@article {pmid35968005,
year = {2022},
author = {Peng, Y and Xie, T and Wu, Z and Zheng, W and Zhang, T and Howe, S and Chai, J and Deng, F and Li, Y and Zhao, J},
title = {Archaea: An under-estimated kingdom in livestock animals.},
journal = {Frontiers in veterinary science},
volume = {9},
number = {},
pages = {973508},
doi = {10.3389/fvets.2022.973508},
pmid = {35968005},
issn = {2297-1769},
abstract = {Archaea are considered an essential group of gut microorganisms in both humans and animals. However, they have been neglected in previous studies, especially those involving non-ruminants. In this study, we re-analyzed published metagenomic and metatranscriptomic data sequenced from matched samples to explore the composition and the expression activity of gut archaea in ruminants (cattle and sheep) and monogastric animals (pig and chicken). Our results showed that the alpha and beta diversity of each host species, especially cattle and chickens, calculated from metagenomic and metatranscriptomic data were significantly different, suggesting that metatranscriptomic data better represent the functional status of archaea. We detected that the relative abundance of 17 (cattle), 7 (sheep), 20 (pig), and 2 (chicken) archaeal species were identified in the top 100 archaeal taxa when analyzing the metagenomic datasets, and these species were classified as the "active archaeal species" for each host species by comparison with corresponding metatranscriptomic data. For example, The expressive abundance in metatranscriptomic dataset of Methanosphaera cuniculi and Methanosphaera stadtmanae were 30- and 27-fold higher than that in metagenomic abundance, indicating their potentially important function in the pig gut. Here we aim to show the potential importance of archaea in the livestock digestive tract and encourage future research in this area, especially on the gut archaea of monogastric animals.},
}
@article {pmid35965098,
year = {2022},
author = {Zhao, H and Zhang, L},
title = {Metagenome-assembled Genomes of Six Novel Ammonia-oxidizing Archaea (AOA) from Agricultural Upland Soil.},
journal = {Microbes and environments},
volume = {37},
number = {3},
pages = {},
doi = {10.1264/jsme2.ME22035},
pmid = {35965098},
issn = {1347-4405},
abstract = {Ammonia-oxidizing archaea (AOA), key players in agricultural upland soil nitrification, convert soil ammonium to nitrite. The microbial oxidation of ammonia to nitrite is an important part of the global biogeochemical nitrogen cycle. In the present study, we recovered six novel AOA metagenome-assembled genomes (MAGs) containing genes for carbon (C) fixation and nitrogen (N) metabolism by using a deep shotgun metagenomic sequencing strategy. We also found that these AOA MAGs possessed cobalamin synthesis genes, suggesting that AOA are vitamin suppliers in agricultural upland soil. Collectively, the present results deepen our understanding of the metabolic potential and phylogeny of AOA in agroecosystems.},
}
@article {pmid35922624,
year = {2022},
author = {Ledesma, L and Hernandez-Guerrero, R and Perez-Rueda, E},
title = {Prediction of DNA-Binding Transcription Factors in Bacteria and Archaea Genomes.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2516},
number = {},
pages = {103-112},
pmid = {35922624},
issn = {1940-6029},
abstract = {DNA-binding transcription factors (TFs) play a central role in the gene expression of all organisms, from viruses to humans, including bacteria and archaea. The role of these proteins is the fate of gene expression in the context of environmental challenges. Because thousands of genomes have been sequenced to date, predictions of the encoded proteins are validated through the use of bioinformatics tools to obtain the necessary experimental, posterior knowledge. In this chapter, we describe three approaches to identify TFs in protein sequences. The first approach integrates the results of sequence comparisons and PFAM assignments, using as reference a manually curated collection of TFs. The second approach considers the prediction of DNA-binding structures, such as the classical helix-turn-helix (HTH); and the third approach considers a deep learning model. We suggest that all approaches must be considered together to increase the possibility of identifying new TFs in bacterial and archaeal genomes.},
}
@article {pmid35922623,
year = {2022},
author = {Sybers, D and Charlier, D and Peeters, E},
title = {In Vitro Transcription Assay for Archaea Belonging to Sulfolobales.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2516},
number = {},
pages = {81-102},
pmid = {35922623},
issn = {1940-6029},
abstract = {Archaeal transcription and its regulation are characterized by a mosaic of eukaryotic and bacterial features. Molecular analysis of the functioning of the archaeal RNA polymerase, basal transcription factors, and specific promoter-containing DNA templates allows to unravel the mechanisms of transcription regulation in archaea. In vitro transcription is a technique that allows the study of this process in a simplified and controlled environment less complex than the archaeal cell. In this chapter, we present an in vitro transcription methodology for the study of transcription in Sulfolobales. It is described how to purify the RNA polymerase and the basal transcription factors TATA-binding protein and transcription factor B of Saccharolobus solfataricus and how to perform in vitro transcription reactions and transcript detection. Application of this protocol for other archaeal species could require minor modifications to protein overexpression and purification conditions.},
}
@article {pmid35922619,
year = {2022},
author = {Maruyama, H},
title = {Micrococcal Nuclease Digestion Assays for the Analysis of Chromosome Structure in Archaea.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2516},
number = {},
pages = {29-38},
pmid = {35922619},
issn = {1940-6029},
abstract = {The digestion of chromosomes using micrococcal nuclease (MNase) enables the analysis of their fundamental structural units. For example, the digestion of eukaryotic chromatin using MNase results in laddered DNA fragments (~150 bp increment), which reflects the length of the DNA wrapped around regularly spaced nucleosomes. Here, we describe the application of MNase to examine the chromosome structure in Archaea. We used Thermococcus kodakarensis, a hyperthermophilic euryarchaeon that encodes proteins homologous to eukaryotic histones. Methods for chromosome extraction and agarose gel electrophoresis of MNase-digested DNA including small fragments (~30 bp) are also described.},
}
@article {pmid35922618,
year = {2022},
author = {Rashid, FM and Detmar, L and Dame, RT},
title = {Chromosome Conformation Capture in Bacteria and Archaea.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2516},
number = {},
pages = {1-28},
pmid = {35922618},
issn = {1940-6029},
abstract = {The three-dimensional structure of the chromosome is encoded within its sequence and regulates activities such as replication and transcription. This necessitates the study of the spatial organization of the chromosome in relation to the underlying sequence. Chromosome conformation capture (3C) techniques are proximity ligation-based approaches that simplify the three-dimensional architecture of the chromosome into a one-dimensional library of hybrid ligation junctions. Deciphering the information contained in these libraries resolves chromosome architecture in a sequence-specific manner. This chapter describes the preparation of 3C libraries for bacteria and archaea. It details how the three-dimensional architecture of local chromatin can be extracted from the 3C library using qPCR (3C-qPCR), and it summarizes the processing of 3C libraries for next-generation sequencing (3C-Seq) for a study of global chromosome organization.},
}
@article {pmid35922580,
year = {2022},
author = {Wang, BB and Sun, YP and Wu, ZP and Zheng, XW and Hou, J and Cui, HL},
title = {Halorientalis salina sp. nov., Halorientalis marina sp. nov., Halorientalis litorea sp. nov.: three extremely halophilic archaea isolated from a salt lake and coarse sea salt.},
journal = {Extremophiles : life under extreme conditions},
volume = {26},
number = {3},
pages = {26},
pmid = {35922580},
issn = {1433-4909},
support = {32070003//National Natural Science Foundation of China/ ; },
abstract = {Three halophilic archaeal strains, NEN8T, GDY88T and ZY14T, were isolated from a salt lake in Tibet and coarse sea salt samples from Guangdong and Hebei, China, respectively. These strains formed three separate clades (showing 94.4-95.8% and 87.1-89.4% similarities, respectively) and then clustered with the current Halorientalis members (showing 90.7-97.6% and 87.0-91.2% similarities, respectively), as revealed by phylogenetic analyses based on 16S rRNA and rpoB' genes. The overall genome-related index, average nucleotide identity (ANI), in silico DNA-DNA hybridization (DDH), average amino acid identity (AAI) and the percentage of conserved proteins (POCP) values, among the three strains and members of the genus Halorientalis were 76.0-88.0%, 21.3-37.2%, 69.0-88.3% and 57.7-78.1%, clearly below the threshold values for species demarcation. Strains NEN8T, GDY88T and ZY14T could be distinguished from current Halorientalis species according to differential phenotypic characteristics. The major polar lipids of the three strains were phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), sulfated mannosyl glucosyl diether (S-DGD-1) and disulfated mannosyl glucosyl diether (S2-DGD). In addition, mannosyl glucosyl diether (DGD-1) was detected in strain NEN8T and phosphatidic acid (PA), posssulfated galactosyl mannosyl glucosyl diether (S-TGD-1) and sulfated mannosyl glucosyl diether-phosphatidic acid (S-DGD-PA) were observed in strain ZY14T. These results revealed that strains NEN8T (= CGMCC 1.17213T = JCM 34155T), GDY88T (= CGMCC 1.18548T = JCM 34481T) and ZY14T (= CGMCC 1.17178T = JCM 34154T) represent three novel species of the genus Halorientalis, for which the names Halorientalis salina sp. nov., Halorientalis marina sp. nov. and Halorientalis litorea sp. nov. are proposed.},
}
@article {pmid35917471,
year = {2022},
author = {Wegener, G and Laso-Pérez, R and Orphan, VJ and Boetius, A},
title = {Anaerobic Degradation of Alkanes by Marine Archaea.},
journal = {Annual review of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-micro-111021-045911},
pmid = {35917471},
issn = {1545-3251},
abstract = {Alkanes are saturated apolar hydrocarbons that range from its simplest form, methane, to high-molecular-weight compounds. Although alkanes were once considered biologically recalcitrant under anaerobic conditions, microbiological investigations have now identified several microbial taxa that can anaerobically degrade alkanes. Here we review recent discoveries in the anaerobic oxidation of alkanes with a specific focus on archaea that use specific methyl coenzyme M reductases to activate their substrates. Our understanding of the diversity of uncultured alkane-oxidizing archaea has expanded through the use of environmental metagenomics and enrichment cultures of syntrophic methane-, ethane-, propane-, and butane-oxidizing marine archaea with sulfate-reducing bacteria. A recently cultured group of archaea directly couples long-chain alkane degradation with methane formation, expanding the range of substrates used for methanogenesis. This article summarizes the rapidly growing knowledge of the diversity, physiology, and habitat distribution of alkane-degrading archaea. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.},
}
@article {pmid35852729,
year = {2022},
author = {Flusche, T and Rajan, R},
title = {Molecular Details of DNA Integration by CRISPR-Associated Proteins During Adaptation in Bacteria and Archaea.},
journal = {Advances in experimental medicine and biology},
volume = {},
number = {},
pages = {},
pmid = {35852729},
issn = {0065-2598},
abstract = {Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins constitute an adaptive immune system in bacteria and archaea, where immunological memory is retained in the CRISPR locus as short pieces of the intruding nucleic acid, termed spacers. The adaptation to new infections occurs through the integration of a new spacer into the CRISPR array. For immune protection, spacers are transcribed into CRISPR RNAs (crRNA) that are used to guide the effector nuclease of the system in sequence-dependent target cleavage. Spacers originate as a prespacer from either DNA or RNA depending on the CRISPR-Cas system being observed, and the nearly universal Cas proteins, Cas1 and Cas2, insert the prespacer into the CRISPR locus during adaptation in all systems that contain them. The mechanism of site-specific prespacer integration varies across CRISPR classes and types, and distinct differences can even be found within the same subtype. In this review, the current knowledge on the mechanisms of prespacer integration in type II-A CRISPR-Cas systems will be described. Comparisons of the currently characterized type II-A systems show that distinct mechanisms exist within different members of this subtype and are correlated to sequence-specific interactions of Cas proteins and the DNA elements present in the CRISPR array. These observations indicate that nature has fine-tuned the mechanistic details while performing the basic step of DNA integration by Cas proteins, which offers unique advantages to develop Cas1-Cas2-based biotechnology.},
}
@article {pmid35905325,
year = {2022},
author = {Rattanasriampaipong, R and Zhang, YG and Pearson, A and Hedlund, BP and Zhang, S},
title = {Archaeal lipids trace ecology and evolution of marine ammonia-oxidizing archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {31},
pages = {e2123193119},
doi = {10.1073/pnas.2123193119},
pmid = {35905325},
issn = {1091-6490},
support = {26G(GG009393-04)//Columbia | LDEO | U.S. Science Support Program, Lamont-Doherty Earth Observatory (USSSP, LDEO)/ ; },
abstract = {Archaeal membrane lipids are widely used for paleotemperature reconstructions, yet these molecular fossils also bear rich information about ecology and evolution of marine ammonia-oxidizing archaea (AOA). Here we identified thermal and nonthermal behaviors of archaeal glycerol dialkyl glycerol tetraethers (GDGTs) by comparing the GDGT-based temperature index (TEX86) to the ratio of GDGTs with two and three cyclopentane rings (GDGT-2/GDGT-3). Thermal-dependent biosynthesis should increase TEX86 and decrease GDGT-2/GDGT-3 when the ambient temperature increases. This presumed temperature-dependent (PTD) trend is observed in GDGTs derived from cultures of thermophilic and mesophilic AOA. The distribution of GDGTs in suspended particulate matter (SPM) and sediments collected from above the pycnocline-shallow water samples-also follows the PTD trend. These similar GDGT distributions between AOA cultures and shallow water environmental samples reflect shallow ecotypes of marine AOA. While there are currently no cultures of deep AOA clades, GDGTs derived from deep water SPM and marine sediment samples exhibit nonthermal behavior deviating from the PTD trend. The presence of deep AOA increases the GDGT-2/GDGT-3 ratio and distorts the temperature-controlled correlation between GDGT-2/GDGT-3 and TEX86. We then used Gaussian mixture models to statistically characterize these diagnostic patterns of modern AOA ecology from paleo-GDGT records to infer the evolution of marine AOA from the Mid-Mesozoic to the present. Long-term GDGT-2/GDGT-3 trends suggest a suppression of today's deep water marine AOA during the Mesozoic-early Cenozoic greenhouse climates. Our analysis provides invaluable insights into the evolutionary timeline and the expansion of AOA niches associated with major oceanographic and climate changes.},
}
@article {pmid35886964,
year = {2022},
author = {Chong, PL and Chang, A and Yu, A and Mammedova, A},
title = {Vesicular and Planar Membranes of Archaea Lipids: Unusual Physical Properties and Biomedical Applications.},
journal = {International journal of molecular sciences},
volume = {23},
number = {14},
pages = {},
doi = {10.3390/ijms23147616},
pmid = {35886964},
issn = {1422-0067},
mesh = {*Archaea ; Lipids ; *Liposomes ; Membranes ; Protons ; },
abstract = {Liposomes and planar membranes made of archaea or archaea-like lipids exhibit many unusual physical properties compared to model membranes composed of conventional diester lipids. Here, we review several recent findings in this research area, which include (1) thermosensitive archaeosomes with the capability to drastically change the membrane surface charge, (2) MthK channel's capability to insert into tightly packed tetraether black lipid membranes and exhibit channel activity with surprisingly high calcium sensitivity, and (3) the intercalation of apolar squalane into the midplane space of diether bilayers to impede proton permeation. We also review the usage of tetraether archaeosomes as nanocarriers of therapeutics and vaccine adjuvants, as well as the biomedical applications of planar archaea lipid membranes. The discussion on archaeosomal therapeutics is focused on partially purified tetraether lipid fractions such as the polar lipid fraction E (PLFE) and glyceryl caldityl tetraether (GCTE), which are the main components of PLFE with the sugar and phosphate removed.},
}
@article {pmid35880875,
year = {2022},
author = {Boswinkle, K and McKinney, J and Allen, KD},
title = {Highlighting the Unique Roles of Radical S-Adenosylmethionine Enzymes in Methanogenic Archaea.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0019722},
doi = {10.1128/jb.00197-22},
pmid = {35880875},
issn = {1098-5530},
abstract = {Radical S-adenosylmethionine (SAM) enzymes catalyze an impressive variety of difficult biochemical reactions in various pathways across all domains of life. These metalloenzymes employ a reduced [4Fe-4S] cluster and SAM to generate a highly reactive 5'-deoxyadenosyl radical that is capable of initiating catalysis on otherwise unreactive substrates. Interestingly, the genomes of methanogenic archaea encode many unique radical SAM enzymes with underexplored or completely unknown functions. These organisms are responsible for the yearly production of nearly 1 billion tons of methane, a potent greenhouse gas as well as a valuable energy source. Thus, understanding the details of methanogenic metabolism and elucidating the functions of essential enzymes in these organisms can provide insights into strategies to decrease greenhouse gas emissions as well as inform advances in bioenergy production processes. This minireview provides an overview of the current state of the field regarding the functions of radical SAM enzymes in methanogens and discusses gaps in knowledge that should be addressed.},
}
@article {pmid35811376,
year = {2022},
author = {Villain, P and Catchpole, R and Forterre, P and Oberto, J and da Cunha, V and Basta, T},
title = {Expanded dataset reveals the emergence and evolution of DNA gyrase in Archaea.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msac155},
pmid = {35811376},
issn = {1537-1719},
abstract = {DNA gyrase is a type II topoisomerase with the unique capacity to introduce negative supercoiling in DNA. In bacteria, DNA gyrase has an essential role in the homeostatic regulation of supercoiling. While ubiquitous in Bacteria, DNA gyrase was previously reported to have a patchy distribution in Archaea but its emergent function and evolutionary history in this domain of life remains elusive. In this study, we used phylogenomic approaches and an up-to date sequence dataset to establish global and archaea-specific phylogenies of DNA gyrases. The most parsimonious evolutionary scenario infers that DNA gyrase was introduced into the lineage leading to Euryarchaeal group II via a single horizontal gene transfer from a bacterial donor which we identified as an ancestor of Gracilicutes and/or Terrabacteria. The archaea-focused trees indicate that DNA gyrase spread from Euryarchaeal group II to some DPANN and Asgard lineages via rare horizontal gene transfers. The analysis of successful recent transfers suggests a requirement for syntropic or symbiotic/parasitic relationship between donor and recipient organisms. We further show that the ubiquitous archaeal Topoisomerase VI may have co-evolved with DNA gyrase to allow the division of labour in the management of topological constraints. Collectively, our study reveals the evolutionary history of DNA gyrase in Archaea and provides testable hypotheses to understand the prerequisites for successful establishment of DNA gyrase in a naïve archaeon and the associated adaptations in the management of topological constraints.},
}
@article {pmid35810262,
year = {2022},
author = {Ou, YF and Dong, HP and McIlroy, SJ and Crowe, SA and Hallam, SJ and Han, P and Kallmeyer, J and Simister, RL and Vuillemin, A and Leu, AO and Liu, Z and Zheng, YL and Sun, QL and Liu, M and Tyson, GW and Hou, LJ},
title = {Expanding the phylogenetic distribution of cytochrome b-containing methanogenic archaea sheds light on the evolution of methanogenesis.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
pmid = {35810262},
issn = {1751-7370},
support = {41725002//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030411//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Methane produced by methanogenic archaea has an important influence on Earth's changing climate. Methanogenic archaea are phylogenetically diverse and widespread in anoxic environments. These microorganisms can be divided into two subgroups based on whether or not they use b-type cytochromes for energy conservation. Methanogens with b-type cytochromes have a wider substrate range and higher growth yields than those without them. To date, methanogens with b-type cytochromes were found exclusively in the phylum "Ca. Halobacteriota" (formerly part of the phylum Euryarchaeota). Here, we present the discovery of metagenome-assembled genomes harboring methyl-coenzyme M reductase genes reconstructed from mesophilic anoxic sediments, together with the previously reported thermophilic "Ca. Methylarchaeum tengchongensis", representing a novel archaeal order, designated the "Ca. Methylarchaeales", of the phylum Thermoproteota (formerly the TACK superphylum). These microorganisms contain genes required for methyl-reducing methanogenesis and the Wood-Ljundahl pathway. Importantly, the genus "Ca. Methanotowutia" of the "Ca. Methylarchaeales" encode a cytochrome b-containing heterodisulfide reductase (HdrDE) and methanophenazine-reducing hydrogenase complex that have similar gene arrangements to those found in methanogenic Methanosarcinales. Our results indicate that members of the "Ca. Methylarchaeales" are methanogens with cytochromes and can conserve energy via membrane-bound electron transport chains. Phylogenetic and amalgamated likelihood estimation analyses indicate that methanogens with cytochrome b-containing electron transfer complexes likely evolved before diversification of Thermoproteota or "Ca. Halobacteriota" in the early Archean Eon. Surveys of public sequence databases suggest that members of the lineage are globally distributed in anoxic sediments and may be important players in the methane cycle.},
}
@article {pmid35796992,
year = {2022},
author = {Kern, M and Ferreira-Cerca, S},
title = {Differential Translation Activity Analysis Using Bioorthogonal Noncanonical Amino Acid Tagging (BONCAT) in Archaea.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2533},
number = {},
pages = {229-246},
pmid = {35796992},
issn = {1940-6029},
abstract = {The study of protein production and degradation in a quantitative and time-dependent manner is a major challenge to better understand cellular physiological response. Among available technologies bioorthogonal noncanonical amino acid tagging (BONCAT) is an efficient approach allowing for time-dependent labeling of proteins through the incorporation of chemically reactive noncanonical amino acids like L-azidohomoalanine (L-AHA). The azide-containing amino-acid derivative enables a highly efficient and specific reaction termed click chemistry, whereby the azide group of the L-AHA reacts with a reactive alkyne derivate, like dibenzocyclooctyne (DBCO) derivatives, using strain-promoted alkyne-azide cycloaddition (SPAAC). Moreover, available DBCO containing reagents are versatile and can be coupled to fluorophore (e.g., Cy7) or affinity tag (e.g., biotin) derivatives, for easy visualization and affinity purification, respectively.Here, we describe a step-by-step BONCAT protocol optimized for the model archaeon Haloferax volcanii , but which is also suitable to harness other biological systems. Finally, we also describe examples of downstream visualization, affinity purification of L-AHA-labeled proteins and differential expression analysis.In conclusion, the following BONCAT protocol expands the available toolkit to explore proteostasis using time-resolved semiquantitative proteomic analysis in archaea .},
}
@article {pmid35773279,
year = {2022},
author = {Buessecker, S and Palmer, M and Lai, D and Dimapilis, J and Mayali, X and Mosier, D and Jiao, JY and Colman, DR and Keller, LM and St John, E and Miranda, M and Gonzalez, C and Gonzalez, L and Sam, C and Villa, C and Zhuo, M and Bodman, N and Robles, F and Boyd, ES and Cox, AD and St Clair, B and Hua, ZS and Li, WJ and Reysenbach, AL and Stott, MB and Weber, PK and Pett-Ridge, J and Dekas, AE and Hedlund, BP and Dodsworth, JA},
title = {An essential role for tungsten in the ecology and evolution of a previously uncultivated lineage of anaerobic, thermophilic Archaea.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {3773},
pmid = {35773279},
issn = {2041-1723},
support = {91951205//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Trace metals have been an important ingredient for life throughout Earth's history. Here, we describe the genome-guided cultivation of a member of the elusive archaeal lineage Caldarchaeales (syn. Aigarchaeota), Wolframiiraptor gerlachensis, and its growth dependence on tungsten. A metagenome-assembled genome (MAG) of W. gerlachensis encodes putative tungsten membrane transport systems, as well as pathways for anaerobic oxidation of sugars probably mediated by tungsten-dependent ferredoxin oxidoreductases that are expressed during growth. Catalyzed reporter deposition-fluorescence in-situ hybridization (CARD-FISH) and nanoscale secondary ion mass spectrometry (nanoSIMS) show that W. gerlachensis preferentially assimilates xylose. Phylogenetic analyses of 78 high-quality Wolframiiraptoraceae MAGs from terrestrial and marine hydrothermal systems suggest that tungsten-associated enzymes were present in the last common ancestor of extant Wolframiiraptoraceae. Our observations imply a crucial role for tungsten-dependent metabolism in the origin and evolution of this lineage, and hint at a relic metabolic dependence on this trace metal in early anaerobic thermophiles.},
}
@article {pmid35770746,
year = {2022},
author = {Cai, M and Tang, X},
title = {Human Archaea and Associated Metabolites in Health and Disease.},
journal = {Biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.biochem.2c00232},
pmid = {35770746},
issn = {1520-4995},
abstract = {Trillions of microorganisms, including bacteria, archaea, fungi, and viruses, live in or on the human body. Microbe-microbe and microbe-host interactions are often influenced by diffusible and microbe-associated small molecules. Over the past few years, it has become evident that these interactions have a substantial impact on human health and disease. In this Perspective, we summarize the research involving the discovery of methanogenic and non-methanogenic archaea associated with the human body. In particular, we emphasize the importance of some archaeal metabolites in mediating intra- and interspecies interactions in the ecological environment of the human body. A deep understanding of the archaeal metabolites as well as their biological functions may reveal in more detail whether and how archaea are involved in maintaining human health and/or causing certain diseases.},
}
@article {pmid35765181,
year = {2022},
author = {Kropp, C and Lipp, J and Schmidt, AL and Seisenberger, C and Linde, M and Hinrichs, KU and Babinger, P},
title = {Identification of acetylated diether lipids in halophilic Archaea.},
journal = {MicrobiologyOpen},
volume = {11},
number = {3},
pages = {e1299},
doi = {10.1002/mbo3.1299},
pmid = {35765181},
issn = {2045-8827},
support = {//None/ ; },
abstract = {As a hallmark of Archaea, their cell membranes are comprised of ether lipids. However, Archaea-type ether lipids have recently been identified in Bacteria as well, with a somewhat different composition: In Bacillales, sn-glycerol 1-phosphate is etherified with one C35 isoprenoid chain, which is longer than the typical C20 chain in Archaea, and instead of a second isoprenoid chain, the product heptaprenylglyceryl phosphate becomes dephosphorylated and afterward diacetylated by the O-acetyltransferase YvoF. Interestingly, database searches have revealed YvoF homologs in Halobacteria (Archaea), too. Here, we demonstrate that YvoF from Haloferax volcanii can acetylate geranylgeranylglycerol in vitro. Additionally, we present the first-time identification of acetylated diether lipids in H. volcanii and Halobacterium salinarum by mass spectrometry. A variety of different acetylated lipids, namely acetylated archaeol, and acetylated archaetidylglycerol, were found, suggesting that halobacterial YvoF has a broad substrate range. We suppose that the acetyl group might serve to modify the polarity of the lipid headgroup, with still unknown biological effects.},
}
@article {pmid35761090,
year = {2022},
author = {Banciu, HL and Gridan, IM and Zety, AV and Baricz, A},
title = {Asgard archaea in saline environments.},
journal = {Extremophiles : life under extreme conditions},
volume = {26},
number = {2},
pages = {21},
pmid = {35761090},
issn = {1433-4909},
support = {PN-III-P4-ID-PCE-2020-1559//Ministry of Research, Innovation and Digitization, CNCS/CCCDI - UEFISCDI/ ; },
abstract = {Members of candidate Asgardarchaeota superphylum appear to share numerous eukaryotic-like attributes thus being broadly explored for their relevance to eukaryogenesis. On the contrast, the ecological roles of Asgard archaea remains understudied. Asgard archaea have been frequently associated to low-oxygen aquatic sedimentary environments worldwide spanning a broad but not extreme salinity range. To date, the available information on diversity and potential biogeochemical roles of Asgardarchaeota mostly sourced from marine habitats and to a much lesser extend from true saline environments (i.e., > 3% w/v total salinity). Here, we provide an overview on diversity and ecological implications of Asgard archaea distributed across saline environments and briefly explore their metagenome-resolved potential for osmoadaptation. Loki-, Thor- and Heimdallarchaeota are the dominant Asgard clades in saline habitats where they might employ anaerobic/microaerophilic organic matter degradation and autotrophic carbon fixation. Homologs of primary solute uptake ABC transporters seemingly prevail in Thorarchaeota, whereas those putatively involved in trehalose and ectoine biosynthesis were mostly inferred in Lokiarchaeota. We speculate that Asgardarchaeota might adopt compatible solute-accumulating ('salt-out') strategy as response to salt stress. Our current understanding on the distribution, ecology and salt-adaptive strategies of Asgardarchaeota in saline environments are, however, limited by insufficient sampling and incompleteness of the available metagenome-assembled genomes. Extensive sampling combined with 'omics'- and cultivation-based approaches seem, therefore, crucial to gain deeper knowledge on this particularly intriguing archaeal lineage.},
}
@article {pmid35760837,
year = {2022},
author = {Rambo, IM and Langwig, MV and Leão, P and De Anda, V and Baker, BJ},
title = {Genomes of six viruses that infect Asgard archaea from deep-sea sediments.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {35760837},
issn = {2058-5276},
support = {73592LPI//Simons Foundation/ ; 687165//Simons Foundation/ ; },
abstract = {Asgard archaea are globally distributed prokaryotic microorganisms related to eukaryotes; however, viruses that infect these organisms have not been described. Here, using metagenome sequences recovered from deep-sea hydrothermal sediments, we characterize six relatively large (up to 117 kb) double-stranded DNA (dsDNA) viral genomes that infected two Asgard archaeal phyla, Lokiarchaeota and Helarchaeota. These viruses encode Caudovirales-like structural proteins, as well as proteins distinct from those described in known archaeal viruses. Their genomes contain around 1-5% of genes associated with eukaryotic nucleocytoplasmic large DNA viruses (NCLDVs) and appear to be capable of semi-autonomous genome replication, repair, epigenetic modifications and transcriptional regulation. Moreover, Helarchaeota viruses may hijack host ubiquitin systems similar to eukaryotic viruses. Genomic analysis of these Asgard viruses reveals that they contain features of both prokaryotic and eukaryotic viruses, and provides insights into their potential infection and host interaction mechanisms.},
}
@article {pmid35759872,
year = {2022},
author = {Garcia, PS and Gribaldo, S and Borrel, G},
title = {Diversity and Evolution of Methane-Related Pathways in Archaea.},
journal = {Annual review of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-micro-041020-024935},
pmid = {35759872},
issn = {1545-3251},
abstract = {Methane is one of the most important greenhouse gases on Earth and holds an important place in the global carbon cycle. Archaea are the only organisms that use methanogenesis to produce energy and rely on the methyl-coenzyme M reductase (Mcr) complex. Over the last decade, new results have significantly reshaped our view of the diversity of methane-related pathways in the Archaea. Many new lineages that synthesize or use methane have been identified across the whole archaeal tree, leading to a greatly expanded diversity of substrates and mechanisms. In this review, we present the state of the art of these advances and how they challenge established scenarios of the origin and evolution of methanogenesis, and we discuss the potential trajectories that may have led to this strikingly wide range of metabolisms.Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.},
}
@article {pmid35751084,
year = {2022},
author = {Xiong, X and Rao, Y and Tu, X and Wang, Z and Gong, J and Yang, Y and Wu, H and Liu, X},
title = {Gut archaea associated with bacteria colonization and succession during piglet weaning transitions.},
journal = {BMC veterinary research},
volume = {18},
number = {1},
pages = {243},
pmid = {35751084},
issn = {1746-6148},
abstract = {BACKGROUND: Host-associated gut microbial communities are key players in shaping the fitness and health of animals. However, most current studies have focused on the gut bacteria, neglecting important gut fungal and archaeal components of these communities. Here, we investigated the gut fungi and archaea community composition in Large White piglets using shotgun metagenomic sequencing, and systematically evaluated how community composition association with gut microbiome, functional capacity, and serum metabolites varied across three weaning periods.<br><br>RESULTS: We found that Mucoromycota, Ascomycota and Basidiomycota were the most common fungi phyla and Euryarchaeota was the most common archaea phyla across individuals. We identified that Methanosarcina siciliae was the most significantly different archaea species among three weaning periods, while Parasitella parasitica, the only differential fungi species, was significantly and positively correlated with Methanosarcina siciliae enriched in day 28 group. The random forest analysis also identified Methanosarcina siciliae and Parasitella parasitica as weaning-biased archaea and fungi at the species level. Additionally, Methanosarcina siciliae was significantly correlated with P. copri and the shifts of functional capacities of the gut microbiome and several CAZymes in day 28 group. Furthermore, characteristic successional alterations in gut archaea, fungi, bacteria, and serum metabolites with each weaning step revealed a weaning transition coexpression network, e.g., Methanosarcina siciliae and P. copri were positively and significantly correlated with 15-HEPE, 8-O-Methyloblongine, and Troxilin B3.<br><br>CONCLUSION: Our findings provide a deep insight into the interactions among gut archaea, fungi, bacteria, and serum metabolites and will present a theoretical framework for understanding gut bacterial colonization and succession association with archaea during piglet weaning transitions.},
}
@article {pmid35743947,
year = {2022},
author = {Doytchinov, VV and Dimov, SG},
title = {Microbial Community Composition of the Antarctic Ecosystems: Review of the Bacteria, Fungi, and Archaea Identified through an NGS-Based Metagenomics Approach.},
journal = {Life (Basel, Switzerland)},
volume = {12},
number = {6},
pages = {},
doi = {10.3390/life12060916},
pmid = {35743947},
issn = {2075-1729},
support = {70-25-72 from 03.08.2021//NATIONAL CENTER FOR POLAR STUDIES - SOFIA UNIVERSITY "ST. KLIMENT OHRIDSKI"/ ; },
abstract = {Antarctica represents a unique environment, both due to the extreme meteorological and geological conditions that govern it and the relative isolation from human influences that have kept its environment largely undisturbed. However, recent trends in climate change dictate an unavoidable change in the global biodiversity as a whole, and pristine environments, such as Antarctica, allow us to study and monitor more closely the effects of the human impact. Additionally, due to its inaccessibility, Antarctica contains a plethora of yet uncultured and unidentified microorganisms with great potential for useful biological activities and production of metabolites, such as novel antibiotics, proteins, pigments, etc. In recent years, amplicon-based next-generation sequencing (NGS) has allowed for a fast and thorough examination of microbial communities to accelerate the efforts of unknown species identification. For these reasons, in this review, we present an overview of the archaea, bacteria, and fungi present on the Antarctic continent and the surrounding area (maritime Antarctica, sub-Antarctica, Southern Sea, etc.) that have recently been identified using amplicon-based NGS methods.},
}
@article {pmid35741701,
year = {2022},
author = {Ding, R and Yang, N and Liu, J},
title = {The Osmoprotectant Switch of Potassium to Compatible Solutes in an Extremely Halophilic Archaea Halorubrum kocurii 2020YC7.},
journal = {Genes},
volume = {13},
number = {6},
pages = {},
doi = {10.3390/genes13060939},
pmid = {35741701},
issn = {2073-4425},
abstract = {The main osmoadaptive mechanisms of extremely halophilic archaea include the "salt-in" strategy and the "compatible solutes" strategy. Here we report the osmoadaptive mechanism of an extremely halophilic archaea H. kocurii 2020YC7, isolated from a high salt environment sample. Genomic data revealed that strain 2020YC7 harbors genes trkA, trkH, kch for K+ uptake, kefB for K+ output, treS for trehalose production from polysaccharide, and betaine/carnitine/choline transporter family gene for glycine betaine uptake. Strain 2020YC7 could accumulate 8.17 to 28.67 μmol/mg protein K+ in a defined medium, with its content increasing along with the increasing salinity from 100 to 200 g/L. When exogenous glycine betaine was added, glycine betaine functioned as the primary osmotic solute between 200 and 250 g/L NaCl, which was accumulated up to 15.27 mg/mg protein in 2020YC7 cells. RT-qPCR results completely confirmed these results. Notably, the concentrations of intracellular trehalose decreased from 5.26 to 2.61 mg/mg protein as the NaCl increased from 50 to 250 g/L. In combination with this result, the transcript level of gene treS, which catalyzes the production of trehalose from polysaccharide, was significantly up-regulated at 50-100 g/L NaCl. Therefore, trehalose does not act as an osmotic solute at high NaCl concentrations (more than 100 g/L) but at relatively low NaCl concentrations (50-100 g/L). And we propose that the degradation of cell wall polysaccharide, as a source of trehalose in a low-salt environment, may be one of the reasons for the obligate halophilic characteristics of strain 2020YC7.},
}
@article {pmid35720372,
year = {2022},
author = {Krawczyk, KT and Locht, C and Kowalewicz-Kulbat, M},
title = {Halophilic Archaea Halorhabdus Rudnickae and Natrinema Salaciae Activate Human Dendritic Cells and Orient T Helper Cell Responses.},
journal = {Frontiers in immunology},
volume = {13},
number = {},
pages = {833635},
doi = {10.3389/fimmu.2022.833635},
pmid = {35720372},
issn = {1664-3224},
mesh = {Cytokines ; Dendritic Cells ; *Halobacteriaceae ; Humans ; *Interleukin-13/pharmacology ; T-Lymphocytes, Helper-Inducer ; },
abstract = {Halophilic archaea are procaryotic organisms distinct from bacteria, known to thrive in hypersaline environments, including salt lakes, salterns, brines and salty food. They have also been identified in the human microbiome. The biological significance of halophiles for human health has rarely been examined. The interactions between halophilic archaea and human dendritic cells (DCs) and T cells have not been identified so far. Here, we show for the first time that the halophilic archaea Halorhabdus rudnickae and Natrinema salaciae activate human monocyte-derived DCs, induce DC maturation, cytokine production and autologous T cell activation. In vitro both strains induced DC up-regulation of the cell-surface receptors CD86, CD80 and CD83, and cytokine production, including IL-12p40, IL-10 and TNF-α, but not IL-23 and IL-12p70. Furthermore, autologous CD4+ T cells produced significantly higher amounts of IFN-γ and IL-13, but not IL-17A when co-cultured with halophile-stimulated DCs in comparison to T cells co-cultured with unstimulated DCs. IFN-γ was almost exclusively produced by naïve T cells, while IL-13 was produced by both naïve and memory CD4+ T cells. Our findings thus show that halophilic archaea are recognized by human DCs and are able to induce a balanced cytokine response. The immunomodulatory functions of halophilic archaea and their potential ability to re-establish the immune balance may perhaps participate in the beneficial effects of halotherapies.},
}
@article {pmid35706137,
year = {2022},
author = {Hu, W and Hou, Q and Delgado-Baquerizo, M and Stegen, JC and Du, Q and Dong, L and Ji, M and Sun, Y and Yao, S and Gong, H and Xiong, J and Xia, R and Liu, J and Aqeel, M and Akram, MA and Ran, J and Deng, J},
title = {Continental-scale niche differentiation of dominant topsoil archaea in drylands.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.16099},
pmid = {35706137},
issn = {1462-2920},
abstract = {Archaea represent a diverse group of microorganisms often associated with extreme environments. However, an integrated understanding of biogeographical patterns of the specialist Haloarchaea and the potential generalist ammonia-oxidizing archaea (AOA) across large-scale environmental gradients remains limited. We hypothesize that niche differentiation determines their distinct distributions along environmental gradients. To test the hypothesis, we use a continental-scale research network including 173 dryland sites across northern China. Our results demonstrate that Haloarchaea and AOA dominate topsoil archaeal communities. As hypothesized, Haloarchaea and AOA show strong niche differentiation associated with two ecosystem types mainly found in China's drylands (i.e., deserts vs. grasslands), and they differ in the degree of habitat specialization. The relative abundance and richness of Haloarchaea are higher in deserts due to specialization to relatively high soil salinity and extreme climates, while those of AOA are greater in grassland soils. Our results further indicate a divergence in ecological processes underlying the segregated distributions of Haloarchaea and AOA. Haloarchaea are governed primarily by environmental-based processes while the more generalist AOA are assembled mostly via spatial-based processes. Our findings add to existing knowledge of large-scale biogeography of topsoil archaea, advancing our predictive understanding on changes in topsoil archaeal communities in a drier world. This article is protected by copyright. All rights reserved.},
}
@article {pmid35697693,
year = {2022},
author = {Hatano, T and Palani, S and Papatziamou, D and Salzer, R and Souza, DP and Tamarit, D and Makwana, M and Potter, A and Haig, A and Xu, W and Townsend, D and Rochester, D and Bellini, D and Hussain, HMA and Ettema, TJG and Löwe, J and Baum, B and Robinson, NP and Balasubramanian, M},
title = {Asgard archaea shed light on the evolutionary origins of the eukaryotic ubiquitin-ESCRT machinery.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {3398},
pmid = {35697693},
issn = {2041-1723},
support = {203276/Z/16/Z//Wellcome Trust (Wellcome)/ ; WT101885MA//Wellcome Trust (Wellcome)/ ; RPG-2019-297//Leverhulme Trust/ ; 2018-06609//Svenska Forskningsrådet Formas (Swedish Research Council Formas)/ ; 2018-05973//Svenska Forskningsrådet Formas (Swedish Research Council Formas)/ ; },
abstract = {The ESCRT machinery, comprising of multiple proteins and subcomplexes, is crucial for membrane remodelling in eukaryotic cells, in processes that include ubiquitin-mediated multivesicular body formation, membrane repair, cytokinetic abscission, and virus exit from host cells. This ESCRT system appears to have simpler, ancient origins, since many archaeal species possess homologues of ESCRT-III and Vps4, the components that execute the final membrane scission reaction, where they have been shown to play roles in cytokinesis, extracellular vesicle formation and viral egress. Remarkably, metagenome assemblies of Asgard archaea, the closest known living relatives of eukaryotes, were recently shown to encode homologues of the entire cascade involved in ubiquitin-mediated membrane remodelling, including ubiquitin itself, components of the ESCRT-I and ESCRT-II subcomplexes, and ESCRT-III and Vps4. Here, we explore the phylogeny, structure, and biochemistry of Asgard homologues of the ESCRT machinery and the associated ubiquitylation system. We provide evidence for the ESCRT-I and ESCRT-II subcomplexes being involved in ubiquitin-directed recruitment of ESCRT-III, as it is in eukaryotes. Taken together, our analyses suggest a pre-eukaryotic origin for the ubiquitin-coupled ESCRT system and a likely path of ESCRT evolution via a series of gene duplication and diversification events.},
}
@article {pmid35695998,
year = {2022},
author = {Verma, D and Kumar, V and Satyanarayana, T},
title = {Genomic attributes of thermophilic and hyperthermophilic bacteria and archaea.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {38},
number = {8},
pages = {135},
pmid = {35695998},
issn = {1573-0972},
abstract = {Thermophiles and hyperthermophiles are immensely useful in understanding the evolution of life, besides their utility in environmental and industrial biotechnology. Advancements in sequencing technologies have revolutionized the field of microbial genomics. The massive generation of data enhances the sequencing coverage multi-fold and allows to analyse the entire genomic features of microbes efficiently and accurately. The mandate of a pure isolate can also be bypassed where whole metagenome-assembled genomes and single cell-based sequencing have fulfilled the majority of the criteria to decode various attributes of microbial genomes. A boom has, therefore, been seen in analysing the extremophilic bacteria and archaea using sequence-based approaches. Due to extensive sequence analysis, it becomes easier to understand the gene flow and their evolution among the members of bacteria and archaea. For instance, sequencing unveiled that Thermotoga maritima shares around 24% of genes of archaeal origin. Comparative and functional genomics provide an analytical view to understanding the microbial diversity of thermophilic bacteria and archaea, their interactions with other microbes, their adaptations, gene flow, and evolution over time. In this review, the genomic features of thermophilic bacteria and archaea are dealt with comprehensively.},
}
@article {pmid35667126,
year = {2022},
author = {Gophna, U and Altman-Price, N},
title = {Horizontal Gene Transfer in Archaea-From Mechanisms to Genome Evolution.},
journal = {Annual review of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-micro-040820-124627},
pmid = {35667126},
issn = {1545-3251},
abstract = {Archaea remains the least-studied and least-characterized domain of life despite its significance not just to the ecology of our planet but also to the evolution of eukaryotes. It is therefore unsurprising that research into horizontal gene transfer (HGT) in archaea has lagged behind that of bacteria. Indeed, several archaeal lineages may owe their very existence to large-scale HGT events, and thus understanding both the molecular mechanisms and the evolutionary impact of HGT in archaea is highly important. Furthermore, some mechanisms of gene exchange, such as plasmids that transmit themselves via membrane vesicles and the formation of cytoplasmic bridges that allows transfer of both chromosomal and plasmid DNA, may be archaea specific. This review summarizes what we know about HGT in archaea, and the barriers that restrict it, highlighting exciting recent discoveries and pointing out opportunities for future research. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.},
}
@article {pmid35665142,
year = {2022},
author = {Selim, S and Akhtar, N and Hagagy, N and Alanazi, A and Warrad, M and El Azab, E and Elamir, MYM and Al-Sanea, MM and Jaouni, SKA and Abdel-Mawgoud, M and Shah, AA and Abdelgawad, H},
title = {Selection of Newly Identified Growth-Promoting Archaea Haloferax Species With a Potential Action on Cobalt Resistance in Maize Plants.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {872654},
doi = {10.3389/fpls.2022.872654},
pmid = {35665142},
issn = {1664-462X},
abstract = {Soil contamination with cobalt (Co) negatively impacts plant growth and production. To combat Co toxicity, plant growth-promoting microorganisms for improving plant growth are effectively applied. To this end, unclassified haloarchaeal species strain NRS_31 (OL912833), belonging to Haloferax genus, was isolated, identified for the first time, and applied to mitigate the Co phytotoxic effects on maize plants. This study found that high Co levels in soil lead to Co accumulation in maize leaves. Co accumulation in the leaves inhibited maize growth and photosynthetic efficiency, inducing oxidative damage in the tissue. Interestingly, pre-inoculation with haloarchaeal species significantly reduced Co uptake and mitigated the Co toxicity. Induced photosynthesis improved sugar metabolism, allocating more carbon to defend against Co stress. Concomitantly, the biosynthetic key enzymes involved in sucrose (sucrose-P-synthase and invertases) and proline (pyrroline-5- carboxylate synthetase (P5CS), pyrroline-5-carboxylate reductase (P5CR)) biosynthesis significantly increased to maintain plant osmotic potential. In addition to their osmoregulation potential, soluble sugars and proline can contribute to maintaining ROS hemostasis. Maize leaves managed their oxidative homeostasis by increasing the production of antioxidant metabolites (such as phenolics and tocopherols) and increasing the activity of ROS-scavenging enzymes (such as POX, CAT, SOD, and enzymes involved in the AsA/GSH cycle). Inside the plant tissue, to overcome heavy Co toxicity, maize plants increased the synthesis of heavy metal-binding ligands (metallothionein, phytochelatins) and the metal detoxifying enzymes (glutathione S transferase). Overall, the improved ROS homeostasis, osmoregulation, and Co detoxification systems were the basis underlying Co oxidative stress, mitigating haloarchaeal treatment's impact.},
}
@article {pmid35660788,
year = {2022},
author = {Lim, JK and Yang, JI and Kim, YJ and Park, YJ and Kim, YH},
title = {Bioconversion of CO to formate by artificially designed carbon monoxide:formate oxidoreductase in hyperthermophilic archaea.},
journal = {Communications biology},
volume = {5},
number = {1},
pages = {539},
pmid = {35660788},
issn = {2399-3642},
abstract = {Ferredoxin-dependent metabolic engineering of electron transfer circuits has been developed to enhance redox efficiency in the field of synthetic biology, e.g., for hydrogen production and for reduction of flavoproteins or NAD(P)+. Here, we present the bioconversion of carbon monoxide (CO) gas to formate via a synthetic CO:formate oxidoreductase (CFOR), designed as an enzyme complex for direct electron transfer between non-interacting CO dehydrogenase and formate dehydrogenase using an electron-transferring Fe-S fusion protein. The CFOR-introduced Thermococcus onnurineus mutant strains showed CO-dependent formate production in vivo and in vitro. The maximum formate production rate from purified CFOR complex and specific formate productivity from the bioreactor were 2.2 ± 0.2 μmol/mg/min and 73.1 ± 29.0 mmol/g-cells/h, respectively. The CO-dependent CO2 reduction/formate production activity of synthetic CFOR was confirmed, indicating that direct electron transfer between two unrelated dehydrogenases was feasible via mediation of the FeS-FeS fusion protein.},
}
@article {pmid35651488,
year = {2022},
author = {Zhong, L and Qing, J and Liu, M and Cai, X and Li, G and Li, FY and Chen, G and Xu, X and Xue, K and Wang, Y},
title = {Fungi and Archaea Control Soil N2O Production Potential in Chinese Grasslands Rather Than Bacteria.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {844663},
doi = {10.3389/fmicb.2022.844663},
pmid = {35651488},
issn = {1664-302X},
abstract = {Nitrous oxide (N2O) is a powerful greenhouse gas and the predominant stratospheric ozone-depleting substance. Soil is a major source of N2O but remains largely uncertain due to the complicated processes of nitrification and denitrification performed by various groups of microbes such as bacteria, fungi, and archaea. We used incubation experiments to measure the total fungal, archaeal, and bacterial N2O production potential and the microbial functional genes in soils along 3,000 km Chinese grassland transect, including meadow steppe, typical steppe, desert steppe, alpine meadow, and alpine steppe. The results indicated that fungi, archaea, and bacteria contributed 25, 34, and 19% to nitrification and 46, 29, and 15% to denitrification, respectively. The AOA and AOB genes were notably correlated with the total nitrification enzyme activity (TNEA), whereas both narG and nirK genes were significantly correlated with total denitrification enzyme activity (TDEA) at p < 0.01. The correlations between AOA and ANEA (archaeal nitrification enzyme activity), AOB and BNEA (bacterial nitrification enzyme activity), and narG, nirK, and BDEA (bacterial denitrification enzyme activity) showed higher coefficients than those between the functional genes and TNEA/TDEA. The structural equation modeling (SEM) results showed that fungi are dominant in N2O production processes, followed by archaea in the northern Chinese grasslands. Our findings indicate that the microbial functional genes are powerful predictors of the N2O production potential, after distinguishing bacterial, fungal, and archaeal processes. The key variables of N2O production and the nitrogen (N) cycle depend on the dominant microbial functional groups in the N-cycle in soils.},
}
@article {pmid35639688,
year = {2022},
author = {Thevasundaram, K and Gallagher, JJ and Cherng, F and Chang, MCY},
title = {Engineering nonphotosynthetic carbon fixation for production of bioplastics by methanogenic archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {23},
pages = {e2118638119},
doi = {10.1073/pnas.2118638119},
pmid = {35639688},
issn = {1091-6490},
support = {CW367486 Award 48610//Shell Global | Shell Exploration and Production Company (Shell Exploration &amp; Production Company)/ ; 1 T32 GMO66698//Office of Extramural Research, National Institutes of Health (OER)/ ; Graduate Fellowship//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; },
abstract = {SignificanceBiological carbon fixation provides opportunities to directly utilize CO2 to synthesize a broad range of value-added compounds, potentially displacing petroleum feedstock use in industry. Chemoautotrophs are particularly interesting as their carbon fixation can be driven chemically by renewable H2 in place of light, which can limit industrial fermentation of photosynthetic organisms. We describe the development of a methanogenic host, Methanococcus maripaludis, for metabolic engineering. Since redox cofactors used in upstream archaeal carbon fixation pathways are orthogonal to typical downstream biosynthetic pathways, it was necessary to engineer both NADH biosynthesis and turnover. In doing so, we are able to show that methanogenic archaea can, indeed, serve as a platform for the high-yield production of bioplastics and monomers from CO2 and H2.},
}
@article {pmid35633707,
year = {2022},
author = {Zheng, J and Tao, L and Dini-Andreote, F and Luan, L and Kong, P and Xue, J and Zhu, G and Xu, Q and Jiang, Y},
title = {Dynamic Responses of Ammonia-Oxidizing Archaea and Bacteria Populations to Organic Material Amendments Affect Soil Nitrification and Nitrogen Use Efficiency.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {911799},
doi = {10.3389/fmicb.2022.911799},
pmid = {35633707},
issn = {1664-302X},
abstract = {Organic material amendments have been proposed as an effective strategy to promote soil health by enhancing soil fertility and promoting nitrogen (N) cycling and N use efficiency (NUE). Thus, it is important to investigate the extent to which the structure and function of ammonia-oxidizing archaea (AOA) and bacteria (AOB) differentially respond to the organic material amendments in field settings. Here, we conducted a 9-year field experiment to track the responses of AOA and AOB populations to the organic material amendments and measured the potential nitrification activity (PNA), plant productivity, and NUE in the plant rhizosphere interface. Our results revealed that the organic material amendments significantly enhanced the abundance and diversity of AOA and AOB populations. Further, significant differences were observed in the composition and co-occurrence network of AOA and AOB. A higher occurrence of potential competitive interactions between taxa and enumerated potential keystone taxa was observed in the AOA-AOB network. Moreover, we found that AOA was more important than AOB for PNA under the organic material amendments. Structural equation modeling suggested that the diversity of AOA and AOB populations induced by the potential competitive interactions with keystone taxa dynamically accelerated the rate of PNA, and positively affected plant productivity and NUE under the organic material amendments. Collectively, our study offers new insights into the ecology and functioning of ammonia oxidizers and highlights the positive effects of organic material amendments on nitrogen cycling dynamics.},
}
@article {pmid35630397,
year = {2022},
author = {Liu, H and Zhou, P and Cheung, S and Lu, Y and Liu, H and Jing, H},
title = {Distribution and Oxidation Rates of Ammonia-Oxidizing Archaea Influenced by the Coastal Upwelling off Eastern Hainan Island.},
journal = {Microorganisms},
volume = {10},
number = {5},
pages = {},
doi = {10.3390/microorganisms10050952},
pmid = {35630397},
issn = {2076-2607},
support = {41776147//the National Natural Science Foundation of China/ ; 91751116//the Training Program of the Major Research Plan of the National Natural Science Foundation of China/ ; 2016YFC0304905//the National Key Research and Development Program of China/ ; 420RC677//the Hainan Provincial Natural Science Foundation of China for High-level Talents/ ; },
abstract = {Coastal upwelling causes variations in temperature, salinity and inorganic nutrients in the water column, consequently leading to the shift of microbial populations and their metabolic activities. Impacts of the eastern Hainan upwelling (EHU) on the ammonia-oxidizing archaea (AOA) were investigated based on the amoA gene using pyrosequencing and quantitative PCR at both DNA and cDNA levels, together with the determination of the ammonia oxidation (AO) rate measured with 15N-labelled ammonium. By comparing stations with and without upwelling influence, we found that coastal upwelling correlated with an increase in amoA gene abundance, the dominance of distinct clades for AOA communities at the respective gene and transcript levels, and a large increase in the proportion of the SCM1-like (Nitrosopumilus maritimus-like) cluster as well. The AO rates were generally higher in the deeper water (~25 m), which was in significant positive correlation with the proportion of cluster Water Column A (WCA) at the transcript level, indicating the potential contribution of this cluster to in situ ammonia oxidization. Our study demonstrated that coastal upwelling had a significant impact on the AOA community and ammonia oxidization rate; therefore, this physical forcing should be considered in the future assessment of the global nitrogen budgets and biogeochemical nitrogen cycles.},
}
@article {pmid35625610,
year = {2022},
author = {Pastor, MM and Sakrikar, S and Rodriguez, DN and Schmid, AK},
title = {Comparative Analysis of rRNA Removal Methods for RNA-Seq Differential Expression in Halophilic Archaea.},
journal = {Biomolecules},
volume = {12},
number = {5},
pages = {},
doi = {10.3390/biom12050682},
pmid = {35625610},
issn = {2218-273X},
support = {1651117//National Science Foundation/ ; 1936024//National Science Foundation/ ; },
abstract = {Despite intense recent research interest in archaea, the scientific community has experienced a bottleneck in the study of genome-scale gene expression experiments by RNA-seq due to the lack of commercial and specifically designed rRNA depletion kits. The high rRNA:mRNA ratio (80-90%: ~10%) in prokaryotes hampers global transcriptomic analysis. Insufficient ribodepletion results in low sequence coverage of mRNA, and therefore, requires a substantially higher number of replicate samples and/or sequencing reads to achieve statistically reliable conclusions regarding the significance of differential gene expression between case and control samples. Here, we show that after the discontinuation of the previous version of RiboZero (Illumina, San Diego, CA, USA) that was useful in partially or completely depleting rRNA from archaea, archaeal transcriptomics studies have experienced a slowdown. To overcome this limitation, here, we analyze the efficiency for four different hybridization-based kits from three different commercial suppliers, each with two sets of sequence-specific probes to remove rRNA from four different species of halophilic archaea. We conclude that the key for transcriptomic success with the currently available tools is the probe-specificity for the rRNA sequence hybridization. With this paper, we provide insights into the archaeal community for selecting certain reagents and strategies over others depending on the archaeal species of interest. These methods yield improved RNA-seq sensitivity and enhanced detection of low abundance transcripts.},
}
@article {pmid35623507,
year = {2022},
author = {de Souza, LF and Alvarez, DO and Domeignoz-Horta, LA and Gomes, FV and de Souza Almeida, C and Merloti, LF and Mendes, LW and Andreote, FD and Bohannan, BJM and Mazza Rodrigues, JL and Nüsslein, K and Tsai, SM},
title = {Maintaining grass coverage increases methane uptake in Amazonian pastures, with a reduction of methanogenic archaea in the rhizosphere.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {156225},
doi = {10.1016/j.scitotenv.2022.156225},
pmid = {35623507},
issn = {1879-1026},
abstract = {Cattle ranching is the largest driver of deforestation in the Brazilian Amazon. The rainforest-to-pasture conversion affects the methane cycle in upland soils, changing it from sink to source of atmospheric methane. However, it remains unknown if management practices could reduce the impact of land-use on methane cycling. In this work, we evaluated how pasture management can regulate the soil methane cycle either by maintaining continuous grass coverage on pasture soils, or by liming the soil to amend acidity. Methane fluxes from forest and pasture soils were evaluated in moisture-controlled greenhouse experiments with and without grass cover (Urochloa brizantha cv. Marandu) or liming. We also assessed changes in the soil microbial community structure of both bare (bulk) and rhizospheric pasture soils through high throughput sequencing of the 16S rRNA gene, and quantified the methane cycling microbiota by their respective marker genes related to methane generation (mcrA) or oxidation (pmoA). The experiments used soils from eastern and western Amazonia, and concurrent field studies allowed us to confirm greenhouse data. The presence of a grass cover not only increased methane uptake by up to 35% in pasture soils, but also reduced the abundance of the methane-producing community. In the grass rhizosphere this reduction was up to 10-fold. Methane-producing archaea belonged to the genera Methanosarcina sp., Methanocella sp., Methanobacterium sp., and Rice Cluster I. Further, we showed that soil liming to increasing pH compromised the capacity of forest and pasture soils to be a sink for methane, and instead converted formerly methane-consuming forest soils to become methane sources in only 40-80 days. Liming reduced the relative abundance of Beijerinckiacea family in forest soils, which account for many known methanotrophs. Our results demonstrate that pasture management that maintains grass coverage can mitigate soil methane emissions, compared to bare (bulk) pasture soil.},
}
@article {pmid35618771,
year = {2022},
author = {Badel, C and Samson, RY and Bell, SD},
title = {Chromosome organization affects genome evolution in Sulfolobus archaea.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {35618771},
issn = {2058-5276},
support = {R01GM135178//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R01GM135178//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
abstract = {In all organisms, the DNA sequence and the structural organization of chromosomes affect gene expression. The extremely thermophilic crenarchaeon Sulfolobus has one circular chromosome with three origins of replication. We previously revealed that this chromosome has defined A and B compartments that have high and low gene expression, respectively. As well as higher levels of gene expression, the A compartment contains the origins of replication. To evaluate the impact of three-dimensional organization on genome evolution, we characterized the effect of replication origins and compartmentalization on primary sequence evolution in eleven Sulfolobus species. Using single-nucleotide polymorphism analyses, we found that distance from an origin of replication was associated with increased mutation rates in the B but not in the A compartment. The enhanced polymorphisms distal to replication origins suggest that replication termination may have a causal role in their generation. Further mutational analyses revealed that the sequences in the A compartment are less likely to be mutated, and that there is stronger purifying selection than in the B compartment. Finally, we applied the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) to show that the B compartment is less accessible than the A compartment. Taken together, our data suggest that compartmentalization of chromosomal DNA can influence chromosome evolution in Sulfolobus. We propose that the A compartment serves as a haven for stable maintenance of gene sequences, while sequences in the B compartment can be diversified.},
}
@article {pmid35616996,
year = {2022},
author = {Bao, CX and Li, SY and Xin, YJ and Hou, J and Cui, HL},
title = {Natrinema halophilum sp. nov., Natrinema salinisoli sp. nov., Natrinema amylolyticum sp. nov. and Haloterrigena alkaliphila sp. nov., four extremely halophilic archaea isolated from salt mine, saline soil and salt lake.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {72},
number = {5},
pages = {},
doi = {10.1099/ijsem.0.005385},
pmid = {35616996},
issn = {1466-5034},
abstract = {Four halophilic archaeal strains, YPL8T, SLN56T, LT61T and KZCA68T, were isolated from a salt mine, saline soil and a salt lake located in different regions of China. Sequence similarities of 16S rRNA and rpoB' genes among strains YPL8T, SLN56T, LT61T and the current members of Natrinema were 94.1-98.2 % and 89.3-95.1 %, respectively, while these values among strain KZCA68T and the current members of Haloterrigena were 97.2-97.4 % and 91.7-91.9 %, respectively. The average nucleotide identity, in silico DNA-DNA hybridization and average amino acid identity values among these four strains and their closely related species were all lower than the threshold values for species boundary. All four strains were unable to hydrolyse casein, gelatin, or Tween 80. Strain YPL8T contained phosphatidic acid (PA), phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), sulfated mannosyl glucosyl diether (S-DGD-1), disulfated mannosyl glucosyl diether (S2-DGD) and sulfated mannosyl glucosyl diether-phosphatidic acid (S-DGD-PA). Strain SLN56T contained PA, PG, phosphatidylglycerol sulphate (PGS), PGP-Me, S-DGD-1, S2-DGD and S-DGD-PA. Strain LT61T contained PA, PG, PGS, PGP-Me, S-DGD-1 and S2-DGD. The phospholipids of strain KZCA68T were PA, PG and PGP-Me. These results showed that strains YPL8T (=CGMCC 1.13883T=JCM 31181T), SLN56T (=CGMCC 1.14945T=JCM 30832T) and LT61T (=CGMCC 1.14942T=JCM 30668T) represent novel species of the genus Natrinema, for which the names, Natrinema halophilum sp. nov., Natrinema salinisoli sp. nov. and Natrinema amylolyticum sp. nov. are proposed. Strain KZCA68T (=CGMCC 1.17211T=JCM 34158T) represents a novel species of Haloterrigena, for which the name Haloterrigena alkaliphila sp. nov. is proposed.},
}
@article {pmid35615789,
year = {2022},
author = {Dyksma, S and Gallert, C},
title = {Effect of magnetite addition on transcriptional profiles of syntrophic Bacteria and Archaea during anaerobic digestion of propionate in wastewater sludge.},
journal = {Environmental microbiology reports},
volume = {},
number = {},
pages = {},
doi = {10.1111/1758-2229.13080},
pmid = {35615789},
issn = {1758-2229},
support = {DY 132/1-1//German Research Foundation (Deutsche Forschungsgemeinschaft)/ ; },
abstract = {Anaerobic digestion (AD) is an important technology for the effective conversion of waste and wastewater to methane. Here, syntrophic bacteria transfer molecular hydrogen (H2), formate, or directly supply electrons (direct interspecies electron transfer, DIET) to the methanogens. Evidence is accumulating that the methanation of short-chain fatty acids can be enhanced by the addition of conductive material to the anaerobic digester, which has often been attributed to the stimulation of DIET. Since little is known about the transcriptional response of a complex AD microbial community to the addition of conductive material, we added magnetite to propionate-fed laboratory-scale reactors that were inoculated with wastewater sludge. Compared to the control reactors, the magnetite-amended reactors showed improved methanation of propionate. A genome-centric metatranscriptomics approach identified the active SCFA-oxidizing bacteria that affiliated with Firmicutes, Desulfobacterota and Cloacimonadota. The transcriptional profiles revealed that the syntrophic bacteria transferred acetate, H2 and formate to acetoclastic and hydrogenotrophic methanogens, whereas transcription of potential determinants for DIET such as conductive pili and outer-membrane cytochromes did not significantly change with magnetite addition. Overall, changes in the transcriptional profiles of syntrophic Bacteria and Archaea in propionate-fed lab-scale reactors amended with magnetite refute a major role of DIET in the studied system.},
}
@article {pmid35610383,
year = {2022},
author = {Pierangeli, GMF and Domingues, MR and Choueri, RB and Hanisch, WS and Gregoracci, GB and Benassi, RF},
title = {Spatial Variation and Environmental Parameters Affecting the Abundant and Rare Communities of Bacteria and Archaea in the Sediments of Tropical Urban Reservoirs.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {35610383},
issn = {1432-184X},
abstract = {Microbial communities in freshwater sediments play an important role in organic matter remineralization, contributing to biogeochemical cycles, nutrient release, and greenhouse gases emissions. Bacterial and archaeal communities might show spatial or seasonal patterns and were shown to be influenced by distinct environmental parameters and anthropogenic activities, including pollution and damming. Here, we determined the spatial variation and the environmental variables influencing the abundant and rare bacterial and archaeal communities in the sediments of eutrophic-hypereutrophic reservoirs from a tropical urban area in Brazil. The most abundant microbes included mainly Anaerolineae and Deltaproteobacteria genera from the Bacteria domain, and Methanomicrobia genera from the Archaea domain. Microbial communities differed spatially in each reservoir, reflecting the establishment of specific environmental conditions. Locations with better or worst water quality, or close to a dam, showed more distinct microbial communities. Besides the water column depth, microbial communities were affected by some pollution indicators, including total phosphorus, orthophosphate, electrical conductivity, and biochemical oxygen demand. Distinct proportions of variation were explained by spatial and environmental parameters for each microbial community. Furthermore, spatial variations in environmental parameters affecting these communities, especially the most distinct ones, contributed to microbial variations mediated by spatial and environmental properties together. Finally, our study showed that different pressures in each reservoir affected the sediment microbiota, promoting different responses and possible adaptations of abundant and rare bacterial and archaeal communities.},
}
@article {pmid35607968,
year = {2022},
author = {Semler, AC and Fortney, JL and Fulweiler, RW and Dekas, AE},
title = {Cold Seeps on the Passive Northern U.S. Atlantic Margin Host Globally Representative Members of the Seep Microbiome with Locally Dominant Strains of Archaea.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0046822},
doi = {10.1128/aem.00468-22},
pmid = {35607968},
issn = {1098-5336},
abstract = {Marine cold seeps are natural sites of methane emission and harbor distinct microbial communities capable of oxidizing methane. The majority of known cold seeps are on tectonically active continental margins, but recent discoveries have revealed abundant seeps on passive margins as well, including on the U.S. Atlantic Margin (USAM). We sampled in and around four USAM seeps and combined pore water geochemistry measurements with amplicon sequencing of 16S rRNA and mcrA (DNA and RNA) to investigate the microbial communities present, their assembly processes, and how they compare to communities at previously studied sites. We found that the USAM seeps contained communities consistent with the canonical seep microbiome at the class and order levels but differed markedly at the sequence variant level, especially within the anaerobic methanotrophic (ANME) archaea. The ANME populations were highly uneven, with just a few dominant mcrA sequence variants at each seep. Interestingly, the USAM seeps did not form a distinct phylogenetic cluster when compared with other previously described seeps around the world. Consistent with this, we found only a very weak (though statistically significant) distance-decay trend in seep community similarity across a global data set. Ecological assembly indices suggest that the USAM seep communities were assembled primarily deterministically, in contrast to the surrounding nonseep sediments, where stochastic processes dominated. Together, our results suggest that the primary driver of seep microbial community composition is local geochemistry-specifically methane, sulfide, nitrate, acetate, and ammonium concentrations-rather than the geologic context, the composition of nearby seeps, or random events of dispersal. IMPORTANCE Cold seeps are now known to be widespread features of passive continental margins, including the northern U.S. Atlantic Margin (USAM). Methane seepage is expected to intensify at these relatively shallow seeps as bottom waters warm and underlying methane hydrates dissociate. While methanotrophic microbial communities might reduce or prevent methane release, microbial communities on passive margins have rarely been characterized. In this study, we investigated the Bacteria and Archaea at four cold seeps on the northern USAM and found that despite being colocated on the same continental slope, the communities significantly differ by site at the sequence variant level, particularly methane-cycling community members. Differentiation by site was not observed in similarly spaced background sediments, raising interesting questions about the dispersal pathways of cold seep microorganisms. Understanding the genetic makeup of these discrete seafloor ecosystems and how their microbial communities develop will be increasingly important as the climate changes.},
}
@article {pmid35605022,
year = {2022},
author = {Martinez-Gutierrez, CA and Aylward, FO},
title = {Genome size distributions in bacteria and archaea are strongly linked to evolutionary history at broad phylogenetic scales.},
journal = {PLoS genetics},
volume = {18},
number = {5},
pages = {e1010220},
doi = {10.1371/journal.pgen.1010220},
pmid = {35605022},
issn = {1553-7404},
abstract = {The evolutionary forces that determine genome size in bacteria and archaea have been the subject of intense debate over the last few decades. Although the preferential loss of genes observed in prokaryotes is explained through the deletional bias, factors promoting and preventing the fixation of such gene losses often remain unclear. Importantly, statistical analyses on this topic typically do not consider the potential bias introduced by the shared ancestry of many lineages, which is critical when using species as data points because of the potential dependence on residuals. In this study, we investigated the genome size distributions across a broad diversity of bacteria and archaea to evaluate if this trait is phylogenetically conserved at broad phylogenetic scales. After model fit, Pagel's lambda indicated a strong phylogenetic signal in genome size data, suggesting that the diversification of this trait is influenced by shared evolutionary histories. We used a phylogenetic generalized least-squares analysis (PGLS) to test whether phylogeny influences the predictability of genome size from dN/dS ratios and 16S copy number, two variables that have been previously linked to genome size. These results confirm that failure to account for evolutionary history can lead to biased interpretations of genome size predictors. Overall, our results indicate that although bacteria and archaea can rapidly gain and lose genetic material through gene transfers and deletions, respectively, phylogenetic signal for genome size distributions can still be recovered at broad phylogenetic scales that should be taken into account when inferring the drivers of genome size evolution.},
}
@article {pmid35604119,
year = {2022},
author = {Popp, PF and Gumerov, VM and Andrianova, EP and Bewersdorf, L and Mascher, T and Zhulin, IB and Wolf, D},
title = {Phyletic Distribution and Diversification of the Phage Shock Protein Stress Response System in Bacteria and Archaea.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0134821},
doi = {10.1128/msystems.01348-21},
pmid = {35604119},
issn = {2379-5077},
abstract = {Maintaining cell envelope integrity is of vital importance for all microorganisms. Not surprisingly, evolution has shaped conserved protein protection networks that connect stress perception, transmembrane signal transduction, and mediation of cellular responses upon cell envelope stress. The phage shock protein (Psp) stress response is one such conserved protection network. Most knowledge about the Psp response derives from studies in the Gram-negative model bacterium Escherichia coli, where the Psp system consists of several well-defined protein components. Homologous systems were identified in representatives of the Proteobacteria, Actinobacteria, and Firmicutes. However, the Psp system distribution in the microbial world remains largely unknown. By carrying out a large-scale, unbiased comparative genomics analysis, we found components of the Psp system in many bacterial and archaeal phyla and describe that the predicted Psp systems deviate dramatically from the known prototypes. The core proteins PspA and PspC have been integrated into various (often phylum-specifically) conserved protein networks during evolution. Based on protein domain-based and gene neighborhood analyses of pspA and pspC homologs, we built a natural classification system for Psp networks in bacteria and archaea. We validate our approach by performing a comprehensive in vivo protein interaction study of Psp domains identified in the Gram-positive model organism Bacillus subtilis and found a strong interconnected protein network. Our study highlights the diversity of Psp domain organizations and potentially diverse functions across the plethora of the microbial landscape, thus laying the ground for studies beyond known Psp functions in underrepresented organisms. IMPORTANCE The PspA protein domain is found in all domains of life, highlighting its central role in Psp networks. To date, all insights into the core functions of Psp responses derive mainly from protein network blueprints representing only three bacterial phyla. Despite large overlaps in function and regulation, the evolutionary diversity of Psp networks remains largely elusive. Here, we present an unbiased protein domain- and genomic context-centered approach that describes and classifies Psp systems. Our results suggest so-far-unknown Psp-associated roles with other protein networks giving rise to new functions. We demonstrate the applicability of our approach by dissecting the Psp protein network present in Bacillus subtilis and demonstrate Psp domains working in concert with other cell envelope stress response systems. We find that the Psp-like protein universe reflects a surprising diversity within the bacterial and archaeal microbial world.},
}
@article {pmid35602962,
year = {2022},
author = {Wu, J and Hong, Y and He, X and Liu, X and Ye, J and Jiao, L and Li, Y and Wang, Y and Ye, F and Yang, Y and Du, J},
title = {Niche differentiation of ammonia-oxidizing archaea and related autotrophic carbon fixation potential in the water column of the South China Sea.},
journal = {iScience},
volume = {25},
number = {5},
pages = {104333},
doi = {10.1016/j.isci.2022.104333},
pmid = {35602962},
issn = {2589-0042},
abstract = {The significant primary production by ammonia-oxidizing archaea (AOA) in the ocean was reported, but the carbon fixation process of AOA and its community composition along the water depth remain unclear. Here, we investigated the abundance, community composition, and potential carbon fixation of AOA in water columns of the South China Sea. Higher abundances of the amoA and accA genes of AOA were found below the euphotic zone. Similarly, higher carbon fixation potential of AOA, evaluated by the ratios of amoA to accA gene, was also observed below euphotic zone and the ratios increased with increasing water depth. The vertical niche differentiation of AOA was further evidenced, with the dominant genus shifting from Nitrosopelagicus in the epipelagic zone to uncultured genus in the meso- and bathypelagic zones. Our findings highlight the higher carbon fixation potential of AOA in deep water and the significance of AOA to the ocean carbon budget.},
}
@article {pmid35544775,
year = {2022},
author = {Tunçkanat, T and Gendron, A and Sadler, Z and Neitz, A and Byquist, S and Lie, TJ and Allen, KD},
title = {Lysine 2,3-Aminomutase and a Newly Discovered Glutamate 2,3-Aminomutase Produce β-Amino Acids Involved in Salt Tolerance in Methanogenic Archaea.},
journal = {Biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.biochem.2c00014},
pmid = {35544775},
issn = {1520-4995},
abstract = {Many methanogenic archaea synthesize β-amino acids as osmolytes that allow survival in high salinity environments. Here, we investigated the radical S-adenosylmethionine (SAM) aminomutases involved in the biosynthesis of Nε-acetyl-β-lysine and β-glutamate in Methanococcus maripaludis C7. Lysine 2,3-aminomutase (KAM), encoded by MmarC7_0106, was overexpressed and purified from Escherichia coli, followed by biochemical characterization. In the presence of l-lysine, SAM, and dithionite, this archaeal KAM had a kcat = 14.3 s-1 and a Km = 19.2 mM. The product was shown to be 3(S)-β-lysine, which is like the well-characterized Clostridium KAM as opposed to the E. coli KAM that produces 3(R)-β-lysine. We further describe the function of MmarC7_1783, a putative radical SAM aminomutase with a ∼160 amino acid extension at its N-terminus. Bioinformatic analysis of the possible substrate-binding residues suggested a function as glutamate 2,3-aminomutase, which was confirmed here through heterologous expression in a methanogen followed by detection of β-glutamate in cell extracts. β-Glutamate has been known to serve as an osmolyte in select methanogens for a long time, but its biosynthetic origin remained unknown until now. Thus, this study defines the biosynthetic routes for β-lysine and β-glutamate in M. maripaludis and expands the importance and diversity of radical SAM enzymes in all domains of life.},
}
@article {pmid35508560,
year = {2022},
author = {Fisk, LM and Barton, L and Maccarone, LD and Jenkins, SN and Murphy, DV},
title = {Seasonal dynamics of ammonia-oxidizing bacteria but not archaea influence soil nitrogen cycling in a semi-arid agricultural soil.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {7299},
pmid = {35508560},
issn = {2045-2322},
support = {UWA000139//Grains Research and Development Corporation/ ; },
mesh = {Ammonia/metabolism ; *Archaea/genetics/metabolism ; Bacteria/genetics/metabolism ; *Betaproteobacteria/metabolism ; Nitrification ; Nitrogen/metabolism ; Oxidation-Reduction ; Phylogeny ; Seasons ; Soil/chemistry ; Soil Microbiology ; Water/metabolism ; },
abstract = {Nitrification, a key pathway of nitrogen (N) loss from agricultural soils, is performed by ammonia-oxidizing bacteria (AOB) and archaea (AOA). We examined the seasonal dynamics (2 years) of ammonia oxidizer gene abundances across a gradient of soil carbon (C) and N in a semi-arid soil after 8 years of tillage and crop residue treatments. AOB was more dominant than AOA in the surface soil, as AOA were undetected in 96% of samples. Seasonal variation in AOB abundance was related to substrate availability; AOB gene copy numbers increased at the end of the growing season (during summer fallow) following higher concentrations in dissolved organic matter soil water. This suggests increased co-location between AOB and substrate resources in pores still filled with water as the soils dried. AOB was however not statistically related to soil ammonium concentrations, soil water content, rainfall or temperature. Organic matter inputs enhanced AOB abundance independent of seasonal variation. AOB abundance was greatest in autumn and immediately preceding the start of the growing season, and coincided with elevated soil nitrate concentrations. The growth of the AOB population is likely to contribute to increased risk of N loss through leaching and/or denitrification at the start of the crop growing season following summer fallow.},
}
@article {pmid35500274,
year = {2022},
author = {Lemaire, ON and Wagner, T},
title = {A Structural View of Alkyl-Coenzyme M Reductases, the First Step of Alkane Anaerobic Oxidation Catalyzed by Archaea.},
journal = {Biochemistry},
volume = {61},
number = {10},
pages = {805-821},
doi = {10.1021/acs.biochem.2c00135},
pmid = {35500274},
issn = {1520-4995},
abstract = {Microbial anaerobic oxidation of alkanes intrigues the scientific community by way of its impact on the global carbon cycle, and its biotechnological applications. Archaea are proposed to degrade short- and long-chain alkanes to CO2 by reversing methanogenesis, a theoretically reversible process. The pathway would start with alkane activation, an endergonic step catalyzed by methyl-coenzyme M reductase (MCR) homologues that would generate alkyl-thiols carried by coenzyme M. While the methane-generating MCR found in methanogens has been well characterized, the enzymatic activity of the putative alkane-fixing counterparts has not been validated so far. Such an absence of biochemical investigations contrasts with the current explosion of metagenomics data, which draws new potential alkane-oxidizing pathways in various archaeal phyla. Therefore, validating the physiological function of these putative alkane-fixing machines and investigating how their structures, catalytic mechanisms, and cofactors vary depending on the targeted alkane have become urgent needs. The first structural insights into the methane- and ethane-capturing MCRs highlighted unsuspected differences and proposed some explanations for their substrate specificity. This Perspective reviews the current physiological, biochemical, and structural knowledge of alkyl-CoM reductases and offers fresh ideas about the expected mechanistic and chemical differences among members of this broad family. We conclude with the challenges of the investigation of these particular enzymes, which might one day generate biofuels for our modern society.},
}
@article {pmid35489791,
year = {2022},
author = {Glodowska, M and Welte, CU and Kurth, JM},
title = {Metabolic potential of anaerobic methane oxidizing archaea for a broad spectrum of electron acceptors.},
