ammonia-oxidizing microorganisms in freshwater aquarium biofilters, and that AOA community composition within a given aquarium is stable over time and across biofilter support material types.},
}
@article {pmid25473158,
year = {2014},
author = {Gaci, N and Borrel, G and Tottey, W and O'Toole, PW and Brugère, JF},
title = {Archaea and the human gut: new beginning of an old story.},
journal = {World journal of gastroenterology},
volume = {20},
number = {43},
pages = {16062-16078},
doi = {10.3748/wjg.v20.i43.16062},
pmid = {25473158},
issn = {2219-2840},
mesh = {Breath Tests ; Disease ; Euryarchaeota/classification/genetics/growth &amp; development/*metabolism ; Evolution, Molecular ; Gastrointestinal Tract/metabolism/*physiology ; Host-Pathogen Interactions ; Humans ; Methane/*metabolism ; *Microbiota ; Phylogeny ; },
abstract = {Methanogenic archaea are known as human gut inhabitants since more than 30 years ago through the detection of methane in the breath and isolation of two methanogenic species belonging to the order Methanobacteriales, Methanobrevibacter smithii and Methanosphaera stadtmanae. During the last decade, diversity of archaea encountered in the human gastrointestinal tract (GIT) has been extended by sequence identification and culturing of new strains. Here we provide an updated census of the archaeal diversity associated with the human GIT and their possible role in the gut physiology and health. We particularly focus on the still poorly characterized 7th order of methanogens, the Methanomassiliicoccales, associated to aged population. While also largely distributed in non-GIT environments, our actual knowledge on this novel order of methanogens has been mainly revealed through GIT inhabitants. They enlarge the number of final electron acceptors of the gut metabolites to mono- di- and trimethylamine. Trimethylamine is exclusively a microbiota-derived product of nutrients (lecithin, choline, TMAO, L-carnitine) from normal diet, from which seems originate two diseases, trimethylaminuria (or Fish-Odor Syndrome) and cardiovascular disease through the proatherogenic property of its oxidized liver-derived form. This therefore supports interest on these methanogenic species and its use as archaebiotics, a term coined from the notion of archaea-derived probiotics.},
}
@article {pmid25472601,
year = {2015},
author = {Hugoni, M and Domaizon, I and Taib, N and Biderre-Petit, C and Agogué, H and Galand, PE and Debroas, D and Mary, I},
title = {Temporal dynamics of active Archaea in oxygen-depleted zones of two deep lakes.},
journal = {Environmental microbiology reports},
volume = {7},
number = {2},
pages = {321-329},
doi = {10.1111/1758-2229.12251},
pmid = {25472601},
issn = {1758-2229},
mesh = {Ammonia/analysis ; Archaea/*classification/genetics/*growth &amp; development ; *Biota ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Gene Expression Profiling ; Lakes/*microbiology ; Nitrification ; Oxidoreductases/genetics ; Oxygen/analysis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Spatio-Temporal Analysis ; Water/chemistry ; },
abstract = {Deep lakes are of specific interest in the study of archaeal assemblages as chemical stratification in the water column allows niche differentiation and distinct community structure. Active archaeal community and potential nitrifiers were investigated monthly over 1 year by pyrosequencing 16S rRNA transcripts and genes, and by quantification of archaeal amoA genes in two deep lakes. Our results showed that the active archaeal community patterns of spatial and temporal distribution were different between these lakes. The meromictic lake characterized by a stable redox gradient but variability in nutrient concentrations exhibited large temporal rearrangements of the dominant euryarchaeal phylotypes, suggesting a variety of ecological niches and dynamic archaeal communities in the hypolimnion of this lake. Conversely, Thaumarchaeota Marine Group I (MGI) largely dominated in the second lake where deeper water layers exhibited only short periods of complete anoxia and constant low ammonia concentrations. Investigations conducted on archaeal amoA transcripts abundance suggested that not all lacustrine Thaumarchaeota conduct the process of nitrification. A high number of 16S rRNA transcripts associated to crenarchaeal group C3 or the Miscellaneous Euryarchaeotic Group indicates the potential for these uncharacterized groups to contribute to nutrient cycling in lakes.},
}
@article {pmid25462589,
year = {2014},
author = {Gschwendtner, S and Tejedor, J and Bimüller, C and Dannenmann, M and Kögel-Knabner, I and Schloter, M},
title = {Climate change induces shifts in abundance and activity pattern of bacteria and archaea catalyzing major transformation steps in nitrogen turnover in a soil from a mid-European beech forest.},
journal = {PloS one},
volume = {9},
number = {12},
pages = {e114278},
doi = {10.1371/journal.pone.0114278},
pmid = {25462589},
issn = {1932-6203},
mesh = {Archaea/*metabolism ; Bacteria/*metabolism ; Catalysis ; *Climate Change ; Europe ; Fagus/*metabolism ; Nitrogen/*metabolism ; *Soil ; },
abstract = {Ongoing climate change will lead to more extreme weather events, including severe drought periods and intense drying rewetting cycles. This will directly influence microbial nitrogen (N) turnover rates in soil by changing the water content and the oxygen partial pressure. Therefore, a space for time climate change experiment was conducted by transferring intact beech seedling-soil mesocosms from a northwest (NW) exposed site, representing today's climatic conditions, to a southwest (SW) exposed site, providing a model climate for future conditions with naturally occurring increased soil temperature (+0.8°C in average). In addition, severe drought and intense rainfall was simulated by a rainout shelter at SW and manual rewetting after 39 days drought, respectively. Soil samples were taken in June, at the end of the drought period (August), 24 and 72 hours after rewetting (August) and after a regeneration period of four weeks (September). To follow dynamics of bacterial and archaeal communities involved in N turnover, abundance and activity of nitrifiers, denitrifiers, N2-fixing microbes and N-mineralizers was analyzed based on marker genes and the related transcripts by qPCR from DNA and RNA directly extracted from soil. Abundance of the transcripts was reduced under climate change with most pronounced effects for denitrification. Our results revealed that already a transfer from NW to SW without further treatment resulted in decreased cnor and nosZ transcripts, encoding for nitric oxide reductase and nitrous oxide reductase, respectively, while nirK transcripts, encoding for nitrite reductase, remained unaffected. Severe drought additionally led to reduced nirK and cnor transcripts at SW. After rewetting, nirK transcripts increased rapidly at both sites, while cnor and nosZ transcripts increased only at NW. Our data indicate that the climate change influences activity pattern of microbial communities involved in denitrification processes to a different extend, which may impact emission rates of the greenhouse gas N2O.},
}
@article {pmid25460192,
year = {2015},
author = {Brablcová, L and Buriánková, I and Badurová, P and Chaudhary, PP and Rulík, M},
title = {Methanogenic archaea diversity in hyporheic sediments of a small lowland stream.},
journal = {Anaerobe},
volume = {32},
number = {},
pages = {24-31},
doi = {10.1016/j.anaerobe.2014.11.009},
pmid = {25460192},
issn = {1095-8274},
mesh = {Archaea/classification/*genetics/*metabolism ; *Biodiversity ; Czech Republic ; Denaturing Gradient Gel Electrophoresis ; Environment ; Geologic Sediments/*microbiology ; Methane/*metabolism ; Phylogeny ; *Rivers/microbiology ; Sequence Analysis, DNA ; },