journal = {Advances in microbial physiology},
volume = {80},
number = {},
pages = {157-201},
doi = {10.1016/bs.ampbs.2022.01.003},
pmid = {35489791},
issn = {2162-5468},
mesh = {Anaerobiosis ; *Archaea/metabolism ; Electrons ; Ferric Compounds/metabolism ; Methane/metabolism ; *Microbiota ; Oxidation-Reduction ; },
abstract = {Methane (CH4) is a potent greenhouse gas significantly contributing to the climate warming we are currently facing. Microorganisms play an important role in the global CH4 cycle that is controlled by the balance between anaerobic production via methanogenesis and CH4 removal via methanotrophic oxidation. Research in recent decades advanced our understanding of CH4 oxidation, which until 1976 was believed to be a strictly aerobic process. Anaerobic oxidation of methane (AOM) coupled to sulfate reduction is now known to be an important sink of CH4 in marine ecosystems. Furthermore, in 2006 it was discovered that anaerobic CH4 oxidation can also be coupled to nitrate reduction (N-DAMO), demonstrating that AOM may be much more versatile than previously thought and linked to other electron acceptors. In consequence, an increasing number of studies in recent years showed or suggested that alternative electron acceptors can be used in the AOM process including FeIII, MnIV, AsV, CrVI, SeVI, SbV, VV, and BrV. In addition, humic substances as well as biochar and perchlorate (ClO4-) were suggested to mediate AOM. Anaerobic methanotrophic archaea, the so-called ANME archaea, are key players in the AOM process, yet we are still lacking deeper understanding of their metabolism, electron acceptor preferences and their interaction with other microbial community members. It is still not clear whether ANME archaea can oxidize CH4 and reduce metallic electron acceptors independently or via electron transfer to syntrophic partners, interspecies electron transfer, nanowires or conductive pili. Therefore, the aim of this review is to summarize and discuss the current state of knowledge about ANME archaea, focusing on their physiology, metabolic flexibility and potential to use various electron acceptors.},
}
@article {pmid35437913,
year = {2022},
author = {Campbell, BC and Greenfield, P and Gong, S and Barnhart, EP and Midgley, DJ and Paulsen, IT and George, SC},
title = {Methanogenic archaea in subsurface coal seams are biogeographically distinct: an analysis of metagenomically-derived mcrA sequences.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.16014},
pmid = {35437913},
issn = {1462-2920},
abstract = {The production of methane as an end-product of organic matter degradation in the absence of other terminal electron acceptors is common, and has often been studied in environments such as animal guts, soils and wetlands due to its potency as a greenhouse gas. To date, however, the study of the biogeographic distribution of methanogens across coal seam environments has been minimal. Here, we show that coal seams are host to a diverse range of methanogens, which are distinctive to each geological basin. Based on comparisons to close relatives from other methanogenic environments, the dominant methanogenic pathway in these basins is hydrogenotrophic, with acetoclastic being a second major pathway in the Surat Basin. Finally, mcrA and 16S rRNA gene primer biases were predominantly seen to affect the detection of Methanocellales, Methanomicrobiales and Methanosarcinales taxa in this study. Subsurface coal methanogenic community distributions and pathways presented here provide insights into important metabolites and bacterial partners for in situ coal biodegradation.},
}
@article {pmid35427170,
year = {2022},
author = {Dey, G},
title = {Preprint Highlight: Growth temperature is the principal driver of chromatinization in archaea.},
journal = {Molecular biology of the cell},
volume = {33},
number = {5},
pages = {mbcP22021007},
doi = {10.1091/mbc.P22-02-1007},
pmid = {35427170},
issn = {1939-4586},
mesh = {*Archaea ; Temperature ; },
}
@article {pmid35422794,
year = {2022},
author = {Kamruzzaman, M and Yan, A and Castro-Escarpulli, G},
title = {Editorial: CRISPR-Cas Systems in Bacteria and Archaea.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {887778},
pmid = {35422794},
issn = {1664-302X},
}
@article {pmid35420474,
year = {2022},
author = {He, W and Gao, H and Wu, D and Jiang, S and Huang, W and Chen, C and Deng, Z and Xiong, L and Wu, G and Wang, L},
title = {Structural and Functional Analysis of DndE Involved in DNA Phosphorothioation in the Haloalkaliphilic Archaea Natronorubrum bangense JCM10635.},
journal = {mBio},
volume = {},
number = {},
pages = {e0071622},
doi = {10.1128/mbio.00716-22},
pmid = {35420474},
issn = {2150-7511},
abstract = {Phosphorothioate (PT) modification, a sequence-specific modification that replaces the nonbridging oxygen atom with sulfur in a DNA phosphodiester through the gene products of dndABCDE or sspABCD, is widely distributed in prokaryotes. DNA PT modification functions together with gene products encoded by dndFGH, pbeABCD, or sspE to form defense systems that can protect against invasion by exogenous DNA particles. While the functions of the multiple enzymes in the PT system have been elucidated, the exact role of DndE in the PT process is still obscure. Here, we solved the crystal structure of DndE from the haloalkaliphilic archaeal strain Natronorubrum bangense JCM10635 at a resolution of 2.31 Å. Unlike the tetrameric conformation of DndE in Escherichia coli B7A, DndE from N. bangense JCM10635 exists in a monomeric conformation and can catalyze the conversion of supercoiled DNA to nicked or linearized products. Moreover, DndE exhibits preferential binding affinity to nicked DNA by virtue of the R19- and K23-containing positively charged surface. This work provides insight into how DndE functions in PT modification and the potential sulfur incorporation mechanism of DNA PT modification. IMPORTANCE DndABCDE proteins have been demonstrated to catalyze DNA PT modification with the nonbridging oxygen in the DNA sugar-phosphate backbone replaced by sulfur. In the PT modification pathway, DndA exerts cysteine desulfurase activity capable of catalyzing the mobilization of sulfur from l-cysteine, which involves the ion-sulfur cluster assembly of DndC. This is regarded as the initial step of the DNA PT modification. Moreover, DndD has ATPase activity in vitro, which is believed to provide energy for the oxygen-sulfur swap, while the function of DndE is unknown. However, the exact function of the key enzyme DndE remains to be elucidated. By determining the structure of DndE from the haloalkaliphilic strain Natronorubrum bangense JCM10635, we showed that the archaeal DndE adopts a monomer conformation. Notably, DndE can introduce nicks to supercoiled DNA and exhibits a binding preference for nicked DNA; the nicking is believed to be the initial step for DNA to facilitate the sulfur incorporation.},
}
@article {pmid35408816,
year = {2022},
author = {Huang, C and Liu, X and Chen, Y and Zhou, J and Li, W and Ding, N and Huang, L and Chen, J and Zhang, Z},
title = {A Novel Family of Winged-Helix Single-Stranded DNA-Binding Proteins from Archaea.},
journal = {International journal of molecular sciences},
volume = {23},
number = {7},
pages = {},
pmid = {35408816},
issn = {1422-0067},
support = {2020YFA0906800//National Key R&amp;D Program of China/ ; 32170050//National Natural Science Foundation of China/ ; 92051109//National Natural Science Foundation of China/ ; },
mesh = {Archaea/metabolism ; DNA/chemistry ; DNA, Single-Stranded ; *DNA-Binding Proteins/metabolism ; *Sulfolobus/genetics ; },
abstract = {The winged helix superfamily comprises a large number of structurally related nucleic acid-binding proteins. While these proteins are often shown to bind dsDNA, few are known to bind ssDNA. Here, we report the identification and characterization of Sul7s, a novel winged-helix single-stranded DNA binding protein family highly conserved in Sulfolobaceae. Sul7s from Sulfolobus islandicus binds ssDNA with an affinity approximately 15-fold higher than that for dsDNA in vitro. It prefers binding oligo(dT)30 over oligo(dC)30 or a dG-rich 30-nt oligonucleotide, and barely binds oligo(dA)30. Further, binding by Sul7s inhibits DNA strand annealing, but shows little effect on the melting temperature of DNA duplexes. The solution structure of Sul7s determined by NMR shows a winged helix-turn-helix fold, consisting of three α-helices, three β-strands, and two short wings. It interacts with ssDNA via a large positively charged binding surface, presumably resulting in ssDNA deformation. Our results shed significant light on not only non-OB fold single-stranded DNA binding proteins in Archaea, but also the divergence of the winged-helix proteins in both function and structure during evolution.},
}
@article {pmid35405221,
year = {2022},
author = {Yang, P and Tang, KW and Tong, C and Lai, DYF and Wu, L and Yang, H and Zhang, L and Tang, C and Hong, Y and Zhao, G},
title = {Changes in sediment methanogenic archaea community structure and methane production potential following conversion of coastal marsh to aquaculture ponds.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {305},
number = {},
pages = {119276},
doi = {10.1016/j.envpol.2022.119276},
pmid = {35405221},
issn = {1873-6424},
mesh = {Aquaculture ; Archaea ; Ecosystem ; Methane ; *Ponds ; *Wetlands ; },
abstract = {Widespread conversion of coastal wetlands into aquaculture ponds in coastal region often results in degradation of the wetland ecosystems, but its effects on sediment's potential to produce greenhouse gases remain unclear. Using field sampling, incubation experiments and molecular analysis, we studied the sediment CH4 production potential and the relevant microbial communities in a brackish marsh and the nearby aquaculture ponds in the Min River Estuary in southeastern China. Sediment CH4 production potential was higher in the summer and autumn months than in spring and winter months, and it was significantly correlated with sediment carbon content among all environmental variables. The mean sediment CH4 production potential in the aquaculture ponds (20.1 ng g-1 d-1) was significantly lower than that in the marsh (45.2 ng g-1 d-1). While Methanobacterium dominated in both habitats (41-59%), the overall composition of sediment methanogenic archaea communities differed significantly between the two habitats (p < 0.05) and methanogenic archaea alpha diversity was lower in the aquaculture ponds (p < 0.01). Network analysis revealed that interactions between sediment methanogenic archaea were much weaker in the ponds than in the marsh. Overall, these findings suggest that conversion of marsh land to aquaculture ponds significantly altered the sediment methanogenic archaea community structure and diversity and lowered the sediment's capacity to produce CH4.},
}
@article {pmid35402889,
year = {2022},
author = {Al-Ajeel, S and Spasov, E and Sauder, LA and McKnight, MM and Neufeld, JD},
title = {Ammonia-oxidizing archaea and complete ammonia-oxidizing Nitrospira in water treatment systems.},
journal = {Water research X},
volume = {15},
number = {},
pages = {100131},
pmid = {35402889},
issn = {2589-9147},
abstract = {Nitrification, the oxidation of ammonia to nitrate via nitrite, is important for many engineered water treatment systems. The sequential steps of this respiratory process are carried out by distinct microbial guilds, including ammonia-oxidizing bacteria (AOB) and archaea (AOA), nitrite-oxidizing bacteria (NOB), and newly discovered members of the genus Nitrospira that conduct complete ammonia oxidation (comammox). Even though all of these nitrifiers have been identified within water treatment systems, their relative contributions to nitrogen cycling are poorly understood. Although AOA contribute to nitrification in many wastewater treatment plants, they are generally outnumbered by AOB. In contrast, AOA and comammox Nitrospira typically dominate relatively low ammonia environments such as drinking water treatment, tertiary wastewater treatment systems, and aquaculture/aquarium filtration. Studies that focus on the abundance of ammonia oxidizers may misconstrue the actual role that distinct nitrifying guilds play in a system. Understanding which ammonia oxidizers are active is useful for further optimization of engineered systems that rely on nitrifiers for ammonia removal. This review highlights known distributions of AOA and comammox Nitrospira in engineered water treatment systems and suggests future research directions that will help assess their contributions to nitrification and identify factors that influence their distributions and activity.},
}
@article {pmid35384236,
year = {2022},
author = {Vuong, P and Moreira-Grez, B and Wise, MJ and Whiteley, AS and Kumaresan, D and Kaur, P},
title = {From rags to enriched: metagenomic insights into ammonia-oxidizing archaea following ammonia enrichment of a denuded oligotrophic soil ecosystem.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.15994},
pmid = {35384236},
issn = {1462-2920},
support = {//Australian Government and the Government of Western Australia/ ; },
abstract = {Stored topsoil acts as a microbial inoculant for ecological restoration of land after disturbance, but the altered circumstances frequently create unfavourable conditions for microbial survival. Nitrogen cycling is a critical indicator for ecological success and this study aimed to investigate the cornerstone taxa driving the process. Previous in silico studies investigating stored topsoil discovered persistent archaeal taxa with the potential for re-establishing ecological activity. Ammonia oxidization is the limiting step in nitrification and as such, ammonia-oxidizing archaea (AOA) can be considered one of the gatekeepers for the re-establishment of the nitrogen cycle in disturbed soils. Semi-arid soil samples were enriched with ammonium sulfate to promote the selective enrichment of ammonia oxidizers for targeted genomic recovery, and to investigate the microbial response of the microcosm to nitrogen input. Ammonia addition produced an increase in AOA population, particularly within the genus Candidatus Nitrosotalea, from which metagenome-assembled genomes (MAGs) were successfully recovered. The Ca. Nitrosotalea archaeon candidates' ability to survive in extreme conditions and rapidly respond to ammonia input makes it a potential bioprospecting target for application in ecological restoration of semi-arid soils and the recovered MAGs provide a metabolic blueprint for developing potential strategies towards isolation of these acclimated candidates.},
}
@article {pmid35380107,
year = {2022},
author = {Gupta, D and Shalvarjian, KE and Nayak, DD},
title = {An Archaea-specific c-type cytochrome maturation machinery is crucial for methanogenesis in Methanosarcina acetivorans.},
journal = {eLife},
volume = {11},
number = {},
pages = {},
pmid = {35380107},
issn = {2050-084X},
support = {GBMF#9324//Gordon and Betty Moore Foundation/ ; imons Early Career Investigator in Marine Microbial Ecology and Evolution Award (822981)//Simons Foundation/ ; Packard Fellowships for Science and Engineering//David and Lucile Packard Foundation/ ; Searle Scholars Program//Searle Scholars Program/ ; Beckman Young Investigator Program//Arnold and Mabel Beckman Foundation/ ; Simons Early Career Investigator in Marine Microbial Ecology and Evolution Award (822981)//Simons Foundation/ ; },
mesh = {*Archaea/metabolism ; Cytochromes/metabolism ; Electron Transport/genetics ; Methane/metabolism ; *Methanosarcina/genetics ; },
abstract = {c-Type cytochromes (cyt c) are proteins that undergo post-translational modification to covalently bind heme, which allows them to facilitate redox reactions in electron transport chains across all domains of life. Genomic evidence suggests that cyt c are involved in electron transfer processes among the Archaea, especially in members that produce or consume the potent greenhouse gas methane. However, neither the maturation machinery for cyt c in Archaea nor their role in methane metabolism has ever been functionally characterized. Here, we have used CRISPR-Cas9 genome editing tools to map a distinct pathway for cyt c biogenesis in the model methanogenic archaeon Methanosarcina acetivorans, and have also identified substrate-specific functional roles for cyt c during methanogenesis. Although the cyt c maturation machinery from M. acetivorans is universally conserved in the Archaea, our evolutionary analyses indicate that different clades of Archaea acquired this machinery through multiple independent horizontal gene transfer events from different groups of Bacteria. Overall, we demonstrate the convergent evolution of a novel Archaea-specific cyt c maturation machinery and its physiological role during methanogenesis, a process which contributes substantially to global methane emissions.},
}
@article {pmid35369442,
year = {2022},
author = {Thirumalaisamy, G and Malik, PK and Trivedi, S and Kolte, AP and Bhatta, R},
title = {Effect of Long-Term Supplementation With Silkworm Pupae Oil on the Methane Yield, Ruminal Protozoa, and Archaea Community in Sheep.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {780073},
pmid = {35369442},
issn = {1664-302X},
abstract = {Supplementation with lipids and oils is one of the most efficient strategies for reducing enteric methane emission. However, high costs and adverse impacts on fiber degradation restrict the use of conventional oils. Silkworm pupae, a non-conventional oil source rarely used for human consumption in India, could be one of the cheaper alternatives for methane mitigation. The objective of this study was to investigate the effect on sheep of long-term supplementation (180 days) of silkworm pupae oil (SWPO) with two distinct supplementation regimes (daily and biweekly) on daily enteric methane emission, methane yield, nutrient digestibility, rumen fermentation, ruminal archaea community composition, and protozoal population. The effect of the discontinuation of oil supplementation on enteric methane emission was also investigated. Eighteen adult male sheep, randomly divided into three groups (n = 6), were provisioned with a mixed diet consisting of 10.1% crude protein (CP) and 11.7 MJ/kg metabolizable energy formulated using finger millet straw and concentrate in a 55:45 ratio. SWPO was supplemented at 2% of dry matter intake (DMI) in test groups either daily (CON) or biweekly (INT), while no oil was supplemented in the control group (CTR). DMI (p = 0.15) and CP (p = 0.16) in the CON and INT groups were similar to that of the CTR group; however, the energy intake (MJ/kg) in the supplemented groups (CON and INT) was higher (p < 0.001) than in CTR. In the CON group, body weight gain (kg, p = 0.02) and average daily gain (g, p = 0.02) were both higher than in the CTR. The daily methane emission in the CON (17.5 g/day) and INT (18.0 g/day) groups was lower (p = 0.01) than the CTR group (23.6 g/day), indicating a reduction of 23-25% due to SWPO supplementation. Similarly, compared with the CTR group, methane yields (g/kg DMI) in test groups were also significantly lower (p < 0.01). The transient nature of the anti-methanogenic effect of SWPO was demonstrated in the oil discontinuation study, where daily methane emission reverted to pre-supplementation levels after a short period. The recorded methanogens were affiliated to the families Methanobacteriaceae, Methanomassilliicoccaceae, and Methanosarcinaceae. The long-term supplementation of oil did not induce any significant change in the rumen archaeal community, whereas minor species such as Group3b exhibited differing abundance among the groups. Methanobrevibacter, irrespective of treatment, was the largest genus, while Methanobrevibacter gottschalkii was the dominant species. Oil supplementation in CON and INT compared with CTR decreased (p < 0.01) the numbers of total protozoa (× 107 cells/ml), Entodiniomorphs (× 107 cells/ml), and Holotrichs (× 106 cells/ml). SWPO continuous supplementation (CON group) resulted in the largest reduction in enteric methane emission and relatively higher body weight gain (p = 0.02) in sheep.},
}
@article {pmid35347497,
year = {2022},
author = {Yuan, B and Wu, W and Yue, S and Zou, P and Yang, R and Zhou, X},
title = {Community structure, distribution pattern, and influencing factors of soil Archaea in the construction area of a large-scale photovoltaic power station.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {35347497},
issn = {1618-1905},
support = {51979222//National Natural Science Foundation of China/ ; },
abstract = {The photovoltaic power station in Qinghai has been built for 8 years; however, its impact on the regional soil ecological environment has not been studied in depth. To reveal the structure and distribution pattern of archaeal communities in desert soil under the influence of a large photovoltaic power station, a comparative study was carried out between the soil affected by photovoltaic panels and the bare land samples outside the photovoltaic station in Gonghe, Qinghai Province. The abundance, community structure, diversity, and distribution characteristics of archaea were analyzed by quantitative PCR and Illumina-MiSeq high-throughput sequencing, and the main environmental factors affecting the variation in soil archaeal community were identified by RDA. The contribution rate of environmental factors and human factors to microbial community diversity was quantitatively evaluated by VPA. The results showed that there was no significant difference in soil nutrients and other physicochemical factors between the photovoltaic power station and bare land. Thaumarchaeota was the dominant archaeal phylum in the area, accounting for more than 99% of archaeal phylum, while at the level of genus, Nitrososphaera was the dominant archaeal genera. There was no significant difference in archaeal community structure between and under different types of PV panels. The analysis has shown that the construction of a photovoltaic station has little effect on the community structure of soil archaea in a desert area, and it was speculated that the selection of niche played a leading role in the distribution pattern of soil archaeal community. This study provides the basis for a scientific understanding of the characteristics and distribution patterns of soil archaeal communities affected by the construction of a photovoltaic power station.},
}
@article {pmid35340443,
year = {2022},
author = {Schiller, H and Young, C and Schulze, S and Tripepi, M and Pohlschroder, M},
title = {A Twist to the Kirby-Bauer Disk Diffusion Susceptibility Test: an Accessible Laboratory Experiment Comparing Haloferax volcanii and Escherichia coli Antibiotic Susceptibility to Highlight the Unique Cell Biology of Archaea.},
journal = {Journal of microbiology &amp; biology education},
volume = {23},
number = {1},
pages = {},
pmid = {35340443},
issn = {1935-7877},
abstract = {Archaea, once thought to only live in extreme environments, are present in many ecosystems, including the human microbiome, and they play important roles ranging from nutrient cycling to bioremediation. Yet this domain is often overlooked in microbiology classes and rarely included in laboratory exercises. Excluding archaea from high school and undergraduate curricula prevents students from learning the uniqueness and importance of this domain. Here, we have modified a familiar and popular microbiology experiment-the Kirby-Bauer disk diffusion antibiotic susceptibility test-to include, together with the model bacterium Escherichia coli, the model archaeon Haloferax volcanii. Students will learn the differences and similarities between archaea and bacteria by using antibiotics that target, for example, the bacterial peptidoglycan cell wall or the ribosome. Furthermore, the experiment provides a platform to reiterate basic cellular biology concepts that students may have previously discussed. We have developed two versions of this experiment, one designed for an undergraduate laboratory curriculum and the second, limited to H. volcanii, that high school students can perform in their classrooms. This nonpathogenic halophile can be cultured aerobically at ambient temperature in high-salt media, preventing contamination, making the experiment low-cost and safe for use in the high school setting.},
}
@article {pmid35336099,
year = {2022},
author = {Cisek, AA and Bąk, I and Stefańska, I and Binek, M},
title = {Selection and Optimization of High-Yielding DNA Isolation Protocol for Quantitative Analyses of Methanogenic Archaea.},
journal = {Microorganisms},
volume = {10},
number = {3},
pages = {},
pmid = {35336099},
issn = {2076-2607},
support = {2017/25/N/NZ7/02905//National Science Center/ ; },
abstract = {Methanogenic archaea are a functionally important component of the intestinal microbiota of humans and animals, participating in the utilization of detrimental hydrogen produced during gut fermentation. Despite this, archaeal DNA has rarely been found in intestinal microbiome analyses, which prompts the need to optimize detecting procedures of these microorganisms, including the DNA isolation step. Three commercially available kits for DNA isolation and one extra purification kit that removes PCR inhibitors were evaluated on chicken droppings. In addition, different variants of mechanical lysis and a double elution were tested to ensure the maximum efficiency of DNA isolation from archaea as well as bacteria. A quantitative real-time PCR was used to monitor the optimization progress. As a result, the combination of the selected Genomic Mini AX Bacteria+ kit with a 2-min-long sonication by ultrasonic probe and enzymatic pretreatment gave excellent extraction efficiency rates for DNA of methanogenic archaea (an approximate 50-fold increase compared to the standard enzymatic lysis described by the producer) and, at the same time, provided optimal protection of DNA extracted from bacteria susceptible to enzymatic lysis. The presented results indicate that the optimized protocol allows for highly efficient extraction of total DNA, which is well-suited for quantitative microbial analyses by real-time PCR.},
}
@article {pmid35323924,
year = {2022},
author = {Klein, T and Poghosyan, L and Barclay, JE and Murrell, JC and Hutchings, MI and Lehtovirta-Morley, LE},
title = {Cultivation of ammonia-oxidising archaea on solid medium.},
journal = {FEMS microbiology letters},
volume = {369},
number = {1},
pages = {},
pmid = {35323924},
issn = {1574-6968},
support = {NE/S007334/1//Natural Environment Research Council/ ; DH150187//Royal Society/ ; 852993/ERC_/European Research Council/International ; BBS/E/J/000PR9790/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Agar ; *Ammonia ; *Archaea/genetics ; Culture Media ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Soil Microbiology ; },
abstract = {Ammonia-oxidising archaea (AOA) are environmentally important microorganisms involved in the biogeochemical cycling of nitrogen. Routine cultivation of AOA is exclusively performed in liquid cultures and reports on their growth on solid medium are scarce. The ability to grow AOA on solid medium would be beneficial for not only the purification of enrichment cultures but also for developing genetic tools. The aim of this study was to develop a reliable method for growing individual colonies from AOA cultures on solid medium. Three phylogenetically distinct AOA strains were tested: 'Candidatus Nitrosocosmicus franklandus C13', Nitrososphaera viennensis EN76 and 'Candidatus Nitrosotalea sinensis Nd2'. Of the gelling agents tested, agar and Bacto-agar severely inhibited growth of all three strains. In contrast, both 'Ca. N. franklandus C13' and N. viennensis EN76 tolerated Phytagel™ while the acidophilic 'Ca. N. sinensis Nd2' was completely inhibited. Based on these observations, we developed a Liquid-Solid (LS) method that involves immobilising cells in Phytagel™ and overlaying with liquid medium. This approach resulted in the development of visible distinct colonies from 'Ca. N. franklandus C13' and N. viennensis EN76 cultures and lays the groundwork for the genetic manipulation of this group of microorganisms.},
}
@article {pmid35276174,
year = {2022},
author = {Wang, JT and Zhang, YB and Xiao, Q and Zhang, LM},
title = {Archaea is more important than bacteria in driving soil stoichiometry in phosphorus deficient habitats.},
journal = {The Science of the total environment},
volume = {827},
number = {},
pages = {154417},
doi = {10.1016/j.scitotenv.2022.154417},
pmid = {35276174},
issn = {1879-1026},
mesh = {*Archaea ; Bacteria ; Forests ; *Microbiota ; Nitrogen/analysis ; Phosphorus/analysis ; Soil/chemistry ; Soil Microbiology ; },
abstract = {Phosphorus deficiency is a critical limit on the cycling of carbon (C), nitrogen (N) and phosphorus (P) in forest ecosystems. Despite the pivotal roles of microbes in driving the biogeochemical cycling of C/N/P, our knowledge on the relationships of soil bacteria and archaea to P deficiency in forest ecosystems remains scarce. Here, we studied 110 acidic soils (average pH 4.5) collected across 700-km subtropical forests with a gradient of available phosphorus (AP) ranging from 0.21 to 17.6 mg/kg. We analyzed the soil C/N/P stoichiometry and studied soil bacterial and archaeal diversity/abundance via high throughput sequencing and qPCR approaches. Our results show that soil P decoupled with N or C when below 3 mg/kg but coupled with C and N when above 3 mg/kg. Archaeal diversity and abundance were significantly higher in low AP (< 3 mg/kg) soils than in high AP (>3 mg/kg) soils, while bacterial were less changed. Compared with bacteria, archaea are more strongly related with soil stoichiometry (C:N, C:P, N:P), especially when AP was less than 3 mg/kg. Taxonomic and functional composition analysis further confirmed that archaeal rather than bacterial taxonomic composition was significantly related with functional composition of microbial communities. Taken together, our results show that archaea are more important than bacteria in driving soil stoichiometry in phosphorus deficient habitats and suggest a niche differentiation of soil bacteria and archaea in regulating the soil C/N/P cycling in subtropical forests.},
}
@article {pmid35270425,
year = {2022},
author = {Xu, A and Li, L and Xie, J and Gopalakrishnan, S and Zhang, R and Luo, Z and Cai, L and Liu, C and Wang, L and Anwar, S and Jiang, Y},
title = {Changes in Ammonia-Oxidizing Archaea and Bacterial Communities and Soil Nitrogen Dynamics in Response to Long-Term Nitrogen Fertilization.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {5},
pages = {},
pmid = {35270425},
issn = {1660-4601},
mesh = {*Ammonia/metabolism ; *Archaea/genetics/metabolism ; Bacteria/genetics/metabolism ; Fertilization ; Fertilizers ; Nitrogen/metabolism ; Oxidation-Reduction ; Phylogeny ; Soil/chemistry ; Soil Microbiology ; },
abstract = {Ammonia oxidizing archaea (AOA) and bacteria (AOB) mediate a crucial step in nitrogen (N) metabolism. The effect of N fertilizer rates on AOA and AOB communities is less studied in the wheat-fallow system from semi-arid areas. Based on a 17-year wheat field experiment, we explored the effect of five N fertilizer rates (0, 52.5, 105, 157.5, and 210 kg ha-1 yr-1) on the AOA and AOB community composition. This study showed that the grain yield of wheat reached the maximum at 105 kg N ha-1 (49% higher than control), and no further significant increase was observed at higher N rates. With the increase of N, AOA abundance decreased in a regular trend from 4.88 × 107 to 1.05 × 107 copies g-1 dry soil, while AOB abundance increased from 3.63 × 107 up to a maximum of 8.24 × 107 copies g-1 dry soil with the N105 treatment (105 kg N ha-1 yr-1). Application rates of N fertilizer had a more significant impact on the AOB diversity than on AOA diversity, and the highest AOB diversity was found under the N105 treatment in this weak alkaline soil. The predominant phyla of AOA and AOB were Thaumarchaeota and Proteobacteria, respectively, and higher N treatment (N210) resulted in a significant decrease in the relative abundance of genus Nitrosospira. In addition, AOA and AOB communities were significantly associated with grain yield of wheat, soil potential nitrification activity (PNA), and some soil physicochemical parameters such as pH, NH4-N, and NO3-N. Among them, soil moisture was the most influential edaphic factor for structuring the AOA community and NH4-N for the AOB community. Overall, 105 kg N ha-1 yr-1 was optimum for the AOB community and wheat yield in the semi-arid area.},
}
@article {pmid35260828,
year = {2022},
author = {Klotz, F and Kitzinger, K and Ngugi, DK and Büsing, P and Littmann, S and Kuypers, MMM and Schink, B and Pester, M},
title = {Quantification of archaea-driven freshwater nitrification from single cell to ecosystem levels.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
pmid = {35260828},
issn = {1751-7370},
support = {GRK 2272/1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; GRK 2272/1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; GRK 2272/1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
abstract = {Deep oligotrophic lakes sustain large populations of the class Nitrososphaeria (Thaumarchaeota) in their hypolimnion. They are thought to be the key ammonia oxidizers in this habitat, but their impact on N-cycling in lakes has rarely been quantified. We followed this archaeal population in one of Europe's largest lakes, Lake Constance, for two consecutive years using metagenomics and metatranscriptomics combined with stable isotope-based activity measurements. An abundant (8-39% of picoplankton) and transcriptionally active archaeal ecotype dominated the nitrifying community. It represented a freshwater-specific species present in major inland water bodies, for which we propose the name "Candidatus Nitrosopumilus limneticus". Its biomass corresponded to 12% of carbon stored in phytoplankton over the year´s cycle. Ca. N. limneticus populations incorporated significantly more ammonium than most other microorganisms in the hypolimnion and were driving potential ammonia oxidation rates of 6.0 ± 0.9 nmol l‒1 d‒1, corresponding to potential cell-specific rates of 0.21 ± 0.11 fmol cell-1 d-1. At the ecosystem level, this translates to a maximum capacity of archaea-driven nitrification of 1.76 × 109 g N-ammonia per year or 11% of N-biomass produced annually by phytoplankton. We show that ammonia-oxidizing archaea play an equally important role in the nitrogen cycle of deep oligotrophic lakes as their counterparts in marine ecosystems.},
}
@article {pmid35246355,
year = {2022},
author = {Ithurbide, S and Gribaldo, S and Albers, SV and Pende, N},
title = {Spotlight on FtsZ-based cell division in Archaea.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2022.01.005},
pmid = {35246355},
issn = {1878-4380},
abstract = {Compared with the extensive knowledge on cell division in model eukaryotes and bacteria, little is known about how archaea divide. Interestingly, both endosomal sorting complex required for transport (ESCRT)-based and FtsZ-based cell division systems are found in members of the Archaea. In the past couple of years, several studies have started to shed light on FtsZ-based cell division processes in members of the Euryarchaeota. In this review we highlight recent findings in this emerging field of research. We present current knowledge of the cell division machinery of halophiles which relies on two FtsZ proteins, and we compare it with that of methanobacteria, which relies on only one FtsZ. Finally, we discuss how these differences relate to the distinct cell envelopes of these two archaeal model systems.},
}
@article {pmid35221208,
year = {2022},
author = {Stevens, KM and Warnecke, T},
title = {Histone variants in archaea - An undiscovered country.},
journal = {Seminars in cell &amp; developmental biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.semcdb.2022.02.016},
pmid = {35221208},
issn = {1096-3634},
abstract = {Exchanging core histones in the nucleosome for paralogous variants can have important functional ramifications. Many of these variants, and their physiological roles, have been characterized in exquisite detail in model eukaryotes, including humans. In comparison, our knowledge of histone biology in archaea remains rudimentary. This is true in particular for our knowledge of histone variants. Many archaea encode several histone genes that differ in sequence, but do these paralogs make distinct, adaptive contributions to genome organization and regulation in a manner comparable to eukaryotes? Below, we review what we know about histone variants in archaea at the level of structure, regulation, and evolution. In all areas, our knowledge pales when compared to the wealth of insight that has been gathered for eukaryotes. Recent findings, however, provide tantalizing glimpses into a rich and largely undiscovered country that is at times familiar and eukaryote-like and at times strange and uniquely archaeal. We sketch a preliminary roadmap for further exploration of this country; an undertaking that may ultimately shed light not only on chromatin biology in archaea but also on the origin of histone-based chromatin in eukaryotes.},
}
@article {pmid35220398,
year = {2022},
author = {Yin, X and Zhou, G and Cai, M and Zhu, QZ and Richter-Heitmann, T and Aromokeye, DA and Liu, Y and Nimzyk, R and Zheng, Q and Tang, X and Elvert, M and Li, M and Friedrich, MW},
title = {Catabolic protein degradation in marine sediments confined to distinct archaea.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
pmid = {35220398},
issn = {1751-7370},
support = {project-ID 49926684//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; project-ID 390741601//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; No. 2018M633111//China Postdoctoral Science Foundation/ ; No. 91851105, 31622002, 31600093, and 31700430//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Metagenomic analysis has facilitated prediction of a variety of carbon utilization potentials by uncultivated archaea including degradation of protein, which is a wide-spread carbon polymer in marine sediments. However, the activity of detrital catabolic protein degradation is mostly unknown for the vast majority of archaea. Here, we show actively executed protein catabolism in three archaeal phyla (uncultivated Thermoplasmata, SG8-5; Bathyarchaeota subgroup 15; Lokiarchaeota subgroup 2c) by RNA- and lipid-stable isotope probing in incubations with different marine sediments. However, highly abundant potential protein degraders Thermoprofundales (MBG-D) and Lokiarchaeota subgroup 3 were not incorporating 13C-label from protein during incubations. Nonetheless, we found that the pathway for protein utilization was present in metagenome associated genomes (MAGs) of active and inactive archaea. This finding was supported by screening extracellular peptidases in 180 archaeal MAGs, which appeared to be widespread but not correlated to organisms actively executing this process in our incubations. Thus, our results have important implications: (i) multiple low-abundant archaeal groups are actually catabolic protein degraders; (ii) the functional role of widespread extracellular peptidases is not an optimal tool to identify protein catabolism, and (iii) catabolic degradation of sedimentary protein is not a common feature of the abundant archaeal community in temperate and permanently cold marine sediments.},
}
@article {pmid35189237,
year = {2022},
author = {Li, M and He, H and Mi, T and Zhen, Y},
title = {Spatiotemporal dynamics of ammonia-oxidizing archaea and bacteria contributing to nitrification in sediments from Bohai Sea and South Yellow Sea, China.},
journal = {The Science of the total environment},
volume = {825},
number = {},
pages = {153972},
doi = {10.1016/j.scitotenv.2022.153972},
pmid = {35189237},
issn = {1879-1026},
mesh = {*Ammonia ; *Archaea/genetics ; Bacteria/genetics ; China ; Geologic Sediments/microbiology ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Soil Microbiology ; },
abstract = {Nitrification is a central process in nitrogen cycle in the ocean. Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play significant roles in ammonia oxidation which is the first and rate-limiting step in nitrification, and their differential contribution to nitrification is an important issue, attracting extensive attention. In this study, based on the quantification of archaeal and bacterial amoA gene and the measurement of potential nitrification rate (PNR), we investigated the spatiotemporal dynamics of PNRs and the amoA gene abundance and transcript abundance of aerobic ammonia oxidizers in surface sediments collected in summer and spring across ~900 km of the Bohai Sea and Yellow Sea in China. The results revealed that the contribution of AOA to nitrification was greater than that of AOB in coastal sediments, probably due to salinity and ammonia concentration. Besides, seasons had significant effect on amoA gene abundance and transcript abundance, especially for AOA, while both seasons and sea areas had significant influence on PNR of AOA and AOB. Further analysis showed complex relationships among amoA gene abundances, transcript abundances and PNRs. More importantly, both spatial (geographic distance) and environmental factors were vital in explaining the variations of ammonia-oxidizing microorganism abundances and the PNRs.},
}
@article {pmid35181078,
year = {2022},
author = {Wei, W and Hu, X and Yang, S and Wang, K and Zeng, C and Hou, Z and Cui, H and Liu, S and Zhu, L},
title = {Denitrifying halophilic archaea derived from salt dominate the degradation of nitrite in salted radish during pickling.},
journal = {Food research international (Ottawa, Ont.)},
volume = {152},
number = {},
pages = {110906},
doi = {10.1016/j.foodres.2021.110906},
pmid = {35181078},
issn = {1873-7145},
mesh = {China ; Nitrates ; *Nitrites/metabolism ; Nitrogen/metabolism ; *Raphanus/chemistry ; },
abstract = {Salted radish is a popular high-salinity table food in China, and nitrite is always generated during the associated pickling process. However, this nitrite can be naturally degraded, and the underlying mechanism is unknown. Here, we identified the microbial groups that dominate the natural degradation of nitrite in salted radish and clarified the related metabolic mechanism. Based on dynamic monitoring of pH and the concentrations of nitrogen compounds as well as high-throughput sequencing analysis of the structural succession of microbial communities in the tested salted radish, we determined that the halophilic archaea derived from pickling salt dominate the natural degradation of nitrite via denitrification. Based on isolation, identification, nitrite reduction assays, and genome annotation, we further determined that Haloarcula, Halolamina, and Halobacterium were the key genera. These halophilic archaea might cope with high salt stress through the "salt-in" mechanism with the assistance of the accumulation of potassium ions, obtain electrons necessary for "truncated denitrification" from the metabolism of extracellular glucose absorbed from salted radish, and efficiently reduce nitrite to nitrogen, bypassing nitrite generation from nitrate reduction. The present study provides important information for the prevention and control of nitrite hazards in salted vegetables with high salinity, such as salted radish.},
}
@article {pmid35165305,
year = {2022},
author = {Xu, B and Li, F and Cai, L and Zhang, R and Fan, L and Zhang, C},
title = {A holistic genome dataset of bacteria, archaea and viruses of the Pearl River estuary.},
journal = {Scientific data},
volume = {9},
number = {1},
pages = {49},
pmid = {35165305},
issn = {2052-4463},
support = {91951120//National Natural Science Foundation of China (National Science Foundation of China)/ ; 91851210//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Archaea/genetics ; *Bacteria/genetics ; Estuaries ; Genome ; *Microbiota/genetics ; Rivers ; *Viruses/genetics ; },
abstract = {Estuaries are one of the most important coastal ecosystems. While microbiomes and viromes have been separately investigated in some estuaries, few studies holistically deciphered the genomes and connections of viruses and their microbial hosts along an estuarine salinity gradient. Here we applied deep metagenomic sequencing on microbial and viral communities in surface waters of the Pearl River estuary, one of China's largest estuaries with strong anthropogenic impacts. Overall, 1,205 non-redundant prokaryotic genomes with ≥50% completeness and ≤10% contamination, and 78,502 non-redundant viral-like genomes were generated from samples of three size fractions and five salinity levels. Phylogenomic analysis and taxonomy classification show that majority of these estuarine prokaryotic and viral genomes are novel at species level according to public databases. Potential connections between the microbial and viral populations were further investigated by host-virus matching. These combined microbial and viral genomes provide an important complement of global marine genome datasets and should greatly facilitate our understanding of microbe-virus interactions, evolution and their implications in estuarine ecosystems.},
}
@article {pmid35165204,
year = {2022},
author = {Schorn, S and Ahmerkamp, S and Bullock, E and Weber, M and Lott, C and Liebeke, M and Lavik, G and Kuypers, MMM and Graf, JS and Milucka, J},
title = {Diverse methylotrophic methanogenic archaea cause high methane emissions from seagrass meadows.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {9},
pages = {},
pmid = {35165204},
issn = {1091-6490},
mesh = {Aerobiosis ; Alismatales/*metabolism ; Anaerobiosis ; Euryarchaeota/classification/*metabolism ; Geologic Sediments ; Mediterranean Sea ; Methane/*metabolism ; Microbiota ; Oxidation-Reduction ; Phylogeny ; Species Specificity ; },
abstract = {Marine coastlines colonized by seagrasses are a net source of methane to the atmosphere. However, methane emissions from these environments are still poorly constrained, and the underlying processes and responsible microorganisms remain largely unknown. Here, we investigated methane turnover in seagrass meadows of Posidonia oceanica in the Mediterranean Sea. The underlying sediments exhibited median net fluxes of methane into the water column of ca. 106 µmol CH4 ⋅ m-2 ⋅ d-1 Our data show that this methane production was sustained by methylated compounds produced by the plant, rather than by fermentation of buried organic carbon. Interestingly, methane production was maintained long after the living plant died off, likely due to the persistence of methylated compounds, such as choline, betaines, and dimethylsulfoniopropionate, in detached plant leaves and rhizomes. We recovered multiple mcrA gene sequences, encoding for methyl-coenzyme M reductase (Mcr), the key methanogenic enzyme, from the seagrass sediments. Most retrieved mcrA gene sequences were affiliated with a clade of divergent Mcr and belonged to the uncultured Candidatus Helarchaeota of the Asgard superphylum, suggesting a possible involvement of these divergent Mcr in methane metabolism. Taken together, our findings identify the mechanisms controlling methane emissions from these important blue carbon ecosystems.},
}
@article {pmid35145493,
year = {2021},
author = {Chen, S and Tao, J and Chen, Y and Wang, W and Fan, L and Zhang, C},
title = {Interactions Between Marine Group II Archaea and Phytoplankton Revealed by Population Correlations in the Northern Coast of South China Sea.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {785532},
pmid = {35145493},
issn = {1664-302X},
abstract = {Marine Group II (MGII) archaea (Poseidoniales) are the most abundant surface marine planktonic archaea and are widely distributed in both coastal and pelagic waters. The factors affecting their distribution and activity are poorly understood. MGII archaea have the metabolic potential to utilize algae-derived organic matter and are frequently observed in high abundance during or following phytoplankton blooms, suggesting that they are key players of the marine food web. In this study, we studied interactions between MGII archaea and the diverse taxa of phytoplankton in the northern coast of South China Sea. Non-metric multidimensional scaling and cluster analyses demonstrated distinct MGII community patterns in the Pearl River plume (PRP) and the open regions of the northern South China Sea (ONSCS), with MGIIb dominating the former and MGIIa and MGIIb showing remarkable variations in the latter for the same sampling season. Nevertheless, positive correlations (Pearson correlation: R > 0.8 and P < 0.01) in absolute abundances of ribosomal RNA (rRNA)-derived complementary DNA and rRNA genes from network analyses were found between MGII archaea and phytoplankton (cyanobacteria, haptophytes, and stramenopiles in both PRP and ONSCS) among different particle size fractions, indicating their intrinsic relationships under changing environmental conditions. The results of this study may shed light on the multiple interactions between co-existing species in the micro-niches of different oceanic regions.},
}
@article {pmid35142133,
year = {2022},
author = {Cui, L and Fan, X and Zheng, Y},
title = {[Enhanced heterologous expression of the cytochrome c from uncultured anaerobic methanotrophic archaea].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {38},
number = {1},
pages = {226-237},
doi = {10.13345/j.cjb.210193},
pmid = {35142133},
issn = {1872-2075},
mesh = {Anaerobiosis ; Archaea/metabolism ; *Cytochromes c/genetics/metabolism ; *Escherichia coli/genetics/metabolism ; Heme/metabolism ; },
abstract = {Cytochrome c is a type of heme proteins that are widely distributed in living organisms. It consists of heme and apocytochrome c, and has potential applications in bioelectronics, biomedicine and pollutant degradation. However, heterologous overexpression of cytochrome c is still challenging. To date, expression of the cytochrome c from uncultured anaerobic methanotrophic archaea has not been reported, and nothing is known about the function of this cytochrome c. A his tagged cytochrome c was successfully expressed in E. coli by introducing a thrombin at the N-terminus of CytC4 and co-expressing CcmABCDEFGH, which is responsible for the maturation of cytochrome c. Shewanella oneidensis, which naturally has enzymes for cytochrome c maturation, was then used as a host to further increase the expression of CytC4. Indeed, a significantly higher expression of CytC4 was achieved in S. oneidensis when compared with in E. coli. The successful heterologous overexpression of CytC4 will facilitate the exploitation of its physiological functions and biotechnological applications.},
}
@article {pmid35126338,
year = {2021},
author = {Hedlund, BP and Zhang, C and Wang, F and Rinke, C and Martin, WF},
title = {Editorial: Ecology, Metabolism and Evolution of Archaea-Perspectives From Proceedings of the International Workshop on Geo-Omics of Archaea.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {827229},
pmid = {35126338},
issn = {1664-302X},
}
@article {pmid35101434,
year = {2022},
author = {Liu, BB and Govindan, R and Muthuchamy, M and Cheng, S and Li, X and Ye, L and Wang, LY and Guo, SX and Li, WJ and Alharbi, NS and M Khaled, J and Kadaikunnan, S},
title = {Halophilic archaea and their extracellular polymeric compounds in the treatment of high salt wastewater containing phenol.},
journal = {Chemosphere},
volume = {294},
number = {},
pages = {133732},
doi = {10.1016/j.chemosphere.2022.133732},
pmid = {35101434},
issn = {1879-1298},
mesh = {Archaea/metabolism ; Extracellular Polymeric Substance Matrix/metabolism ; *Phenol/metabolism ; Phenols ; *Waste Water ; },
abstract = {Phenol is one of the major organic pollutants in high salt industrial wastewaters. The biological treatment of such waste using microorganisms is considered to be a cost-effective and eco-friendly method. However, in this process, salt tolerance of microorganisms is one of the main limiting factors. Halophilic microorganisms, especially halophilic archaea are thought to be appropriate for such treatment. To develop a novel effective biological method for high salt phenol wastewater treatment, the influence of phenol in high salt phenol wastewater on halophilic archaea and their extracellular polymeric substances (EPS) should be investigated. In the present study, using phenol enrichment method, 75 halophilic archaeal strains were isolated from Wuyongbulake salt lake sediment sample. The majority of the identified strains were phenol-tolerant. Six strains with high phenol tolerance were chosen, and the phenol scavenging effect was observed in the microbial suspension, supernatant, and EPS. It was noticed that the phenol degradation rate of suspensions of both strains 869-1, and 121-1 in salt water exhibited the highest rates of 83.7%, while the supernatant of strain 869-1 reached the highest rate of 78.2%. When combined with the comprehensive analysis of the artificial wastewater simulation experiment, it was discovered that in the artificial wastewater containing phenol, the phenol degradation rate of suspension of strain A387 exhibited the highest rates of 55.74% both, and supernatant of strain 630-3 reached the highest rate of 62.3%. The EPS produced by strains A00135, 558-1, 869-1, 121-1 and A387 removed 100% phenol within 96 h, and the phenol removal efficiency of EPS produced by 869-1 reached 56.1% under an artificial wastewater simulation experiment with high salt (15%NaCl) condition. The present study suggests that halophilic archaea and their EPS play an important role in phenol degradation. This approach could be potentially used for industrial high-salt wastewater treatment.},
}
@article {pmid35098330,
year = {2022},
author = {Shen, LD and Geng, CY and Ren, BJ and Jin, JH and Huang, HC and Liu, X and Yang, WT and Yang, YL and Liu, JQ and Tian, MH},
title = {Detection and Quantification of Candidatus Methanoperedens-Like Archaea in Freshwater Wetland Soils.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {35098330},
issn = {1432-184X},
support = {41977037//National Natural Science Foundation of China/ ; BK20190092//Natural Science Foundation of Jiangsu Province/ ; },
abstract = {Candidatus Methanoperedens-like archaea, which can use multiple electron acceptors (nitrate, iron, manganese, and sulfate) for anaerobic methane oxidation, could play an important role in reducing methane emissions from freshwater wetlands. Currently, very little is known about the distribution and community composition of Methanoperedens-like archaea in freshwater wetlands, particularly based on their alpha subunit of methyl-coenzyme M reductase (mcrA) genes. Here, the community composition, diversity, and abundance of Methanoperedens-like archaea were investigated in a freshwater wetland through high-throughput sequencing and quantitative PCR on their mcrA genes. A large number of Methanoperedens-like mcrA gene sequences (119,250) were recovered, and a total of 31 operational taxonomic units (OTUs) were generated based on 95% sequence similarity cut-off. The majority of Methanoperedens-like sequences can be grouped into three distinct clusters that were closely associated with the known Methanoperedens species which can couple anaerobic methane oxidation to nitrate or iron reduction. The community composition of Methanoperedens-like archaea differed significantly among different sampling sites, and their mcrA gene abundance was 1.49 × 106 ~ 4.62 × 106 copies g-1 dry soil in the examined wetland. In addition, the community composition of Methanoperedens-like archaea was significantly affected by the soil water content, and the archaeal abundance was significantly positively correlated with the water content. Our results suggest that the mcrA gene is a good biomarker for detection and quantification of Methanoperedens-like archaea, and provide new insights into the distribution and environmental regulation of these archaea in freshwater wetlands.},
}
@article {pmid35076275,
year = {2022},
author = {Rasmussen, AN and Francis, CA},
title = {Genome-Resolved Metagenomic Insights into Massive Seasonal Ammonia-Oxidizing Archaea Blooms in San Francisco Bay.},
journal = {mSystems},
volume = {7},
number = {1},
pages = {e0127021},
doi = {10.1128/msystems.01270-21},
pmid = {35076275},
issn = {2379-5077},
support = {OCE-0847266//National Science Foundation (NSF)/ ; },
abstract = {Ammonia-oxidizing archaea (AOA) are key for the transformation of ammonia to oxidized forms of nitrogen in aquatic environments around the globe, including nutrient-rich coastal and estuarine waters such as San Francisco Bay (SFB). Using metagenomics and 16S rRNA gene amplicon libraries, we found that AOA are more abundant than ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB), except in the freshwater stations in SFB. In South SFB, we observed recurrent AOA blooms of "Candidatus Nitrosomarinus catalina" SPOT01-like organisms, which account for over 20% of 16S rRNA gene amplicons in both surface and bottom waters and co-occur with weeks of high nitrite concentrations (>10 μM) in the oxic water column. We observed pronounced nitrite peaks occurring in the autumn for 7 of the last 9 years (2012 to 2020), suggesting that seasonal AOA blooms are common in South SFB. We recovered two high-quality AOA metagenome-assembled genomes (MAGs), including a Nitrosomarinus-like genome from the South SFB bloom and another Nitrosopumilus genome originating from Suisun Bay in North SFB. Both MAGs cluster with genomes from other estuarine/coastal sites. Analysis of Nitrosomarinus-like genomes show that they are streamlined, with low GC content and high coding density, and harbor urease genes. Our findings support the unique niche of Nitrosomarinus-like organisms which dominate coastal/estuarine waters and provide insights into recurring AOA blooms in SFB. IMPORTANCE Ammonia-oxidizing archaea (AOA) carry out key transformations of ammonia in estuarine systems such as San Francisco Bay (SFB)-the largest estuary on the west coast of North America-and play a significant role in both local and global nitrogen cycling. Using metagenomics and 16S rRNA gene amplicon libraries, we document a massive, recurrent AOA bloom in South SFB that co-occurs with months of high nitrite concentrations in the oxic water column. Our study is the first to generate metagenome-assembled genomes (MAGs) from SFB, and through this process we recovered two high-quality AOA MAGs, one of which originated from bloom samples. These AOA MAGs yield new insight into the Nitrosopumilus and Nitrosomarinus-like lineages and their potential niches in coastal and estuarine systems. Nitrosomarinus-like AOA are abundant in coastal regions around the globe, and we highlight the common occurrence of urease genes, low GC content, and range of salinity tolerances within this lineage.},
}
@article {pmid35069467,
year = {2021},
author = {Rodríguez-Gijón, A and Nuy, JK and Mehrshad, M and Buck, M and Schulz, F and Woyke, T and Garcia, SL},
title = {A Genomic Perspective Across Earth's Microbiomes Reveals That Genome Size in Archaea and Bacteria Is Linked to Ecosystem Type and Trophic Strategy.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {761869},
pmid = {35069467},
issn = {1664-302X},
abstract = {Our view of genome size in Archaea and Bacteria has remained skewed as the data has been dominated by genomes of microorganisms that have been cultivated under laboratory settings. However, the continuous effort to catalog Earth's microbiomes, specifically propelled by recent extensive work on uncultivated microorganisms, provides an opportunity to revise our perspective on genome size distribution. We present a meta-analysis that includes 26,101 representative genomes from 3 published genomic databases; metagenomic assembled genomes (MAGs) from GEMs and stratfreshDB, and isolates from GTDB. Aquatic and host-associated microbial genomes present on average the smallest estimated genome sizes (3.1 and 3.0 Mbp, respectively). These are followed by terrestrial microbial genomes (average 3.7 Mbp), and genomes from isolated microorganisms (average 4.3 Mbp). On the one hand, aquatic and host-associated ecosystems present smaller genomes sizes in genera of phyla with genome sizes above 3 Mbp. On the other hand, estimated genome size in phyla with genomes under 3 Mbp showed no difference between ecosystems. Moreover, we observed that when using 95% average nucleotide identity (ANI) as an estimator for genetic units, only 3% of MAGs cluster together with genomes from isolated microorganisms. Although there are potential methodological limitations when assembling and binning MAGs, we found that in genome clusters containing both environmental MAGs and isolate genomes, MAGs were estimated only an average 3.7% smaller than isolate genomes. Even when assembly and binning methods introduce biases, estimated genome size of MAGs and isolates are very similar. Finally, to better understand the ecological drivers of genome size, we discuss on the known and the overlooked factors that influence genome size in different ecosystems, phylogenetic groups, and trophic strategies.},
}
@article {pmid35052563,
year = {2021},
author = {Neira, G and Vergara, E and Cortez, D and Holmes, DS},
title = {A Large-Scale Multiple Genome Comparison of Acidophilic Archaea (pH ≤ 5.0) Extends Our Understanding of Oxidative Stress Responses in Polyextreme Environments.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {11},
number = {1},
pages = {},
pmid = {35052563},
issn = {2076-3921},
support = {1181717//Fondecyt/ ; FB210008//Centro Ciencia &amp; Vida, Financiamiento Basal para Centros Científicos y Tecnológicos de Excelencia de ANID/ ; },
abstract = {Acidophilic archaea thrive in anaerobic and aerobic low pH environments (pH < 5) rich in dissolved heavy metals that exacerbate stress caused by the production of reactive oxygen species (ROS) such as hydrogen peroxide (H2O2), hydroxyl radical (·OH) and superoxide (O2-). ROS react with lipids, proteins and nucleic acids causing oxidative stress and damage that can lead to cell death. Herein, genes and mechanisms potentially involved in ROS mitigation are predicted in over 200 genomes of acidophilic archaea with sequenced genomes. These organisms are often be subjected to simultaneous multiple stresses such as high temperature, high salinity, low pH and high heavy metal loads. Some of the topics addressed include: (1) the phylogenomic distribution of these genes and what this can tell us about the evolution of these mechanisms in acidophilic archaea; (2) key differences in genes and mechanisms used by acidophilic versus non-acidophilic archaea and between acidophilic archaea and acidophilic bacteria and (3) how comparative genomic analysis predicts novel genes or pathways involved in oxidative stress responses in archaea and likely horizontal gene transfer (HGT) events.},
}
@article {pmid35049347,
year = {2022},
author = {McMahon, FT and Lonergan, CM and Gilmore, BF and Megaw, J},
title = {Draft Genome Sequences of Halobacterium sp. Strains KA-4 and KA-6, Two Extremely Halophilic Archaea Isolated from a Triassic Salt Deposit in Northern Ireland.},
journal = {Microbiology resource announcements},
volume = {11},
number = {1},
pages = {e0116521},
pmid = {35049347},
issn = {2576-098X},
abstract = {Here, we report the draft genome sequences of Halobacterium sp. strains KA-4 and KA-6. These extremely halophilic archaea were isolated from a Triassic halite deposit in Northern Ireland. Based on 16S sequence identity, they were deemed to be closely related strains of Halobacterium noricense but with some notable phenotypic differences.},
}
@article {pmid35040218,
year = {2022},
author = {Papenfort, K and Woodson, SA and Schmitz, RA and Winkler, WC},
title = {Special Issue: Regulating with RNA in Microbes: In conjunction with the 6th Meeting on Regulating with RNA in Bacteria and Archaea.},
journal = {Molecular microbiology},
volume = {117},
number = {1},
pages = {1-3},
doi = {10.1111/mmi.14867},
pmid = {35040218},
issn = {1365-2958},
mesh = {Archaea/*genetics/physiology ; Bacteria/*genetics ; Bacterial Physiological Phenomena ; Evolution, Molecular ; *RNA Processing, Post-Transcriptional ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Untranslated/*genetics ; RNA-Binding Proteins/genetics/*metabolism ; },
}
@article {pmid35027677,
year = {2022},
author = {Wu, F and Speth, DR and Philosof, A and Crémière, A and Narayanan, A and Barco, RA and Connon, SA and Amend, JP and Antoshechkin, IA and Orphan, VJ},
title = {Unique mobile elements and scalable gene flow at the prokaryote-eukaryote boundary revealed by circularized Asgard archaea genomes.},
journal = {Nature microbiology},
volume = {7},
number = {2},
pages = {200-212},
pmid = {35027677},
issn = {2058-5276},
mesh = {Archaea/*genetics ; Archaeal Proteins/genetics ; Bacteria/genetics ; Eukaryota/*genetics ; *Evolution, Molecular ; *Gene Flow ; *Genome, Archaeal ; Metagenomics ; Phylogeny ; Prokaryotic Cells/*metabolism ; },
abstract = {Eukaryotic genomes are known to have garnered innovations from both archaeal and bacterial domains but the sequence of events that led to the complex gene repertoire of eukaryotes is largely unresolved. Here, through the enrichment of hydrothermal vent microorganisms, we recovered two circularized genomes of Heimdallarchaeum species that belong to an Asgard archaea clade phylogenetically closest to eukaryotes. These genomes reveal diverse mobile elements, including an integrative viral genome that bidirectionally replicates in a circular form and aloposons, transposons that encode the 5,000 amino acid-sized proteins Otus and Ephialtes. Heimdallaechaeal mobile elements have garnered various genes from bacteria and bacteriophages, likely playing a role in shuffling functions across domains. The number of archaea- and bacteria-related genes follow strikingly different scaling laws in Asgard archaea, exhibiting a genome size-dependent ratio and a functional division resembling the bacteria- and archaea-derived gene repertoire across eukaryotes. Bacterial gene import has thus likely been a continuous process unaltered by eukaryogenesis and scaled up through genome expansion. Our data further highlight the importance of viewing eukaryogenesis in a pan-Asgard context, which led to the proposal of a conceptual framework, that is, the Heimdall nucleation-decentralized innovation-hierarchical import model that accounts for the emergence of eukaryotic complexity.},
}
@article {pmid35022241,
year = {2022},
author = {Sakai, HD and Nur, N and Kato, S and Yuki, M and Shimizu, M and Itoh, T and Ohkuma, M and Suwanto, A and Kurosawa, N},
title = {Insight into the symbiotic lifestyle of DPANN archaea revealed by cultivation and genome analyses.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {3},
pages = {},
pmid = {35022241},
issn = {1091-6490},
mesh = {Archaea/classification/cytology/*genetics/*physiology ; Coculture Techniques ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Archaeal ; Genomics ; Nanoarchaeota ; Phylogeny ; Symbiosis/*genetics/*physiology ; },
abstract = {Decades of culture-independent analyses have resulted in proposals of many tentative archaeal phyla with no cultivable representative. Members of DPANN (an acronym of the names of the first included phyla Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanohaloarchaeota, and Nanoarchaeota), an archaeal superphylum composed of at least 10 of these tentative phyla, are generally considered obligate symbionts dependent on other microorganisms. While many draft/complete genome sequences of DPANN archaea are available and their biological functions have been considerably predicted, only a few examples of their successful laboratory cultivation have been reported, limiting our knowledge of their symbiotic lifestyles. Here, we investigated physiology, morphology, and host specificity of an archaeon of the phylum "Candidatus Micrarchaeota" (ARM-1) belonging to the DPANN superphylum by cultivation. We constructed a stable coculture system composed of ARM-1 and its original host Metallosphaera sp. AS-7 belonging to the order Sulfolobales Further host-switching experiments confirmed that ARM-1 grew on five different archaeal species from three genera-Metallosphaera, Acidianus, and Saccharolobus-originating from geologically distinct hot, acidic environments. The results suggested the existence of DPANN archaea that can grow by relying on a range of hosts. Genomic analyses showed inferred metabolic capabilities, common/unique genetic contents of ARM-1 among cultivated micrarchaeal representatives, and the possibility of horizontal gene transfer between ARM-1 and members of the order Sulfolobales Our report sheds light on the symbiotic lifestyles of DPANN archaea and will contribute to the elucidation of their biological/ecological functions.},
}
@article {pmid35021862,
year = {2022},
author = {Salter, TL and Magee, BA and Waite, JH and Sephton, MA},
title = {Mass Spectrometric Fingerprints of Bacteria and Archaea for Life Detection on Icy Moons.},
journal = {Astrobiology},
volume = {22},
number = {2},
pages = {143-157},
doi = {10.1089/ast.2020.2394},
pmid = {35021862},
issn = {1557-8070},
mesh = {Archaea ; Bacteria ; *Exobiology/methods ; Extraterrestrial Environment/chemistry ; Mass Spectrometry ; *Moon ; },
abstract = {The icy moons of the outer Solar System display evidence of subsurface liquid water and, therefore, potential habitability for life. Flybys of Saturn's moon Enceladus by the Cassini spacecraft have provided measurements of material from plumes that suggest hydrothermal activity and the presence of organic matter. Jupiter's moon Europa may have similar plumes and is the target for the forthcoming Europa Clipper mission that carries a high mass resolution and high sensitivity mass spectrometer, called the MAss Spectrometer for Planetary EXploration (MASPEX), with the capability for providing detailed characterization of any organic materials encountered. We have performed a series of experiments using pyrolysis-gas chromatography-mass spectrometry to characterize the mass spectrometric fingerprints of microbial life. A range of extremophile Archaea and Bacteria have been analyzed and the laboratory data converted to MASPEX-type signals. Molecular characteristics of protein, carbohydrate, and lipid structures were detected, and the characteristic fragmentation patterns corresponding to these different biological structures were identified. Protein pyrolysis fragments included phenols, nitrogen heterocycles, and cyclic dipeptides. Oxygen heterocycles, such as furans, were detected from carbohydrates. Our data reveal how mass spectrometry on Europa Clipper can aid in the identification of the presence of life, by looking for characteristic bacterial fingerprints that are similar to those from simple Earthly organisms.},
}
@article {pmid34987183,
year = {2022},
author = {Diamond, S and Lavy, A and Crits-Christoph, A and Matheus Carnevali, PB and Sharrar, A and Williams, KH and Banfield, JF},
title = {Soils and sediments host Thermoplasmata archaea encoding novel copper membrane monooxygenases (CuMMOs).},
journal = {The ISME journal},
volume = {16},
number = {5},
pages = {1348-1362},
pmid = {34987183},
issn = {1751-7370},
mesh = {Ammonia/metabolism ; *Archaea/metabolism ; Carbon/metabolism ; Copper/metabolism ; *Euryarchaeota/metabolism ; Mixed Function Oxygenases/genetics ; Phylogeny ; Soil ; },
abstract = {Copper membrane monooxygenases (CuMMOs) play critical roles in the global carbon and nitrogen cycles. Organisms harboring these enzymes perform the first, and rate limiting, step in aerobic oxidation of ammonia, methane, or other simple hydrocarbons. Within archaea, only organisms in the order Nitrososphaerales (Thaumarchaeota) encode CuMMOs, which function exclusively as ammonia monooxygenases. From grassland and hillslope soils and aquifer sediments, we identified 20 genomes from distinct archaeal species encoding divergent CuMMO sequences. These archaea are phylogenetically clustered in a previously unnamed Thermoplasmatota order, herein named the Ca. Angelarchaeales. The CuMMO proteins in Ca. Angelarchaeales are more similar in structure to those in Nitrososphaerales than those of bacteria, and contain all functional residues required for general monooxygenase activity. Ca. Angelarchaeales genomes are significantly enriched in blue copper proteins (BCPs) relative to sibling lineages, including plastocyanin-like electron carriers and divergent nitrite reductase-like (nirK) 2-domain cupredoxin proteins co-located with electron transport machinery. Ca. Angelarchaeales also encode significant capacity for peptide/amino acid uptake and degradation and share numerous electron transport mechanisms with the Nitrososphaerales. Ca. Angelarchaeales are detected at high relative abundance in some of the environments where their genomes originated from. While the exact substrate specificities of the novel CuMMOs identified here have yet to be determined, activity on ammonia is possible given their metabolic and ecological context. The identification of an archaeal CuMMO outside of the Nitrososphaerales significantly expands the known diversity of CuMMO enzymes in archaea and suggests previously unaccounted organisms contribute to critical global nitrogen and/or carbon cycling functions.},
}
@article {pmid34986784,
year = {2022},
author = {Aouad, M and Flandrois, JP and Jauffrit, F and Gouy, M and Gribaldo, S and Brochier-Armanet, C},
title = {A divide-and-conquer phylogenomic approach based on character supermatrices resolves early steps in the evolution of the Archaea.},
journal = {BMC ecology and evolution},
volume = {22},
number = {1},
pages = {1},
pmid = {34986784},
issn = {2730-7182},
mesh = {*Archaea/genetics ; *Eukaryota ; Phylogeny ; },
abstract = {BACKGROUND: The recent rise in cultivation-independent genome sequencing has provided key material to explore uncharted branches of the Tree of Life. This has been particularly spectacular concerning the Archaea, projecting them at the center stage as prominently relevant to understand early stages in evolution and the emergence of fundamental metabolisms as well as the origin of eukaryotes. Yet, resolving deep divergences remains a challenging task due to well-known tree-reconstruction artefacts and biases in extracting robust ancient phylogenetic signal, notably when analyzing data sets including the three Domains of Life. Among the various strategies aimed at mitigating these problems, divide-and-conquer approaches remain poorly explored, and have been primarily based on reconciliation among single gene trees which however notoriously lack ancient phylogenetic signal.<br><br>RESULTS: We analyzed sub-sets of full supermatrices covering the whole Tree of Life with specific taxonomic sampling to robustly resolve different parts of the archaeal phylogeny in light of their current diversity. Our results strongly support the existence and early emergence of two main clades, Cluster I and Cluster II, which we name Ouranosarchaea and Gaiarchaea, and we clarify the placement of important novel archaeal lineages within these two clades. However, the monophyly and branching of the fast evolving nanosized DPANN members remains unclear and worth of further study.<br><br>CONCLUSIONS: We inferred a well resolved rooted phylogeny of the Archaea that includes all recently described phyla of high taxonomic rank. This phylogeny represents a valuable reference to study the evolutionary events associated to the early steps of the diversification of the archaeal domain. Beyond the specifics of archaeal phylogeny, our results demonstrate the power of divide-and-conquer approaches to resolve deep phylogenetic relationships, which should be applied to progressively resolve the entire Tree of Life.},
}
@article {pmid34986141,
year = {2022},
author = {Chadwick, GL and Skennerton, CT and Laso-Pérez, R and Leu, AO and Speth, DR and Yu, H and Morgan-Lang, C and Hatzenpichler, R and Goudeau, D and Malmstrom, R and Brazelton, WJ and Woyke, T and Hallam, SJ and Tyson, GW and Wegener, G and Boetius, A and Orphan, VJ},
title = {Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea.},
journal = {PLoS biology},
volume = {20},
number = {1},
pages = {e3001508},
pmid = {34986141},
issn = {1545-7885},
mesh = {Anaerobiosis ; *Archaea/genetics/metabolism ; *Electrons ; Genomics ; Geologic Sediments/microbiology ; Methane/metabolism ; Oxidation-Reduction ; Phylogeny ; Sulfates/metabolism ; },
abstract = {The anaerobic oxidation of methane coupled to sulfate reduction is a microbially mediated process requiring a syntrophic partnership between anaerobic methanotrophic (ANME) archaea and sulfate-reducing bacteria (SRB). Based on genome taxonomy, ANME lineages are polyphyletic within the phylum Halobacterota, none of which have been isolated in pure culture. Here, we reconstruct 28 ANME genomes from environmental metagenomes and flow sorted syntrophic consortia. Together with a reanalysis of previously published datasets, these genomes enable a comparative analysis of all marine ANME clades. We review the genomic features that separate ANME from their methanogenic relatives and identify what differentiates ANME clades. Large multiheme cytochromes and bioenergetic complexes predicted to be involved in novel electron bifurcation reactions are well distributed and conserved in the ANME archaea, while significant variations in the anabolic C1 pathways exists between clades. Our analysis raises the possibility that methylotrophic methanogenesis may have evolved from a methanotrophic ancestor.},
}
@article {pmid34984789,
year = {2022},
author = {Chazan, A and Rozenberg, A and Mannen, K and Nagata, T and Tahan, R and Yaish, S and Larom, S and Inoue, K and Béjà, O and Pushkarev, A},
title = {Diverse heliorhodopsins detected via functional metagenomics in freshwater Actinobacteria, Chloroflexi and Archaea.},
journal = {Environmental microbiology},
volume = {24},
number = {1},
pages = {110-121},
doi = {10.1111/1462-2920.15890},
pmid = {34984789},
issn = {1462-2920},
mesh = {*Actinobacteria/genetics ; Archaea/genetics ; *Chloroflexi ; Fresh Water ; Metagenomics ; Rhodopsins, Microbial ; },
abstract = {The recently discovered rhodopsin family of heliorhodopsins (HeRs) is abundant in diverse microbial environments. So far, the functional and biological roles of HeRs remain unknown. To tackle this issue, we combined experimental and computational screens to gain some novel insights. Here, 10 readily expressed HeR genes were found using functional metagenomics on samples from two freshwater environments. These HeRs originated from diverse prokaryotic groups: Actinobacteria, Chloroflexi and Archaea. Heterologously expressed HeRs absorbed light in the green and yellow wavelengths (543-562 nm) and their photocycles exhibited diverse kinetic characteristics. To approach the physiological function of the HeRs, we used our environmental clones along with thousands of microbial genomes to analyze genes neighbouring HeRs. The strongest association was found with the DegV family involved in activation of fatty acids, which allowed us to hypothesize that HeRs might be involved in light-induced membrane lipid modifications.},
}
@article {pmid34962596,
year = {2021},
author = {Li, SY and Xin, YJ and Bao, CX and Hou, J and Cui, HL},
title = {Haloprofundus salilacus sp. nov., Haloprofundus halobius sp. nov. and Haloprofundus salinisoli sp. nov.: three extremely halophilic archaea isolated from salt lake and saline soil.},
journal = {Extremophiles : life under extreme conditions},
volume = {26},
number = {1},
pages = {6},
pmid = {34962596},
issn = {1433-4909},
support = {31770005//National Natural Science Foundation of China/ ; },
mesh = {Base Composition ; China ; DNA, Archaeal ; Glycolipids ; *Halobacteriaceae/genetics ; *Lakes ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil ; },
abstract = {Three halophilic archaeal strains, Gai1-5T, SEDH52T and SQT7-1T were isolated from Gaize salt lake and Xiadi salt lake in Tibet, and saline soil from Xinjiang, respectively. Phylogenetic analysis based on 16S rRNA gene and rpoB' gene sequences showed that these three strains formed different branches separating them from Haloprofundus halophilus NK23T (97.7-98.3% similarities for 16S rRNA gene and 94.7-94.8% similarities for rpoB' gene, respectively) and Haloprofundus marisrubri SB9T (94.7-96.4% similarities for 16S rRNA gene and 92.3-93.2% similarities for rpoB' gene, respectively). Several phenotypic characteristics distinguish the strains Gai1-5 T, SEDH52T and SQT7-1T from Haloprofundus halophilus NK23T and Haloprofundus marisrubri SB9T. The average nucleotide identity (ANI) and in silico DNA-DNA hybridization (isDDH) values among the three strains and current Haloprofundus members were in the range of 83.3-88.3% and 27.2-35.7%, respectively, far below the species boundary threshold values. The major polar lipids of three strains were phosphatidic acid (PA), phosphatidylglycerol (PG), phosphatidylglycerol sulphate (PGS), phosphatidylglycerol phosphate methyl ester (PGP-Me), sulfated mannosyl glucosyl diether (S-DGD-1), mannosyl glucosyl diether-phosphatidic acid (DGD-PA) and sulfated mannosyl glucosyl diether-phosphatidic acid (S-DGD-PA). These results showed that strains Gai1-5T (= CGMCC 1.16079T = JCM 33561T), SQT7-1T (= CGMCC 1.16063T = JCM 33553 T) and SEDH52T (= CGMCC 1.17434T) represented three novel species in the genus Haloprofundus, for which the names Haloprofundus salilacus sp. nov., Haloprofundus salinisoli sp. nov., and Haloprofundus halobius sp. nov. are proposed.},
}
@article {pmid34948099,
year = {2021},
author = {De Falco, M and De Felice, M},
title = {Take a Break to Repair: A Dip in the World of Double-Strand Break Repair Mechanisms Pointing the Gaze on Archaea.},
journal = {International journal of molecular sciences},
volume = {22},
number = {24},
pages = {},
pmid = {34948099},
issn = {1422-0067},
support = {FOE-2019, DSB.AD004.271//CNR project NUTR-AGE/ ; F/200050/01-03/X45//NUTRABEST/ ; },
mesh = {*Archaea/genetics/metabolism ; *DNA Breaks, Double-Stranded ; *DNA Repair ; *DNA, Archaeal/genetics/metabolism ; *Genomic Instability ; Humans ; },
abstract = {All organisms have evolved many DNA repair pathways to counteract the different types of DNA damages. The detection of DNA damage leads to distinct cellular responses that bring about cell cycle arrest and the induction of DNA repair mechanisms. In particular, DNA double-strand breaks (DSBs) are extremely toxic for cell survival, that is why cells use specific mechanisms of DNA repair in order to maintain genome stability. The choice among the repair pathways is mainly linked to the cell cycle phases. Indeed, if it occurs in an inappropriate cellular context, it may cause genome rearrangements, giving rise to many types of human diseases, from developmental disorders to cancer. Here, we analyze the most recent remarks about the main pathways of DSB repair with the focus on homologous recombination. A thorough knowledge in DNA repair mechanisms is pivotal for identifying the most accurate treatments in human diseases.},
}
@article {pmid34927901,
year = {2021},
author = {Otzen, DE and Dueholm, MS and Najarzadeh, Z and Knowles, TPJ and Ruggeri, FS},
title = {In situ Sub-Cellular Identification of Functional Amyloids in Bacteria and Archaea by Infrared Nanospectroscopy.},
journal = {Small methods},
volume = {5},
number = {6},
pages = {e2001002},
doi = {10.1002/smtd.202001002},
pmid = {34927901},
issn = {2366-9608},
support = {8021-00208B//Independent Research Foundation Denmark | Natural Sciences/ ; 6111-00241B//Independent Research Foundation Denmark | Technology and Production/ ; 13351//Villum Foundation/ ; },
mesh = {Amyloid/chemistry/*isolation &amp; purification/*metabolism ; Amyloidogenic Proteins/chemistry/isolation &amp; purification/*metabolism ; Archaea/*metabolism ; Bacteria/*metabolism ; Bacterial Outer Membrane ; Biofilms ; Escherichia coli/metabolism ; Escherichia coli Proteins ; Humans ; Protein Structure, Secondary ; Pseudomonas/metabolism ; },
abstract = {Formation of amyloid structures is originally linked to human disease. However, amyloid materials are found extensively in the animal and bacterial world where they stabilize intra- and extra-cellular environments like biofilms or cell envelopes. To date, functional amyloids have largely been studied using optical microscopy techniques in vivo, or after removal from their biological context for higher-resolution studies in vitro. Furthermore, conventional microscopies only indirectly identify amyloids based on morphology or unspecific amyloid dyes. Here, the high chemical and spatial (≈20 nm) resolution of Infrared Nanospectroscopy (AFM-IR) to investigate functional amyloid from Escherichia coli (curli), Pseudomonas (Fap), and the Archaea Methanosaeta (MspA) in situ is exploited. It is demonstrated that AFM-IR identifies amyloid protein within single intact cells through their cross β-sheet secondary structure, which has a unique spectroscopic signature in the amide I band of protein. Using this approach, nanoscale-resolved chemical images and spectra of purified curli and Methanosaeta cell wall sheaths are provided. The results highlight significant differences in secondary structure between E. coli cells with and without curli. Taken together, these results suggest that AFM-IR is a new and powerful label-free tool for in situ investigations of the biophysical state of functional amyloid and biomolecules in general.},
}
@article {pmid34917055,
year = {2021},
author = {Lu, S and Liu, X and Liu, C and Cheng, G and Zhou, R and Li, Y},
title = {A Review of Ammonia-Oxidizing Archaea and Anaerobic Ammonia-Oxidizing Bacteria in the Aquaculture Pond Environment in China.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {775794},
pmid = {34917055},
issn = {1664-302X},
abstract = {The excessive ammonia produced in pond aquaculture processes cannot be ignored. In this review, we present the distribution and diversity of ammonia-oxidizing archaea (AOA) and anaerobic ammonia-oxidizing bacteria (AnAOB) in the pond environment. Combined with environmental conditions, we analyze the advantages of AOA and AnAOB in aquaculture water treatment and discuss the current situation of pond water treatment engineering involving these microbes. AOA and AnAOB play an important role in the nitrogen removal process of aquaculture pond water, especially in seasonal low temperatures and anoxic sediment layers. Finally, we prospect the application of bioreactors to purify pond aquaculture water using AOA and AnAOB, in autotrophic nitrogen removal, which can reduce the production of greenhouse gases (such as nitrous oxide) and is conducive to the development of environmentally sustainable pond aquaculture.},
}
@article {pmid34910467,
year = {2021},
author = {Wang, Y and Xu, J and Cui, D and Kong, L and Chen, S and Xie, W and Zhang, C},
title = {Classification and Identification of Archaea Using Single-Cell Raman Ejection and Artificial Intelligence: Implications for Investigating Uncultivated Microorganisms.},
journal = {Analytical chemistry},
volume = {93},
number = {51},
pages = {17012-17019},
doi = {10.1021/acs.analchem.1c03495},
pmid = {34910467},
issn = {1520-6882},
mesh = {*Artificial Intelligence ; In Situ Hybridization, Fluorescence ; *Lipids ; Phylogeny ; RNA, Ribosomal, 16S ; },
abstract = {Archaea can produce special cellular components such as polyhydroxyalkanoates, carotenoids, rhodopsin, and ether lipids, which have valuable applications in medicine and green energy production. Most of the archaeal species are uncultivated, posing challenges to investigating their biomarker components and biochemical properties. In this study, we applied Raman spectroscopy to examine the biological characteristics of nine archaeal isolates, including halophilic archaea (Haloferax larsenii, Haloarcula argentinensis, Haloferax mediterranei, Halomicrobium mukohataei, Halomicrobium salinus, Halorussus sp., Natrinema gari), thermophilic archaea (Sulfolobus acidocaldarius), and marine group I (MGI) archaea (Nitrosopumilus maritimus). Linear discriminant analysis of the Raman spectra allowed visualization of significant separations among the nine archaeal isolates. Machine-learning classification models based on support vector machine achieved accuracies of 88-100% when classifying the nine archaeal species. The predicted results were validated by DNA sequencing analysis of cells isolated from the mixture by Raman-activated cell sorting. Raman spectra of uncultured archaea (MGII) were also obtained based on Raman spectroscopy and fluorescence in situ hybridization. The results combining multiple Raman-based techniques indicated that MGII may have the ability to produce lipids distinct from other archaeal species. Our study provides a valuable approach for investigating and classifying archaea, especially uncultured species, at the single-cell level.},
}
@article {pmid34894218,
year = {2022},
author = {Stevens, KM and Hocher, A and Warnecke, T},
title = {Deep Conservation of Histone Variants in Thermococcales Archaea.},
journal = {Genome biology and evolution},
volume = {14},
number = {1},
pages = {},
pmid = {34894218},
issn = {1759-6653},
support = {MC_UP_1102/7/MRC_/Medical Research Council/United Kingdom ; MC-A658-5TY40/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Archaea/genetics/metabolism ; Chromatin ; *Histones/genetics ; Nucleosomes/genetics ; Phylogeny ; *Thermococcales/genetics/metabolism ; },
abstract = {Histones are ubiquitous in eukaryotes where they assemble into nucleosomes, binding and wrapping DNA to form chromatin. One process to modify chromatin and regulate DNA accessibility is the replacement of histones in the nucleosome with paralogous variants. Histones are also present in archaea but whether and how histone variants contribute to the generation of different physiologically relevant chromatin states in these organisms remains largely unknown. Conservation of paralogs with distinct properties can provide prima facie evidence for defined functional roles. We recently revealed deep conservation of histone paralogs with different properties in the Methanobacteriales, but little is known experimentally about these histones. In contrast, the two histones of the model archaeon Thermococcus kodakarensis, HTkA and HTkB, have been examined in some depth, both in vitro and in vivo. HTkA and HTkB exhibit distinct DNA-binding behaviors and elicit unique transcriptional responses when deleted. Here, we consider the evolution of HTkA/B and their orthologs across the order Thermococcales. We find histones with signature HTkA- and HTkB-like properties to be present in almost all Thermococcales genomes. Phylogenetic analysis indicates the presence of one HTkA- and one HTkB-like histone in the ancestor of Thermococcales and long-term maintenance of these two paralogs throughout Thermococcales diversification. Our results support the notion that archaea and eukaryotes have convergently evolved histone variants that carry out distinct adaptive functions. Intriguingly, we also detect more highly diverged histone-fold proteins, related to those found in some bacteria, in several Thermococcales genomes. The functions of these bacteria-type histones remain unknown, but structural modeling suggests that they can form heterodimers with HTkA/B-like histones.},
}
@article {pmid34871608,
year = {2022},
author = {Liu, Y and Wang, Q and Pan, Q and Zhou, X and Peng, Z and Jahng, D and Yang, B and Pan, X},
title = {Ventilation induced evolution pattern of archaea, fungi, bacteria and their potential roles during co-bioevaporation treatment of concentrated landfill leachate and food waste.},
journal = {Chemosphere},
volume = {289},
number = {},
pages = {133122},
doi = {10.1016/j.chemosphere.2021.133122},
pmid = {34871608},
issn = {1879-1298},
mesh = {Archaea/genetics ; Bacteria/genetics ; Bioreactors ; Food ; Fungi/genetics ; *Refuse Disposal ; Waste Disposal Facilities ; *Water Pollutants, Chemical/analysis ; },
abstract = {To obtain a favorable aeration type in co-bioevaporation treatment of concentrated landfill leachate and food waste, and to deeply understand the co-bioevaporation mechanisms, the temporal evolution differences of archaea, fungi and bacteria as well as the related microbial metabolism genes and functional enzymes under intermittent ventilation (IV) and continuous ventilation (CV) were investigated. Results through metagenomics analysis showed that the less sufficient oxygen and longer thermophilic phase in IV stimulated the vigorous growth of archaea, while CV was beneficial for fungal growth. Even genes of carbohydrates and lipids metabolism and ATP-associated enzymes (enzyme 2.7.13.3 and 3.6.4.12), as well as peptidoglycan biosynthesis enzyme (enzyme 3.4.16.4), were more abundant in CV, IV hold better DNA repair ability, higher microbial viability, and less dehydrogenase sensitivity to temperatures due to the critical contribution of Pseudomonas (3.1-45.9%). Furthermore, IV consumed a similar amount of heat for water evaporation with nearly half of the ventilation of CV and was a favorable aeration type in the practical application of co-bioevaporation.},
}
@article {pmid34850144,
year = {2021},
author = {Yen, CY and Lin, MG and Chen, BW and Ng, IW and Read, N and Kabli, AF and Wu, CT and Shen, YY and Chen, CH and Barillà, D and Sun, YJ and Hsiao, CD},
title = {Chromosome segregation in Archaea: SegA- and SegB-DNA complex structures provide insights into segrosome assembly.},
journal = {Nucleic acids research},
volume = {49},
number = {22},
pages = {13150-13164},
pmid = {34850144},
issn = {1362-4962},
support = {BB/M007839/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R006369/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Adenosine Diphosphate/metabolism ; Adenosine Triphosphatases/chemistry/genetics/metabolism ; Adenosine Triphosphate/metabolism ; Archaeal Proteins/chemistry/*genetics/metabolism ; Chromatin/genetics/metabolism/ultrastructure ; *Chromosome Segregation ; Chromosomes, Archaeal/*genetics ; Crystallography, X-Ray ; DNA, Archaeal/chemistry/*genetics/metabolism ; DNA-Binding Proteins/chemistry/genetics/metabolism ; Microscopy, Electron ; Models, Molecular ; Multiprotein Complexes/chemistry/metabolism/ultrastructure ; Mutation ; Nucleic Acid Conformation ; Protein Binding ; Protein Conformation ; Sulfolobus solfataricus/*genetics/metabolism ; },
abstract = {Genome segregation is a vital process in all organisms. Chromosome partitioning remains obscure in Archaea, the third domain of life. Here, we investigated the SegAB system from Sulfolobus solfataricus. SegA is a ParA Walker-type ATPase and SegB is a site-specific DNA-binding protein. We determined the structures of both proteins and those of SegA-DNA and SegB-DNA complexes. The SegA structure revealed an atypical, novel non-sandwich dimer that binds DNA either in the presence or in the absence of ATP. The SegB structure disclosed a ribbon-helix-helix motif through which the protein binds DNA site specifically. The association of multiple interacting SegB dimers with the DNA results in a higher order chromatin-like structure. The unstructured SegB N-terminus plays an essential catalytic role in stimulating SegA ATPase activity and an architectural regulatory role in segrosome (SegA-SegB-DNA) formation. Electron microscopy results also provide a compact ring-like segrosome structure related to chromosome organization. These findings contribute a novel mechanistic perspective on archaeal chromosome segregation.},
}
@article {pmid34846953,
year = {2022},
author = {Vavilin, VA and Lokshina, LY and Rytov, SV},
title = {Anaerobic oxidation of methane coupled with sulphate reduction: high concentration of methanotrophic archaea might be responsible for low stable isotope fractionation factors in methane.},
journal = {Isotopes in environmental and health studies},
volume = {58},
number = {1},
pages = {44-59},
doi = {10.1080/10256016.2021.2000405},
pmid = {34846953},
issn = {1477-2639},
mesh = {Anaerobiosis ; *Archaea ; Factor VII ; Geologic Sediments ; Isotopes ; *Methane ; Oxidation-Reduction ; Sulfates ; },
abstract = {The changes in δ13CH4 and δ12C1H32H during sulphate-dependent anaerobic oxidation of methane (AOM) were described using dynamic modelling. The batch sulphate-dependent AOM at the nearly linear dynamics of methane oxidation with different enriched cultures originating from three marine sediments was simulated. The traditional Rayleigh equation for carbon and hydrogen stable isotopes in methane was derived from the basic dynamic isotope equation. The general and reduced models, taking into account the reaction stoichiometry and based on balances of chemical elements and their isotopes, describes a redistribution of stable isotope values in the sulphate-dependent AOM process. It was shown that AOM is the first and rate-limiting step in the whole AOM + SR (sulphate reduction) process. The different fractionation factors of carbon and hydrogen isotopes in methane were obtained for three marine sediments. It was concluded that during incubation the highest concentration of methanotrophic archaea might be responsible for the lowest fractionation factors of stable isotopes of carbon and hydrogen in methane. The interpretation of this phenomenon was suggested. Different concentrations of methanotrophic archaea can lead to variations of isotope fractionation factors.},
}
@article {pmid34841354,
year = {2021},
author = {Tan, RSG and Zhou, M and Li, F and Guan, LL},
title = {Identifying active rumen epithelial associated bacteria and archaea in beef cattle divergent in feed efficiency using total RNA-seq.},
journal = {Current research in microbial sciences},
volume = {2},
number = {},
pages = {100064},
pmid = {34841354},
issn = {2666-5174},
abstract = {To date, the role of ruminal epithelial attached microbiota in cattle feed efficiency is undefined. In this study, we aimed to characterize transcriptionally active bacteria and archaea attached to the rumen epithelial wall and to determine whether they differ in cattle with varied feed efficiency. RNA-sequencing was performed to obtain the rumen epithelial transcriptomes from 9 of the most efficient (low RFI) and 9 of the most inefficient (high RFI) animals. The bacteria and archaea 16S rRNA transcripts were identified using an in-house developed pipeline, enriched from filtered reads that did not map to the bovine genome. Archaea from unclassified genera belonging to the Euryarchaeota phylum showed the most activity on the rumen epithelium of low RFI (81.3 ± 1.9%) and high RFI (76.4 ± 3.0%) steers. Bacteria from the Succinivibrionaceae family showed the greatest activity of bacteria on the low RFI (28.7 ± 9.0%) and high RFI (33.9± 8.8%) epithelium. Of the bacterial families, Campylobacteraceae and Neisseriaceae had significantly greater activity on the low RFI epithelium (p < 0.05) and are known to play a role in oxygen scavenging. Greater activity of rumen epithelial attached oxygen scavenging bacteria may provide more optimal feed fermentation conditions, which contributes to high fermentation efficiency in the rumen.},
}
@article {pmid34827555,
year = {2021},
author = {Amin, K and Tranchimand, S and Benvegnu, T and Abdel-Razzak, Z and Chamieh, H},
title = {Glycoside Hydrolases and Glycosyltransferases from Hyperthermophilic Archaea: Insights on Their Characteristics and Applications in Biotechnology.},
journal = {Biomolecules},
volume = {11},
number = {11},
pages = {},
pmid = {34827555},
issn = {2218-273X},
mesh = {Biotechnology ; *Glycoside Hydrolases ; Temperature ; },
abstract = {Hyperthermophilic Archaea colonizing unnatural habitats of extremes conditions such as volcanoes and deep-sea hydrothermal vents represent an unmeasurable bioresource for enzymes used in various industrial applications. Their enzymes show distinct structural and functional properties and are resistant to extreme conditions of temperature and pressure where their mesophilic homologs fail. In this review, we will outline carbohydrate-active enzymes (CAZymes) from hyperthermophilic Archaea with specific focus on the two largest families, glycoside hydrolases (GHs) and glycosyltransferases (GTs). We will present the latest advances on these enzymes particularly in the light of novel accumulating data from genomics and metagenomics sequencing technologies. We will discuss the contribution of these enzymes from hyperthermophilic Archaea to industrial applications and put the emphasis on newly identifed enzymes. We will highlight their common biochemical and distinct features. Finally, we will overview the areas that remain to be explored to identify novel promising hyperthermozymes.},
}
@article {pmid34825404,
year = {2022},
author = {Coker, OO},
title = {Non-bacteria microbiome (virus, fungi, and archaea) in gastrointestinal cancer.},
journal = {Journal of gastroenterology and hepatology},
volume = {37},
number = {2},
pages = {256-262},
doi = {10.1111/jgh.15738},
pmid = {34825404},
issn = {1440-1746},
mesh = {Archaea ; Fungi ; *Gastrointestinal Microbiome ; *Gastrointestinal Neoplasms/microbiology/prevention &amp; control ; Humans ; Viruses ; },
abstract = {The gastrointestinal tract houses millions of microbes collectively referred to as the gut microbiome. The gut microbes comprise of bacteria, viruses, fungi, archaea, and microscopic eukaryotes, which co-evolved or colonize the gut forming complex symbiotic and mutualistic relationships. A state of homeostasis is required between host and gut microbiome relationship to maintain several host beneficial processes. Alterations in the taxonomic and functional composition of the gut microbes are associated with several human diseases including gastrointestinal cancers. Owed to their overwhelming abundance and ease of characterization, several studies focus on the role of bacteria in gastrointestinal cancers. There is however growing evidence that non-bacteria gut microbes are associated with the pathogenesis of gastrointestinal cancers. This review details the association of non-bacteria gut microbes including fungi, viruses, and archaea and their potential manipulation in the prevention and treatment of human gastrointestinal cancers.},
}
@article {pmid34808316,
year = {2022},
author = {Fan, Q and Fan, X and Fu, P and Li, Y and Zhao, Y and Hua, D},
title = {Anaerobic digestion of wood vinegar wastewater using domesticated sludge: Focusing on the relationship between organic degradation and microbial communities (archaea, bacteria, and fungi).},
journal = {Bioresource technology},
volume = {347},
number = {},
pages = {126384},
doi = {10.1016/j.biortech.2021.126384},
pmid = {34808316},
issn = {1873-2976},
mesh = {Acetic Acid ; Anaerobiosis ; Archaea ; Bacteria ; Bioreactors ; Fungi ; Methane ; Methanol ; *Microbiota ; *Sewage ; Waste Water ; },
abstract = {Thermochemical process of biomass is one of the promising renewable energy technologies; however, the by-product (wood vinegar wastewater) is rich in refractory organics, which is harmful to the environment and inhibits the conversion efficiency of microorganisms. Consequently, the dominant functional microbial communities corresponding to the various substrate were obtained through the continuous domestication, and the relationship between the dominant functional communities and the degradation of organic compounds was comprehensively analyzed. The bacterial community was absolutely dominant (approximately 85%), while archaea and fungi had similar relative abundance. The diversity showed that glucose was not conducive to the development of microbial diversity, while the substrate containing wood vinegar wastewater showed the opposite trend. The functional analysis revealed that the enrichment of bacteria associated with the hydrolysis and acidification of organics increased in the domestication process. Glucose facilitated hydrogen-trophic methanogenesis as the main methanogenic pathway in the methanogenic stage.},
}
@article {pmid34803972,
year = {2021},
author = {Durán-Viseras, A and Sánchez-Porro, C and Ventosa, A},
title = {Genomic Insights Into New Species of the Genus Halomicroarcula Reveals Potential for New Osmoadaptative Strategies in Halophilic Archaea.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {751746},
pmid = {34803972},
issn = {1664-302X},
abstract = {Metagenomic studies on prokaryotic diversity of hypersaline soils from the Odiel saltmarshes, South-west Spain, revealed a high proportion of genomic sequences not related to previously cultivated taxa, that might be related to haloarchaea with a high environmental and nutritional flexibility. In this study, we used a culturomics approach in order to isolate new haloarchaeal microorganisms from these hypersaline soils. Four haloarchaeal strains, designated strains F24AT, F28, F27T, and F13T, phylogenetically related to the genus Halomicroarcula, were isolated and characterized in detail. The phylogenomic tree based on the 100 orthologous single-copy genes present in the genomes of these four strains as well as those of the type strains of the species Halomicroarcula pellucida CECT 7537T, Halomicroarcula salina JCM 18369T and Halomicroarcula limicola JCM 18640T, that were determined in this study, revealed that these four new isolates clustered on three groups, with strains F24AT and F28 within a single cluster, and altogether with the species of Halomicroarcula. Additionally, Orthologous Average Nucleotide Identity (OrthoANI), digital DNA-DNA hybridization (dDDH) and Average Amino-acid Identity (AAI) values, likewise phenotypic characteristics, including their polar lipids profiles, permitted to determine that they represent three new species, for which we propose the names Halomicroarcula rubra sp. nov. (type strain F13T), Halomicroarcula nitratireducens sp. nov. (type strain F27T) and Halomicroarcula salinisoli sp. nov. (type strain F24AT). An in deep comparative genomic analysis of species of the genus Halomicroarcula, including their metabolism, their capability to biosynthesize secondary metabolites and their osmoregulatory adaptation mechanisms was carried out. Although they use a salt-in strategy, the identification of the complete pathways for the biosynthesis of the compatible solutes trehalose and glycine betaine, not identified before in any other haloarchaea, might suggest alternative osmoadaptation strategies for this group. This alternative osmoregulatory mechanism would allow this group of haloarchaea to be versatile and eco-physiologically successful in hypersaline environments and would justify the capability of the species of this genus to grow not only on environments with high salt concentrations [up to 30% (w/v) salts], but also under intermediate to low salinities.},
}
@article {pmid34796612,
year = {2022},
author = {Saghaï, A and Banjeree, S and Degrune, F and Edlinger, A and García-Palacios, P and Garland, G and van der Heijden, MGA and Herzog, C and Maestre, FT and Pescador, DS and Philippot, L and Rillig, MC and Romdhane, S and Hallin, S},
title = {Diversity of archaea and niche preferences among putative ammonia-oxidizing Nitrososphaeria dominating across European arable soils.},
journal = {Environmental microbiology},
volume = {24},
number = {1},
pages = {341-356},
doi = {10.1111/1462-2920.15830},
pmid = {34796612},
issn = {1462-2920},
mesh = {*Ammonia ; *Archaea ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Soil ; Soil Microbiology ; },
abstract = {Archaeal communities in arable soils are dominated by Nitrososphaeria, a class within Thaumarchaeota comprising all known ammonia-oxidizing archaea (AOA). AOA are key players in the nitrogen cycle and defining their niche specialization can help predicting effects of environmental change on these communities. However, hierarchical effects of environmental filters on AOA and the delineation of niche preferences of nitrososphaerial lineages remain poorly understood. We used phylogenetic information at fine scale and machine learning approaches to identify climatic, edaphic and geomorphological drivers of Nitrososphaeria and other archaea along a 3000 km European gradient. Only limited insights into the ecology of the low-abundant archaeal classes could be inferred, but our analyses underlined the multifactorial nature of niche differentiation within Nitrososphaeria. Mean annual temperature, C:N ratio and pH were the best predictors of their diversity, evenness and distribution. Thresholds in the predictions could be defined for C:N ratio and cation exchange capacity. Furthermore, multiple, independent and recent specializations to soil pH were detected in the Nitrososphaeria phylogeny. The coexistence of widespread ecophysiological differences between closely related soil Nitrososphaeria highlights that their ecology is best studied at fine phylogenetic scale.},
}
@article {pmid34790173,
year = {2021},
author = {Trouche, B and Brandt, MI and Belser, C and Orejas, C and Pesant, S and Poulain, J and Wincker, P and Auguet, JC and Arnaud-Haond, S and Maignien, L},
title = {Diversity and Biogeography of Bathyal and Abyssal Seafloor Bacteria and Archaea Along a Mediterranean-Atlantic Gradient.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {702016},
pmid = {34790173},
issn = {1664-302X},
abstract = {Seafloor sediments cover the majority of planet Earth and microorganisms inhabiting these environments play a central role in marine biogeochemical cycles. Yet, description of the biogeography and distribution of sedimentary microbial life is still too sparse to evaluate the relative contribution of processes driving this distribution, such as the levels of drift, connectivity, and specialization. To address this question, we analyzed 210 archaeal and bacterial metabarcoding libraries from a standardized and horizon-resolved collection of sediment samples from 18 stations along a longitudinal gradient from the eastern Mediterranean to the western Atlantic. Overall, we found that biogeographic patterns depended on the scale considered: while at local scale the selective influence of contemporary environmental conditions appeared strongest, the heritage of historic processes through dispersal limitation and drift became more apparent at regional scale, and ended up superseding contemporary influences at inter-regional scale. When looking at environmental factors, the structure of microbial communities was correlated primarily with water depth, with a clear transition between 800 and 1,200 meters below sea level. Oceanic basin, water temperature, and sediment depth were other important explanatory parameters of community structure. Finally, we propose increasing dispersal limitation and ecological drift with sediment depth as a probable factor for the enhanced divergence of deeper horizons communities.},
}
@article {pmid34777272,
year = {2021},
author = {Satari, L and Guillén, A and Latorre-Pérez, A and Porcar, M},
title = {Beyond Archaea: The Table Salt Bacteriome.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {714110},
pmid = {34777272},
issn = {1664-302X},
abstract = {Commercial table salt is a condiment with food preservative properties by decreasing water activity and increasing osmotic pressure. Salt is also a source of halophilic bacteria and archaea. In the present research, the diversity of halotolerant and halophilic microorganisms was studied in six commercial table salts by culture-dependent and culture-independent techniques. Three table salts were obtained from marine origins: Atlantic Ocean, Mediterranean (Ibiza Island), and Odiel marshes (supermarket marine salt). Other salts supplemented with mineral and nutritional ingredients were also used: Himalayan pink, Hawaiian black, and one with dried vegetables known as Viking salt. The results of 16S rRNA gene sequencing reveal that the salts from marine origins display a similar archaeal taxonomy, but with significant variations among genera. Archaeal taxa Halorubrum, Halobacterium, Hallobellus, Natronomonas, Haloplanus, Halonotius, Halomarina, and Haloarcula were prevalent in those three marine salts. Furthermore, the most abundant archaeal genera present in all salts were Natronomonas, Halolamina, Halonotius, Halapricum, Halobacterium, Haloarcula, and uncultured Halobacterales. Sulfitobacter sp. was the most frequent bacteria, represented almost in all salts. Other genera such as Bacillus, Enterococcus, and Flavobacterium were the most frequent taxa in the Viking, Himalayan pink, and black salts, respectively. Interestingly, the genus Salinibacter was detected only in marine-originated salts. A collection of 76 halotolerant and halophilic bacterial and haloarchaeal species was set by culturing on different media with a broad range of salinity and nutrient composition. Comparing the results of 16S rRNA gene metataxonomic and culturomics revealed that culturable bacteria Acinetobacter, Aquibacillus, Bacillus, Brevundimonas, Fictibacillus, Gracilibacillus, Halobacillus, Micrococcus, Oceanobacillus, Salibacterium, Salinibacter, Terribacillus, Thalassobacillus, and also Archaea Haloarcula, Halobacterium, and Halorubrum were identified at least in one sample by both methods. Our results show that salts from marine origins are dominated by Archaea, whereas salts from other sources or salt supplemented with ingredients are dominated by bacteria.},
}
@article {pmid34740642,
year = {2022},
author = {Zou, W and Lang, M and Zhang, L and Liu, B and Chen, X},
title = {Ammonia-oxidizing bacteria rather than ammonia-oxidizing archaea dominate nitrification in a nitrogen-fertilized calcareous soil.},
journal = {The Science of the total environment},
volume = {811},
number = {},
pages = {151402},
doi = {10.1016/j.scitotenv.2021.151402},
pmid = {34740642},
issn = {1879-1026},
mesh = {Ammonia ; *Archaea/genetics ; *Betaproteobacteria ; Ecosystem ; Fertilization ; Nitrification ; Nitrogen ; Oxidation-Reduction ; Phylogeny ; Soil ; Soil Microbiology ; },
abstract = {Microbe-driven nitrification is a key process that affects nitrogen (N) utilization by plants and N loss to the environment in agro-ecosystems. Ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) are important microorganisms that dominate the ammonia oxidation process (the first and rate-limiting step of nitrification). Calcareous soils are widely distributed, accounting for more than 30% of the Earth's land. However, the effects of long-term N fertilization on the potential nitrification rate (PNR) and on AOA and AOB in calcareous soils are poorly understood. In this study, we comprehensively assessed the effects of N application (applied at five rates as urea with 0, 73.5, 105, 136.5 and 250 kg N ha-1 for 12 years) on soil chemical characteristics, PNR, N use efficiency (NUE) and the community characteristics of AOB and AOA in a calcareous soil. N application rate affected AOB beta diversity more than that of AOA. Compared to no N control, N application significantly decreased the relative abundance of Group I.1b clade A of AOA and Nitrosospira cluster 3a.2 of AOB, but increased Nitrosomonas cluster 7 of AOB. The relative abundance of Nitrosospira cluster 3a.2 of AOB was negatively correlated with PNR. A structural equation model showed a direct effect of N application rate on the content of soil organic matter and nitrate, the alpha and beta diversity of AOA and AOB. Nitrate and AOB beta diversity were the key factors affecting PNR. Overall, the alpha, beta diversity and community composition of AOB contribute more to PNR than AOA in calcareous soils with high organic matter content. Understanding the relationship between the characteristics of AOA and AOB in calcareous soils and PNR will help to improve NUE.},
}
@article {pmid34737728,
year = {2021},
author = {Vázquez-Campos, X and Kinsela, AS and Bligh, MW and Payne, TE and Wilkins, MR and Waite, TD},
title = {Genomic Insights Into the Archaea Inhabiting an Australian Radioactive Legacy Site.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {732575},
pmid = {34737728},
issn = {1664-302X},
abstract = {During the 1960s, small quantities of radioactive materials were co-disposed with chemical waste at the Little Forest Legacy Site (LFLS, Sydney, Australia). The microbial function and population dynamics in a waste trench during a rainfall event have been previously investigated revealing a broad abundance of candidate and potentially undescribed taxa in this iron-rich, radionuclide-contaminated environment. Applying genome-based metagenomic methods, we recovered 37 refined archaeal MAGs, mainly from undescribed DPANN Archaea lineages without standing in nomenclature and 'Candidatus Methanoperedenaceae' (ANME-2D). Within the undescribed DPANN, the newly proposed orders 'Ca. Gugararchaeales', 'Ca. Burarchaeales' and 'Ca. Anstonellales', constitute distinct lineages with a more comprehensive central metabolism and anabolic capabilities within the 'Ca. Micrarchaeota' phylum compared to most other DPANN. The analysis of new and extant 'Ca. Methanoperedens spp.' MAGs suggests metal ions as the ancestral electron acceptors during the anaerobic oxidation of methane while the respiration of nitrate/nitrite via molybdopterin oxidoreductases would have been a secondary acquisition. The presence of genes for the biosynthesis of polyhydroxyalkanoates in most 'Ca. Methanoperedens' also appears to be a widespread characteristic of the genus for carbon accumulation. This work expands our knowledge about the roles of the Archaea at the LFLS, especially, DPANN Archaea and 'Ca. Methanoperedens', while exploring their diversity, uniqueness, potential role in elemental cycling, and evolutionary history.},
}
@article {pmid34725736,
year = {2021},
author = {Sutter, JM and Johnsen, U and Reinhardt, A and Schönheit, P},
title = {Correction to: Pentose degradation in archaea: Halorhabdus species degrade D-xylose, L-arabinose and D-ribose via bacterial-type pathways.},
journal = {Extremophiles : life under extreme conditions},
volume = {25},
number = {5-6},
pages = {527},
doi = {10.1007/s00792-021-01248-7},
pmid = {34725736},
issn = {1433-4909},
}
@article {pmid34721370,
year = {2021},
author = {Liu, LJ and Jiang, Z and Wang, P and Qin, YL and Xu, W and Wang, Y and Liu, SJ and Jiang, CY},
title = {Physiology, Taxonomy, and Sulfur Metabolism of the Sulfolobales, an Order of Thermoacidophilic Archaea.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {768283},
pmid = {34721370},
issn = {1664-302X},
abstract = {The order Sulfolobales (phylum Crenarchaeota) is a group of thermoacidophilic archaea. The first member of the Sulfolobales was discovered in 1972, and current 23 species are validly named under the International Code of Nomenclature of Prokaryotes. The majority of members of the Sulfolobales is obligately or facultatively chemolithoautotrophic. When they grow autotrophically, elemental sulfur or reduced inorganic sulfur compounds are their energy sources. Therefore, sulfur metabolism is the most important physiological characteristic of the Sulfolobales. The functions of some enzymes and proteins involved in sulfur reduction, sulfur oxidation, sulfide oxidation, thiosulfate oxidation, sulfite oxidation, tetrathionate hydrolysis, and sulfur trafficking have been determined. In this review, we describe current knowledge about the physiology, taxonomy, and sulfur metabolism of the Sulfolobales, and note future challenges in this field.},
}
@article {pmid34691003,
year = {2021},
author = {Anchal, and Kaushik, V and Goel, M},
title = {Distribution of Peptidyl-Prolyl Isomerase (PPIase) in the Archaea.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {751049},
pmid = {34691003},
issn = {1664-302X},
abstract = {Cis-trans isomerization of the peptide bond prior to proline is an intrinsically slow process but plays an essential role in protein folding. In vivo cis-trans isomerization reaction is catalyzed by Peptidyl-prolyl isomerase (PPIases), a category of proteins widely distributed among all the three domains of life. The present study is majorly focused on the distribution of different types of PPIases in the archaeal domain. All the three hitherto known families of PPIases (namely FKBP, Cyclophilin and parvulin) were studied to identify the evolutionary conservation across the phylum archaea. The basic function of cyclophilin, FKBP and parvulin has been conserved whereas the sequence alignment suggested variations in each clade. The conserved residues within the predicted motif of each family are unique. The available protein structures of different PPIase across various domains were aligned to ascertain the structural variation in the catalytic site. The structural alignment of native PPIase proteins among various groups suggested that the apo-protein may have variable conformations but when bound to their specific inhibitors, they attain similar active site configuration. This is the first study of its kind which explores the distribution of archaeal PPIases, along with detailed structural and functional analysis of each type of PPIase found in archaea.},
}
@article {pmid34688753,
year = {2022},
author = {Wunderer, M and Markt, R and Lackner, N and Wagner, AO},
title = {The glutamyl tail length of the cofactor F420 in the methanogenic Archaea Methanosarcina thermophila and Methanoculleus thermophilus.},
journal = {The Science of the total environment},
volume = {809},
number = {},
pages = {151112},
doi = {10.1016/j.scitotenv.2021.151112},
pmid = {34688753},
issn = {1879-1026},
mesh = {Methane ; *Methanomicrobiaceae/enzymology ; Methanosarcina/*enzymology ; Riboflavin/analogs &amp; derivatives ; },
abstract = {The cofactor F420 is synthesized by many different organisms and as a redox cofactor, it plays a crucial role in the redox reactions of catabolic and biosynthetic metabolic pathways. It consists of a deazaflavin structure, which is linked via lactate to an oligoglutamate chain, that can vary in length. In the present study, the methanogenic Archaea Methanosarcina thermophila and Methanoculleus thermophilus were cultivated on different carbon sources and their coenzyme F420 composition has been assayed by reversed-phase ion-pair high-performance liquid chromatography with fluorometric detection regarding both, overall cofactor F420 production and distribution of F420 glutamyl tail length. In Methanosarcina thermophila cultivated on methanol, acetate, and a mixture of acetate and methanol, the most abundant cofactors were F420-5 and F420-4, whereby the last digit refers to the number of expressed glutamyl rests. By contrast, in the obligate CO2 reducing Methanoculleus thermophilus the most abundant cofactors were F420-3 and F420-4. In Methanosarcina thermophila, the relative proportions of the expressed F420 tail length changed during batch growth on all three carbon sources. Over time F420-3 and F420-4 decreased while F420-5 and F420-6 increased in their relative proportion in comparison to total F420 content. In contrast, in Methanoculleus thermophilus the relative abundance of the different F420 cofactors remained stable. It was also possible to differentiate the two methanogenic Archaea based on the glutamyl tail length of the cofactor F420. The cofactor F420-5 in concentrations >2% could only be assigned to Methanosarcina thermophila. In all four variants a trend for a positive correlation between the DNA concentration and the total concentration of the cofactor could be shown. Except for the variant Methanosarcinathermophila with acetate as sole carbon source the same could be shown between the concentration of the mcrA gene copy number and the total concentration of the cofactor.},
}
@article {pmid34666825,
year = {2021},
author = {Wang, B and Liu, N and Yang, M and Wang, L and Liang, X and Liu, CQ},
title = {Co-occurrence of planktonic bacteria and archaea affects their biogeographic patterns in China's coastal wetlands.},
journal = {Environmental microbiome},
volume = {16},
number = {1},
pages = {19},
pmid = {34666825},
issn = {2524-6372},
support = {U1612441//national natural science foundation of china/ ; 2016YFA0601001//key technologies research and development program/ ; },
abstract = {Planktonic bacteria and archaea play a key role in maintaining ecological functions in aquatic ecosystems; however, their biogeographic patterns and underlying mechanisms have not been well known in coastal wetlands including multiple types and at a large space scale. Therefore, planktonic bacteria and archaea and related environmental factors were investigated in twenty-one wetlands along China's coast to understand the above concerns. The results indicated that planktonic bacteria had different biogeographic pattern from planktonic archaea, and both patterns were not dependent on the wetland's types. Deterministic selection shapes the former's community structure, whereas stochastic processes regulate the latter's, being consistent with the fact that planktonic archaea have a larger niche breadth than planktonic bacteria. Planktonic bacteria and archaea co-occur, and their co-occurrence rather than salinity is more important in shaping their community structure although salinity is found to be a main environmental deterministic factor in the coastal wetland waters. This study highlights the role of planktonic bacteria-archaea co-occurrence on their biogeographic patterns, and thus provides a new insight into studying underlying mechanisms of microbial biogeography in coastal wetlands.},
}
@article {pmid34665251,
year = {2021},
author = {Westoby, M and Nielsen, DA and Gillings, MR and Gumerov, VM and Madin, JS and Paulsen, IT and Tetu, SG},
title = {Strategic traits of bacteria and archaea vary widely within substrate-use groups.},
journal = {FEMS microbiology ecology},
volume = {97},
number = {11},
pages = {},
doi = {10.1093/femsec/fiab142},
pmid = {34665251},
issn = {1574-6941},
mesh = {*Archaea/genetics ; *Bacteria/genetics ; Genome Size ; Phenotype ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Quantitative traits such as maximum growth rate and cell radial diameter are one facet of ecological strategy variation across bacteria and archaea. Another facet is substrate-use pathways, such as iron reduction or methylotrophy. Here, we ask how these two facets intersect, using a large compilation of data for culturable species and examining seven quantitative traits (genome size, signal transduction protein count, histidine kinase count, growth temperature, temperature-adjusted maximum growth rate, cell radial diameter and 16S rRNA operon copy number). Overall, quantitative trait variation within groups of organisms possessing a particular substrate-use pathway was very broad, outweighing differences between substrate-use groups. Although some substrate-use groups had significantly different means for some quantitative traits, standard deviation of quantitative trait values within each substrate-use pathway mostly averaged between 1.6 and 1.8 times larger than standard deviation across group means. Most likely, this wide variation reflects ecological strategy: for example, fast maximum growth rate is likely to express an early successional or copiotrophic strategy, and maximum growth varies widely within most substrate-use pathways. In general, it appears that these quantitative traits express different and complementary information about ecological strategy, compared with substrate use.},
}
@article {pmid34661841,
year = {2022},
author = {Ye, H and Tang, C and Cao, Y and Li, X and Huang, P},
title = {Contribution of ammonia-oxidizing archaea and bacteria to nitrification under different biogeochemical factors in acidic soils.},
journal = {Environmental science and pollution research international},
volume = {29},
number = {12},
pages = {17209-17222},
doi = {10.1007/s11356-021-16887-8},
pmid = {34661841},
issn = {1614-7499},
support = {No. 2017B020236001//Applied Science and Technology Research and Development Project of Guangdong Province, China/ ; No.41877470//General Program of the National Natural Science Foundation of China/ ; No.42077154//General Program of the National Natural Science Foundation of China/ ; },
mesh = {Ammonia/chemistry ; *Archaea/genetics ; Bacteria/genetics ; Ecosystem ; *Nitrification ; Oxidation-Reduction ; Phylogeny ; Soil/chemistry ; Soil Microbiology ; },
abstract = {Nitrification in soils is an essential process that involves archaeal and bacterial ammonia-oxidizers. Despite its importance, the relative contributions of soil factors to the abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and their nitrification performances are seldom discussed. The aim of this study was to determine the effects of AOA and AOB abundance and different environmental conditions (pH, TC, TN, moisture, and temperature) on nitrification performance. The soils of the long-term fertilized tea orchards and forests were sampled in the field, and nitrification experiments were conducted in the laboratory. The acid soils were collected from the field and used in laboratory incubation experiments to calculate the nitrification rate, including the net nitrification rate (NN rate), nitrification potential (NP), and nitrification kinetics. The basic parameters, different forms of nitrogen content, and AOA and AOB amoA gene copies were also analyzed. Compared with the forest soil, the tea orchard soil had a lower pH and higher nitrogen content (p < 0.05). The AOA and AOB abundance in the soils of the forests and tea orchards were pH-dependent. The NN rate and NP had good relationships with AOA or AOB in the forest soil; however, poor relationships were observed in the tea orchard soil. When pH < 4, the performances of AOA and AOB were restricted by pH and the environment, especially in long-term fertilized farmlands. Long-term fertilization can cause soil acidification, which regulates the abundance of AOA and AOB and their nitrifying ability. The soil environment rather than AOA or AOB could control nitrification in long-term fertilized farmlands with a pH below 4. These findings could improve fertilization efficiency and control nutrient runoff in hilly agricultural ecosystems.},
}
@article {pmid34655277,
year = {2022},
author = {Chouhan, BPS and Gade, M and Martinez, D and Toledo-Patino, S and Laurino, P},
title = {Implications of divergence of methionine adenosyltransferase in archaea.},
journal = {FEBS open bio},
volume = {12},
number = {1},
pages = {130-145},
pmid = {34655277},
issn = {2211-5463},
mesh = {*Archaea/genetics/metabolism ; Catalytic Domain ; Methionine ; *Methionine Adenosyltransferase/chemistry/genetics/metabolism ; S-Adenosylmethionine/chemistry ; },
abstract = {Methionine adenosyltransferase (MAT) catalyzes the biosynthesis of S-adenosyl methionine from l-methionine and ATP. MAT enzymes are ancient, believed to share a common ancestor, and are highly conserved in all three domains of life. However, the sequences of archaeal MATs show considerable divergence compared with their bacterial and eukaryotic counterparts. Furthermore, the structural significance and functional significance of this sequence divergence are not well understood. In the present study, we employed structural analysis and ancestral sequence reconstruction to investigate archaeal MAT divergence. We observed that the dimer interface containing the active site (which is usually well conserved) diverged considerably between the bacterial/eukaryotic MATs and archaeal MAT. A detailed investigation of the available structures supports the sequence analysis outcome: The protein domains and subdomains of bacterial and eukaryotic MAT are more similar than those of archaea. Finally, we resurrected archaeal MAT ancestors. Interestingly, archaeal MAT ancestors show substrate specificity, which is lost during evolution. This observation supports the hypothesis of a common MAT ancestor for the three domains of life. In conclusion, we have demonstrated that archaeal MAT is an ideal system for studying an enzyme family that evolved differently in one domain compared with others while maintaining the same catalytic activity.},
}
@article {pmid34650523,
year = {2021},
author = {Bhattarai, B and Bhattacharjee, AS and Coutinho, FH and Goel, RK},
title = {Viruses and Their Interactions With Bacteria and Archaea of Hypersaline Great Salt Lake.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {701414},
pmid = {34650523},
issn = {1664-302X},
abstract = {Viruses play vital biogeochemical and ecological roles by (a) expressing auxiliary metabolic genes during infection, (b) enhancing the lateral transfer of host genes, and (c) inducing host mortality. Even in harsh and extreme environments, viruses are major players in carbon and nutrient recycling from organic matter. However, there is much that we do not yet understand about viruses and the processes mediated by them in the extreme environments such as hypersaline habitats. The Great Salt Lake (GSL) in Utah, United States is a hypersaline ecosystem where the biogeochemical role of viruses is poorly understood. This study elucidates the diversity of viruses and describes virus-host interactions in GSL sediments along a salinity gradient. The GSL sediment virosphere consisted of Haloviruses (32.07 ± 19.33%) and members of families Siphoviridae (39.12 ± 19.8%), Myoviridae (13.7 ± 6.6%), and Podoviridae (5.43 ± 0.64%). Our results demonstrate that salinity alongside the concentration of organic carbon and inorganic nutrients (nitrogen and phosphorus) governs the viral, bacteria, and archaeal diversity in this habitat. Computational host predictions for the GSL viruses revealed a wide host range with a dominance of viruses that infect Proteobacteria, Actinobacteria, and Firmicutes. Identification of auxiliary metabolic genes for photosynthesis (psbA), carbon fixation (rbcL, cbbL), formaldehyde assimilation (SHMT), and nitric oxide reduction (NorQ) shed light on the roles played by GSL viruses in biogeochemical cycles of global relevance.},
}
@article {pmid34628131,
year = {2021},
author = {Castro, I and Costa, H and Turgeman-Grott, I and Allers, T and Mendo, S and Caetano, T},
title = {The lanthipeptide biosynthetic clusters of the domain Archaea.},
journal = {Microbiological research},
volume = {253},
number = {},
pages = {126884},
doi = {10.1016/j.micres.2021.126884},
pmid = {34628131},
issn = {1618-0623},
mesh = {*Archaea/genetics ; Eukaryota ; Euryarchaeota ; *Peptides/genetics ; },
abstract = {Research on Archaea's secondary metabolites is still lagging behind that of Bacteria and Eukarya. Our goal was to contribute to this knowledge gap by analyzing the lanthipeptide's clusters in Archaea. As previously proposed, Archaea encodes only class II synthetases (LanMs), which we found to be confined to the class Halobacteria (also known as haloarchaea). In total, we analyzed the phylogeny and the domains of 42 LanMs. Four types were identified, and the majority of them belong to the CCG group due to their cyclization domain, which includes LanMs of Cyanobacteria. Putative cognate peptides were predicted for most of LanMs and are a very diverse group of molecules that share a Kx(Y/F)(D/E)xx(F/Y) motif in their leader peptides. According to their homology, some of them were categorized into subfamilies, including Halolancins, Haladacins, Haloferaxcins and Halobiforcins. Many LanM genes were associated with mobile genetic elements, and their vicinities mainly encode ABC and MFS transporters, tailoring enzymes and uncharacterized proteins. Our results suggest that the biosynthesis of lanthipeptides in haloarchaea can entail distinct enzymology that must lead to the production of peptides with novel structures and unpredicted biological and ecological roles. Finally, an Haloferax mediterranei knockout, lacking its three lanM genes, was generated, and it was concluded that its antimicrobial activity is not primarily related to the production of lanthipeptides.},
}
@article {pmid34606606,
year = {2021},
author = {Payne, LJ and Todeschini, TC and Wu, Y and Perry, BJ and Ronson, CW and Fineran, PC and Nobrega, FL and Jackson, SA},
title = {Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types.},
journal = {Nucleic acids research},
volume = {49},
number = {19},
pages = {10868-10878},
pmid = {34606606},
issn = {1362-4962},
mesh = {Adenosine Triphosphatases/genetics/metabolism ; Antibiosis/*genetics ; Archaea/classification/*genetics/metabolism/virology ; Archaeal Proteins/*genetics/metabolism ; Bacteria/classification/*genetics/metabolism/virology ; Bacterial Proteins/*genetics/metabolism ; Bacteriophages/*genetics/growth &amp; development ; CRISPR-Cas Systems ; DNA Helicases/genetics/metabolism ; DNA Modification Methylases/genetics/metabolism ; Markov Chains ; Phylogeny ; *Software ; Terminology as Topic ; },
abstract = {To provide protection against viral infection and limit the uptake of mobile genetic elements, bacteria and archaea have evolved many diverse defence systems. The discovery and application of CRISPR-Cas adaptive immune systems has spurred recent interest in the identification and classification of new types of defence systems. Many new defence systems have recently been reported but there is a lack of accessible tools available to identify homologs of these systems in different genomes. Here, we report the Prokaryotic Antiviral Defence LOCator (PADLOC), a flexible and scalable open-source tool for defence system identification. With PADLOC, defence system genes are identified using HMM-based homologue searches, followed by validation of system completeness using gene presence/absence and synteny criteria specified by customisable system classifications. We show that PADLOC identifies defence systems with high accuracy and sensitivity. Our modular approach to organising the HMMs and system classifications allows additional defence systems to be easily integrated into the PADLOC database. To demonstrate application of PADLOC to biological questions, we used PADLOC to identify six new subtypes of known defence systems and a putative novel defence system comprised of a helicase, methylase and ATPase. PADLOC is available as a standalone package (https://github.com/padlocbio/padloc) and as a webserver (https://padloc.otago.ac.nz).},
}
@article {pmid34578152,
year = {2021},
author = {Krawczyk, A and Salamon, D and Kowalska-Duplaga, K and Bogiel, T and Gosiewski, T},
title = {Association of Fungi and Archaea of the Gut Microbiota with Crohn's Disease in Pediatric Patients-Pilot Study.},
journal = {Pathogens (Basel, Switzerland)},
volume = {10},
number = {9},
pages = {},
pmid = {34578152},
issn = {2076-0817},
support = {2019/33/N/NZ5/00698//National Science Center in Poland/ ; },
abstract = {The composition of bacteria is often altered in Crohn's disease (CD), but its connection to the disease is not fully understood. Gut archaea and fungi have recently been suggested to play a role as well. In our study, the presence and number of selected species of fungi and archaea in pediatric patients with CD and healthy controls were evaluated. Stool samples were collected from children with active CD (n = 54), non-active CD (n = 37) and control subjects (n = 33). The prevalence and the number of selected microorganisms were assessed by real-time PCR. The prevalence of Candida tropicalis was significantly increased in active CD compared to non-active CD and the control group (p = 0.011 and p = 0.036, respectively). The number of Malassezia spp. cells was significantly lower in patients with active CD compared to the control group, but in non-active CD, a significant increase was observed (p = 0.005 and p = 0.020, respectively). There were no statistically significant differences in the colonization by archaea. The obtained results indicate possible correlations with the course of the CD; however, further studies of the entire archeobiome and the mycobiome are necessary in order to receive a complete picture.},
}
@article {pmid34575103,
year = {2021},
author = {Merkel, AY and Chernyh, NA and Pimenov, NV and Bonch-Osmolovskaya, EA and Slobodkin, AI},
title = {Diversity and Metabolic Potential of the Terrestrial Mud Volcano Microbial Community with a High Abundance of Archaea Mediating the Anaerobic Oxidation of Methane.},
journal = {Life (Basel, Switzerland)},
volume = {11},
number = {9},
pages = {},
pmid = {34575103},
issn = {2075-1729},
support = {. 17-74-30025//Russian Science Foundation/ ; n/a//Ministry of Science and Higher Education of the Russian Federation/ ; },
abstract = {Terrestrial mud volcanoes (TMVs) are important natural sources of methane emission. The microorganisms inhabiting these environments remain largely unknown. We studied the phylogenetic composition and metabolic potential of the prokaryotic communities of TMVs located in the Taman Peninsula, Russia, using a metagenomic approach. One of the examined sites harbored a unique community with a high abundance of anaerobic methane-oxidizing archaea belonging to ANME-3 group (39% of all 16S rRNA gene reads). The high number of ANME-3 archaea was confirmed by qPCR, while the process of anaerobic methane oxidation was demonstrated by radioisotopic experiments. We recovered metagenome-assembled genomes (MAGs) of archaeal and bacterial community members and analyzed their metabolic capabilities. The ANME-3 MAG contained a complete set of genes for methanogenesis as well as of ribosomal RNA and did not encode proteins involved in dissimilatory nitrate or sulfate reduction. The presence of multiheme c-type cytochromes suggests that ANME-3 can couple methane oxidation with the reduction of metal oxides or with the interspecies electron transfer to a bacterial partner. The bacterial members of the community were mainly represented by autotrophic, nitrate-reducing, sulfur-oxidizing bacteria, as well as by fermentative microorganisms. This study extends the current knowledge of the phylogenetic and metabolic diversity of prokaryotes in TMVs and provides a first insight into the genomic features of ANME-3 archaea.},
}
@article {pmid34543104,
year = {2022},
author = {Weidenbach, K and Gutt, M and Cassidy, L and Chibani, C and Schmitz, RA},
title = {Small Proteins in Archaea, a Mainly Unexplored World.},
journal = {Journal of bacteriology},
volume = {204},
number = {1},
pages = {e0031321},
pmid = {34543104},
issn = {1098-5530},
mesh = {Archaea/genetics/*metabolism ; Archaeal Proteins/genetics/*metabolism ; Gene Expression Regulation, Archaeal/*physiology ; Genome, Archaeal ; },
abstract = {In recent years, increasing numbers of small proteins have moved into the focus of science. Small proteins have been identified and characterized in all three domains of life, but the majority remains functionally uncharacterized, lack secondary structure, and exhibit limited evolutionary conservation. While quite a few have already been described for bacteria and eukaryotic organisms, the amount of known and functionally analyzed archaeal small proteins is still very limited. In this review, we compile the current state of research, show strategies for systematic approaches for global identification of small archaeal proteins, and address selected functionally characterized examples. Besides, we document exemplarily for one archaeon the tool development and optimization to identify small proteins using genome-wide approaches.},
}
@article {pmid34535658,
year = {2021},
author = {Blombach, F and Fouqueau, T and Matelska, D and Smollett, K and Werner, F},
title = {Promoter-proximal elongation regulates transcription in archaea.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {5524},
pmid = {34535658},
issn = {2041-1723},
support = {/WT_/Wellcome Trust/United Kingdom ; WT 207446/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {CRISPR-Cas Systems/genetics ; DNA/metabolism ; DNA-Directed RNA Polymerases/metabolism ; Oxidative Stress/genetics ; *Promoter Regions, Genetic ; Regression Analysis ; Sulfolobus solfataricus/*genetics/growth &amp; development ; *Transcription Elongation, Genetic ; },
abstract = {Recruitment of RNA polymerase and initiation factors to the promoter is the only known target for transcription activation and repression in archaea. Whether any of the subsequent steps towards productive transcription elongation are involved in regulation is not known. We characterised how the basal transcription machinery is distributed along genes in the archaeon Saccharolobus solfataricus. We discovered a distinct early elongation phase where RNA polymerases sequentially recruit the elongation factors Spt4/5 and Elf1 to form the transcription elongation complex (TEC) before the TEC escapes into productive transcription. TEC escape is rate-limiting for transcription output during exponential growth. Oxidative stress causes changes in TEC escape that correlate with changes in the transcriptome. Our results thus establish that TEC escape contributes to the basal promoter strength and facilitates transcription regulation. Impaired TEC escape coincides with the accumulation of initiation factors at the promoter and recruitment of termination factor aCPSF1 to the early TEC. This suggests two possible mechanisms for how TEC escape limits transcription, physically blocking upstream RNA polymerases during transcription initiation and premature termination of early TECs.},
}
@article {pmid34531846,
year = {2021},
author = {Lin, T and Zhang, L and Wu, M and Jiang, D and Li, Z and Yang, Z},
title = {Repair of Hypoxanthine in DNA Revealed by DNA Glycosylases and Endonucleases From Hyperthermophilic Archaea.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {736915},
pmid = {34531846},
issn = {1664-302X},
abstract = {Since hyperthermophilic Archaea (HA) thrive in high-temperature environments, which accelerate the rates of deamination of base in DNA, their genomic stability is facing a severe challenge. Hypoxanthine (Hx) is one of the common deaminated bases in DNA. Generally, replication of Hx in DNA before repaired causes AT → GC mutation. Biochemical data have demonstrated that 3-methyladenine DNA glycosylase II (AlkA) and Family V uracil DNA glycosylase (UDG) from HA could excise Hx from DNA, thus triggering a base excision repair (BER) process for Hx repair. Besides, three endonucleases have been reported from HA: Endonuclease V (EndoV), Endonuclease Q (EndoQ), and Endonuclease NucS (EndoNucS), capable of cleaving Hx-containing DNA, thereby providing alternative pathways for Hx repair. Both EndoV and EndoQ could cleave one DNA strand with Hx, thus forming a nick and further initiating an alternative excision repair (AER) process for the follow-up repair. By comparison, EndoNucS cleaves both strands of Hx-containing DNA in a restriction endonuclease manner, thus producing a double-stranded break (DSB). This created DSB might be repaired by homologous recombination (HR) or by a combination activity of DNA polymerase (DNA pol), flap endonuclease 1 (FEN1), and DNA ligase (DNA lig). Herein, we reviewed the most recent advances in repair of Hx in DNA triggered by DNA glycosylases and endonucleases from HA, and proposed future research directions.},
}
@article {pmid34526983,
year = {2021},
author = {Franke, JD and Fuerst, JA and Poole, AM},
title = {Editorial: Structure, Function and Evolution of Complex Cellular Organization in Bacteria and Archaea.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {751416},
pmid = {34526983},
issn = {1664-302X},
}
@article {pmid34516368,
year = {2021},
author = {Pallen, MJ},
title = {The status Candidatus for uncultured taxa of Bacteria and Archaea: SWOT analysis.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {71},
number = {9},
pages = {},
pmid = {34516368},
issn = {1466-5034},
mesh = {*Archaea/classification ; *Bacteria/classification ; Phylogeny ; Terminology as Topic ; },
abstract = {The status Candidatus was introduced to bacterial taxonomy in the 1990s to accommodate uncultured taxa defined by analyses of DNA sequences. Here I review the strengths, weaknesses, opportunities and threats (SWOT) associated with the status Candidatus in the light of a quarter century of use, twinned with recent developments in bacterial taxonomy and sequence-based taxonomic discovery. Despite ambiguities as to its scope, philosophical objections to its use and practical problems in implementation, the status Candidatus has now been applied to over 1000 taxa and has been widely adopted by journals and databases. Although lacking priority under the International Code for Nomenclature of Prokaryotes, many Candidatus names have already achieved de facto standing in the academic literature and in databases via description of a taxon in a peer-reviewed publication, alongside deposition of a genome sequence and there is a clear path to valid publication of such names on culture. Continued and increased use of Candidatus names provides an alternative to the potential upheaval that might accompany creation of a new additional code of nomenclature and provides a ready solution to the urgent challenge of naming many thousands of newly discovered but uncultured species.},
}
@article {pmid34509601,
year = {2021},
author = {Kumar, V and Singh, B and van Belkum, MJ and Diep, DB and Chikindas, ML and Ermakov, AM and Tiwari, SK},
title = {Halocins, natural antimicrobials of Archaea: Exotic or special or both?.},
journal = {Biotechnology advances},
volume = {53},
number = {},
pages = {107834},
doi = {10.1016/j.biotechadv.2021.107834},
pmid = {34509601},
issn = {1873-1899},
mesh = {Anti-Bacterial Agents ; *Anti-Infective Agents/pharmacology ; *Archaea ; Sodium Chloride ; },
abstract = {Haloarchaea are adapted to survive under extreme saline conditions by accumulating osmolytes and salts to counteract the high osmotic pressure in their habitats. As a consequence, their proteins have evolved to remain active, or even most active, at very high ionic strength. Halocins are proteinaceous antimicrobial substances that are ribosomally-synthesized by haloarchaea and they provide the producers an advantage in the competition for nutrients and ecological niches. These antimicrobials are stable at high temperature, elevated salt concentrations, and alkaline pH conditions. These properties have endowed them with great potential in diverse biotechnological applications, which involve extreme processing conditions (such as high salt concentrations, high pressure, or high temperatures). They kill target cells by inhibition of Na+/H+ antiporter in the membrane or modification/disruption of the cell membrane leading to cell lysis. In general, the taxonomy of haloarchaea and their typical phenotypic and genotypic characteristics are well studied; however, information regarding their halocins, especially aspects related to genetics, biosynthetic pathways, mechanism of action, and structure-function relationship is very limited. A few studies have demonstrated the potential applications of halocins in the preservation of salted food products and brine-cured hides in leather industries, protecting the myocardium from ischemia and reperfusion injury, as well as from life-threatening diseases such as cardiac arrest and cancers. In recent years, genome mining has been an essential tool to decipher the genetic basis of halocin biosynthesis. Nevertheless, this is likely the tip of the iceberg as genome analyses have revealed many putative halocins in databases waiting for further investigation. Identification and characterization of this source of halocins may lead to antimicrobials for future therapeutics and/or food preservation. Hence, the present review analyzes different aspects of halocins such as biosynthesis, mechanism of action against target cells, and potential biotechnological applications.},
}
@article {pmid34491083,
year = {2021},
author = {Li, L and Zhang, W and Zhang, S and Song, L and Sun, Q and Zhang, H and Xiang, H and Dong, X},
title = {Bacteria and Archaea Synergistically Convert Glycine Betaine to Biogenic Methane in the Formosa Cold Seep of the South China Sea.},
journal = {mSystems},
volume = {6},
number = {5},
pages = {e0070321},
pmid = {34491083},
issn = {2379-5077},
support = {2018YFC0310801//Ministry of Science and Technology of the People's Republic of China (MOST)/ ; },
abstract = {Cold seeps are globally widespread seafloor ecosystems that feature abundant methane production and flourishing chemotrophic benthic communities. Chemical evidence indicates that cold seep methane is largely biogenic; however, the primary methane-producing organisms and associated pathways involved in methanogenesis remain elusive. This work detected methane production when glycine betaine (GBT) or trimethylamine (TMA) was added to the sediment microcosms of the Formosa cold seep, South China Sea. The methane production was suppressed by antibiotic inhibition of bacteria, while GBT was accumulated. This suggests that the widely used osmoprotectant GBT could be converted to cold seep biogenic methane via the synergistic activity of bacteria and methanogenic archaea because archaea are not sensitive to antibiotics and no bacteria are known to produce ample methane (mM). 16S rRNA gene diversity analyses revealed that the predominant bacterial and archaeal genera in the GBT-amended methanogenic microcosms included Oceanirhabdus and Methanococcoides. Moreover, metagenomic analyses detected the presence of grdH and mtgB genes that are involved in GBT reduction and demethylation, respectively. Two novel species were obtained, including bacterium Oceanirhabdus seepicola, which reduces GBT to TMA, and a methanogenic archaeon, Methanococcoides seepicolus, which produces methane from TMA and GBT. The two strains reconstituted coculture efficiently converted GBT to methane at 18°C; however, at 4°C addition of dimethylglycine (DMG), the GBT demethylation product, was necessary. Therefore, this work demonstrated that GBT is the precursor not only of the biogenic methane but also of the cryoprotectant DMG to the microorganisms at the Formosa cold seep. IMPORTANCE Numerous cold seeps have been found in global continental margins where methane is enriched in pore waters that are forced upward from sediments. Therefore, high concerns have been focused on the methane-producing organisms and the metabolic pathways in these environments because methane is a potent greenhouse gas. In this study, GBT was identified as the main precursor for methane in the Formosa cold seep of the South China Sea. Further, synergism of bacteria and methanogenic archaea was identified in GBT conversion to methane via the GBT reduction pathway, while methanogen-mediated GBT demethylation to methane was also observed. In addition, GBT-demethylated product dimethyl glycine acted as a cryoprotectant that promoted the cold seep microorganisms at cold temperatures. GBT is an osmoprotectant that is widely used by marine organisms, and therefore, the GBT-derived methanogenic pathway reported here could be widely distributed among global cold seep environments.},
}
@article {pmid34490397,
year = {2021},
author = {Hu, D and Yang, J and Qi, Y and Li, B and Li, K and Mok, KM},
title = {Metagenomic Analysis of Fecal Archaea, Bacteria, Eukaryota, and Virus in Przewalski's Horses Following Anthelmintic Treatment.},
journal = {Frontiers in veterinary science},
volume = {8},
number = {},
pages = {708512},
pmid = {34490397},
issn = {2297-1769},
abstract = {Intestinal microbiota is involved in immune response and metabolism of the host. The frequent use of anthelmintic compounds for parasite expulsion causes disturbance to the equine intestinal microbiota. However, most studies were on the effects of such treatment on the intestinal bacterial microbes; none is on the entire microbial community including archaea and eukaryotic and viral community in equine animals. This study is the first to explore the differences of the microbial community composition and structure in Przewalski's horses prior to and following anthelmintic treatment, and to determine the corresponding changes of their functional attributes based on metagenomic sequencing. Results showed that in archaea, the methanogen of Euryarchaeota was the dominant phylum. Under this phylum, anthelmintic treatment increased the Methanobrevibacter genus and decreased the Methanocorpusculum genus and two other dominant archaea species, Methanocorpusculum labreanum and Methanocorpusculum bavaricum. In bacteria, Firmicutes and Bacteroidetes were the dominant phyla. Anthelmintic treatment increased the genera of Clostridium and Eubacterium and decreased those of Bacteroides and Prevotella and dominant bacteria species. These altered genera were associated with immunity and digestion. In eukaryota, anthelmintic treatment also changed the genera related to digestion and substantially decreased the relative abundances of identified species. In virus, anthelmintic treatment increased the genus of unclassified_d__Viruses and decreased those of unclassified_f__Siphoviridae and unclassified_f__Myoviridae. Most of the identified viral species were classified into phage, which were more sensitive to anthelmintic treatment than other viruses. Furthermore, anthelmintic treatment was found to increase the number of pathogens related to some clinical diseases in horses. The COG and KEGG function analysis showed that the intestinal microbiota of Przewalski's horse mainly participated in the carbohydrate and amino acid metabolism. The anthelmintic treatment did not change their overall function; however, it displaced the population of the functional microbes involved in each function or pathway. These results provide a complete view on the changes caused by anthelmintic treatment in the intestinal microbiota of the Przewalski's horses.},
}
@article {pmid34489912,
year = {2021},
author = {Makarova, KS and Wolf, YI and Karamycheva, S and Koonin, EV},
title = {A Unique Gene Module in Thermococcales Archaea Centered on a Hypervariable Protein Containing Immunoglobulin Domains.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {721392},
pmid = {34489912},
issn = {1664-302X},
abstract = {Molecular mechanisms involved in biological conflicts and self vs nonself recognition in archaea remain poorly characterized. We apply phylogenomic analysis to identify a hypervariable gene module that is widespread among Thermococcales. These loci consist of an upstream gene coding for a large protein containing several immunoglobulin (Ig) domains and unique combinations of downstream genes, some of which also contain Ig domains. In the large Ig domain containing protein, the C-terminal Ig domain sequence is hypervariable, apparently, as a result of recombination between genes from different Thermococcales. To reflect the hypervariability, we denote this gene module VARTIG (VARiable Thermococcales IG). The overall organization of the VARTIG modules is similar to the organization of Polymorphic Toxin Systems (PTS). Archaeal genomes outside Thermococcales encode a variety of Ig domain proteins, but no counterparts to VARTIG and no Ig domains with comparable levels of variability. The specific functions of VARTIG remain unknown but the identified features of this system imply three testable hypotheses: (i) involvement in inter-microbial conflicts analogous to PTS, (ii) role in innate immunity analogous to the vertebrate complement system, and (iii) function in self vs nonself discrimination analogous to the vertebrate Major Histocompatibility Complex. The latter two hypotheses seem to be of particular interest given the apparent analogy to the vertebrate immunity.},
}
@article {pmid34487604,
year = {2022},
author = {Haiming, T and Chao, L and Kaikai, C and Lihong, S and Li, W and Weiyan, L and Xiaoping, X and Ke, W},
title = {Effects of short-term soil tillage practice on activity and community structure of ammonia-oxidizing bacteria and archaea under the double-cropping rice field.},
journal = {Journal of applied microbiology},
volume = {132},
number = {2},
pages = {1307-1318},
doi = {10.1111/jam.15289},
pmid = {34487604},
issn = {1365-2672},
support = {//National Natural Science Foundation of China/ ; 2019JJ10003//Innovative Research Groups of the Natural Science Foundation of Hunan Province/ ; },
mesh = {Ammonia ; Archaea/genetics ; *Betaproteobacteria ; Nitrification ; *Oryza ; Oxidation-Reduction ; Phylogeny ; Soil ; Soil Microbiology ; },
abstract = {AIMS: The potential nitrification activity (PNA), population size and community composition of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in paddy soil from a short-term (5 years) tillage field experiment conducted at tillering stage of late rice were investigated using the shaken slurry method and quantitative real-time polymerase chain reaction.<br><br>METHODS AND RESULTS: The experiment included four tillage treatments: conventional tillage with crop residue incorporation (CT), rotary tillage with crop residue incorporation (RT), no-tillage with crop residue returning (NT) and rotary tillage with all crop residues removed as a control (RTO). The results showed that PNA in paddy soil of CT, RT and NT treatments was higher than that of RTO treatment, and the abundance of AOA and AOB was much higher in paddy soil of CT, RT and NT treatments than RTO treatment. Meanwhile, PNA and the abundance of AOB and AOA in paddy soil were greatly enhanced by combined application of tillage and crop residue, whereas PNA and the abundance of AOB and AOA in paddy soil were decreased by combined application of no-tillage and crop residue. Moreover, PNA was closely correlated with the abundance and community structure of AOB rather than AOA. The results also showed that PNA and the population sizes of AOB and AOA in crop incorporation treatments were higher than that of crop residue removed treatment. Cluster and redundancy analyses indicated that crop residue effect played a more important role in shaping AOA community structure compared to short-term tillage management.<br><br>CONCLUSIONS: The results indicated that AOB rather than AOA functionally dominated ammonia oxidation in the double-cropping rice paddy soil, the activities of AOB and AOA were increased and the community structure was also changed under the combination of conventional tillage, rotary tillage and crop residue condition.<br><br>The activity and community structure of AOB and AOA, which were affected by the combination of tillage and crop residue managements, play an important role in cycling of nitrogen.},
}
@article {pmid34464803,
year = {2022},
author = {Cai, M and Yin, X and Tang, X and Zhang, C and Zheng, Q and Li, M},
title = {Metatranscriptomics reveals different features of methanogenic archaea among global vegetated coastal ecosystems.},
journal = {The Science of the total environment},
volume = {802},
number = {},
pages = {149848},
doi = {10.1016/j.scitotenv.2021.149848},
pmid = {34464803},
issn = {1879-1026},
mesh = {*Archaea/genetics ; *Ecosystem ; Methane ; Methanosarcinaceae ; Methanosarcinales ; Phylogeny ; },
abstract = {Vegetated coastal ecosystems (VCEs; i.e., mangroves, saltmarshes, and seagrasses) represent important sources of natural methane emission. Despite recent advances in the understanding of novel taxa and pathways associated with methanogenesis in these ecosystems, the key methanogenic players and the contribution of different substrates to methane formation remain elusive. Here, we systematically investigate the community and activity of methanogens using publicly available metatranscriptomes at a global scale together with our in-house metatranscriptomic dataset. Taxonomic profiling reveals that 13 groups of methanogenic archaea were transcribed in the investigated VCEs, and they were predominated by Methanosarcinales. Among these VCEs, methanogens exhibited all the three known methanogenic pathways in some mangrove sediments, where methylotrophic methanogens Methanosarcinales/Methanomassiliicoccales grew on diverse methyl compounds and coexisted with hydrogenotrophic (mainly Methanomicrobiales) and acetoclastic (mainly Methanothrix) methanogens. Contrastingly, the predominant methanogenic pathway in saltmarshes and seagrasses was constrained to methylotrophic methanogenesis. These findings reveal different archaeal methanogens in VCEs and suggest the potentially distinct methanogenesis contributions in these VCEs to the global warming.},
}
@article {pmid34442741,
year = {2021},
author = {Koirala, A and Brözel, VS},
title = {Phylogeny of Nitrogenase Structural and Assembly Components Reveals New Insights into the Origin and Distribution of Nitrogen Fixation across Bacteria and Archaea.},
journal = {Microorganisms},
volume = {9},
number = {8},
pages = {},
pmid = {34442741},
issn = {2076-2607},
abstract = {The phylogeny of nitrogenase has only been analyzed using the structural proteins NifHDK. As nifHDKENB has been established as the minimum number of genes necessary for in silico prediction of diazotrophy, we present an updated phylogeny of diazotrophs using both structural (NifHDK) and cofactor assembly proteins (NifENB). Annotated Nif sequences were obtained from InterPro from 963 culture-derived genomes. Nif sequences were aligned individually and concatenated to form one NifHDKENB sequence. Phylogenies obtained using PhyML, FastTree, RapidNJ, and ASTRAL from individuals and concatenated protein sequences were compared and analyzed. All six genes were found across the Actinobacteria, Aquificae, Bacteroidetes, Chlorobi, Chloroflexi, Cyanobacteria, Deferribacteres, Firmicutes, Fusobacteria, Nitrospira, Proteobacteria, PVC group, and Spirochaetes, as well as the Euryarchaeota. The phylogenies of individual Nif proteins were very similar to the overall NifHDKENB phylogeny, indicating the assembly proteins have evolved together. Our higher resolution database upheld the three cluster phylogeny, but revealed undocumented horizontal gene transfers across phyla. Only 48% of the 325 genera containing all six nif genes are currently supported by biochemical evidence of diazotrophy. In addition, this work provides reference for any inter-phyla comparison of Nif sequences and a quality database of Nif proteins that can be used for identifying new Nif sequences.},
}
@article {pmid34436605,
year = {2021},
author = {Martinez-Gutierrez, CA and Aylward, FO},
title = {Phylogenetic Signal, Congruence, and Uncertainty across Bacteria and Archaea.},
journal = {Molecular biology and evolution},
volume = {38},
number = {12},
pages = {5514-5527},
pmid = {34436605},
issn = {1537-1719},
mesh = {*Archaea/genetics ; *Bacteria/genetics ; Biological Evolution ; Phylogeny ; Uncertainty ; },
abstract = {Reconstruction of the Tree of Life is a central goal in biology. Although numerous novel phyla of bacteria and archaea have recently been discovered, inconsistent phylogenetic relationships are routinely reported, and many inter-phylum and inter-domain evolutionary relationships remain unclear. Here, we benchmark different marker genes often used in constructing multidomain phylogenetic trees of bacteria and archaea and present a set of marker genes that perform best for multidomain trees constructed from concatenated alignments. We use recently-developed Tree Certainty metrics to assess the confidence of our results and to obviate the complications of traditional bootstrap-based metrics. Given the vastly disparate number of genomes available for different phyla of bacteria and archaea, we also assessed the impact of taxon sampling on multidomain tree construction. Our results demonstrate that biases between the representation of different taxonomic groups can dramatically impact the topology of resulting trees. Inspection of our highest-quality tree supports the division of most bacteria into Terrabacteria and Gracilicutes, with Thermatogota and Synergistota branching earlier from these superphyla. This tree also supports the inclusion of the Patescibacteria within the Terrabacteria as a sister group to the Chloroflexota instead of as a basal-branching lineage. For the Archaea, our tree supports three monophyletic lineages (DPANN, Euryarchaeota, and TACK/Asgard), although we note the basal placement of the DPANN may still represent an artifact caused by biased sequence composition. Our findings provide a robust and standardized framework for multidomain phylogenetic reconstruction that can be used to evaluate inter-phylum relationships and assess uncertainty in conflicting topologies of the Tree of Life.},
}
@article {pmid34394058,
year = {2021},
author = {Kostygov, AY and Alves, JMP and Yurchenko, V},
title = {Editorial: Symbioses Between Protists and Bacteria/Archaea.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {709184},
pmid = {34394058},
issn = {1664-302X},
}
@article {pmid34391833,
year = {2021},
author = {Moghimipour, E and Abedishirehjin, S and Baghbadorani, MA and Handali, S},
title = {Bacteria and Archaea: A new era of cancer therapy.},
journal = {Journal of controlled release : official journal of the Controlled Release Society},
volume = {338},
number = {},
pages = {1-7},
doi = {10.1016/j.jconrel.2021.08.019},
pmid = {34391833},
issn = {1873-4995},
mesh = {*Antineoplastic Agents ; Archaea ; Bacteria ; Drug Delivery Systems ; Nanotechnology ; *Neoplasms/drug therapy ; },
abstract = {Cancer is one of the most important mortality in the world. The major drawbacks of chemotherapy are the poor absorption of drugs into tumor tissues and development of resistance against anti-cancer agents. To overcome these limitations, the use of microorganisms has been extensively considered in the treatment of cancer. Microorganisms (bacteria/Archaea) secrete different bioactive compounds that can efficiently inhibit cancer cells growth. Biological nanocarriers derived from microorganisms including outer membrane vesicles (OMVs), bacterial ghosts (BGs) and archaeosomes have also been considered as drug delivery systems. Conjugation of drug loaded nanocarriers to bacteria strongly kills the cancer cells after internalization through the bacteria. Merging of microbiology and nanotechnology may provide versatile microbial nano-hybrids for promising treatment of cancer. This strategy causes more amount of drug to enter into cancer cells. In this review, we present evidence that microorganism, their derivatives as well as their intervention with nanotechnology can be a powerful vehicle for eradication cancer.},
}
@article {pmid34379636,
year = {2021},
author = {Acharya, S and Dahal, A and Bhattarai, HK},
title = {Evolution and origin of sliding clamp in bacteria, archaea and eukarya.},
journal = {PloS one},
volume = {16},
number = {8},
pages = {e0241093},
pmid = {34379636},
issn = {1932-6203},
mesh = {Amino Acid Sequence ; Archaea/*genetics ; Bacteria/*genetics ; DNA/genetics ; DNA Replication/genetics ; DNA-Directed DNA Polymerase/genetics ; Eukaryota/*genetics ; Evolution, Molecular ; Firmicutes/genetics ; Phylogeny ; Proliferating Cell Nuclear Antigen/genetics ; Pyrococcus furiosus/genetics ; },
abstract = {The replication of DNA is an essential process in all domains of life. A protein often involved in replication is the sliding clamp. The sliding clamp encircles the DNA and helps replicative polymerase stay attached to the replication machinery increasing the processivity of the polymerase. In eukaryotes and archaea, the sliding clamp is called the Proliferating Cell Nuclear Antigen (PCNA) and consists of two domains. This PCNA forms a trimer encircling the DNA as a hexamer. In bacteria, the structure of the sliding clamp is highly conserved, but the protein itself, called beta clamp, contains three domains, which dimerize to form a hexamer. The bulk of literature touts a conservation of the structure of the sliding clamp, but fails to recognize the conservation of protein sequence among sliding clamps. In this paper, we have used PSI blast to the second iteration in NCBI to show a statistically significant sequence homology between Pyrococcus furiosus PCNA and Kallipyga gabonensis beta clamp. The last two domains of beta clamp align with the two domains of PCNA. This homology data demonstrates that PCNA and beta clamp arose from a common ancestor. In this paper, we have further used beta clamp and PCNA sequences from diverse bacteria, archaea and eukarya to build maximum likelihood phylogenetic tree. Most, but not all, species in different domains of life harbor one sliding clamp from vertical inheritance. Some of these species that have two or more sliding clamps have acquired them from gene duplication or horizontal gene transfer events.},
}
@article {pmid34378142,
year = {2022},
author = {Xie, R and Wang, Y and Huang, D and Hou, J and Li, L and Hu, H and Zhao, X and Wang, F},
title = {Expanding Asgard members in the domain of Archaea sheds new light on the origin of eukaryotes.},
journal = {Science China. Life sciences},
volume = {65},
number = {4},
pages = {818-829},
pmid = {34378142},
issn = {1869-1889},
mesh = {*Archaea/genetics/metabolism ; *Eukaryota/genetics ; Eukaryotic Cells/metabolism ; Phylogeny ; },
abstract = {The hypothesis that eukaryotes originated from within the domain Archaea has been strongly supported by recent phylogenomic analyses placing Heimdallarchaeota-Wukongarchaeota branch from the Asgard superphylum as the closest known archaeal sister-group to eukaryotes. However, our understanding is still limited in terms of the relationship between eukaryotes and archaea, as well as the evolution and ecological functions of the Asgard archaea. Here, we describe three previously unknown phylum-level Asgard archaeal lineages, tentatively named Sigyn-, Freyr- and Njordarchaeota. Additional members in Wukongarchaeota and Baldrarchaeota from distinct environments are also reported here, further expanding their ecological roles and metabolic capacities. Comprehensive phylogenomic analyses further supported the origin of eukaryotes within Asgard archaea and a new lineage Njordarchaeota was supposed as the known closest branch with the eukaryotic nuclear host lineage. Metabolic reconstruction suggests that Njordarchaeota may have a heterotrophic lifestyle with capability of peptides and amino acids utilization, while Sigynarchaeota and Freyrarchaeota also have the potentials to fix inorganic carbon via the Wood-Ljungdahl pathway and degrade organic matters. Additionally, the Ack/Pta pathway for homoacetogenesis and de novo anaerobic cobalamin biosynthesis pathway were found in Freyrarchaeota and Wukongrarchaeota, respectively. Some previously unidentified eukaryotic signature proteins for intracellular membrane trafficking system, and the homologue of mu/sigma subunit of adaptor protein complex, were identified in Freyrarchaeota. This study expands the Asgard superphylum, sheds new light on the evolution of eukaryotes and improves our understanding of ecological functions of the Asgard archaea.},
}
@article {pmid34367583,
year = {2021},
author = {Wu, D and Zhao, C and Bai, H and Feng, F and Sui, X and Sun, G},
title = {Characteristics and metabolic patterns of soil methanogenic archaea communities in the high-latitude natural forested wetlands of China.},
journal = {Ecology and evolution},
volume = {11},
number = {15},
pages = {10396-10408},
pmid = {34367583},
issn = {2045-7758},
abstract = {Soil methanogenic microorganisms are one of the primary methane-producing microbes in wetlands. However, we still poorly understand the community characteristic and metabolic patterns of these microorganisms according to vegetation type and seasonal changes. Therefore, to better elucidate the effects of the vegetation type and seasonal factors on the methanogenic community structure and metabolic patterns, we detected the characteristics of the soil methanogenic mcrA gene from three types of natural wetlands in different seasons in the Xiaoxing'an Mountain region, China. The results indicated that the distribution of Methanobacteriaceae (hydrogenotrophic methanogens) was higher in winter, while Methanosarcinaceae and Methanosaetaceae accounted for a higher proportion in summer. Hydrogenotrophic methanogenesis was the dominant trophic pattern in each wetland. The results of principal coordinate analysis and cluster analysis showed that the vegetation type considerably influenced the methanogenic community composition. The methanogenic community structure in the Betula platyphylla-Larix gmelinii wetland was relatively different from the structure of the other two wetland types. Indicator species analysis further demonstrated that the corresponding species of indicator operational taxonomic units from the Alnus sibirica wetland and the Betula ovalifolia wetland were similar. Network analysis showed that cooperative and competitive relationships exist both within and between the same or different trophic methanogens. The core methanogens with higher abundance in each wetland were conducive to the adaptation to environmental disturbances. This information is crucial for the assessment of metabolic patterns of soil methanogenic archaea and future fluxes in the wetlands of the Xiaoxing'an Mountain region given their vulnerability.},
}
@article {pmid34367089,
year = {2021},
author = {Londei, P and Ferreira-Cerca, S},
title = {Ribosome Biogenesis in Archaea.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {686977},
pmid = {34367089},
issn = {1664-302X},
abstract = {Making ribosomes is a major cellular process essential for the maintenance of functional ribosome homeostasis and to ensure appropriate gene expression. Strikingly, although ribosomes are universally conserved ribonucleoprotein complexes decoding the genetic information contained in messenger RNAs into proteins, their biogenesis shows an intriguing degree of variability across the tree of life. In this review, we summarize our knowledge on the least understood ribosome biogenesis pathway: the archaeal one. Furthermore, we highlight some evolutionary conserved and divergent molecular features of making ribosomes across the tree of life.},
}
@article {pmid34364295,
year = {2021},
author = {Xiao, L and Liu, G and Gong, F and Cai, Z and Li, Y},
title = {The reductive carboxylation activity of heterotetrameric pyruvate synthases from hyperthermophilic archaea.},
journal = {Biochemical and biophysical research communications},
volume = {572},
number = {},
pages = {151-156},
doi = {10.1016/j.bbrc.2021.07.091},
pmid = {34364295},
issn = {1090-2104},
mesh = {Archaea/*enzymology ; Carboxylic Acids/metabolism ; Oxidation-Reduction ; Pyruvate Synthase/*metabolism ; },
abstract = {Pyruvate synthase (pyruvate:ferredoxin oxidoreductase, PFOR) catalyzes the interconversion of acetyl-CoA and pyruvate, but the reductive carboxylation activities of heterotetrameric PFORs remain largely unknown. In this study, we cloned, expressed, and purified selected six heterotetrameric PFORs from hyperthermophilic archaea. The reductive carboxylation activities of these heterotetrameric PFORs were measured at 70 °C and the ratio of reductive carboxylation activity to oxidative decarboxylation activity (red/ox ratio) were calculated. Four out of six showed reductive decarboxylation activities. Among them, the PFORpfm from Pyrolobus fumarii showed the highest reductive carboxylation activities and the highest red/ox ratio, which were 54.32 mU/mg and 0.51, respectively. The divergence of the reductive carboxylation activities and the red/ox ratios of heterotetrameric PFORs in hyperthermophilic archaea indicate the diversity of the functions of PFOR over long-term evolution. This can help us better understand the autotrophic CO2 fixation process in thermal vent, or in other CO2-rich high temperature habitat.},
}
@article {pmid34359268,
year = {2021},
author = {Deng, F and Li, Y and Peng, Y and Wei, X and Wang, X and Howe, S and Yang, H and Xiao, Y and Li, H and Zhao, J and Li, Y},
title = {The Diversity, Composition, and Metabolic Pathways of Archaea in Pigs.},
journal = {Animals : an open access journal from MDPI},
volume = {11},
number = {7},
pages = {},
pmid = {34359268},
issn = {2076-2615},
support = {2019KSYS011//Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Educa-tion Institutes/ ; 2019B030301010//Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding/ ; },