abstract = {Abundance and diversity of methanogenic archaea were studied at five localities along a longitudinal profile of a Sitka stream (Czech Republic). Samples of hyporheic sediments were collected from two sediment depths (0-25 cm and 25-50 cm) by freeze-core method. Methanogen community was analyzed by fluorescence in situ hybridization (FISH), denaturing gradient gel electrophoresis (DGGE) and sequencing method. The proportion of methanogens to the DAPI-stained cells varied among all localities and depths with an average value 2.08 × 10(5) per g of dry sediment with the range from 0.37 to 4.96 × 10(5) cells per g of dry sediment. A total of 73 bands were detected at 19 different positions on the DGGE gel and the highest methanogen diversity was found at the downstream located sites. There was no relationship between methanogen diversity and sediment depth. Cluster analysis of DGGE image showed three main clusters consisting of localities that differed in the number and similarity of the DGGE bands. Sequencing analysis of representative DGGE bands revealed phylotypes affiliated with members belonging to the orders Methanosarcinales, Methanomicrobiales and Methanocellales. The knowledge about occurrence and diversity of methanogenic archaea in freshwater ecosystems are essential for methane dynamics in river sediments and can contribute to the understanding of global warming process.},
}
@article {pmid25427790,
year = {2015},
author = {Mueller, TJ and Grisewood, MJ and Nazem-Bokaee, H and Gopalakrishnan, S and Ferry, JG and Wood, TK and Maranas, CD},
title = {Methane oxidation by anaerobic archaea for conversion to liquid fuels.},
journal = {Journal of industrial microbiology &amp; biotechnology},
volume = {42},
number = {3},
pages = {391-401},
doi = {10.1007/s10295-014-1548-7},
pmid = {25427790},
issn = {1476-5535},
mesh = {Anaerobiosis ; Archaea/*metabolism ; Biofuels/*supply &amp; distribution ; Carbon Cycle ; Carbon Dioxide/metabolism ; Methane/*metabolism ; Oxidation-Reduction ; Oxidoreductases/metabolism ; },
abstract = {Given the recent increases in natural gas reserves and associated drawbacks of current gas-to-liquids technologies, the development of a bioconversion process to directly convert methane to liquid fuels would generate considerable industrial interest. Several clades of anaerobic methanotrophic archaea (ANME) are capable of performing anaerobic oxidation of methane (AOM). AOM carried out by ANME offers carbon efficiency advantages over aerobic oxidation by conserving the entire carbon flux without losing one out of three carbon atoms to carbon dioxide. This review highlights the recent advances in understanding the key enzymes involved in AOM (i.e., methyl-coenzyme M reductase), the ecological niches of a number of ANME, the putative metabolic pathways for AOM, and the syntrophic consortia that they typically form.},
}
@article {pmid25420929,
year = {2015},
author = {Martens-Habbena, W and Qin, W and Horak, RE and Urakawa, H and Schauer, AJ and Moffett, JW and Armbrust, EV and Ingalls, AE and Devol, AH and Stahl, DA},
title = {The production of nitric oxide by marine ammonia-oxidizing archaea and inhibition of archaeal ammonia oxidation by a nitric oxide scavenger.},
journal = {Environmental microbiology},
volume = {17},
number = {7},
pages = {2261-2274},
doi = {10.1111/1462-2920.12677},
pmid = {25420929},
issn = {1462-2920},
mesh = {Ammonia/*metabolism ; Ammonium Compounds/metabolism ; Aquatic Organisms/metabolism ; Archaea/*metabolism ; Betaproteobacteria/metabolism ; Cyclic N-Oxides/*pharmacology ; Denitrification ; Imidazoles/*pharmacology ; Nitric Oxide/biosynthesis/*metabolism ; *Nitrification ; Nitrogen/metabolism ; Oxidation-Reduction ; Thiourea/*analogs &amp; derivatives/pharmacology ; },
abstract = {Nitrification is a critical process for the balance of reduced and oxidized nitrogen pools in nature, linking mineralization to the nitrogen loss processes of denitrification and anammox. Recent studies indicate a significant contribution of ammonia-oxidizing archaea (AOA) to nitrification. However, quantification of the relative contributions of AOA and ammonia-oxidizing bacteria (AOB) to in situ ammonia oxidation remains challenging. We show here the production of nitric oxide (NO) by Nitrosopumilus maritimus SCM1. Activity of SCM1 was always associated with the release of NO with quasi-steady state concentrations between 0.05 and 0.08 μM. NO production and metabolic activity were inhibited by the nitrogen free radical scavenger 2-phenyl-4,4,5,5,-tetramethylimidazoline-1-oxyl-3-oxide (PTIO). Comparison of marine and terrestrial AOB strains with SCM1 and the recently isolated marine AOA strain HCA1 demonstrated a differential sensitivity of AOB and AOA to PTIO and allylthiourea (ATU). Similar to the investigated AOA strains, bulk water column nitrification at coastal and open ocean sites with sub-micromolar ammonia/ammonium concentrations was inhibited by PTIO and insensitive to ATU. These experiments support predictions from kinetic, molecular and biogeochemical studies, indicating that marine nitrification at low ammonia/ammonium concentrations is largely driven by archaea and suggest an important role of NO in the archaeal metabolism.},
}
@article {pmid25420454,
year = {2014},
author = {Rzechorzek, NJ and Blackwood, JK and Bray, SM and Maman, JD and Pellegrini, L and Robinson, NP},
title = {Structure of the hexameric HerA ATPase reveals a mechanism of translocation-coupled DNA-end processing in archaea.},
journal = {Nature communications},
volume = {5},
number = {},
pages = {5506},
doi = {10.1038/ncomms6506},
pmid = {25420454},
issn = {2041-1723},
support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; G0701443//Medical Research Council/United Kingdom ; 104641//Wellcome Trust/United Kingdom ; 084279//Wellcome Trust/United Kingdom ; 08279/Z/07/Z//Wellcome Trust/United Kingdom ; },
mesh = {Adenosine Triphosphatases/*chemistry/genetics/*metabolism ; Amino Acid Sequence ; Archaea/chemistry/*enzymology/genetics ; Archaeal Proteins/chemistry/genetics/*metabolism ; DNA Breaks, Double-Stranded ; DNA, Archaeal/*genetics/metabolism ; Deoxyribonucleases/genetics/metabolism ; Models, Molecular ; Molecular Sequence Data ; Sequence Alignment ; *Translocation, Genetic ; },
abstract = {The HerA ATPase cooperates with the NurA nuclease and the Mre11-Rad50 complex for the repair of double-strand DNA breaks in thermophilic archaea. Here we extend our structural knowledge of this minimal end-resection apparatus by presenting the first crystal structure of hexameric HerA. The full-length structure visualizes at atomic resolution the N-terminal HerA-ATP synthase domain and a conserved C-terminal extension, which acts as a physical brace between adjacent protomers. The brace also interacts in trans with nucleotide-binding residues of the neighbouring subunit. Our observations support a model in which the coaxial interaction of the HerA ring with the toroidal NurA dimer generates a continuous channel traversing the complex. HerA-driven translocation would propel the DNA towards the narrow annulus of NurA, leading to duplex melting and nucleolytic digestion. This system differs substantially from the bacterial end-resection paradigms. Our findings suggest a novel mode of DNA-end processing by this integrated archaeal helicase-nuclease machine.},
}
@article {pmid25414355,
year = {2015},
author = {Stoddard, SF and Smith, BJ and Hein, R and Roller, BR and Schmidt, TM},
title = {rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development.},
journal = {Nucleic acids research},
volume = {43},
number = {Database issue},
pages = {D593-8},
doi = {10.1093/nar/gku1201},
pmid = {25414355},
issn = {1362-4962},
support = {R01 GM099549/GM/NIGMS NIH HHS/United States ; M0099549//PHS HHS/United States ; },
mesh = {Archaea/classification ; Bacteria/classification ; *Databases, Nucleic Acid ; Gene Dosage ; *Genes, Archaeal ; *Genes, Bacterial ; *Genes, rRNA ; Genome, Archaeal ; Genome, Bacterial ; Internet ; Operon ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Software ; },
abstract = {Microbiologists utilize ribosomal RNA genes as molecular markers of taxonomy in surveys of microbial communities. rRNA genes are often co-located as part of an rrn operon, and multiple copies of this operon are present in genomes across the microbial tree of life. rrn copy number variability provides valuable insight into microbial life history, but introduces systematic bias when measuring community composition in molecular surveys. Here we present an update to the ribosomal RNA operon copy number database (rrnDB), a publicly available, curated resource for copy number information for bacteria and archaea. The redesigned rrnDB (http://rrndb.umms.med.umich.edu/) brings a substantial increase in the number of genomes described, improved curation, mapping of genomes to both NCBI and RDP taxonomies, and refined tools for querying and analyzing these data. With these changes, the rrnDB is better positioned to remain a comprehensive resource under the torrent of microbial genome sequencing. The enhanced rrnDB will contribute to the analysis of molecular surveys and to research linking genomic characteristics to life history.},