abstract = {Archaea are an essential class of gut microorganisms in humans and animals. Despite the substantial progress in gut microbiome research in the last decade, most studies have focused on bacteria, and little is known about archaea in mammals. In this study, we investigated the composition, diversity, and functional potential of gut archaeal communities in pigs by re-analyzing a published metagenomic dataset including a total of 276 fecal samples from three countries: China (n = 76), Denmark (n = 100), and France (n = 100). For alpha diversity (Shannon Index) of the archaeal communities, Chinese pigs were less diverse than Danish and French pigs (p < 0.001). Consistently, Chinese pigs also possessed different archaeal community structures from the other two groups based on the Bray-Curtis distance matrix. Methanobrevibacter was the most dominant archaeal genus in Chinese pigs (44.94%) and French pigs (15.41%), while Candidatus methanomethylophilus was the most predominant in Danish pigs (15.71%). At the species level, the relative abundance of Candidatus methanomethylophilus alvus, Natrialbaceae archaeon XQ INN 246, and Methanobrevibacter gottschalkii were greatest in Danish, French, and Chinese pigs with a relative abundance of 14.32, 11.67, and 16.28%, respectively. In terms of metabolic potential, the top three pathways in the archaeal communities included the MetaCyc pathway related to the biosynthesis of L-valine, L-isoleucine, and isobutanol. Interestingly, the pathway related to hydrogen consumption (METHANOGENESIS-PWY) was only observed in archaeal reads, while the pathways participating in hydrogen production (FERMENTATION-PWY and PWY4LZ-257) were only detected in bacterial reads. Archaeal communities also possessed CAZyme gene families, with the top five being AA3, GH43, GT2, AA6, and CE9. In terms of antibiotic resistance genes (ARGs), the class of multidrug resistance was the most abundant ARG, accounting for 87.41% of archaeal ARG hits. Our study reveals the diverse composition and metabolic functions of archaea in pigs, suggesting that archaea might play important roles in swine nutrition and metabolism.},
}
@article {pmid34354121,
year = {2021},
author = {Clark, IM and Hughes, DJ and Fu, Q and Abadie, M and Hirsch, PR},
title = {Metagenomic approaches reveal differences in genetic diversity and relative abundance of nitrifying bacteria and archaea in contrasting soils.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {15905},
pmid = {34354121},
issn = {2045-2322},
support = {BBS/E/C/00005196/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/C/000I0310/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Ammonia/analysis ; Archaea/*genetics ; Bacteria/*genetics ; Fertilizers/analysis ; Genetic Variation/genetics ; Metagenome/genetics ; Metagenomics/methods ; Nitrification/*genetics/physiology ; Nitrites/analysis ; Oxidation-Reduction ; Phylogeny ; Soil/chemistry ; Soil Microbiology ; },
abstract = {The abundance and phylogenetic diversity of functional genes involved in nitrification were assessed in Rothamsted field plots under contrasting management regimes-permanent bare fallow, grassland, and arable (wheat) cultivation maintained for more than 50 years. Metagenome and metatranscriptome analysis indicated nitrite oxidizing bacteria (NOB) were more abundant than ammonia oxidizing archaea (AOA) and bacteria (AOB) in all soils. The most abundant AOA and AOB in the metagenomes were, respectively, Nitrososphaera and Ca. Nitrososcosmicus (family Nitrososphaeraceae) and Nitrosospira and Nitrosomonas (family Nitrosomonadaceae). The most abundant NOB were Nitrospira including the comammox species Nitrospira inopinata, Ca. N. nitrificans and Ca. N. nitrosa. Anammox bacteria were also detected. Nitrospira and the AOA Nitrososphaeraceae showed most transcriptional activity in arable soil. Similar numbers of sequences were assigned to the amoA genes of AOA and AOB, highest in the arable soil metagenome and metatranscriptome; AOB amoA reads included those from comammox Nitrospira clades A and B, in addition to Nitrosomonadaceae. Nitrification potential assessed in soil from the experimental sites (microcosms amended or not with DCD at concentrations inhibitory to AOB but not AOA), was highest in arable samples and lower in all assays containing DCD, indicating AOB were responsible for oxidizing ammonium fertilizer added to these soils.},
}
@article {pmid34350672,
year = {2021},
author = {Wakai, M and Hayashi, S and Chiba, Y and Koike, S and Nagashima, K and Kobayashi, Y},
title = {Growth and morphologic response of rumen methanogenic archaea and bacteria to cashew nut shell liquid and its alkylphenol components.},
journal = {Animal science journal = Nihon chikusan Gakkaiho},
volume = {92},
number = {1},
pages = {e13598},
doi = {10.1111/asj.13598},
pmid = {34350672},
issn = {1740-0929},
support = {JPJ009237//Cabinet Office, Government of Japan, Cross-ministerial Moonshot Agriculture, Forestry and Fisheries Research and Development Program/ ; },
mesh = {*Anacardium ; Animals ; Archaea ; Bacteria ; Methane ; Nuts ; *Rumen ; },
abstract = {The growth and morphology of rumen methanogenic archaea (15 strains of 10 species in 5 genera, including 7 strains newly isolated in the present study) and bacteria (14 species in 12 genera) were investigated using unsupplemented in vitro pure cultures and cultures supplemented with cashew nut shell liquid (CNSL) and its phenolic compound components, anti-methanogenic agents for ruminant animals. Growth of most of the methanogens tested was inhibited by CNSL and alkylphenols at different concentrations ranging from 1.56 to 12.5 μg/ml. Of the alkylphenols tested, anacardic acid exhibited the most potent growth inhibition. Three gram-negative bacterial species involved in propionate production were resistant to CNSL and alkylphenols (>50 μg/ml). All the methanogens and bacteria that were sensitive to CNSL and alkylphenols exhibited altered morphology; disruption of the cell surface was notable, possibly due to surfactant activity of the tested materials. Cells division was inhibited in some organisms, with cell elongation and unclear septum formation observed. These results indicate that CNSL and alkylphenols, particularly anacardic acid, inhibit both rumen bacteria and methanogens in a selective manner, which could help mitigate rumen methane generation.},
}
@article {pmid34347515,
year = {2021},
author = {French, E and Kozlowski, JA and Bollmann, A},
title = {Competition between Ammonia-Oxidizing Archaea and Bacteria from Freshwater Environments.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {20},
pages = {e0103821},
pmid = {34347515},
issn = {1098-5336},
mesh = {Ammonia/*metabolism ; Archaea/genetics/growth &amp; development/*metabolism ; Fresh Water/*microbiology ; *Microbial Interactions ; Nitrosomonas/genetics/growth &amp; development/*metabolism ; Oxidation-Reduction ; Phylogeny ; },
abstract = {In the environment, nutrients are rarely available in a constant supply. Therefore, microorganisms require strategies to compete for limiting nutrients. In freshwater systems, ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) compete with heterotrophic bacteria, photosynthetic microorganisms, and each other for ammonium, which AOA and AOB utilize as their sole source of energy and nitrogen. We investigated the competition between highly enriched cultures of AOA (AOA-AC1) and AOB (AOB-G5-7) for ammonium. Based on the amoA gene, the newly enriched archaeal ammonia oxidizer in AOA-AC1 was closely related to Nitrosotenuis spp., and the bacterial ammonia oxidizer in AOB-G5-7, Nitrosomonas sp. strain Is79, belonged to the Nitrosomonas oligotropha group (Nitrosomonas cluster 6a). Growth experiments in batch cultures showed that AOB-G5-7 had higher growth rates than AOA-AC1 at higher ammonium concentrations. During chemostat competition experiments under ammonium-limiting conditions, AOA-AC1 dominated the cultures, while AOB-G5-7 decreased in abundance. In batch cultures, the outcome of the competition between AOA and AOB was determined by the initial ammonium concentrations. AOA-AC1 was the dominant ammonia oxidizer at an initial ammonium concentration of 50 μM, and AOB-G5-7 was dominant at 500 μM. These findings indicate that during direct competition, AOA-AC1 was able to use ammonium that was unavailable to AOB-G5-7, while AOB-G5-7 dominated at higher ammonium concentrations. The results are in strong accordance with environmental survey data suggesting that AOA are mainly responsible for ammonia oxidation under more oligotrophic conditions, whereas AOB dominate under eutrophic conditions. IMPORTANCE Nitrification is an important process in the global nitrogen cycle. The first step, ammonia oxidation to nitrite, can be carried out by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). In many natural environments, these ammonia oxidizers coexist. Therefore, it is important to understand the population dynamics in response to increasing ammonium concentrations. Here, we study the competition between AOA and AOB enriched from freshwater systems. The results demonstrate that AOA are more abundant in systems with low ammonium availabilities and that AOB are more abundant when the ammonium availability increases. These results will help to predict potential shifts in the community composition of ammonia oxidizers in the environment due to changes in ammonium availability.},
}
@article {pmid34346295,
year = {2021},
author = {Santos, MVD and Goes, RHTB and Takiya, CS and Cabral, LDS and Mombach, MA and Oliveira, RT and Silva, NGD and Anschau, DG and Freitas Júnior, JE and de Araújo, MLGML and Gandra, JR},
title = {Effect of increasing doses of chitosan to grazing beef steers on the relative population and transcript abundance of Archaea and cellulolytic and amylolytic bacterias.},
journal = {Animal biotechnology},
volume = {},
number = {},
pages = {1-7},
doi = {10.1080/10495398.2021.1954936},
pmid = {34346295},
issn = {1532-2378},
abstract = {This paper aims to investigate the influence of increasing chitosan doses on the relative proportion and abundance of cellulotytic, amylolytic bacteria, and Archaea transcripts for grazing cattle. Five rumen cannulated crossbread steers [3.6 months and 300 ± 25 kg body LW (live weight), mean ± standard deviation] were used in a 5 × 5 latin square design, randomly assigned to treatment sequence containing chitosan added to 0, 400, 800, 1200, or 1600 mg/kg concentrate. There was the effect of chitosan on the population of Fibrobacter succinogenes, Ruminococcus albus, and Archaea. The lowest population of these bacteria of 576.60 mg/kg DM (dry matter), 1010.40 mg/kg DM, and 634.80 mg/kg DM were noted when chitosan was added at levels of 3.87, 4.16, and 3.52. Except for Ruminococcus albus, which was not affected by increasing chitosan doses, supplementation of this additive in the concentrate quadratically increased the relative abundance of Fibrobacter succinogenes and Archaea Supplemental 740 mg CHI/kg concentrate for grazing steers receiving concentrate at 150 grams/100 kg LW is recommended to promote minimal effect on the relative population and abundance of cellulolytics and amylomatics and to restrict Archaea growth.},
}
@article {pmid34343555,
year = {2022},
author = {Zhu, J and Yan, X and Zhou, L and Li, N and Liao, C and Wang, X},
title = {Insight of bacteria and archaea in Feammox community enriched from different soils.},
journal = {Environmental research},
volume = {203},
number = {},
pages = {111802},
doi = {10.1016/j.envres.2021.111802},
pmid = {34343555},
issn = {1096-0953},
mesh = {*Ammonium Compounds ; Archaea ; Bacteria ; Ferric Compounds ; Nitrogen/analysis ; Oxidation-Reduction ; *Soil ; Soil Microbiology ; },
abstract = {Anaerobic ammonium oxidation coupled to Fe(III) reduction, known as Feammox, is a newly discovered nitrogen-cycling process, which serves an important role in the pathways of nitrogen loss in the environment. However, the specific types of microorganisms involved in Feammox currently remain unclear. In this study, we selected two groups of soil samples (paddy and mine), from considerably different habitats in South China, to acclimate Feammox colonies. The Paddy Group had a shorter lag period than the Mine Group, while the ammonium transformation rate was nearly equal in both groups in the mature period. The emergence of the Feammox activity was found to be associated with the increased abundance of iron-reducing bacteria, especially Clostridium_sensu_stricto_12, Desulfitobacterium, Thermoanaerobaculum, Anaeromyxobacter and Geobacter. Ammonium oxidizing archaea and methanogens were dominant among the known archaea. These findings extend our knowledge of the microbial community composition of the potential Feammox microbes from soils under different environmental conditions, which broadens our understanding of this important Fe/N transformation process.},
}
@article {pmid34327792,
year = {2021},
author = {Li, C and Hambright, KD and Bowen, HG and Trammell, MA and Grossart, HP and Burford, MA and Hamilton, DP and Jiang, H and Latour, D and Meyer, EI and Padisák, J and Zamor, RM and Krumholz, LR},
title = {Global co-occurrence of methanogenic archaea and methanotrophic bacteria in Microcystis aggregates.},
journal = {Environmental microbiology},
volume = {23},
number = {11},
pages = {6503-6519},
doi = {10.1111/1462-2920.15691},
pmid = {34327792},
issn = {1462-2920},
mesh = {Archaea/genetics ; *Euryarchaeota/genetics ; Eutrophication ; Lakes/microbiology ; Methane ; *Microcystis/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Global warming and eutrophication contribute to the worldwide increase in cyanobacterial blooms, and the level of cyanobacterial biomass is strongly associated with rises in methane emissions from surface lake waters. Hence, methane-metabolizing microorganisms may be important for modulating carbon flow in cyanobacterial blooms. Here, we surveyed methanogenic and methanotrophic communities associated with floating Microcystis aggregates in 10 lakes spanning four continents, through sequencing of 16S rRNA and functional marker genes. Methanogenic archaea (mainly Methanoregula and Methanosaeta) were detectable in 5 of the 10 lakes and constituted the majority (~50%-90%) of the archaeal community in these lakes. Three of the 10 lakes contained relatively more abundant methanotrophs than the other seven lakes, with the methanotrophic genera Methyloparacoccus, Crenothrix, and an uncultured species related to Methylobacter dominating and nearly exclusively found in each of those three lakes. These three are among the five lakes in which methanogens were observed. Operational taxonomic unit (OTU) richness and abundance of methanotrophs were strongly positively correlated with those of methanogens, suggesting that their activities may be coupled. These Microcystis-aggregate-associated methanotrophs may be responsible for a hitherto overlooked sink for methane in surface freshwaters, and their co-occurrence with methanogens sheds light on the methane cycle in cyanobacterial aggregates.},
}
@article {pmid34316016,
year = {2022},
author = {Jung, MY and Sedlacek, CJ and Kits, KD and Mueller, AJ and Rhee, SK and Hink, L and Nicol, GW and Bayer, B and Lehtovirta-Morley, L and Wright, C and de la Torre, JR and Herbold, CW and Pjevac, P and Daims, H and Wagner, M},
title = {Ammonia-oxidizing archaea possess a wide range of cellular ammonia affinities.},
journal = {The ISME journal},
volume = {16},
number = {1},
pages = {272-283},
pmid = {34316016},
issn = {1751-7370},
mesh = {*Ammonia/metabolism ; *Archaea/genetics/metabolism ; Bacteria/genetics/metabolism ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Soil Microbiology ; },
abstract = {Nitrification, the oxidation of ammonia to nitrate, is an essential process in the biogeochemical nitrogen cycle. The first step of nitrification, ammonia oxidation, is performed by three, often co-occurring guilds of chemolithoautotrophs: ammonia-oxidizing bacteria (AOB), archaea (AOA), and complete ammonia oxidizers (comammox). Substrate kinetics are considered to be a major niche-differentiating factor between these guilds, but few AOA strains have been kinetically characterized. Here, the ammonia oxidation kinetic properties of 12 AOA representing all major cultivated phylogenetic lineages were determined using microrespirometry. Members of the genus Nitrosocosmicus have the lowest affinity for both ammonia and total ammonium of any characterized AOA, and these values are similar to previously determined ammonia and total ammonium affinities of AOB. This contrasts previous assumptions that all AOA possess much higher substrate affinities than their comammox or AOB counterparts. The substrate affinity of ammonia oxidizers correlated with their cell surface area to volume ratios. In addition, kinetic measurements across a range of pH values supports the hypothesis that-like for AOB-ammonia and not ammonium is the substrate for the ammonia monooxygenase enzyme of AOA and comammox. Together, these data will facilitate predictions and interpretation of ammonia oxidizer community structures and provide a robust basis for establishing testable hypotheses on competition between AOB, AOA, and comammox.},
}
@article {pmid34286299,
year = {2021},
author = {Coutinho, FH and Zaragoza-Solas, A and López-Pérez, M and Barylski, J and Zielezinski, A and Dutilh, BE and Edwards, R and Rodriguez-Valera, F},
title = {RaFAH: Host prediction for viruses of Bacteria and Archaea based on protein content.},
journal = {Patterns (New York, N.Y.)},
volume = {2},
number = {7},
pages = {100274},
pmid = {34286299},
issn = {2666-3899},
support = {RC2 DK116713/DK/NIDDK NIH HHS/United States ; },
abstract = {Culture-independent approaches have recently shed light on the genomic diversity of viruses of prokaryotes. One fundamental question when trying to understand their ecological roles is: which host do they infect? To tackle this issue we developed a machine-learning approach named Random Forest Assignment of Hosts (RaFAH), that uses scores to 43,644 protein clusters to assign hosts to complete or fragmented genomes of viruses of Archaea and Bacteria. RaFAH displayed performance comparable with that of other methods for virus-host prediction in three different benchmarks encompassing viruses from RefSeq, single amplified genomes, and metagenomes. RaFAH was applied to assembled metagenomic datasets of uncultured viruses from eight different biomes of medical, biotechnological, and environmental relevance. Our analyses led to the identification of 537 sequences of archaeal viruses representing unknown lineages, whose genomes encode novel auxiliary metabolic genes, shedding light on how these viruses interfere with the host molecular machinery. RaFAH is available at https://sourceforge.net/projects/rafah/.},
}
@article {pmid34285362,
year = {2022},
author = {Yu, H and Skennerton, CT and Chadwick, GL and Leu, AO and Aoki, M and Tyson, GW and Orphan, VJ},
title = {Sulfate differentially stimulates but is not respired by diverse anaerobic methanotrophic archaea.},
journal = {The ISME journal},
volume = {16},
number = {1},
pages = {168-177},
pmid = {34285362},
issn = {1751-7370},
mesh = {Anaerobiosis ; *Archaea/metabolism ; Geologic Sediments/microbiology ; Humans ; Methane/metabolism ; Oxidation-Reduction ; Phylogeny ; *Sulfates/metabolism ; },
abstract = {Sulfate-coupled anaerobic oxidation of methane (AOM) is a major methane sink in marine sediments. Multiple lineages of anaerobic methanotrophic archaea (ANME) often coexist in sediments and catalyze this process syntrophically with sulfate-reducing bacteria (SRB), but the potential differences in ANME ecophysiology and mechanisms of syntrophy remain unresolved. A humic acid analog, anthraquinone 2,6-disulfonate (AQDS), could decouple archaeal methanotrophy from bacterial sulfate reduction and serve as the terminal electron acceptor for AOM (AQDS-coupled AOM). Here in sediment microcosm experiments, we examined variations in physiological response between two co-occurring ANME-2 families (ANME-2a and ANME-2c) and tested the hypothesis of sulfate respiration by ANME-2. Sulfate concentrations as low as 100 µM increased AQDS-coupled AOM nearly 2-fold matching the rates of sulfate-coupled AOM. However, the SRB partners remained inactive in microcosms with sulfate and AQDS and neither ANME-2 families respired sulfate, as shown by their cellular sulfur contents and anabolic activities measured using nanoscale secondary ion mass spectrometry. ANME-2a anabolic activity was significantly higher than ANME-2c, suggesting that ANME-2a was primarily responsible for the observed sulfate stimulation of AQDS-coupled AOM. Comparative transcriptomics showed significant upregulation of ANME-2a transcripts linked to multiple ABC transporters and downregulation of central carbon metabolism during AQDS-coupled AOM compared to sulfate-coupled AOM. Surprisingly, genes involved in sulfur anabolism were not differentially expressed during AQDS-coupled AOM with and without sulfate amendment. Collectively, this data indicates that ANME-2 archaea are incapable of respiring sulfate, but sulfate availability differentially stimulates the growth and AOM activity of different ANME lineages.},
}
@article {pmid34282942,
year = {2021},
author = {Umbach, AK and Stegelmeier, AA and Neufeld, JD},
title = {Archaea Are Rare and Uncommon Members of the Mammalian Skin Microbiome.},
journal = {mSystems},
volume = {6},
number = {4},
pages = {e0064221},
pmid = {34282942},
issn = {2379-5077},
support = {NA//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; },
abstract = {Although previous research demonstrates that skin-associated archaea are rarely detected within human skin microbiome data, exist at relatively low abundance, and are primarily affiliated with the Methanobacteriota and Halobacteriota phyla, other studies suggest that archaea are consistently detected and relatively abundant on human skin, with skin "archaeomes" dominated by putative ammonia oxidizers of the Nitrososphaeria class (Thermoproteota phylum, formerly Thaumarchaeota). Here, we evaluated new and existing 16S rRNA gene sequence data sourced from mammalian skin and skin-associated surfaces and generated with two commonly used universal prokaryotic primer sets to assess archaeal prevalence, relative abundance, and taxonomic distribution. Archaeal 16S rRNA gene sequences were detected in only 17.5% of 1,688 samples by high-throughput sequence data, with most of the archaeon-positive samples associated with nonhuman mammalian skin. Only 5.9% of human-associated skin sample data sets contained sequences affiliated with archaeal 16S rRNA genes. When detected, the relative abundance of sequences affiliated with archaeal amplicon sequence variants (ASVs) was less than 1% for most mammalian skin samples and did not exceed 2% for any samples. Although several computer keyboard microbial profiles were dominated by Nitrososphaeria sequences, all other skin microbiome data sets tested were primarily composed of sequences affiliated with Methanobacteriota and Halobacteriota phyla. Our findings revise downward recent estimates of human skin archaeal distributions and relative abundances, especially those affiliated with the Nitrososphaeria, reflecting a limited and infrequent archaeal presence within the mammalian skin microbiome. IMPORTANCE The current state of research on mammalian skin-associated archaea is limited, with the few papers focusing on potential skin archaeal communities often in disagreement with each other. As such, there is no consensus on the prevalence or taxonomic composition of archaea on mammalian skin. Mammalian skin health is in part influenced by its complex microbiota and consortium of bacteria and potential archaea. Without a clear foundational analysis and characterization of the mammalian skin archaeome, it will be difficult for future research to explore the potential impact of skin-associated archaea on skin health and function. The current work provides a much-needed analysis of the mammalian skin archaeome and contributes to building a foundation from which further discussion and exploration of the skin archaeome might continue.},
}
@article {pmid34276623,
year = {2021},
author = {Dong, Y and Shan, Y and Xia, K and Shi, L},
title = {The Proposed Molecular Mechanisms Used by Archaea for Fe(III) Reduction and Fe(II) Oxidation.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {690918},
pmid = {34276623},
issn = {1664-302X},
abstract = {Iron (Fe) is the fourth most abundant element in the Earth's crust where ferrous Fe [Fe(II)] and ferric Fe [Fe(III)] can be used by archaea for energy conservation. In these archaea-Fe interactions, Fe(III) serves as terminal electron acceptor for anaerobic respiration by a variety of archaea, while Fe(II) serves as electron donor and/or energy sources for archaeal growth. As no Fe is incorporated into the archaeal cells, these redox reactions are referred to as dissimilatory Fe(III) reduction and Fe(II) oxidation, respectively. Dissimilatory Fe(III)-reducing archaea (FeRA) and Fe(II)-oxidizing archaea (FeOA) are widespread on Earth where they play crucial roles in biogeochemical cycling of not only Fe, but also carbon and sulfur. To reduce extracellular Fe(III) (oxyhydr)oxides, some FeRA transfer electrons directly to the Fe(III) (oxyhydr)oxides most likely via multiheme c-type cytochromes (c-Cyts). These multiheme c-Cyts may form the pathways similar to those found in bacteria for transferring electrons from the quinone/quinol pool in the cytoplasmic membrane to the Fe(III) (oxyhydr)oxides external to the archaeal cells. Use of multiheme c-Cyts for extracellular Fe(III) reduction by both Domains of Archaea and Bacteria emphasizes an ancient mechanism of extracellular electron transfer, which is well conserved. Other FeRA, however, reduce Fe(III) (oxyhydr)oxides indirectly via electron shuttles. Similarly, it is proposed that FeOA use pathways to oxidize Fe(II) on the surface of the cytoplasmic membrane and then to transfer the released electrons across the cytoplasmic membrane inward to the O2 and NAD+ in the cytoplasm. In this review, we focus on the latest understandings of the molecular mechanisms used by FeRA and FeOA for Fe(III) reduction and Fe(II) oxidation, respectively.},
}
@article {pmid34267287,
year = {2021},
author = {Wang, L and Huang, D},
title = {Soil ammonia-oxidizing archaea in a paddy field with different irrigation and fertilization managements.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {14563},
pmid = {34267287},
issn = {2045-2322},
mesh = {Agricultural Irrigation/*methods ; Ammonia/*metabolism ; Archaea/*metabolism ; China ; Crenarchaeota/metabolism ; *Fertilizers ; Hydrogen-Ion Concentration ; Oryza/growth &amp; development ; Oxidation-Reduction ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {Because ammonia-oxidizing archaea (AOA) are ubiquitous and highly abundant in almost all terrestrial soils, they play an important role in soil nitrification. However, the changes in the structure and function of AOA communities and their edaphic drivers in paddy soils under different fertilization and irrigation regimes remain unclear. In this study, we investigated AOA abundance, diversity and activity in acid paddy soils by a field experiment. Results indicated that the highest potential ammonia oxidation (PAO) (0.011 μg NO 2 - -N g-1 d.w.day-1) was found in T2 (optimal irrigation and fertilization)-treated soils, whereas the lowest PAO (0.004 μg NO 2 - -N g-1 d.w.day-1) in T0 (traditional irrigation)- treated soils. Compared with the T0-treated soil, the T2 treatment significantly (P < 0.05) increased AOA abundances. Furthermore, the abundance of AOA was significantly (P < 0.01) positively correlated with pH, soil organic carbon (SOC), and PAO. Meanwhile, pH and SOC content were significantly (P < 0.05) higher in the T2-treated soil than those in the T1 (traditional irrigation and fertilization)- treated soil. In addition, these two edaphic factors further influenced the AOA community composition. The AOA phylum Crenarchaeota was mainly found in the T2-treated soils. Phylogenetic analysis revealed that most of the identified OTUs of AOA were mainly affiliated with Crenarchaeota. Furthermore, the T2 treatment had higher rice yield than the T0 and T1 treatments. Together, our findings confirm that T2 might ameliorate soil chemical properties, regulate the AOA community structure, increase the AOA abundance, enhance PAO and consequently maintain rice yields in the present study.},
}
@article {pmid34253852,
year = {2022},
author = {Jørgensen, BB},
title = {Do methanogenic archaea cause reductive pyrite dissolution in subsurface sediments?.},
journal = {The ISME journal},
volume = {16},
number = {1},
pages = {1-2},
pmid = {34253852},
issn = {1751-7370},
mesh = {*Archaea/genetics ; *Euryarchaeota ; Iron ; Solubility ; Sulfides ; },
}
@article {pmid34248899,
year = {2021},
author = {Christakis, CA and Barkay, T and Boyd, ES},
title = {Expanded Diversity and Phylogeny of mer Genes Broadens Mercury Resistance Paradigms and Reveals an Origin for MerA Among Thermophilic Archaea.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {682605},
pmid = {34248899},
issn = {1664-302X},
abstract = {Mercury (Hg) is a highly toxic element due to its high affinity for protein sulfhydryl groups, which upon binding, can destabilize protein structure and decrease enzyme activity. Prokaryotes have evolved enzymatic mechanisms to detoxify inorganic Hg and organic Hg (e.g., MeHg) through the activities of mercuric reductase (MerA) and organomercury lyase (MerB), respectively. Here, the taxonomic distribution and evolution of MerAB was examined in 84,032 archaeal and bacterial genomes, metagenome assembled genomes, and single-cell genomes. Homologs of MerA and MerB were identified in 7.8 and 2.1% percent of genomes, respectively. MerA was identified in the genomes of 10 archaeal and 28 bacterial phyla previously unknown to code for this functionality. Likewise, MerB was identified in 2 archaeal and 11 bacterial phyla previously unknown to encode this functionality. Surprisingly, homologs of MerB were identified in a number of genomes (∼50% of all MerB-encoding genomes) that did not encode MerA, suggesting alternative mechanisms to detoxify Hg(II) once it is generated in the cytoplasm. Phylogenetic reconstruction of MerA place its origin in thermophilic Thermoprotei (Crenarchaeota), consistent with high levels of Hg(II) in geothermal environments, the natural habitat of this archaeal class. MerB appears to have been recruited to the mer operon relatively recently and likely among a mesophilic ancestor of Euryarchaeota and Thaumarchaeota. This is consistent with the functional dependence of MerB on MerA and the widespread distribution of mesophilic microorganisms that methylate Hg(II) at lower temperature. Collectively, these results expand the taxonomic and ecological distribution of mer-encoded functionalities, and suggest that selection for Hg(II) and MeHg detoxification is dependent not only on the availability and type of mercury compounds in the environment but also the physiological potential of the microbes who inhabit these environments. The expanded diversity and environmental distribution of MerAB identify new targets to prioritize for future research.},
}
@article {pmid34245190,
year = {2021},
author = {Wang, S and Narsing Rao, MP and Wei, D and Sun, L and Fang, BZ and Li, WQ and Yu, LH and Li, WJ},
title = {Complete genome sequencing and comparative genome analysis of the extremely halophilic archaea, Haloterrigena daqingensis.},
journal = {Biotechnology and applied biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1002/bab.2220},
pmid = {34245190},
issn = {1470-8744},
abstract = {In the present study, we report the complete genome sequencing of Haloterrigena daqingensis species. The genome of H. daqingensis JX313T consisted of a circular chromosome with three plasmids. The genome size and G+C content were estimated to be 3835796 bp and 61.7%, respectively. A total of 4158 genes were predicted with six rRNAs and 45 tRNAs. Metabolic pathway analysis suggests that H. daqingensis JX313T codes for all the necessary genes responsible to sustain its life at saline environment. The pan-genome analysis suggests that the number of singleton-gene between H. daqingensis and other Haloterrigena species varied. The study not only helps us understand H. daqingensis strategy for dealing with high stress, but it also provides an overview of its genomic makeup.},
}
@article {pmid34217274,
year = {2021},
author = {Kakuk, B and Wirth, R and Maróti, G and Szuhaj, M and Rakhely, G and Laczi, K and Kovács, KL and Bagi, Z},
title = {Early response of methanogenic archaea to H2 as evaluated by metagenomics and metatranscriptomics.},
journal = {Microbial cell factories},
volume = {20},
number = {1},
pages = {127},
pmid = {34217274},
issn = {1475-2859},
support = {FK123902//Nemzeti Kutatási Fejlesztési és Innovációs Hivatal/ ; PD132145//Nemzeti Kutatási Fejlesztési és Innovációs Hivatal/ ; FK123899//Nemzeti Kutatási Fejlesztési és Innovációs Hivatal/ ; GINOP- 2.2.1-15-2017-00081//Nemzeti Kutatási és Technológiai Hivatal/ ; EFOP- 3.6.2-16-2017-00010//Nemzeti Kutatási és Technológiai Hivatal/ ; 2020-1.1.2-PIACI-KFI-2020-00117//Nemzeti Kutatási és Technológiai Hivatal/ ; LP2020-5/2020//Magyar Tudományos Akadémia/ ; 2020-3.1.2.-ZFR-KVG-2020-00009//nemzeti kutatási és technológiai hivatal/ ; },
mesh = {Anaerobiosis ; Bacteria/genetics/metabolism ; Carbon Dioxide/metabolism ; Fermentation ; Gene Expression Regulation, Archaeal ; Genome, Archaeal ; Hydrogen/*metabolism ; Metagenome ; Metagenomics ; Methane/*biosynthesis ; Methanomicrobiaceae/genetics/*metabolism ; Methanosarcina/genetics/*metabolism ; Microbiota ; *Transcriptome ; },
abstract = {BACKGROUND: The molecular machinery of the complex microbiological cell factory of biomethane production is not fully understood. One of the process control elements is the regulatory role of hydrogen (H2). Reduction of carbon dioxide (CO2) by H2 is rate limiting factor in methanogenesis, but the community intends to keep H2 concentration low in order to maintain the redox balance of the overall system. H2 metabolism in methanogens becomes increasingly important in the Power-to-Gas renewable energy conversion and storage technologies.<br><br>RESULTS: The early response of the mixed mesophilic microbial community to H2 gas injection was investigated with the goal of uncovering the first responses of the microbial community in the CH4 formation and CO2 mitigation Power-to-Gas process. The overall microbial composition changes, following a 10 min excessive bubbling of H2 through the reactor, was investigated via metagenome and metatranscriptome sequencing. The overall composition and taxonomic abundance of the biogas producing anaerobic community did not change appreciably 2 hours after the H2 treatment, indicating that this time period was too short to display differences in the proliferation of the members of the microbial community. There was, however, a substantial increase in the expression of genes related to hydrogenotrophic methanogenesis of certain groups of Archaea. As an early response to H2 exposure the activity of the hydrogenotrophic methanogenesis in the genus Methanoculleus was upregulated but the hydrogenotrophic pathway in genus Methanosarcina was downregulated. The RT-qPCR data corroborated the metatranscriptomic RESULTS: H2 injection also altered the metabolism of a number of microbes belonging in the kingdom Bacteria. Many Bacteria possess the enzyme sets for the Wood-Ljungdahl pathway. These and the homoacetogens are partners for syntrophic community interactions between the distinct kingdoms of Archaea and Bacteria.<br><br>CONCLUSIONS: External H2 regulates the functional activity of certain Bacteria and Archaea. The syntrophic cross-kingdom interactions in H2 metabolism are important for the efficient operation of the Power-to-Gas process. Therefore, mixed communities are recommended for the large scale Power-to-Gas process rather than single hydrogenotrophic methanogen strains. Fast and reproducible response from the microbial community can be exploited in turn-off and turn-on of the Power-to-Gas microbial cell factories.},
}
@article {pmid34213183,
year = {2020},
author = {Wang, X and He, Z and Li, X and Song, Q and Zou, X and Song, X and Feng, L},
title = {[Comparison of pretreatment methods in lipid analysis and ultra-performance liquid chromatography-mass spectrometry analysis of archaea].},
journal = {Se pu = Chinese journal of chromatography},
volume = {38},
number = {8},
pages = {914-922},
doi = {10.3724/SP.J.1123.2019.12009},
pmid = {34213183},
issn = {1000-8713},
mesh = {*Archaea/chemistry ; Chromatography, High Pressure Liquid ; *Lipidomics ; Lipids/*analysis ; Mass Spectrometry ; Pyrococcus/chemistry ; Reproducibility of Results ; },
abstract = {Archaea are single-cell microorganisms, structurally and biochemically similar to bacteria and fungi. Most of them live in extreme environments, such as high salt, extremely acidic, extremely hot, and anaerobicenvironments. The membrane structure and related metabolic pathways of archaea are different from those of other microorganisms. Therefore, studying the lipid metabolism of archaea is of great significance for exploring the life activities in extreme environments. As the first step in lipidomic analysis, lipid extraction and pretreatment methods play an important role, as they influence the accuracy and reliability of the final results. We harnessed ultra-performance liquid chromatography coupled with high-resolution mass spectrometry (UPLC-HRMS) to detect the total normal lipids. The hyperthermophilic archaeon Pyrococcus yayanosii was selected as the model. The Bligh-Dyer acidic method, Folch method, methyl tert-butyl ether (MTBE) method, and solid-phase extraction (SPE) method were compared by multi-component analysis in terms of extraction efficiency, reproducibility, and extraction discrimination. Comprehensive analysis revealed that the SPE and MTBE methods showed the best extraction repeatability and extraction efficiency, and were suitable for high-throughput microbial lipid extraction. Finally, normal lipid components of P. yayanosii were comprehensively analyzed by SPE coupled with UPLC-HRMS. A total of 1402 lipid components were identified. This article aims to provide a reference for non-targeted lipidomic analysis of archaea and other microorganisms towards understanding their lipid metabolism.},
}
@article {pmid34207561,
year = {2021},
author = {Abellan-Schneyder, I and Siebert, A and Hofmann, K and Wenning, M and Neuhaus, K},
title = {Full-Length SSU rRNA Gene Sequencing Allows Species-Level Detection of Bacteria, Archaea, and Yeasts Present in Milk.},
journal = {Microorganisms},
volume = {9},
number = {6},
pages = {},
pmid = {34207561},
issn = {2076-2607},
support = {n/a (grant for a scientist//Research Foundation of Dairy Science at the Technical University of Munich (VFMF)/ ; n/a (grant for a doctorate position)//ZIEL-Institute for Food &amp; Health at the Technical University of Munich/ ; 281A105616//Federal Ministry of Food and Agriculture (BMEL)/ ; AiF 20027N//IGF Project of the FEI via AiF/ ; },
abstract = {Full-length SSU rRNA gene sequencing allows species-level identification of the microorganisms present in milk samples. Here, we used bulk-tank raw milk samples of two German dairies and detected, using this method, a great diversity of bacteria, archaea, and yeasts within the samples. Moreover, the species-level classification was improved in comparison to short amplicon sequencing. Therefore, we anticipate that this approach might be useful for the detection of possible mastitis-causing species, as well as for the control of spoilage-associated microorganisms. In a proof of concept, we showed that we were able to identify several putative mastitis-causing or mastitis-associated species such as Streptococcusuberis, Streptococcusagalactiae, Streptococcusdysgalactiae, Escherichiacoli and Staphylococcusaureus, as well as several Candida species. Overall, the presented full-length approach for the sequencing of SSU rRNA is easy to conduct, able to be standardized, and allows the screening of microorganisms in labs with Illumina sequencing machines.},
}
@article {pmid34202810,
year = {2021},
author = {Pfeiffer, F and Dyall-Smith, M},
title = {Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea.},
journal = {Genes},
volume = {12},
number = {7},
pages = {},
pmid = {34202810},
issn = {2073-4425},
mesh = {Archaeal Proteins/classification/*genetics ; Halobacteriales/classification/*genetics ; Haloferax volcanii/*genetics ; Molecular Sequence Annotation ; },
abstract = {BACKGROUND: Annotation ambiguities and annotation errors are a general challenge in genomics. While a reliable protein function assignment can be obtained by experimental characterization, this is expensive and time-consuming, and the number of such Gold Standard Proteins (GSP) with experimental support remains very low compared to proteins annotated by sequence homology, usually through automated pipelines. Even a GSP may give a misleading assignment when used as a reference: the homolog may be close enough to support isofunctionality, but the substrate of the GSP is absent from the species being annotated. In such cases, the enzymes cannot be isofunctional. Here, we examined a variety of such issues in halophilic archaea (class Halobacteria), with a strong focus on the model haloarchaeon Haloferax volcanii.<br><br>RESULTS: Annotated proteins of Hfx. volcanii were identified for which public databases tend to assign a function that is probably incorrect. In some cases, an alternative, probably correct, function can be predicted or inferred from the available evidence, but this has not been adopted by public databases because experimental validation is lacking. In other cases, a probably invalid specific function is predicted by homology, and while there is evidence that this assigned function is unlikely, the true function remains elusive. We listed 50 of those cases, each with detailed background information, so that a conclusion about the most likely biological function can be drawn. For reasons of brevity and comprehension, only the key aspects are listed in the main text, with detailed information being provided in a corresponding section of the Supplementary Materials.<br><br>CONCLUSIONS: Compiling, describing and summarizing these open annotation issues and functional predictions will benefit the scientific community in the general effort to improve the evaluation of protein function assignments and more thoroughly detail them. By highlighting the gaps and likely annotation errors currently in the databases, we hope this study will provide a framework for experimentalists to systematically confirm (or disprove) our function predictions or to uncover yet more unexpected functions.},
}
@article {pmid34190386,
year = {2022},
author = {Tamisier, M and Schmidt, M and Vogt, C and Kümmel, S and Stryhanyuk, H and Musat, N and Richnow, HH and Musat, F},
title = {Iron corrosion by methanogenic archaea characterized by stable isotope effects and crust mineralogy.},
journal = {Environmental microbiology},
volume = {24},
number = {2},
pages = {583-595},
doi = {10.1111/1462-2920.15658},
pmid = {34190386},
issn = {1462-2920},
mesh = {*Archaea ; Carbon Isotopes/analysis ; Corrosion ; *Euryarchaeota ; Iron ; Isotopes ; Methane ; },
abstract = {Carbon and hydrogen stable isotope effects associated with methane formation by the corrosive archaeon Methanobacterium strain IM1 were determined during growth with hydrogen and iron. Isotope analyses were complemented by structural, elemental and molecular composition analyses of corrosion crusts. During growth with H2 , strain IM1 formed methane with average δ13 C of -43.5‰ and δ2 H of -370‰. Corrosive growth led to methane more depleted in 13 C, with average δ13 C ranging from -56‰ to -64‰ during the early and the late growth phase respectively. The corresponding δ2 H were less impacted by the growth phase, with average values ranging from -316 to -329‰. The stable isotope fractionation factors, α 13 C CO 2 / CH 4 , were 1.026 and 1.042 for hydrogenotrophic and corrosive growth respectively. Corrosion crusts formed by strain IM1 have a domed structure, appeared electrically conductive and were composed of siderite, calcite and iron sulfide, the latter formed by precipitation of sulfide (from culture medium) with ferrous iron generated during corrosion. Strain IM1 cells were found attached to crust surfaces and encrusted deep inside crust domes. Our results may assist to diagnose methanogens-induced corrosion in the field and suggest that intrusion of sulfide in anoxic settings may stimulate corrosion by methanogenic archaea via formation of semiconductive crusts.},
}
@article {pmid34158628,
year = {2021},
author = {Zhao, R and Mogollón, JM and Roerdink, DL and Thorseth, IH and Økland, I and Jørgensen, SL},
title = {Ammonia-oxidizing archaea have similar power requirements in diverse marine oxic sediments.},
journal = {The ISME journal},
volume = {15},
number = {12},
pages = {3657-3667},
pmid = {34158628},
issn = {1751-7370},
mesh = {*Ammonia ; *Archaea/genetics ; Bacteria ; Geologic Sediments ; Nitrification ; Oxidation-Reduction ; Phylogeny ; },
abstract = {Energy/power availability is regarded as one of the ultimate controlling factors of microbial abundance in the deep biosphere, where fewer cells are found in habitats of lower energy availability. A critical assumption driving the proportional relationship between total cell abundance and power availability is that the cell-specific power requirement keeps constant or varies over smaller ranges than other variables, which has yet to be validated. Here we present a quantitative framework to determine the cell-specific power requirement of the omnipresent ammonia-oxidizing archaea (AOA) in eight sediment cores with 3-4 orders of magnitude variations of organic matter flux and oxygen penetration depth. Our results show that despite the six orders of magnitude variations in the rates and power supply of nitrification and AOA abundances across these eight cores, the cell-specific power requirement of AOA from different cores and depths overlaps within the narrow range of 10-19-10-17 W cell-1, where the lower end may represent the basal power requirement of microorganisms persisting in subseafloor sediments. In individual cores, AOA also exhibit similar cell-specific power requirements, regardless of the AOA population size or sediment depth/age. Such quantitative insights establish a relationship between the power supply and the total abundance of AOA, and therefore lay a foundation for a first-order estimate of the standing stock of AOA in global marine oxic sediments.},
}
@article {pmid34153824,
year = {2021},
author = {Chen, Z and Liu, WS and Zhong, X and Zheng, M and Fei, YH and He, H and Ding, K and Chao, Y and Tang, YT and Wang, S and Qiu, R},
title = {Genome- and community-level interaction insights into the ecological role of archaea in rare earth element mine drainage in South China.},
journal = {Water research},
volume = {201},
number = {},
pages = {117331},
doi = {10.1016/j.watres.2021.117331},
pmid = {34153824},
issn = {1879-2448},
mesh = {*Archaea/genetics ; China ; Genome, Archaeal ; Metagenome ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S ; },
abstract = {Microbial communities play crucial roles in mine drainage generation and remediation. Despite the wide distribution of archaea in the mine ecosystem, their diversity and ecological roles remain less understood than bacteria. Here, we retrieved 56 archaeal metagenome-assembled genomes from a river impacted by rare earth element (REE) mining activities in South China. Genomic analysis showed that archaea represented four distinct lineages, including phyla of Thaumarchaeota, Micrarchaeota, Nanoarchaeota and Thermoplasmata. These archaea represented a considerable fraction (up to 40%) of the total prokaryote community, which might contribute to nitrogen and sulfur cycling in the REE mine drainage. Reconstructed metabolic potential among diverse archaea taxa revealed that archaea were involved in the network of ammonia oxidation, denitrification, sulfate redox reaction, and required substrates supplied by other community members. As the dominant driver of ammonia oxidation, Thaumarchaeota might provide substrates to support the survival of two nano-sized archaea belonging to Micrarchaeota and Nanoarchaeota. Despite the absence of biosynthesis pathways for amino acids and nucleotides, the potential capacity for nitrite reduction (nirD) was observed in Micrarchaeota, indicating that these nano-sized archaea encompassed diverse metabolisms. Moreover, Thermoplasmata, as keystone taxa in community, might be the main genetic donor for the other three archaeal phyla, transferring many environmental resistance related genes (e.g., V/A-type ATPase and Vitamin B12-transporting ATPase). The genetic interactions within archaeal community through horizontal gene transfer might be the key to the formation of archaeal resistance and functional partitioning. This study provides putative metabolic and genetic insights into the diverse archaea taxa from community-level perspectives, and highlights the ecological roles of archaea in REE contaminated aquatic environment.},
}
@article {pmid34151666,
year = {2021},
author = {Ziegler, CA and Freddolino, PL},
title = {The leucine-responsive regulatory proteins/feast-famine regulatory proteins: an ancient and complex class of transcriptional regulators in bacteria and archaea.},
journal = {Critical reviews in biochemistry and molecular biology},
volume = {56},
number = {4},
pages = {373-400},
doi = {10.1080/10409238.2021.1925215},
pmid = {34151666},
issn = {1549-7798},
support = {R35 GM128637/GM/NIGMS NIH HHS/United States ; T32 GM007544/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/genetics/*metabolism ; Archaeal Proteins/genetics/*metabolism ; Escherichia coli/genetics/*metabolism ; Escherichia coli Proteins/genetics/*metabolism ; Leucine-Responsive Regulatory Protein/genetics/*metabolism ; },
abstract = {Since the discovery of the Escherichia coli leucine-responsive regulatory protein (Lrp) almost 50 years ago, hundreds of Lrp homologs have been discovered, occurring in 45% of sequenced bacteria and almost all sequenced archaea. Lrp-like proteins are often referred to as the feast/famine regulatory proteins (FFRPs), reflecting their common regulatory roles. Acting as either global or local transcriptional regulators, FFRPs detect the environmental nutritional status by sensing small effector molecules (usually amino acids) and regulate the expression of genes involved in metabolism, virulence, motility, nutrient transport, stress tolerance, and antibiotic resistance to implement appropriate behaviors for the specific ecological niche of each organism. Despite FFRPs' complexity, a significant role in gene regulation, and prevalence throughout prokaryotes, the last comprehensive review on this family of proteins was published about a decade ago. In this review, we integrate recent notable findings regarding E. coli Lrp and other FFRPs across bacteria and archaea with previous observations to synthesize a more complete view on the mechanistic details and biological roles of this ancient class of transcription factors.},
}
@article {pmid34149676,
year = {2021},
author = {De Lise, F and Strazzulli, A and Iacono, R and Curci, N and Di Fenza, M and Maurelli, L and Moracci, M and Cobucci-Ponzano, B},
title = {Programmed Deviations of Ribosomes From Standard Decoding in Archaea.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {688061},
pmid = {34149676},
issn = {1664-302X},
abstract = {Genetic code decoding, initially considered to be universal and immutable, is now known to be flexible. In fact, in specific genes, ribosomes deviate from the standard translational rules in a programmed way, a phenomenon globally termed recoding. Translational recoding, which has been found in all domains of life, includes a group of events occurring during gene translation, namely stop codon readthrough, programmed ± 1 frameshifting, and ribosome bypassing. These events regulate protein expression at translational level and their mechanisms are well known and characterized in viruses, bacteria and eukaryotes. In this review we summarize the current state-of-the-art of recoding in the third domain of life. In Archaea, it was demonstrated and extensively studied that translational recoding regulates the decoding of the 21st and the 22nd amino acids selenocysteine and pyrrolysine, respectively, and only one case of programmed -1 frameshifting has been reported so far in Saccharolobus solfataricus P2. However, further putative events of translational recoding have been hypothesized in other archaeal species, but not extensively studied and confirmed yet. Although this phenomenon could have some implication for the physiology and adaptation of life in extreme environments, this field is still underexplored and genes whose expression could be regulated by recoding are still poorly characterized. The study of these recoding episodes in Archaea is urgently needed.},
}
@article {pmid34145392,
year = {2021},
author = {Kurth, JM and Nobu, MK and Tamaki, H and de Jonge, N and Berger, S and Jetten, MSM and Yamamoto, K and Mayumi, D and Sakata, S and Bai, L and Cheng, L and Nielsen, JL and Kamagata, Y and Wagner, T and Welte, CU},
title = {Methanogenic archaea use a bacteria-like methyltransferase system to demethoxylate aromatic compounds.},
journal = {The ISME journal},
volume = {15},
number = {12},
pages = {3549-3565},
pmid = {34145392},
issn = {1751-7370},
mesh = {*Euryarchaeota/enzymology/genetics ; Methane/*metabolism ; *Methyltransferases/genetics ; },
abstract = {Methane-generating archaea drive the final step in anaerobic organic compound mineralization and dictate the carbon flow of Earth's diverse anoxic ecosystems in the absence of inorganic electron acceptors. Although such Archaea were presumed to be restricted to life on simple compounds like hydrogen (H2), acetate or methanol, an archaeon, Methermicoccus shengliensis, was recently found to convert methoxylated aromatic compounds to methane. Methoxylated aromatic compounds are important components of lignin and coal, and are present in most subsurface sediments. Despite the novelty of such a methoxydotrophic archaeon its metabolism has not yet been explored. In this study, transcriptomics and proteomics reveal that under methoxydotrophic growth M. shengliensis expresses an O-demethylation/methyltransferase system related to the one used by acetogenic bacteria. Enzymatic assays provide evidence for a two step-mechanisms in which the methyl-group from the methoxy compound is (1) transferred on cobalamin and (2) further transferred on the C1-carrier tetrahydromethanopterin, a mechanism distinct from conventional methanogenic methyl-transfer systems which use coenzyme M as final acceptor. We further hypothesize that this likely leads to an atypical use of the methanogenesis pathway that derives cellular energy from methyl transfer (Mtr) rather than electron transfer (F420H2 re-oxidation) as found for methylotrophic methanogenesis.},
}
@article {pmid34145390,
year = {2021},
author = {Murali, R and Gennis, RB and Hemp, J},
title = {Evolution of the cytochrome bd oxygen reductase superfamily and the function of CydAA' in Archaea.},
journal = {The ISME journal},
volume = {15},
number = {12},
pages = {3534-3548},
pmid = {34145390},
issn = {1751-7370},
support = {R01 AI148160/AI/NIAID NIH HHS/United States ; },
mesh = {Archaea/enzymology/*genetics ; Archaeal Proteins/*genetics ; Cytochrome b Group/*genetics ; Electron Transport Chain Complex Proteins/*genetics ; Evolution, Molecular ; Oxidation-Reduction ; *Oxidoreductases/genetics ; Oxygen ; },
abstract = {Cytochrome bd-type oxygen reductases (cytbd) belong to one of three enzyme superfamilies that catalyze oxygen reduction to water. They are widely distributed in Bacteria and Archaea, but the full extent of their biochemical diversity is unknown. Here we used phylogenomics to identify three families and several subfamilies within the cytbd superfamily. The core architecture shared by all members of the superfamily consists of four transmembrane helices that bind two active site hemes, which are responsible for oxygen reduction. While previously characterized cytochrome bd-type oxygen reductases use quinol as an electron donor to reduce oxygen, sequence analysis shows that only one of the identified families has a conserved quinol binding site. The other families are missing this feature, suggesting that they use an alternative electron donor. Multiple gene duplication events were identified within the superfamily, resulting in significant evolutionary and structural diversity. The CydAA' cytbd, found exclusively in Archaea, is formed by the co-association of two superfamily paralogs. We heterologously expressed CydAA' from Caldivirga maquilingensis and demonstrated that it performs oxygen reduction with quinol as an electron donor. Strikingly, CydAA' is the first isoform of cytbd containing only b-type hemes shown to be active when isolated from membranes, demonstrating that oxygen reductase activity in this superfamily is not dependent on heme d.},
}
@article {pmid34142100,
year = {2021},
author = {Takemata, N and Bell, SD},
title = {Chromosome conformation capture assay combined with biotin enrichment for hyperthermophilic archaea.},
journal = {STAR protocols},
volume = {2},
number = {2},
pages = {100576},
pmid = {34142100},
issn = {2666-1667},
support = {R01 GM135178/GM/NIGMS NIH HHS/United States ; },
mesh = {Biotin/*metabolism ; *Chromosomes, Archaeal ; Genes, Archaeal ; Sequence Analysis, DNA/methods ; Sulfolobus acidocaldarius/genetics/*metabolism ; },
abstract = {Chromosome organization in archaea has long been enigmatic due, in part, to the typically small cell size of archaea and the extremophilic nature of many of the model archaeal species studies, rendering live-cell imaging technically challenging. To circumvent these problems, we recently applied chromosome conformation capture combined with biotin enrichment and deep sequencing (Hi-C) to members of hyperthermophilic archaeal genus Sulfolobus. Our optimized Hi-C protocol described here permits delineation of how Sulfolobus species organize their chromosomes. For complete details on the use and execution of this protocol, please refer to Takemata et al. (2019).},
}
@article {pmid34140936,
year = {2021},
author = {Castelle, CJ and Méheust, R and Jaffe, AL and Seitz, K and Gong, X and Baker, BJ and Banfield, JF},
title = {Protein Family Content Uncovers Lineage Relationships and Bacterial Pathway Maintenance Mechanisms in DPANN Archaea.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {660052},
pmid = {34140936},
issn = {1664-302X},
abstract = {DPANN are small-celled archaea that are generally predicted to be symbionts, and in some cases are known episymbionts of other archaea. As the monophyly of the DPANN remains uncertain, we hypothesized that proteome content could reveal relationships among DPANN lineages, constrain genetic overlap with bacteria, and illustrate how organisms with hybrid bacterial and archaeal protein sets might function. We tested this hypothesis using protein family content that was defined in part using 3,197 genomes including 569 newly reconstructed genomes. Protein family content clearly separates the final set of 390 DPANN genomes from other archaea, paralleling the separation of Candidate Phyla Radiation (CPR) bacteria from all other bacteria. This separation is partly driven by hypothetical proteins, some of which may be symbiosis-related. Pacearchaeota with the most limited predicted metabolic capacities have Form II/III and III-like Rubisco, suggesting metabolisms based on scavenged nucleotides. Intriguingly, the Pacearchaeota and Woesearchaeota with the smallest genomes also tend to encode large extracellular murein-like lytic transglycosylase domain proteins that may bind and degrade components of bacterial cell walls, indicating that some might be episymbionts of bacteria. The pathway for biosynthesis of bacterial isoprenoids is widespread in Woesearchaeota genomes and is encoded in proximity to genes involved in bacterial fatty acids synthesis. Surprisingly, in some DPANN genomes we identified a pathway for synthesis of queuosine, an unusual nucleotide in tRNAs of bacteria. Other bacterial systems are predicted to be involved in protein refolding. For example, many DPANN have the complete bacterial DnaK-DnaJ-GrpE system and many Woesearchaeota and Pacearchaeota possess bacterial group I chaperones. Thus, many DPANN appear to have mechanisms to ensure efficient protein folding of both archaeal and laterally acquired bacterial proteins.},
}
@article {pmid34138841,
year = {2021},
author = {Schulze, S and Pfeiffer, F and Garcia, BA and Pohlschroder, M},
title = {Comprehensive glycoproteomics shines new light on the complexity and extent of glycosylation in archaea.},
journal = {PLoS biology},
volume = {19},
number = {6},
pages = {e3001277},
pmid = {34138841},
issn = {1545-7885},
support = {P01 CA196539/CA/NCI NIH HHS/United States ; R01 AI118891/AI/NIAID NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Archaeal Proteins/chemistry/*metabolism ; Biological Assay ; Cell Shape/drug effects ; Databases, Protein ; Glycopeptides/chemistry/*metabolism ; Glycoproteins/chemistry/*metabolism ; Glycosylation/drug effects ; Haloferax volcanii/drug effects/*metabolism ; Mutation/genetics ; Phenotype ; Phylogeny ; Proteomics ; Sodium Chloride/pharmacology ; },
abstract = {Glycosylation is one of the most complex posttranslational protein modifications. Its importance has been established not only for eukaryotes but also for a variety of prokaryotic cellular processes, such as biofilm formation, motility, and mating. However, comprehensive glycoproteomic analyses are largely missing in prokaryotes. Here, we extend the phenotypic characterization of N-glycosylation pathway mutants in Haloferax volcanii and provide a detailed glycoproteome for this model archaeon through the mass spectrometric analysis of intact glycopeptides. Using in-depth glycoproteomic datasets generated for the wild-type (WT) and mutant strains as well as a reanalysis of datasets within the Archaeal Proteome Project (ArcPP), we identify the largest archaeal glycoproteome described so far. We further show that different N-glycosylation pathways can modify the same glycosites under the same culture conditions. The extent and complexity of the Hfx. volcanii N-glycoproteome revealed here provide new insights into the roles of N-glycosylation in archaeal cell biology.},
}
@article {pmid34119867,
year = {2021},
author = {Shen, LD and Yang, YL and Liu, JQ and Hu, ZH and Liu, X and Tian, MH and Yang, WT and Jin, JH and Wang, HY and Wang, YY and Wu, HS},
title = {Different responses of ammonia-oxidizing archaea and bacteria in paddy soils to elevated CO2 concentration.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {286},
number = {},
pages = {117558},
doi = {10.1016/j.envpol.2021.117558},
pmid = {34119867},
issn = {1873-6424},
mesh = {*Ammonia ; *Archaea/genetics ; Bacteria/genetics ; Carbon Dioxide ; Ecosystem ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Soil ; Soil Microbiology ; },
abstract = {The elevated atmospheric CO2 concentration is well known to have an important effect on soil nutrient cycling. Ammonia oxidation, mediated by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), is the rate-limiting step in soil nitrification, which controls the availability of two key soil nutrients (ammonium and nitrate) for crops. Until now, how the AOA and AOB communities in paddy soils respond to elevated CO2 remains largely unknown. Here, we examined the communities of AOA and AOB and nitrification potential at both surface (0-5 cm) and subsurface (5-10 cm) soil layers of paddy fields under three different CO2 treatments, including CK (ambient CO2 concentration), LT (CK + 160 ppm of CO2) and HT (CK + 200 ppm of CO2). The elevated CO2 was found to have a greater impact on the community structure of AOB than that of AOA in surface soils as revealed by high-throughput sequencing of their amoA genes. However, no obvious variation of AOA or AOB communities was observed in subsurface soils among different CO2 treatments. The abundance of AOA and AOB, and nitrification potential were significantly increased in surface soils under elevated CO2. The variation of AOB abundance correlated well with the variation of nitrification potential. The soil water content and dissolved organic carbon content had important impacts on the dynamic of AOB communities and nitrification potential. Overall, our results showed different responses of AOA and AOB communities to elevated CO2 in paddy ecosystems, and AOB were more sensitive to the rising CO2 concentration.},
}
@article {pmid34113850,
year = {2021},
author = {Takemata, N and Bell, SD},
title = {High-resolution analysis of chromosome conformation in hyperthermophilic archaea.},
journal = {STAR protocols},
volume = {2},
number = {2},
pages = {100562},
pmid = {34113850},
issn = {2666-1667},
support = {R01 GM135178/GM/NIGMS NIH HHS/United States ; },
mesh = {*Chromosomes ; DNA, Archaeal/genetics ; High-Throughput Nucleotide Sequencing/methods ; Polymerase Chain Reaction/methods ; Sulfolobus/*genetics ; },
abstract = {Chromosome conformation capture (3C) techniques are emerging as promising approaches to study genome organization in Archaea, the least understood domain of life in terms of chromosome biology. Here, we describe a 3C technique combined with deep sequencing for the hyperthermophilic archaeal genus Sulfolobus. Instead of using restriction enzymes compatible with fill-in labeling, this protocol uses the 4-bp blunt cutter AluI to generate high-resolution (up to 2 kb) contact maps from Sulfolobus species. For complete details on the use and execution of this protocol, please refer to Takemata and Bell (2021).},
}
@article {pmid34113328,
year = {2021},
author = {Garnier, F and Couturier, M and Débat, H and Nadal, M},
title = {Archaea: A Gold Mine for Topoisomerase Diversity.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {661411},
pmid = {34113328},
issn = {1664-302X},
abstract = {The control of DNA topology is a prerequisite for all the DNA transactions such as DNA replication, repair, recombination, and transcription. This global control is carried out by essential enzymes, named DNA-topoisomerases, that are mandatory for the genome stability. Since many decades, the Archaea provide a significant panel of new types of topoisomerases such as the reverse gyrase, the type IIB or the type IC. These more or less recent discoveries largely contributed to change the understanding of the role of the DNA topoisomerases in all the living world. Despite their very different life styles, Archaea share a quasi-homogeneous set of DNA-topoisomerases, except thermophilic organisms that possess at least one reverse gyrase that is considered a marker of the thermophily. Here, we discuss the effect of the life style of Archaea on DNA structure and topology and then we review the content of these essential enzymes within all the archaeal diversity based on complete sequenced genomes available. Finally, we discuss their roles, in particular in the processes involved in both the archaeal adaptation and the preservation of the genome stability.},
}
@article {pmid34112969,
year = {2021},
author = {Payne, D and Spietz, RL and Boyd, ES},
title = {Reductive dissolution of pyrite by methanogenic archaea.},
journal = {The ISME journal},
volume = {15},
number = {12},
pages = {3498-3507},
pmid = {34112969},
issn = {1751-7370},
mesh = {*Archaea/genetics ; Iron ; Solubility ; *Sulfides ; },
abstract = {The formation and fate of pyrite (FeS2) modulates global iron, sulfur, carbon, and oxygen biogeochemical cycles and has done so since early in Earth's geological history. A longstanding paradigm is that FeS2 is stable at low temperature and is unavailable to microorganisms in the absence of oxygen and oxidative weathering. Here, we show that methanogens can catalyze the reductive dissolution of FeS2 at low temperature (≤38 °C) and utilize dissolution products to meet cellular iron and sulfur demands associated with the biosynthesis of simple and complex co-factors. Direct access to FeS2 is required to catalyze its reduction and/or to assimilate iron monosulfide that likely forms through coupled reductive dissolution and precipitation, consistent with close associations observed between cells and FeS2. These findings demonstrate that FeS2 is bioavailable to anaerobic methanogens and can be mobilized in low temperature anoxic environments. Given that methanogens evolved at least 3.46 Gya, these data indicate that the microbial contribution to the iron and sulfur cycles in ancient and contemporary anoxic environments may be more complex and robust than previously recognized, with impacts on the sources and sinks of iron and sulfur and other bio-essential and thiophilic elements such as nickel and cobalt.},
}
@article {pmid34099860,
year = {2021},
author = {Watanabe, S and Murase, Y and Watanabe, Y and Sakurai, Y and Tajima, K},
title = {Crystal structures of aconitase X enzymes from bacteria and archaea provide insights into the molecular evolution of the aconitase superfamily.},
journal = {Communications biology},
volume = {4},
number = {1},
pages = {687},
pmid = {34099860},
issn = {2399-3642},
mesh = {Aconitate Hydratase/*chemistry ; Agrobacterium tumefaciens/chemistry/*enzymology ; Catalytic Domain ; Crystallography, X-Ray ; Evolution, Molecular ; Models, Molecular ; Protein Conformation ; Thermococcus/chemistry/*enzymology ; },
abstract = {Aconitase superfamily members catalyze the homologous isomerization of specific substrates by sequential dehydration and hydration and contain a [4Fe-4S] cluster. However, monomeric and heterodimeric types of function unknown aconitase X (AcnX) have recently been characterized as a cis-3-hydroxy-L-proline dehydratase (AcnXType-I) and mevalonate 5-phosphate dehydratase (AcnXType-II), respectively. We herein elucidated the crystal structures of AcnXType-I from Agrobacterium tumefaciens (AtAcnX) and AcnXType-II from Thermococcus kodakarensis (TkAcnX) without a ligand and in complex with substrates. AtAcnX and TkAcnX contained the [2Fe-2S] and [3Fe-4S] clusters, respectively, conforming to UV and EPR spectroscopy analyses. The binding sites of the [Fe-S] cluster and substrate were clearlydifferent from those that were completely conserved in other aconitase enzymes; however, theoverall structural frameworks and locations of active sites were partially similar to each other.These results provide novel insights into the evolutionary scenario of the aconitase superfamilybased on the recruitment hypothesis.},
}
@article {pmid34088904,
year = {2021},
author = {Pende, N and Sogues, A and Megrian, D and Sartori-Rupp, A and England, P and Palabikyan, H and Rittmann, SKR and Graña, M and Wehenkel, AM and Alzari, PM and Gribaldo, S},
title = {SepF is the FtsZ anchor in archaea, with features of an ancestral cell division system.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {3214},
pmid = {34088904},
issn = {2041-1723},
mesh = {Archaeal Proteins/chemistry/genetics/*metabolism ; Bacterial Proteins/chemistry/genetics/metabolism ; Cell Cycle ; Cell Division/genetics/*physiology ; Conserved Sequence ; Crystallography, X-Ray ; Evolution, Molecular ; Methanobrevibacter/genetics/*metabolism/ultrastructure ; Microscopy, Electron, Transmission ; Models, Molecular ; Phylogeny ; Protein Binding ; Protein Interaction Domains and Motifs ; Protein Structure, Quaternary ; Recombinant Proteins/genetics/metabolism/ultrastructure ; },
abstract = {Most archaea divide by binary fission using an FtsZ-based system similar to that of bacteria, but they lack many of the divisome components described in model bacterial organisms. Notably, among the multiple factors that tether FtsZ to the membrane during bacterial cell constriction, archaea only possess SepF-like homologs. Here, we combine structural, cellular, and evolutionary analyses to demonstrate that SepF is the FtsZ anchor in the human-associated archaeon Methanobrevibacter smithii. 3D super-resolution microscopy and quantitative analysis of immunolabeled cells show that SepF transiently co-localizes with FtsZ at the septum and possibly primes the future division plane. M. smithii SepF binds to membranes and to FtsZ, inducing filament bundling. High-resolution crystal structures of archaeal SepF alone and in complex with the FtsZ C-terminal domain (FtsZCTD) reveal that SepF forms a dimer with a homodimerization interface driving a binding mode that is different from that previously reported in bacteria. Phylogenetic analyses of SepF and FtsZ from bacteria and archaea indicate that the two proteins may date back to the Last Universal Common Ancestor (LUCA), and we speculate that the archaeal mode of SepF/FtsZ interaction might reflect an ancestral feature. Our results provide insights into the mechanisms of archaeal cell division and pave the way for a better understanding of the processes underlying the divide between the two prokaryotic domains.},
}
@article {pmid34065163,
year = {2021},
author = {Vázquez-Madrigal, AS and Barbachano-Torres, A and Arellano-Plaza, M and Kirchmayr, MR and Finore, I and Poli, A and Nicolaus, B and De la Torre Zavala, S and Camacho-Ruiz, RM},
title = {Effect of Carbon Sources in Carotenoid Production from Haloarcula sp. M1, Halolamina sp. M3 and Halorubrum sp. M5, Halophilic Archaea Isolated from Sonora Saltern, Mexico.},
journal = {Microorganisms},
volume = {9},
number = {5},
pages = {},
pmid = {34065163},
issn = {2076-2607},
abstract = {The isolation and molecular and chemo-taxonomic identification of seventeen halophilic archaea from the Santa Bárbara saltern, Sonora, México, were performed. Eight strains were selected based on pigmentation. Molecular identification revealed that the strains belonged to the Haloarcula, Halolamina and Halorubrum genera. Neutral lipids (quinones) were identified in all strains. Glycolipid S-DGD was found only in Halolamina sp. strain M3; polar phospholipids 2,3-O-phytanyl-sn-glycerol-1-phosphoryl-3-sn-glycerol (PG), 2,3-di-O-phytanyl-sn-glycero-1-phospho-3'-sn-glycerol-1'-methyl phosphate (PGP-Me) and sodium salt 1-(3-sn-phosphatidyl)-rac-glycerol were found in all the strains; and one unidentified glyco-phospholipid in strains M1, M3 and M4. Strains M1, M3 and M5 were selected for further studies based on carotenoid production. The effect of glucose and succinic and glutamic acid on carotenoid production was assessed. In particular, carotenoid production and growth significantly improved in the presence of glucose in strains Haloarcula sp. M1 and Halorubrum sp. M5 but not in Halolamina sp. M3. Glutamic and succinic acid had no effect on carotenoid production, and even was negative for Halorubrum sp. M5. Growth was increased by glutamic and succinic acid on Haloarcula sp. M1 but not in the other strains. This work describes for first time the presence of halophilic archaea in the Santa Bárbara saltern and highlights the differences in the effect of carbon sources on the growth and carotenoid production of haloarchaea.},
}
@article {pmid34060911,
year = {2021},
author = {McNichol, J and Berube, PM and Biller, SJ and Fuhrman, JA},
title = {Evaluating and Improving Small Subunit rRNA PCR Primer Coverage for Bacteria, Archaea, and Eukaryotes Using Metagenomes from Global Ocean Surveys.},
journal = {mSystems},
volume = {6},
number = {3},
pages = {e0056521},
pmid = {34060911},
issn = {2379-5077},
support = {3779//Gordon and Betty Moore Foundation (GBMF)/ ; OCE-1737409//National Science Foundation (NSF)/ ; 549943//Simons Foundation (SF)/ ; },
abstract = {Small subunit rRNA (SSU rRNA) amplicon sequencing can quantitatively and comprehensively profile natural microbiomes, representing a critically important tool for studying diverse global ecosystems. However, results will only be accurate if PCR primers perfectly match the rRNA of all organisms present. To evaluate how well marine microorganisms across all 3 domains are detected by this method, we compared commonly used primers with >300 million rRNA gene sequences retrieved from globally distributed marine metagenomes. The best-performing primers compared to 16S rRNA of bacteria and archaea were 515Y/926R and 515Y/806RB, which perfectly matched over 96% of all sequences. Considering cyanobacterial and chloroplast 16S rRNA, 515Y/926R had the highest coverage (99%), making this set ideal for quantifying marine primary producers. For eukaryotic 18S rRNA sequences, 515Y/926R also performed best (88%), followed by V4R/V4RB (18S rRNA specific; 82%)-demonstrating that the 515Y/926R combination performs best overall for all 3 domains. Using Atlantic and Pacific Ocean samples, we demonstrate high correspondence between 515Y/926R amplicon abundances (generated for this study) and metagenomic 16S rRNA (median R2 = 0.98, n = 272), indicating amplicons can produce equally accurate community composition data compared with shotgun metagenomics. Our analysis also revealed that expected performance of all primer sets could be improved with minor modifications, pointing toward a nearly completely universal primer set that could accurately quantify biogeochemically important taxa in ecosystems ranging from the deep sea to the surface. In addition, our reproducible bioinformatic workflow can guide microbiome researchers studying different ecosystems or human health to similarly improve existing primers and generate more accurate quantitative amplicon data. IMPORTANCE PCR amplification and sequencing of marker genes is a low-cost technique for monitoring prokaryotic and eukaryotic microbial communities across space and time but will work optimally only if environmental organisms match PCR primer sequences exactly. In this study, we evaluated how well primers match globally distributed short-read oceanic metagenomes. Our results demonstrate that primer sets vary widely in performance, and that at least for marine systems, rRNA amplicon data from some primers lack significant biases compared to metagenomes. We also show that it is theoretically possible to create a nearly universal primer set for diverse saline environments by defining a specific mixture of a few dozen oligonucleotides, and present a software pipeline that can guide rational design of primers for any environment with available meta'omic data.},
}
@article {pmid34027477,
year = {2021},
author = {Cockram, C and Thierry, A and Koszul, R},
title = {Generation of gene-level resolution chromosome contact maps in bacteria and archaea.},
journal = {STAR protocols},
volume = {2},
number = {2},
pages = {100512},
pmid = {34027477},
issn = {2666-1667},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Chromosome Mapping ; Chromosomes, Archaeal/*genetics ; Chromosomes, Bacterial/*genetics ; Genome, Archaeal ; Genome, Bacterial ; },
abstract = {Chromosome conformation capture (Hi-C) has become a routine method for probing the 3D organization of genomes. However, when applied to bacteria and archaea, current protocols are expensive and limited in their resolution. By dissecting the different steps of published eukaryotic and prokaryotic Hi-C protocols, we have developed a cost- and time-effective approach to generate high-resolution (down to 500 bp - 1 kb) contact matrices of both bacteria and archaea genomes. For complete details on the use and execution of this protocol, please refer to Cockram et al. (2020).},
}
@article {pmid34027378,
year = {2021},
author = {Inkinen, J and Siponen, S and Jayaprakash, B and Tiwari, A and Hokajärvi, AM and Pursiainen, A and Ikonen, J and Kauppinen, A and Miettinen, IT and Paananen, J and Torvinen, E and Kolehmainen, M and Pitkänen, T},
title = {Diverse and active archaea communities occur in non-disinfected drinking water systems-Less activity revealed in disinfected and hot water systems.},
journal = {Water research X},
volume = {12},
number = {},
pages = {100101},
pmid = {34027378},
issn = {2589-9147},
abstract = {The knowledge about the members of active archaea communities in DWDS is limited. The current understanding is based on high-throughput 16S ribosomal RNA gene (DNA-based) amplicon sequencing that reveals the diversity of active, dormant, and dead members of the prokaryote (bacteria, archaea) communities. The sequencing primers optimized for bacteria community analysis may underestimate the share of the archaea community. This study characterized archaea communities at five full-scale drinking water distribution systems (DWDS), representing a variety of drinking water production units (A-E); A&amp;B use artificially recharged non-disinfected groundwater (ARG), the other DWDS's supplied water disinfected by using ultraviolet (UV) light and chlorine compounds, C&amp;D were surface waterworks and E was a ground waterworks. For the first time for archaea community analyses, this study employed the archaea-specific high-throughput sequencing primers for 16S ribosomal RNA (rRNA) as a target (reverse-transcribed cDNA; an RNA-based approach) in addition to the previously used 16S rRNA gene target (rDNA; a DNA-based approach) to reveal the active fraction of the archaea present in DWDS. The archaea community structure in varying environmental conditions in the water and biofilm of the five DWDSs were investigated by taking into consideration the system properties (cold or hot water system) and water age (distance from the treatment plants) in samples from each season of one year. The RNA-based archaea amplicon reads were obtained mostly from cold water samples from DWDSs (A-B) distributing water without disinfection where the DNA-based and RNA-based analysis created separate clusters in a weighted beta-diversity analysis. The season and location in DWDS A further affected the diversity of these archaea communities as was seen by different clusters in beta-diversity plots. The recovery of archaea reads was not adequate for analysis in any of the disinfected samples in DWDSs C-E or non-disinfected hot water in DWDSs A-B when utilizing RNA-based template. The metabolically active archaea community of DWDSs thus seemed to be effectively controlled by disinfection of water and in the hot water systems by the temperature. All biofilms regardless of DWDS showed lower species richness values (mainly Nitrososphaeria class) than non-disinfected water from DWDSs A-B where several archaea classes occurred (e.g. Woesearchaeia, Nitrososphaeria, Micrarchaeia, Methanomicrobia, Iairchaeia, Bathyarchaeia) indicating only part of the archaea members were able to survive in biofilms. Thus, Archaea has been shown as a significant part of normal DWDS biota, and their role especially in non-disinfected DWDS may be more important than previously considered.},
}
@article {pmid34026962,
year = {2020},
author = {Bomberg, M and Miettinen, H},
title = {Data on the optimization of an archaea-specific probe-based qPCR assay.},
journal = {Data in brief},
volume = {33},
number = {},
pages = {106610},
pmid = {34026962},
issn = {2352-3409},
abstract = {Estimation of archaeal numbers by use of fluorescent DNA binding dyes is challenging, because primers targeting the archaeal 16SrRNA genes readily also bind to bacterial 16S rRNA gene sequences, especially when the relative abundance of bacteria is greater than that of archaea. In order to increase specificity, we optimized a fluorescent probe-based assay using previously published archaeal primers and probe. The assay was tested on genomic DNA of pure bacterial and archaeal cultures and optimized using PCR amplicons of the archaeal pure cultures. The used bacterial strains showed slight amplification using the fluorescent dye assay, whereas all archaeal strains could be amplified with the archaea primers used. Due to differences in genome size and number of 16S rRNA gene copies between the tested archaeal strains, the amplification level varied greatly between the strains. Therefore, we also tested the amplification using PCR amplified fragments of the archaeal 16S rRNA genes. The tests with the archaeal 16S rRNA gene amplicons showed good amplification, although the amplification efficiency still varied between archaeal strains. The qPCR assay was used to estimate the archaeal numbers in process water of a multi-metal mine's metallurgical plant [1] and will be used in similar future microbiological analysis included in the H2020 ITERAMS project (Grant agreement# 730480).},
}
@article {pmid34026831,
year = {2021},
author = {Lei, L and Burton, ZF},
title = {Early Evolution of Transcription Systems and Divergence of Archaea and Bacteria.},
journal = {Frontiers in molecular biosciences},
volume = {8},
number = {},
pages = {651134},
pmid = {34026831},
issn = {2296-889X},
abstract = {DNA template-dependent multi-subunit RNA polymerases (RNAPs) found in all three domains of life and some viruses are of the two-double-Ψ-β-barrel (DPBB) type. The 2-DPBB protein format is also found in some RNA template-dependent RNAPs and a major replicative DNA template-dependent DNA polymerase (DNAP) from Archaea (PolD). The 2-DPBB family of RNAPs and DNAPs probably evolved prior to the last universal common cellular ancestor (LUCA). Archaeal Transcription Factor B (TFB) and bacterial σ factors include homologous strings of helix-turn-helix units. The consequences of TFB-σ homology are discussed in terms of the evolution of archaeal and bacterial core promoters. Domain-specific DPBB loop inserts functionally connect general transcription factors to the RNAP active site. Archaea appear to be more similar to LUCA than Bacteria. Evolution of bacterial σ factors from TFB appears to have driven divergence of Bacteria from Archaea, splitting the prokaryotic domains.},
}
@article {pmid34019119,
year = {2021},
author = {Naitam, MG and Kaushik, R},
title = {Archaea: An Agro-Ecological Perspective.},
journal = {Current microbiology},
volume = {78},
number = {7},
pages = {2510-2521},
pmid = {34019119},
issn = {1432-0991},
support = {BT/PR6540/BCE/8/917/2012//Department of Biotechnology , Ministry of Science and Technology/ ; },
mesh = {*Archaea/genetics ; Bacteria/genetics ; Fungi/genetics ; Rhizosphere ; Soil ; *Soil Microbiology ; },
abstract = {Microorganisms inhabiting bulk soil and rhizosphere play an important role in soil biogeochemical cycles leading to enhanced plant growth and productivity. In this context, the role of bacteria is well established, however, not much reports are available about the role archaea plays in this regard. Literature suggests that archaea also play a greater role in nutrient cycling of carbon, nitrogen, sulfur, and other minerals, possess various plant growth promoting attributes, and can impart tolerance to various abiotic stresses (especially osmotic and oxidative) in areas of high salinity, low and high temperatures and hydrogen ion concentrations. Thermoacidophilic archaea have been found to potentially involve in bioleaching of mineral ores and bioremediation of chemical pollutants and aromatic compounds. Looking at immense potential of archaea in promoting plant growth, alleviating abiotic stresses, and remediating contaminated sites, detailed studies are required to establish their role in different ecological processes, and their interactions in rhizosphere with plant and other microflora (bacteria and fungi) in different ecosystems. In this review, a brief discussion on archaea from the agro-ecological point of view is presented.},
}
@article {pmid34017110,
year = {2021},
author = {Graham, F},
title = {Daily briefing: Enigmatic archaea might be key to complex life.},
journal = {Nature},
volume = {},
number = {},
pages = {},
doi = {10.1038/d41586-021-01366-4},
pmid = {34017110},
issn = {1476-4687},
}
@article {pmid33997611,
year = {2021},
author = {Clemmons, BA and Schneider, LG and Melchior, EA and Lindholm-Perry, AK and Hales, KE and Wells, JE and Freetly, HC and Hansen, SL and Drewnoski, ME and Hartman, SJ and Myer, PR},
title = {The effects of feeding ferric citrate on ruminal bacteria, methanogenic archaea and methane production in growing beef steers.},
journal = {Access microbiology},
volume = {3},
number = {1},
pages = {acmi000180},
pmid = {33997611},
issn = {2516-8290},
abstract = {Methane produced by cattle is one of the contributors of anthropogenic greenhouse gas. Methods to lessen methane emissions from cattle have been met with varying success; thus establishing consistent methods for decreasing methane production are imperative. Ferric iron may possibly act to decrease methane by acting as an alternative electron acceptor. The objective of this study was to assess the effect of ferric citrate on the rumen bacterial and archaeal communities and its impact on methane production. In this study, eight steers were used in a repeated Latin square design with 0, 250, 500 or 750 mg Fe/kg DM of ferric iron (as ferric citrate) in four different periods. Each period consisted of a 16 day adaptation period and 5 day sampling period. During each sampling period, methane production was measured, and rumen content was collected for bacterial and archaeal community analyses. Normally distributed data were analysed using a mixed model ANOVA using the GLIMMIX procedure of SAS, and non-normally distributed data were analysed in the same manner following ranking. Ferric citrate did not have any effect on bacterial community composition, methanogenic archaea nor methane production (P>0.05). Ferric citrate may not be a viable option to observe a ruminal response for decreases in enteric methane production.},
}
@article {pmid33995325,
year = {2021},
author = {Weixlbaumer, A and Grünberger, F and Werner, F and Grohmann, D},
title = {Coupling of Transcription and Translation in Archaea: Cues From the Bacterial World.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {661827},
pmid = {33995325},
issn = {1664-302X},
abstract = {The lack of a nucleus is the defining cellular feature of bacteria and archaea. Consequently, transcription and translation are occurring in the same compartment, proceed simultaneously and likely in a coupled fashion. Recent cryo-electron microscopy (cryo-EM) and tomography data, also combined with crosslinking-mass spectrometry experiments, have uncovered detailed structural features of the coupling between a transcribing bacterial RNA polymerase (RNAP) and the trailing translating ribosome in Escherichia coli and Mycoplasma pneumoniae. Formation of this supercomplex, called expressome, is mediated by physical interactions between the RNAP-bound transcription elongation factors NusG and/or NusA and the ribosomal proteins including uS10. Based on the structural conservation of the RNAP core enzyme, the ribosome, and the universally conserved elongation factors Spt5 (NusG) and NusA, we discuss requirements and functional implications of transcription-translation coupling in archaea. We furthermore consider additional RNA-mediated and co-transcriptional processes that potentially influence expressome formation in archaea.},
}
@article {pmid33993308,
year = {2021},
author = {Yang, Y and Zhang, C and Lenton, TM and Yan, X and Zhu, M and Zhou, M and Tao, J and Phelps, TJ and Cao, Z},
title = {The Evolution Pathway of Ammonia-Oxidizing Archaea Shaped by Major Geological Events.},
journal = {Molecular biology and evolution},
volume = {38},
number = {9},
pages = {3637-3648},
doi = {10.1093/molbev/msab129},
pmid = {33993308},
issn = {1537-1719},
mesh = {*Ammonia/metabolism ; *Archaea/genetics/metabolism ; Bacteria/genetics ; Oxidation-Reduction ; Soil Microbiology ; },
abstract = {Primordial nitrification processes have been studied extensively using geochemical approaches, but the biological origination of nitrification remains unclear. Ammonia-oxidizing archaea (AOA) are widely distributed nitrifiers and implement the rate-limiting step in nitrification. They are hypothesized to have been important players in the global nitrogen cycle in Earth's early history. We performed systematic phylogenomic and marker gene analyses to elucidate the diversification timeline of AOA evolution. Our results suggested that the AOA ancestor experienced terrestrial geothermal environments at ∼1,165 Ma (1,928-880 Ma), and gradually evolved into mesophilic soil at ∼652 Ma (767-554 Ma) before diversifying into marine settings at ∼509 Ma (629-412 Ma) and later into shallow and deep oceans, respectively. Corroborated by geochemical evidence and modeling, the timing of key diversification nodes can be linked to the global magmatism and glaciation associated with the assembly and breakup of the supercontinent Rodinia, and the later oxygenation of the deep ocean. Results of this integrated study shed light on the geological forces that may have shaped the evolutionary pathways of the AOA, which played an important role in the ancient global nitrogen cycle.},
}
@article {pmid33976787,
year = {2021},
author = {Westoby, M and Nielsen, DA and Gillings, MR and Litchman, E and Madin, JS and Paulsen, IT and Tetu, SG},
title = {Cell size, genome size, and maximum growth rate are near-independent dimensions of ecological variation across bacteria and archaea.},
journal = {Ecology and evolution},
volume = {11},
number = {9},
pages = {3956-3976},
pmid = {33976787},
issn = {2045-7758},
abstract = {Among bacteria and archaea, maximum relative growth rate, cell diameter, and genome size are widely regarded as important influences on ecological strategy. Via the most extensive data compilation so far for these traits across all clades and habitats, we ask whether they are correlated and if so how. Overall, we found little correlation among them, indicating they should be considered as independent dimensions of ecological variation. Nor was correlation evident within particular habitat types. A weak nonlinearity (6% of variance) was found whereby high maximum growth rates (temperature-adjusted) tended to occur in the midrange of cell diameters. Species identified in the literature as oligotrophs or copiotrophs were clearly separated on the dimension of maximum growth rate, but not on the dimensions of genome size or cell diameter.},
}
@article {pmid33941062,
year = {2021},
author = {Mikhaylina, AO and Nikonova, EY and Kostareva, OS and Piendl, W and Erlacher, M and Tishchenko, SV},
title = {Characterization of Regulatory Elements of L11 and L1 Operons in Thermophilic Bacteria and Archaea.},
journal = {Biochemistry. Biokhimiia},
volume = {86},
number = {4},
pages = {397-408},
doi = {10.1134/S0006297921040027},
pmid = {33941062},
issn = {1608-3040},
support = {P 30486/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Gene Expression Regulation, Archaeal ; Gene Expression Regulation, Bacterial ; Haloarcula marismortui/*genetics/metabolism ; Hot Temperature ; Operon/*genetics ; *Regulatory Sequences, Nucleic Acid ; Ribosomal Proteins/*genetics ; Thermotoga maritima/*genetics/metabolism ; Thermus thermophilus/*genetics/metabolism ; },
abstract = {Ribosomal protein L1 is a conserved two-domain protein that is involved in formation of the L1 stalk of the large ribosomal subunit. When there are no free binding sites available on the ribosomal 23S RNA, the protein binds to the specific site on the mRNA of its own operon (L11 operon in bacteria and L1 operon in archaea) preventing translation. Here we show that the regulatory properties of the r-protein L1 and its domain I are conserved in the thermophilic bacteria Thermus and Thermotoga and in the halophilic archaeon Haloarcula marismortui. At the same time the revealed features of the operon regulation in thermophilic bacteria suggest presence of two regulatory regions.},
}
@article {pmid33935987,
year = {2021},
author = {Schnakenberg, A and Aromokeye, DA and Kulkarni, A and Maier, L and Wunder, LC and Richter-Heitmann, T and Pape, T and Ristova, PP and Bühring, SI and Dohrmann, I and Bohrmann, G and Kasten, S and Friedrich, MW},
title = {Electron Acceptor Availability Shapes Anaerobically Methane Oxidizing Archaea (ANME) Communities in South Georgia Sediments.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {617280},
pmid = {33935987},
issn = {1664-302X},
abstract = {Anaerobic methane oxidizing archaea (ANME) mediate anaerobic oxidation of methane (AOM) in marine sediments and are therefore important for controlling atmospheric methane concentrations in the water column and ultimately the atmosphere. Numerous previous studies have revealed that AOM is coupled to the reduction of different electron acceptors such as sulfate, nitrate/nitrite or Fe(III)/Mn(IV). However, the influence of electron acceptor availability on the in situ ANME community composition in sediments remains largely unknown. Here, we investigated the electron acceptor availability and compared the microbial in situ communities of three methane-rich locations offshore the sub-Antarctic island South Georgia, by Illumina sequencing and qPCR of mcrA genes. The methanic zone (MZ) sediments of Royal Trough and Church Trough comprised high sulfide concentrations of up to 4 and 19 mM, respectively. In contrast, those of the Cumberland Bay fjord accounted for relatively high concentrations of dissolved iron (up to 186 μM). Whereas the ANME community in the sulfidic sites Church Trough and Royal Trough mainly comprised members of the ANME-1 clade, the order-level clade "ANME-1-related" (Lever and Teske, 2015) was most abundant in the iron-rich site in Cumberland Bay fjord, indicating that the availability of electron acceptors has a strong selective effect on the ANME community. This study shows that potential electron acceptors for methane oxidation may serve as environmental filters to select for the ANME community composition and adds to a better understanding of the global importance of AOM.},
}
@article {pmid33911286,
year = {2021},
author = {Liu, Y and Makarova, KS and Huang, WC and Wolf, YI and Nikolskaya, AN and Zhang, X and Cai, M and Zhang, CJ and Xu, W and Luo, Z and Cheng, L and Koonin, EV and Li, M},
title = {Expanded diversity of Asgard archaea and their relationships with eukaryotes.},
journal = {Nature},
volume = {593},
number = {7860},
pages = {553-557},
pmid = {33911286},
issn = {1476-4687},
mesh = {Archaea/*classification ; Biological Evolution ; Eukaryota ; *Genome, Archaeal ; Metagenomics ; *Phylogeny ; },
abstract = {Asgard is a recently discovered superphylum of archaea that appears to include the closest archaeal relatives of eukaryotes1-5. Debate continues as to whether the archaeal ancestor of eukaryotes belongs within the Asgard superphylum or whether this ancestor is a sister group to all other archaea (that is, a two-domain versus a three-domain tree of life)6-8. Here we present a comparative analysis of 162 complete or nearly complete genomes of Asgard archaea, including 75 metagenome-assembled genomes that-to our knowledge-have not previously been reported. Our results substantially expand the phylogenetic diversity of Asgard and lead us to propose six additional phyla that include a deep branch that we have provisionally named Wukongarchaeota. Our phylogenomic analysis does not resolve unequivocally the evolutionary relationship between eukaryotes and Asgard archaea, but instead-depending on the choice of species and conserved genes used to build the phylogeny-supports either the origin of eukaryotes from within Asgard (as a sister group to the expanded Heimdallarchaeota-Wukongarchaeota branch) or a deeper branch for the eukaryote ancestor within archaea. Our comprehensive protein domain analysis using the 162 Asgard genomes results in a major expansion of the set of eukaryotic signature proteins. The Asgard eukaryotic signature proteins show variable phyletic distributions and domain architectures, which is suggestive of dynamic evolution through horizontal gene transfer, gene loss, gene duplication and domain shuffling. The phylogenomics of the Asgard archaea points to the accumulation of the components of the mobile archaeal 'eukaryome' in the archaeal ancestor of eukaryotes (within or outside Asgard) through extensive horizontal gene transfer.},
}
@article {pmid33907062,
year = {2021},
author = {Kitamura, R and Kozaki, T and Ishii, K and Iigo, M and Kurokura, T and Yamane, K and Maeda, I and Iwabuchi, K and Saito, T},
title = {Utilizing Cattle Manure Compost Increases Ammonia Monooxygenase A Gene Expression and Ammonia-oxidizing Activity of Both Bacteria and Archaea in Biofiltration Media for Ammonia Deodorization.},
journal = {Microbes and environments},
volume = {36},
number = {2},
pages = {},
pmid = {33907062},
issn = {1347-4405},
mesh = {Ammonia/metabolism ; Animals ; Archaea/classification/*enzymology/genetics/metabolism ; Archaeal Proteins/genetics/*metabolism ; Bacteria/classification/*enzymology/genetics/metabolism ; Bacterial Proteins/genetics/*metabolism ; Cattle ; Composting ; Filtration ; Manure/analysis/*microbiology ; Oxidation-Reduction ; Oxidoreductases/genetics/*metabolism ; Phylogeny ; },
abstract = {Malodorous emissions are a crucial and inevitable issue during the decomposition of biological waste and contain a high concentration of ammonia. Biofiltration technology is a feasible, low-cost, energy-saving method that reduces and eliminates malodors without environmental impact. In the present study, we evaluated the effectiveness of compost from cattle manure and food waste as deodorizing media based on their removal of ammonia and the expression of ammonia-oxidizing genes, and identified the bacterial and archaeal communities in these media. Ammonia was removed by cattle manure compost, but not by food waste compost. The next-generation sequencing of 16S ribosomal RNA obtained from cattle manure compost revealed the presence of ammonia-oxidizing bacteria (AOB), including Cytophagia, Alphaproteobacteria, and Gammaproteobacteria, and ammonia-oxidizing archaea (AOA), such as Thaumarchaeota. In cattle manure compost, the bacterial and archaeal ammonia monooxygenase A (amoA) genes were both up-regulated after exposure to ammonia (fold ratio of 14.2±11.8 after/before), and the bacterial and archaeal communities were more homologous after than before exposure to ammonia, which indicates the adaptation of these communities to ammonia. These results suggest the potential of cattle manure compost as an efficient biological deodorization medium due to the activation of ammonia-oxidizing microbes, such as AOB and AOA, and the up-regulation of their amoA genes.},
}
@article {pmid33901216,
year = {2021},
author = {Płaza, G and Jałowiecki, Ł and Głowacka, D and Hubeny, J and Harnisz, M and Korzeniewska, E},
title = {Insights into the microbial diversity and structure in a full-scale municipal wastewater treatment plant with particular regard to Archaea.},
journal = {PloS one},
volume = {16},
number = {4},
pages = {e0250514},
pmid = {33901216},
issn = {1932-6203},
mesh = {Archaea/*isolation &amp; purification ; Bacteria/isolation &amp; purification ; *Biodiversity ; Cities ; *Microbiota ; Phylogeny ; Principal Component Analysis ; *Water Purification ; },
abstract = {Due to limited description of the role and diversity of archaea in WWTPs, the aim of the study was to analyze microbial community structures and diversities with particular regard to Archaea in the samples taken from different stages of the full-scale municipal wastewater treatment plant and effluent receiving water (upstream and downstream discharge point). Our study was focused on showing how the treatment processes influenced the Eubacteria and Archaea composition. Alpha and Beta diversity were used to evaluate the microbial diversity changes in the collected samples. Proteobacteria was the largest fraction ranging from 28% to 67% with 56% relative abundance across all samples. Archaea were present in all stages of WWTP ranged from 1 to 8%. Among the Archaea, two groups of methanogens, acetoclastic (Methanosarcina, Methanosaeta) and hydrogenotrophic methanogens (Methanospirillium, Methanoculleus, Methanobrevibacter) were dominant in the technological stages. The obtained results indicate that the treated wastewater did not significantly affect eubacterial and archaeal composition in receiving water. However, differences in richness, diversity and microbial composition of Eubacteria and Archaea between the wastewater samples taken from the primary and secondary treatment were observed.},
}
@article {pmid33896087,
year = {2021},
author = {Westoby, M and Gillings, MR and Madin, JS and Nielsen, DA and Paulsen, IT and Tetu, SG},
title = {Trait dimensions in bacteria and archaea compared to vascular plants.},
journal = {Ecology letters},
volume = {24},
number = {7},
pages = {1487-1504},
doi = {10.1111/ele.13742},
pmid = {33896087},
issn = {1461-0248},
support = {//Macquarie U/ ; //Australian Research Council/ ; },
mesh = {*Archaea/genetics ; Bacteria/genetics ; *Ecology ; Phenotype ; Plants ; },
abstract = {Bacteria and archaea have very different ecology compared to plants. One similarity, though, is that much discussion of their ecological strategies has invoked concepts such as oligotrophy or stress tolerance. For plants, so-called 'trait ecology'-strategy description reframed along measurable trait dimensions-has made global syntheses possible. Among widely measured trait dimensions for bacteria and archaea three main axes are evident. Maximum growth rate in association with rRNA operon copy number expresses a rate-yield trade-off that is analogous to the acquisitive-conservative spectrum in plants, though underpinned by different trade-offs. Genome size in association with signal transduction expresses versatility. Cell size has influence on diffusive uptake and on relative wall costs. These trait dimensions, and potentially others, offer promise for interpreting ecology. At the same time, there are very substantial differences from plant trait ecology. Traits and their underpinning trade-offs are different. Also, bacteria and archaea use a variety of different substrates. Bacterial strategies can be viewed both through the facet of substrate-use pathways, and also through the facet of quantitative traits such as maximum growth rate. Preliminary evidence shows the quantitative traits vary widely within substrate-use pathways. This indicates they convey information complementary to substrate use.},
}
@article {pmid33892429,
year = {2021},
author = {Thema, M and Weidlich, T and Kaul, A and Böllmann, A and Huber, H and Bellack, A and Karl, J and Sterner, M},
title = {Optimized biological CO2-methanation with a pure culture of thermophilic methanogenic archaea in a trickle-bed reactor.},
journal = {Bioresource technology},
volume = {333},
number = {},
pages = {125135},
doi = {10.1016/j.biortech.2021.125135},
pmid = {33892429},
issn = {1873-2976},
mesh = {Bioreactors ; *Carbon Dioxide ; *Euryarchaeota ; Hydrogen ; Methane ; },
abstract = {In this study, a fully automated process converting hydrogen and carbon dioxide to methane in a high temperature trickle-bed reactor was developed from lab scale to field test level. The reactor design and system performance was optimized to yield high methane content in the product gas for direct feed-in to the gas grid. The reaction was catalyzed by a pure culture of Methanothermobacter thermoautotrophicus IM5, which formed a biofilm on ceramic packing elements. During 600 h in continuous and semi-continuous operation in countercurrent flow, the 0.05 m3 reactor produced up to95.3 % of methane at a methane production rate of 0.35 [Formula: see text] . Adding nitrogen as carrier gas during startup, foam control and dosing of ammonium and sodium sulfide as nitrogen and sulfur source were important factors for process automation.},
}
@article {pmid33851978,
year = {2021},
author = {Grinter, R and Greening, C},
title = {Cofactor F420: an expanded view of its distribution, biosynthesis and roles in bacteria and archaea.},
journal = {FEMS microbiology reviews},
volume = {45},
number = {5},
pages = {},
pmid = {33851978},
issn = {1574-6976},
support = {APP1178715//NHMRC/ ; },
mesh = {*Archaea/genetics/metabolism ; Bacteria/genetics/metabolism ; Biosynthetic Pathways ; *Euryarchaeota/metabolism ; Humans ; Riboflavin/metabolism ; },
abstract = {Many bacteria and archaea produce the redox cofactor F420. F420 is structurally similar to the cofactors FAD and FMN but is catalytically more similar to NAD and NADP. These properties allow F420 to catalyze challenging redox reactions, including key steps in methanogenesis, antibiotic biosynthesis and xenobiotic biodegradation. In the last 5 years, there has been much progress in understanding its distribution, biosynthesis, role and applications. Whereas F420 was previously thought to be confined to Actinobacteria and Euryarchaeota, new evidence indicates it is synthesized across the bacterial and archaeal domains, as a result of extensive horizontal and vertical biosynthetic gene transfer. F420 was thought to be synthesized through one biosynthetic pathway; however, recent advances have revealed variants of this pathway and have resolved their key biosynthetic steps. In parallel, new F420-dependent biosynthetic and metabolic processes have been discovered. These advances have enabled the heterologous production of F420 and identified enantioselective F420H2-dependent reductases for biocatalysis. New research has also helped resolve how microorganisms use F420 to influence human and environmental health, providing opportunities for tuberculosis treatment and methane mitigation. A total of 50 years since its discovery, multiple paradigms associated with F420 have shifted, and new F420-dependent organisms and processes continue to be discovered.},
}
@article {pmid33847950,
year = {2021},
author = {Taib, N and Gribaldo, S and MacNeill, SA},
title = {Single-Stranded DNA-Binding Proteins in the Archaea.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2281},
number = {},
pages = {23-47},
pmid = {33847950},
issn = {1940-6029},
mesh = {Archaea/classification/genetics/*metabolism ; Archaeal Proteins/chemistry/metabolism ; DNA Repair ; DNA Replication ; DNA, Archaeal/metabolism ; DNA, Single-Stranded/chemistry/*metabolism ; DNA-Binding Proteins/*chemistry/*metabolism ; Models, Molecular ; Phylogeny ; Protein Binding ; Protein Domains ; Species Specificity ; },
abstract = {Single-stranded (ss) DNA-binding proteins are found in all three domains of life where they play vital roles in nearly all aspects of DNA metabolism by binding to and stabilizing exposed ssDNA and acting as platforms onto which DNA-processing activities can assemble. The ssDNA-binding factors SSB and RPA are extremely well conserved across bacteria and eukaryotes, respectively, and comprise one or more OB-fold ssDNA-binding domains. In the third domain of life, the archaea, multiple types of ssDNA-binding protein are found with a variety of domain architectures and subunit compositions, with OB-fold ssDNA-binding domains being a characteristic of most, but not all. This chapter summarizes current knowledge of the distribution, structure, and biological function of the archaeal ssDNA-binding factors, highlighting key features shared between clades and those that distinguish the proteins of different clades from one another. The likely cellular functions of the proteins are discussed and gaps in current knowledge identified.},
}
@article {pmid33828536,
year = {2021},
author = {Gao, K and Lu, Y},
title = {Putative Extracellular Electron Transfer in Methanogenic Archaea.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {611739},
pmid = {33828536},
issn = {1664-302X},
abstract = {It has been suggested that a few methanogens are capable of extracellular electron transfers. For instance, Methanosarcina barkeri can directly capture electrons from the coexisting microbial cells of other species. Methanothrix harundinacea and Methanosarcina horonobensis retrieve electrons from Geobacter metallireducens via direct interspecies electron transfer (DIET). Recently, Methanobacterium, designated strain YSL, has been found to grow via DIET in the co-culture with Geobacter metallireducens. Methanosarcina acetivorans can perform anaerobic methane oxidation and respiratory growth relying on Fe(III) reduction through the extracellular electron transfer. Methanosarcina mazei is capable of electromethanogenesis under the conditions where electron-transfer mediators like H2 or formate are limited. The membrane-bound multiheme c-type cytochromes (MHC) and electrically-conductive cellular appendages have been assumed to mediate the extracellular electron transfer in bacteria like Geobacter and Shewanella species. These molecules or structures are rare but have been recently identified in a few methanogens. Here, we review the current state of knowledge for the putative extracellular electron transfers in methanogens and highlight the opportunities and challenges for future research.},
}
@article {pmid33821466,
year = {2021},
author = {Chuphal, N and Singha, KP and Sardar, P and Sahu, NP and Shamna, N and Kumar, V},
title = {Scope of Archaea in Fish Feed: a New Chapter in Aquafeed Probiotics?.},
journal = {Probiotics and antimicrobial proteins},
volume = {13},
number = {6},
pages = {1668-1695},
pmid = {33821466},
issn = {1867-1314},
mesh = {Animal Feed/*microbiology ; *Archaea/genetics ; *Probiotics ; },
abstract = {The outbreak of diseases leading to substantial loss is a major bottleneck in aquaculture. Over the last decades, the concept of using feed probiotics was more in focus to address the growth and health of cultivable aquatic organisms. The objective of this review is to provide an overview of the distinct functionality of archaea from conventional probiotics in nutrient utilization, specific caloric contribution, evading immune response and processing thermal resistance. The prime limitation of conventional probiotics is the viability of desired microbes under harsh feed processing conditions. To overcome the constraints of commercial probiotics pertaining to incompatibility towards industrial processing procedure, a super microbe, archaea, appears to be a potential alternative approach in aquaculture. The peculiarity of the archaeal cell wall provides them with heat stability and rigidity under industrial processing conditions. Besides, archaea being one of the gut microbial communities participates in various health-oriented biological functions in animals. Thus, the current review devoted that administration of archaea in aquafeed could be a promising strategy in aquaculture. Archaea may be used as a potential probiotic with the possible modes of functions and advantages over conventional probiotics in aquafeed preparation. The present review also provides the challenges associated with the use of archaea for aquaculture and a brief outline of the patents on archaea to highlight the various use of archaea in different sectors.},
}
@article {pmid33807612,
year = {2021},
author = {Gonzalez-Bosquet, J and Pedra-Nobre, S and Devor, EJ and Thiel, KW and Goodheart, MJ and Bender, DP and Leslie, KK},
title = {Bacterial, Archaea, and Viral Transcripts (BAVT) Expression in Gynecological Cancers and Correlation with Regulatory Regions of the Genome.},
journal = {Cancers},
volume = {13},
number = {5},
pages = {},
pmid = {33807612},
issn = {2072-6694},
support = {2018 Bridge Funding Award//American Association of Obstetricians and Gynecologists Foundation (AAOGF) Bridge Funding Award/ ; R01 CA99908/NH/NIH HHS/United States ; R01 CA184101/NH/NIH HHS/United States ; },
abstract = {Bacteria, archaea, and viruses are associated with numerous human cancers. To date, microbiome variations in transcription have not been evaluated relative to upper female genital tract cancer risk. Our aim was to assess differences in bacterial, archaea, and viral transcript (BAVT) expression between different gynecological cancers and normal fallopian tubes. In this case-control study we performed RNA sequencing on 12 normal tubes, 112 serous ovarian cancers (HGSC) and 62 endometrioid endometrial cancers (EEC). We used the centrifuge algorithm to classify resultant transcripts into four indexes: bacterial, archaea, viral, and human genomes. We then compared BAVT expression from normal samples, HGSC and EEC. T-test was used for univariate comparisons (correcting for multiple comparison) and lasso for multivariate modelling. For validation we performed DNA sequencing of normal tubes in comparison to HGSC and EEC BAVTs in the TCGA database. Pathway analyses were carried out to evaluate the function of significant BAVTs. Our results show that BAVT expression levels vary between different gynecological cancers. Finally, we mapped some of these BAVTs to the human genome. Numerous map locations were close to regulatory genes and long non-coding RNAs based on the pathway enrichment analysis. BAVTs may affect gynecological cancer risk and may be part of potential targets for cancer therapy.},
}
@article {pmid33798878,
year = {2021},
author = {Fan, C and Zhang, W and Chen, X and Li, N and Li, W and Wang, Q and Duan, P and Chen, M},
title = {Residual effects of four-year amendments of organic material on N2O production driven by ammonia-oxidizing archaea and bacteria in a tropical vegetable soil.},
journal = {The Science of the total environment},
volume = {781},
number = {},
pages = {146746},
doi = {10.1016/j.scitotenv.2021.146746},
pmid = {33798878},
issn = {1879-1026},
mesh = {*Ammonia ; *Archaea ; Bacteria ; Ecosystem ; Fertilizers/analysis ; Nitrification ; Oxidation-Reduction ; Soil ; Soil Microbiology ; Vegetables ; },
abstract = {Organic material (OM) applied to cropland not only enhances soil fertility but also profoundly affects soil nitrogen cycling. However, little is known about the relative contributions of soil ammonia-oxidizing archaea (AOA) and bacteria (AOB) to nitrous oxide (N2O) production during ammonia oxidation in response to the additions of diverse types of OMs in the tropical soil for vegetable production. Herein, the soils were sampled from a tropical vegetable field subjected to 4-year consecutive amendments of straw or manure. All the soils were amended with ammonium sulfate ((NH4)2SO4, applied at a dose of 150 mg N kg-1) and incubated aerobically for four weeks under 50% water holding capacity. 1-octyne or acetylene inhibition technique was used to differentiate the relative contributions of AOA and AOB to N2O production. Results showed that AOA dominated N2O production in soil managements of unfertilized control (CK), chemical fertilization (NPK), and NPK with straw (NPKS), whereas AOB contributed more in soil under NPK with manure (NPKM). Straw addition stimulated AOA-dependent N2O production by 94.8% despite the decreased AOA-amoA abundance. Moreover, manure incorporation triggered both AOA- and AOB-dependent N2O production by 147.2% and 233.7%, respectively, accompanied with increased AOA and AOB abundances. Those stimulating effects were stronger for AOB, owing to its sensitivity to the alleviated soil acidification and decreased soil C/N ratio. Our findings highlight the stimulated N2O emissions during ammonia oxidation by historical OM amendments in tropical vegetable soil, with the magnitude of those priming effects dependent on the types of OM, and appropriate measures need to be taken to counter this challenge in tropical agriculture ecosystems.},
}
@article {pmid33782110,
year = {2021},
author = {Liu, J and Cvirkaite-Krupovic, V and Baquero, DP and Yang, Y and Zhang, Q and Shen, Y and Krupovic, M},
title = {Virus-induced cell gigantism and asymmetric cell division in archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {15},
pages = {},
pmid = {33782110},
issn = {1091-6490},
mesh = {Archaeal Proteins/metabolism ; Archaeal Viruses/*pathogenicity ; *Asymmetric Cell Division ; CRISPR-Cas Systems ; Endosomal Sorting Complexes Required for Transport/metabolism ; Giant Cells/*metabolism/virology ; Sulfolobales/genetics/physiology/*virology ; },
abstract = {Archaeal viruses represent one of the most mysterious parts of the global virosphere, with many virus groups sharing no evolutionary relationship to viruses of bacteria or eukaryotes. How these viruses interact with their hosts remains largely unexplored. Here we show that nonlytic lemon-shaped virus STSV2 interferes with the cell cycle control of its host, hyperthermophilic and acidophilic archaeon Sulfolobus islandicus, arresting the cell cycle in the S phase. STSV2 infection leads to transcriptional repression of the cell division machinery, which is homologous to the eukaryotic endosomal sorting complexes required for transport (ESCRT) system. The infected cells grow up to 20-fold larger in size, have 8,000-fold larger volume compared to noninfected cells, and accumulate massive amounts of viral and cellular DNA. Whereas noninfected Sulfolobus cells divide symmetrically by binary fission, the STSV2-infected cells undergo asymmetric division, whereby giant cells release normal-sized cells by budding, resembling the division of budding yeast. Reinfection of the normal-sized cells produces a new generation of giant cells. If the CRISPR-Cas system is present, the giant cells acquire virus-derived spacers and terminate the virus spread, whereas in its absence, the cycle continues, suggesting that CRISPR-Cas is the primary defense system in Sulfolobus against STSV2. Collectively, our results show how an archaeal virus manipulates the cell cycle, transforming the cell into a giant virion-producing factory.},
}
@article {pmid33776986,
year = {2021},
author = {Teske, A and Amils, R and Ramírez, GA and Reysenbach, AL},
title = {Editorial: Archaea in the Environment: Views on Archaeal Distribution, Activity, and Biogeography.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {667596},
pmid = {33776986},
issn = {1664-302X},
}
@article {pmid33776984,
year = {2021},
author = {Czekay, DP and Kothe, U},
title = {H/ACA Small Ribonucleoproteins: Structural and Functional Comparison Between Archaea and Eukaryotes.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {654370},
pmid = {33776984},
issn = {1664-302X},
abstract = {During ribosome synthesis, ribosomal RNA is modified through the formation of many pseudouridines and methylations which contribute to ribosome function across all domains of life. In archaea and eukaryotes, pseudouridylation of rRNA is catalyzed by H/ACA small ribonucleoproteins (sRNPs) utilizing different H/ACA guide RNAs to identify target uridines for modification. H/ACA sRNPs are conserved in archaea and eukaryotes, as they share a common general architecture and function, but there are also several notable differences between archaeal and eukaryotic H/ACA sRNPs. Due to the higher protein stability in archaea, we have more information on the structure of archaeal H/ACA sRNPs compared to eukaryotic counterparts. However, based on the long history of yeast genetic and other cellular studies, the biological role of H/ACA sRNPs during ribosome biogenesis is better understood in eukaryotes than archaea. Therefore, this review provides an overview of the current knowledge on H/ACA sRNPs from archaea, in particular their structure and function, and relates it to our understanding of the roles of eukaryotic H/ACA sRNP during eukaryotic ribosome synthesis and beyond. Based on this comparison of our current insights into archaeal and eukaryotic H/ACA sRNPs, we discuss what role archaeal H/ACA sRNPs may play in the formation of ribosomes.},
}
@article {pmid33771626,
year = {2021},
author = {Orona-Navar, A and Aguilar-Hernández, I and Nigam, KDP and Cerdán-Pasarán, A and Ornelas-Soto, N},
title = {Alternative sources of natural pigments for dye-sensitized solar cells: Algae, cyanobacteria, bacteria, archaea and fungi.},
journal = {Journal of biotechnology},
volume = {332},
number = {},
pages = {29-53},
doi = {10.1016/j.jbiotec.2021.03.013},
pmid = {33771626},
issn = {1873-4863},
mesh = {*Archaea ; Carotenoids ; *Cyanobacteria ; Fungi ; Plants ; },
abstract = {Dye-sensitized solar cells have been of great interest in photovoltaic technology due to their capacity to convert energy at a low cost. The use of natural pigments means replacing expensive chemical synthesis processes by easily extractable pigments that are non-toxic and environmentally friendly. Although most of the pigments used for this purpose are obtained from higher plants, there are potential alternative sources that have been underexploited and have shown encouraging results, since pigments can also be obtained from organisms like bacteria, cyanobacteria, microalgae, yeast, and molds, which have the potential of being cultivated in bioreactors or optimized by biotechnological processes. The aforementioned organisms are sources of diverse sensitizers like photosynthetic pigments, accessory pigments, and secondary metabolites such as chlorophylls, bacteriochlorophylls, carotenoids, and phycobiliproteins. Moreover, retinal proteins, photosystems, and reaction centers from these organisms can also act as sensitizers. In this review, the use of natural sensitizers extracted from algae, cyanobacteria, bacteria, archaea, and fungi is assessed. The reported photoconversion efficiencies vary from 0.001 % to 4.6 % for sensitizers extracted from algae and microalgae, 0.004 to 1.67 % for bacterial sensitizers, 0.07-0.23 % for cyanobacteria, 0.09 to 0.049 % for archaea and 0.26-2.3 % for pigments from fungi.},
}
@article {pmid33753464,
year = {2021},
author = {Galperin, MY and Wolf, YI and Garushyants, SK and Vera Alvarez, R and Koonin, EV},
title = {Non-essential ribosomal proteins in bacteria and archaea identified using COGs.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {},
pmid = {33753464},
issn = {1098-5530},
abstract = {Ribosomal proteins (RPs) are highly conserved across the bacterial and archaeal domains. Although many RPs are essential for survival, genome analysis demonstrates the absence of some RP genes in many bacterial and archaeal genomes. Furthermore, global transposon mutagenesis and/or targeted deletion showed that elimination of some RP genes had only a moderate effect on the bacterial growth rate. Here, we systematically analyze the evolutionary conservation of RPs in prokaryotes by compiling the list of the ribosomal genes that are missing from one or more genomes in the recently updated version of the Clusters of Orthologous Genes (COG) database. Some of these absences occurred because the respective genes carried frameshifts, presumably, resulting from sequencing errors, while others were overlooked and not translated during genome annotation. Apart from these annotation errors, we identified multiple genuine losses of RP genes in a variety of bacteria and archaea. Some of these losses are clade-specific, whereas others occur in symbionts and parasites with dramatically reduced genomes. The lists of computationally and experimentally defined non-essential ribosomal genes show a substantial overlap, revealing a common trend in prokaryote ribosome evolution that could be linked to the architecture and assembly of the ribosomes. Thus, RPs that are located at the surface of the ribosome and/or are incorporated at a late stage of ribosome assembly are more likely to be non-essential and to be lost during microbial evolution, particularly, in the course of genome compaction.IMPORTANCEIn many prokaryote genomes, one or more ribosomal protein (RP) genes are missing. Analysis of 1,309 prokaryote genomes included in the COG database shows that only about half of the RPs are universally conserved in bacteria and archaea. In contrast, up to 16 other RPs are missing in some genomes, primarily, tiny (<1 Mb) genomes of host-associated bacteria and archaea. Ten universal and nine archaea-specific ribosomal proteins show clear patterns of lineage-specific gene loss. Most of the RPs that are frequently lost from bacterial genomes are located on the ribosome periphery and are non-essential in Escherichia coli and Bacillus subtilis These results reveal general trends and common constraints in the architecture and evolution of ribosomes in prokaryotes.},
}
@article {pmid33726663,
year = {2021},
author = {Bize, A and Midoux, C and Mariadassou, M and Schbath, S and Forterre, P and Da Cunha, V},
title = {Exploring short k-mer profiles in cells and mobile elements from Archaea highlights the major influence of both the ecological niche and evolutionary history.},
journal = {BMC genomics},
volume = {22},
number = {1},
pages = {186},
pmid = {33726663},
issn = {1471-2164},
support = {ANR-17-CE05-0011-01//Agence Nationale de la Recherche/ ; 340440/ERC_/European Research Council/International ; },
mesh = {*Archaea/genetics ; Ecosystem ; Phylogeny ; Plasmids ; *Viruses/genetics ; },
abstract = {BACKGROUND: K-mer-based methods have greatly advanced in recent years, largely driven by the realization of their biological significance and by the advent of next-generation sequencing. Their speed and their independence from the annotation process are major advantages. Their utility in the study of the mobilome has recently emerged and they seem a priori adapted to the patchy gene distribution and the lack of universal marker genes of viruses and plasmids. To provide a framework for the interpretation of results from k-mer based methods applied to archaea or their mobilome, we analyzed the 5-mer DNA profiles of close to 600 archaeal cells, viruses and plasmids. Archaea is one of the three domains of life. Archaea seem enriched in extremophiles and are associated with a high diversity of viral and plasmid families, many of which are specific to this domain. We explored the dataset structure by multivariate and statistical analyses, seeking to identify the underlying factors.<br><br>RESULTS: For cells, the 5-mer profiles were inconsistent with the phylogeny of archaea. At a finer taxonomic level, the influence of the taxonomy and the environmental constraints on 5-mer profiles was very strong. These two factors were interdependent to a significant extent, and the respective weights of their contributions varied according to the clade. A convergent adaptation was observed for the class Halobacteria, for which a strong 5-mer signature was identified. For mobile elements, coevolution with the host had a clear influence on their 5-mer profile. This enabled us to identify one previously known and one new case of recent host transfer based on the atypical composition of the mobile elements involved. Beyond the effect of coevolution, extrachromosomal elements strikingly retain the specific imprint of their own viral or plasmid taxonomic family in their 5-mer profile.<br><br>CONCLUSION: This specific imprint confirms that the evolution of extrachromosomal elements is driven by multiple parameters and is not restricted to host adaptation. In addition, we detected only recent host transfer events, suggesting the fast evolution of short k-mer profiles. This calls for caution when using k-mers for host prediction, metagenomic binning or phylogenetic reconstruction.},
}
@article {pmid33720296,
year = {2021},
author = {Zhang, C and Meckenstock, RU and Weng, S and Wei, G and Hubert, CRJ and Wang, JH and Dong, X},
title = {Marine sediments harbor diverse archaea and bacteria with the potential for anaerobic hydrocarbon degradation via fumarate addition.},
journal = {FEMS microbiology ecology},
volume = {97},
number = {5},
pages = {},
doi = {10.1093/femsec/fiab045},
pmid = {33720296},
issn = {1574-6941},
mesh = {Anaerobiosis ; *Archaea/genetics ; Bacteria/genetics ; *Fumarates ; Geologic Sediments ; Hydrocarbons ; Phylogeny ; },
abstract = {Marine sediments can contain large amounts of alkanes and methylated aromatic hydrocarbons that are introduced by natural processes or anthropogenic activities. These compounds can be biodegraded by anaerobic microorganisms via enzymatic addition of fumarate. However, the identity and ecological roles of a significant fraction of hydrocarbon degraders containing fumarate-adding enzymes (FAE) in various marine sediments remains unknown. By combining phylogenetic reconstructions, protein homolog modelling, and functional profiling of publicly available metagenomes and genomes, 61 draft bacterial and archaeal genomes encoding anaerobic hydrocarbon degradation via fumarate addition were obtained. Besides Desulfobacterota (previously known as Deltaproteobacteria) that are well-known to catalyze these reactions, Chloroflexi are dominant FAE-encoding bacteria in hydrocarbon-impacted sediments, potentially coupling sulfate reduction or fermentation to anaerobic hydrocarbon degradation. Among Archaea, besides Archaeoglobi previously shown to have this capability, genomes of Heimdallarchaeota, Lokiarchaeota, Thorarchaeota and Thermoplasmata also suggest fermentative hydrocarbon degradation using archaea-type FAE. These bacterial and archaeal hydrocarbon degraders occur in a wide range of marine sediments, including high abundances of FAE-encoding Asgard archaea associated with natural seeps and subseafloor ecosystems. Our results expand the knowledge of diverse archaeal and bacterial lineages engaged in anaerobic degradation of alkanes and methylated aromatic hydrocarbons.},
}
@article {pmid33694023,
year = {2021},
author = {Jain, A and Krishnan, KP},
title = {Marine Group-II archaea dominate particle-attached as well as free-living archaeal assemblages in the surface waters of Kongsfjorden, Svalbard, Arctic Ocean.},
journal = {Antonie van Leeuwenhoek},
volume = {114},
number = {5},
pages = {633-647},
pmid = {33694023},
issn = {1572-9699},
support = {Indian Arctic Programme//Ministry of Earth Sciences/ ; },
mesh = {*Archaea/genetics ; Ecosystem ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Seawater ; Svalbard ; },
abstract = {Marine archaea are a significant component of the global oceanic ecosystems, including the polar oceans. However, only a few attempts have been made to study archaea in the high Arctic fjords. Given the importance of Archaea in carbon and nitrogen cycling, it is imperative to explore their diversity and community composition in the high Arctic fjords, such as Kongsfjorden (Svalbard). In the present study, we evaluated archaeal diversity and community composition in the size-fractionated microbial population, viz-a-viz free-living (FL; 0.2-3 μm) and particle-attached (PA; > 3 μm) using archaeal V3-V4 16S rRNA gene amplicon sequencing. Our results indicate that the overall archaeal community in the surface water of Kongsfjorden was dominated by the members of the marine group-II (MGII) archaea, followed by the MGI group members, including Nitrosopumilaceae and Nitrososphaeraceae. Although a clear niche partitioning between PA and FL archaeal communities was not observed, 2 OTUs among 682 OTUs, and 3 ASVs out of 1932 ASVs were differentially abundant among the fractions. OTU001/ASV0002, classified as MGIIa, was differentially abundant in the PA fraction. OTU006/ASV0006/ASV0010 affiliated with MGIIb were differentially abundant in the FL fraction. Particulate organic nitrogen and C:N ratio were the most significant variables (P < 0.05) explaining the observed variation in the FL and PA archaeal communities, respectively. These results indicate an exchange between archaeal communities or a generalist lifestyle switching between FL and PA fractions. Besides, the particles' elemental composition (carbon and nitrogen) seems to play an essential role in shaping the PA archaeal communities in the surface waters of Kongsfjorden.},
}
@article {pmid33674723,
year = {2021},
author = {Mauerhofer, LM and Zwirtmayr, S and Pappenreiter, P and Bernacchi, S and Seifert, AH and Reischl, B and Schmider, T and Taubner, RS and Paulik, C and Rittmann, SKR},
title = {Hyperthermophilic methanogenic archaea act as high-pressure CH4 cell factories.},
journal = {Communications biology},
volume = {4},
number = {1},
pages = {289},
pmid = {33674723},
issn = {2399-3642},
mesh = {Amino Acid Motifs ; High-Throughput Screening Assays ; *Industrial Microbiology ; Kinetics ; Membrane Glycoproteins/metabolism ; Methane/*metabolism ; Methanocaldococcaceae/growth &amp; development/*metabolism ; Methanocaldococcus/growth &amp; development/*metabolism ; Oxidoreductases/metabolism ; Pressure ; Renewable Energy ; },
abstract = {Bioprocesses converting carbon dioxide with molecular hydrogen to methane (CH4) are currently being developed to enable a transition to a renewable energy production system. In this study, we present a comprehensive physiological and biotechnological examination of 80 methanogenic archaea (methanogens) quantifying growth and CH4 production kinetics at hyperbaric pressures up to 50 bar with regard to media, macro-, and micro-nutrient supply, specific genomic features, and cell envelope architecture. Our analysis aimed to systematically prioritize high-pressure and high-performance methanogens. We found that the hyperthermophilic methanococci Methanotorris igneus and Methanocaldococcoccus jannaschii are high-pressure CH4 cell factories. Furthermore, our analysis revealed that high-performance methanogens are covered with an S-layer, and that they harbour the amino acid motif Tyrα444 Glyα445 Tyrα446 in the alpha subunit of the methyl-coenzyme M reductase. Thus, high-pressure biological CH4 production in pure culture could provide a purposeful route for the transition to a carbon-neutral bioenergy sector.},
}
@article {pmid33637253,
year = {2021},
author = {Zheng, M and He, S and Feng, Y and Wang, M and Liu, YX and Dang, C and Wang, J},
title = {Active ammonia-oxidizing bacteria and archaea in wastewater treatment systems.},
journal = {Journal of environmental sciences (China)},
volume = {102},
number = {},
pages = {273-282},
doi = {10.1016/j.jes.2020.09.039},
pmid = {33637253},
issn = {1001-0742},
mesh = {Ammonia ; *Archaea/genetics ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Soil Microbiology ; *Water Purification ; },
abstract = {Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are two microbial groups mediating nitrification, yet little is presently known about their abundances and community structures at the transcriptional level in wastewater treatment systems (WWTSs). This is a significant issue, as the numerical abundance of AOA or AOB at the gene level may not necessarily represent their functional role in ammonia oxidation. Using amoA genes as molecular markers, this study investigated the transcriptional abundance and community structure of active AOA and AOB in 14 WWTSs. Quantitative PCR results indicated that the transcriptional abundances of AOB amoA (averaged: 1.6 × 108 copies g-1 dry sludge) were higher than those of AOA (averaged: 3.4 × 107 copies g-1 dry sludge) in all WWTSs despite several higher abundances of AOA amoA at the gene level. Moreover, phylogenetic analysis demonstrated that Nitrosomonas europaea and unknown clusters accounted for 37.66% and 49.96% of the total AOB amoA transcripts, respectively, suggesting their dominant role in driving ammonia oxidation. Meanwhile, AOA amoA transcripts were only successfully retrieved from 3 samples, and the Nitrosospaera sister cluster dominated, accounting for 83.46%. Finally, the substrate utilization kinetics of different AOA and AOB species might play a fundamental role in shaping their niche differentiation, community composition, and functional activity. This study provides a basis for evaluating the relative contributions of ammonia-oxidizing microorganisms (AOMs) to nitrogen conversions in WWTSs.},
}
@article {pmid33624267,
year = {2021},
author = {Kim, JG and Gazi, KS and Awala, SI and Jung, MY and Rhee, SK},
title = {Ammonia-oxidizing archaea in biological interactions.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {59},
number = {3},
pages = {298-310},
pmid = {33624267},
issn = {1976-3794},
mesh = {Ammonia/*metabolism ; Archaea/classification/genetics/isolation &amp; purification/*metabolism ; Ecosystem ; Nitrification ; Oxidation-Reduction ; Phylogeny ; },
abstract = {The third domain Archaea was known to thrive in extreme or anoxic environments based on cultivation studies. Recent metagenomics-based approaches revealed a widespread abundance of archaea, including ammonia-oxidizing archaea (AOA) of Thaumarchaeota in non-extreme and oxic environments. AOA alter nitrogen species availability by mediating the first step of chemolithoautotrophic nitrification, ammonia oxidation to nitrite, and are important primary producers in ecosystems, which affects the distribution and activity of other organisms in ecosystems. Thus, information on the interactions of AOA with other cohabiting organisms is a crucial element in understanding nitrogen and carbon cycles in ecosystems as well as the functioning of whole ecosystems. AOA are self-nourishing, and thus interactions of AOA with other organisms can often be indirect and broad. Besides, there are possibilities of specific and obligate interactions. Mechanisms of interaction are often not clearly identified but only inferred due to limited knowledge on the interaction factors analyzed by current technologies. Here, we overviewed different types of AOA interactions with other cohabiting organisms, which contribute to understanding AOA functions in ecosystems.},
}
@article {pmid33620581,
year = {2021},
author = {Sorokin, DY and Roman, P and Kolganova, TV},
title = {Halo(natrono)archaea from hypersaline lakes can utilize sulfoxides other than DMSO as electron acceptors for anaerobic respiration.},
journal = {Extremophiles : life under extreme conditions},
volume = {25},
number = {2},
pages = {173-180},
pmid = {33620581},
issn = {1433-4909},
support = {19-04-00401//Russuan Foundation for Basic Research/ ; },
mesh = {Anaerobiosis ; *Dimethyl Sulfoxide ; Electrons ; *Lakes ; Phylogeny ; RNA, Ribosomal, 16S ; Respiration ; Russia ; Siberia ; },
abstract = {Dimethylsulfoxide (DMSO) has long been known to support anaerobic respiration in a few species of basically aerobic extremely halophilic euryarchaea living in hypersaline lakes. Recently, it has also been shown to be utilized as an additional electron acceptor in basically anaerobic sulfur-reducing haloarchaea. Here we investigated whether haloarchaea would be capable of anaerobic respiration with other two sulfoxides, methionine sulfoxide (MSO) and tetramethylene sulfoxide (TMSO). For this, anaerobic enrichment cultures were inoculated with sediments from hypersaline salt and soda lakes in southwestern Siberia and southern Russia. Positive enrichments were obtained for both MSO and TMSO with yeast extract but not with formate or acetate as the electron donor. Two pure cultures obtained from salt lakes, either with MSO or TMSO, were obligate anaerobes closely related to sulfur-reducing Halanaeroarchaeum sulfurireducens, although the type strain of this genus was unable to utilize any sulfoxides. Two pure cultures isolated from soda lakes were facultatively anaerobic alkaliphilic haloarchaea using O2, sulfur and sulfoxides as the electron acceptors. One isolate was identical to the previously described sulfur-reducing Natrarchaeobaculum sulfurireducens, while another one, enriched at lower alkalinity, is forming a new species in the genus Halobiforma. Since all isolates enriched with either MSO or TMSO were able to respire all three sulfoxides including DMSO and the corresponding activities were cross-induced, it suggest that a single enzyme of the DMSO-reductase family with a broad substrate specificity is responsible for various sulfoxide-dependent respiration in haloarchaea.},
}
@article {pmid33608296,
year = {2021},
author = {Cai, R and Zhang, J and Liu, R and Sun, C},
title = {Metagenomic Insights into the Metabolic and Ecological Functions of Abundant Deep-Sea Hydrothermal Vent DPANN Archaea.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {9},
pages = {},
pmid = {33608296},
issn = {1098-5336},
mesh = {Amino Acids/biosynthesis ; Archaea/*genetics/metabolism ; Genome, Archaeal ; Glucose/metabolism ; Hydrothermal Vents/*microbiology ; Metagenome ; Nucleotides/biosynthesis ; Phylogeny ; },
abstract = {Due to their unique metabolism and important ecological roles, deep-sea hydrothermal archaea have attracted great scientific interest. Among these archaea, DPANN superphylum archaea are widely distributed in hydrothermal vent environments. However, DPANN metabolism and ecology remain largely unknown. In this study, we assembled 20 DPANN genomes among 43 reconstructed genomes obtained from deep-sea hydrothermal vent sediments. Phylogenetic analysis suggests 6 phyla, comprised of Aenigmarchaeota, Diapherotrites, Nanoarchaeota, Pacearchaeota, Woesearchaeota, and a new candidate phylum we have designated Kexuearchaeota These are included in the 20 DPANN archaeal members, indicating their broad diversity in this special environment. Analyses of their metabolism reveal deficiencies due to their reduced genome size, including gluconeogenesis and de novo nucleotide and amino acid biosynthesis. However, DPANN archaea possess alternate strategies to address these deficiencies. DPANN archaea also have the potential to assimilate nitrogen and sulfur compounds, indicating an important ecological role in the hydrothermal vent system.IMPORTANCE DPANN archaea show high distribution in the hydrothermal system, although they display small genome size and some incomplete biological processes. Exploring their metabolism is helpful to understand how such small forms of life adapt to this unique environment and what ecological roles they play. In this study, we obtained 20 high-quality metagenome-assembled genomes (MAGs) corresponding to 6 phyla of the DPANN group (Aenigmarchaeota, Diapherotrites, Nanoarchaeota, Pacearchaeota, Woesearchaeota, and a new candidate phylum designated Kexuearchaeota). Further metagenomic analyses provided insights on the metabolism and ecological functions of DPANN archaea to adapt to deep-sea hydrothermal environments. Our study contributes to a deeper understanding of their special lifestyles and should provide clues to cultivate this important archaeal group in the future.},
}
@article {pmid33584634,
year = {2021},
author = {Distaso, MA and Bargiela, R and Brailsford, FL and Williams, GB and Wright, S and Lunev, EA and Toshchakov, SV and Yakimov, MM and Jones, DL and Golyshin, PN and Golyshina, OV},
title = {Corrigendum: High Representation of Archaea Across All Depths in Oxic and Low-pH Sediment Layers Underlying an Acidic Stream.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {633015},
doi = {10.3389/fmicb.2021.633015},
pmid = {33584634},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2020.576520.].},
}
@article {pmid33582288,
year = {2021},
author = {Starke, R and Siles, JA and Fernandes, MLP and Schallert, K and Benndorf, D and Plaza, C and Jehmlich, N and Delgado-Baquerizo, M and Bastida, F},
title = {The structure and function of soil archaea across biomes.},
journal = {Journal of proteomics},
volume = {237},
number = {},
pages = {104147},
doi = {10.1016/j.jprot.2021.104147},
pmid = {33582288},
issn = {1876-7737},
mesh = {*Archaea/genetics ; Ecosystem ; RNA, Ribosomal, 16S ; *Soil ; Soil Microbiology ; },
abstract = {We lack a predictive understanding of the environmental drivers determining the structure and function of archaeal communities as well as the proteome associated with these important soil organisms. Here, we characterized the structure (by 16S rRNA gene sequencing) and function (by metaproteomics) of archaea from 32 soil samples across terrestrial ecosystems with contrasting climate and vegetation types. Our multi-"omics" approach unveiled that genes from Nitrosophaerales and Thermoplasmata dominated soils collected from four continents, and that archaea comprise 2.3 ± 0.3% of microbial proteins in these soils. Aridity positively correlated with the proportion of Nitrosophaerales genes and the number of archaeal proteins. The interaction of climate x vegetation shaped the functional profile of the archaeal community. Our study provides novel insights into the structure and function of soil archaea across climates, and highlights that these communities may be influenced by increasing global aridity.},
}
@article {pmid33561735,
year = {2021},
author = {Shalvarjian, KE and Nayak, DD},
title = {Transcriptional regulation of methanogenic metabolism in archaea.},
journal = {Current opinion in microbiology},
volume = {60},
number = {},
pages = {8-15},
doi = {10.1016/j.mib.2021.01.005},
pmid = {33561735},
issn = {1879-0364},
mesh = {*Archaea/genetics ; Gene Expression Regulation, Archaeal ; *Methane ; Methanococcus/genetics ; Methanosarcina/genetics ; },
abstract = {Methanogenesis is a widespread metabolism of evolutionary and environmental importance that is likely to have originated on early Earth. Microorganisms that perform methanogenesis, termed methanogens, belong exclusively to the domain Archaea. Despite maintaining eukaryotic transcription machinery and homologs of bacterial regulators, archaeal transcription and gene regulation appear to be distinct from either domain. While genes involved in methanogenic metabolism have been identified and characterized, their regulation in response to both extracellular and intracellular signals is less understood. Here, we review recent reports on transcriptional regulation of methanogenesis using two model methanogens, Methanococcus maripaludis and Methanosarcina acetivorans, and highlight directions for future research in this nascent field.},
}
@article {pmid33558390,
year = {2021},
author = {Kuprat, T and Ortjohann, M and Johnsen, U and Schönheit, P},
title = {Glucose Metabolism and Acetate Switch in Archaea: the Enzymes in Haloferax volcanii.},
journal = {Journal of bacteriology},
volume = {203},
number = {8},
pages = {},
pmid = {33558390},
issn = {1098-5530},
mesh = {Acetate-CoA Ligase/genetics/metabolism ; Acetates/*metabolism ; Acetyl Coenzyme A/metabolism ; Archaeal Proteins/genetics/metabolism ; Glucose/*metabolism ; Haloferax volcanii/*enzymology/genetics/growth &amp; development/metabolism ; Phosphoenolpyruvate Carboxylase/genetics/metabolism ; Phosphoglycerate Mutase/genetics/metabolism ; Phosphopyruvate Hydratase/genetics/metabolism ; Pyruvic Acid/metabolism ; },
abstract = {The halophilic archaeon Haloferax volcanii has been proposed to degrade glucose via the semiphosphorylative Entner-Doudoroff (spED) pathway. Following our previous studies on key enzymes of this pathway, we now focus on the characterization of enzymes involved in 3-phosphoglycerate conversion to pyruvate, in anaplerosis, and in acetyl coenzyme A (acetyl-CoA) formation from pyruvate. These enzymes include phosphoglycerate mutase, enolase, pyruvate kinase, phosphoenolpyruvate carboxylase, and pyruvate-ferredoxin oxidoreductase. The essential function of these enzymes were shown by transcript analyses and growth experiments with respective deletion mutants. Furthermore, we show that H. volcanii-during aerobic growth on glucose-excreted significant amounts of acetate, which was consumed in the stationary phase (acetate switch). The enzyme catalyzing the conversion of acetyl-CoA to acetate as part of the acetate overflow mechanism, an ADP-forming acetyl-CoA synthetase (ACD), was characterized. The functional involvement of ACD in acetate formation and of AMP-forming acetyl-CoA synthetases (ACSs) in activation of excreted acetate was proven by using respective deletion mutants. Together, the data provide a comprehensive analysis of enzymes of the spED pathway and of anaplerosis and report the first genetic evidence of the functional involvement of enzymes of the acetate switch in archaea.IMPORTANCE In this work, we provide a comprehensive analysis of glucose degradation via the semiphosphorylative Entner-Doudoroff pathway in the haloarchaeal model organism Haloferax volcanii The study includes transcriptional analyses, growth experiments with deletion mutants. and characterization of all enzymes involved in the conversion of 3-phosphoglycerate to acetyl coenzyme A (acetyl-CoA) and in anaplerosis. Phylogenetic analyses of several enzymes indicate various lateral gene transfer events from bacteria to haloarchaea. Furthermore, we analyzed the key players involved in the acetate switch, i.e., in the formation (overflow) and subsequent consumption of acetate during aerobic growth on glucose. Together, the data provide novel aspects of glucose degradation, anaplerosis, and acetate switch in H. volcanii and thus expand our understanding of the unusual sugar metabolism in archaea.},
}
@article {pmid33556662,
year = {2021},
author = {Du, H and Sun, T and Liu, Y and An, S and Xie, H and Wang, D and Igarashi, Y and Imanaka, T and Luo, F and Ma, M},
title = {Bacteria and archaea involved in anaerobic mercury methylation and methane oxidation in anaerobic sulfate-rich reactors.},
journal = {Chemosphere},
volume = {274},
number = {},
pages = {129773},
doi = {10.1016/j.chemosphere.2021.129773},
pmid = {33556662},
issn = {1879-1298},
mesh = {Anaerobiosis ; Animals ; *Archaea/genetics ; Bacteria/genetics ; *Mercury ; Methane ; Methylation ; Oxidation-Reduction ; Phylogeny ; Sulfates ; Swine ; },
abstract = {The identification of dominant microbes in anaerobic mercury (Hg) methylation, methylmercury (MeHg) demethylation, and methane oxidation as sulfate-reducing bacteria, methanogens or, probably, anaerobic methanotrophic archaea (ANMEs) is of great interest. To date, however, the interrelationship of bacteria and archaea involved in these processes remains unclear. Here, we demonstrated the dynamics of microorganisms participating in these processes. Anaerobic fixed-bed reactors were operated with swine manure and sludge to produce methane stably, and then, sulfate (reactor C), sulfate and Hg(II) (reactor H), and sulfate and MeHg (reactor M) were added, and the reactors were operated for 120 d, divided equally into four periods, P1-P4. The bacterial compositions changed nonsignificantly, whereas Methanosaeta in reactors H and M decreased significantly, revealing that it was irrelevant for Hg transformation. The abundances of Syntrophomonadaceae, Methanoculleus, Candidatus Methanogranum and Candidatus Methanoplasma increased continuously with time; these species probably functioned in these processes, but further evidence is needed. Desulfocella and Desulfobacterium dominated first but eventually almost vanished, while the dominant archaeal genera Methanogenium, Methanoculleus and Methanocorpusculum were closely related to ANME-1 and ANME-2. PLS-DA results indicated that both bacteria and archaea in different periods in the three reactors were clustered separately, implying that the microbial compositions in the same periods were similar and changed markedly with time.},
}
@article {pmid33555973,
year = {2020},
author = {Makarova, KS and Wolf, YI and Shmakov, SA and Liu, Y and Li, M and Koonin, EV},
title = {Unprecedented Diversity of Unique CRISPR-Cas-Related Systems and Cas1 Homologs in Asgard Archaea.},
journal = {The CRISPR journal},
volume = {3},
number = {3},
pages = {156-163},
pmid = {33555973},
issn = {2573-1602},
mesh = {Archaea/classification/*genetics/metabolism ; Archaeal Proteins/genetics/metabolism ; *CRISPR-Cas Systems ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Endonucleases/genetics ; Genome, Archaeal ; Metagenome ; Phylogeny ; },
abstract = {The principal function of archaeal and bacterial CRISPR-Cas systems is antivirus adaptive immunity. However, recent genome analyses identified a variety of derived CRISPR-Cas variants at least some of which appear to perform different functions. Here, we describe a unique repertoire of CRISPR-Cas-related systems that we discovered by searching archaeal metagenome-assemble genomes of the Asgard superphylum. Several of these variants contain extremely diverged homologs of Cas1, the integrase involved in CRISPR adaptation as well as casposon transposition. Strikingly, the diversity of Cas1 in Asgard archaea alone is greater than that detected so far among the rest of archaea and bacteria. The Asgard CRISPR-Cas derivatives also encode distinct forms of Cas4, Cas5, and Cas7 proteins, and/or additional nucleases. Some of these systems are predicted to perform defense functions, but possibly not programmable ones, whereas others are likely to represent previously unknown mobile genetic elements.},
}
@article {pmid33554274,
year = {2021},
author = {Zhu, D and Shen, G and Wang, Z and Han, R and Long, Q and Gao, X and Xing, J and Li, Y and Wang, R},
title = {Distinctive distributions of halophilic Archaea across hypersaline environments within the Qaidam Basin of China.},
journal = {Archives of microbiology},
volume = {203},
number = {5},
pages = {2029-2042},
pmid = {33554274},
issn = {1432-072X},
support = {31760034//National Natural Science Foundation of China/ ; 31860030//National Natural Science Foundation of China/ ; 21967018//National Natural Science Foundation of China/ ; 2019SF121//Key Research Foundation of Development and Transformation of Qinghai Province/ ; 2018ZJ778//Applied Basic Research Program of Qinghai Province/ ; 2018ZJ930Q//Applied Basic Research Program of Qinghai Province/ ; 2020ZJ767//Applied Basic Research Program of Qinghai Province/ ; },
mesh = {China ; *Ecosystem ; *Environmental Microbiology ; Euryarchaeota/*classification/genetics ; RNA, Ribosomal, 16S/genetics ; Salinity ; Seawater/microbiology ; },
abstract = {Halophilic Archaea are widely distributed globally in hypersaline environments. However, little is known of how dominant halophilic archaeal genera are distributed across environments and how they may co-associate across ecosystems. Here, the archaeal community composition and diversity from hypersaline environments (> 300 g/L salinity; total of 33 samples) in the Qaidam Basin of China were investigated using high-throughput Illumina sequencing of 16S rRNA genes. The archaeal communities (total of 3,419 OTUs) were dominated by the class Halobacteria (31.7-99.6% relative abundances) within the phylum Euryarchaeota (90.8-99.9%). Five predominant taxa, including Halorubrum, Halobacterium, Halopenitus, Methanothrix, and Halomicrobium, were observed across most samples. However, several distinct genera were associated with individual samples and were inconsistently distributed across samples, which contrast with previous studies of hypersaline archaeal communities. Additionally, co-occurrence network analysis indicated that five network clusters were present and potentially reflective of interspecies interactions among the environments, including three clusters (clusters II, III, and IV) comprising halophilic archaeal taxa within the Halobacteriaceae and Haloferacaceae families. In addition, two other clusters (clusters I and V) were identified that comprised methanogens. Finally, salinity comprising ionic concentrations (in the order of Na+ > Ca2+ > Mg2+) and pH were most correlated with taxonomic distributions across sample sites.},
}
@article {pmid33545473,
year = {2021},
author = {Wei, H and Lin, X},
title = {Shifts in the relative abundance and potential rates of sediment ammonia-oxidizing archaea and bacteria along environmental gradients of an urban river-estuary-adjacent sea continuum.},
journal = {The Science of the total environment},
volume = {771},
number = {},
pages = {144824},
doi = {10.1016/j.scitotenv.2020.144824},
pmid = {33545473},
issn = {1879-1026},
mesh = {*Ammonia ; *Archaea/genetics ; Bacteria/genetics ; China ; Estuaries ; Humans ; Oxidation-Reduction ; Phylogeny ; Rivers ; Soil Microbiology ; },
abstract = {Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play important roles in N cycling in sediments globally. However, little is known about their ammonia oxidation rates along a river-estuary-sea continuum. In this study, we investigated how the potential ammonia oxidation rates (PARs) of AOA and AOB changed spatially along a continuum comprising three habitats: the Shanghai urban river network, the Yangtze Estuary, and the adjacent East China Sea, in summer and winter. The AOA and AOB PARs (0.53 ± 0.49 and 0.72 ± 0.69 μg N g-1 d-1, mean ± SD, respectively) and their amoA gene abundance (0.47 ± 0.85 × 106 and 2.4 ± 3.54 × 106 copies g-1, respectively) decreased along the continuum, particularly from the urban river to the estuary, driven by decreasing sediment total organic C and N and other correlated inorganic nutrients (e.g., NH4+) along the gradient of anthropogenic influences. These spatial patterns were consistent between the seasons. The urban river network, where the anthropogenic influences were strongest, saw the largest seasonal differences, as both AOA and AOB had higher PARs and abundance in summer than in winter. The ratios between AOA and AOB PARs (~0.87 ± 0.51) and gene abundances (~0.25 ± 0.24), however, were predominantly <1, indicating an AOB-dominated community. Comparing the different NH4+ consumption pathways, total aerobic oxidation accounted for 12-26% of the total consumption, with the largest proportion in the estuary, where the system was well oxygenated, and the lowest in the adjacent sea, where inorganic N was highly depleted. This study revealed the spatiotemporal patterns of AOA and AOB potential rates and gene abundance along gradients of human influences and identified organic matter and nutrients as key environmental factors that shaped the variation of AOA and AOB along the continuum.},
}
@article {pmid33539079,
year = {2021},
author = {Wang, Y and Qin, W and Jiang, X and Ju, F and Mao, Y and Zhang, A and Stahl, DA and Zhang, T},
title = {Seasonal Prevalence of Ammonia-Oxidizing Archaea in a Full-Scale Municipal Wastewater Treatment Plant Treating Saline Wastewater Revealed by a 6-Year Time-Series Analysis.},
journal = {Environmental science &amp; technology},
volume = {55},
number = {4},
pages = {2662-2673},
doi = {10.1021/acs.est.0c07703},
pmid = {33539079},
issn = {1520-5851},
mesh = {Ammonia ; *Archaea/genetics ; Bacteria/genetics ; Extracellular Polymeric Substance Matrix ; Hong Kong ; Oxidation-Reduction ; Phylogeny ; Prevalence ; RNA, Ribosomal, 16S/genetics ; Seasons ; Waste Water ; *Water Purification ; },
abstract = {Although several molecular-based studies have demonstrated the involvement of ammonia-oxidizing archaea (AOA) in ammonia oxidation in wastewater treatment plants (WWTPs), factors affecting the persistence and growth of AOA in these engineered systems have not been resolved. Here, we show a seasonal prevalence of AOA in a full-scale WWTP (Shatin, Hong Kong SAR) over a 6-year period of observation, even outnumbering ammonia-oxidizing bacteria in the seasonal peaks in 3 years, which may be due to the high bioavailable copper concentrations. Comparative analysis of three metagenome-assembled genomes of group I.1a AOA obtained from the activated sludge and 16S rRNA gene sequences recovered from marine sediments suggested that the seawater used for toilet flushing was the primary source of the WWTP AOA. A rare AOA population in the estuarine source water became transiently abundant in the WWTP with a metagenome-based relative abundance of up to 1.3% over three seasons of observation. Correlation-based network analysis revealed a robust co-occurrence relationship between these AOA and organisms potentially active in nitrite oxidation. Moreover, a strong correlation between the dominant AOA and an abundant proteobacterial organism suggested that capacity for extracellular polymeric substance production by the proteobacterium could provide a niche for AOA within bioaggregates. Together, the study highlights the importance of long-term observation in identifying biotic and abiotic factors governing population dynamics in open systems such as full-scale WWTPs.},
}
@article {pmid33538376,
year = {2021},
author = {Sorokin, DY and Messina, E and Smedile, F and La Cono, V and Hallsworth, JE and Yakimov, MM},
title = {Carbohydrate-dependent sulfur respiration in halo(alkali)philic archaea.},
journal = {Environmental microbiology},
volume = {23},
number = {7},
pages = {3789-3808},
doi = {10.1111/1462-2920.15421},
pmid = {33538376},
issn = {1462-2920},
mesh = {*Alkalies ; *Archaea ; Carbohydrates ; Phylogeny ; Respiration ; Sulfur ; },
abstract = {Archaea are environmentally ubiquitous on Earth, and their extremophilic and metabolically versatile phenotypes make them useful as model systems for astrobiology. Here, we reveal a new functional group of halo(natrono)archaea able to utilize alpha-d-glucans (amylopectin, amylose and glycogen), sugars, and glycerol as electron donors and carbon sources for sulfur respiration. They are facultative anaerobes enriched from hypersaline sediments with either amylopectin, glucose or glycerol as electron/carbon sources and elemental sulfur as the terminal electron acceptor. They include 10 strains of neutrophilic haloarchaea from circum pH-neutral lakes and one natronoarchaeon from soda-lake sediments. The neutrophilic isolates can grow by fermentation, although addition of S0 or dimethyl sulfoxide increased growth rate and biomass yield (with a concomitant decrease in H2). Natronoarchaeal isolate AArc-S grew only by respiration, either anaerobically with S0 or thiosulfate as the terminal electron acceptor, or aerobically. Through genome analysis of five representative strains, we detected the full set of enzymes required for the observed catabolic and respiratory phenotypes. These findings provide evidence that sulfur-respiring haloarchaea partake in biogeochemical sulfur cycling, linked to terminal anaerobic carbon mineralization in hypersaline anoxic habitats. We discuss the implications for life detection in analogue environments such as the polar subglacial brine-lakes of Mars.},
}
@article {pmid33527146,
year = {2021},
author = {Ali, MM and Khanom, A and Nahar, K and Ali, MY and Azad, MAK and Rahman, MM},
title = {Effect of Manure Application on Net Nitrification Rates, Heavy Metal Concentrations and Nitrifying Archaea/Bacteria in Soils.},
journal = {Bulletin of environmental contamination and toxicology},
volume = {106},
number = {4},
pages = {707-713},
pmid = {33527146},
issn = {1432-0800},
mesh = {Ammonia ; *Archaea ; Bacteria/genetics ; Manure ; *Metals, Heavy ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Soil ; Soil Microbiology ; },
abstract = {In this study, we determined the effect of manure application on net nitrification rates (NNRs), heavy metal concentrations (HMCs), and abundance of ammonia-oxidizing archaea (AOA)/bacteria (AOB), and nitrite-oxidizing bacteria (NOB) in soil. HMCs were measured by atomic absorption spectroscopy. Abundance of AOA, AOB, and NOB was enumerated by q-PCR. NNRs ranged from 2.8 to 14.7 mg kg-1 h-1 and were significantly (p < 0.05) increased in manure soils as compared to control soils. NNRs were affected by pH 7 and temperature 30°C. Cd, Fe and Pb concentrations were classified as excessively polluted, moderate contamination and slight pollution, respectively, in the manure soils. NNRs and concentrations of Fe and Pb were significantly (p < 0.00) positive correlated, but Cu and Cd were significantly (p < 0.00) negative correlated with NNRs. Application of manure significantly (p < 0.05) increased HMCs (Fe, Cu, and Pb), which have indirect and direct effects on NNRs and nitrifying bacteria.},
}
@article {pmid33519774,
year = {2020},
author = {DeLong, EF},
title = {Exploring Marine Planktonic Archaea: Then and Now.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {616086},
pmid = {33519774},
issn = {1664-302X},
abstract = {In 1977, Woese and Fox leveraged molecular phylogenetic analyses of ribosomal RNAs and identified a new microbial domain of life on Earth, the Archaebacteria (now known as Archaea). At the time of their discovery, only one archaebacterial group, the strictly anaerobic methanogens, was known. But soon, other phenotypically unrelated microbial isolates were shown to belong to the Archaea, many originating from extreme habitats, including extreme halophiles, extreme thermophiles, and thermoacidophiles. Since most Archaea seemed to inhabit extreme or strictly anoxic habitats, it came as a surprise in 1992 when two new lineages of archaea were reported to be abundant in oxygen rich, temperate marine coastal waters and the deep ocean. Since that time, studies of marine planktonic archaea have revealed many more surprises, including their unexpected ubiquity, unusual symbiotic associations, unpredicted physiologies and biogeochemistry, and global abundance. In this Perspective, early work conducted on marine planktonic Archaea by my lab group and others is discussed in terms of the relevant historical context, some of the original research motivations, and surprises and discoveries encountered along the way.},
}
@article {pmid33501490,
year = {2021},
author = {Mueller, RC and Peach, JT and Skorupa, DJ and Copié, V and Bothner, B and Peyton, BM},
title = {An emerging view of the diversity, ecology and function of Archaea in alkaline hydrothermal environments.},
journal = {FEMS microbiology ecology},
volume = {97},
number = {2},
pages = {},
doi = {10.1093/femsec/fiaa246},
pmid = {33501490},
issn = {1574-6941},
mesh = {*Archaea/genetics ; Bacteria ; Ecology ; Ecosystem ; *Hot Springs ; Phylogeny ; },
abstract = {The described diversity within the domain Archaea has recently expanded due to advances in sequencing technologies, but many habitats that likely harbor novel lineages of archaea remain understudied. Knowledge of archaea within natural and engineered hydrothermal systems, such as hot springs and engineered subsurface habitats, has been steadily increasing, but the majority of the work has focused on archaea living in acidic or circumneutral environments. The environmental pressures exerted by the combination of high temperatures and high pH likely select for divergent communities and distinct metabolic pathways from those observed in acidic or circumneutral systems. In this review, we examine what is currently known about the archaea found in thermoalkaline environments, focusing on the detection of novel lineages and knowledge of the ecology, metabolic pathways and functions of these populations and communities. We also discuss the potential of emerging multi-omics approaches, including proteomics and metabolomics, to enhance our understanding of archaea within extreme thermoalkaline systems.},
}
@article {pmid33499367,
year = {2021},
author = {Tittes, C and Schwarzer, S and Quax, TEF},
title = {Viral Hijack of Filamentous Surface Structures in Archaea and Bacteria.},
journal = {Viruses},
volume = {13},
number = {2},
pages = {},
pmid = {33499367},
issn = {1999-4915},
mesh = {Archaea/*virology ; Archaeal Viruses/*physiology ; Bacteria/*virology ; Bacteriophages/*physiology ; Cytoskeleton/*virology ; Fimbriae Proteins ; Fimbriae, Bacterial/virology ; Flagella/virology ; },
abstract = {The bacterial and archaeal cell surface is decorated with filamentous surface structures that are used for different functions, such as motility, DNA exchange and biofilm formation. Viruses hijack these structures and use them to ride to the cell surface for successful entry. In this review, we describe currently known mechanisms for viral attachment, translocation, and entry via filamentous surface structures. We describe the different mechanisms used to exploit various surface structures bacterial and archaeal viruses. This overview highlights the importance of filamentous structures at the cell surface for entry of prokaryotic viruses.},
}
@article {pmid33495623,
year = {2021},
author = {He, C and Keren, R and Whittaker, ML and Farag, IF and Doudna, JA and Cate, JHD and Banfield, JF},
title = {Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems.},
journal = {Nature microbiology},
volume = {6},
number = {3},
pages = {354-365},
pmid = {33495623},
issn = {2058-5276},
support = {/HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Agriculture ; Archaea/classification/*physiology/ultrastructure ; Bacteria/classification/ultrastructure ; *Bacterial Physiological Phenomena ; Cell Adhesion ; Cell Proliferation ; *Ecosystem ; Groundwater/chemistry/*microbiology ; Humans ; Metagenome ; Metagenomics/*methods ; Microbiota ; Phylogeny ; Symbiosis ; },
abstract = {Candidate phyla radiation (CPR) bacteria and DPANN archaea are unisolated, small-celled symbionts that are often detected in groundwater. The effects of groundwater geochemistry on the abundance, distribution, taxonomic diversity and host association of CPR bacteria and DPANN archaea has not been studied. Here, we performed genome-resolved metagenomic analysis of one agricultural and seven pristine groundwater microbial communities and recovered 746 CPR and DPANN genomes in total. The pristine sites, which serve as local sources of drinking water, contained up to 31% CPR bacteria and 4% DPANN archaea. We observed little species-level overlap of metagenome-assembled genomes (MAGs) across the groundwater sites, indicating that CPR and DPANN communities may be differentiated according to physicochemical conditions and host populations. Cryogenic transmission electron microscopy imaging and genomic analyses enabled us to identify CPR and DPANN lineages that reproducibly attach to host cells and showed that the growth of CPR bacteria seems to be stimulated by attachment to host-cell surfaces. Our analysis reveals site-specific diversity of CPR bacteria and DPANN archaea that coexist with diverse hosts in groundwater aquifers. Given that CPR and DPANN organisms have been identified in human microbiomes and their presence is correlated with diseases such as periodontitis, our findings are relevant to considerations of drinking water quality and human health.},
}
@article {pmid33476388,
year = {2021},
author = {Lewis, AM and Recalde, A and Bräsen, C and Counts, JA and Nussbaum, P and Bost, J and Schocke, L and Shen, L and Willard, DJ and Quax, TEF and Peeters, E and Siebers, B and Albers, SV and Kelly, RM},
title = {The biology of thermoacidophilic archaea from the order Sulfolobales.},
journal = {FEMS microbiology reviews},
volume = {45},
number = {4},
pages = {},
pmid = {33476388},
issn = {1574-6976},
support = {GM008776-16/NH/NIH HHS/United States ; Pr-2013-0010//MERCUR/ ; T32 GM008776/GM/NIGMS NIH HHS/United States ; T32 GM133366/GM/NIGMS NIH HHS/United States ; CBET-1802939//National Science Foundation/ ; //Mercator Foundation/ ; 031L0078A//Federal Ministry of Education and Research/ ; FA9550-17-1-0268//AFOSR/ ; T32 AI007392/AI/NIAID NIH HHS/United States ; 411069969//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Archaea/genetics ; Biology ; Iron ; *Sulfolobales ; },
abstract = {Thermoacidophilic archaea belonging to the order Sulfolobales thrive in extreme biotopes, such as sulfuric hot springs and ore deposits. These microorganisms have been model systems for understanding life in extreme environments, as well as for probing the evolution of both molecular genetic processes and central metabolic pathways. Thermoacidophiles, such as the Sulfolobales, use typical microbial responses to persist in hot acid (e.g. motility, stress response, biofilm formation), albeit with some unusual twists. They also exhibit unique physiological features, including iron and sulfur chemolithoautotrophy, that differentiate them from much of the microbial world. Although first discovered >50 years ago, it was not until recently that genome sequence data and facile genetic tools have been developed for species in the Sulfolobales. These advances have not only opened up ways to further probe novel features of these microbes but also paved the way for their potential biotechnological applications. Discussed here are the nuances of the thermoacidophilic lifestyle of the Sulfolobales, including their evolutionary placement, cell biology, survival strategies, genetic tools, metabolic processes and physiological attributes together with how these characteristics make thermoacidophiles ideal platforms for specialized industrial processes.},
}
@article {pmid33469805,
year = {2021},
author = {Lyu, Z},
title = {Back to the Source: Molecular Identification of Methanogenic Archaea as Markers of Colonic Methane Production.},
journal = {Digestive diseases and sciences},
volume = {66},
number = {11},
pages = {3661-3664},
pmid = {33469805},
issn = {1573-2568},
mesh = {*Archaea/genetics ; *Euryarchaeota ; Humans ; Methane ; },
}
@article {pmid33462984,
year = {2021},
author = {Kevorkian, RT and Callahan, S and Winstead, R and Lloyd, KG},
title = {ANME-1 archaea may drive methane accumulation and removal in estuarine sediments.},
journal = {Environmental microbiology reports},
volume = {13},
number = {2},
pages = {185-194},
doi = {10.1111/1758-2229.12926},
pmid = {33462984},
issn = {1758-2229},
mesh = {Anaerobiosis ; *Archaea ; Geologic Sediments/microbiology ; *Methane/metabolism ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {ANME-1 archaea subsist on the very low energy of anaerobic oxidation of methane (AOM). Most marine sediments shift from net AOM in the sulfate methane transition zone (SMTZ) to methanogenesis in the methane zone (MZ) below it. In White Oak River estuarine sediments, ANME-1 comprised 99.5% of 16S rRNA genes from amplicons and 100% of 16S rRNA genes from metagenomes of the Methanomicrobia in the SMTZ and 99.9% and 98.3%, respectively, in the MZ. Each of the 16 ANME-1 OTUs (97% similarity) had peaks in the SMTZ that coincided with peaks of putative sulfate-reducing bacteria Desulfatiglans sp. and SEEP-SRB1. In the MZ, ANME-1, but none of the putative sulfate-reducing bacteria or cultured methanogens, increased with depth. Our meta-analysis of public data showed only ANME-1 expressed methanogenic genes during both net AOM and net methanogenesis in an enrichment culture. We conclude that ANME-1 perform AOM in the SMTZ and methanogenesis in the MZ of White Oak River sediments. This metabolic flexibility may expand habitable zones in extraterrestrial environments, since it enables greater energy yields in a fluctuating energetic landscape.},
}
@article {pmid33462601,
year = {2021},
author = {Garg, SG and Kapust, N and Lin, W and Knopp, M and Tria, FDK and Nelson-Sathi, S and Gould, SB and Fan, L and Zhu, R and Zhang, C and Martin, WF},
title = {Anomalous Phylogenetic Behavior of Ribosomal Proteins in Metagenome-Assembled Asgard Archaea.},
journal = {Genome biology and evolution},
volume = {13},
number = {1},
pages = {},
pmid = {33462601},
issn = {1759-6653},
mesh = {Archaea/*genetics ; Ecosystem ; Eukaryota/genetics ; Eukaryotic Cells ; Evolution, Molecular ; *Genome, Archaeal ; Genomics ; *Metagenome ; Metagenomics ; *Phylogeny ; Ribosomal Proteins/*classification/*genetics ; },
abstract = {Metagenomic studies permit the exploration of microbial diversity in a defined habitat, and binning procedures enable phylogenomic analyses, taxon description, and even phenotypic characterizations in the absence of morphological evidence. Such lineages include asgard archaea, which were initially reported to represent archaea with eukaryotic cell complexity, although the first images of such an archaeon show simple cells with prokaryotic characteristics. However, these metagenome-assembled genomes (MAGs) might suffer from data quality problems not encountered in sequences from cultured organisms due to two common analytical procedures of bioinformatics: assembly of metagenomic sequences and binning of assembled sequences on the basis of innate sequence properties and abundance across samples. Consequently, genomic sequences of distantly related taxa, or domains, can in principle be assigned to the same MAG and result in chimeric sequences. The impacts of low-quality or chimeric MAGs on phylogenomic and metabolic prediction remain unknown. Debates that asgard archaeal data are contaminated with eukaryotic sequences are overshadowed by the lack of evidence indicating that individual asgard MAGs stem from the same chromosome. Here, we show that universal proteins including ribosomal proteins of asgard archaeal MAGs fail to meet the basic phylogenetic criterion fulfilled by genome sequences of cultured archaea investigated to date: These proteins do not share common evolutionary histories to the same extent as pure culture genomes do, pointing to a chimeric nature of asgard archaeal MAGs. Our analysis suggests that some asgard archaeal MAGs represent unnatural constructs, genome-like patchworks of genes resulting from assembly and/or the binning process.},
}
@article {pmid33453701,
year = {2021},
author = {Tao, R and Li, J and Hu, B and Chu, G},
title = {Mitigating N2O emission by synthetic inhibitors mixed with urea and cattle manure application via inhibiting ammonia-oxidizing bacteria, but not archaea, in a calcareous soil.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {273},
number = {},
pages = {116478},
doi = {10.1016/j.envpol.2021.116478},
pmid = {33453701},
issn = {1873-6424},