}
@article {pmid25409591,
year = {2015},
author = {Flood, M and Frabutt, D and Floyd, D and Powers, A and Ezegwe, U and Devol, A and Tiquia-Arashiro, SM},
title = {Ammonia-oxidizing bacteria and archaea in sediments of the Gulf of Mexico.},
journal = {Environmental technology},
volume = {36},
number = {1-4},
pages = {124-135},
doi = {10.1080/09593330.2014.942385},
pmid = {25409591},
issn = {0959-3330},
mesh = {Ammonia/*metabolism ; Archaea/classification/isolation &amp; purification/*physiology ; Bacteria/classification/*isolation &amp; purification ; *Bacterial Physiological Phenomena ; Geologic Sediments/*microbiology ; Gulf of Mexico ; Oxidation-Reduction ; Seawater/*microbiology ; Species Specificity ; },
abstract = {The diversity (richness and community composition) of ammonia-oxidizing archaea (AOA) and bacteria (AOB) within sediments of the Gulf of Mexico was examined. Using polymerase chain reaction primers designed to specifically target the archaeal ammonia monooxygenase-subunit (amoA) gene and bacterial amoA gene, we found AOA and AOB to be present in all three sampling sites. Archaeal amoA libraries were dominated by a few widely distributed Nitrosopumilus-like sequence types, whereas AOB diversity showed significant variation in both richness and community composition. Majority of the bacterial amoA sequences recovered belong to Betaproteobacteria and very few belong to Gammaproteobacteria. Results suggest that water depth and nutrient availability were identified as potential drivers that affected the selection of the AOA and AOB communities. Besides influencing the abundance of individual taxa, these environmental factors also had an impact on the overall richness of the overall AOA and AOB communities. The richness and diversity of AOA and AOB genes were higher at the shallowest sediments (100 m depth) and the deepest sediments (1300 m depth). The reduced diversity in the deepest sediments could be explained by much lower nutrient availability.},
}
@article {pmid25406237,
year = {2015},
author = {Liu, Q and Ren, M and Zhang, LL},
title = {Natribaculum breve gen. nov., sp. nov. and Natribaculum longum sp. nov., halophilic archaea isolated from saline soil.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {65},
number = {Pt 2},
pages = {604-608},
doi = {10.1099/ijs.0.060541-0},
pmid = {25406237},
issn = {1466-5034},
mesh = {Base Composition ; China ; DNA, Archaeal/genetics ; Genes, Archaeal ; Glycolipids/chemistry ; Halobacteriaceae/*classification/genetics/isolation &amp; purification ; Lipids/chemistry ; Molecular Sequence Data ; Nucleic Acid Hybridization ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Salinity ; Sequence Analysis, DNA ; *Soil Microbiology ; },
abstract = {Two halophilic archaeal strains, TRM20010(T) and TRM20345(T), were isolated from saline soil of the Lop Nur region in Xinjiang, north-west China. Cells from the two strains were pleomorphic rods, stained Gram-negative and produced red-pigmented colonies. Strains TRM20010(T) and TRM20345(T) were able to grow at 30-62 °C (optimum 37 °C), 0.9-5.1 M NaCl (optimum 2.6 and 3.4 M, respectively) and pH 6.0-10.0 (optimum pH 7.0-7.5) and neither strain required Mg(2+) for growth. The major polar lipids of the two strains were phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), two glycolipids chromatographically identical to galactosyl mannosyl glucosyl diether (TGD-1) and disulfated mannosyl glucosyl diether (S2-DGD). Phylogenetic analysis based on 16S rRNA and rpoB' genes revealed that strains TRM20010(T) and TRM20345(T) clustered together and formed a distinct clade separated from the related genera Halovivax, Haloterrigena, Halostagnicola, Natronolimnobius and Natrinema. The DNA G+C contents of strains TRM20010(T) and TRM20345(T) were 63.9 and 63.8 mol%, respectively. The DNA-DNA hybridization value between strain TRM20010(T) and strain TRM20345(T) was 42.8 %. The phenotypic, chemotaxonomic and phylogenetic properties suggested that strains TRM20010(T) and TRM20345(T) represent two novel species in a new genus within the family Halobacteriaceae, for which the names Natribaculum breve gen. nov., sp. nov. (type strain TRM20010(T) = CCTCC AB2013112(T) = NRRL B-59996(T)) and Natribaculum longum sp. nov. (type strain TRM20345(T) = CCTCC AB2013113(T) = NRRL B-59997(T)) are proposed.},
}
@article {pmid25404694,
year = {2015},
author = {Leyn, SA and Rodionov, DA},
title = {Comparative genomics of DtxR family regulons for metal homeostasis in Archaea.},
journal = {Journal of bacteriology},
volume = {197},
number = {3},
pages = {451-458},
doi = {10.1128/JB.02386-14},
pmid = {25404694},
issn = {1098-5530},
mesh = {Archaea/*genetics/*metabolism ; Binding Sites ; Computational Biology ; DNA, Archaeal/genetics ; Gene Order ; Genomics ; *Homeostasis ; Metals/*metabolism ; Phylogeny ; *Regulon ; Transcription Factors/*genetics/*metabolism ; },
abstract = {The DtxR family consists of metal-dependent transcription factors (DtxR-TFs) that regulate the expression of genes involved in metal homeostasis in the cell. The majority of characterized DtxR-TFs belong to Bacteria. In the current work, we applied a comparative genomics approach to predict DNA-binding sites and reconstruct regulons for DtxR-TFs in Archaea. As a result, we inferred 575 candidate binding sites for 139 DtxR-TFs in 77 genomes from 15 taxonomic orders. Novel DNA motifs of archaeal DtxR-TFs that have a common palindromic structure were classified into 10 distinct groups. By combining functional regulon reconstructions with phylogenetic analysis, we selected 28 DtxR-TF clades and assigned them metal specificities and regulator names. The reconstructed FetR (ferrous iron), MntR (manganese), and ZntR (zinc) regulons largely contain known or putative metal uptake transporters from the FeoAB, NRAMP, ZIP, and TroA families. A novel family of putative iron transporters (named Irt), including multiple FetR-regulated paralogs, was identified in iron-oxidizing Archaea from the Sulfolobales order. The reconstructed DtxR-TF regulons were reconciled with available transcriptomics data in Archaeoglobus, Halobacterium, and Thermococcus spp.},
}
@article {pmid25402442,
year = {2014},
author = {Hayden, CJ and Beman, JM},
title = {High abundances of potentially active ammonia-oxidizing bacteria and archaea in oligotrophic, high-altitude lakes of the Sierra Nevada, California, USA.},
journal = {PloS one},
volume = {9},
number = {11},
pages = {e111560},
doi = {10.1371/journal.pone.0111560},
pmid = {25402442},
issn = {1932-6203},
mesh = {*Altitude ; Ammonia/*metabolism ; Archaea/genetics/*metabolism ; Bacteria/genetics/*metabolism ; Biodiversity ; California ; Genes, Archaeal ; Genes, Bacterial ; Geography ; Lakes/*microbiology ; Nitrification ; Nitrogen Cycle ; Oxidation-Reduction ; },
abstract = {Nitrification plays a central role in the nitrogen cycle by determining the oxidation state of nitrogen and its subsequent bioavailability and cycling. However, relatively little is known about the underlying ecology of the microbial communities that carry out nitrification in freshwater ecosystems--and particularly within high-altitude oligotrophic lakes, where nitrogen is frequently a limiting nutrient. We quantified ammonia-oxidizing archaea (AOA) and bacteria (AOB) in 9 high-altitude lakes (2289-3160 m) in the Sierra Nevada, California, USA, in relation to spatial and biogeochemical data. Based on their ammonia monooxygenase (amoA) genes, AOB and AOA were frequently detected. AOB were present in 88% of samples and were more abundant than AOA in all samples. Both groups showed >100 fold variation in abundance between different lakes, and were also variable through time within individual lakes. Nutrient concentrations (ammonium, nitrite, nitrate, and phosphate) were generally low but also varied across and within lakes, suggestive of active internal nutrient cycling; AOB abundance was significantly correlated with phosphate (r(2) = 0.32, p<0.1), whereas AOA abundance was inversely correlated with lake elevation (r(2) = 0.43, p<0.05). We also measured low rates of ammonia oxidation--indicating that AOB, AOA, or both, may be biogeochemically active in these oligotrophic ecosystems. Our data indicate that dynamic populations of AOB and AOA are found in oligotrophic, high-altitude, freshwater lakes.},
}
@article {pmid25393412,
year = {2014},