abstract = {Synthetic inhibitors and organic amendment have been proposed for mitigating greenhouse gas N2O emissions. However, their combined effect on the N2O emissions and ammonia-oxidizer (ammonia-oxidizing bacteria and archaea, AOB and AOA) communities remains unclear in calcareous soils under climate warming. We conducted two incubation experiments (25 and 35 °C) to examine how N2O emissions and AOA and AOB communities responded to organic amendment (urea plus cattle manure, UCM), and in combination with urease (N-(n-butyl) thiophosphoric triamide, NBPT) and nitrification inhibitor (nitrapyrin). The treatments of UCM + nitrapyrin and UCM + nitrapyrin + NBPT significantly lowered total N2O emissions by average 64.5 and 71.05% at 25 and 35 °C, respectively, compared with UCM treatment. AOB gene abundance and α-diversity (Chao1 and Shannon indices) were significantly increased by the application of urea and manure (P < 0.05). However, relative to UCM treatment, nitrapyrin addition treatments decreased AOB gene abundance and Chao 1 index by average 115.4 and 30.4% at 25 and 35 °C, respectively. PCA analysis showed that UCM or UCM plus nitrapyrin notably shifted AOB structure at both temperatures. However, fertilization had little effects on AOA community (P > 0.05). Potential nitrification rate (PNR) was greatly decreased by nitrapyrin addition, and PNR significantly positively correlated with AOB gene abundance (P = 0.0179 at 25 °C and P = 0.0029 at 35 °C) rather than AOA (P > 0.05). Structural equation model analysis showed that temperature directly increased AOA abundance but decrease AOB abundance, while fertilization indirectly influenced AOB community by altering soil NH4+, pH and SOC. In conclusion, the combined application of organic amendment, NBPT and nitrapyrin significantly lowered N2O emissions via reducing AOB community in calcareous soil even at high temperature. Our findings provide a solid theoretical basis in mitigating N2O emissions from calcareous soil under climate warming.},
}
@article {pmid33452484,
year = {2021},
author = {Zhang, JW and Dong, HP and Hou, LJ and Liu, Y and Ou, YF and Zheng, YL and Han, P and Liang, X and Yin, GY and Wu, DM and Liu, M and Li, M},
title = {Newly discovered Asgard archaea Hermodarchaeota potentially degrade alkanes and aromatics via alkyl/benzyl-succinate synthase and benzoyl-CoA pathway.},
journal = {The ISME journal},
volume = {15},
number = {6},
pages = {1826-1843},
pmid = {33452484},
issn = {1751-7370},
mesh = {Acyl Coenzyme A ; *Alkanes ; *Archaea/genetics ; Geologic Sediments ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Succinic Acid ; },
abstract = {Asgard archaea are widely distributed in anaerobic environments. Previous studies revealed the potential capability of Asgard archaea to utilize various organic substrates including proteins, carbohydrates, fatty acids, amino acids and hydrocarbons, suggesting that Asgard archaea play an important role in sediment carbon cycling. Here, we describe a previously unrecognized archaeal phylum, Hermodarchaeota, affiliated with the Asgard superphylum. The genomes of these archaea were recovered from metagenomes generated from mangrove sediments, and were found to encode alkyl/benzyl-succinate synthases and their activating enzymes that are similar to those identified in alkane-degrading sulfate-reducing bacteria. Hermodarchaeota also encode enzymes potentially involved in alkyl-coenzyme A and benzoyl-coenzyme A oxidation, the Wood-Ljungdahl pathway and nitrate reduction. These results indicate that members of this phylum have the potential to strictly anaerobically degrade alkanes and aromatic compounds, coupling the reduction of nitrate. By screening Sequence Read Archive, additional genes encoding 16S rRNA and alkyl/benzyl-succinate synthases analogous to those in Hermodarchaeota were identified in metagenomic datasets from a wide range of marine and freshwater sediments. These findings suggest that Asgard archaea capable of degrading alkanes and aromatics via formation of alkyl/benzyl-substituted succinates are ubiquitous in sediments.},
}
@article {pmid33452028,
year = {2021},
author = {Aldridge, J and Carr, S and Weber, KA and Buan, NR},
title = {Anaerobic Production of Isoprene by Engineered Methanosarcina Species Archaea.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {6},
pages = {},
pmid = {33452028},
issn = {1098-5336},
mesh = {Anaerobiosis ; Butadienes ; Hemiterpenes/*biosynthesis ; Methanol/metabolism ; Methanosarcina/genetics/*metabolism ; Mevalonic Acid ; Microorganisms, Genetically-Modified/metabolism ; },
abstract = {Isoprene is a valuable petrochemical used for a wide variety of consumer goods, such as adhesives and synthetic rubber. We were able to achieve a high yield of renewable isoprene by taking advantage of the naturally high-flux mevalonate lipid synthesis pathway in anaerobic methane-producing archaea (methanogens). Our study illustrates that by genetically manipulating Methanosarcina species methanogens, it is possible to create organisms that grow by producing the hemiterpene isoprene. Mass balance measurements show that engineered methanogens direct up to 4% of total carbon flux to isoprene, demonstrating that methanogens produce higher isoprene yields than engineered yeast, bacteria, or cyanobacteria, and from inexpensive feedstocks. Expression of isoprene synthase resulted in increased biomass and changes in gene expression that indicate that isoprene synthesis depletes membrane precursors and redirects electron flux, enabling isoprene to be a major metabolic product. Our results demonstrate that methanogens are a promising engineering chassis for renewable isoprene synthesis.IMPORTANCE A significant barrier to implementing renewable chemical technologies is high production costs relative to those for petroleum-derived products. Existing technologies using engineered organisms have difficulty competing with petroleum-derived chemicals due to the cost of feedstocks (such as glucose), product extraction, and purification. The hemiterpene monomer isoprene is one such chemical that cannot currently be produced using cost-competitive renewable biotechnologies. To reduce the cost of renewable isoprene, we have engineered methanogens to synthesize it from inexpensive feedstocks such as methane, methanol, acetate, and carbon dioxide. The "isoprenogen" strains we developed have potential to be used for industrial production of inexpensive renewable isoprene.},
}
@article {pmid33444853,
year = {2021},
author = {Yang, Y and Herbold, CW and Jung, MY and Qin, W and Cai, M and Du, H and Lin, JG and Li, X and Li, M and Gu, JD},
title = {Survival strategies of ammonia-oxidizing archaea (AOA) in a full-scale WWTP treating mixed landfill leachate containing copper ions and operating at low-intensity of aeration.},
journal = {Water research},
volume = {191},
number = {},
pages = {116798},
doi = {10.1016/j.watres.2020.116798},
pmid = {33444853},
issn = {1879-2448},
mesh = {Ammonia ; *Archaea/genetics ; Bacteria ; Copper ; Ions ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Soil Microbiology ; *Water Pollutants, Chemical ; },
abstract = {Recent studies indicate that ammonia-oxidizing archaea (AOA) may play an important role in nitrogen removal by wastewater treatment plants (WWTPs). However, our knowledge of the mechanisms employed by AOA for growth and survival in full-scale WWTPs is still limited. Here, metagenomic and metatranscriptomic analyses combined with a laboratory cultivation experiment revealed that three active AOAs (WS9, WS192, and WS208) belonging to family Nitrososphaeraceae were active in the deep oxidation ditch (DOD) of a full-scale WWTP treating landfill leachate, which is configured with three continuous aerobic-anoxic (OA) modules with low-intensity aeration (≤ 1.5 mg/L). AOA coexisted with AOB and complete ammonia oxidizers (Comammox), while the ammonia-oxidizing microbial (AOM) community was unexpectedly dominated by the novel AOA strain WS9. The low aeration, long retention time, and relatively high inputs of ammonium and copper might be responsible for the survival of AOA over AOB and Comammox, while the dominance of WS9, specifically may be enhanced by substrate preference and uniquely encoded retention strategies. The urease-negative WS9 is specifically adapted for ammonia acquisition as evidenced by the high expression of an ammonium transporter, whereas two metabolically versatile urease-positive AOA strains (WS192 and WS208) can likely supplement ammonia needs with urea. This study provides important information for the survival and application of the eutrophic Nitrososphaeraceae AOA and advances our understanding of archaea-dominated ammonia oxidation in a full-scale wastewater treatment system.},
}
@article {pmid33434266,
year = {2021},
author = {Knüppel, R and Trahan, C and Kern, M and Wagner, A and Grünberger, F and Hausner, W and Quax, TEF and Albers, SV and Oeffinger, M and Ferreira-Cerca, S},
title = {Insights into synthesis and function of KsgA/Dim1-dependent rRNA modifications in archaea.},
journal = {Nucleic acids research},
volume = {49},
number = {3},
pages = {1662-1687},
pmid = {33434266},
issn = {1362-4962},
support = {PJT 386315//CIHR/Canada ; },
mesh = {Archaea/*enzymology/genetics ; Cell Movement ; Crenarchaeota/enzymology ; Euryarchaeota/enzymology ; Haloferax volcanii/enzymology ; Methyltransferases/*metabolism/physiology ; Protein Biosynthesis ; RNA, Archaeal/chemistry/*metabolism ; RNA, Ribosomal/chemistry/*metabolism ; Ribosome Subunits, Small, Archaeal/enzymology ; },
abstract = {Ribosomes are intricate molecular machines ensuring proper protein synthesis in every cell. Ribosome biogenesis is a complex process which has been intensively analyzed in bacteria and eukaryotes. In contrast, our understanding of the in vivo archaeal ribosome biogenesis pathway remains less characterized. Here, we have analyzed the in vivo role of the almost universally conserved ribosomal RNA dimethyltransferase KsgA/Dim1 homolog in archaea. Our study reveals that KsgA/Dim1-dependent 16S rRNA dimethylation is dispensable for the cellular growth of phylogenetically distant archaea. However, proteomics and functional analyses suggest that archaeal KsgA/Dim1 and its rRNA modification activity (i) influence the expression of a subset of proteins and (ii) contribute to archaeal cellular fitness and adaptation. In addition, our study reveals an unexpected KsgA/Dim1-dependent variability of rRNA modifications within the archaeal phylum. Combining structure-based functional studies across evolutionary divergent organisms, we provide evidence on how rRNA structure sequence variability (re-)shapes the KsgA/Dim1-dependent rRNA modification status. Finally, our results suggest an uncoupling between the KsgA/Dim1-dependent rRNA modification completion and its release from the nascent small ribosomal subunit. Collectively, our study provides additional understandings into principles of molecular functional adaptation, and further evolutionary and mechanistic insights into an almost universally conserved step of ribosome synthesis.},
}
@article {pmid33432457,
year = {2021},
author = {Wang, YF and Gu, JD and Dick, RP and Han, W and Yang, HX and Liao, HQ and Zhou, Y and Meng, H},
title = {Distribution of ammonia-oxidizing archaea and bacteria along an engineered coastal ecosystem in subtropical China.},
journal = {Ecotoxicology (London, England)},
volume = {30},
number = {8},
pages = {1769-1779},
pmid = {33432457},
issn = {1573-3017},
support = {2018KJCX011//Guangdong Forestry Scientific and Technological Innovation Key Program/ ; },
mesh = {*Ammonia ; *Archaea/genetics ; Bacteria/genetics ; China ; Ecosystem ; Humans ; Oxidation-Reduction ; Phylogeny ; Soil ; Soil Microbiology ; },
abstract = {Ammonia-oxidizing archaea (AOA) and bacteria (AOB) are the crucial players in nitrogen cycle. Both AOA and AOB were examined along a gradient of human activity in a coastal ecosystem from intertidal zone, grassland, and Casuarina equisetifolia forest to farmland. Results showed that the farmland soils had noticeably higher nitrate-N, available P than soils in the other three sites. Generally, AOA and AOB community structures varied across sites. The farmland mainly had Nitrosotalea-like AOA, intertidal zone was dominated by Nitrosopumilus AOA, while grassland and C. equisetifolia forest primarily harbored Nitrososphaera-like AOA. The farmland and C. equisetifolia forest owned Nitrosospira-like AOB, intertidal zone possessed Nitrosomonas-like AOB, and no AOB was detected in the grassland. AOA abundance was significantly greater than AOB in this coastal ecosystem (p < 0.05, n = 8). AOB diversity and abundance in the farmland were significantly higher than those in the other three sites (p < 0.05, n = 2). The biodiversity and abundance of AOA were not significantly correlated with any soil property (p < 0.05, n = 8). However, the diversity of AOB was significantly correlated with pH, available P and total P (p < 0.05, n = 6). The abundance of AOB was significantly correlated with pH, nitrite, available N, available P and total P (p < 0.05, n = 6). This study suggested that the community structures of AOA and AOB vary in the different parts in the bio-engineered coastal ecosystem and agricultural activity appears to influence these nitrifiers.},
}
@article {pmid33385817,
year = {2021},
author = {Zheng, T and Li, W and Ma, Y and Liu, J},
title = {Time-based succession existed in rural sewer biofilms: Bacterial communities, sulfate-reducing bacteria and methanogenic archaea, and sulfide and methane generation.},
journal = {The Science of the total environment},
volume = {765},
number = {},
pages = {144397},
doi = {10.1016/j.scitotenv.2020.144397},
pmid = {33385817},
issn = {1879-1026},
mesh = {*Archaea ; Bacteria ; Biofilms ; Family Characteristics ; *Methane ; Sewage ; Sulfates ; Sulfides ; },
abstract = {Rural sewers are applied widely to collect rural sewage and biofilm characteristics in rural sewers may be different with municipal sewers. The succession of bacteria communities, sulfate-reducing bacteria (SRB) and methanogenic archaea (MA) need to be studied since rural sewers have a potential risk of sulfide and methane accumulation. In this study, lab-scale rural sewer facilities were established to analyze the characteristics of sewer biofilm and the generation of sulfide and methane. The results indicate that the variation tendency of biofilm thickness in rural sewers was different with municipal sewers. Time-based bacterial succession existed in rural sewer biofilms and the predominant genus was changed from Acinetobacter (approximately 19.10%) to Pseudomonas (approximately 12.61%). SRB (mean 1.49 × 106dsrA copies/cm2) were abundant than MA (mean 2.57 × 105mcrA copies/cm2) while MA were eliminated gradually in rural sewer biofilms. The tendency of sulfide and methane generation was similar with the number variation of SRB and MA, indicating sulfide accumulation might be more serious trouble than methane accumulation in a long-run rural sewer. Overall, this study deeply analyzed the succession of rural sewer biofilms and found that MA and methane were automatically inhibited in rural sewers.},
}
@article {pmid33383035,
year = {2021},
author = {Laursen, SP and Bowerman, S and Luger, K},
title = {Archaea: The Final Frontier of Chromatin.},
journal = {Journal of molecular biology},
volume = {433},
number = {6},
pages = {166791},
pmid = {33383035},
issn = {1089-8638},
support = {/HHMI/Howard Hughes Medical Institute/United States ; F32 GM137496/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Archaea/classification/*genetics/metabolism ; Archaeal Proteins/*chemistry/genetics/metabolism ; Chromatin/chemistry/metabolism/*ultrastructure ; Conserved Sequence ; DNA, Archaeal/*chemistry/genetics/metabolism ; DNA-Binding Proteins/*chemistry/genetics/metabolism ; Histones/*chemistry/genetics/metabolism ; Nucleic Acid Conformation ; Phylogeny ; Protein Binding ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Protein Interaction Domains and Motifs ; Protein Multimerization ; },
abstract = {The three domains of life employ various strategies to organize their genomes. Archaea utilize features similar to those found in both eukaryotic and bacterial chromatin to organize their DNA. In this review, we discuss the current state of research regarding the structure-function relationships of several archaeal chromatin proteins (histones, Alba, Cren7, and Sul7d). We address individual structures as well as inferred models for higher-order chromatin formation. Each protein introduces a unique phenotype to chromatin organization, and these structures are put into the context of in vivo and in vitro data. We close by discussing the present gaps in knowledge that are preventing further studies of the organization of archaeal chromatin, on both the organismal and domain level.},
}
@article {pmid33343547,
year = {2020},
author = {Kuprat, T and Johnsen, U and Ortjohann, M and Schönheit, P},
title = {Acetate Metabolism in Archaea: Characterization of an Acetate Transporter and of Enzymes Involved in Acetate Activation and Gluconeogenesis in Haloferax volcanii.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {604926},
pmid = {33343547},
issn = {1664-302X},
abstract = {The haloarchaeon Haloferax volcanii grows on acetate as sole carbon and energy source. The genes and proteins involved in uptake and activation of acetate and in gluconeogenesis were identified and analyzed by characterization of enzymes and by growth experiments with the respective deletion mutants. (i) An acetate transporter of the sodium: solute-symporter family (SSF) was characterized by kinetic analyses of acetate uptake into H. volcanii cells. The functional involvement of the transporter was proven with a Δssf mutant. (ii) Four paralogous AMP-forming acetyl-CoA synthetases that belong to different phylogenetic clades were shown to be functionally involved in acetate activation. (iii) The essential involvement of the glyoxylate cycle as an anaplerotic sequence was concluded from growth experiments with an isocitrate lyase knock-out mutant excluding the operation of the methylaspartate cycle reported for Haloarcula species. (iv) Enzymes involved in phosphoenolpyruvate synthesis from acetate, namely two malic enzymes and a phosphoenolpyruvate synthetase, were identified and characterized. Phylogenetic analyses of haloarchaeal malic enzymes indicate a separate evolutionary line distinct from other archaeal homologs. The exclusive function of phosphoenolpyruvate synthetase in gluconeogenesis was proven by the respective knock-out mutant. Together, this is a comprehensive study of acetate metabolism in archaea.},
}
@article {pmid33329506,
year = {2020},
author = {Skretas, G and Ventura, S},
title = {Editorial: Protein Aggregation and Solubility in Microorganisms (Archaea, Bacteria and Unicellular Eukaryotes): Implications and Applications.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {620239},
pmid = {33329506},
issn = {1664-302X},
}
@article {pmid33329479,
year = {2020},
author = {Schwarz, TS and Berkemer, SJ and Bernhart, SH and Weiß, M and Ferreira-Cerca, S and Stadler, PF and Marchfelder, A},
title = {Splicing Endonuclease Is an Important Player in rRNA and tRNA Maturation in Archaea.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {594838},
pmid = {33329479},
issn = {1664-302X},
abstract = {In all three domains of life, tRNA genes contain introns that must be removed to yield functional tRNA. In archaea and eukarya, the first step of this process is catalyzed by a splicing endonuclease. The consensus structure recognized by the splicing endonuclease is a bulge-helix-bulge (BHB) motif which is also found in rRNA precursors. So far, a systematic analysis to identify all biological substrates of the splicing endonuclease has not been carried out. In this study, we employed CRISPRi to repress expression of the splicing endonuclease in the archaeon Haloferax volcanii to identify all substrates of this enzyme. Expression of the splicing endonuclease was reduced to 1% of its normal level, resulting in a significant extension of lag phase in H. volcanii growth. In the repression strain, 41 genes were down-regulated and 102 were up-regulated. As an additional approach in identifying new substrates of the splicing endonuclease, we isolated and sequenced circular RNAs, which identified excised introns removed from tRNA and rRNA precursors as well as from the 5' UTR of the gene HVO_1309. In vitro processing assays showed that the BHB sites in the 5' UTR of HVO_1309 and in a 16S rRNA-like precursor are processed by the recombinant splicing endonuclease. The splicing endonuclease is therefore an important player in RNA maturation in archaea.},
}
@article {pmid33329440,
year = {2020},
author = {Distaso, MA and Bargiela, R and Brailsford, FL and Williams, GB and Wright, S and Lunev, EA and Toshchakov, SV and Yakimov, MM and Jones, DL and Golyshin, PN and Golyshina, OV},
title = {High Representation of Archaea Across All Depths in Oxic and Low-pH Sediment Layers Underlying an Acidic Stream.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {576520},
pmid = {33329440},
issn = {1664-302X},
abstract = {Parys Mountain or Mynydd Parys (Isle of Anglesey, United Kingdom) is a mine-impacted environment, which accommodates a variety of acidophilic organisms. Our previous research of water and sediments from one of the surface acidic streams showed a high proportion of archaea in the total microbial community. To understand the spatial distribution of archaea, we sampled cores (0-20 cm) of sediment and conducted chemical analyses and taxonomic profiling of microbiomes using 16S rRNA gene amplicon sequencing in different core layers. The taxonomic affiliation of sequencing reads indicated that archaea represented between 6.2 and 54% of the microbial community at all sediment depths. Majority of archaea were associated with the order Thermoplasmatales, with the most abundant group of sequences being clustered closely with the phylotype B_DKE, followed by "E-plasma," "A-plasma," other yet uncultured Thermoplasmatales with Ferroplasma and Cuniculiplasma spp. represented in minor proportions. Thermoplasmatales were found at all depths and in the whole range of chemical conditions with their abundance correlating with sediment Fe, As, Cr, and Mn contents. The bacterial microbiome component was largely composed in all layers of sediment by members of the phyla Proteobacteria, Actinobacteria, Nitrospirae, Firmicutes, uncultured Chloroflexi (AD3 group), and Acidobacteria. This study has revealed a high abundance of Thermoplasmatales in acid mine drainage-affected sediment layers and pointed at these organisms being the main contributors to carbon, and probably to iron and sulfur cycles in this ecosystem.},
}
@article {pmid33325687,
year = {2021},
author = {Stein, LY and Klotz, MG and Lancaster, KM and Nicol, GW and Qin, W and Schleper, C and Stahl, D and Ward, BB and Yoon, S},
title = {Comment on"A Critical Review on Nitrous Oxide Production by Ammonia-Oxidizing Archaea" by Lan Wu, Xueming Chen, Wei Wei, Yiwen Liu, Dongbo Wang, and Bing-Jie Ni.},
journal = {Environmental science &amp; technology},
volume = {55},
number = {1},
pages = {797-798},
doi = {10.1021/acs.est.0c06792},
pmid = {33325687},
issn = {1520-5851},
mesh = {*Ammonia ; *Archaea ; Nitrification ; Nitrous Oxide ; Oxidation-Reduction ; },
}
@article {pmid33325686,
year = {2021},
author = {Wu, L and Wei, W and Ni, BJ},
title = {Response to Comment on "A Critical Review on Nitrous Oxide Production by Ammonia-Oxidizing Archaea".},
journal = {Environmental science &amp; technology},
volume = {55},
number = {1},
pages = {799-800},
doi = {10.1021/acs.est.0c08136},
pmid = {33325686},
issn = {1520-5851},
mesh = {*Ammonia ; *Archaea ; Nitrification ; Nitrous Oxide ; Oxidation-Reduction ; },
}
@article {pmid33320181,
year = {2021},
author = {Thomès, L and Lescure, A},
title = {Mosaic Evolution of the Phosphopantothenate Biosynthesis Pathway in Bacteria and Archaea.},
journal = {Genome biology and evolution},
volume = {13},
number = {2},
pages = {},
pmid = {33320181},
issn = {1759-6653},
mesh = {Archaea/*enzymology/genetics ; Bacteria/*enzymology/genetics ; Biosynthetic Pathways/genetics ; Coenzyme A/*biosynthesis ; *Evolution, Molecular ; Genes, Bacterial ; Symbiosis ; },
abstract = {Phosphopantothenate is a precursor to synthesis of coenzyme A, a molecule essential to many metabolic pathways. Organisms of the archaeal phyla were shown to utilize a different phosphopantothenate biosynthetic pathway from the eukaryotic and bacterial one. In this study, we report that symbiotic bacteria from the group Candidatus poribacteria present enzymes of the archaeal pathway, namely pantoate kinase and phosphopantothenate synthetase, mirroring what was demonstrated for Picrophilus torridus, an archaea partially utilizing the bacterial pathway. Our results not only support the ancient origin of the coenzyme A pathway in the three domains of life but also highlight its complex and dynamic evolution. Importantly, this study helps to improve protein annotation for this pathway in the C. poribacteria group and other related organisms.},
}
@article {pmid33316511,
year = {2021},
author = {Ding, J and Zeng, RJ},
title = {Fundamentals and potential environmental significance of denitrifying anaerobic methane oxidizing archaea.},
journal = {The Science of the total environment},
volume = {757},
number = {},
pages = {143928},
doi = {10.1016/j.scitotenv.2020.143928},
pmid = {33316511},
issn = {1879-1026},
mesh = {Anaerobiosis ; *Archaea ; Bioreactors ; Denitrification ; *Methane ; Nitrites ; Oxidation-Reduction ; },
abstract = {Many properties of denitrifying anaerobic methane oxidation (DAMO) bacteria have been explored since their first discovery, while DAMO archaea have attracted less attention. Since nitrate is more abundant than nitrite not only in wastewater but also in the natural environment, in depth investigations of the nitrate-DAMO process should be conducted to determine its environmental significance in the global carbon and nitrogen cycles. This review summarizes the status of research on DAMO archaea and the catalyzed nitrate-dependent anaerobic methane oxidation, including such aspects as laboratory enrichment, environmental distribution, and metabolic mechanism. It is shown that appropriate inocula and enrichment parameters are important for the culture enrichment and thus the subsequent DAMO activity, but there are still relatively few studies on the environmental distribution and physiological metabolism of DAMO archaea. Finally, some hypotheses and directions for future research on DAMO archaea, anaerobic methanotrophic archaea, and even anaerobically metabolizing archaea are also discussed.},
}
@article {pmid33288720,
year = {2020},
author = {Stevens, KM and Swadling, JB and Hocher, A and Bang, C and Gribaldo, S and Schmitz, RA and Warnecke, T},
title = {Histone variants in archaea and the evolution of combinatorial chromatin complexity.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {117},
number = {52},
pages = {33384-33395},
pmid = {33288720},
issn = {1091-6490},
support = {MC_UP_1102/7/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Amino Acids/genetics ; Archaea/*genetics ; Chromatin/*metabolism ; DNA/metabolism ; *Evolution, Molecular ; *Genetic Variation ; Histones/chemistry/*genetics/metabolism ; Molecular Dynamics Simulation ; Mutation/genetics ; Phylogeny ; Protein Binding ; },
abstract = {Nucleosomes in eukaryotes act as platforms for the dynamic integration of epigenetic information. Posttranslational modifications are reversibly added or removed and core histones exchanged for paralogous variants, in concert with changing demands on transcription and genome accessibility. Histones are also common in archaea. Their role in genome regulation, however, and the capacity of individual paralogs to assemble into histone-DNA complexes with distinct properties remain poorly understood. Here, we combine structural modeling with phylogenetic analysis to shed light on archaeal histone paralogs, their evolutionary history, and capacity to generate combinatorial chromatin states through hetero-oligomeric assembly. Focusing on the human commensal Methanosphaera stadtmanae as a model archaeal system, we show that the heteromeric complexes that can be assembled from its seven histone paralogs vary substantially in DNA binding affinity and tetramer stability. Using molecular dynamics simulations, we go on to identify unique paralogs in M. stadtmanae and Methanobrevibacter smithii that are characterized by unstable interfaces between dimers. We propose that these paralogs act as capstones that prevent stable tetramer formation and extension into longer oligomers characteristic of model archaeal histones. Importantly, we provide evidence from phylogeny and genome architecture that these capstones, as well as other paralogs in the Methanobacteriales, have been maintained for hundreds of millions of years following ancient duplication events. Taken together, our findings indicate that at least some archaeal histone paralogs have evolved to play distinct and conserved functional roles, reminiscent of eukaryotic histone variants. We conclude that combinatorially complex histone-based chromatin is not restricted to eukaryotes and likely predates their emergence.},
}
@article {pmid33288384,
year = {2021},
author = {Pallen, MJ and Telatin, A and Oren, A},
title = {The Next Million Names for Archaea and Bacteria.},
journal = {Trends in microbiology},
volume = {29},
number = {4},
pages = {289-298},
doi = {10.1016/j.tim.2020.10.009},
pmid = {33288384},
issn = {1878-4380},
support = {BBS/E/F/000PR10355/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; MR/T030062/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Archaea/*classification/*genetics ; Bacteria/*classification/*genetics ; Metagenomics ; *Phylogeny ; },
abstract = {Latin binomials, popularised in the 18th century by the Swedish naturalist Linnaeus, have stood the test of time in providing a stable, clear, and memorable system of nomenclature across biology. However, relentless and ever-deeper exploration and analysis of the microbial world has created an urgent need for huge numbers of new names for Archaea and Bacteria. Manual creation of such names remains difficult and slow and typically relies on expert-driven nomenclatural quality control. Keen to ensure that the legacy of Linnaeus lives on in the age of microbial genomics and metagenomics, we propose an automated approach, employing combinatorial concatenation of roots from Latin and Greek to create linguistically correct names for genera and species that can be used off the shelf as needed. As proof of principle, we document over a million new names for Bacteria and Archaea. We are confident that our approach provides a road map for how to create new names for decades to come.},
}
@article {pmid33276555,
year = {2020},
author = {Urbonavičius, J and Tauraitė, D},
title = {Biochemical Pathways Leading to the Formation of Wyosine Derivatives in tRNA of Archaea.},
journal = {Biomolecules},
volume = {10},
number = {12},
pages = {},
pmid = {33276555},
issn = {2218-273X},
support = {S-MIP-19-61//Lietuvos Mokslo Taryba/International ; },
mesh = {Archaea/*genetics/*metabolism ; Guanosine/*analogs &amp; derivatives/biosynthesis ; RNA, Transfer/*genetics ; },
abstract = {Tricyclic wyosine derivatives are present at position 37 in tRNAPhe of both eukaryotes and archaea. In eukaryotes, five different enzymes are needed to form a final product, wybutosine (yW). In archaea, 4-demethylwyosine (imG-14) is an intermediate for the formation of three different wyosine derivatives, yW-72, imG, and mimG. In this review, current knowledge regarding the archaeal enzymes involved in this process and their reaction mechanisms are summarized. The experiments aimed to elucidate missing steps in biosynthesis pathways leading to the formation of wyosine derivatives are suggested. In addition, the chemical synthesis pathways of archaeal wyosine nucleosides are discussed, and the scheme for the formation of yW-86 and yW-72 is proposed. Recent data demonstrating that wyosine derivatives are present in the other tRNA species than those specific for phenylalanine are discussed.},
}
@article {pmid33274598,
year = {2021},
author = {More, KD and Wuchter, C and Irigoien, X and Tierney, JE and Giosan, L and Grice, K and Coolen, MJL},
title = {Subseafloor Archaea reflect 139 kyrs of paleodepositional changes in the northern Red Sea.},
journal = {Geobiology},
volume = {19},
number = {2},
pages = {162-172},
doi = {10.1111/gbi.12421},
pmid = {33274598},
issn = {1472-4669},
mesh = {*Archaea/genetics ; DNA, Archaeal/genetics ; *Euryarchaeota ; Geologic Sediments ; Indian Ocean ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The vertical distribution of subseafloor archaeal communities is thought to be primarily controlled by in situ conditions in sediments such as the availability of electron acceptors and donors, although sharp community shifts have also been observed at lithological boundaries suggesting that at least a subset of vertically stratified Archaea form a long-term genetic record of coinciding environmental conditions that occurred at the time of sediment deposition. To substantiate this possibility, we performed a highly resolved 16S rRNA gene survey of vertically stratified archaeal communities paired with paleo-oceanographic proxies in a sedimentary record from the northern Red Sea spanning the last glacial-interglacial cycle (i.e., marine isotope stages 1-6; MIS1-6). Our results show a strong significant correlation between subseafloor archaeal communities and drastic paleodepositional changes associated with glacial low vs. interglacial high stands (ANOSIM; R = .73; p = .001) and only a moderately strong correlation with lithological changes. Bathyarchaeota, Lokiarchaeota, MBGA, and DHVEG-1 were the most abundant identified archaeal groups. Whether they represented ancient cell lines from the time of deposition or migrated to the specific sedimentary horizons after deposition remains speculative. However, we show that the majority of sedimentary archaeal tetraether membrane lipids were of allochthonous origin and not produced in situ. Slow post-burial growth under energy-limited conditions would explain why the downcore distribution of these dominant archaeal groups still indirectly reflect changes in the paleodepositional environment that prevailed during the analyzed marine isotope stages. In addition, archaea seeded from the overlying water column such as Thaumarchaeota and group II and III Euryarchaeota, which were likely not have been able to subsist after burial, were identified from a lower abundance of preserved sedimentary DNA signatures, and represented direct markers of paleoenvironmental changes in the Red Sea spanning the last six marine isotope stages.},
}
@article {pmid33272134,
year = {2022},
author = {Kumar, V and Behl, A and Shoaib, R and Abid, M and Shevtsov, M and Singh, S},
title = {Comparative structural insight into prefoldin subunints of archaea and eukaryotes with special emphasis on unexplored prefoldin of Plasmodium falciparum.},
journal = {Journal of biomolecular structure &amp; dynamics},
volume = {40},
number = {8},
pages = {3804-3818},
doi = {10.1080/07391102.2020.1850527},
pmid = {33272134},
issn = {1538-0254},
mesh = {*Archaea/metabolism ; Chaperonins/metabolism ; Eukaryota/metabolism ; Humans ; *Malaria ; Molecular Chaperones/chemistry ; Plasmodium falciparum/genetics/metabolism ; },
abstract = {Prefoldin (PFD) is a heterohexameric molecular chaperone which bind unfolded proteins and subsequently deliver them to a group II chaperonin for correct folding. Although there is structural and functional information available for humans and archaea PFDs, their existence and functions in malaria parasite remains uncharacterized. In the present review, we have collected the available information on prefoldin family members of archaea and humans and attempted to analyze unexplored PFD subunits of Plasmodium falciparum (Pf). Our review enhances the understanding of probable functions, structure and mechanism of substrate binding of Pf prefoldin by comparing with the available information of its homologs in archaea and H. sapiens. Three PfPFD out of six and a Pf prefoldin-like protein are reported to be essential for parasite survival that signifies their importance in malaria parasite biology. Transcriptome analyses suggest that PfPFD subunits are up-regulated at the mRNA level during asexual and sexual stages of parasite life cycle. Our in silico analysis suggested several pivotal proteins like myosin E, cytoskeletal protein (tubulin), merozoite surface protein and ring exported protein 3 as their interacting partners. Based on structural information of archaeal and H. sapiens PFDs, P. falciparum counterparts have been modelled and key interface residues were identified that are critical for oligomerization of PfPFD subunits. We collated information on PFD-substrate binding and PFD-chaperonin interaction in detail to understand the mechanism of substrate delivery in archaea and humans. Overall, our review enables readers to view the PFD family comprehensively. Communicated by Ramaswamy H. SarmaAbbreviations: HSP: Heat shock proteins; CCT: Chaperonin containing TCP-1; PFD: Prefoldin; PFLP: Prefoldin like protein; PfPFD: Plasmodium falciparum prefoldin; Pf: Plasmodium falciparum; H. sapiens: Homo sapiens; M. thermoautotrophicus: Methanobacterium thermoautotrophicus; P. horikoshii: Pyrococcus horikoshii.},
}
@article {pmid33271237,
year = {2021},
author = {Pfeifer, K and Ergal, İ and Koller, M and Basen, M and Schuster, B and Rittmann, SKR},
title = {Archaea Biotechnology.},
journal = {Biotechnology advances},
volume = {47},
number = {},
pages = {107668},
doi = {10.1016/j.biotechadv.2020.107668},
pmid = {33271237},
issn = {1873-1899},
support = {P 29399/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {*Archaea/genetics ; Bacteria ; *Biotechnology ; Fungi ; *Industrial Microbiology ; Polyhydroxyalkanoates ; },
abstract = {Archaea are a domain of prokaryotic organisms with intriguing physiological characteristics and ecological importance. In Microbial Biotechnology, archaea are historically overshadowed by bacteria and eukaryotes in terms of public awareness, industrial application, and scientific studies, although their biochemical and physiological properties show a vast potential for a wide range of biotechnological applications. Today, the majority of microbial cell factories utilized for the production of value-added and high value compounds on an industrial scale are bacterial, fungal or algae based. Nevertheless, archaea are becoming ever more relevant for biotechnology as their cultivation and genetic systems improve. Some of the main advantages of archaeal cell factories are the ability to cultivate many of these often extremophilic organisms under non-sterile conditions, and to utilize inexpensive feedstocks often toxic to other microorganisms, thus drastically reducing cultivation costs. Currently, the only commercially available products of archaeal cell factories are bacterioruberin, squalene, bacteriorhodopsin and diether-/tetraether-lipids, all of which are produced utilizing halophiles. Other archaeal products, such as carotenoids and biohydrogen, as well as polyhydroxyalkanoates and methane are in early to advanced development stages, respectively. The aim of this review is to provide an overview of the current state of Archaea Biotechnology by describing the actual state of research and development as well as the industrial utilization of archaeal cell factories, their role and their potential in the future of sustainable bioprocessing, and to illustrate their physiological and biotechnological potential.},
}
@article {pmid33264986,
year = {2021},
author = {Cai, Y and Zheng, Z and Wang, X},
title = {Obstacles faced by methanogenic archaea originating from substrate-driven toxicants in anaerobic digestion.},
journal = {Journal of hazardous materials},
volume = {403},
number = {},
pages = {123938},
doi = {10.1016/j.jhazmat.2020.123938},
pmid = {33264986},
issn = {1873-3336},
mesh = {Ammonia ; Anaerobiosis ; *Archaea/genetics ; *Bioreactors ; Methane ; },
abstract = {Anaerobic digestion (AD) is used to treat waste and produce bioenergy. However, toxicants, which originate from the substrate, can inhibit or damage the digestion process. Methanogenic archaea (MA), which are the executor in the methanogenesis stage, are more sensitive than bacteria to these toxicants. This review discusses the effects of substrate-driven toxicants, namely, antibiotics, H2S and sulfate, heavy metals (HMs), long-chain fatty acids (LCFAs), and ammonia nitrogen, on the activity of MAs, methanogenic pathways, and the inter-genus succession of MAs. The adverse effects of these five toxicants on MA include effects on pH, damages to cell membranes, the prevention of protein synthesis, changes in hydrogen partial pressure, a reduction in the bioavailability of trace elements, and hindrance of mass transfer. These effects cause a reduction in MA activity and the succession of MAs and methanogenic pathways, which affect AD performance. Under the stress of these toxicants, succession occurs among HA (hydrogenotrophic methanogen), AA (acetoclastic methanogen), and MM (methylotrophic methanogen), especially HA gradually replaces AA as the dominant MA. Simultaneously, the dominant methanogenic pathway also changes from the aceticlastic pathway to other methanogenic pathways. A comprehensive understanding of the impact of toxicants on MA permits more specific targeting when developing strategies to mitigate or eliminate the effects of these toxicants.},
}
@article {pmid33264482,
year = {2021},
author = {Wilkens, D and Meusinger, R and Hein, S and Simon, J},
title = {Sequence analysis and specificity of distinct types of menaquinone methyltransferases indicate the widespread potential of methylmenaquinone production in bacteria and archaea.},
journal = {Environmental microbiology},
volume = {23},
number = {3},
pages = {1407-1421},
doi = {10.1111/1462-2920.15344},
pmid = {33264482},
issn = {1462-2920},
mesh = {*Actinobacteria ; *Archaea/enzymology ; Gammaproteobacteria ; *Methyltransferases/genetics ; Phylogeny ; Sequence Analysis ; Vitamin K 2 ; },
abstract = {Menaquinone (MK) serves as an essential membranous redox mediator in various electron transport chains of aerobic and anaerobic respiration. In addition, the composition of the quinone/quinol pool has been widely used as a biomarker in microbial taxonomy. The HemN-like class C radical SAM methyltransferases (RSMTs) MqnK, MenK and MenK2 have recently been shown to facilitate specific menaquinone methylation reactions at position C-8 (MqnK/MenK) or C-7 (MenK2) to synthesize 8-methylmenaquinone, 7-methylmenaquinone and 7,8-dimethylmenaquinone. However, the vast majority of protein sequences from the MqnK/MenK/MenK2 family belong to organisms, whose capacity to produce methylated menaquinones has not been investigated biochemically. Here, representative putative menK and menK2 genes from Collinsella tanakaei and Ferrimonas marina were individually expressed in Escherichia coli (wild-type or ubiE deletion mutant) and the corresponding cells were found to produce methylated derivatives of the endogenous MK and 2-demethylmenaquinone. Cluster and phylogenetic analyses of 828 (methyl)menaquinone methyltransferase sequences revealed signature motifs that allowed to discriminate enzymes of the MqnK/MenK/MenK2 family from other radical SAM enzymes and to identify C-7-specific menaquinone methyltransferases of the MenK2 subfamily. This study will help to predict the methylation status of the quinone/quinol pool of a microbial species (or even a microbial community) from its (meta)genome and contribute to the future design of microbial quinone/quinol pools in a Synthetic Biology approach.},
}
@article {pmid33257309,
year = {2021},
author = {Lahme, S and Mand, J and Longwell, J and Smith, R and Enning, D},
title = {Severe Corrosion of Carbon Steel in Oil Field Produced Water Can Be Linked to Methanogenic Archaea Containing a Special Type of [NiFe] Hydrogenase.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {3},
pages = {},
pmid = {33257309},
issn = {1098-5336},
mesh = {Archaea/genetics/metabolism ; Archaeal Proteins/*chemistry/genetics/metabolism ; Carbon ; Corrosion ; Hydrogenase/*chemistry/genetics/metabolism ; *Industrial Waste ; Methane/metabolism ; *Oil and Gas Fields ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Steel/*chemistry ; Waste Water/*microbiology ; },
abstract = {Methanogenic archaea have long been implicated in microbially influenced corrosion (MIC) of oil and gas infrastructure, yet a first understanding of the underlying molecular mechanisms has only recently emerged. We surveyed pipeline-associated microbiomes from geographically distinct oil field facilities and found methanogens to account for 0.2 to 9.3% of the 16S rRNA gene sequencing reads. Neither the type nor the abundance of the detected methanogens was correlated with the perceived severity of MIC in these pipelines. Using fluids from one pipeline, MIC was reproduced in the laboratory, both under stagnant conditions and in customized corrosion reactors simulating pipeline flow. High corrosion rates (up to 2.43 mm Fe0 · yr-1) with macroscopic, localized corrosion features were attributed to lithotrophic, mesophilic microbial activity. Other laboratory tests with the same waters yielded negligible corrosion rates (<0.08 mm Fe0 · yr-1). Recently, a novel [NiFe] hydrogenase from Methanococcus maripaludis strain OS7 was demonstrated to accelerate corrosion. We developed a specific quantitative PCR (qPCR) assay and detected the gene encoding the large subunit of this hydrogenase (labeled micH) in corrosive (>0.15 mm Fe0 · yr-1) biofilms. The micH gene, on the other hand, was absent in noncorrosive biofilms, despite an abundance of methanogens. Reconstruction of a nearly complete Methanococcus maripaludis genome from a highly corrosive mixed biofilm revealed micH and associated genes in nearly identical genetic configuration to that in strain OS7, thereby supporting our hypothesis that the encoded molecular mechanism contributed to corrosion. Lastly, the proposed MIC biomarker was detected in multiple oil fields, indicating a geographically widespread involvement of this [NiFe] hydrogenase in MIC.IMPORTANCE Microorganisms can deteriorate built environments, which is particularly problematic in the case of pipelines transporting hydrocarbons to industrial end users. MIC is notoriously difficult to detect and monitor and, as a consequence, is a particularly difficult corrosion mechanism to manage. Despite the advent of molecular tools and improved microbial monitoring strategies for oil and gas operations, specific underlying MIC mechanisms in pipelines remain largely enigmatic. Emerging mechanistic understanding of methanogenic MIC derived from pure culture work allowed us to develop a qPCR assay that distinguishes technically problematic from benign methanogens in a West African oil field. Detection of the same gene in geographically diverse samples from North America hints at the widespread applicability of this assay. The research presented here offers a step toward a mechanistic understanding of biocorrosion in oil fields and introduces a binary marker for (methanogenic) MIC that can find application in corrosion management programs in industrial settings.},
}
@article {pmid33241850,
year = {2021},
author = {Kasirajan, L and Maupin-Furlow, JA},
title = {Halophilic archaea and their potential to generate renewable fuels and chemicals.},
journal = {Biotechnology and bioengineering},
volume = {118},
number = {3},
pages = {1066-1090},
pmid = {33241850},
issn = {1097-0290},
support = {R01 GM057498/GM/NIGMS NIH HHS/United States ; },
mesh = {*Biofuels ; Biological Products/*metabolism ; *Halobacteriales/genetics/growth &amp; development ; Hydrogen-Ion Concentration ; Salinity ; Sodium Chloride ; },
abstract = {Lignocellulosic biofuels and chemicals have great potential to reduce our dependence on fossil fuels and mitigate air pollution by cutting down on greenhouse gas emissions. Chemical, thermal, and enzymatic processes are used to release the sugars from the lignocellulosic biomass for conversion to biofuels. These processes often operate at extreme pH conditions, high salt concentrations, and/or high temperature. These harsh treatments add to the cost of the biofuels, as most known biocatalysts do not operate under these conditions. To increase the economic feasibility of biofuel production, microorganisms that thrive in extreme conditions are considered as ideal resources to generate biofuels and value-added products. Halophilic archaea (haloarchaea) are isolated from hypersaline ecosystems with high salt concentrations approaching saturation (1.5-5 M salt concentration) including environments with extremes in pH and/or temperature. The unique traits of haloarchaea and their enzymes that enable them to sustain catalytic activity in these environments make them attractive resources for use in bioconversion processes that must occur across a wide range of industrial conditions. Biocatalysts (enzymes) derived from haloarchaea occupy a unique niche in organic solvent, salt-based, and detergent industries. This review focuses on the use of haloarchaea and their enzymes to develop and improve biofuel production. The review also highlights how haloarchaea produce value-added products, such as antibiotics, carotenoids, and bioplastic precursors, and can do so using feedstocks considered "too salty" for most microbial processes including wastes from the olive-mill, shell fish, and biodiesel industries.},
}
@article {pmid33232349,
year = {2020},
author = {Euler, S and Jeffrey, LC and Maher, DT and Mackenzie, D and Tait, DR},
title = {Shifts in methanogenic archaea communities and methane dynamics along a subtropical estuarine land use gradient.},
journal = {PloS one},
volume = {15},
number = {11},
pages = {e0242339},
pmid = {33232349},
issn = {1932-6203},
mesh = {Agriculture ; Ammonium Compounds/metabolism ; Animal Husbandry ; Archaea/*isolation &amp; purification/metabolism ; Carbon/metabolism ; Ecosystem ; *Estuaries ; Fresh Water/analysis/microbiology ; Greenhouse Gases/analysis ; Housing ; Industry ; Methane/*metabolism ; Methanococcales/*isolation &amp; purification/metabolism ; Methylocystaceae/*isolation &amp; purification/metabolism ; *Microbiota ; Nitrates/metabolism ; Oxidation-Reduction ; Queensland ; *Saline Waters/analysis ; Salinity ; Sulfates/metabolism ; Temperature ; Thermodynamics ; *Water Microbiology ; Water Purification ; },
abstract = {In coastal aquatic ecosystems, prokaryotic communities play an important role in regulating the cycling of nutrients and greenhouse gases. In the coastal zone, estuaries are complex and delicately balanced systems containing a multitude of specific ecological niches for resident microbes. Anthropogenic influences (i.e. urban, industrial and agricultural land uses) along the estuarine continuum can invoke physical and biochemical changes that impact these niches. In this study, we investigate the relative abundance of methanogenic archaea and other prokaryotic communities, distributed along a land use gradient in the subtropical Burnett River Estuary, situated within the Great Barrier Reef catchment, Australia. Microbiological assemblages were compared to physicochemical, nutrient and greenhouse gas distributions in both pore and surface water. Pore water samples from within the most urbanised site showed a high relative abundance of methanogenic Euryarchaeota (7.8% of all detected prokaryotes), which coincided with elevated methane concentrations in the water column, ranging from 0.51 to 0.68 μM at the urban and sewage treatment plant (STP) sites, respectively. These sites also featured elevated dissolved organic carbon (DOC) concentrations (0.66 to 1.16 mM), potentially fuelling methanogenesis. At the upstream freshwater site, both methane and DOC concentrations were considerably higher (2.68 μM and 1.8 mM respectively) than at the estuarine sites (0.02 to 0.66 μM and 0.39 to 1.16 mM respectively) and corresponded to the highest relative abundance of methanotrophic bacteria. The proportion of sulfate reducing bacteria in the prokaryotic community was elevated within the urban and STP sites (relative abundances of 8.0%- 10.5%), consistent with electron acceptors with higher redox potentials (e.g. O2, NO3-) being scarce. Overall, this study showed that ecological niches in anthropogenically altered environments appear to give an advantage to specialized prokaryotes invoking a potential change in the thermodynamic landscape of the ecosystem and in turn facilitating the generation of methane-a potent greenhouse gas.},
}
@article {pmid33229086,
year = {2021},
author = {Amin, FR and Khalid, H and El-Mashad, HM and Chen, C and Liu, G and Zhang, R},
title = {Functions of bacteria and archaea participating in the bioconversion of organic waste for methane production.},
journal = {The Science of the total environment},
volume = {763},
number = {},
pages = {143007},
doi = {10.1016/j.scitotenv.2020.143007},
pmid = {33229086},
issn = {1879-1026},
mesh = {Anaerobiosis ; *Archaea ; Bacteria ; Biofuels ; *Bioreactors ; Methane ; },
abstract = {Anaerobic digestion (AD) is a widely applied technology for treating organic wastes to generate renewable energy in the form of biogas. The effectiveness of AD process depends on many factors, among which the most important is the presence of active and healthy microbial community in the anaerobic digesters, which needs to be explored. However, the deciphering of microbial populations and their functions during the AD process of different materials is still incomplete, which restricts the understanding of its long-term performance under different operational conditions. This review describes the type, morphology, functions, and specific growth conditions of commonly found hydrolytic, acidogenic, acetogenic bacteria, and archaea during the AD process. The effects of microbes on the performance and stability of the digestion process are also presented. Furthermore, the article offers a deep understanding of the AD management strategies for the enhancement of methane production and the efficiency of the energy conversion process of various organic wastes.},
}
@article {pmid33226731,
year = {2021},
author = {Diaz, PI},
title = {Subgingival fungi, Archaea, and viruses under the omics loupe.},
journal = {Periodontology 2000},
volume = {85},
number = {1},
pages = {82-89},
doi = {10.1111/prd.12352},
pmid = {33226731},
issn = {1600-0757},
mesh = {Archaea/genetics ; Bacteria/genetics ; DNA ; Fungi ; *Gingiva/microbiology ; Humans ; *Microbiota ; *Viruses ; },
abstract = {The microbial communities that inhabit the gingival crevice are responsible for the pathological processes that affect the periodontium. The changes in composition and function of subgingival bacteria as disease develops have been extensively studied. Subgingival communities, however, also contain fungi, Archaea, and viruses, which could contribute to the dysbiotic processes associated with periodontal diseases. High-throughput DNA sequencing has facilitated a better understanding of the mycobiome, archaeome, and virome. However, the number of studies available on the nonbacterial components of the subgingival microbiome remains limited in comparison with publications focusing on bacteria. Difficulties in characterizing fungal, archaeal, and viral populations arise from the small portion of the total metagenome mass they occupy and lack of comprehensive reference genome databases. In addition, specialized approaches potentially introducing bias are required to enrich for viral particles, while harsh methods of cell lysis are needed to recover nuclei acids from certain fungi. While the characterization of the subgingival diversity of fungi, Archaea and viruses is incomplete, emerging evidence suggests that they could contribute in different ways to subgingival dysbiosis. Certain fungi, such as Candida albicans are suggested to facilitate colonization of bacterial pathogens. Methanogenic Archaea are associated with periodontitis severity and are thought to partner synergistically with bacterial fermenters, while viruses may affect immune responses or shape microbial communities in ways incompletely understood. This review describes the manner in which omics approaches have improved our understanding of the diversity of fungi, Archaea, and viruses within subgingival communities. Further characterization of these understudied components of the subgingival microbiome is required, together with mechanistic studies to unravel their ecological role and potential contributions to dysbiosis.},
}
@article {pmid33223169,
year = {2021},
author = {Cai, M and Richter-Heitmann, T and Yin, X and Huang, WC and Yang, Y and Zhang, C and Duan, C and Pan, J and Liu, Y and Liu, Y and Friedrich, MW and Li, M},
title = {Ecological features and global distribution of Asgard archaea.},
journal = {The Science of the total environment},
volume = {758},
number = {},
pages = {143581},
doi = {10.1016/j.scitotenv.2020.143581},
pmid = {33223169},
issn = {1879-1026},
mesh = {*Archaea/genetics ; *Eukaryota ; Geologic Sediments ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Salinity ; },
abstract = {Asgard is a newly proposed archaeal superphylum, which has been suggested to hold the key to decipher the origin of Eukaryotes. However, their ecology remains largely unknown. Here, we conducted a meta-analysis of publicly available Asgard-associated 16S rRNA gene fragments, and found that just three previously proposed clades (Lokiarchaeota, Thorarchaeota, and Asgard clade 4) are widely distributed, whereas the other seven clades (phylum or class level) are restricted to the sediment biosphere. Asgard archaea, especially Loki- and Thorarchaeota, seem to adapt to marine sediments, and water depth (the depth of the sediment below water surface) and salinity might be crucial factors for the proportion of these microorganisms as revealed by multivariate regression analyses. However, the abundance of Asgard archaea exhibited distinct environmental drivers at the clade-level; for instance, the proportion of Asgard clade 4 was higher in less saline environments (salinity <6.35 psu), while higher for Heimdallarchaeota-AAG and Asgard clade 2 in more saline environment (salinity ≥35 psu). Furthermore, co-occurrence analysis allowed us to find a significant non-random association of different Asgard clades with other groups (e.g., Lokiarchaeota with Deltaproteobacteria and Anaerolineae; Odinarchaeota with Bathyarchaeota), suggesting different interaction potentials among these clades. Overall, these findings reveal Asgard archaea as a ubiquitous group worldwide and provide initial insights into their ecological features on a global scale.},
}
@article {pmid33202677,
year = {2020},
author = {Diene, SM and Pinault, L and Armstrong, N and Azza, S and Keshri, V and Khelaifia, S and Chabrière, E and Caetano-Anolles, G and Rolain, JM and Pontarotti, P and Raoult, D},
title = {Dual RNase and β-lactamase Activity of a Single Enzyme Encoded in Archaea.},
journal = {Life (Basel, Switzerland)},
volume = {10},
number = {11},
pages = {},
pmid = {33202677},
issn = {2075-1729},
abstract = {β-lactam antibiotics have a well-known activity which disturbs the bacterial cell wall biosynthesis and may be cleaved by β-lactamases. However, these drugs are not active on archaea microorganisms, which are naturally resistant because of the lack of β-lactam target in their cell wall. Here, we describe that annotation of genes as β-lactamases in Archaea on the basis of homologous genes is a remnant of identification of the original activities of this group of enzymes, which in fact have multiple functions, including nuclease, ribonuclease, β-lactamase, or glyoxalase, which may specialized over time. We expressed class B β-lactamase enzyme from Methanosarcina barkeri that digest penicillin G. Moreover, while weak glyoxalase activity was detected, a significant ribonuclease activity on bacterial and synthetic RNAs was demonstrated. The β-lactamase activity was inhibited by β-lactamase inhibitor (sulbactam), but its RNAse activity was not. This gene appears to have been transferred to the Flavobacteriaceae group especially the Elizabethkingia genus, in which the expressed gene shows a more specialized activity on thienamycin, but no glyoxalase activity. The expressed class C-like β-lactamase gene, from Methanosarcina sp., also shows hydrolysis activity on nitrocefin and is more closely related to DD-peptidase enzymes. Our findings highlight the need to redefine the nomenclature of β-lactamase enzymes and the specification of multipotent enzymes in different ways in Archaea and bacteria over time.},
}
@article {pmid33193193,
year = {2020},
author = {Wang, H and Bier, R and Zgleszewski, L and Peipoch, M and Omondi, E and Mukherjee, A and Chen, F and Zhang, C and Kan, J},
title = {Distinct Distribution of Archaea From Soil to Freshwater to Estuary: Implications of Archaeal Composition and Function in Different Environments.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {576661},
pmid = {33193193},
issn = {1664-302X},
abstract = {In addition to inhabiting extreme territories, Archaea are widely distributed in common environments spanning from terrestrial to aquatic environments. This study investigated and compared archaeal community structures from three different habitats (representing distinct environments): agriculture soils (from farming system trials FST, PA, United States), freshwater biofilms (from White Clay Creek, PA, United States), and estuary water (Chesapeake Bay, United States). High-throughput sequencing of 16S rRNA genes indicated that Thaumarchaeota, Euryarchaeota, Nanoarchaeota, Crenarchaeota, and Diapherotrites were the commonly found dominant phyla across these three environments. Similar to Bacteria, distinct community structure and distribution patterns for Archaea were observed in soils vs. freshwater vs. estuary. However, the abundance, richness, evenness, and diversity of archaeal communities were significantly greater in soils than it was in freshwater and estuarine environments. Indicator species (or amplicon sequence variants, ASVs) were identified from different nitrogen and carbon cycling archaeal groups in soils (Nitrososphaerales, Nitrosotaleales, Nitrosopumilales, Methanomassiliicoccales, Lainarchaeales), freshwater biofilms (Methanobacteria, Nitrososphaerales) and Chesapeake Bay (Marine Group II, Nitrosopumilales), suggesting the habitat-specificity of their biogeochemical contributions to different environments. Distinct functional aspects of Archaea were also confirmed by functional predictions (PICRUSt2 analysis). Further, co-occurrence network analysis indicated that only soil Archaea formed stable modules. Keystone species (ASVs) were identified mainly from Methanomassiliicoccales, Nitrososphaerales, Nitrosopumilales. Overall, these results indicate a strong habitat-dependent distribution of Archaea and their functional partitions within the local environments.},
}
@article {pmid33184503,
year = {2021},
author = {Murray, AE and Freudenstein, J and Gribaldo, S and Hatzenpichler, R and Hugenholtz, P and Kämpfer, P and Konstantinidis, KT and Lane, CE and Papke, RT and Parks, DH and Rossello-Mora, R and Stott, MB and Sutcliffe, IC and Thrash, JC and Venter, SN and Whitman, WB and Acinas, SG and Amann, RI and Anantharaman, K and Armengaud, J and Baker, BJ and Barco, RA and Bode, HB and Boyd, ES and Brady, CL and Carini, P and Chain, PSG and Colman, DR and DeAngelis, KM and de Los Rios, MA and Estrada-de Los Santos, P and Dunlap, CA and Eisen, JA and Emerson, D and Ettema, TJG and Eveillard, D and Girguis, PR and Hentschel, U and Hollibaugh, JT and Hug, LA and Inskeep, WP and Ivanova, EP and Klenk, HP and Li, WJ and Lloyd, KG and Löffler, FE and Makhalanyane, TP and Moser, DP and Nunoura, T and Palmer, M and Parro, V and Pedrós-Alió, C and Probst, AJ and Smits, THM and Steen, AD and Steenkamp, ET and Spang, A and Stewart, FJ and Tiedje, JM and Vandamme, P and Wagner, M and Wang, FP and Yarza, P and Hedlund, BP and Reysenbach, AL},
title = {Author Correction: Roadmap for naming uncultivated Archaea and Bacteria.},
journal = {Nature microbiology},
volume = {6},
number = {1},
pages = {136},
doi = {10.1038/s41564-020-00827-2},
pmid = {33184503},
issn = {2058-5276},
support = {DEB-1841658//National Science Foundation (NSF)/ ; },
}
@article {pmid33172134,
year = {2020},
author = {Zink, IA and Wimmer, E and Schleper, C},
title = {Heavily Armed Ancestors: CRISPR Immunity and Applications in Archaea with a Comparative Analysis of CRISPR Types in Sulfolobales.},
journal = {Biomolecules},
volume = {10},
number = {11},
pages = {},
pmid = {33172134},
issn = {2218-273X},
support = {695192/ERC_/European Research Council/International ; P29399//Austrian Science Fund/ ; DOC-fellowship//Österreichischen Akademie der Wissenschaften/ ; DOC completion grant//Universität Wien/ ; },
mesh = {Clustered Regularly Interspaced Short Palindromic Repeats/*immunology ; RNA/genetics ; Species Specificity ; Sulfolobales/*genetics/*immunology ; },
abstract = {Prokaryotes are constantly coping with attacks by viruses in their natural environments and therefore have evolved an impressive array of defense systems. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) is an adaptive immune system found in the majority of archaea and about half of bacteria which stores pieces of infecting viral DNA as spacers in genomic CRISPR arrays to reuse them for specific virus destruction upon a second wave of infection. In detail, small CRISPR RNAs (crRNAs) are transcribed from CRISPR arrays and incorporated into type-specific CRISPR effector complexes which further degrade foreign nucleic acids complementary to the crRNA. This review gives an overview of CRISPR immunity to newcomers in the field and an update on CRISPR literature in archaea by comparing the functional mechanisms and abundances of the diverse CRISPR types. A bigger fraction is dedicated to the versatile and prevalent CRISPR type III systems, as tremendous progress has been made recently using archaeal models in discerning the controlled molecular mechanisms of their unique tripartite mode of action including RNA interference, DNA interference and the unique cyclic-oligoadenylate signaling that induces promiscuous RNA shredding by CARF-domain ribonucleases. The second half of the review spotlights CRISPR in archaea outlining seminal in vivo and in vitro studies in model organisms of the euryarchaeal and crenarchaeal phyla, including the application of CRISPR-Cas for genome editing and gene silencing. In the last section, a special focus is laid on members of the crenarchaeal hyperthermophilic order Sulfolobales by presenting a thorough comparative analysis about the distribution and abundance of CRISPR-Cas systems, including arrays and spacers as well as CRISPR-accessory proteins in all 53 genomes available to date. Interestingly, we find that CRISPR type III and the DNA-degrading CRISPR type I complexes co-exist in more than two thirds of these genomes. Furthermore, we identified ring nuclease candidates in all but two genomes and found that they generally co-exist with the above-mentioned CARF domain ribonucleases Csx1/Csm6. These observations, together with published literature allowed us to draft a working model of how CRISPR-Cas systems and accessory proteins cross talk to establish native CRISPR anti-virus immunity in a Sulfolobales cell.},
}
@article {pmid33171029,
year = {2020},
author = {Dong, L and Gao, Y and Guo, H and Zhang, H and Lai, Q and Diao, Q},
title = {Pretreatments of Broussonetia papyrifera: In vitro assessment on gas and methane production, fermentation characteristic, and methanogenic archaea profile.},
journal = {Asian-Australasian journal of animal sciences},
volume = {},
number = {},
pages = {},
doi = {10.5713/ajas.20.0503},
pmid = {33171029},
issn = {1011-2367},
abstract = {OBJECTIVE: The present study was conducted to examine the gas production, fermentation characteristics, nutrient degradation, and methanogenic community composition of the rumen fluid culture with Broussonetia papyrifera (B. papyrifera) subjected to ensiling or steam explosion (SE) pretreatment.<br><br>METHODS: Fresh B. papyrifera was collected and pretreated by ensiling or steam explosion, which was then fermented with ruminal fluids as ensiled B. papyrifera (BPS) group, steam-exploded B. papyrifera (BP-SE) group, and untreated B. papyrifera (BP) group. The gas and methane production, fermentation characteristics, nutrient degradation, and methanogenic community were determined during the fermentation.<br><br>RESULTS: Cumulative methane production was significantly improved with SE pretreatment compared with ensiled or untreated biomass accompanied with more volatile fatty acids production. After 72 h incubation, SE and ensiling pretreatments decreased the acid detergent fiber contents by 39.4% and 22.9%, and neutral detergent fiber contents by 10.6% and 47.2%, respectively. Changes of methanogenic diversity and abundance of methanogenic archaea corresponded to the variations in fermentation pattern and methane production.<br><br>CONCLUSION: Compared with ensiling pretreatment, SE can be a promising technique for the efficient utilization of B. papyrifera, which would contribute to the sustainable livestock production systems.},
}
@article {pmid33161088,
year = {2021},
author = {Kajale, S and Jani, K and Sharma, A},
title = {Contribution of archaea and bacteria in sustaining climate change by oxidizing ammonia and sulfur in an Arctic Fjord.},
journal = {Genomics},
volume = {113},
number = {1 Pt 2},
pages = {1272-1276},
doi = {10.1016/j.ygeno.2020.11.005},
pmid = {33161088},
issn = {1089-8646},
mesh = {Ammonia/*metabolism ; Archaea/genetics/*metabolism ; Arctic Regions ; Bacteria/genetics/*metabolism ; *Climate Change ; Microbiota ; Oxidation-Reduction ; Sulfur/*metabolism ; },
abstract = {The present study attempts to investigate the microbial communities and their potential to oxidize ammonia and sulfur at different sites of Arctic Fjord by targeted metagenomics. The high throughput sequencing revealed archaeal Thaumarchaeota (79.3%), Crenarchaeota (10.9%), Euryarchaeota (5.4%), and Woesearchaeota (2.9%) across different depths. In contrast, the bacterial communities depict predominance of Proteobacteria (52.6%), which comprises of dominant genera viz. Sulfurovum (11.2%) and Sulfurimonas (6.3%). Characterizing the metabolic potential of microbial communities with prime focus on the ammonia and sulfur cycling revealed the presence of amoABC and narGHYZ/ nxrAB genes encoding key enzymes. The ammonia cycling coupled with an augmentation of members of Nitrosopumilus belonging to the phylum Thaumarcheaota suggests the vital role of archaeal communities. Similarly, the persistence of chemolithoautotrophic members of Sulfurovum and Sulfurimonas along with the anaerobic genera Desulfocapsa and Desulfobulbus harboring SOX (sulfur-oxidation) system indicates the modulatory role of bacterial communities in sulfur cycling.},
}
@article {pmid33157448,
year = {2021},
author = {Yang, S and Li, L and Peng, X and Song, L},
title = {Leachate microbiome profile reveals bacteria, archaea and eukaryote dynamics and methanogenic function during solid waste decomposition.},
journal = {Bioresource technology},
volume = {320},
number = {Pt A},
pages = {124359},
doi = {10.1016/j.biortech.2020.124359},
pmid = {33157448},
issn = {1873-2976},
mesh = {*Archaea/genetics ; Bacteria/genetics ; Bioreactors ; Eukaryota ; Methane ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S ; Solid Waste ; },
abstract = {Bacterial, archaeal, and eukaryotic community composition and dynamics in leachate during solid waste decomposition were investigated using Illumina MiSeq sequencing. The functional enzyme-encoding genes of methanogenic pathways were also predicted via PICRUSt. Succession of bacterial, archaeal, and eukaryotic community composition in aerobic phase (AP), anaerobic acid phase (ACP), and methanogenic phase (MP) was observed. The main representatives of microbial phyla, genera, and species significantly (p < 0.05) differed at least two phases. Protist Ciliophora occurred at ACP and was prevalent in MP, suggesting a short food chain establishment in the methanogenesis. Bacterial, archaeal, fungi and eukaryotic community structure were all pH and biochemical oxygen demand (BOD5) dependent patter. Acetoclastic and hydrogenotrophic methanogenesis pathways with associated functional genes differed during solid waste decomposition and were inhibited in ACP.},
}
@article {pmid33125862,
year = {2020},
author = {Nußbaum, P and Ithurbide, S and Walsh, JC and Patro, M and Delpech, F and Rodriguez-Franco, M and Curmi, PMG and Duggin, IG and Quax, TEF and Albers, SV},
title = {An Oscillating MinD Protein Determines the Cellular Positioning of the Motility Machinery in Archaea.},
journal = {Current biology : CB},
volume = {30},
number = {24},
pages = {4956-4972.e4},
doi = {10.1016/j.cub.2020.09.073},
pmid = {33125862},
issn = {1879-0445},
mesh = {Archaeal Proteins/genetics/*metabolism ; Cell Membrane/metabolism ; Chemotaxis/*physiology ; Haloferax volcanii/*physiology ; Intravital Microscopy ; Time-Lapse Imaging ; },
abstract = {MinD proteins are well studied in rod-shaped bacteria such as E. coli, where they display self-organized pole-to-pole oscillations that are important for correct positioning of the Z-ring at mid-cell for cell division. Archaea also encode proteins belonging to the MinD family, but their functions are unknown. MinD homologous proteins were found to be widespread in Euryarchaeota and form a sister group to the bacterial MinD family, distinct from the ParA and other related ATPase families. We aimed to identify the function of four archaeal MinD proteins in the model archaeon Haloferax volcanii. Deletion of the minD genes did not cause cell division or size defects, and the Z-ring was still correctly positioned. Instead, one of the deletions (ΔminD4) reduced swimming motility and hampered the correct formation of motility machinery at the cell poles. In ΔminD4 cells, there is reduced formation of the motility structure and chemosensory arrays, which are essential for signal transduction. In bacteria, several members of the ParA family can position the motility structure and chemosensory arrays via binding to a landmark protein, and consequently these proteins do not oscillate along the cell axis. However, GFP-MinD4 displayed pole-to-pole oscillation and formed polar patches or foci in H. volcanii. The MinD4 membrane-targeting sequence (MTS), homologous to the bacterial MinD MTS, was essential for the oscillation. Surprisingly, mutant MinD4 proteins failed to form polar patches. Thus, MinD4 from H. volcanii combines traits of different bacterial ParA/MinD proteins.},
}
@article {pmid33123879,
year = {2021},
author = {Liu, X and Shao, Y and Dong, Y and Dong, M and Xu, Z and Hu, X and Liu, A},
title = {Response of ammonia-oxidizing archaea and bacteria to sulfadiazine and copper and their interaction in black soils.},
journal = {Environmental science and pollution research international},
volume = {28},
number = {9},
pages = {11357-11368},
pmid = {33123879},
issn = {1614-7499},
support = {No.41671322//Natural Science Foundation of China/ ; No. 41877122//Natural Science Foundation of China/ ; NO. 2019GSF109058.//Shandong Skate R&amp;D Project/ ; },
mesh = {*Ammonia ; Animals ; *Archaea ; Bacteria ; Copper ; Nitrification ; Oxidation-Reduction ; Soil ; Soil Microbiology ; Sulfadiazine ; },
abstract = {The large-scale development of animal husbandry and the wide agricultural application of livestock manure lead to more and more serious co-pollution of heavy metals and antibiotics in soil. In this study, two common feed additives, copper (Cu) and sulfadiazine (SDZ), were selected as target pollutants to evaluate the toxicity and interaction of antibiotics and heavy metals on ammonia oxidizers diversity, potential nitrification rate (PNR), and enzymatic activity in black soils. The results showed that soil enzyme activity was significantly inhibited by single Cu pollution, but the toxicity could be reduced by introducing low-concentration SDZ (5 mg · kg-1), which showed an antagonistic effect between Cu and SDZ (5 mg · kg-1), while the combined toxicity of high-concentration SDZ (10 mg · kg-1) and Cu were strengthened compared with the single Cu contamination on soil enzymes. In contrast, soil PNR was more sensitive to single Cu pollution and its combined pollution with SDZ than the enzyme activity. Real-time fluorescence quota PCR and Illumina Hiseq/Miseq sequencing results showed that ammonia-oxidizing archaea (AOA) was decreased in C2 (200 mg · kg-1 Cu treatment) and ammonia-oxidizing bacteria (AOB) was obviously stimulated in soil contaminated in C2, while in S5 (5 mg · kg-1 SDZ treatment), AOB was decreased; both AOA and AOB were significantly decreased at gene level in soils with combined pollutants (C2S5, 200 mg · kg-1 Cu combined with 5 mg · kg-1 SDZ). So, it can be concluded that combined pollution can cause more serious toxicity on the enzymatic activity, PNR, and ammonia-oxidizing microorganisms in soil through the synergistic effect between heavy metals and antibiotics pollutants.},
}
@article {pmid33093799,
year = {2020},
author = {Jha, P and Singh, J and Vidyarthi, AS and Prasad, R},
title = {Unveiling the Biodiversity of Hyperthermophilic Archaea in Jharia Coal Mines: Potential Threat to Methanogenesis?.},
journal = {Current genomics},
volume = {21},
number = {5},
pages = {363-371},
pmid = {33093799},
issn = {1389-2029},
abstract = {AIM: To examine the biodiversity of archaeal sulfate reducers and methanogens present in the underground coal mines of Jharia using metagenomics and pyrosequencing.<br><br>OBJECTIVES: 1) Bioinformatical analysis of the metagenomic data related to a taxonomic analysis obtained from the coal to investigate complete archaeal taxonomic features of the coal bed methane (CBM) microbiome. 2) Bioinformatical analysis of the metagenomic data related to a functional analysis obtained from the coal to investigate functional features relating to taxonomic diversity of the CBM microbiome. 3) The functional attributes have been examined specifically for ORFs related to sulfite reduction and methanogenesis.The taxonomic and functional biodiversity related to euryarchaeota will help in a better understanding of the obstacles associated with methane production imposed by the sulfate reducers.<br><br>BACKGROUND: The microbial methanogenesis in the coal microbiome is a resultant of substrate utilization by primarily fermentative bacteria and methanogens. The present work reveals the biodiversity of archaeal sulfate reducers and methanogens present in the underground coal mines of Jharia using metagenomics and pyrosequencing.<br><br>METHODOLOGY: Bioinformatical analysis for structural and functional attributes was accomplished using MG-RAST. The structural analysis was accomplished using RefSeq database, whereas the functional analysis was done via CoG database with a cut off value, a sequence percent identity, and sequence alignment length cut off of 1e-5, 60% and 45, respectively.<br><br>RESULTS: Attained communities revealed the dominance of hyperthermophilic archaea Pyrococcus furiosus along with Thermococcus kodakarensis in the coal metagenome.The obtained results also suggest the presence of dissimilatory sulfite reductase and formylmethanofuran dehydrogenase, formylmethanofuran: tetrahydromethanopterin formyltransferase involved in sulfite reduction and methanogenesis, respectively, in the microbiome.<br><br>CONCLUSION: This report is the first attempt to showcase the existence of specific euryarchaeal diversity and their related functional attributes from Jharia coal mines through high throughput sequencing. The study helps in developing a better understanding of the presence of indigenous microbes (archaea) and their functions in the coal microbiome, which can be utilized further to resolve the energy crisis.},
}
@article {pmid33077635,
year = {2020},
author = {Chávez, J and Devos, DP and Merino, E},
title = {Complementary Tendencies in the Use of Regulatory Elements (Transcription Factors, Sigma Factors, and Riboswitches) in Bacteria and Archaea.},
journal = {Journal of bacteriology},
volume = {203},
number = {2},
pages = {},
pmid = {33077635},
issn = {1098-5530},
mesh = {Archaea/classification/genetics/*physiology ; Bacteria/classification/*genetics ; Genome, Archaeal/physiology ; Genome, Bacterial/physiology ; Phylogeny ; Riboswitch/*physiology ; Sigma Factor/*physiology ; Transcription Factors/*physiology ; },
abstract = {In prokaryotes, the key players in transcription initiation are sigma factors and transcription factors that bind to DNA to modulate the process, while premature transcription termination at the 5' end of the genes is regulated by attenuation and, in particular, by attenuation associated with riboswitches. In this study, we describe the distribution of these regulators across phylogenetic groups of bacteria and archaea and find that their abundance not only depends on the genome size, as previously described, but also varies according to the phylogeny of the organism. Furthermore, we observed a tendency for organisms to compensate for the low frequencies of a particular type of regulatory element (i.e., transcription factors) with a high frequency of other types of regulatory elements (i.e., sigma factors). This study provides a comprehensive description of the more abundant COG, KEGG, and Rfam families of transcriptional regulators present in prokaryotic genomes.IMPORTANCE In this study, we analyzed the relationship between the relative frequencies of the primary regulatory elements in bacteria and archaea, namely, transcription factors, sigma factors, and riboswitches. In bacteria, we reveal a compensatory behavior for transcription factors and sigma factors, meaning that in phylogenetic groups in which the relative number of transcription factors was low, we found a tendency for the number of sigma factors to be high and vice versa. For most of the phylogenetic groups analyzed here, except for Firmicutes and Tenericutes, a clear relationship with other mechanisms was not detected for transcriptional riboswitches, suggesting that their low frequency in most genomes does not constitute a significant impact on the global variety of transcriptional regulatory elements in prokaryotic organisms.},
}
@article {pmid33068423,
year = {2020},
author = {L Bräuer, S and Basiliko, N and M P Siljanen, H and H Zinder, S},
title = {Methanogenic archaea in peatlands.},
journal = {FEMS microbiology letters},
volume = {367},
number = {20},
pages = {},
doi = {10.1093/femsle/fnaa172},
pmid = {33068423},
issn = {1574-6968},
mesh = {Archaea/*classification ; Methane/metabolism ; Microbiota/physiology ; *Soil ; *Soil Microbiology ; *Wetlands ; },
abstract = {Methane emission feedbacks in wetlands are predicted to influence global climate under climate change and other anthropogenic stressors. Herein, we review the taxonomy and physiological ecology of the microorganisms responsible for methane production in peatlands. Common in peat soils are five of the eight described orders of methanogens spanning three phyla (Euryarchaeota, Halobacterota and Thermoplasmatota). The phylogenetic affiliation of sequences found in peat suggest that members of the thus-far-uncultivated group Candidatus Bathyarchaeota (representing a fourth phylum) may be involved in methane cycling, either anaerobic oxidation of methane and/or methanogenesis, as at least a few organisms within this group contain the essential gene, mcrA, according to metagenomic data. Methanogens in peatlands are notoriously challenging to enrich and isolate; thus, much remains unknown about their physiology and how methanogen communities will respond to environmental changes. Consistent patterns of changes in methanogen communities have been reported across studies in permafrost peatland thaw where the resulting degraded feature is thermokarst. However much remains to be understood regarding methanogen community feedbacks to altered hydrology and warming in other contexts, enhanced atmospheric pollution (N, S and metals) loading and direct anthropogenic disturbances to peatlands like drainage, horticultural peat extraction, forestry and agriculture, as well as post-disturbance reclamation.},
}
@article {pmid33051370,
year = {2020},
author = {Abby, SS and Kerou, M and Schleper, C},
title = {Ancestral Reconstructions Decipher Major Adaptations of Ammonia-Oxidizing Archaea upon Radiation into Moderate Terrestrial and Marine Environments.},
journal = {mBio},
volume = {11},
number = {5},
pages = {},
pmid = {33051370},
issn = {2150-7511},
mesh = {Adaptation, Physiological/*genetics ; Ammonia/*metabolism ; Aquatic Organisms/*genetics ; Archaea/*genetics/metabolism ; Carbon Cycle ; Evolution, Molecular ; *Genome, Archaeal ; Oxidation-Reduction ; *Soil Microbiology ; },
abstract = {Unlike all other archaeal lineages, ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota are widespread and abundant in all moderate and oxic environments on Earth. The evolutionary adaptations that led to such unprecedented ecological success of a microbial clade characterized by highly conserved energy and carbon metabolisms have, however, remained underexplored. Here, we reconstructed the genomic content and growth temperature of the ancestor of all AOA, as well as the ancestors of the marine and soil lineages, based on 39 available complete or nearly complete genomes of AOA. Our evolutionary scenario depicts an extremely thermophilic, autotrophic, aerobic ancestor from which three independent lineages of a marine and two terrestrial groups radiated into moderate environments. Their emergence was paralleled by (i) a continuous acquisition of an extensive collection of stress tolerance genes mostly involved in redox maintenance and oxygen detoxification, (ii) an expansion of regulatory capacities in transcription and central metabolic functions, and (iii) an extended repertoire of cell appendages and modifications related to adherence and interactions with the environment. Our analysis provides insights into the evolutionary transitions and key processes that enabled the conquest of the diverse environments in which contemporary AOA are found.},
}
@article {pmid33045546,
year = {2021},
author = {Park, JG and Lee, B and Heo, TY and Cheon, AI and Jun, HB},
title = {Metagenomics approach and canonical correspondence analysis of novel nitrifiers and ammonia-oxidizing archaea in full scale anaerobic-anoxic-oxic (A2/O) and oxidation ditch processes.},
journal = {Bioresource technology},
volume = {319},
number = {},
pages = {124205},
doi = {10.1016/j.biortech.2020.124205},
pmid = {33045546},
issn = {1873-2976},
mesh = {*Ammonia ; Anaerobiosis ; *Archaea/genetics ; Metagenomics ; Nitrification ; Nitrites ; Oxidation-Reduction ; Phylogeny ; },
abstract = {Various microorganisms are involved in nitrogen removal, and their group compositions depend closely on operating parameters. The structures and functions of nitrification microorganisms in full-scale anaerobic-anoxic-oxic (A2/O) and oxidation ditch processes were analyzed using metagenomics and canonical correspondence analysis. The community structure of ammonia-oxidizing archaea in the oxidation ditch was 3.8 (winter) - 6.3 (summer) times higher than in A2/O, and the complete ammonia oxidizer was only found in the oxidation ditch process. The canonical correspondence analysis of various environmental variables showed that Nitrosomonadales, Crenarchaeota, and Nitrospira inopinata correlate highly with nitrification, and Nitrospira was involved in NO2--N oxidation rather than Nitrobacter. The longer solid and hydraulic retention times in the oxidation ditch were more effective in achieving a wider range of novel nitrification than A2/O. This result indicates that microbial communities of novel nitrifiers and ammonia-oxidizing archaea improved in the oxidation ditch process, significantly contributing to stable nitrogen removal.},
}
@article {pmid33040791,
year = {2020},
author = {Song, W and Sun, C},
title = {Diversity and distribution of bacteria and archaea in Tuosu Lake in Qaidam Basin.},
journal = {Cellular and molecular biology (Noisy-le-Grand, France)},
volume = {66},
number = {6},
pages = {86-92},
pmid = {33040791},
issn = {1165-158X},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; Biodiversity ; Lakes ; Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Salinity ; },
abstract = {Microbes in plateau lakes are important participants of material circulation and energy flow in plateau ecosystems. Knowledge of the microbiota, such as bacteria and archaea, community distribution and diversity in plateau lakes is the basis to understand the species succession, adaptation, maintenance and metabolic mechanisms of specific environmental microbial ecosystems. This work aimed to reveal the diversity and# succession of the microbiota in Tuosu Lake to provide a biological basis for the exploration and development of microbial resources in the plateau lakes. The distribution and diversity of microflora in Tuosu Lake, hypoxia, high altitude, alkaline, closed plateau lake with fresh water supply, was investigated. The total DNA was extracted from six samples with different salinity from different geographical locations of Tuosu Lake. The 16S rRNA gene of bacteria and archaea were determined by using high-throughput sequencing-based on an Illumina Miseq sequencing platform. The microbiota in Tuosu Lake has a high diversity and complexity and there are a large number of unclassified microbial species. The bacterial communities in Tuosu Lake are dominated by Proteobacteria (44.3%) and Actbacteria (17.2%). Among them, β-Proteobacteria is the dominant genus in the low-salt sample, while γ-Proteobacteria is more advantageous in the samples with higher salinity. The archaeal communities are dominated by Euryarchaeota (50%) and Woesearchaeota__DHVEG-6 (42.6%). The vast majority of the methanogenic archaea in Tuosu Lake samples belong to Methanomicrobia, and the methanogens in low-salinity samples are significantly more abundant than those in high-salt samples. Diversity and distribution appear to be highly influenced by water salinity and pH.},
}
@article {pmid33025566,
year = {2021},
author = {Takamura, E and Taki, S and Sakamoto, H and Satomura, T and Sakuraba, H and Ohshima, T and Suye, SI},
title = {Site-Directed Mutagenesis of Multicopper Oxidase from Hyperthermophilic Archaea for High-Voltage Biofuel Cells.},
journal = {Applied biochemistry and biotechnology},
volume = {193},
number = {2},
pages = {492-501},
pmid = {33025566},
issn = {1559-0291},
mesh = {Amino Acid Substitution ; *Archaeal Proteins/chemistry/genetics ; *Bioelectric Energy Sources ; *Mutagenesis, Site-Directed ; *Mutation, Missense ; *Oxidoreductases/chemistry/genetics ; *Pyrobaculum/enzymology/genetics ; },
abstract = {Enzymes from hyperthermophilic archaea are potential candidates for industrial use because of their superior pH, thermal, and long-term stability, and are expected to improve the long-term stability of biofuel cells (BFCs). However, the reported multicopper oxidase (MCO) from hyperthermophilic archaea has lower redox potential than MCOs from other organisms, which leads to a decrease in the cell voltage of BFCs. In this study, we attempted to positively shift the redox potential of the MCO from hyperthermophilic archaeon Pyrobaculum aerophilum (McoP). Mutations (M470L and M470F) were introduced into the axial ligand of the T1 copper atom of McoP, and the enzymatic chemistry and redox potentials were compared with that of the parent (M470). The redox potentials of M470L and M470F shifted positively by about 0.07 V compared with that of M470. In addition, the catalytic activity of the mutants towards 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) increased 1.2-1.3-fold. The thermal stability of the mutants and the electrocatalytic performance for O2 reduction of M470F was slightly reduced compared with that of M470. This research provides useful enzymes for application as biocathode catalysts for high-voltage BFCs.},
}
@article {pmid33022088,
year = {2021},
author = {Thiroux, S and Dupont, S and Nesbø, CL and Bienvenu, N and Krupovic, M and L'Haridon, S and Marie, D and Forterre, P and Godfroy, A and Geslin, C},
title = {The first head-tailed virus, MFTV1, infecting hyperthermophilic methanogenic deep-sea archaea.},
journal = {Environmental microbiology},
volume = {23},
number = {7},
pages = {3614-3626},
doi = {10.1111/1462-2920.15271},
pmid = {33022088},
issn = {1462-2920},
mesh = {Archaea/genetics ; *Archaeal Viruses/genetics ; Ecosystem ; Methanocaldococcus ; *Viruses ; },
abstract = {Deep-sea hydrothermal vents are inhabited by complex communities of microbes and their viruses. Despite the importance of viruses in controlling the diversity, adaptation and evolution of their microbial hosts, to date, only eight bacterial and two archaeal viruses isolated from abyssal ecosystems have been described. Thus, our efforts focused on gaining new insights into viruses associated with deep-sea autotrophic archaea. Here, we provide the first evidence of an infection of hyperthermophilic methanogenic archaea by a head-tailed virus, Methanocaldococcus fervens tailed virus 1 (MFTV1). MFTV1 has an isometric head of 50 nm in diameter and a 150 nm-long non-contractile tail. Virions are released continuously without causing a sudden drop in host growth. MFTV1 infects Methanocaldococcus species and is the first hyperthermophilic head-tailed virus described thus far. The viral genome is a double-stranded linear DNA of 31 kb. Interestingly, our results suggest potential strategies adopted by the plasmid pMEFER01, carried by M. fervens, to spread horizontally in hyperthermophilic methanogens. The data presented here open a new window of understanding on how the abyssal mobilome interacts with hyperthermophilic marine archaea.},
}
@article {pmid33021028,
year = {2021},
author = {Wei, D and Zeng, S and Hou, D and Zhou, R and Xing, C and Deng, X and Yu, L and Wang, H and Deng, Z and Weng, S and Huang, Z and He, J},
title = {Community diversity and abundance of ammonia-oxidizing archaea and bacteria in shrimp pond sediment at different culture stages.},
journal = {Journal of applied microbiology},
volume = {130},
number = {5},
pages = {1442-1455},
doi = {10.1111/jam.14846},
pmid = {33021028},
issn = {1365-2672},
support = {CARS-48//China Agriculture Research System/ ; //China-ASEAN Maritime Cooperation Fund/ ; //China-ASEAN Center for Joint Research and Promotion of Marine Aquaculture Technology/ ; GDOE (2019) A21//Guangdong MEPP Fund/ ; //Guangzhou Science Technology and Innovation Commission Project/ ; 20164200042090023//Guangdong Ocean and Fishery Bureau Project/ ; },
mesh = {Ammonia/*metabolism ; Animals ; *Aquaculture ; Archaea/classification/genetics/growth &amp; development/*metabolism ; Bacteria/classification/genetics/growth &amp; development/*metabolism ; Ecosystem ; Geologic Sediments/chemistry/*microbiology ; Microbiota/*physiology ; Nitrogen Cycle ; Nitrosomonadaceae/classification/growth &amp; development/metabolism ; Oxidation-Reduction ; Penaeidae/*growth &amp; development ; Phylogeny ; Ponds/microbiology ; RNA, Ribosomal, 16S ; },
abstract = {AIMS: Ammonia oxidation is a significant process of nitrogen cycles in a lot of ecosystems sediments while there are few studies in shrimp culture pond (SCP) sediments. This paper attempted to explore the community diversity and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in SCP sediments at different culture stages.<br><br>METHODS AND RESULTS: We collected SCP sediments and analysed the community diversity and abundance of AOA and bacteria in shrimp pond sediment at different culture stages using the ammonia monooxygenase (amoA) gene with quantitative PCR (qPCR) and 16S rRNA gene sequencing. The AOB-amoA gene abundance was showed higher than AOA-amoA gene abundance in SCP sediments on Day 50 and Day 60 after shrimp larvae introducing into the pond, and the diversity of AOA in SCP sediments was higher than that of AOB. The phylogenetic tree revealed that the most of AOA were the member of Nitrosopumilus and Nitrososphaera, and the majority of AOB sequences were clustered into Nitrosospira, Nitrosomonas clusters 6a and 7. The AOA community has close relationship with total organic carbon (TOC), pH, total phosphorus (TP), nitrate reductase, urease, acid phosphatase and β-glucosidase. The AOB community was related to TOC, C/N and nitrate reductase.<br><br>CONCLUSIONS: AOA and AOB play the different ecological roles in SCP sediments at different culture stages.<br><br>Our results suggested that the different community diversity and abundance of AOA and AOB in SCP sediments, which may improve our ecological cognition of shrimp culture stages in SCP ecosystems.},
}
@article {pmid33013726,
year = {2020},
author = {Mani, K and Taib, N and Hugoni, M and Bronner, G and Bragança, JM and Debroas, D},
title = {Transient Dynamics of Archaea and Bacteria in Sediments and Brine Across a Salinity Gradient in a Solar Saltern of Goa, India.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {1891},
pmid = {33013726},
issn = {1664-302X},
abstract = {The microbial fluctuations along an increasing salinity gradient during two different salt production phases - initial salt harvesting (ISH) phase and peak salt harvesting (PSH) phase of Siridao solar salterns in Goa, India were examined through high-throughput sequencing of 16S rRNA genes on Illumina MiSeq platform. Elemental analysis of the brine samples showed high concentration of sodium (Na+) and chloride (Cl-) ions thereby indicating its thalassohaline nature. Comparison of relative abundance of sequences revealed that Archaea transited from sediment to brine while Bacteria transited from brine to sediment with increasing salinity. Frequency of Archaea was found to be significantly enriched even in low and moderate salinity sediments with their relative sequence abundance reaching as high as 85%. Euryarchaeota was found to be the dominant archaeal phylum containing 19 and 17 genera in sediments and brine, respectively. Phylotypes belonging to Halorubrum, Haloarcula, Halorhabdus, and Haloplanus were common in both sediments and brine. Occurence of Halobacterium and Natronomonas were exclusive to sediments while Halonotius was exclusive to brine. Among sediments, relative sequence frequency of Halorubrum, and Halorhabdus decreased while Haloarcula, Haloplanus, and Natronomonas increased with increasing salinity. Similarly, the relative abundance of Haloarcula and Halorubrum increased with increasing salinity in brine. Sediments and brine samples harbored about 20 and 17 bacterial phyla, respectively. Bacteroidetes, Proteobacteria, and Chloroflexi were the common bacterial phyla in both sediments and brine while Firmicutes were dominant albeit in sediments alone. Further, Gammaproteobacteria, Alphaproteobacteria, and Deltaproteobacteria were observed to be the abundant class within the Proteobacteria. Among the bacterial genera, phylotypes belonging to Rubricoccus and Halomonas were widely detected in both brine and sediment while Thioalkalispira, Desulfovermiculus, and Marinobacter were selectively present in sediments. This study suggests that Bacteria are more susceptible to salinity fluctuations than Archaea, with many bacterial genera being compartment and phase-specific. Our study further indicated that Archaea rather than Bacteria could withstand the wide salinity fluctuation and attain a stable community structure within a short time-frame.},
}
@article {pmid33005311,
year = {2020},
author = {Jung, J and Kim, JS and Taffner, J and Berg, G and Ryu, CM},
title = {Archaea, tiny helpers of land plants.},
journal = {Computational and structural biotechnology journal},
volume = {18},
number = {},
pages = {2494-2500},
pmid = {33005311},
issn = {2001-0370},
abstract = {Archaea are members of most microbiomes. While archaea are highly abundant in extreme environments, they are less abundant and diverse in association with eukaryotic hosts. Nevertheless, archaea are a substantial constituent of plant-associated ecosystems in the aboveground and belowground phytobiome. Only a few studies have investigated the role of archaea in plant health and its potential symbiosis in ecosystems. This review discusses recent progress in identifying how archaea contribute to plant traits such as growth, adaptation to abiotic stresses, and immune activation. We synthesized the most recent functional and molecular data on archaea, including root colonization and the volatile emission to activate plant systemic immunity. These data represent a paradigm shift in our understanding of plant-microbiota interactions.},
}
@article {pmid33002447,
year = {2021},
author = {Berger, S and Cabrera-Orefice, A and Jetten, MSM and Brandt, U and Welte, CU},
title = {Investigation of central energy metabolism-related protein complexes of ANME-2d methanotrophic archaea by complexome profiling.},
journal = {Biochimica et biophysica acta. Bioenergetics},
volume = {1862},
number = {1},
pages = {148308},
doi = {10.1016/j.bbabio.2020.148308},
pmid = {33002447},
issn = {1879-2650},
support = {339880/ERC_/European Research Council/International ; },
mesh = {Archaea/*enzymology ; Archaeal Proteins/chemistry/*metabolism ; Electron Transport ; *Energy Metabolism ; },
abstract = {The anaerobic oxidation of methane is important for mitigating emissions of this potent greenhouse gas to the atmosphere and is mediated by anaerobic methanotrophic archaea. In a 'Candidatus Methanoperedens BLZ2' enrichment culture used in this study, methane is oxidized to CO2 with nitrate being the terminal electron acceptor of an anaerobic respiratory chain. Energy conservation mechanisms of anaerobic methanotrophs have mostly been studied at metagenomic level and hardly any protein data is available at this point. To close this gap, we used complexome profiling to investigate the presence and subunit composition of protein complexes involved in energy conservation processes. All enzyme complexes and their subunit composition involved in reverse methanogenesis were identified. The membrane-bound enzymes of the respiratory chain, such as F420H2:quinone oxidoreductase, membrane-bound heterodisulfide reductase, nitrate reductases and Rieske cytochrome bc1 complex were all detected. Additional or putative subunits such as an octaheme subunit as part of the Rieske cytochrome bc1 complex were discovered that will be interesting targets for future studies. Furthermore, several soluble proteins were identified, which are potentially involved in oxidation of reduced ferredoxin produced during reverse methanogenesis leading to formation of small organic molecules. Taken together these findings provide an updated, refined picture of the energy metabolism of the environmentally important group of anaerobic methanotrophic archaea.},
}
@article {pmid32994183,
year = {2020},
author = {Wolff, P and Villette, C and Zumsteg, J and Heintz, D and Antoine, L and Chane-Woon-Ming, B and Droogmans, L and Grosjean, H and Westhof, E},
title = {Comparative patterns of modified nucleotides in individual tRNA species from a mesophilic and two thermophilic archaea.},
journal = {RNA (New York, N.Y.)},
volume = {26},
number = {12},
pages = {1957-1975},
pmid = {32994183},
issn = {1469-9001},
mesh = {Base Sequence ; Methanococcus/*genetics ; Nucleic Acid Conformation ; Nucleotides/*chemistry ; Pyrococcus furiosus/*genetics ; RNA, Archaeal/chemistry/genetics ; RNA, Transfer/*chemistry/*genetics ; Sulfolobus acidocaldarius/*genetics ; },
abstract = {To improve and complete our knowledge of archaeal tRNA modification patterns, we have identified and compared the modification pattern (type and location) in tRNAs of three very different archaeal species, Methanococcus maripaludis (a mesophilic methanogen), Pyrococcus furiosus (a hyperthermophile thermococcale), and Sulfolobus acidocaldarius (an acidophilic thermophilic sulfolobale). Most abundant isoacceptor tRNAs (79 in total) for each of the 20 amino acids were isolated by two-dimensional gel electrophoresis followed by in-gel RNase digestions. The resulting oligonucleotide fragments were separated by nanoLC and their nucleotide content analyzed by mass spectrometry (MS/MS). Analysis of total modified nucleosides obtained from complete digestion of bulk tRNAs was also performed. Distinct base- and/or ribose-methylations, cytidine acetylations, and thiolated pyrimidines were identified, some at new positions in tRNAs. Novel, some tentatively identified, modifications were also found. The least diversified modification landscape is observed in the mesophilic Methanococcus maripaludis and the most complex one in Sulfolobus acidocaldarius Notable observations are the frequent occurrence of ac4C nucleotides in thermophilic archaeal tRNAs, the presence of m7G at positions 1 and 10 in Pyrococcus furiosus tRNAs, and the use of wyosine derivatives at position 37 of tRNAs, especially those decoding U1- and C1-starting codons. These results complete those already obtained by others with sets of archaeal tRNAs from Methanocaldococcus jannaschii and Haloferax volcanii.},
}
@article {pmid32991817,
year = {2021},
author = {Chen, T and Hu, W and He, S and Zhang, X and Niu, Y},
title = {Diversity and community structure of ammonia-oxidizing archaea in rhizosphere soil of four plant groups in Ebinur Lake wetland.},
journal = {Canadian journal of microbiology},
volume = {67},
number = {4},
pages = {271-280},
doi = {10.1139/cjm-2020-0228},
pmid = {32991817},
issn = {1480-3275},
mesh = {Ammonia/*metabolism ; Archaea/classification/genetics/*isolation &amp; purification/metabolism ; Lakes ; *Microbiota ; Plants/classification ; *Rhizosphere ; Seasons ; Soil/chemistry ; *Soil Microbiology ; Wetlands ; },
abstract = {The aim of this study was to reveal the differences in the community structure of ammonia-oxidizing archaea (AOA) between rhizosphere and non-rhizosphere soil, to provide a theoretical basis for further study on the relationship between halophyte rhizosphere soil microorganisms and salt tolerance. The results of diversity and community structure showed that the diversity of the AOA community in rhizosphere soil of Reeds was higher than that in non-rhizosphere soil in spring and lower than that in non-rhizosphere soil in summer and autumn. In summer, the diversity of rhizosphere soil of Karelinia caspica was higher than that of non-rhizosphere soil and lower than that of non-rhizosphere soil in spring and autumn. The diversity of rhizosphere soil of Halocnemum strobilaceum in 3 seasons was lower than that in non-rhizosphere soil. The diversity of rhizosphere soil of Salicornia was higher than that in non-rhizosphere soil in 3 seasons. In addition, the relative abundance of AOA in rhizosphere soil of 4 plants was higher than that in non-rhizosphere soil. The AOA community in all soil samples was mainly concentrated in Crenarchaeota and Thaumarchaeota. Redundancy analysis results showed salinity, soil water moisture, pH, and soil organic matter were important factors affecting the differentiation of AOA communities.},
}
@article {pmid32983044,
year = {2020},
author = {Zou, D and Liu, H and Li, M},
title = {Community, Distribution, and Ecological Roles of Estuarine Archaea.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {2060},
pmid = {32983044},
issn = {1664-302X},
abstract = {Archaea are diverse and ubiquitous prokaryotes present in both extreme and moderate environments. Estuaries, serving as links between the land and ocean, harbor numerous microbes that are relatively highly active because of massive terrigenous input of nutrients. Archaea account for a considerable portion of the estuarine microbial community. They are diverse and play key roles in the estuarine biogeochemical cycles. Ammonia-oxidizing archaea (AOA) are an abundant aquatic archaeal group in estuaries, greatly contributing estuarine ammonia oxidation. Bathyarchaeota are abundant in sediments, and they may involve in sedimentary organic matter degradation, acetogenesis, and, potentially, methane metabolism, based on genomics. Other archaeal groups are also commonly detected in estuaries worldwide. They include Euryarchaeota, and members of the DPANN and Asgard archaea. Based on biodiversity surveys of the 16S rRNA gene and some functional genes, the distribution and abundance of estuarine archaea are driven by physicochemical factors, such as salinity and oxygen concentration. Currently, increasing amount of genomic information for estuarine archaea is becoming available because of the advances in sequencing technologies, especially for AOA and Bathyarchaeota, leading to a better understanding of their functions and environmental adaptations. Here, we summarized the current knowledge on the community composition and major archaeal groups in estuaries, focusing on AOA and Bathyarchaeota. We also highlighted the unique genomic features and potential adaptation strategies of estuarine archaea, pointing out major unknowns in the field and scope for future research.},
}
@article {pmid32967357,
year = {2020},
author = {Brázda, V and Luo, Y and Bartas, M and Kaura, P and Porubiaková, O and Šťastný, J and Pečinka, P and Verga, D and Da Cunha, V and Takahashi, TS and Forterre, P and Myllykallio, H and Fojta, M and Mergny, JL},
title = {G-Quadruplexes in the Archaea Domain.},
journal = {Biomolecules},
volume = {10},
number = {9},
pages = {},
pmid = {32967357},
issn = {2218-273X},
support = {CZ.02.1.01/0.0/0.0/15_003/0000477//ERDF/International ; 18-15548S//Grantová Agentura České Republiky/International ; },
mesh = {Archaea/classification/*genetics/metabolism ; Archaeal Proteins/genetics/metabolism ; Circular Dichroism ; DNA/*chemistry/genetics/metabolism ; DNA-Binding Proteins/genetics/metabolism ; *G-Quadruplexes ; Genome, Archaeal/*genetics ; Genomics/methods ; Nucleic Acid Conformation ; Phylogeny ; RNA/*chemistry/genetics/metabolism ; Species Specificity ; },
abstract = {The importance of unusual DNA structures in the regulation of basic cellular processes is an emerging field of research. Amongst local non-B DNA structures, G-quadruplexes (G4s) have gained in popularity during the last decade, and their presence and functional relevance at the DNA and RNA level has been demonstrated in a number of viral, bacterial, and eukaryotic genomes, including humans. Here, we performed the first systematic search of G4-forming sequences in all archaeal genomes available in the NCBI database. In this article, we investigate the presence and locations of G-quadruplex forming sequences using the G4Hunter algorithm. G-quadruplex-prone sequences were identified in all archaeal species, with highly significant differences in frequency, from 0.037 to 15.31 potential quadruplex sequences per kb. While G4 forming sequences were extremely abundant in Hadesarchaea archeon (strikingly, more than 50% of the Hadesarchaea archaeon isolate WYZ-LMO6 genome is a potential part of a G4-motif), they were very rare in the Parvarchaeota phylum. The presence of G-quadruplex forming sequences does not follow a random distribution with an over-representation in non-coding RNA, suggesting possible roles for ncRNA regulation. These data illustrate the unique and non-random localization of G-quadruplexes in Archaea.},
}
@article {pmid32955155,
year = {2020},
author = {Stahl, DA},
title = {The path leading to the discovery of the ammoniaoxidizing archaea.},
journal = {Environmental microbiology},
volume = {22},
number = {11},
pages = {4507-4519},
doi = {10.1111/1462-2920.15239},
pmid = {32955155},
issn = {1462-2920},
support = {//DOE Biological and Environmental Research/ ; //Defense Advanced Research Projects Agency/ ; /EPA/EPA/United States ; /NASA/NASA/United States ; /DE/NIDCR NIH HHS/United States ; //National Science Foundation/ ; //Office of Naval Research/ ; /EPA/EPA/United States ; /NASA/NASA/United States ; /DE/NIDCR NIH HHS/United States ; },
}
@article {pmid32936753,
year = {2020},
author = {Yin, XM and Yang, XY and Hou, J and Zhu, L and Cui, HL},
title = {Natronomonas halophila sp. nov. and Natronomonas salina sp. nov., two novel halophilic archaea.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {70},
number = {11},
pages = {5686-5692},
doi = {10.1099/ijsem.0.004463},
pmid = {32936753},
issn = {1466-5034},
mesh = {China ; DNA, Archaeal/genetics ; Fatty Acids/chemistry ; Glycolipids/chemistry ; Halobacteriaceae/*classification/isolation &amp; purification ; Lakes/*microbiology ; *Mining ; Nucleic Acid Hybridization ; Phospholipids/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Saline Waters ; Sequence Analysis, DNA ; },
abstract = {Two halophilic archaeal strains, C90T and YPL13T, were isolated from a salt lake and a salt mine in PR China. The two strains were found to form two clusters (97.5 and 89.5 % similarity between them, respectively) separating them from the three current members of the genus Natronomonas (95.4-97.0 % and 86.6-89.3 % similarity, respectively) on the basis of the 16S rRNA and rpoB' gene sequence similarities and phylogenetic analysis. Diverse phenotypic characteristics differentiate strains C90T and YPL13T from current Natronomonas members. The polar lipids of strain C90T were phosphatidic acid, phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), phosphatidylglycerol sulphate, two unidentified glycolipids, a major glycolipid and a minor glycolipid, while those of strain YPL13T were PG, PGP-Me, two unidentified phospholipids and a glycolipid. The average nucleotide identity (ANI) and in silico DNA-DNA hybridization (isDDH) values between the two strains were 79.8 and 27.1 %, respectively, which were much lower than the threshold values proposed as a species boundaries (ANI 95-96 % and isDDH 70 %), which revealed that the two strains represent two novel species; these values (ANI 76.6-80.0 % and isDDH 21.6-27.0 %) of the strains examined in this study and the current members of Natronomonas are much lower than the recommended threshold values, suggesting that strains C90T and YPL13T represent two genomically different species of Natronomonas. These results showed that strains C90T (=CGMCC 1.13738T=JCM 32961T) and YPL13T (=CGMCC 1.13884T=JCM 31111T) represent two novel species of Natronomonas, for which the names Natronomonas halophila sp. nov. and Natronomonas salina sp. nov. are proposed.},
}
@article {pmid32935184,
year = {2021},
author = {He, Y and Zhou, Y and Weng, R and Wang, J and Chen, J and Huang, M},
title = {Responses of Ammonia-Oxidizing Archaea and Bacteria in Malodorous River Sediments to Different Remediation Techniques.},
journal = {Microbial ecology},
volume = {81},
number = {2},
pages = {314-322},
pmid = {32935184},
issn = {1432-184X},
support = {41877477//National Natural Science Foundation of China/ ; 18DZ1203806//Shanghai Science and Technology Development Funds/ ; 2017ZX07207001//National Science and Technology Major Project for Water Pollution Control and Treatment/ ; 2018ZX07208008//National Science and Technology Major Project for Water Pollution Control and Treatment/ ; },
mesh = {Ammonia/analysis/*metabolism ; Archaea/classification/genetics/isolation &amp; purification/*metabolism ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Calcium Compounds/analysis ; Environmental Restoration and Remediation/*methods ; Geologic Sediments/chemistry/*microbiology ; Nitrates/analysis ; Oxidation-Reduction ; Oxygen/analysis ; Rivers/chemistry/*microbiology ; Species Specificity ; Water Pollutants, Chemical/metabolism ; },
abstract = {In this study, the joint use of high throughput sequencing, real-time quantitative PCR, and ammonia-oxidizing bacteria (AOB)-inhibiting allylthiourea was used to differentiate between the contributions of ammonia-oxidizing archaea (AOA) vs AOB to ammonia oxidation and ascertain how AOA and AOB responded to two widely used river remediation techniques (aeration and Ca(NO3)2 injection). Results showed that ammonia oxidation was largely attributed to ATU-sensitive AOB rather than AOA and Nitrosomonas was the predominant AOB-related genus (53.86%) in the malodorous river. The contribution of AOB to ammonia oxidation in the context of aeration and Ca(NO3)2 injection was 75.51 ± 2.77% and 60.19 ± 10.44%, respectively. The peak of AOB/AOA ratio and the marked increase of relative abundances of Nitrosomonas and Nitrosospira in aeration runs further demonstrated aeration favored the ammonia oxidation of AOB. Comparatively, Ca(NO3)2 injection could increase the ammonia oxidation contribution of AOA from 31.32 ± 6.06 to 39.81 ± 10.44% and was significantly correlated with Nitrosococcus of AOB (r = 0.796, p < 0.05), Candidatus_Nitrosopelagicus of AOA (r = 0.986, p < 0.01), and AOA Simpson diversity (r = - 0.791, p < 0.05). Moreover, Candidatus_Nitrosopelagicus was only present in Ca(NO3)2 runs. Taken together, Ca(NO3)2 was recognized as an important factor in mediating the growth and ecological niches of ammonia oxidizers.Graphical abstract.},
}
@article {pmid32925997,
year = {2020},
author = {Aleksandrowicz, P and Brzezińska-Błaszczyk, E and Dudko, A and Agier, J},
title = {Archaea Occurrence in the Subgingival Biofilm in Patients with Peri-implantitis and Periodontitis.},
journal = {The International journal of periodontics &amp; restorative dentistry},
volume = {40},
number = {5},
pages = {677-683},
doi = {10.11607/prd.4670},
pmid = {32925997},
issn = {1945-3388},
mesh = {Archaea ; Biofilms ; *Dental Implants ; Humans ; *Peri-Implantitis ; *Periodontitis ; RNA, Ribosomal, 16S ; },
abstract = {This study aimed to determine the prevalence and diversity of archaea and select bacteria in the subgingival biofilm of patients with peri-implantitis in comparison to patients with unaffected implants and patients with periodontitis. Samples of subgingival biofilm from oral sites were collected for DNA extraction (n = 139). A 16S rRNA gene-based polymerase chain reaction assay was used to determine the presence of archaea and select bacteria. Seven samples were selected for direct sequencing. Archaea were detected in 10% of samples from peri-implantitis sites, but not in samples from the unaffected dental implant. Archaea were present in 53% and 64% of samples from mild and moderate/advanced periodontitis sites, respectively. The main representative of the Archaea domain found in biofilm from periodontitis and peri-implantitis sites was Methanobrevibacter oralis. The present results revealed that archaea are present in diseased but not healthy implants. It was also found that archaea were more abundant in periodontitis than in peri-implantitis sites. Hence, the potential role of archaea in peri-implantitis and periodontitis should be taken into consideration.},
}
@article {pmid32919036,
year = {2020},
author = {Di Giulio, M},
title = {LUCA as well as the ancestors of archaea, bacteria and eukaryotes were progenotes: Inference from the distribution and diversity of the reading mechanism of the AUA and AUG codons in the domains of life.},
journal = {Bio Systems},
volume = {198},
number = {},
pages = {104239},
doi = {10.1016/j.biosystems.2020.104239},
pmid = {32919036},
issn = {1872-8324},
mesh = {Anticodon/genetics ; Archaea/classification/*genetics ; Bacteria/classification/*genetics ; Codon/genetics ; Eukaryota/classification/*genetics ; *Evolution, Molecular ; *Genetic Code ; Genetic Variation ; Open Reading Frames/genetics ; Origin of Life ; Phylogeny ; RNA, Transfer/genetics ; },
abstract = {Here I use the rationale assuming that if of a certain trait that exerts its function in some aspect of the genetic code or, more generally, in protein synthesis, it is possible to identify the evolutionary stage of its origin then it would imply that this evolutionary moment would be characterized by a high translational noise because this trait would originate for the first time during that evolutionary stage. That is to say, if this trait had a non-marginal role in the realization of the genetic code, or in protein synthesis, then the origin of this trait would imply that, more generally, it was the genetic code itself that was still originating. But if the genetic code were still originating - at that precise evolutionary stage - then this would imply that there was a high translational noise which in turn would imply that it was in the presence of a protocell, i.e. a progenote that was by definition characterized by high translational noise. I apply this rationale to the mechanism of modification of the base 34 of the anticodon of an isoleucine tRNA that leads to the reading of AUA and AUG codons in archaea, bacteria and eukaryotes. The phylogenetic distribution of this mechanism in these phyletic lineages indicates that this mechanism originated only after the evolutionary stage of the last universal common ancestor (LUCA), namely, during the formation of cellular domains, i.e., at the stage of ancestors of these main phyletic lineages. Furthermore, given that this mechanism of modification of the base 34 of the anticodon of the isoleucine tRNA would result to emerge at a stage of the origin of the genetic code - despite in its terminal phases - then all this would imply that the ancestors of bacteria, archaea and eukaryotes were progenotes. If so, all the more so, the LUCA would also be a progenote since it preceded these ancestors temporally. A consequence of all this reasoning might be that since these three ancestors were of the progenotes that were different from each other, if at least one of them had evolved into at least two real and different cells - basically different from each other - then the number of cellular domains would not be three but it would be greater than three.},
}
@article {pmid32892054,
year = {2021},
author = {Qi, L and Ma, Z and Chang, SX and Zhou, P and Huang, R and Wang, Y and Wang, Z and Gao, M},
title = {Biochar decreases methanogenic archaea abundance and methane emissions in a flooded paddy soil.},
journal = {The Science of the total environment},
volume = {752},
number = {},
pages = {141958},
doi = {10.1016/j.scitotenv.2020.141958},
pmid = {32892054},
issn = {1879-1026},
mesh = {Archaea/genetics ; Charcoal ; Methane ; *Oryza ; *Soil ; Soil Microbiology ; },
abstract = {Biochar addition can reduce methane (CH4) emissions from paddy soils while the mechanisms involved are not entirely clear. Here, we studied the effect of biochar addition on CH4 emissions, and the abundance and community composition of methanogens and methanotrophs over two rice cultivation seasons. The experiment had the following five treatments: control (CK), chemical fertilizer application only (BC0), and 0.5% (w/w) (BC1), 1% (BC2), and 2% of biochar applied with chemical fertilizers (BC3). The season-wide CH4 emissions were decreased (P < 0.05) by 22.2-95.7% in biochar application compared with BC0 in the two rice seasons (2017 and 2018). In 2017, biochar application decreased methanogenic archaea (mcrA) but increased methanotrophic bacteria (pmoA) abundances, and decreased the ratio of mcrA/pmoA, as compared with BC0 (P < 0.05). In 2018, the abundance of mcrA was lower in BC2 and BC3 than in BC0 (P < 0.05) but was not different between BC0 and BC1, and the abundance of pmoA was lower in BC1, BC2 and BC3 than in BC0 (P < 0.05). The CH4 emissions were positively related to abundances of the mcrA gene (P < 0.01) but not to that of the pmoA gene in two rice seasons. Rice grain yield was increased by 62.2-94.1% in biochar addition treatments compared with BC0 in the first year (P < 0.01) and by 29.9-37.6% in BC2 and BC3 compared with BC0 in the second year (P < 0.05). Biochar application decreased CH4 emissions by reducing methanogenic archaea abundance in the studied flooded paddy soil.},
}
@article {pmid32892037,
year = {2021},
author = {Niu, M and Zhou, F and Yang, Y and Sun, Y and Zhu, T and Shen, F},
title = {Abundance and composition of airborne archaea during springtime mixed dust and haze periods in Beijing, China.},
journal = {The Science of the total environment},
volume = {752},
number = {},
pages = {141641},
doi = {10.1016/j.scitotenv.2020.141641},
pmid = {32892037},
issn = {1879-1026},
mesh = {*Air Pollution ; Archaea/genetics ; Beijing ; China ; *Dust/analysis ; Humans ; Phylogeny ; },
abstract = {Archaea have an important role in the elemental biogeochemical cycle and human health. However, characteristics of airborne archaea affected by anthropogenic and natural processes are unclear. In this study, we investigated the abundance, structures, influencing factors and assembly processes of the archaeal communities in the air samples collected from Beijing in springtime using quantitative polymerase chain reaction (qPCR), high-throughput sequencing technology and statistical analysis. The concentrations of airborne archaea ranged from 101 to 103 copies m-3 (455 ± 211 copies m-3), accounting for 0.67% of the total prokaryote (sum of archaea and bacteria). An increase in airborne archaea was seen when the air quality shifted from clean to slightly polluted conditions. Sandstorm dust imported a large number of archaea to the local atmosphere. Euryarchaeota, Thaumarchaeota and Crenarchaeota were the dominant phyla, revealing the primary role of soil in releasing archaea to the ambient environment. Dispersal-related neutral processes play an important role in shaping the structure of airborne archaeal assembly. Of all phyla, methanogenic Euryarchaeota were most abundant in the air parcels come from the south of Beijing. Air masses from the west of Beijing, which brought sandstorm to Beijing, carried large amounts of ammonia oxidizing archaea Nitrososphaera. The results demonstrate the importance of air mass sources and local weather conditions in shaping the local airborne archaea community.},
}
@article {pmid32889138,
year = {2020},
author = {Nikolayev, S and Cohen-Rosenzweig, C and Eichler, J},
title = {Evolutionary considerations of the oligosaccharyltransferase AglB and other aspects of N-glycosylation across Archaea.},
journal = {Molecular phylogenetics and evolution},
volume = {153},
number = {},
pages = {106951},
doi = {10.1016/j.ympev.2020.106951},
pmid = {32889138},
issn = {1095-9513},
mesh = {Archaea/*classification/*enzymology/genetics ; Archaeal Proteins/*genetics ; Glycosylation ; Hexosyltransferases/*genetics ; Membrane Proteins/*genetics ; *Phylogeny ; },
abstract = {Various biological markers in members of the TACK and Asgard archaeal super-phyla show Eukarya-like traits. These include the oligosaccharyltransferase, responsible for transferring glycans from the lipid carrier upon which they are assembled onto selected asparagine residues of target proteins during N-glycosylation. In Archaea, oligosaccharyltransferase activity is catalyzed by AglB. To gain deeper insight into AglB and N-glycosylation across archaeal phylogeny, bioinformatics approaches were employed to address variability in AglB sequence motifs involved in enzyme activity, construct a phylogenetic tree based on AglB sequences, search for archaeal homologues of non-catalytic subunits of the multimeric eukaryal oligosaccharyltransferase complex and predict the presence of aglB-based clusters of glycosylation-related genes in the Euryarchaeota and the DPANN, TACK and Asgard super-phyla. In addition, site-directed mutagenesis and mass spectrometry were employed to study the natural variability in the WWDXG motif central to oligosaccharyltransferase activity seen in archaeal AglB. The results clearly distinguish AglB from members of the DPANN super-phylum and the Euryarchaeota from the same enzyme in members of the TACK and Asgard super-phyla, which showed considerable similarity to its eukaryal homologue Stt3. The results thus support the evolutionary proximity of Eukarya and the TACK and Asgard archaea.},
}
@article {pmid32887961,
year = {2020},
author = {Parks, DH and Chuvochina, M and Chaumeil, PA and Rinke, C and Mussig, AJ and Hugenholtz, P},
title = {Author Correction: A complete domain-to-species taxonomy for Bacteria and Archaea.},
journal = {Nature biotechnology},
volume = {38},
number = {9},
pages = {1098},
doi = {10.1038/s41587-020-0539-7},
pmid = {32887961},
issn = {1546-1696},
abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.},
}
@article {pmid32887944,
year = {2020},
author = {Reichart, NJ and Jay, ZJ and Krukenberg, V and Parker, AE and Spietz, RL and Hatzenpichler, R},
title = {Activity-based cell sorting reveals responses of uncultured archaea and bacteria to substrate amendment.},
journal = {The ISME journal},
volume = {14},
number = {11},
pages = {2851-2861},
pmid = {32887944},
issn = {1751-7370},
support = {80NSSC19K0449/ImNASA/Intramural NASA/United States ; 80NSSC19K1633/ImNASA/Intramural NASA/United States ; },
mesh = {*Archaea/genetics ; Bacteria/genetics ; *Hot Springs ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Wyoming ; },
abstract = {Metagenomic studies have revolutionized our understanding of the metabolic potential of uncultured microorganisms in various ecosystems. However, many of these genomic predictions have yet to be experimentally tested, and the functional expression of genomic potential often remains unaddressed. In order to obtain a more thorough understanding of cell physiology, novel techniques capable of testing microbial metabolism under close to in situ conditions must be developed. Here, we provide a benchmark study to demonstrate that bioorthogonal non-canonical amino acid tagging (BONCAT) in combination with fluorescence-activated cell sorting (FACS) and 16S rRNA gene sequencing can be used to identify anabolically active members of a microbial community incubated in the presence of various growth substrates or under changing physicochemical conditions. We applied this approach to a hot spring sediment microbiome from Yellowstone National Park (Wyoming, USA) and identified several microbes that changed their activity levels in response to substrate addition, including uncultured members of the phyla Thaumarchaeota, Acidobacteria, and Fervidibacteria. Because shifts in activity in response to substrate amendment or headspace changes are indicative of microbial preferences for particular growth conditions, results from this and future BONCAT-FACS studies could inform the development of cultivation media to specifically enrich uncultured microbes. Most importantly, BONCAT-FACS is capable of providing information on the physiology of uncultured organisms at as close to in situ conditions as experimentally possible.},
}
@article {pmid32857850,
year = {2020},
author = {Yue, L and Li, J and Zhang, B and Qi, L and Li, Z and Zhao, F and Li, L and Zheng, X and Dong, X},
title = {The conserved ribonuclease aCPSF1 triggers genome-wide transcription termination of Archaea via a 3'-end cleavage mode.},
journal = {Nucleic acids research},
volume = {48},
number = {17},
pages = {9589-9605},
pmid = {32857850},
issn = {1362-4962},
mesh = {Archaeal Proteins/*genetics/metabolism ; DNA, Complementary/genetics ; DNA-Directed RNA Polymerases/genetics/metabolism ; Genome, Archaeal ; Methanococcus/*genetics ; Mutation ; Phylogeny ; Ribonucleases/*genetics/metabolism ; Transcription, Genetic ; Uridine ; },
abstract = {Transcription termination defines accurate transcript 3'-ends and ensures programmed transcriptomes, making it critical to life. However, transcription termination mechanisms remain largely unknown in Archaea. Here, we reported the physiological significance of the newly identified general transcription termination factor of Archaea, the ribonuclease aCPSF1, and elucidated its 3'-end cleavage triggered termination mechanism. The depletion of Mmp-aCPSF1 in Methanococcus maripaludis caused a genome-wide transcription termination defect and disordered transcriptome. Transcript-3'end-sequencing revealed that transcriptions primarily terminate downstream of a uridine-rich motif where Mmp-aCPSF1 performed an endoribonucleolytic cleavage, and the endoribonuclease activity was determined to be essential to the in vivo transcription termination. Co-immunoprecipitation and chromatin-immunoprecipitation detected interactions of Mmp-aCPSF1 with RNA polymerase and chromosome. Phylogenetic analysis revealed that the aCPSF1 orthologs are ubiquitously distributed among the archaeal phyla, and two aCPSF1 orthologs from Lokiarchaeota and Thaumarchaeota could replace Mmp-aCPSF1 to terminate transcription of M. maripaludis. Therefore, the aCPSF1 dependent termination mechanism could be widely employed in Archaea, including Lokiarchaeota belonging to Asgard Archaea, the postulated archaeal ancestor of Eukaryotes. Strikingly, aCPSF1-dependent archaeal transcription termination reported here exposes a similar 3'-cleavage mode as the eukaryotic RNA polymerase II termination, thus would shed lights on understanding the evolutionary linking between archaeal and eukaryotic termination machineries.},
}
@article {pmid32852144,
year = {2021},
author = {Tang, HM and Xiao, XP and Li, C and Shi, LH and Cheng, KK and Wen, L and Li, WY and Wang, K},
title = {Influences of different manure N input on soil ammonia-oxidizing archaea and bacterial activity and community structure in a double-cropping rice field.},
journal = {Journal of applied microbiology},
volume = {130},
number = {3},
pages = {937-947},
doi = {10.1111/jam.14830},
pmid = {32852144},
issn = {1365-2672},
support = {31872851//National Natural Science Foundation of China/ ; 2019JJ10003//Innovative Research Groups of the Natural Science Foundation of Hunan Province/ ; },
mesh = {Ammonia/metabolism ; Archaea/classification/genetics/isolation &amp; purification/*metabolism ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; China ; Fertilizers/analysis ; Manure/*analysis ; *Microbiota ; Nitrogen/analysis/*metabolism ; Oryza/growth &amp; development/microbiology ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {AIMS: The short-term effects of different organic manure nitrogen (N) input on soil ammonia-oxidizing archaea (AOA) and bacterial (AOB) activity and community structure at maturity stages of early rice and late rice were investigated in the present paper, in a double-cropping rice system in southern China.<br><br>METHODS AND RESULTS: A field experiment was done by applying five different organic and inorganic N input treatments: (i) 100% N of chemical fertilizer (M0), (ii) 30% N of organic manure and 70% N of chemical fertilizer (M30), (iii) 50% N of organic manure and 50% N of chemical fertilizer (M50), (iv) 100% N of organic manure (M100) and (v) without N fertilizer input as control (CK). Microbial community changes were assessed using fatty acid methyl esters, and ammonia oxidizer (AO) changes were followed using quantitative PCR. The results showed that AOA were higher than that of AOB based upon amoA gene copy at maturity stages of early rice and late rice. Also, the abundance of AOB and AOA with M30, M50 and M100 treatments was significantly higher than that of CK treatment. Manure N input treatments had significant effect on AOB and AOA abundance, and a higher correlation between AOB and manure N input was observed. AOB correlated moderately with soil organic carbon content, and AOA correlated moderately with water-filled pore space.<br><br>CONCLUSIONS: This study found that abundance of AOB and AOA was increased under the given organic N conditions, and the soil AOB and AOA community and diversity were changed by different short-term organic manure N input treatments.<br><br>Soil microbial community and specific N-utilizing microbial groups were affected by organic manure N input practices.},
}
@article {pmid32851593,
year = {2020},
author = {Cendron, F and Niero, G and Carlino, G and Penasa, M and Cassandro, M},
title = {Characterizing the fecal bacteria and archaea community of heifers and lactating cows through 16S rRNA next-generation sequencing.},
journal = {Journal of applied genetics},
volume = {61},
number = {4},
pages = {593-605},
pmid = {32851593},
issn = {2190-3883},
mesh = {Animals ; Archaea/genetics/*isolation &amp; purification ; Bacteria/genetics/*isolation &amp; purification ; Breeding ; Cattle ; Feces/microbiology ; Female ; High-Throughput Nucleotide Sequencing ; Lactation/*genetics ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The aim of this study was to describe the fecal bacteria and archaea composition of Holstein-Friesian and Simmental heifers and lactating cows, using 16S rRNA gene sequencing. Bacteria and archaea communities were characterized and compared between heifers and cows of the same breed. Two breeds from different farms were considered, just to speculate about the conservation of the microbiome differences between cows and heifers that undergo different management conditions. The two breeds were from two different herds. Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria were the most abundant phyla in all experimental groups. Alpha- and beta-diversity metrics showed significant differences between heifers and cows within the same breed, supported by principal coordinate analysis. The analysis of Holstein-Friesian fecal microbiome composition revealed 3 different bacteria families, 2 genera, and 2 species that differed between heifers and cows; on the other hand, Simmental heifers and cows differed only for one bacteria family, one archaeal genus, and one bacteria species. Results of the present study suggest that fecal communities of heifers and cows are different, and that fecal microbiome is maintained across experimental groups.},
}
@article {pmid32849470,
year = {2020},
author = {Nagler, M and Podmirseg, SM and Mayr, M and Ascher-Jenull, J and Insam, H},
title = {Quantities of Intra- and Extracellular DNA Reveal Information About Activity and Physiological State of Methanogenic Archaea.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {1894},
pmid = {32849470},
issn = {1664-302X},
abstract = {Although being a common aim of many microbial ecology studies, measuring individual physiological conditions of a microbial group or species within a complex consortium is still a challenge. Here, we propose a novel approach that is based on the quantification of sequentially extracted extracellular (exDNA) and intracellular DNA (iDNA) and reveals information about cell lysis and activity of methanogenic archaea within a biogas-producing microbial community. We monitored the methane production rates of differently treated batch anaerobic cultures and compared the concentrations of the alpha subunit of the methyl coenzyme M reductase gene of methanogenic archaea in extracellular and intracellular DNA fractions and in the classically extracted total DNA pool. Our results showed that this fine-tuned DNA approach coupled with the interpretation of the ratio between free exDNA and iDNA considerably improved microbial activity tracking compared to the classical extraction/quantification of total DNA. Additionally, it allowed to identify and quantify methanogenic populations that are inactive and those that are strongly influenced by cell lysis. We argue that despite the need of further studies, this method represents a novel approach to gain specific physiological information from a complex environmental sample and holds the potential to be applied to other microbes of interest.},
}
@article {pmid32829441,
year = {2021},
author = {Silveira, R and Silva, MRSS and de Roure Bandeira de Mello, T and Alvim, EACC and Marques, NCS and Kruger, RH and da Cunha Bustamante, MM},
title = {Bacteria and Archaea Communities in Cerrado Natural Pond Sediments.},
journal = {Microbial ecology},
volume = {81},
number = {3},
pages = {563-578},
pmid = {32829441},
issn = {1432-184X},
support = {process number 193.000.567/2009//Fundação de Apoio à Pesquisa do Distrito Federal/ ; },
mesh = {*Archaea/genetics ; Bacteria/genetics ; Biodiversity ; Geologic Sediments ; Phylogeny ; *Ponds ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Natural ponds in the Brazilian Cerrado harbor high biodiversity but are still poorly studied, especially their microbial assemblage. The characterization of the microbial community in aquatic environments is fundamental for understanding its functioning, particularly under the increasing pressure posed by land conversion and climate change. Here, we aim to characterize the structure (abundance, richness, and diversity) and composition of the Bacteria and Archaea in the sediment of two natural ponds belonging to different basins that primarily differ in size and depth in the Cerrado. Sediment samples were collected in the dry and rainy seasons and the transition periods between both. The structure and composition of Bacteria and Archaea were assessed by 16S rRNA gene pyrosequencing. We identified 45 bacterial and four archaeal groups. Proteobacteria and Acidobacteria dominated the bacterial community, while Euryarchaeota and Thaumarchaeota dominated the archaeal community. Seasonal fluctuations in the relative abundance of microbial taxa were observed, but pond characteristics were more determinant to community composition differences. Microbial communities are highly diverse, and local variability could partially explain the microbial structure's main differences. Functional predictions based in 16S rRNA gene accessed with Tax4Fun indicated an enriched abundance of predicted methane metabolism in the deeper pond, where higher abundance of methanogenic archaea Methanocella, Methanosaeta, and Methanomicrobiaceae was detected. Our dataset encompasses the more comprehensive survey of prokaryotic microbes in Cerrado's aquatic environments. Here, we present basic and essential information about composition and diversity, for initial insights into the ecology of Bacteria and Archaea in these environments.},
}
@article {pmid32826220,
year = {2020},
author = {Dhamad, AE and Lessner, DJ},
title = {A CRISPRi-dCas9 System for Archaea and Its Use To Examine Gene Function during Nitrogen Fixation by Methanosarcina acetivorans.},
journal = {Applied and environmental microbiology},
volume = {86},
number = {21},
pages = {},
pmid = {32826220},
issn = {1098-5336},
mesh = {Archaeal Proteins/*genetics/metabolism ; *CRISPR-Cas Systems ; Gene Expression ; Genes, Archaeal/*genetics ; Methanosarcina/*genetics/metabolism ; Nitrogen Fixation/*genetics ; },
abstract = {CRISPR-based systems are emerging as the premier method to manipulate many cellular processes. In this study, a simple and efficient CRISPR interference (CRISPRi) system for targeted gene repression in archaea was developed. The Methanosarcina acetivorans CRISPR-Cas9 system was repurposed by replacing Cas9 with the catalytically dead Cas9 (dCas9) to generate a CRISPRi-dCas9 system for targeted gene repression. To test the utility of the system, genes involved in nitrogen (N2) fixation were targeted for dCas9-mediated repression. First, the nif operon (nifHI 1 I 2 DKEN) that encodes molybdenum nitrogenase was targeted by separate guide RNAs (gRNAs), one targeting the promoter and the other targeting nifD Remarkably, growth of M. acetivorans with N2 was abolished by dCas9-mediated repression of the nif operon with each gRNA. The abundance of nif transcripts was >90% reduced in both strains expressing the gRNAs, and NifD was not detected in cell lysate. Next, we targeted NifB, which is required for nitrogenase cofactor biogenesis. Expression of a gRNA targeting the coding sequence of NifB decreased nifB transcript abundance >85% and impaired but did not abolish growth of M. acetivorans with N2 Finally, to ascertain the ability to study gene regulation using CRISPRi-dCas9, nrpR1, encoding a subunit of the repressor of the nif operon, was targeted. The nrpR1 repression strain grew normally with N2 but had increased nif operon transcript abundance, consistent with NrpR1 acting as a repressor. These results highlight the utility of the system, whereby a single gRNA when expressed with dCas9 can block transcription of targeted genes and operons in M. acetivorans IMPORTANCE Genetic tools are needed to understand and manipulate the biology of archaea, which serve critical roles in the biosphere. Methanogenic archaea (methanogens) are essential for the biological production of methane, an intermediate in the global carbon cycle, an important greenhouse gas, and a biofuel. The CRISPRi-dCas9 system in the model methanogen Methanosarcina acetivorans is, to our knowledge, the first Cas9-based CRISPR interference system in archaea. Results demonstrate that the system is remarkably efficient in targeted gene repression and provide new insight into nitrogen fixation by methanogens, the only archaea with nitrogenase. Overall, the CRISPRi-dCas9 system provides a simple, yet powerful, genetic tool to control the expression of target genes and operons in methanogens.},
}
@article {pmid32822422,
year = {2020},
author = {Flores-Bautista, E and Hernandez-Guerrero, R and Huerta-Saquero, A and Tenorio-Salgado, S and Rivera-Gomez, N and Romero, A and Ibarra, JA and Perez-Rueda, E},
title = {Deciphering the functional diversity of DNA-binding transcription factors in Bacteria and Archaea organisms.},
journal = {PloS one},
volume = {15},
number = {8},
pages = {e0237135},
pmid = {32822422},
issn = {1932-6203},
mesh = {Archaea/*genetics/pathogenicity ; Archaeal Proteins/*genetics/metabolism ; Bacterial Proteins/*genetics/metabolism ; Binding Sites ; DNA, Archaeal/metabolism ; DNA, Bacterial/metabolism ; DNA-Binding Proteins/*genetics/metabolism ; Escherichia coli K12/*genetics/pathogenicity ; Gene Expression Regulation, Archaeal ; Gene Expression Regulation, Bacterial ; Genome, Archaeal ; Genome, Bacterial ; Protein Binding ; Transcription Factors/*genetics/metabolism ; Virulence/genetics ; },
abstract = {DNA-binding Transcription Factors (TFs) play a central role in regulation of gene expression in prokaryotic organisms, and similarities at the sequence level have been reported. These proteins are predicted with different abundances as a consequence of genome size, where small organisms contain a low proportion of TFs and large genomes contain a high proportion of TFs. In this work, we analyzed a collection of 668 experimentally validated TFs across 30 different species from diverse taxonomical classes, including Escherichia coli K-12, Bacillus subtilis 168, Corynebacterium glutamicum, and Streptomyces coelicolor, among others. This collection of TFs, together with 111 hidden Markov model profiles associated with DNA-binding TFs collected from diverse databases such as PFAM and DBD, was used to identify the repertoire of proteins putatively devoted to gene regulation in 1321 representative genomes of Archaea and Bacteria. The predicted regulatory proteins were posteriorly analyzed in terms of their genomic context, allowing the prediction of functions for TFs and their neighbor genes, such as genes involved in virulence, enzymatic functions, phosphorylation mechanisms, and antibiotic resistance. The functional analysis associated with PFAM groups showed diverse functional categories were significantly enriched in the collection of TFs and the proteins encoded by the neighbor genes, in particular, small-molecule binding and amino acid transmembrane transporter activities associated with the LysR family and proteins devoted to cellular aromatic compound metabolic processes or responses to drugs, stress, or abiotic stimuli in the MarR family. We consider that with the increasing data derived from new technologies, novel TFs can be identified and help improve the predictions for this class of proteins in complete genomes. The complete collection of experimentally characterized and predicted TFs is available at http://web.pcyt.unam.mx/EntrafDB/.},
}
@article {pmid32817089,
year = {2020},
author = {Fonseca, DR and Halim, MFA and Holten, MP and Costa, KC},
title = {Type IV-Like Pili Facilitate Transformation in Naturally Competent Archaea.},
journal = {Journal of bacteriology},
volume = {202},
number = {21},
pages = {},
pmid = {32817089},
issn = {1098-5530},
mesh = {Archaeal Proteins/*metabolism ; *DNA, Archaeal ; *Gene Transfer, Horizontal ; Methanococcus/*genetics ; Methanomicrobiaceae/*genetics ; },
abstract = {Naturally competent organisms are capable of DNA uptake directly from the environment through the process of transformation. Despite the importance of transformation to microbial evolution, DNA uptake remains poorly characterized outside of the bacterial domain. Here, we identify the pilus as a necessary component of the transformation machinery in archaea. We describe two naturally competent organisms, Methanococcus maripaludis and Methanoculleus thermophilus In M. maripaludis, replicative vectors were transferred with an average efficiency of 2.4 × 103 transformants μg-1 DNA. In M. thermophilus, integrative vectors were transferred with an average efficiency of 2.7 × 103 transformants μg-1 DNA. Additionally, natural transformation of M. thermophilus could be used to introduce chromosomal mutations. To our knowledge, this is the first demonstration of a method to introduce targeted mutations in a member of the order Methanomicrobiales For both organisms, mutants lacking structural components of the type IV-like pilus filament were defective for DNA uptake, demonstrating the importance of pili for natural transformation. Interestingly, competence could be induced in a noncompetent strain of M. maripaludis by expressing pilin genes from a replicative vector. These results expand the known natural competence pili to include examples from the archaeal domain and highlight the importance of pili for DNA uptake in diverse microbial organisms.IMPORTANCE Microbial organisms adapt and evolve by acquiring new genetic material through horizontal gene transfer. One way that this occurs is natural transformation, the direct uptake and genomic incorporation of environmental DNA by competent organisms. Archaea represent up to a third of the biodiversity on Earth, yet little is known about transformation in these organisms. Here, we provide the first characterization of a component of the archaeal DNA uptake machinery. We show that the type IV-like pilus is essential for natural transformation in two archaeal species. This suggests that pili are important for transformation across the tree of life and further expands our understanding of gene flow in archaea.},
}
@article {pmid32812678,
year = {2020},
author = {Wang, K and Yan, H and Peng, X and Hu, H and Zhang, H and Hou, D and Chen, W and Qian, P and Liu, J and Cai, J and Chai, X and Zhang, D},
title = {Community assembly of bacteria and archaea in coastal waters governed by contrasting mechanisms: A seasonal perspective.},
journal = {Molecular ecology},
volume = {29},
number = {19},
pages = {3762-3776},
doi = {10.1111/mec.15600},
pmid = {32812678},
issn = {1365-294X},
mesh = {*Archaea/genetics ; *Bacteria/genetics ; China ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seasons ; },
abstract = {Marine planktonic bacteria and archaea commonly exhibit pronounced seasonal succession in community composition. But the existence of seasonality in their assembly processes and between-domain differences in underlying mechanism are largely unassessed. Using a high-coverage sampling strategy (including single sample for each station during four cruises in different seasons), 16S rRNA gene sequencing, and null models, we investigated seasonal patterns in the processes governing spatial turnover of bacteria and archaea in surface coastal waters across a sampling grid over ~300 km in the East China Sea. We found that archaea only bloomed in prokaryotic communities during autumn and winter cruises. Seasonality mostly overwhelmed spatial variability in the compositions of both domains. Bacterial and archaeal communities were dominantly governed by deterministic and stochastic assembly processes, respectively, in autumn cruise, probably due to the differences in niche breadths (bacteria < archaea) and relative abundance (bacteria > archaea). Stochasticity dominated assembly mechanisms of both domains but was driven by distinct processes in winter cruise. Determinism-dominated assembly mechanisms of bacteria rebounded in spring and summer cruises, reflecting seasonal variability in bacterial community assembly. This could be attributed to seasonal changes in bacterial niche breadths and habitat heterogeneity across the study area. There were seasonal changes in environmental factors mediating the determinism-stochasticity balance of bacterial community assembly, holding a probability of the existence of unmeasured mediators. Our results suggest contrasting assembly mechanisms of bacteria and archaea in terms of determinism-vs.-stochasticity pattern and its seasonality, highlighting the importance of seasonal perspective on microbial community assembly in marine ecosystems.},
}
@article {pmid32788376,
year = {2020},
author = {Darnell, CL and Zheng, J and Wilson, S and Bertoli, RM and Bisson-Filho, AW and Garner, EC and Schmid, AK},
title = {The Ribbon-Helix-Helix Domain Protein CdrS Regulates the Tubulin Homolog ftsZ2 To Control Cell Division in Archaea.},
journal = {mBio},
volume = {11},
number = {4},
pages = {},
pmid = {32788376},
issn = {2150-7511},
support = {203276/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; DP2 AI117923/AI/NIAID NIH HHS/United States ; },
mesh = {Archaea/*genetics/growth &amp; development ; Archaeal Proteins/*genetics ; Cell Division/*genetics ; *Gene Expression Regulation, Archaeal ; Protein Domains ; Transcription Factors/*genetics ; Transcription, Genetic ; },
abstract = {Precise control of the cell cycle is central to the physiology of all cells. In prior work we demonstrated that archaeal cells maintain a constant size; however, the regulatory mechanisms underlying the cell cycle remain unexplored in this domain of life. Here, we use genetics, functional genomics, and quantitative imaging to identify and characterize the novel CdrSL gene regulatory network in a model species of archaea. We demonstrate the central role of these ribbon-helix-helix family transcription factors in the regulation of cell division through specific transcriptional control of the gene encoding FtsZ2, a putative tubulin homolog. Using time-lapse fluorescence microscopy in live cells cultivated in microfluidics devices, we further demonstrate that FtsZ2 is required for cell division but not elongation. The cdrS-ftsZ2 locus is highly conserved throughout the archaeal domain, and the central function of CdrS in regulating cell division is conserved across hypersaline adapted archaea. We propose that the CdrSL-FtsZ2 transcriptional network coordinates cell division timing with cell growth in archaea.IMPORTANCE Healthy cell growth and division are critical for individual organism survival and species long-term viability. However, it remains unknown how cells of the domain Archaea maintain a healthy cell cycle. Understanding the archaeal cell cycle is of paramount evolutionary importance given that an archaeal cell was the host of the endosymbiotic event that gave rise to eukaryotes. Here, we identify and characterize novel molecular players needed for regulating cell division in archaea. These molecules dictate the timing of cell septation but are dispensable for growth between divisions. Timing is accomplished through transcriptional control of the cell division ring. Our results shed light on mechanisms underlying the archaeal cell cycle, which has thus far remained elusive.},
}
@article {pmid32785681,
year = {2020},
author = {Penev, PI and Fakhretaha-Aval, S and Patel, VJ and Cannone, JJ and Gutell, RR and Petrov, AS and Williams, LD and Glass, JB},
title = {Supersized Ribosomal RNA Expansion Segments in Asgard Archaea.},
journal = {Genome biology and evolution},
volume = {12},
number = {10},
pages = {1694-1710},
pmid = {32785681},
issn = {1759-6653},
support = {80NSSC18K1139/ImNASA/Intramural NASA/United States ; },
mesh = {Archaea/*chemistry/genetics ; *Evolution, Molecular ; *Models, Molecular ; *RNA Folding ; RNA, Ribosomal/*chemistry/genetics ; },
abstract = {The ribosome's common core, comprised of ribosomal RNA (rRNA) and universal ribosomal proteins, connects all life back to a common ancestor and serves as a window to relationships among organisms. The rRNA of the common core is similar to rRNA of extant bacteria. In eukaryotes, the rRNA of the common core is decorated by expansion segments (ESs) that vastly increase its size. Supersized ESs have not been observed previously in Archaea, and the origin of eukaryotic ESs remains enigmatic. We discovered that the large ribosomal subunit (LSU) rRNA of two Asgard phyla, Lokiarchaeota and Heimdallarchaeota, considered to be the closest modern archaeal cell lineages to Eukarya, bridge the gap in size between prokaryotic and eukaryotic LSU rRNAs. The elongated LSU rRNAs in Lokiarchaeota and Heimdallarchaeota stem from two supersized ESs, called ES9 and ES39. We applied chemical footprinting experiments to study the structure of Lokiarchaeota ES39. Furthermore, we used covariation and sequence analysis to study the evolution of Asgard ES39s and ES9s. By defining the common eukaryotic ES39 signature fold, we found that Asgard ES39s have more and longer helices than eukaryotic ES39s. Although Asgard ES39s have sequences and structures distinct from eukaryotic ES39s, we found overall conservation of a three-way junction across the Asgard species that matches eukaryotic ES39 topology, a result consistent with the accretion model of ribosomal evolution.},
}
@article {pmid32783333,
year = {2020},
author = {Aigle, A and Gubry-Rangin, C and Thion, C and Estera-Molina, KY and Richmond, H and Pett-Ridge, J and Firestone, MK and Nicol, GW and Prosser, JI},
title = {Experimental testing of hypotheses for temperature- and pH-based niche specialization of ammonia oxidizing archaea and bacteria.},
journal = {Environmental microbiology},
volume = {22},
number = {9},
pages = {4032-4045},
doi = {10.1111/1462-2920.15192},
pmid = {32783333},
issn = {1462-2920},
support = {//AXA Research Fund/International ; DOE Contract DE-AC52- 07NA27344, award SCW1632//Lawrence Livermore National Laboratory/International ; NE/L006286/1//Natural Environment Research Council/International ; UF150571//Royal Society/International ; },
mesh = {Ammonia/*metabolism ; Archaea/genetics/isolation &amp; purification/*metabolism ; Bacteria/genetics/isolation &amp; purification/*metabolism ; Hydrogen-Ion Concentration ; Microbiota ; Nitrification ; Oxidation-Reduction ; Soil/*chemistry ; *Soil Microbiology ; Temperature ; },
abstract = {Investigation of niche specialization in microbial communities is important in assessing consequences of environmental change for ecosystem processes. Ammonia oxidizing bacteria (AOB) and archaea (AOA) present a convenient model for studying niche specialization. They coexist in most soils and effects of soil characteristics on their relative abundances have been studied extensively. This study integrated published information on the influence of temperature and pH on AOB and AOA into several hypotheses, generating predictions that were tested in soil microcosms. The influence of perturbations in temperature was determined in pH 4.5, 6 and 7.5 soils and perturbations in pH were investigated at 15°C, 25°C and 35°C. AO activities were determined by analysing changes in amoA gene and transcript abundances, stable isotope probing and nitrate production. Experimental data supported major predictions of the effects of temperature and pH, but with several significant discrepancies, some of which may have resulted from experimental limitations. The study also provided evidence for unpredicted activity of AOB in pH 4.5 soil. Other discrepancies highlighted important deficiencies in current knowledge, particularly lack of consideration of niche overlap and the need to consider combinations of factors when assessing the influence of environmental change on microbial communities and their activities.},
}
@article {pmid32772189,
year = {2020},
author = {Alori, ET and Emmanuel, OC and Glick, BR and Babalola, OO},
title = {Plant-archaea relationships: a potential means to improve crop production in arid and semi-arid regions.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {36},
number = {9},
pages = {133},
doi = {10.1007/s11274-020-02910-6},
pmid = {32772189},
issn = {1573-0972},
mesh = {Agriculture ; Archaea/classification/*physiology ; Crop Production ; Microbiota ; *Plant Development ; Plant Roots/microbiology ; Plants/*microbiology ; Soil Microbiology ; },
abstract = {Crop production in arid and semi-arid regions of the world is limited by several abiotic factors, including water stress, temperature extremes, low soil fertility, high soil pH, low soil water-holding capacity, and low soil organic matter. Moreover, arid and semi-arid areas experience low levels of rainfall with high spatial and temporal variability. Also, the indiscriminate use of chemicals, a practice that characterizes current agricultural practice, promotes crop and soil pollution potentially resulting in serious human health and environmental hazards. A reliable and sustainable alternative to current farming practice is, therefore, a necessity. One such option includes the use of plant growth-promoting microbes that can help to ameliorate some of the adverse effects of these multiple stresses. In this regard, archaea, functional components of the plant microbiome that are found both in the rhizosphere and the endosphere may contribute to the promotion of plant growth. Archaea can survive in extreme habitats such as areas with high temperatures and hypersaline water. No cases of archaea pathogenicity towards plants have been reported. Archaea appear to have the potential to promote plant growth, improve nutrient supply and protect plants against various abiotic stresses. A better understanding of recent developments in archaea functional diversity, plant colonizing ability, and modes of action could facilitate their eventual usage as reliable components of sustainable agricultural systems. The research discussed herein, therefore, addresses the potential role of archaea to improve sustainable crop production in arid and semi-arid areas.},
}
@article {pmid32770005,
year = {2020},
author = {Yang, S and Lv, Y and Liu, X and Wang, Y and Fan, Q and Yang, Z and Boon, N and Wang, F and Xiao, X and Zhang, Y},
title = {Genomic and enzymatic evidence of acetogenesis by anaerobic methanotrophic archaea.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {3941},
pmid = {32770005},
issn = {2041-1723},
mesh = {Acetates/*metabolism ; Anaerobiosis ; Archaea/*enzymology/genetics ; Bacterial Proteins/genetics/*metabolism ; Carbon Cycle/physiology ; Coenzyme A Ligases/genetics/*metabolism ; Genome, Archaeal ; Geologic Sediments/microbiology ; Metabolic Networks and Pathways/genetics ; Methane/*metabolism ; Oxidation-Reduction ; Seawater/microbiology ; },
abstract = {Anaerobic oxidation of methane (AOM) mediated by anaerobic methanotrophic archaea (ANME) is the primary process that provides energy to cold seep ecosystems by converting methane into inorganic carbon. Notably, cold seep ecosystems are dominated by highly divergent heterotrophic microorganisms. The role of the AOM process in supporting heterotrophic population remains unknown. We investigate the acetogenic capacity of ANME-2a in a simulated cold seep ecosystem using high-pressure biotechnology, where both AOM activity and acetate production are detected. The production of acetate from methane is confirmed by isotope-labeling experiments. A complete archaeal acetogenesis pathway is identified in the ANME-2a genome, and apparent acetogenic activity of the key enzymes ADP-forming acetate-CoA ligase and acetyl-CoA synthetase is demonstrated. Here, we propose a modified model of carbon cycling in cold seeps: during AOM process, methane can be converted into organic carbon, such as acetate, which further fuels the heterotrophic community in the ecosystem.},
}
@article {pmid32761262,
year = {2020},
author = {Sutter, JM and Johnsen, U and Reinhardt, A and Schönheit, P},
title = {Pentose degradation in archaea: Halorhabdus species degrade D-xylose, L-arabinose and D-ribose via bacterial-type pathways.},
journal = {Extremophiles : life under extreme conditions},
volume = {24},
number = {5},
pages = {759-772},
pmid = {32761262},
issn = {1433-4909},
support = {SCHO 316/11-1//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Arabinose/metabolism ; Bacteria ; *Halobacteriaceae/enzymology ; Pentoses ; Ribose ; *Xylose/metabolism ; },
abstract = {The degradation of the pentoses D-xylose, L-arabinose and D-ribose in the domain of archaea, in Haloferax volcanii and in Haloarcula and Sulfolobus species, has been shown to proceed via oxidative pathways to generate α-ketoglutarate. Here, we report that the haloarchaeal Halorhabdus species utilize the bacterial-type non-oxidative degradation pathways for pentoses generating xylulose-5-phosphate. The genes of these pathways are each clustered and were constitutively expressed. Selected enzymes involved in D-xylose degradation, xylose isomerase and xylulokinase, and those involved in L-arabinose degradation, arabinose isomerase and ribulokinase, were characterized. Further, D-ribose degradation in Halorhabdus species involves ribokinase, ribose-5-phosphate isomerase and D-ribulose-5-phosphate-3-epimerase. Ribokinase of Halorhabdus tiamatea and ribose-5-phosphate isomerase of Halorhabdus utahensis were characterized. This is the first report of pentose degradation via the bacterial-type pathways in archaea, in Halorhabdus species that likely acquired these pathways from bacteria. The utilization of bacterial-type pathways of pentose degradation rather than the archaeal oxidative pathways generating α-ketoglutarate might be explained by an incomplete gluconeogenesis in Halorhabdus species preventing the utilization of α-ketoglutarate in the anabolism.},
}
@article {pmid32759221,
year = {2020},
author = {Wang, F and Baquero, DP and Beltran, LC and Su, Z and Osinski, T and Zheng, W and Prangishvili, D and Krupovic, M and Egelman, EH},
title = {Structures of filamentous viruses infecting hyperthermophilic archaea explain DNA stabilization in extreme environments.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {117},
number = {33},
pages = {19643-19652},
pmid = {32759221},
issn = {1091-6490},
support = {R35 GM122510/GM/NIGMS NIH HHS/United States ; HHSN261200800001E/CA/NCI NIH HHS/United States ; },
mesh = {Archaeal Viruses/*chemistry/classification/genetics/ultrastructure ; Biological Evolution ; Capsid/chemistry/ultrastructure ; DNA Viruses/*chemistry/classification/genetics/ultrastructure ; DNA, Viral/*chemistry/genetics ; Extreme Environments ; Genome, Viral ; Phylogeny ; Sulfolobales/*virology ; Sulfolobus/*virology ; },
abstract = {Living organisms expend metabolic energy to repair and maintain their genomes, while viruses protect their genetic material by completely passive means. We have used cryo-electron microscopy (cryo-EM) to solve the atomic structures of two filamentous double-stranded DNA viruses that infect archaeal hosts living in nearly boiling acid: Saccharolobus solfataricus rod-shaped virus 1 (SSRV1), at 2.8-Å resolution, and Sulfolobus islandicus filamentous virus (SIFV), at 4.0-Å resolution. The SIFV nucleocapsid is formed by a heterodimer of two homologous proteins and is membrane enveloped, while SSRV1 has a nucleocapsid formed by a homodimer and is not enveloped. In both, the capsid proteins wrap around the DNA and maintain it in an A-form. We suggest that the A-form is due to both a nonspecific desolvation of the DNA by the protein, and a specific coordination of the DNA phosphate groups by positively charged residues. We extend these observations by comparisons with four other archaeal filamentous viruses whose structures we have previously determined, and show that all 10 capsid proteins (from four heterodimers and two homodimers) have obvious structural homology while sequence similarity can be nonexistent. This arises from most capsid residues not being under any strong selective pressure. The inability to detect homology at the sequence level arises from the sampling of viruses in this part of the biosphere being extremely sparse. Comparative structural and genomic analyses suggest that nonenveloped archaeal viruses have evolved from enveloped viruses by shedding the membrane, indicating that this trait may be relatively easily lost during virus evolution.},
}
@article {pmid32756530,
year = {2020},
author = {Pedone, E and Fiorentino, G and Bartolucci, S and Limauro, D},
title = {Enzymatic Antioxidant Signatures in Hyperthermophilic Archaea.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {9},
number = {8},
pages = {},
pmid = {32756530},
issn = {2076-3921},
support = {MIUR 2017-JTNK78.006//"FLAshMoB: FunctionalAmyloid Chimera for Marine Biosensing"; GoodbyWaste: ObtainGOOD products - exploit BY-products - reduce WASTE, MIUR 2017-JTNK78.006, Italy/ ; FFABR 2017//Fondo per il Finanziamento delleAttivita' Base di Ricerca (FFABR 2017) Ministero dell'Università e della Ricerca (MIUR) Italy/ ; },
abstract = {To fight reactive oxygen species (ROS) produced by both the metabolism and strongly oxidative habitats, hyperthermophilic archaea are equipped with an array of antioxidant enzymes whose role is to protect the biological macromolecules from oxidative damage. The most common ROS, such as superoxide radical (O2-.) and hydrogen peroxide (H2O2), are scavenged by superoxide dismutase, peroxiredoxins, and catalase. These enzymes, together with thioredoxin, protein disulfide oxidoreductase, and thioredoxin reductase, which are involved in redox homeostasis, represent the core of the antioxidant system. In this review, we offer a panorama of progression of knowledge on the antioxidative system in aerobic or microaerobic (hyper)thermophilic archaea and possible industrial applications of these enzymes.},
}
@article {pmid32747565,
year = {2020},
author = {Akıl, C and Tran, LT and Orhant-Prioux, M and Baskaran, Y and Manser, E and Blanchoin, L and Robinson, RC},
title = {Insights into the evolution of regulated actin dynamics via characterization of primitive gelsolin/cofilin proteins from Asgard archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {117},
number = {33},
pages = {19904-19913},
pmid = {32747565},
issn = {1091-6490},
mesh = {Actin Depolymerizing Factors/chemistry/genetics/*metabolism ; Actins/chemistry/genetics/*metabolism ; Amino Acid Sequence ; Archaea/chemistry/genetics/*metabolism ; Archaeal Proteins/chemistry/genetics/*metabolism ; Cytoskeleton/chemistry/genetics/metabolism ; Evolution, Molecular ; Gelsolin/chemistry/genetics/*metabolism ; Genome, Archaeal ; Polymerization ; Protein Conformation, alpha-Helical ; Sequence Alignment ; },
abstract = {Asgard archaea genomes contain potential eukaryotic-like genes that provide intriguing insight for the evolution of eukaryotes. The eukaryotic actin polymerization/depolymerization cycle is critical for providing force and structure in many processes, including membrane remodeling. In general, Asgard genomes encode two classes of actin-regulating proteins from sequence analysis, profilins and gelsolins. Asgard profilins were demonstrated to regulate actin filament nucleation. Here, we identify actin filament severing, capping, annealing and bundling, and monomer sequestration activities by gelsolin proteins from Thorarchaeota (Thor), which complete a eukaryotic-like actin depolymerization cycle, and indicate complex actin cytoskeleton regulation in Asgard organisms. Thor gelsolins have homologs in other Asgard archaea and comprise one or two copies of the prototypical gelsolin domain. This appears to be a record of an initial preeukaryotic gene duplication event, since eukaryotic gelsolins are generally comprise three to six domains. X-ray structures of these proteins in complex with mammalian actin revealed similar interactions to the first domain of human gelsolin or cofilin with actin. Asgard two-domain, but not one-domain, gelsolins contain calcium-binding sites, which is manifested in calcium-controlled activities. Expression of two-domain gelsolins in mammalian cells enhanced actin filament disassembly on ionomycin-triggered calcium release. This functional demonstration, at the cellular level, provides evidence for a calcium-controlled Asgard actin cytoskeleton, indicating that the calcium-regulated actin cytoskeleton predates eukaryotes. In eukaryotes, dynamic bundled actin filaments are responsible for shaping filopodia and microvilli. By correlation, we hypothesize that the formation of the protrusions observed from Lokiarchaeota cell bodies may involve the gelsolin-regulated actin structures.},
}
@article {pmid32714287,
year = {2020},
author = {Zhang, L and Jiang, D and Wu, M and Yang, Z and Oger, PM},
title = {New Insights Into DNA Repair Revealed by NucS Endonucleases From Hyperthermophilic Archaea.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {1263},
pmid = {32714287},
issn = {1664-302X},
abstract = {Hyperthermophilic Archaea (HA) thrive in high temperature environments and their genome is facing severe stability challenge due to the increased DNA damage levels caused by high temperature. Surprisingly, HA display spontaneous mutation frequencies similar to mesophilic microorganisms, thereby indicating that the former must possess more efficient DNA repair systems than the latter to counteract the potentially enhanced mutation rates under the harsher environment. Although a few repair proteins or enzymes from HA have been biochemically and structurally characterized, the molecular mechanisms of DNA repair of HA remain largely unknown. Genomic analyses of HA revealed that they lack MutS/MutL homologues of the mismatch repair (MMR) pathway and the recognition proteins of the nucleotide excision repair (NER) pathway. Endonucleases play an essential role in DNA repair. NucS endonuclease, a novel endonuclease recently identified in some HA and bacteria, has been shown to act on branched, mismatched, and deaminated DNA, suggesting that this endonuclease is a multifunctional enzyme involved in NER, MMR, and deaminated base repair in a non-canonical manner. However, the catalytic mechanism and the physiological function of NucS endonucleases from HA need to be further clarified to determine how they participate in the different DNA repair pathways in cells from HA. In this review, we focus on recent advances in our understanding of the function of NucS endonucleases from HA in NER, MMR, and deaminated DNA repair, and propose directions for future studies of the NucS family of endonucleases.},
}
@article {pmid32691824,
year = {2020},
author = {Charlesworth, J and Kimyon, O and Manefield, M and Beloe, CJ and Burns, BP},
title = {Archaea join the conversation: detection of AHL-like activity across a range of archaeal isolates.},
journal = {FEMS microbiology letters},
volume = {367},
number = {16},
pages = {},
doi = {10.1093/femsle/fnaa123},
pmid = {32691824},
issn = {1574-6968},
mesh = {Archaea/*physiology ; Biosensing Techniques ; Plasmids/genetics ; Quorum Sensing/*genetics ; Signal Transduction ; },
abstract = {Quorum sensing is a mechanism of genetic control allowing single cell organisms to coordinate phenotypic response(s) across a local population and is often critical for ecosystem function. Although quorum sensing has been extensively studied in bacteria comparatively less is known about this mechanism in Archaea. Given the growing significance of Archaea in both natural and anthropogenic settings, it is important to delineate how widespread this phenomenon of signaling is in this domain. Employing a plasmid-based AHL biosensor in conjunction with thin-layer chromatography (TLC), the present study screened a broad range of euryarchaeota isolates for potential signaling activity. Data indicated the presence of 11 new Archaeal isolates with AHL-like activity against the LuxR-based AHL biosensor, including for the first time putative AHL activity in a thermophile. The presence of multiple signals and distinct changes between growth phases were also shown via TLC. Multiple signal molecules were detected using TLC in Haloferax mucosum, Halorubrum kocurii, Natronococcus occultus and Halobacterium salinarium. The finding of multiple novel signal producers suggests the potential for quorum sensing to play an important role not only in the regulation of complex phenotypes within Archaea but the potential for cross-talk with bacterial systems.},
}
@article {pmid32674430,
year = {2020},
author = {Hogrel, G and Lu, Y and Alexandre, N and Bossé, A and Dulermo, R and Ishino, S and Ishino, Y and Flament, D},
title = {Role of RadA and DNA Polymerases in Recombination-Associated DNA Synthesis in Hyperthermophilic Archaea.},
journal = {Biomolecules},
volume = {10},
number = {7},
pages = {},
pmid = {32674430},
issn = {2218-273X},
support = {-//Institut Français de Recherche pour l'Exploitation de la Mer/International ; -//LIA1211 MICROBSEA/International ; },
mesh = {Archaeal Proteins/*metabolism ; DNA Polymerase III/*metabolism ; DNA Polymerase beta/*metabolism ; DNA Replication ; DNA, Archaeal/chemistry/*metabolism ; DNA-Binding Proteins/*metabolism ; Homologous Recombination ; Nucleic Acid Conformation ; Pyrococcus abyssi/*genetics/metabolism ; },
abstract = {Among the three domains of life, the process of homologous recombination (HR) plays a central role in the repair of double-strand DNA breaks and the restart of stalled replication forks. Curiously, main protein actors involved in the HR process appear to be essential for hyperthermophilic Archaea raising interesting questions about the role of HR in replication and repair strategies of those Archaea living in extreme conditions. One key actor of this process is the recombinase RadA, which allows the homologous strand search and provides a DNA substrate required for following DNA synthesis and restoring genetic information. DNA polymerase operation after the strand exchange step is unclear in Archaea. Working with Pyrococcus abyssi proteins, here we show that both DNA polymerases, family-B polymerase (PolB) and family-D polymerase (PolD), can take charge of processing the RadA-mediated recombination intermediates. Our results also indicate that PolD is far less efficient, as compared with PolB, to extend the invaded DNA at the displacement-loop (D-loop) substrate. These observations coincide with previous genetic analyses obtained on Thermococcus species showing that PolB is mainly involved in DNA repair without being essential probably because PolD could take over combined with additional partners.},
}
@article {pmid32671380,
year = {2021},
author = {Rasmussen, M and Collin, M},
title = {Archaea in Blood Cultures: Coincidence or Coinfection?.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {73},
number = {9},
pages = {e2580-e2581},
doi = {10.1093/cid/ciaa993},
pmid = {32671380},
issn = {1537-6591},
mesh = {Archaea ; *Bacteremia ; Blood Culture ; *Coinfection ; Humans ; *Staphylococcal Infections ; },
}
@article {pmid32657581,
year = {2020},
author = {Wu, L and Chen, X and Wei, W and Liu, Y and Wang, D and Ni, BJ},
title = {A Critical Review on Nitrous Oxide Production by Ammonia-Oxidizing Archaea.},
journal = {Environmental science &amp; technology},
volume = {54},
number = {15},
pages = {9175-9190},
doi = {10.1021/acs.est.0c03948},
pmid = {32657581},
issn = {1520-5851},
mesh = {*Ammonia ; *Archaea ; Nitrification ; Nitrous Oxide ; Oxidation-Reduction ; Soil Microbiology ; },
abstract = {The continuous increase of nitrous oxide (N2O) in the atmosphere has become a global concern because of its property as a potent greenhouse gas. Given the important role of ammonia-oxidizing archaea (AOA) in ammonia oxidation and their involvement in N2O production, a clear understanding of the knowledge on archaeal N2O production is necessary for global N2O mitigation. Compared to bacterial N2O production by ammonia-oxidizing bacteria (AOB), AOA-driven N2O production pathways are less-well elucidated. In this Critical Review, we synthesized the currently proposed AOA-driven N2O production pathways in combination with enzymology distinction, analyzed the role of AOA species involved in N2O production pathways, discussed the relative contribution of AOA to N2O production in both natural and anthropogenic environments, summarized the factors affecting archaeal N2O yield, and compared the distinctions among approaches used to differentiate ammonia oxidizer-associated N2O production. We, then, put forward perspectives for archaeal N2O production and future challenges to further improve our understanding of the production pathways, putative enzymes involved and potential approaches for identification in order to potentially achieve effective N2O mitigations.},
}
@article {pmid32655535,
year = {2020},
author = {Wang, L and Pang, Q and Peng, F and Zhang, A and Zhou, Y and Lian, J and Zhang, Y and Yang, F and Zhu, Y and Ding, C and Zhu, X and Li, Y and Cui, Y},
title = {Response Characteristics of Nitrifying Bacteria and Archaea Community Involved in Nitrogen Removal and Bioelectricity Generation in Integrated Tidal Flow Constructed Wetland-Microbial Fuel Cell.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {1385},
pmid = {32655535},
issn = {1664-302X},