author = {Becker, EA and Seitzer, PM and Tritt, A and Larsen, D and Krusor, M and Yao, AI and Wu, D and Madern, D and Eisen, JA and Darling, AE and Facciotti, MT},
title = {Phylogenetically driven sequencing of extremely halophilic archaea reveals strategies for static and dynamic osmo-response.},
journal = {PLoS genetics},
volume = {10},
number = {11},
pages = {e1004784},
doi = {10.1371/journal.pgen.1004784},
pmid = {25393412},
issn = {1553-7404},
mesh = {Adaptation, Physiological/*genetics ; Archaea/*genetics ; Base Sequence ; Evolution, Molecular ; Genome, Archaeal ; Humans ; *Metagenomics ; Molecular Sequence Annotation ; Osmolar Concentration ; Phylogeny ; Salinity ; TATA-Box Binding Protein/*genetics ; },
abstract = {Organisms across the tree of life use a variety of mechanisms to respond to stress-inducing fluctuations in osmotic conditions. Cellular response mechanisms and phenotypes associated with osmoadaptation also play important roles in bacterial virulence, human health, agricultural production and many other biological systems. To improve understanding of osmoadaptive strategies, we have generated 59 high-quality draft genomes for the haloarchaea (a euryarchaeal clade whose members thrive in hypersaline environments and routinely experience drastic changes in environmental salinity) and analyzed these new genomes in combination with those from 21 previously sequenced haloarchaeal isolates. We propose a generalized model for haloarchaeal management of cytoplasmic osmolarity in response to osmotic shifts, where potassium accumulation and sodium expulsion during osmotic upshock are accomplished via secondary transport using the proton gradient as an energy source, and potassium loss during downshock is via a combination of secondary transport and non-specific ion loss through mechanosensitive channels. We also propose new mechanisms for magnesium and chloride accumulation. We describe the expansion and differentiation of haloarchaeal general transcription factor families, including two novel expansions of the TATA-binding protein family, and discuss their potential for enabling rapid adaptation to environmental fluxes. We challenge a recent high-profile proposal regarding the evolutionary origins of the haloarchaea by showing that inclusion of additional genomes significantly reduces support for a proposed large-scale horizontal gene transfer into the ancestral haloarchaeon from the bacterial domain. The combination of broad (17 genera) and deep (≥5 species in four genera) sampling of a phenotypically unified clade has enabled us to uncover both highly conserved and specialized features of osmoadaptation. Finally, we demonstrate the broad utility of such datasets, for metagenomics, improvements to automated gene annotation and investigations of evolutionary processes.},
}
@article {pmid25387612,
year = {2015},
author = {Kishishita, S and Fujii, T and Ishikawa, K},
title = {Heterologous expression of hyperthermophilic cellulases of archaea Pyrococcus sp. by fungus Talaromyces cellulolyticus.},
journal = {Journal of industrial microbiology &amp; biotechnology},
volume = {42},
number = {1},
pages = {137-141},
doi = {10.1007/s10295-014-1532-2},
pmid = {25387612},
issn = {1476-5535},
mesh = {Cellulases/*biosynthesis ; *Gene Expression Regulation, Enzymologic ; Glucan 1,4-alpha-Glucosidase/genetics ; Promoter Regions, Genetic ; Pyrococcus/*enzymology/genetics ; Talaromyces/*metabolism ; },
abstract = {Talaromyces cellulolyticus (formerly known as Acremonium cellulolyticus) is one of the high cellulolytic enzyme-producing fungi. T. cellulolyticus exhibits the potential ability for high amount production of enzyme proteins. Using the homologous expression system under the control of a glucoamylase promoter, some kinds of cellulases of T. cellulolyticus can be expressed by T. cellulolyticus. On the other hand, hyperthermophilic cellulase has been expected to be useful in the industrial applications to biomass. The hyperthermophilic archaea Pyrococcus horikoshii and P. furiosus have GH family 5 and 12 hyperthermophilic endocellulase, respectively. The two kinds of hyperthermophilic endocellulases were successfully produced by T. cellulolyticus using the above expression system under the control of a glucoamylase promoter of T. cellulolyticus. These recombinant cellulases exhibited the same characteristics as those of the recombinant cellulases prepared in E. coli. The productions of the recombinant enzymes were estimated to be over 100 mg/L. In this study, we first report the overexpression of the hyperthermophilic enzymes of archaea using the fungal expression system.},
}
@article {pmid25381908,
year = {2015},
author = {Ding, K and Wen, X and Li, Y and Shen, B and Zhang, B},
title = {Ammonia-oxidizing archaea versus bacteria in two soil aquifer treatment systems.},
journal = {Applied microbiology and biotechnology},
volume = {99},
number = {3},
pages = {1337-1347},
doi = {10.1007/s00253-014-6188-3},
pmid = {25381908},
issn = {1432-0614},
mesh = {Ammonia/*metabolism ; Archaea/classification/genetics/isolation &amp; purification/*metabolism ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Groundwater/*microbiology ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; Soil Microbiology ; Waste Water/*microbiology ; Water Purification/instrumentation/methods ; },
abstract = {So far, the contribution of ammonia-oxidizing archaea (AOA) to ammonia oxidation in wastewater treatment processes has not been well understood. In this study, two soil aquifer treatment (SATs) systems were built up to treat synthetic domestic wastewater (column 1) and secondary effluent (column 4), accomplishing an average of 95% ammonia removal during over 550 days of operation. Except at day 322, archaeal amoA genes always outnumbered bacterial amoA genes in both SATs as determined by using quantitative polymerase chain reaction (q-PCR). The ratios of archaeal amoA to 16S rRNA gene averaged at 0.70 ± 0.56 and 0.82 ± 0.62 in column 1 and column 4, respectively, indicating that all the archaea could be AOA carrying amoA gene in the SATs. The results of MiSeq-pyrosequencing targeting on archaeal and bacterial 16S rRNA genes with the primer pair of modified 515R/806R indicated that Nitrososphaera cluster affiliated with thaumarchaeal group I.1b was the dominant AOA species, while Nitrosospira cluster was the dominant ammonia-oxidizing bacteria (AOB). The statistical analysis showed significant relationship between AOA abundance (compared to AOB abundance) and inorganic and total nitrogen concentrations. Based on the mathematical model calculation for microbial growth, AOA had much greater capacity of ammonia oxidation as compared to the specific influent ammonia loading for AOA in the SATs, implying that a small fraction of the total AOA would actively work to oxidize ammonia chemoautotrophically whereas most of AOA would exhibit some level of functional redundancy. These results all pointed that AOA involved in microbial ammonia oxidation in the SATs.},
}
@article {pmid25370029,
year = {2014},
author = {Leuko, S and Rettberg, P and Pontifex, AL and Burns, BP},
title = {On the response of halophilic archaea to space conditions.},
journal = {Life (Basel, Switzerland)},
volume = {4},
number = {1},
pages = {66-76},
doi = {10.3390/life4010066},
pmid = {25370029},
issn = {2075-1729},
abstract = {Microorganisms are ubiquitous and can be found in almost every habitat and ecological niche on Earth. They thrive and survive in a broad spectrum of environments and adapt to rapidly changing external conditions. It is of great interest to investigate how microbes adapt to different extreme environments and with modern human space travel, we added a new extreme environment: outer space. Within the last 50 years, technology has provided tools for transporting microbial life beyond Earth's protective shield in order to study in situ responses to selected conditions of space. This review will focus on halophilic archaea, as, due to their ability to survive in extremes, they are often considered a model group of organisms to study responses to the harsh conditions associated with space. We discuss ground-based simulations, as well as space experiments, utilizing archaea, examining responses and/or resistance to the effects of microgravity and UV in particular. Several halophilic archaea (e.g., Halorubrum chaoviator) have been exposed to simulated and actual space conditions and their survival has been determined as well as the protective effects of halite shown. Finally, the intriguing potential of archaea to survive on other planets or embedded in a meteorite is postulated.},
}
@article {pmid25368347,
year = {2014},
author = {Oren, A},
title = {Halophilic archaea on Earth and in space: growth and survival under extreme conditions.},
journal = {Philosophical transactions. Series A, Mathematical, physical, and engineering sciences},
volume = {372},
number = {2030},
pages = {},
doi = {10.1098/rsta.2014.0194},
pmid = {25368347},
issn = {1364-503X},
abstract = {Salts are abundant on Mars, and any liquid water that is present or may have been present on the planet is expected to be hypersaline. Halophilic archaea (family Halobacteriaceae) are the microorganisms best adapted to life at extremes of salinity on Earth. This paper reviews the properties of the Halobacteriaceae that may make the group good candidates for life also on Mars. Many species resist high UV and gamma radiation levels; one species has survived exposure to vacuum and radiation during a space flight; and there is at least one psychrotolerant species. Halophilic archaea may survive for millions of years within brine inclusions in salt crystals. Many species have different modes of anaerobic metabolism, and some can use light as an energy source using the light-driven proton pump bacteriorhodopsin. They are also highly tolerant to perchlorate, recently shown to be present in Martian soils, and some species can even use perchlorate as an electron acceptor to support anaerobic growth. The presence of characteristic carotenoid pigments (α-bacterioruberin and derivatives) makes the Halobacteriaceae easy to identify by Raman spectroscopy. Thus, if present on Mars, such organisms may be detected by Raman instrumentation planned to explore Mars during the upcoming ExoMars mission.},
}
@article {pmid25367104,
year = {2015},
author = {Pump, J and Pratscher, J and Conrad, R},
title = {Colonization of rice roots with methanogenic archaea controls photosynthesis-derived methane emission.},
journal = {Environmental microbiology},
volume = {17},
number = {7},
pages = {2254-2260},
doi = {10.1111/1462-2920.12675},
pmid = {25367104},
issn = {1462-2920},
mesh = {Euryarchaeota/classification/genetics/*metabolism ; Methane/*biosynthesis ; Oryza/*metabolism/*microbiology ; Oxidoreductases/genetics ; Photosynthesis/physiology ; Plant Roots/*microbiology ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Soil ; Soil Microbiology ; },
abstract = {The methane emitted from rice fields originates to a large part (up to 60%) from plant photosynthesis and is formed on the rice roots by methanogenic archaea. To investigate to which extent root colonization controls methane (CH4) emission, we pulse-labeled rice microcosms with (13) CO2 to determine the rates of (13) CH4 emission exclusively derived from photosynthates. We also measured emission of total CH4 ((12+13) CH4), which was largely produced in the soil. The total abundances of archaea and methanogens on the roots and in the soil were analysed by quantitative polymerase chain reaction of the archaeal 16S rRNA gene and the mcrA gene coding for a subunit of the methyl coenzyme M reductase respectively. The composition of archaeal and methanogenic communities was determined with terminal restriction fragment length polymorphism (T-RFLP). During the vegetative growth stages, emission rates of (13) CH4 linearly increased with the abundance of methanogenic archaea on the roots and then decreased during the last plant growth stage. Rates of (13) CH4 emission and the abundance of methanogenic archaea were lower when the rice was grown in quartz-vermiculite with only 10% rice soil. Rates of total CH4 emission were not systematically related to the abundance of methanogenic archaea in soil plus roots. The composition of the archaeal communities was similar under all conditions; however, the analysis of mcrA genes indicated that the methanogens differed between the soil and root. Our results support the hypothesis that rates of photosynthesis-driven CH4 emission are limited by the abundance of methanogens on the roots.},
}
@article {pmid25352841,
year = {2014},
author = {Oren, A},
title = {DNA as genetic material and as a nutrient in halophilic Archaea.},
journal = {Frontiers in microbiology},
volume = {5},
number = {},
pages = {539},
doi = {10.3389/fmicb.2014.00539},
pmid = {25352841},
issn = {1664-302X},
}
@article {pmid25351144,
year = {2015},
author = {Cersosimo, LM and Lachance, H and St-Pierre, B and van Hoven, W and Wright, AD},
title = {Examination of the rumen bacteria and methanogenic archaea of wild impalas (Aepyceros melampus melampus) from Pongola, South Africa.},
journal = {Microbial ecology},
volume = {69},
number = {3},
pages = {577-585},
doi = {10.1007/s00248-014-0521-3},
pmid = {25351144},
issn = {1432-184X},
mesh = {Animals ; Antelopes/*microbiology ; Archaea/classification/genetics/*isolation &amp; purification ; Bacteria/classification/genetics/*isolation &amp; purification ; *Gastrointestinal Microbiome ; Male ; Molecular Sequence Data ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Rumen/microbiology ; South Africa ; },
abstract = {Although the rumen microbiome of domesticated ruminants has been evaluated, few studies have explored the rumen microbiome of wild ruminants, and no studies have identified the rumen microbiome in the impala (Aepyceros melampus melampus). In the present study, next-generation sequencing and real-time polymerase chain reaction were used to investigate the diversity and density of the bacteria and methanogenic archaea residing in the rumen of five adult male impalas, culled during the winter dry season in Pongola, South Africa. A total of 15,323 bacterial 16S rRNA gene sequences (from five impala), representing 3,892 different phylotypes, were assigned to 1,902 operational taxonomic units (OTUs). A total of 20,124 methanogen 16S rRNA gene sequence reads (from four impala), of which 5,028 were unique, were assigned to 344 OTUs. From the total sequence reads, Bacteroidetes, Proteobacteria, and Firmicutes were the most abundant bacterial phyla. While the majority of the bacterial genera found were unclassified, Prevotella and Cupriavidus were the most abundant classified genera. For methanogens, the genera Methanobrevibacter and Methanosphaera represented 94.3% and 4.0% of the classified sequences, respectively. Most notable was the identification of Methanobrevibacter thaueri-like 16S rRNA gene sequence reads in all four impala samples, representing greater than 30% of each individual's total sequences. Both data sets are accessible through NCBI's Sequence Read Archive (SRA), under study accession number SRP [048619]. The densities of bacteria (1.26 × 10(10)-3.82 × 10(10) cells/ml whole rumen contents) and methanogens (4.48 × 10(8)-7.2 × 10(9) cells/ml of whole rumen contents) from five individual impala were similar to those typically observed in domesticated ruminants.},
}
@article {pmid25344977,
year = {2014},
author = {Efenberger, M and Wódz, K and Brzezińska-Błaszczyk, E},
title = {[Archaea--the significant inhabitants of human microbiome].},
journal = {Przeglad lekarski},
volume = {71},
number = {6},
pages = {346-351},
pmid = {25344977},
issn = {0033-2240},
mesh = {Archaea/*cytology/drug effects/*physiology ; Drug Resistance, Microbial ; Gastrointestinal Diseases/microbiology ; Humans ; Microbiota/*physiology ; },
abstract = {Archaea, along with bacteria and eucarya are the three domains of life. These microorganisms inhabit variable natural environments but they are also important part of human physiological flora. In this paper we describe archaeal morphology and physiology. We also review the state of knowledge about archaea associated with human microbiome. The potential role of these microorganisms in etiopathogenesis of some human diseases is discussed, as well. Finally, we consider archaeal susceptibility/resistance to antimicrobial agents, including antibiotics.},
}
@article {pmid25344857,
year = {2015},
author = {Puthiya Veettil, V and Abdulaziz, A and Chekidhenkuzhiyil, J and Kalanthingal Ramkollath, L and Karayadi Hamza, F and Kizhakkepat Kalam, B and Kallungal Ravunnikutty, M and Nair, S},
title = {Bacterial domination over archaea in ammonia oxidation in a monsoon-driven tropical estuary.},
journal = {Microbial ecology},
volume = {69},
number = {3},
pages = {544-553},
doi = {10.1007/s00248-014-0519-x},
pmid = {25344857},
issn = {1432-184X},
mesh = {Ammonia/*metabolism ; Archaea/genetics/*physiology ; *Bacterial Physiological Phenomena/genetics ; DNA, Bacterial/genetics/metabolism ; Estuaries ; India ; Molecular Sequence Data ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics/metabolism ; Seawater/*microbiology ; Sequence Analysis, DNA ; Tropical Climate ; },
abstract = {Autotrophic ammonia oxidizing microorganisms, which are responsible for the rate-limiting step of nitrification in most aquatic systems, have not been studied in tropical estuaries. Cochin estuary (CE) is one of the largest, productive, and monsoon-driven estuary in India opening into the southeast Arabian Sea. CE receives surplus quantities of ammonia through industrial and domestic discharges. The distribution of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and anaerobic ammonia-oxidizing bacteria (anammox) were studied using fluorescence in situ hybridization (FISH) and their relative contribution to the process as well as the governing factors were examined and reported for the first time from CE. The order of occurrence of these assemblages was β-proteobacteria (0.79 to 2 × 10(5) cells ml(-1)) > γ-proteobacteria (0.9 to 4.6 × 10(4) cells ml(-1)) > anammox (0.49 to 1.9 × 10(4) cells ml(-1)) > AOA (0.56 to 6.3 × 10(3) cells ml(-1)). Phylogenetic analysis of DGGE bands showed major affiliation of AOB to β-proteobacteria, while AOA was affiliated to Crenarchaeota. The abundance of AOB was mostly influenced by ammonia concentrations. The recovered ammonia oxidation rate of AOB was in the range of 45-65%, whereas for AOA, it was 15-45%, indicating that AOB were mostly responsible for the ammonia oxidation in CE during the study period. Overall, the present study provides an insight into the relevance and contribution of different groups of ammonia oxidizing bacteria in CE and emphasizes the need for further in depth studies across space and on season scale.},
}
@article {pmid25338080,
year = {2014},
author = {Jaakkola, ST and Zerulla, K and Guo, Q and Liu, Y and Ma, H and Yang, C and Bamford, DH and Chen, X and Soppa, J and Oksanen, HM},
title = {Halophilic archaea cultivated from surface sterilized middle-late eocene rock salt are polyploid.},
journal = {PloS one},
volume = {9},
number = {10},
pages = {e110533},
doi = {10.1371/journal.pone.0110533},
pmid = {25338080},
issn = {1932-6203},
mesh = {Base Sequence ; Biological Evolution ; China ; DNA, Archaeal/*genetics ; *Genome, Archaeal ; Geologic Sediments/microbiology ; Halobacteriaceae/classification/*genetics/isolation &amp; purification ; Molecular Sequence Data ; Phylogeny ; *Polyploidy ; RNA, Ribosomal, 16S/*genetics ; Salts ; },
abstract = {Live bacteria and archaea have been isolated from several rock salt deposits of up to hundreds of millions of years of age from all around the world. A key factor affecting their longevity is the ability to keep their genomic DNA intact, for which efficient repair mechanisms are needed. Polyploid microbes are known to have an increased resistance towards mutations and DNA damage, and it has been suggested that microbes from deeply buried rock salt would carry several copies of their genomes. Here, cultivable halophilic microbes were isolated from a surface sterilized middle-late Eocene (38-41 million years ago) rock salt sample, drilled from the depth of 800 m at Yunying salt mine, China. Eight unique isolates were obtained, which represented two haloarchaeal genera, Halobacterium and Halolamina. We used real-time PCR to show that our isolates are polyploid, with genome copy numbers of 11-14 genomes per cell in exponential growth phase. The ploidy level was slightly downregulated in stationary growth phase, but the cells still had an average genome copy number of 6-8. The polyploidy of halophilic archaea living in ancient rock salt might be a factor explaining how these organisms are able to overcome the challenge of prolonged survival during their entombment.},
}
@article {pmid25331558,
year = {2015},
author = {Lazar, CS and Biddle, JF and Meador, TB and Blair, N and Hinrichs, KU and Teske, AP},
title = {Environmental controls on intragroup diversity of the uncultured benthic archaea of the miscellaneous Crenarchaeotal group lineage naturally enriched in anoxic sediments of the White Oak River estuary (North Carolina, USA).},
journal = {Environmental microbiology},
volume = {17},
number = {7},
pages = {2228-2238},
doi = {10.1111/1462-2920.12659},
pmid = {25331558},
issn = {1462-2920},
mesh = {Adaptation, Physiological/*genetics ; Biodiversity ; Crenarchaeota/*classification/genetics ; DNA, Archaeal/genetics ; *Estuaries ; Geologic Sediments/*microbiology ; North Carolina ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Rivers ; },
abstract = {Sediments of the White Oak River (WOR) estuary are situated on the coast of North Carolina harbour, one of the most diverse known populations of uncultured Archaea, specifically the miscellaneous Crenarchaeotal group (MCG). In order to constrain the environmental factors influencing the uncultured archaeal groups in the WOR estuary, biogeochemical profiles as well as archaeal 16S rRNA genes from sediment pushcores were analysed. The relative fraction of MCG Archaea in clone libraries decreased at shallow sediment depths (27% of the total MCG). A LINKTREE analysis of the MCG intragroup diversity reinforced the observation that the MCG subgroup 6 was found predominantly within sulfide-depleted shallow sediment layers; other subgroups (especially MCG-1 and MCG-5/8) occurred preferentially in deeper, more strongly reducing sediment layers. The available evidence from this study and published MCG distribution patterns indicates that the MCG-6 subgroup is a specialized MCG lineage that, in contrast to other MCG subgroups, prefers suboxic sediment horizons with minimal or no free sulfide. Collectively, our results reveal the habitat preferences of different MCG subgroups in the WOR sediments and suggest that physiological adaptations to distinct sedimentary geochemical niches evolved in different MCG subgroups.},
}
@article {pmid25330320,
year = {2014},
author = {Barreto, DP and Conrad, R and Klose, M and Claus, P and Enrich-Prast, A},
title = {Distance-decay and taxa-area relationships for bacteria, archaea and methanogenic archaea in a tropical lake sediment.},
journal = {PloS one},
volume = {9},
number = {10},
pages = {e110128},
doi = {10.1371/journal.pone.0110128},
pmid = {25330320},
issn = {1932-6203},
mesh = {Archaea/*classification/genetics/*metabolism ; Bacteria/*classification/genetics ; Geologic Sediments/*microbiology ; Lakes/*microbiology ; Methane/*biosynthesis ; *Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The study of of the distribution of microorganisms through space (and time) allows evaluation of biogeographic patterns, like the species-area index (z). Due to their high dispersal ability, high reproduction rates and low rates of extinction microorganisms tend to be widely distributed, and they are thought to be virtually cosmopolitan and selected primarily by environmental factors. Recent studies have shown that, despite these characteristics, microorganisms may behave like larger organisms and exhibit geographical distribution. In this study, we searched patterns of spatial diversity distribution of bacteria and archaea in a contiguous environment. We collected 26 samples of a lake sediment, distributed in a nested grid, with distances between samples ranging from 0.01 m to 1000 m. The samples were analyzed using T-RFLP (Terminal restriction fragment length polymorphism) targeting mcrA (coding for a subunit of methyl-coenzyme M reductase) and the genes of Archaeal and Bacterial 16S rRNA. From the qualitative and quantitative results (relative abundance of operational taxonomic units) we calculated the similarity index for each pair to evaluate the taxa-area and distance decay relationship slopes by linear regression. All results were significant, with mcrA genes showing the highest slope, followed by Archaeal and Bacterial 16S rRNA genes. We showed that the microorganisms of a methanogenic community, that is active in a contiguous environment, display spatial distribution and a taxa-area relationship.},
}
@article {pmid25326317,
year = {2014},
author = {Li, GP and Jiang, L and Ni, JZ and Liu, Q and Zhang, Y},
title = {Computational identification of a new SelD-like family that may participate in sulfur metabolism in hyperthermophilic sulfur-reducing archaea.},
journal = {BMC genomics},
volume = {15},
number = {},
pages = {908},
doi = {10.1186/1471-2164-15-908},
pmid = {25326317},
issn = {1471-2164},
mesh = {Amino Acid Sequence ; Archaeal Proteins/chemistry/*genetics ; Computational Biology/*methods ; Conserved Sequence ; Crenarchaeota/chemistry/*enzymology/genetics ; Gene Expression Regulation, Archaeal ; Phosphotransferases/chemistry/*genetics ; Phylogeny ; Selenium/metabolism ; Sulfur/*metabolism ; },
abstract = {BACKGROUND: Selenium (Se) and sulfur (S) are closely related elements that exhibit similar chemical properties. Some genes related to S metabolism are also involved in Se utilization in many organisms. However, the evolutionary relationship between the two utilization traits is unclear.<br><br>RESULTS: In this study, we conducted a comparative analysis of the selenophosphate synthetase (SelD) family, a key protein for all known Se utilization traits, in all sequenced archaea. Our search showed a very limited distribution of SelD and Se utilization in this kingdom. Interestingly, a SelD-like protein was detected in two orders of Crenarchaeota: Sulfolobales and Thermoproteales. Sequence and phylogenetic analyses revealed that SelD-like protein contains the same domain and conserved functional residues as those of SelD, and might be involved in S metabolism in these S-reducing organisms. Further genome-wide analysis of patterns of gene occurrence in different thermoproteales suggested that several genes, including SirA-like, Prx-like and adenylylsulfate reductase, were strongly related to SelD-like gene. Based on these findings, we proposed a simple model wherein SelD-like may play an important role in the biosynthesis of certain thiophosphate compound.<br><br>CONCLUSIONS: Our data suggest novel genes involved in S metabolism in hyperthermophilic S-reducing archaea, and may provide a new window for understanding the complex relationship between Se and S metabolism in archaea.},
}
@article {pmid25326303,
year = {2015},
author = {Li, J and Nedwell, DB and Beddow, J and Dumbrell, AJ and McKew, BA and Thorpe, EL and Whitby, C},
title = {amoA Gene abundances and nitrification potential rates suggest that benthic ammonia-oxidizing bacteria and not Archaea dominate N cycling in the Colne Estuary, United Kingdom.},
journal = {Applied and environmental microbiology},
volume = {81},
number = {1},
pages = {159-165},
doi = {10.1128/AEM.02654-14},
pmid = {25326303},
issn = {1098-5336},
mesh = {Ammonia/*metabolism ; Archaea/*classification/genetics/isolation &amp; purification/*metabolism ; Bacteria/*classification/genetics/isolation &amp; purification/*metabolism ; Denaturing Gradient Gel Electrophoresis ; *Estuaries ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Nitrification ; Oxidation-Reduction ; Oxidoreductases/genetics ; Seasons ; Sequence Analysis, DNA ; United Kingdom ; },
abstract = {Nitrification, mediated by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), is important in global nitrogen cycling. In estuaries where gradients of salinity and ammonia concentrations occur, there may be differential selections for ammonia-oxidizer populations. The aim of this study was to examine the activity, abundance, and diversity of AOA and AOB in surface oxic sediments of a highly nutrified estuary that exhibits gradients of salinity and ammonium. AOB and AOA communities were investigated by measuring ammonia monooxygenase (amoA) gene abundance and nitrification potentials both spatially and temporally. Nitrification potentials differed along the estuary and over time, with the greatest nitrification potentials occurring mid-estuary (8.2 μmol N grams dry weight [gdw](-1) day(-1) in June, increasing to 37.4 μmol N gdw(-1) day(-1) in January). At the estuary head, the nitrification potential was 4.3 μmol N gdw(-1) day(-1) in June, increasing to 11.7 μmol N gdw(-1) day(-1) in January. At the estuary head and mouth, nitrification potentials fluctuated throughout the year. AOB amoA gene abundances were significantly greater (by 100-fold) than those of AOA both spatially and temporally. Nitrosomonas spp. were detected along the estuary by denaturing gradient gel electrophoresis (DGGE) band sequence analysis. In conclusion, AOB dominated over AOA in the estuarine sediments, with the ratio of AOB/AOA amoA gene abundance increasing from the upper (freshwater) to lower (marine) regions of the Colne estuary. These findings suggest that in this nutrified estuary, AOB (possibly Nitrosomonas spp.) were of major significance in nitrification.},
}
@article {pmid25324835,
year = {2014},
author = {Magalhães, CM and Machado, A and Frank-Fahle, B and Lee, CK and Cary, SC},
title = {The ecological dichotomy of ammonia-oxidizing archaea and bacteria in the hyper-arid soils of the Antarctic Dry Valleys.},
journal = {Frontiers in microbiology},
volume = {5},
number = {},
pages = {515},
doi = {10.3389/fmicb.2014.00515},
pmid = {25324835},
issn = {1664-302X},
abstract = {The McMurdo Dry Valleys of Antarctica are considered to be one of the most physically and chemically extreme terrestrial environments on the Earth. However, little is known about the organisms involved in nitrogen transformations in these environments. In this study, we investigated the diversity and abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in four McMurdo Dry Valleys with highly variable soil geochemical properties and climatic conditions: Miers Valley, Upper Wright Valley, Beacon Valley and Battleship Promontory. The bacterial communities of these four Dry Valleys have been examined previously, and the results suggested that the extremely localized bacterial diversities are likely driven by the disparate physicochemical conditions associated with these locations. Here we showed that AOB and AOA amoA gene diversity was generally low; only four AOA and three AOB operational taxonomic units (OTUs) were identified from a total of 420 AOA and AOB amoA clones. Quantitative PCR analysis of amoA genes revealed clear differences in the relative abundances of AOA and AOB amoA genes among samples from the four dry valleys. Although AOB amoA gene dominated the ammonia-oxidizing community in soils from Miers Valley and Battleship Promontory, AOA amoA gene were more abundant in samples from Upper Wright and Beacon Valleys, where the environmental conditions are considerably harsher (e.g., extremely low soil C/N ratios and much higher soil electrical conductivity). Correlations between environmental variables and amoA genes copy numbers, as examined by redundancy analysis (RDA), revealed that higher AOA/AOB ratios were closely related to soils with high salts and Cu contents and low pH. Our findings hint at a dichotomized distribution of AOA and AOB within the Dry Valleys, potentially driven by environmental constraints.},
}
@article {pmid25320442,
year = {2014},
author = {Devivaraprasad Reddy, A and Subrahmanyam, G and Shivani Kallappa, G and Karunasagar, I and Karunasagar, I},
title = {Detection of ammonia-oxidizing archaea in fish processing effluent treatment plants.},
journal = {Indian journal of microbiology},
volume = {54},
number = {4},
pages = {434-438},
doi = {10.1007/s12088-014-0484-6},
pmid = {25320442},
issn = {0046-8991},
abstract = {Ammonia oxidation is the rate limiting step in nitrification and thus have an important role in removal of ammonia in natural and engineered systems with participation of both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). However, their relative distribution and activity in fish processing effluent treatment plants (FPETPs) though significant, is hitherto unreported. Presence of AOA in sludge samples obtained from FPETPs was studied by amplification and sequencing of thaumarchaeal ammonia monooxygenase subunit A (AOA-amoA) gene. Different primer sets targeting 16S rRNA and AOA-amoA gene were used for the detection of AOA in FPETPs. Phylogenetic analysis of the gene revealed that the AOA was affiliated with thaumarchaeal group 1.1a lineage (marine cluster). Quantitative real time PCR of amoA gene was used to study the copy number of AOA and AOB in FPETPs. The AOA-amoA and AOB-amoA gene copy numbers of sludge samples ranged from 2.2 × 10(6) to 4.2 × 10(8) and 1.1 × 10(7) to 8.5 × 10(8) mg(-1) sludge respectively. Primer sets Arch-amoAF/Arch-amoAR and 340F/1000R were found to be useful for the sensitive detection of AOA-amoA and Archaeal 16S rRNA genes respectively in FPETPs. Their presence suggests the widespread occurrence and possible usefulness in removing ammonia from FPETPs which is in line with reports from other waste water treatment plants.},
}
@article {pmid25293379,
year = {2014},
author = {Chai, J and Kora, G and Ahn, TH and Hyatt, D and Pan, C},
title = {Functional phylogenomics analysis of bacteria and archaea using consistent genome annotation with UniFam.},
journal = {BMC evolutionary biology},
volume = {14},
number = {},
pages = {207},
doi = {10.1186/s12862-014-0207-y},
pmid = {25293379},
issn = {1471-2148},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; Databases, Protein ; Genome, Archaeal ; Genome, Bacterial ; Molecular Sequence Annotation/*methods ; Phylogeny ; },
abstract = {BACKGROUND: Phylogenetic studies have provided detailed knowledge on the evolutionary mechanisms of genes and species in Bacteria and Archaea. However, the evolution of cellular functions, represented by metabolic pathways and biological processes, has not been systematically characterized. Many clades in the prokaryotic tree of life have now been covered by sequenced genomes in GenBank. This enables a large-scale functional phylogenomics study of many computationally inferred cellular functions across all sequenced prokaryotes.<br><br>RESULTS: A total of 14,727 GenBank prokaryotic genomes were re-annotated using a new protein family database, UniFam, to obtain consistent functional annotations for accurate comparison. The functional profile of a genome was represented by the biological process Gene Ontology (GO) terms in its annotation. The GO term enrichment analysis differentiated the functional profiles between selected archaeal taxa. 706 prokaryotic metabolic pathways were inferred from these genomes using Pathway Tools and MetaCyc. The consistency between the distribution of metabolic pathways in the genomes and the phylogenetic tree of the genomes was measured using parsimony scores and retention indices. The ancestral functional profiles at the internal nodes of the phylogenetic tree were reconstructed to track the gains and losses of metabolic pathways in evolutionary history.<br><br>CONCLUSIONS: Our functional phylogenomics analysis shows divergent functional profiles of taxa and clades. Such function-phylogeny correlation stems from a set of clade-specific cellular functions with low parsimony scores. On the other hand, many cellular functions are sparsely dispersed across many clades with high parsimony scores. These different types of cellular functions have distinct evolutionary patterns reconstructed from the prokaryotic tree.},
}
@article {pmid25279954,
year = {2014},
author = {Anderson, RE and Sogin, ML and Baross, JA},
title = {Evolutionary strategies of viruses, bacteria and archaea in hydrothermal vent ecosystems revealed through metagenomics.},
journal = {PloS one},
volume = {9},
number = {10},
pages = {e109696},
doi = {10.1371/journal.pone.0109696},
pmid = {25279954},
issn = {1932-6203},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Biological Evolution ; Ecosystem ; Host-Pathogen Interactions ; Hydrothermal Vents/*microbiology/*virology ; Lysogeny ; Metagenomics/*methods ; Phylogeny ; Seawater/microbiology/virology ; Viruses/*genetics ; },
abstract = {The deep-sea hydrothermal vent habitat hosts a diverse community of archaea and bacteria that withstand extreme fluctuations in environmental conditions. Abundant viruses in these systems, a high proportion of which are lysogenic, must also withstand these environmental extremes. Here, we explore the evolutionary strategies of both microorganisms and viruses in hydrothermal systems through comparative analysis of a cellular and viral metagenome, collected by size fractionation of high temperature fluids from a diffuse flow hydrothermal vent. We detected a high enrichment of mobile elements and proviruses in the cellular fraction relative to microorganisms in other environments. We observed a relatively high abundance of genes related to energy metabolism as well as cofactors and vitamins in the viral fraction compared to the cellular fraction, which suggest encoding of auxiliary metabolic genes on viral genomes. Moreover, the observation of stronger purifying selection in the viral versus cellular gene pool suggests viral strategies that promote prolonged host integration. Our results demonstrate that there is great potential for hydrothermal vent viruses to integrate into hosts, facilitate horizontal gene transfer, and express or transfer genes that manipulate the hosts' functional capabilities.},
}
@article {pmid25257534,
year = {2014},
author = {Visone, V and Vettone, A and Serpe, M and Valenti, A and Perugino, G and Rossi, M and Ciaramella, M},
title = {Chromatin structure and dynamics in hot environments: architectural proteins and DNA topoisomerases of thermophilic archaea.},
journal = {International journal of molecular sciences},
volume = {15},
number = {9},
pages = {17162-17187},
doi = {10.3390/ijms150917162},
pmid = {25257534},
issn = {1422-0067},
mesh = {Archaea/genetics/*physiology ; Archaeal Proteins/chemistry/genetics/*physiology ; Chromatin/metabolism/*ultrastructure ; Climate ; DNA Topoisomerases/genetics/*physiology ; DNA Topoisomerases, Type I/chemistry/physiology ; DNA, Archaeal/chemistry/genetics/metabolism ; DNA-Binding Proteins/chemistry/genetics/physiology ; Gene Expression Regulation, Archaeal ; Genes, Archaeal ; Histones/chemistry/genetics/physiology ; *Hot Temperature ; Nucleic Acid Conformation ; Nucleosomes/metabolism/ultrastructure ; Protein Binding ; Protein Conformation ; Structure-Activity Relationship ; },
abstract = {In all organisms of the three living domains (Bacteria, Archaea, Eucarya) chromosome-associated proteins play a key role in genome functional organization. They not only compact and shape the genome structure, but also regulate its dynamics, which is essential to allow complex genome functions. Elucidation of chromatin composition and regulation is a critical issue in biology, because of the intimate connection of chromatin with all the essential information processes (transcription, replication, recombination, and repair). Chromatin proteins include architectural proteins and DNA topoisomerases, which regulate genome structure and remodelling at two hierarchical levels. This review is focussed on architectural proteins and topoisomerases from hyperthermophilic Archaea. In these organisms, which live at high environmental temperature (>80 °C <113 °C), chromatin proteins and modulation of the DNA secondary structure are concerned with the problem of DNA stabilization against heat denaturation while maintaining its metabolic activity.},
}
@article {pmid25250654,
year = {2014},
author = {Snelling, TJ and Genç, B and McKain, N and Watson, M and Waters, SM and Creevey, CJ and Wallace, RJ},
title = {Diversity and community composition of methanogenic archaea in the rumen of Scottish upland sheep assessed by different methods.},
journal = {PloS one},
volume = {9},
number = {9},
pages = {e106491},
doi = {10.1371/journal.pone.0106491},
pmid = {25250654},
issn = {1932-6203},
support = {BB/J004235/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J004243/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J004413/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; Biodiversity ; DNA, Archaeal/chemistry/genetics ; Euryarchaeota/genetics/growth &amp; development ; *Genetic Variation ; Geography ; Metagenome/genetics ; Methanobacteriaceae/growth &amp; development ; Methanobacteriales/classification/*genetics/growth &amp; development ; Methanobrevibacter/genetics/growth &amp; development ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Rumen/*microbiology ; Scotland ; Sequence Analysis, DNA ; Sheep ; },
abstract = {Ruminal archaeomes of two mature sheep grazing in the Scottish uplands were analysed by different sequencing and analysis methods in order to compare the apparent archaeal communities. All methods revealed that the majority of methanogens belonged to the Methanobacteriales order containing the Methanobrevibacter, Methanosphaera and Methanobacteria genera. Sanger sequenced 1.3 kb 16S rRNA gene amplicons identified the main species of Methanobrevibacter present to be a SGMT Clade member Mbb. millerae (≥ 91% of OTUs); Methanosphaera comprised the remainder of the OTUs. The primers did not amplify ruminal Thermoplasmatales-related 16S rRNA genes. Illumina sequenced V6-V8 16S rRNA gene amplicons identified similar Methanobrevibacter spp. and Methanosphaera clades and also identified the Thermoplasmatales-related order as 13% of total archaea. Unusually, both methods concluded that Mbb. rum