abstract = {This study explores nitrogen removal performance, bioelectricity generation, and the response of microbial community in two novel tidal flow constructed wetland-microbial fuel cells (TFCW-MFCs) when treating synthetic wastewater under two different chemical oxygen demand/total nitrogen (COD/TN, or simplified as C/N) ratios (10:1 and 5:1). The results showed that they achieved high and stable COD, NH4 +-N, and TN removal efficiencies. Besides, TN removal rate of TFCW-MFC was increased by 5-10% compared with that of traditional CW-MFC. Molecular biological analysis revealed that during the stabilization period, a low C/N ratio remarkably promoted diversities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the cathode layer, whereas a high one enhanced the richness of nitrite-oxidizing bacteria (NOB) in each medium; the dominant genera in AOA, AOB, and NOB were Candidatus Nitrosotenuis, Nitrosomonas, and Nitrobacter. Moreover, a high C/N ratio facilitated the growth of Nitrosomonas, while it inhibited the growth of Candidatus Nitrosotenuis. The distribution of microbial community structures in NOB was separated by space rather than time or C/N ratio, except for Nitrobacter. This is caused by the differences of pH, dissolved oxygen (DO), and nitrogen concentration. The response of microbial community characteristics to nitrogen transformations and bioelectricity generation demonstrated that TN concentration is significantly negatively correlated with AOA-shannon, AOA-chao, 16S rRNA V4-V5-shannon, and 16S rRNA V4-V5-chao, particularly due to the crucial functions of Nitrosopumilus, Planctomyces, and Aquicella. Additionally, voltage output was primarily influenced by microorganisms in the genera of Nitrosopumilus, Nitrosospira, Altererythrobacter, Gemmata, and Aquicella. This study not only presents an applicable tool to treat high nitrogen-containing wastewater, but also provides a theoretical basis for the use of TFCW-MFC and the regulation of microbial community in nitrogen removal and electricity production.},
}
@article {pmid32636492,
year = {2020},
author = {Qin, W and Zheng, Y and Zhao, F and Wang, Y and Urakawa, H and Martens-Habbena, W and Liu, H and Huang, X and Zhang, X and Nakagawa, T and Mende, DR and Bollmann, A and Wang, B and Zhang, Y and Amin, SA and Nielsen, JL and Mori, K and Takahashi, R and Virginia Armbrust, E and Winkler, MH and DeLong, EF and Li, M and Lee, PH and Zhou, J and Zhang, C and Zhang, T and Stahl, DA and Ingalls, AE},
title = {Alternative strategies of nutrient acquisition and energy conservation map to the biogeography of marine ammonia-oxidizing archaea.},
journal = {The ISME journal},
volume = {14},
number = {10},
pages = {2595-2609},
pmid = {32636492},
issn = {1751-7370},
mesh = {*Ammonia ; *Archaea/genetics ; Nitrification ; Nutrients ; Oxidation-Reduction ; Phylogeny ; },
abstract = {Ammonia-oxidizing archaea (AOA) are among the most abundant and ubiquitous microorganisms in the ocean, exerting primary control on nitrification and nitrogen oxides emission. Although united by a common physiology of chemoautotrophic growth on ammonia, a corresponding high genomic and habitat variability suggests tremendous adaptive capacity. Here, we compared 44 diverse AOA genomes, 37 from species cultivated from samples collected across diverse geographic locations and seven assembled from metagenomic sequences from the mesopelagic to hadopelagic zones of the deep ocean. Comparative analysis identified seven major marine AOA genotypic groups having gene content correlated with their distinctive biogeographies. Phosphorus and ammonia availabilities as well as hydrostatic pressure were identified as selective forces driving marine AOA genotypic and gene content variability in different oceanic regions. Notably, AOA methylphosphonate biosynthetic genes span diverse oceanic provinces, reinforcing their importance for methane production in the ocean. Together, our combined comparative physiological, genomic, and metagenomic analyses provide a comprehensive view of the biogeography of globally abundant AOA and their adaptive radiation into a vast range of marine and terrestrial habitats.},
}
@article {pmid32634668,
year = {2020},
author = {Shi, X and Gao, G and Tian, J and Wang, XC and Jin, X and Jin, P},
title = {Symbiosis of sulfate-reducing bacteria and methanogenic archaea in sewer systems.},
journal = {Environment international},
volume = {143},
number = {},
pages = {105923},
doi = {10.1016/j.envint.2020.105923},
pmid = {32634668},
issn = {1873-6750},
mesh = {*Archaea/genetics ; Bacteria ; *Sewage ; Sulfates ; Symbiosis ; },
abstract = {Sulfide and methane emissions always simultaneously exist in natural environment and constitute a major topic of societal concern. However, the metabolic environments between sulfate-reducing bacteria (SRB) and methanogenic archaea (MA) exist a great difference, which seems to be opposite to the coexisting phenomenon. To explore this issue, the comprehensive biofilm structures, substrate consuming and metabolism pathways of SRB and MA were investigated in a case study of urban sewers. The results showed that, due to the stricter environmental requirements of MA than SRB, SRB became the preponderant microorganism which promoted the rapid generation of sulfide in the initial period of biofilm formation. According to a metagenomic analysis, the SRB appeared to be more preferential than MA in sewers, and the preponderant SRB could provide a key medium (Methyl-coenzyme M) for methane metabolism. Therefore, the diversity of MA gradually increased, and the symbiosis system formed preliminarily. In addition, via L-cysteine, methane metabolism also participated in sulfide consumption which was involved in cysteine and methionine metabolism. This phenomenon of sulfide consumption led to the forward reaction of sulfide metabolism, which could promote sulfide generation while stabilizing the pH value (H+ concentration) and S2- concentrations which should have inhibited SRB and MA production. Therefore, the heavily intertwined interactions between sulfide and methane metabolism provided environmental security for SRB and MA, and completely formed the symbiosis between SRB and MA. Based on these findings, an ecological model involving synergistic mechanism between sulfide and methane generation is proposed and this model can also improve understanding on the symbiosis of SRB and MA in the natural environment.},
}
@article {pmid32634643,
year = {2020},
author = {Lin, Z and Huang, W and Zhou, J and He, X and Wang, J and Wang, X and Zhou, J},
title = {The variation on nitrogen removal mechanisms and the succession of ammonia oxidizing archaea and ammonia oxidizing bacteria with temperature in biofilm reactors treating saline wastewater.},
journal = {Bioresource technology},
volume = {314},
number = {},
pages = {123760},
doi = {10.1016/j.biortech.2020.123760},
pmid = {32634643},
issn = {1873-2976},
mesh = {*Ammonia ; *Archaea ; Bacteria ; Biofilms ; Denitrification ; Nitrification ; Nitrogen ; Oxidation-Reduction ; Phylogeny ; Temperature ; Waste Water ; },
abstract = {To reveal nitrogen removal mechanisms under environmental stresses, biofilm reactors were operated at different temperatures (10 °C-35 °C) treating saline wastewater (salinity 3%). The results showed nitrogen removal efficiency was 98.46% at 30 °C and 60.85% at 10 °C, respectively. Both ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB) participated in nitrification. 94.9% of the overall ammonia oxidation was attributed to AOA at 10 °C, but only 48.2% of that was undertaken by AOA at 35 °C. AOA had a greater contribution at low temperature, which demonstrated that nitrogen removal pathway varied with temperature. Aerobic denitrification was more stable than anoxic denitrification. High-throughput sequencing showed Crenarchaeota was the dominant AOA (97.02-34.47%), cooperating with various heterotrophic AOB. Real-time PCR indicated that AOA was three orders of magnitude more abundant than AOB. AOA was more resistant to low temperature and high-saline stresses. Ammonia oxidizers had distinct responses to temperature change and showed diverse relationships at different temperatures.},
}
@article {pmid32633872,
year = {2020},
author = {Eichler, J},
title = {N-glycosylation in Archaea-New roles for an ancient posttranslational modification.},
journal = {Molecular microbiology},
volume = {114},
number = {5},
pages = {735-741},
doi = {10.1111/mmi.14569},
pmid = {32633872},
issn = {1365-2958},
mesh = {Archaea/*metabolism ; Archaeal Proteins/metabolism ; Biological Evolution ; Evolution, Molecular ; Genes, Archaeal/genetics ; Glycoproteins/metabolism ; *Glycosylation ; Polysaccharides/genetics/*metabolism ; Protein Processing, Post-Translational/genetics/physiology ; },
abstract = {Genome analysis points to N-glycosylation as being an almost universal posttranslational modification in Archaea. Although such predictions have been confirmed in only a limited number of species, such studies are making it increasingly clear that the N-linked glycans which decorate archaeal glycoproteins present diversity in terms of both glycan composition and architecture far beyond what is seen in the other two domains of life. In addition to continuing to decipher pathways of N-glycosylation, recent efforts have revealed how Archaea exploit this variability in novel roles. As well as encouraging glycoprotein synthesis, folding and assembly into properly functioning higher ordered complexes, N-glycosylation also provides Archaea with a strategy to cope with changing environments. Archaea can, moreover, exploit the apparent species-specific nature of N-glycosylation for selectivity in mating, and hence, to maintain species boundaries, and in other events where cell-selective interactions are required. At the same time, addressing components of N-glycosylation pathways across archaeal phylogeny offers support for the concept of an archaeal origin for eukaryotes. In this MicroReview, these and other recent discoveries related to N-glycosylation in Archaea are considered.},
}
@article {pmid32631866,
year = {2020},
author = {Zou, D and Wan, R and Han, L and Xu, MN and Liu, Y and Liu, H and Kao, SJ and Li, M},
title = {Genomic Characteristics of a Novel Species of Ammonia-Oxidizing Archaea from the Jiulong River Estuary.},
journal = {Applied and environmental microbiology},
volume = {86},
number = {18},
pages = {},
pmid = {32631866},
issn = {1098-5336},
mesh = {Ammonia/*metabolism ; Archaea/classification/*genetics/metabolism ; China ; Estuaries ; *Genome, Archaeal ; Oxidation-Reduction ; Rivers/microbiology ; },
abstract = {Ammonia-oxidizing archaea (AOA) are ubiquitous in diverse ecosystems and play a pivotal role in global nitrogen and carbon cycling. Although AOA diversity and distribution are widely studied, mainly based on the amoA (alpha subunit of ammonia monooxygenase) genotypes, only limited investigations have addressed the relationship between AOA genetic adaptation, metabolic features, and ecological niches, especially in estuaries. Here, we describe the AOA communities along the Jiulong River estuary in southern China. Nine high-quality AOA metagenome-assembled genomes (MAGs) were obtained by metagenomics. Five of the MAGs are proposed to constitute a new species, "Candidatus Nitrosopumilus aestuariumsis" sp. nov., based on the phylogenies of the 16S and 23S rRNA genes and concatenated ribosomal proteins, as well as the average amino acid identity. Comparative genomic analysis revealed unique features of the new species, including a high number of genes related to diverse carbohydrate-active enzymes, phosphatases, heavy-metal transport systems, flagellation, and chemotaxis. These genes may be crucial for AOA adaptation to the eutrophic and heavy-metal-contaminated Jiulong River estuary. The uncovered detailed genomic characteristics of the new estuarine AOA species highlight AOA contributions to ammonia oxidation in the Jiulong River estuary.IMPORTANCE In this study, AOA communities along a river in southern China were characterized, and metagenome-assembled genomes (MAGs) of a novel AOA clade were also obtained. Based on the characterization of AOA genomes, the study suggests adaptation of the novel AOAs to estuarine environments, providing new information on the ecology of estuarine AOA and the nitrogen cycle in contaminated estuarine environments.},
}
@article {pmid32608808,
year = {2020},
author = {Zhang, Y and Zuo, JE and Wang, SK and Alisa, S and Li, AJ and Li, LL},
title = {[Spatial Distribution of Nitrogen Metabolism Functional Genes of Eubacteria and Archaebacteria in Dianchi Lake].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {41},
number = {6},
pages = {2908-2917},
doi = {10.13227/j.hjkx.201909196},
pmid = {32608808},
issn = {0250-3301},
mesh = {*Archaea ; *Bacteria/genetics ; Biodiversity ; *Genes, Bacterial ; *Lakes ; Nitrogen ; *Nitrogen Cycle ; Phylogeny ; },
abstract = {Nitrogen metabolism plays an important role in the nitrogen cycle and transformation in Dianchi Lake. Not only do eukaryotes participate in nitrogen transformation but prokaryotes, as the main drivers of the nitrogen cycle, also play an extremely important role in the nitrogen cycle. Based on 16S rDNA high-throughput sequencing technology, 13 sites in Caohai and Waihai of Dianchi Lake were monitored, and PICRUSt function analysis method was adopted to analyze the microbial community diversity and key genes of nitrogen metabolism in Dianchi Lake. Bacteria belonging to 35 phyla and 427 genera were found in Dianchi Lake water and mainly included Proteobacteria and Bacteroidetes. Archaea had 14 phyla and 61 genera and mainly belonged to Euryarchaeota. The overall bacterial richness index of Dianchi Lake was higher than that of archaea, and the bacterial diversity index of Caohai was higher than that of Waihai. Functional prediction showed functional richness of bacteria and archaea. There were 35 KO pathways involved in nitrogen metabolism in bacteria, including key genes such as nitrogenous nitrate-reducing gene nirB, nitric oxide reductase gene norB in denitrification, and nitroreductase gene nasK. There were 23 KO pathways involved in nitrogen metabolism in archaea, involving nifH, nifK, and nifD nitrogenase genes in nitrogen fixation. The copy number of nitrogenase genes was significantly higher than that of other nitrogenase genes. The copy number of nitrogen-fixing genes of archaea was higher than that of bacteria, the nitrogen metabolism capacity of archaea in Caohai was higher than that in Waihai, and the potential of nitrogen-fixation of archaea in Dianchi Lake water was higher than that of bacteria. From the perspective of community structure and function prediction of bacteria and archaea, this study discussed the differences of nitrogen cycle in bacteria and archaea in different areas of Dianchi Lake and provided a decision basis for water environment management in Dianchi Lake.},
}
@article {pmid32602260,
year = {2021},
author = {Song, Y and Zhu, Z and Zhou, W and Zhang, YPJ},
title = {High-efficiency transformation of archaea by direct PCR products with its application to directed evolution of a thermostable enzyme.},
journal = {Microbial biotechnology},
volume = {14},
number = {2},
pages = {453-464},
pmid = {32602260},
issn = {1751-7915},
mesh = {Hot Temperature ; Plasmids ; Polymerase Chain Reaction ; *Thermococcus/genetics ; },
abstract = {Hyperthermophilic archaea with unique biochemical and physiological characteristics are important organisms for fundamental research of life science and have great potential for biotechnological applications. However, low transformation efficiency of foreign DNA molecules impedes developments in genetic modification tools and industrial applications. In this study, we applied prolonged overlap extension PCR (POE-PCR) to generate multimeric DNA molecules and then transformed them into two hyperthermophilic archaea, Thermococcus kodakarensis KOD1 and Pyrococcus yayanosii A1. This study was the first example to demonstrate the enhanced transformation efficiencies of POE-PCR products by a factor of approximately 100 for T. kodakarensis KOD1 and 8 for P. yayanosii A1, respectively, relative to circular shuttle plasmids. Furthermore, directed evolution of a modestly thermophilic enzyme, Methanothermococcus okinawensis 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR), was conducted to obtain more stable ones due to high transformation efficiency of T. kodakarensis (i.e. ~3 × 104 CFU per μg DNA). T. kodakarensis harbouring the most thermostable MoHMGR mutant can grow in the presence of a thermostable antibiotic simvastatin at 85°C and even higher temperatures. This high transformation efficiency technique could not only help develop more hyperthermophilic enzyme mutants via directed evolution but also simplify genetical modification of archaea, which could be novel hosts for industrial biotechnology.},
}
@article {pmid32580393,
year = {2020},
author = {Leoni, C and Volpicella, M and Fosso, B and Manzari, C and Piancone, E and Dileo, MCG and Arcadi, E and Yakimov, M and Pesole, G and Ceci, LR},
title = {A Differential Metabarcoding Approach to Describe Taxonomy Profiles of Bacteria and Archaea in the Saltern of Margherita di Savoia (Italy).},
journal = {Microorganisms},
volume = {8},
number = {6},
pages = {},
pmid = {32580393},
issn = {2076-2607},
support = {634486//Horizon 2020/ ; 97/2018//Banca d'Italia/ ; },
abstract = {Microorganisms inhabiting saline environments are an interesting ecological model for the study of the adaptation of organisms to extreme living conditions and constitute a precious resource of enzymes and bioproducts for biotechnological applications. We analyzed the microbial communities in nine ponds with increasing salt concentrations (salinity range 4.9-36.0%) of the Saltern of Margherita di Savoia (Italy), the largest thalassohaline saltern in Europe. A deep-metabarcoding NGS procedure addressing separately the V5-V6 and V3-V4 hypervariable regions of the 16S rRNA gene of Bacteria and Archaea, respectively, and a CARD-FISH (catalyzed reporter deposition fluorescence in situ hybridization) analysis allowed us to profile the dynamics of microbial populations at the different salt concentrations. Both the domains were detected throughout the saltern, even if the low relative abundance of Archaea in the three ponds with the lowest salinities prevented the construction of the relative amplicon libraries. The highest cell counts were recorded at 14.5% salinity for Bacteria and at 24.1% salinity for Archaea. While Bacteria showed the greatest number of genera in the first ponds (salinity range 4.9-14.5%), archaeal genera were more numerous in the last ponds of the saltern (salinity 24.1-36.0%). Among prokaryotes, Salinibacter was the genus with the maximum abundance (~49% at 34.6% salinity). Other genera detected at high abundance were the archaeal Haloquadratum (~43% at 36.0% salinity) and Natronomonas (~18% at 13.1% salinity) and the bacterial "Candidatus Aquiluna" (~19% at 14.5% salinity). Interestingly, "Candidatus Aquiluna" had not been identified before in thalassohaline waters.},
}
@article {pmid32569776,
year = {2020},
author = {Coker, OO and Wu, WKK and Wong, SH and Sung, JJY and Yu, J},
title = {Altered Gut Archaea Composition and Interaction With Bacteria Are Associated With Colorectal Cancer.},
journal = {Gastroenterology},
volume = {159},
number = {4},
pages = {1459-1470.e5},
doi = {10.1053/j.gastro.2020.06.042},
pmid = {32569776},
issn = {1528-0012},
mesh = {Adenoma/*microbiology/*pathology ; Aged ; Archaea/*isolation &amp; purification ; Case-Control Studies ; Cohort Studies ; Colorectal Neoplasms/*microbiology/*pathology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Middle Aged ; Sensitivity and Specificity ; },
abstract = {BACKGROUND &amp; AIMS: Changes in the intestinal microbiota have been associated with development and progression of colorectal cancer (CRC). Archaea are stable components of the microbiota, but little is known about their composition or contribution to colorectal carcinogenesis. We analyzed archaea in fecal microbiomes of 2 large cohorts of patients with CRC.<br><br>METHODS: We performed shotgun metagenomic analyses of fecal samples from 585 participants (184 patients with CRC, 197 patients with adenomas, and 204 healthy individuals) from discovery (165 individuals) and validation (420 individuals) cohorts. Assignment of taxonomies was performed by exact k-mer alignment against an integrated microbial reference genome database.<br><br>RESULTS: Principal component analysis of archaeomes showed distinct clusters in fecal samples from patients with CRC, patients with adenomas, and control individuals (P < .001), indicating an alteration in the composition of enteric archaea during tumorigenesis. Fecal samples from patients with CRC had significant enrichment of halophilic and depletion of methanogenic archaea. The halophilic Natrinema sp. J7-2 increased progressively in samples from control individuals, to patients with adenomas, to patients with CRC. Abundances of 9 archaea species that were enriched in fecal samples from patients with CRC distinguished them from control individuals with areas under the receiver operating characteristic curve of 0.82 in the discovery cohort and 0.83 in the validation cohort. An association between archaea and bacteria diversities was observed in fecal samples from control individuals but not from patients with CRC. Archaea that were enriched in fecal samples from patients with CRC had an extensive mutual association with bacteria that were enriched in the same samples and exclusivity with bacteria that were lost from these samples.<br><br>CONCLUSIONS: Archaeomes of fecal samples from patients with CRC are characterized by enrichment of halophiles and depletion of methanogens. Studies are needed to determine whether associations between specific archaea and bacteria species in samples from patients with CRC contribute to or are a response to colorectal tumorigenesis.},
}
@article {pmid32546672,
year = {2020},
author = {Zhao, J and Meng, Y and Drewer, J and Skiba, UM and Prosser, JI and Gubry-Rangin, C},
title = {Differential Ecosystem Function Stability of Ammonia-Oxidizing Archaea and Bacteria following Short-Term Environmental Perturbation.},
journal = {mSystems},
volume = {5},
number = {3},
pages = {},
pmid = {32546672},
issn = {2379-5077},
abstract = {Rapidly expanding conversion of tropical forests to oil palm plantations in Southeast Asia leads to soil acidification following intensive nitrogen fertilization. Changes in soil pH are predicted to have an impact on archaeal ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and complete (comammox) ammonia oxidizers and, consequently, on nitrification. It is therefore critical to determine whether the predicted effects of pH on ammonia oxidizers and nitrification activity apply in tropical soils subjected to various degrees of anthropogenic activity. This was investigated by experimental manipulation of pH in soil microcosms from a land-use gradient (forest, riparian, and oil palm soils). The nitrification rate was greater in forest soils with native neutral pH than in converted acidic oil palm soils. Ammonia oxidizer activity decreased following acidification of the forest soils but increased after liming of the oil palm soils, leading to a trend of a reversed net nitrification rate after pH modification. AOA and AOB nitrification activity was dependent on pH, but AOB were more sensitive to pH modification than AOA, which demonstrates a greater stability of AOA than AOB under conditions of short-term perturbation. In addition, these results predict AOB to be a good bioindicator of nitrification response following pH perturbation during land-use conversion. AOB and/or comammox species were active in all soils along the land-use gradient, even, unexpectedly, under acidic conditions, suggesting their adaptation to native acidic or acidified soils. The present study therefore provided evidence for limited stability of soil ammonia oxidizer activity following intensive anthropogenic activities, which likely aggravates the vulnerability of nitrogen cycle processes to environmental disturbance.IMPORTANCE Physiological and ecological studies have provided evidence for pH-driven niche specialization of ammonia oxidizers in terrestrial ecosystems. However, the functional stability of ammonia oxidizers following pH change has not been investigated, despite its importance in understanding the maintenance of ecosystem processes following environmental perturbation. This is particularly true after anthropogenic perturbation, such as the conversion of tropical forest to oil palm plantations. This study demonstrated a great impact of land-use conversion on nitrification, which is linked to changes in soil pH due to common agricultural practices (intensive fertilization). In addition, the different communities of ammonia oxidizers were differently affected by short-term pH perturbations, with implications for future land-use conversions but also for increased knowledge of associated global nitrous oxide emissions and current climate change concerns.},
}
@article {pmid32535177,
year = {2020},
author = {Di Giulio, M},
title = {The phylogenetic distribution of the glutaminyl-tRNA synthetase and Glu-tRNAGln amidotransferase in the fundamental lineages would imply that the ancestor of archaea, that of eukaryotes and LUCA were progenotes.},
journal = {Bio Systems},
volume = {196},
number = {},
pages = {104174},
doi = {10.1016/j.biosystems.2020.104174},
pmid = {32535177},
issn = {1872-8324},
mesh = {Amino Acyl-tRNA Synthetases/*genetics/metabolism ; Archaea/enzymology/*genetics ; Eukaryota/enzymology/*genetics ; *Evolution, Molecular ; Nitrogenous Group Transferases/*genetics/metabolism ; *Phylogeny ; },
abstract = {The function of the glutaminyl-tRNA synthetase and Glu-tRNAGln amidotransferase might be related to the origin of the genetic code because, for example, glutaminyl-tRNA synthetase catalyses the fundamental reaction that makes the genetic code. If the evolutionary stage of the origin of these two enzymes could be unambiguously identified, then the genetic code should still have been originating at that particular evolutionary stage because the fundamental reaction that makes the code itself was still evidently evolving. This would result in that particular evolutionary moment being attributed to the evolutionary stage of the progenote because it would have a relationship between the genotype and the phenotype not yet fully realized because the genetic code was precisely still originating. I then analyzed the distribution of the glutaminyl-tRNA synthetase and Glu-tRNAGln aminodotrasferase in the main phyletic lineages. Since in some cases the origin of these two enzymes can be related to the evolutionary stages of ancestors of archaea and eukaryotes, this would indicate these ancestors as progenotes because at that evolutionary moment the genetic code was evidently still evolving, thus realizing the definition of progenote. The conclusion that the ancestor of archaea and that of eukaryotes were progenotes would imply that even the last universal common ancestor (LUCA) was a progenote because it appeared, on the tree of life, temporally before these ancestors.},
}
@article {pmid32534168,
year = {2020},
author = {Pinevich, AV},
title = {The ambiguity of the basic terms related to eukaryotes and the more consistent etymology based on eukaryotic signatures in Asgard archaea.},
journal = {Bio Systems},
volume = {197},
number = {},
pages = {104178},
doi = {10.1016/j.biosystems.2020.104178},
pmid = {32534168},
issn = {1872-8324},
mesh = {Actin Cytoskeleton/genetics ; Archaea/*classification/genetics ; Bacteria/genetics ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Endosomal Sorting Complexes Required for Transport/genetics ; *Eukaryota ; *Eukaryotic Cells ; Euryarchaeota/*classification/genetics ; GTP Phosphohydrolases/genetics ; Genome, Archaeal/*genetics ; Phylogeny ; Symbiosis/*genetics ; *Terminology as Topic ; },
abstract = {The endosymbiosis theory most widely accepted variant surmises the engulfment of a bacterial cell by an archaeal cell. For decades, this scenario was reputed to be an unconfirmed hypothesis, and only recently it has obtained an indirect proof in Asgard archaea environmental DNA encoding eukaryotic signatures - actin cytoskeleton, small GTPases, and ESCRT complex. In view of growing interest to this aspect of the endosymbiosis theory, it seemed timely to revisit the basic terms eukaryotic cell/eukaryotes/nucleated organisms. The article highlights the ambiguous applications of these terms, and seeks for their consistency with regard to phylogeny and taxonomy. Additionally, new name Caryosignifera is proposed for the phylum represented by: (1) the underexplored Asgard archaea manifested by above-mentioned environmental DNA; (2) cultured species of engulfing Asgard archaea; (3) eukaryotic host cells in nucleated organisms (protists, algae, plants, fungi, and animals).},
}
@article {pmid32527006,
year = {2020},
author = {Gryta, A and Frąc, M},
title = {Methodological Aspects of Multiplex Terminal Restriction Fragment Length Polymorphism-Technique to Describe the Genetic Diversity of Soil Bacteria, Archaea and Fungi.},
journal = {Sensors (Basel, Switzerland)},
volume = {20},
number = {11},
pages = {},
pmid = {32527006},
issn = {1424-8220},
support = {2018/02/X/NZ9/00515//National Science Center/ ; BIOSTRATEG3/347464/5/NCBR/2017//The National Centre for Research and Development/ ; },
mesh = {Archaea/*classification ; Bacteria/*classification ; Fungi/*classification ; Polymerase Chain Reaction ; *Polymorphism, Restriction Fragment Length ; *Soil Microbiology ; },
abstract = {The molecular fingerprinting methods used to evaluate soil microbial diversity could also be used as effective biosensors for the purposes of monitoring ecological soil status. The biodiversity of microorganisms is a relevant index of soil activity and there is a necessity to develop tools to generate reliable results for an emerging approach in the field of environmental control using microbial diversity biosensors. This work reports a method under development for determining soil microbial diversity using high efficiency Multiplex PCR-Terminal Restriction Fragment Length Polymorphism (M-T-RFLP) for the simultaneous detection of bacteria, archaea and fungi. Three different primer sets were used in the reaction and the analytical conditions were optimized. Optimal analytical conditions were achieved using 0.5 µM of primer for bacteria and 1 µM for archaea and fungi, 4 ng of soil DNA template, and HaeIII restriction enzyme. Comparative tests using the proposed analytical approach and a single analysis of each microorganism group were carried out to indicate that both genetic profiles were similar. The Jaccard similarity coefficient between single and multiplexing approach ranged from 0.773 to 0.850 for bacteria and fungi, and 0.208 to 0.905 for archaea. In conclusion, the multiplexing and pooling approaches significantly reduced the costs and time required to perform the analyses, while maintaining a proper effectiveness.},
}
@article {pmid32514073,
year = {2020},
author = {Murray, AE and Freudenstein, J and Gribaldo, S and Hatzenpichler, R and Hugenholtz, P and Kämpfer, P and Konstantinidis, KT and Lane, CE and Papke, RT and Parks, DH and Rossello-Mora, R and Stott, MB and Sutcliffe, IC and Thrash, JC and Venter, SN and Whitman, WB and Acinas, SG and Amann, RI and Anantharaman, K and Armengaud, J and Baker, BJ and Barco, RA and Bode, HB and Boyd, ES and Brady, CL and Carini, P and Chain, PSG and Colman, DR and DeAngelis, KM and de Los Rios, MA and Estrada-de Los Santos, P and Dunlap, CA and Eisen, JA and Emerson, D and Ettema, TJG and Eveillard, D and Girguis, PR and Hentschel, U and Hollibaugh, JT and Hug, LA and Inskeep, WP and Ivanova, EP and Klenk, HP and Li, WJ and Lloyd, KG and Löffler, FE and Makhalanyane, TP and Moser, DP and Nunoura, T and Palmer, M and Parro, V and Pedrós-Alió, C and Probst, AJ and Smits, THM and Steen, AD and Steenkamp, ET and Spang, A and Stewart, FJ and Tiedje, JM and Vandamme, P and Wagner, M and Wang, FP and Yarza, P and Hedlund, BP and Reysenbach, AL},
title = {Roadmap for naming uncultivated Archaea and Bacteria.},
journal = {Nature microbiology},
volume = {5},
number = {8},
pages = {987-994},
pmid = {32514073},
issn = {2058-5276},
mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; DNA, Bacterial ; Metagenome ; Phylogeny ; Prokaryotic Cells/classification ; Sequence Analysis, DNA ; Terminology as Topic ; },
abstract = {The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as 'type material', thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity.},
}
@article {pmid32507415,
year = {2020},
author = {Zhou, S and Xiang, H and Liu, JL},
title = {CTP synthase forms cytoophidia in archaea.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {47},
number = {4},
pages = {213-223},
doi = {10.1016/j.jgg.2020.03.004},
pmid = {32507415},
issn = {1673-8527},
mesh = {Archaea/enzymology/metabolism ; Carbon-Nitrogen Ligases/*genetics/metabolism ; Cytoskeleton/*enzymology/genetics/metabolism ; Gene Expression Regulation, Archaeal/drug effects ; Glutamine/metabolism/pharmacology ; Haloarcula/*enzymology/genetics ; },
abstract = {CTP synthase (CTPS) is an important metabolic enzyme that catalyzes the rate-limiting reaction of nucleotide CTP de novo synthesis. Since 2010, a series of studies have demonstrated that CTPS can form filamentous structures in bacteria and eukaryotes, which are termed cytoophidia. However, it is unknown whether cytoophidia exist in the third domain of life, archaea. Using Haloarcula hispanica as a model system, here we demonstrate that CTPS forms distinct intracellular compartments in archaea. Under stimulated emission depletion microscopy, we find that the structures of H. hispanica CTPS are elongated, similar to cytoophidia in bacteria and eukaryotes. When Haloarcula cells are cultured in low-salt medium, the occurrence of cytoophidia increases dramatically. In addition, treatment of H. hispanica with a glutamine analog or overexpression of CTPS can promote cytoophidium assembly. Our study reveals that CTPS can form cytoophidia in all three domains of life, suggesting that forming cytoophidia is an ancient property of CTPS.},
}
@article {pmid32503045,
year = {2020},
author = {},
title = {Corrigendum to: D-Galactose catabolism in archaea: Operation of the DeLey-Doudoroff pathway in Haloferax volcanii.},
journal = {FEMS microbiology letters},
volume = {367},
number = {11},
pages = {},
doi = {10.1093/femsle/fnaa069},
pmid = {32503045},
issn = {1574-6968},
}
@article {pmid32499624,
year = {2020},
author = {Tang, L},
title = {Taxonomy of Bacteria and Archaea.},
journal = {Nature methods},
volume = {17},
number = {6},
pages = {562},
doi = {10.1038/s41592-020-0863-3},
pmid = {32499624},
issn = {1548-7105},
mesh = {*Archaea ; *Bacteria ; Phylogeny ; },
}
@article {pmid32499102,
year = {2020},
author = {Peng, X and Mayo-Muñoz, D and Bhoobalan-Chitty, Y and Martínez-Álvarez, L},
title = {Anti-CRISPR Proteins in Archaea.},
journal = {Trends in microbiology},
volume = {28},
number = {11},
pages = {913-921},
doi = {10.1016/j.tim.2020.05.007},
pmid = {32499102},
issn = {1878-4380},
mesh = {Archaea/genetics/*immunology/virology ; Archaeal Proteins/genetics/*immunology ; Archaeal Viruses/genetics/*physiology ; *CRISPR-Cas Systems ; Rudiviridae/genetics/*physiology ; },
abstract = {Anti-CRISPR (Acr) proteins are natural inhibitors of CRISPR-Cas immune systems. To date, Acrs inhibiting types I, II, III, V, and VI CRISPR-Cas systems have been characterized. While most known Acrs are derived from bacterial phages and prophages, very few have been characterized in the domain Archaea, despite the nearly ubiquitous presence of CRISPR-Cas in archaeal cells. Here we summarize the discovery and characterization of the archaeal Acrs with the representatives encoded by a model archaeal virus, Sulfolobus islandicus rod-shaped virus 2 (SIRV2). AcrID1 inhibits subtype I-D CRISPR-Cas immunity through direct interaction with the large subunit Cas10d of the effector complex, and AcrIIIB1 inhibits subtype III-B CRISPR-Cas immunity through a mechanism interfering with middle/late gene targeting. Future development of efficient screening methods will be key to uncovering the diversity of archaeal Acrs.},
}
@article {pmid32449429,
year = {2020},
author = {Qi, L and Li, J and Jia, J and Yue, L and Dong, X},
title = {Comprehensive analysis of the pre-ribosomal RNA maturation pathway in a methanoarchaeon exposes the conserved circularization and linearization mode in archaea.},
journal = {RNA biology},
volume = {17},
number = {10},
pages = {1427-1441},
pmid = {32449429},
issn = {1555-8584},
mesh = {Archaea/*physiology ; Base Sequence ; Conserved Sequence ; Endodeoxyribonucleases/chemistry/metabolism ; *Gene Expression Regulation, Archaeal ; Models, Biological ; Nucleic Acid Conformation ; RNA Cleavage ; RNA Precursors/chemistry/*genetics ; *RNA Processing, Post-Transcriptional ; RNA Splicing ; RNA, Ribosomal/chemistry/*genetics ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; RNA, Ribosomal, 5S/genetics ; RNA, Transfer/genetics ; RNA-Binding Motifs ; },
abstract = {The ribosomal RNA (rRNA) genes are generally organized as an operon and cotranscribed into a polycistronic precursor; therefore, processing and maturation of pre-rRNAs are essential for ribosome biogenesis. However, rRNA maturation pathways of archaea, particularly of methanoarchaea, are scarcely known. Here, we thoroughly elucidated the maturation pathway of the rRNA operon (16S-tRNAAla-23S-tRNACys-5S) in Methanolobus psychrophilus, one representative of methanoarchaea. Enzymatic assay demonstrated that EndA, a tRNA splicing endoribonuclease, cleaved bulge-helix-bulge (BHB) motifs buried in the processing stems of pre-16S and pre-23S rRNAs. Northern blot and quantitative PCR detected splicing-coupled circularization of pre-16S and pre-23S rRNAs, which accounted for 2% and 12% of the corresponding rRNAs, respectively. Importantly, endoribonuclease Nob1 was determined to linearize circular pre-16S rRNA at the mature 3' end so to expose the anti-Shine-Dalgarno sequence, while circular pre-23S rRNA was linearized at the mature 5' end by an unknown endoribonuclease. The resultant 5' and 3' extension in linearized pre-16S and pre-23S rRNAs were finally matured through 5'-3' and 3'-5' exoribonucleolytic trimming, respectively. Additionally, a novel processing pathway of endoribonucleolysis coupled with exoribonucleolysis was identified for the pre-5S rRNA maturation in this methanogen, which could be also conserved in most methanogenic euryarchaea. Based on evaluating the phylogenetic conservation of the key elements that are involved in circularization and linearization of pre-rRNA maturation, we predict that the rRNA maturation mode revealed here could be prevalent among archaea.},
}
@article {pmid32448158,
year = {2020},
author = {Eckert, I and Weinberg, Z},
title = {Discovery of 20 novel ribosomal leader candidates in bacteria and archaea.},
journal = {BMC microbiology},
volume = {20},
number = {1},
pages = {130},
pmid = {32448158},
issn = {1471-2180},
support = {WE6322/1-1//Deutsche Forschungsgemeinschaft/International ; },
mesh = {*5' Untranslated Regions ; Archaea/*genetics/metabolism ; Bacillus subtilis/genetics ; Bacteria/*genetics/metabolism ; Escherichia coli/genetics ; Gene Expression Regulation, Archaeal ; Gene Expression Regulation, Bacterial ; Models, Molecular ; Nucleic Acid Conformation ; Protein Biosynthesis ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal/*chemistry/genetics ; Ribosomal Proteins/metabolism ; },
abstract = {BACKGROUND: RNAs perform many functions in addition to supplying coding templates, such as binding proteins. RNA-protein interactions are important in multiple processes in all domains of life, and the discovery of additional protein-binding RNAs expands the scope for studying such interactions. To find such RNAs, we exploited a form of ribosomal regulation. Ribosome biosynthesis must be tightly regulated to ensure that concentrations of rRNAs and ribosomal proteins (r-proteins) match. One regulatory mechanism is a ribosomal leader (r-leader), which is a domain in the 5' UTR of an mRNA whose genes encode r-proteins. When the concentration of one of these r-proteins is high, the protein binds the r-leader in its own mRNA, reducing gene expression and thus protein concentrations. To date, 35 types of r-leaders have been validated or predicted.<br><br>RESULTS: By analyzing additional conserved RNA structures on a multi-genome scale, we identified 20 novel r-leader structures. Surprisingly, these included new r-leaders in the highly studied organisms Escherichia coli and Bacillus subtilis. Our results reveal several cases where multiple unrelated RNA structures likely bind the same r-protein ligand, and uncover previously unknown r-protein ligands. Each r-leader consistently occurs upstream of r-protein genes, suggesting a regulatory function. That the predicted r-leaders function as RNAs is supported by evolutionary correlations in the nucleotide sequences that are characteristic of a conserved RNA secondary structure. The r-leader predictions are also consistent with the locations of experimentally determined transcription start sites.<br><br>CONCLUSIONS: This work increases the number of known or predicted r-leader structures by more than 50%, providing additional opportunities to study structural and evolutionary aspects of RNA-protein interactions. These results provide a starting point for detailed experimental studies.},
}
@article {pmid32442771,
year = {2020},
author = {Shi, LD and Lv, PL and Wang, M and Lai, CY and Zhao, HP},
title = {A mixed consortium of methanotrophic archaea and bacteria boosts methane-dependent selenate reduction.},
journal = {The Science of the total environment},
volume = {732},
number = {},
pages = {139310},
doi = {10.1016/j.scitotenv.2020.139310},
pmid = {32442771},
issn = {1879-1026},
mesh = {Anaerobiosis ; *Archaea ; Bacteria ; Biofilms ; Bioreactors ; In Situ Hybridization, Fluorescence ; Methane ; Oxidation-Reduction ; RNA, Ribosomal, 16S ; Selenic Acid ; },
abstract = {Though methane-based selenate reduction has been reported, neither the selenate load nor the removal rate could satisfy practical applications, thus limiting this technique to bio-remediate selenate pollution. In the present study, using a membrane biofilm batch reactor (MBBR), we successfully enriched a consortium performing methane-dependent selenate reduction, with enhanced reduction rates from 16.1 to 28.9 μM-day-1 under a comparable Se concentration to industrial wastewaters (i.e., ~500 μM). During active reduction, 16S rRNA gene copies of Archaea and Bacteria were both increased more than one order of magnitude. Clone library construction and high-throughput sequencing indicated that Methanosarcina and Methylocystis were the only methane-oxidizing microorganisms. The presence of 20 mM bromoethanesulphonate or 0.15 mM acetylene both significantly, but not completely, inhibited methane-dependent selenate reduction, indicating the concurrent contributions of methanotrophic archaea and bacteria. Fluorescence in situ hybridization (FISH) revealed that archaea directly adhered to the surface of the membrane while bacteria were in the outer layer, together forming the mature biofilm. This study highlights the crucial role of both methanotrophic archaea and bacteria in methane-dependent selenate reduction, and lays foundations in applying methane to bio-remediate practical selenate pollution.},
}
@article {pmid32440868,
year = {2020},
author = {Yang, D and Xiao, X and He, N and Zhu, W and Liu, M and Xie, G},
title = {Effects of reducing chemical fertilizer combined with organic amendments on ammonia-oxidizing bacteria and archaea communities in a low-fertility red paddy field.},
journal = {Environmental science and pollution research international},
volume = {27},
number = {23},
pages = {29422-29432},
doi = {10.1007/s11356-020-09120-5},
pmid = {32440868},
issn = {1614-7499},
support = {2016YFD0201200//the National Key Research and Development Program of China/ ; },
mesh = {Ammonia ; Animals ; *Archaea ; Bacteria ; Ecosystem ; Fertility ; *Fertilizers ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Soil ; Soil Microbiology ; Swine ; },
abstract = {Ammonia oxidation process in soil has a great contribution to the emission of nitrous oxide, which is a hot issue in the study of N cycle of rice field ecosystem. Organic amendments which partially substitute chemical nitrogen fertilizer are widely adopted to optimizing N management and reduce the use of chemical nitrogen fertilizers in the paddy ecosystem, but their long-term effects on ammonia-oxidizing archaea (AOA) and bacteria (AOB) were not well understood. Thus, based on a 6-year field trial that comprised four fertilization strategies (CF, chemical fertilizer; PM, pig manure substituting for 20% chemical N; BF, biogas slurry substituting for 20% chemical N; and GM, milk vetch substituting for 20% chemical N) and no N fertilizer application as CK, the abundance and community structure of ammonia oxidizers were examined by using qPCR and Illumina Miseq sequencing approaches based on the functional marker genes (amoA) in a low-fertility paddy field. The results revealed that 6 years of organic-substitute fertilization significantly increased AOA abundance in comparison with NF and CF. However, only CF and PM had a higher AOB abundance than those in NF and no significant difference between CF and organic-substitute treatments was observed. Both AOA and AOB were significantly correlated with soil potential nitrification rate (PNR). Moreover, organic-substitute treatments showed the evident changes in the AOA community, while little were observed in the AOB community. Soil pH was the main predictor for AOA abundance, while NH4+-N and NO3--N were the main predictors for AOB abundance. This study suggests that both AOA and AOB were jointly contributed to the variation of soil potential nitrification rate, while the AOA community was shown to be more responsive to organic-substitute fertilization strategies than AOB in the tested soils.},
}
@article {pmid32430468,
year = {2020},
author = {Lu, Z and Fu, T and Li, T and Liu, Y and Zhang, S and Li, J and Dai, J and Koonin, EV and Li, G and Chu, H and Li, M},
title = {Coevolution of Eukaryote-like Vps4 and ESCRT-III Subunits in the Asgard Archaea.},
journal = {mBio},
volume = {11},
number = {3},
pages = {},
pmid = {32430468},
issn = {2150-7511},
mesh = {Adenosine Triphosphatases/genetics ; Archaea/*classification ; Archaeal Proteins/*genetics/metabolism ; Biological Transport ; Endosomal Sorting Complexes Required for Transport/*genetics/metabolism ; *Evolution, Molecular ; Models, Molecular ; Molecular Docking Simulation ; *Phylogeny ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins/genetics ; },
abstract = {The emergence of the endomembrane system is a key step in the evolution of cellular complexity during eukaryogenesis. The endosomal sorting complex required for transport (ESCRT) machinery is essential and required for the endomembrane system functions in eukaryotic cells. Recently, genes encoding eukaryote-like ESCRT protein components have been identified in the genomes of Asgard archaea, a newly proposed archaeal superphylum that is thought to include the closest extant prokaryotic relatives of eukaryotes. However, structural and functional features of Asgard ESCRT remain uncharacterized. Here, we show that Vps4, Vps2/24/46, and Vps20/32/60, the core functional components of the Asgard ESCRT, coevolved eukaryote-like structural and functional features. Phylogenetic analysis shows that Asgard Vps4, Vps2/24/46, and Vps20/32/60 are closely related to their eukaryotic counterparts. Molecular dynamics simulation and biochemical assays indicate that Asgard Vps4 contains a eukaryote-like microtubule-interacting and transport (MIT) domain that binds the distinct type 1 MIT-interacting motif and type 2 MIT-interacting motif in Vps2/24/46 and Vps20/32/60, respectively. The Asgard Vps4 partly, but much more efficiently than homologs from other archaea, complements the vps4 null mutant of Saccharomyces cerevisiae, further supporting the functional similarity between the membrane remodeling machineries of Asgard archaea and eukaryotes. Thus, this work provides evidence that the ESCRT complexes from Asgard archaea and eukaryotes are evolutionarily related and functionally similar. Thus, despite the apparent absence of endomembranes in Asgard archaea, the eukaryotic ESCRT seems to have been directly inherited from an Asgard ancestor, to become a key component of the emerging endomembrane system.IMPORTANCE The discovery of Asgard archaea has changed the existing ideas on the origins of eukaryotes. Researchers propose that eukaryotic cells evolved from Asgard archaea. This hypothesis partly stems from the presence of multiple eukaryotic signature proteins in Asgard archaea, including homologs of ESCRT proteins that are essential components of the endomembrane system in eukaryotes. However, structural and functional features of Asgard ESCRT remain unknown. Our study provides evidence that Asgard ESCRT is functionally comparable to the eukaryotic counterparts, suggesting that despite the apparent absence of endomembranes in archaea, eukaryotic ESCRT was inherited from an Asgard archaeal ancestor, alongside the emergence of endomembrane system during eukaryogenesis.},
}
@article {pmid32427979,
year = {2020},
author = {Baker, BJ and De Anda, V and Seitz, KW and Dombrowski, N and Santoro, AE and Lloyd, KG},
title = {Author Correction: Diversity, ecology and evolution of Archaea.},
journal = {Nature microbiology},
volume = {5},
number = {7},
pages = {976},
doi = {10.1038/s41564-020-0741-x},
pmid = {32427979},
issn = {2058-5276},
abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.},
}
@article {pmid32426487,
year = {2020},
author = {Meador, TB and Schoffelen, N and Ferdelman, TG and Rebello, O and Khachikyan, A and Könneke, M},
title = {Carbon recycling efficiency and phosphate turnover by marine nitrifying archaea.},
journal = {Science advances},
volume = {6},
number = {19},
pages = {eaba1799},
pmid = {32426487},
issn = {2375-2548},
abstract = {Thaumarchaeotal nitrifiers are among the most abundant organisms in the ocean, but still unknown is the carbon (C) yield from nitrification and the coupling of these fluxes to phosphorus (P) turnover and release of metabolites from the cell. Using a dual radiotracer approach, we found that Nitrosopumilus maritimus fixed roughly 0.3 mol C, assimilated 2 mmol P, and released ca. 10-2 mol C and 10-5 mol P as dissolved organics (DOC and DOP) per mole ammonia respired. Phosphate turnover may influence assimilation fluxes by nitrifiers in the euphotic zone, which parallel those of the dark ocean. Collectively, marine nitrifiers assimilate up to 2 Pg C year-1 and 0.05 Pg P year-1 and thereby recycle roughly 5% of mineralized C and P into marine biomass. Release of roughly 50 Tg DOC and 0.2 Tg DOP by thaumarchaea each year represents a small but fresh input of reduced substrates throughout the ocean.},
}
@article {pmid32423947,
year = {2020},
author = {Takemata, N and Bell, SD},
title = {Emerging views of genome organization in Archaea.},
journal = {Journal of cell science},
volume = {133},
number = {10},
pages = {},
pmid = {32423947},
issn = {1477-9137},
support = {R01 GM125579/GM/NIGMS NIH HHS/United States ; R01 GM135178/GM/NIGMS NIH HHS/United States ; },
mesh = {*Archaea/genetics ; *Chromatin ; Chromosomes ; Eukaryota ; Genome/genetics ; },
abstract = {Over the past decade, advances in methodologies for the determination of chromosome conformation have provided remarkable insight into the local and higher-order organization of bacterial and eukaryotic chromosomes. Locally folded domains are found in both bacterial and eukaryotic genomes, although they vary in size. Importantly, genomes of metazoans also possess higher-order organization into A- and B-type compartments, regions of transcriptionally active and inactive chromatin, respectively. Until recently, nothing was known about the organization of genomes of organisms in the third domain of life - the archaea. However, despite archaea possessing simple circular genomes that are morphologically reminiscent of those seen in many bacteria, a recent study of archaea of the genus Sulfolobus has revealed that it organizes its genome into large-scale domains. These domains further interact to form defined A- and B-type compartments. The interplay of transcription and localization of a novel structural maintenance of chromosomes (SMC) superfamily protein, termed coalescin, defines compartment identity. In this Review, we discuss the mechanistic and evolutionary implications of these findings.},
}
@article {pmid32422160,
year = {2020},
author = {Lekontseva, N and Mikhailina, A and Fando, M and Kravchenko, O and Balobanov, V and Tishchenko, S and Nikulin, A},
title = {Crystal structures and RNA-binding properties of Lsm proteins from archaea Sulfolobus acidocaldarius and Methanococcus vannielii: Similarity and difference of the U-binding mode.},
journal = {Biochimie},
volume = {175},
number = {},
pages = {1-12},
doi = {10.1016/j.biochi.2020.05.001},
pmid = {32422160},
issn = {1638-6183},
mesh = {Archaeal Proteins/*chemistry ; Binding Sites ; Crystallography, X-Ray ; Methanococcus/*chemistry ; Poly U/*chemistry ; RNA-Binding Proteins/*chemistry ; Sulfolobus acidocaldarius/*chemistry ; },
abstract = {Sm and Sm-like (Lsm) proteins are considered as an evolutionary conserved family involved in RNA metabolism in organisms from bacteria and archaea to human. Currently, the function of Sm-like archaeal proteins (SmAP) is not well understood. Here, we report the crystal structures of SmAP proteins from Sulfolobus acidocaldarius and Methanococcus vannielii and a comparative analysis of their RNA-binding sites. Our data show that these SmAPs have only a uridine-specific RNA-binding site, unlike their bacterial homolog Hfq, which has three different RNA-binding sites. Moreover, variations in the amino acid composition of the U-binding sites of the two SmAPs lead to a difference in protein affinity for oligo(U) RNA. Surface plasmon resonance data and nucleotide-binding analysis confirm the high affinity of SmAPs for uridine nucleotides and oligo(U) RNA and the reduced affinity for adenines, guanines, cytidines and corresponding oligo-RNAs. In addition, we demonstrate that MvaSmAP1 and SacSmAP2 are capable of melting an RNA hairpin and, apparently, promote its interaction with complementary RNA.},
}
@article {pmid32382758,
year = {2020},
author = {Gelsinger, DR and Dallon, E and Reddy, R and Mohammad, F and Buskirk, AR and DiRuggiero, J},
title = {Ribosome profiling in archaea reveals leaderless translation, novel translational initiation sites, and ribosome pausing at single codon resolution.},
journal = {Nucleic acids research},
volume = {48},
number = {10},
pages = {5201-5216},
pmid = {32382758},
issn = {1362-4962},
support = {R01 GM110113/GM/NIGMS NIH HHS/United States ; T32 GM007445/GM/NIGMS NIH HHS/United States ; },
mesh = {5' Untranslated Regions/genetics ; Codon/genetics/*metabolism ; Haloferax volcanii/drug effects/*genetics/*metabolism ; Harringtonines/pharmacology ; Peptide Chain Elongation, Translational/drug effects/genetics ; Peptide Chain Initiation, Translational/drug effects/genetics ; *Protein Biosynthesis/drug effects ; Protein Footprinting ; Reading Frames/genetics ; Ribosomes/drug effects/*metabolism ; Transcriptome/drug effects ; },
abstract = {High-throughput methods, such as ribosome profiling, have revealed the complexity of translation regulation in Bacteria and Eukarya with large-scale effects on cellular functions. In contrast, the translational landscape in Archaea remains mostly unexplored. Here, we developed ribosome profiling in a model archaeon, Haloferax volcanii, elucidating, for the first time, the translational landscape of a representative of the third domain of life. We determined the ribosome footprint of H. volcanii to be comparable in size to that of the Eukarya. We linked footprint lengths to initiating and elongating states of the ribosome on leadered transcripts, operons, and on leaderless transcripts, the latter representing 70% of H. volcanii transcriptome. We manipulated ribosome activity with translation inhibitors to reveal ribosome pausing at specific codons. Lastly, we found that the drug harringtonine arrested ribosomes at initiation sites in this archaeon. This drug treatment allowed us to confirm known translation initiation sites and also reveal putative novel initiation sites in intergenic regions and within genes. Ribosome profiling revealed an uncharacterized complexity of translation in this archaeon with bacteria-like, eukarya-like, and potentially novel translation mechanisms. These mechanisms are likely to be functionally essential and to contribute to an expanded proteome with regulatory roles in gene expression.},
}
@article {pmid32380716,
year = {2020},
author = {Rawat, M and Maupin-Furlow, JA},
title = {Redox and Thiols in Archaea.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {9},
number = {5},
pages = {},
pmid = {32380716},
issn = {2076-3921},
support = {R01 GM057498/GM/NIGMS NIH HHS/United States ; DE-FG02-05ER15650//U.S. Department of Energy/ ; MCB-1642283//National Science Foundation/ ; R01 GM57498/NH/NIH HHS/United States ; SC3GM-100855-03/NH/NIH HHS/United States ; MCB1244611//National Science Foundation/ ; },
abstract = {Low molecular weight (LMW) thiols have many functions in bacteria and eukarya, ranging from redox homeostasis to acting as cofactors in numerous reactions, including detoxification of xenobiotic compounds. The LMW thiol, glutathione (GSH), is found in eukaryotes and many species of bacteria. Analogues of GSH include the structurally different LMW thiols: bacillithiol, mycothiol, ergothioneine, and coenzyme A. Many advances have been made in understanding the diverse and multiple functions of GSH and GSH analogues in bacteria but much less is known about distribution and functions of GSH and its analogues in archaea, which constitute the third domain of life, occupying many niches, including those in extreme environments. Archaea are able to use many energy sources and have many unique metabolic reactions and as a result are major contributors to geochemical cycles. As LMW thiols are major players in cells, this review explores the distribution of thiols and their biochemistry in archaea.},
}
@article {pmid32375092,
year = {2020},
author = {Li, Y and Fan, C and Wang, L and Wang, L and Zhang, W and Zhang, H and Niu, L},
title = {Interaction type of tetrabromobisphenol A and copper manipulates ammonia-oxidizing archaea and bacteria communities in co-contaminated river sediments.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {264},
number = {},
pages = {114671},
doi = {10.1016/j.envpol.2020.114671},
pmid = {32375092},
issn = {1873-6424},
mesh = {*Ammonia ; *Archaea ; Bacteria ; Copper ; Oxidation-Reduction ; Phylogeny ; Polybrominated Biphenyls ; Rivers ; Soil Microbiology ; },
abstract = {The combined contamination of brominated flame retardants (BFRs) and heavy metals in electronic waste (e-waste) recycling and disposal areas has been a serious concern owing to their environmental persistence and chronic toxicities. Ammonia oxidizers, e.g., ammonia-oxidizing archaea (AOA) and bacteria (AOB) play essential roles in nitrogen cycling and can serve as ideal indicators that reflect the changes in sediment health in response to environmental variables. There is currently very little information available on the combined toxic effects of BFRs and heavy metals on AOA and AOB communities. In this study, two typical e-waste pollutants, tetrabromobisphenol A (TBBPA) and copper (Cu), were selected as target contaminants to investigate the individual and combined effects of both pollutants on AOA and AOB communities in river sediments. Respective treatments of TBBPA (1, 10, and 20 mg/kg wet weight), Cu (100 mg/kg wet weight) and their combined treatments (weight ratios of 1:100, 1:10, and 1:5) were performed in laboratory experiments. High-throughput sequencing was applied to explore the response of ammonia oxidizers to TBBPA and Cu. The interaction types of TBBPA and Cu were calculated by the directional classification system to reveal the individual and combined toxicities of both contaminants to the ammonia oxidizers. On days 15 and 30, the dominant interaction type of TBBPA and Cu was synergistic (62.50%), and the combined contamination exacted selective pressure and inhibition on the AOB and AOA communities. On days 45 and 90, the interaction type shifted to be antagonistic (83.33%), with both the AOB and AOA communities gradually reaching stable population equilibria. The alteration of the interaction type is attributed to the elevated TBBPA/Cu tolerance as the incubation time increased. This study disclosed the interaction types of TBBPA and Cu in contaminated river sediments, and revealed that the combined effect could potentially manipulate AOB and AOA communities.},
}
@article {pmid32372550,
year = {2020},
author = {Juottonen, H and Fontaine, L and Wurzbacher, C and Drakare, S and Peura, S and Eiler, A},
title = {Archaea in boreal Swedish lakes are diverse, dominated by Woesearchaeota and follow deterministic community assembly.},
journal = {Environmental microbiology},
volume = {22},
number = {8},
pages = {3158-3171},
doi = {10.1111/1462-2920.15058},
pmid = {32372550},
issn = {1462-2920},
support = {2012-4592//Swedish University of Agricultural Sciences/International ; //Swedish Research Council VR/International ; //University of Oslo/International ; 265902//Academy of Finland/International ; CTS:13-113//Carl Tryggers Foundation/International ; },
mesh = {Archaea/classification/genetics/*isolation &amp; purification ; Biodiversity ; Geologic Sediments/microbiology ; Lakes/*microbiology ; Molecular Typing ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S ; Sequence Analysis, RNA ; Sweden ; *Water Microbiology ; },
abstract = {Despite their key role in biogeochemical processes, particularly the methane cycle, archaea are widely underrepresented in molecular surveys because of their lower abundance compared with bacteria and eukaryotes. Here, we use parallel high-resolution small subunit rRNA gene sequencing to explore archaeal diversity in 109 Swedish lakes and correlate archaeal community assembly mechanisms to large-scale latitudinal, climatic (nemoral to arctic) and nutrient (oligotrophic to eutrophic) gradients. Sequencing with universal primers showed the contribution of archaea was on average 0.8% but increased up to 1.5% of the three domains in forest lakes. Archaea-specific sequencing revealed that freshwater archaeal diversity could be partly explained by lake variables associated with nutrient status. Combined with deterministic co-occurrence patterns this finding suggests that ecological drift is overridden by environmental sorting, as well as other deterministic processes such as biogeographic and evolutionary history, leading to lake-specific archaeal biodiversity. Acetoclastic, hydrogenotrophic and methylotrophic methanogens as well as ammonia-oxidizing archaea were frequently detected across the lakes. Archaea-specific sequencing also revealed representatives of Woesearchaeota and other phyla of the DPANN superphylum. This study adds to our understanding of the ecological range of key archaea in freshwaters and links these taxa to hypotheses about processes governing biogeochemical cycles in lakes.},
}
@article {pmid32371309,
year = {2020},
author = {Xie, F and Ma, A and Zhou, H and Liang, Y and Yin, J and Ma, K and Zhuang, X and Zhuang, G},
title = {Niche differentiation of denitrifying anaerobic methane oxidizing bacteria and archaea leads to effective methane filtration in a Tibetan alpine wetland.},
journal = {Environment international},
volume = {140},
number = {},
pages = {105764},
doi = {10.1016/j.envint.2020.105764},
pmid = {32371309},
issn = {1873-6750},
mesh = {Anaerobiosis ; *Archaea/genetics ; Methane ; *Methylococcaceae ; Oxidation-Reduction ; Tibet ; Wetlands ; },
abstract = {Denitrifying anaerobic methane oxidation (DAMO) is a vital methane sink in wetlands. However, the interactions and niche partitioning of DAMO bacteria and archaea in freshwater wetland soils, in addition to the interactions among microorganisms that couple methane and nitrogen cycling is still unclear, despite that these factors may govern the fate of methane and nitrogen in wetlands. Here, we evaluated the vertical distribution of DAMO bacteria and archaea in soil layers along with the potential interactions among populations in the methane-coupled nitrogen cycling microbial community of Tibetan freshwater wetlands. A combination of molecular biology, stable isotope tracer technology, and microbial bioinformatics was used to evaluate these interrelated dynamics. The abundances and potential methane oxidation rates indicated that DAMO bacteria and archaea differentially occupy surface and subsurface soil layers, respectively. The inferred interactions between DAMO bacteria and nitrogen cycling microorganisms within their communities are complex, DAMO bacteria apparently achieve an advantage in the highly competitive environment of surface soils layers and occupy a specific niche in those environments. Conversely, the apparent relationships between DAMO archaea and nitrogen cycling microorganisms are relatively simple, wherein high levels of cooperation are inferred between DAMO archaea and nitrate-producing organisms in subsurface soils layers. These results suggest that the vertical distribution patterns of DAMO bacteria and archaea enable them to play significant roles in the methane oxidation activity of different soil layers and collectively form an effective methane filtration consortium.},
}
@article {pmid32367670,
year = {2021},
author = {Wang, Y and Wegener, G and Ruff, SE and Wang, F},
title = {Methyl/alkyl-coenzyme M reductase-based anaerobic alkane oxidation in archaea.},
journal = {Environmental microbiology},
volume = {23},
number = {2},
pages = {530-541},
doi = {10.1111/1462-2920.15057},
pmid = {32367670},
issn = {1462-2920},
support = {DY135-B2-12//COMRA Project/ ; 41525011,//National Natural Science Foundation of China/ ; 41902313,//National Natural Science Foundation of China/ ; 91751205//National Natural Science Foundation of China/ ; GKZD010075//State Key Laboratory of Ocean Engineering Foundation/ ; 2016YFA0601102,//State Key R&amp;D Project of China/ ; 2018YFC0310800//State Key R&amp;D Project of China/ ; //DFG Cluster of Excellence 2077/ ; },
mesh = {Alkanes/*metabolism ; Anaerobiosis ; Archaea/chemistry/classification/*enzymology/genetics ; Archaeal Proteins/chemistry/genetics/*metabolism ; Oxidation-Reduction ; Oxidoreductases/chemistry/genetics/*metabolism ; Phylogeny ; },
abstract = {Methyl-coenzyme M reductase (MCR) has been originally identified to catalyse the final step of the methanogenesis pathway. About 20 years ago anaerobic methane-oxidizing archaea (ANME) were discovered that use MCR enzymes to activate methane. ANME thrive at the thermodynamic limit of life, are slow-growing, and in most cases form syntrophic consortia with sulfate-reducing bacteria. Recently, archaea that have the ability to anaerobically oxidize non-methane multi-carbon alkanes such as ethane and n-butane were described in both enrichment cultures and environmental samples. These anaerobic multi-carbon alkane-oxidizing archaea (ANKA) use enzymes homologous to MCR named alkyl-coenzyme M reductase (ACR). Here we review the recent progresses on the diversity, distribution and functioning of both ANME and ANKA by presenting a detailed MCR/ACR-based phylogeny, compare their metabolic pathways and discuss the gaps in our knowledge of physiology of these organisms. To improve our understanding of alkane oxidation in archaea, we identified three directions for future research: (i) expanding cultivation attempts to validate omics-based metabolic models of yet-uncultured organisms, (ii) performing biochemical and structural analyses of key enzymes to understand thermodynamic and steric constraints and (iii) investigating the evolution of anaerobic alkane metabolisms and their impact on biogeochemical cycles.},
}
@article {pmid32367054,
year = {2020},
author = {Baker, BJ and De Anda, V and Seitz, KW and Dombrowski, N and Santoro, AE and Lloyd, KG},
title = {Diversity, ecology and evolution of Archaea.},
journal = {Nature microbiology},
volume = {5},
number = {7},
pages = {887-900},
pmid = {32367054},
issn = {2058-5276},
mesh = {*Archaea/classification/genetics/growth &amp; development/metabolism ; *Biodiversity ; *Biological Evolution ; *Ecology ; Energy Metabolism ; Environmental Microbiology ; Genetic Variation ; Genome, Archaeal ; Phylogeny ; },
abstract = {Compared to bacteria, our knowledge of archaeal biology is limited. Historically, microbiologists have mostly relied on culturing and single-gene diversity surveys to understand Archaea in nature. However, only six of the 27 currently proposed archaeal phyla have cultured representatives. Advances in genomic sequencing and computational approaches are revolutionizing our understanding of Archaea. The recovery of genomes belonging to uncultured groups from the environment has resulted in the description of several new phyla, many of which are globally distributed and are among the predominant organisms on the planet. In this Review, we discuss how these genomes, together with long-term enrichment studies and elegant in situ measurements, are providing insights into the metabolic capabilities of the Archaea. We also debate how such studies reveal how important Archaea are in mediating an array of ecological processes, including global carbon and nutrient cycles, and how this increase in archaeal diversity has expanded our view of the tree of life and early archaeal evolution, and has provided new insights into the origin of eukaryotes.},
}
@article {pmid32345641,
year = {2020},
author = {DeWerff, SJ and Bautista, MA and Pauly, M and Zhang, C and Whitaker, RJ},
title = {Killer Archaea: Virus-Mediated Antagonism to CRISPR-Immune Populations Results in Emergent Virus-Host Mutualism.},
journal = {mBio},
volume = {11},
number = {2},
pages = {},
pmid = {32345641},
issn = {2150-7511},
mesh = {Archaea/*virology ; *Bacteriophages ; Biological Evolution ; CRISPR-Cas Systems/*immunology ; Evolution, Molecular ; Genome, Viral ; *Host Microbial Interactions ; *Sulfolobus/genetics/virology ; Symbiosis ; },
abstract = {Theory, simulation, and experimental evolution demonstrate that diversified CRISPR-Cas immunity to lytic viruses can lead to stochastic virus extinction due to a limited number of susceptible hosts available to each potential new protospacer escape mutation. Under such conditions, theory predicts that to evade extinction, viruses evolve toward decreased virulence and promote vertical transmission and persistence in infected hosts. To better understand the evolution of host-virus interactions in microbial populations with active CRISPR-Cas immunity, we studied the interaction between CRISPR-immune Sulfolobus islandicus cells and immune-deficient strains that are infected by the chronic virus SSV9. We demonstrate that Sulfolobus islandicus cells infected with SSV9, and with other related SSVs, kill uninfected, immune strains through an antagonistic mechanism that is a protein and is independent of infectious virus. Cells that are infected with SSV9 are protected from killing and persist in the population. We hypothesize that this infection acts as a form of mutualism between the host and the virus by removing competitors in the population and ensuring continued vertical transmission of the virus within populations with diversified CRISPR-Cas immunity.IMPORTANCE Multiple studies, especially those focusing on the role of lytic viruses in key model systems, have shown the importance of viruses in shaping microbial populations. However, it has become increasingly clear that viruses with a long host-virus interaction, such as those with a chronic lifestyle, can be important drivers of evolution and have large impacts on host ecology. In this work, we describe one such interaction with the acidic crenarchaeon Sulfolobus islandicus and its chronic virus Sulfolobus spindle-shaped virus 9. Our work expands the view in which this symbiosis between host and virus evolved, describing a killing phenotype which we hypothesize has evolved in part due to the high prevalence and diversity of CRISPR-Cas immunity seen in natural populations. We explore the implications of this phenotype in population dynamics and host ecology, as well as the implications of mutualism between this virus-host pair.},
}
@article {pmid32341564,
year = {2020},
author = {Parks, DH and Chuvochina, M and Chaumeil, PA and Rinke, C and Mussig, AJ and Hugenholtz, P},
title = {A complete domain-to-species taxonomy for Bacteria and Archaea.},
journal = {Nature biotechnology},
volume = {38},
number = {9},
pages = {1079-1086},
pmid = {32341564},
issn = {1546-1696},
mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Databases, Genetic ; Genome, Archaeal/genetics ; Genome, Bacterial/genetics ; Nucleic Acid Hybridization ; *Phylogeny ; Reproducibility of Results ; },
abstract = {The Genome Taxonomy Database is a phylogenetically consistent, genome-based taxonomy that provides rank-normalized classifications for ~150,000 bacterial and archaeal genomes from domain to genus. However, almost 40% of the genomes in the Genome Taxonomy Database lack a species name. We address this limitation by using commonly accepted average nucleotide identity criteria to set bounds on species and propose species clusters that encompass all publicly available bacterial and archaeal genomes. Unlike previous average nucleotide identity studies, we chose a single representative genome to serve as the effective nomenclatural 'type' defining each species. Of the 24,706 proposed species clusters, 8,792 are based on published names. We assigned placeholder names to the remaining 15,914 species clusters to provide names to the growing number of genomes from uncultivated species. This resource provides a complete domain-to-species taxonomic framework for bacterial and archaeal genomes, which will facilitate research on uncultivated species and improve communication of scientific results.},
}
@article {pmid32317322,
year = {2020},
author = {Hahn, CJ and Laso-Pérez, R and Vulcano, F and Vaziourakis, KM and Stokke, R and Steen, IH and Teske, A and Boetius, A and Liebeke, M and Amann, R and Knittel, K and Wegener, G},
title = {"Candidatus Ethanoperedens," a Thermophilic Genus of Archaea Mediating the Anaerobic Oxidation of Ethane.},
journal = {mBio},
volume = {11},
number = {2},
pages = {},
pmid = {32317322},
issn = {2150-7511},
mesh = {*Anaerobiosis ; Archaea/classification/genetics/*metabolism ; Bacteria/classification/genetics/metabolism ; Biomarkers ; Energy Metabolism ; Ethane/*metabolism ; Genome, Archaeal ; Genomics/methods ; Geologic Sediments/microbiology ; Hydrothermal Vents/microbiology ; Metabolic Networks and Pathways ; Molecular Typing ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Cold seeps and hydrothermal vents deliver large amounts of methane and other gaseous alkanes into marine surface sediments. Consortia of archaea and partner bacteria thrive on the oxidation of these alkanes and its coupling to sulfate reduction. The inherently slow growth of the involved organisms and the lack of pure cultures have impeded the understanding of the molecular mechanisms of archaeal alkane degradation. Here, using hydrothermal sediments of the Guaymas Basin (Gulf of California) and ethane as the substrate, we cultured microbial consortia of a novel anaerobic ethane oxidizer, "Candidatus Ethanoperedens thermophilum" (GoM-Arc1 clade), and its partner bacterium "Candidatus Desulfofervidus auxilii," previously known from methane-oxidizing consortia. The sulfate reduction activity of the culture doubled within one week, indicating a much faster growth than in any other alkane-oxidizing archaea described before. The dominance of a single archaeal phylotype in this culture allowed retrieval of a closed genome of "Ca. Ethanoperedens," a sister genus of the recently reported ethane oxidizer "Candidatus Argoarchaeum." The metagenome-assembled genome of "Ca. Ethanoperedens" encoded a complete methanogenesis pathway including a methyl-coenzyme M reductase (MCR) that is highly divergent from those of methanogens and methanotrophs. Combined substrate and metabolite analysis showed ethane as the sole growth substrate and production of ethyl-coenzyme M as the activation product. Stable isotope probing demonstrated that the enzymatic mechanism of ethane oxidation in "Ca. Ethanoperedens" is fully reversible; thus, its enzymatic machinery has potential for the biotechnological development of microbial ethane production from carbon dioxide.IMPORTANCE In the seabed, gaseous alkanes are oxidized by syntrophic microbial consortia that thereby reduce fluxes of these compounds into the water column. Because of the immense quantities of seabed alkane fluxes, these consortia are key catalysts of the global carbon cycle. Due to their obligate syntrophic lifestyle, the physiology of alkane-degrading archaea remains poorly understood. We have now cultivated a thermophilic, relatively fast-growing ethane oxidizer in partnership with a sulfate-reducing bacterium known to aid in methane oxidation and have retrieved the first complete genome of a short-chain alkane-degrading archaeon. This will greatly enhance the understanding of nonmethane alkane activation by noncanonical methyl-coenzyme M reductase enzymes and provide insights into additional metabolic steps and the mechanisms underlying syntrophic partnerships. Ultimately, this knowledge could lead to the biotechnological development of alkanogenic microorganisms to support the carbon neutrality of industrial processes.},
}
@article {pmid32316034,
year = {2020},
author = {Berkemer, SJ and McGlynn, SE},
title = {A New Analysis of Archaea-Bacteria Domain Separation: Variable Phylogenetic Distance and the Tempo of Early Evolution.},
journal = {Molecular biology and evolution},
volume = {37},
number = {8},
pages = {2332-2340},
pmid = {32316034},
issn = {1537-1719},
mesh = {Archaea/*genetics ; Archaeal Proteins/genetics ; Bacteria/*genetics ; Bacterial Proteins/genetics ; *Phylogeny ; },
abstract = {Comparative genomics and molecular phylogenetics are foundational for understanding biological evolution. Although many studies have been made with the aim of understanding the genomic contents of early life, uncertainty remains. A study by Weiss et al. (Weiss MC, Sousa FL, Mrnjavac N, Neukirchen S, Roettger M, Nelson-Sathi S, Martin WF. 2016. The physiology and habitat of the last universal common ancestor. Nat Microbiol. 1(9):16116.) identified a number of protein families in the last universal common ancestor of archaea and bacteria (LUCA) which were not found in previous works. Here, we report new research that suggests the clustering approaches used in this previous study undersampled protein families, resulting in incomplete phylogenetic trees which do not reflect protein family evolution. Phylogenetic analysis of protein families which include more sequence homologs rejects a simple LUCA hypothesis based on phylogenetic separation of the bacterial and archaeal domains for a majority of the previously identified LUCA proteins (∼82%). To supplement limitations of phylogenetic inference derived from incompletely populated orthologous groups and to test the hypothesis of a period of rapid evolution preceding the separation of the domains, we compared phylogenetic distances both within and between domains, for thousands of orthologous groups. We find a substantial diversity of interdomain versus intradomain branch lengths, even among protein families which exhibit a single domain separating branch and are thought to be associated with the LUCA. Additionally, phylogenetic trees with long interdomain branches relative to intradomain branches are enriched in information categories of protein families in comparison to those associated with metabolic functions. These results provide a new view of protein family evolution and temper claims about the phenotype and habitat of the LUCA.},
}
@article {pmid32302567,
year = {2020},
author = {López-García, P and Moreira, D},
title = {Cultured Asgard Archaea Shed Light on Eukaryogenesis.},
journal = {Cell},
volume = {181},
number = {2},
pages = {232-235},
doi = {10.1016/j.cell.2020.03.058},
pmid = {32302567},
issn = {1097-4172},
mesh = {*Archaea/genetics ; *Eukaryota/genetics ; Eukaryotic Cells ; Genome, Archaeal ; Phylogeny ; },
abstract = {The first cultured Asgard archaeon lives in metabolic symbiosis with hydrogen-scavenging microbes. Its full-genome analysis authenticates the existence of Asgard archaea, previously only known from metagenome-assembled genomes, confirms their closer phylogenetic relatedness to eukaryotes and reinforces the idea that the eukaryotic cell evolved from an integrated archaeal-bacterial syntrophic consortium.},
}
@article {pmid32302368,
year = {2020},
author = {Molnár, J and Magyar, B and Schneider, G and Laczi, K and Valappil, SK and Kovács, ÁL and Nagy, IK and Rákhely, G and Kovács, T},
title = {Identification of a novel archaea virus, detected in hydrocarbon polluted Hungarian and Canadian samples.},
journal = {PloS one},
volume = {15},
number = {4},
pages = {e0231864},
pmid = {32302368},
issn = {1932-6203},
mesh = {Archaea/isolation &amp; purification/*virology ; Archaeal Viruses/genetics/*isolation &amp; purification ; Canada ; DNA, Viral/chemistry/metabolism ; Environmental Pollution/*analysis ; Genome, Viral ; Hungary ; Hydrocarbons/*analysis ; Soil Microbiology ; Water Microbiology ; },
abstract = {Metagenomics is a helpful tool for the analysis of unculturable organisms and viruses. Viruses that target bacteria and archaea play important roles in the microbial diversity of various ecosystems. Here we show that Methanosarcina virus MV (MetMV), the second Methanosarcina sp. virus with a completely determined genome, is characteristic of hydrocarbon pollution in environmental (soil and water) samples. It was highly abundant in Hungarian hydrocarbon polluted samples and its genome was also present in the NCBI SRA database containing reads from hydrocarbon polluted samples collected in Canada, indicating the stability of its niche and the marker feature of this virus. MetMV, as the only currently identified marker virus for pollution in environmental samples, could contribute to the understanding of the complicated network of prokaryotes and their viruses driving the decomposition of environmental pollutants.},
}
@article {pmid32300653,
year = {2020},
author = {Inoue, K and Tsunoda, SP and Singh, M and Tomida, S and Hososhima, S and Konno, M and Nakamura, R and Watanabe, H and Bulzu, PA and Banciu, HL and Andrei, AŞ and Uchihashi, T and Ghai, R and Béjà, O and Kandori, H},
title = {Schizorhodopsins: A family of rhodopsins from Asgard archaea that function as light-driven inward H+ pumps.},
journal = {Science advances},
volume = {6},
number = {15},
pages = {eaaz2441},
pmid = {32300653},
issn = {2375-2548},
mesh = {Archaea/genetics/*metabolism ; Cell Membrane/metabolism ; Fluorescent Antibody Technique ; Ion Channel Gating/*radiation effects ; Light ; Models, Molecular ; Multigene Family ; Mutation ; Protein Conformation ; Proton Pumps/chemistry/genetics/*metabolism ; Rhodopsin/chemistry/genetics/*metabolism ; Spectroscopy, Fourier Transform Infrared ; Structure-Activity Relationship ; },
abstract = {Schizorhodopsins (SzRs), a rhodopsin family first identified in Asgard archaea, the archaeal group closest to eukaryotes, are present at a phylogenetically intermediate position between typical microbial rhodopsins and heliorhodopsins. However, the biological function and molecular properties of SzRs have not been reported. Here, SzRs from Asgardarchaeota and from a yet unknown microorganism are expressed in Escherichia coli and mammalian cells, and ion transport assays and patch clamp analyses are used to demonstrate SzR as a novel type of light-driven inward H+ pump. The mutation of a cytoplasmic glutamate inhibited inward H+ transport, suggesting that it functions as a cytoplasmic H+ acceptor. The function, trimeric structure, and H+ transport mechanism of SzR are similar to that of xenorhodopsin (XeR), a light-driven inward H+ pumping microbial rhodopsins, implying that they evolved convergently. The inward H+ pump function of SzR provides new insight into the photobiological life cycle of the Asgardarchaeota.},
}
@article {pmid32296409,
year = {2020},
author = {Tourte, M and Schaeffer, P and Grossi, V and Oger, PM},
title = {Functionalized Membrane Domains: An Ancestral Feature of Archaea?.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {526},
pmid = {32296409},
issn = {1664-302X},
abstract = {Bacteria and Eukarya organize their plasma membrane spatially into domains of distinct functions. Due to the uniqueness of their lipids, membrane functionalization in Archaea remains a debated area. A novel membrane ultrastructure predicts that monolayer and bilayer domains would be laterally segregated in the hyperthermophilic archaeon Thermococcus barophilus. With very different physico-chemical parameters of the mono- and bilayer, each domain type would thus allow the docking of different membrane proteins and express different biological functions in the membrane. To estimate the ubiquity of this putative membrane ultrastructure in and out of the order Thermococcales, we re-analyzed the core lipid composition of all the Thermococcales type species and collected all the literature data available for isolated archaea. We show that all species of Thermococcales synthesize a mixture of diether bilayer forming and tetraether monolayer forming lipids, in various ratio from 10 to 80% diether in Pyrococcus horikoshii and Thermococcus gorgonarius, respectively. Since the domain formation prediction rests only on the coexistence of di- and tetraether lipids, we show that all Thermococcales have the ability for domain formation, i.e., differential functionalization of their membrane. Extrapolating this view to the whole Archaea domain, we show that almost all archaea also have the ability to synthesize di- and tetraether lipids, which supports the view that functionalized membrane domains may be shared between all Archaea. Hence domain formation and membrane compartmentalization may have predated the separation of the three domains of life and be essential for the cell cycle.},
}
@article {pmid32281023,
year = {2020},
author = {Fadhlaoui, K and Arnal, ME and Martineau, M and Camponova, P and Ollivier, B and O'Toole, PW and Brugère, JF},
title = {Archaea, specific genetic traits, and development of improved bacterial live biotherapeutic products: another face of next-generation probiotics.},
journal = {Applied microbiology and biotechnology},
volume = {104},
number = {11},
pages = {4705-4716},
doi = {10.1007/s00253-020-10599-8},
pmid = {32281023},
issn = {1432-0614},
support = {16-IDEX-0001 CAP 20-25//ANR program ''Investissements d'Avenir'' CAP 20-25 "Innovation-Research" grant from Hub Innovergne/ ; },
mesh = {Animals ; Archaea/*genetics/*metabolism ; *Biological Therapy ; Cardiovascular Diseases/prevention &amp; control ; Diet ; Gastrointestinal Microbiome/*physiology ; Humans ; Metabolism, Inborn Errors/prevention &amp; control ; Methylamines/blood/metabolism/urine ; Mice ; Probiotics/*therapeutic use ; },
abstract = {Trimethylamine (TMA) and its oxide TMAO are important biomolecules involved in disease-associated processes in humans (e.g., trimethylaminuria and cardiovascular diseases). TMAO in plasma (pTMAO) stems from intestinal TMA, which is formed from various components of the diet in a complex interplay between diet, gut microbiota, and the human host. Most approaches to prevent the occurrence of such deleterious molecules focus on actions to interfere with gut microbiota metabolism to limit the synthesis of TMA. Some human gut archaea however use TMA as terminal electron acceptor for producing methane, thus indicating that intestinal TMA does not accumulate in some human subjects. Therefore, a rational alternative approach is to eliminate neo-synthesized intestinal TMA. This can be achieved through bioremediation of TMA by these peculiar methanogenic archaea, either by stimulating or providing them, leading to a novel kind of next-generation probiotics referred to as archaebiotics. Finally, specific components which are involved in this archaeal metabolism could also be used as intestinal TMA sequesters, facilitating TMA excretion along with stool. Referring to a standard pharmacological approach, these TMA traps could be synthesized ex vivo and then delivered into the human gut. Another approach is the engineering of known probiotic strain in order to metabolize TMA, i.e., live engineered biotherapeutic products. These alternatives would require, however, to take into account the necessity of synthesizing the 22nd amino acid pyrrolysine, i.e., some specificities of the genetics of TMA-consuming archaea. Here, we present an overview of these different strategies and recent advances in the field that will sustain such biotechnological developments. KEY POINTS: • Some autochthonous human archaea can use TMA for their essential metabolism, a methyl-dependent hydrogenotrophic methanogenesis. • They could therefore be used as next-generation probiotics for preventing some human diseases, especially cardiovascular diseases and trimethylaminuria. • Their genetic capacities can also be used to design live recombinant biotherapeutic products. • Encoding of the 22nd amino acid pyrrolysine is necessary for such alternative developments.},
}
@article {pmid32267873,
year = {2020},
author = {Compte-Port, S and Fillol, M and Gich, F and Borrego, CM},
title = {Metabolic versatility of freshwater sedimentary archaea feeding on different organic carbon sources.},
journal = {PloS one},
volume = {15},
number = {4},
pages = {e0231238},
pmid = {32267873},
issn = {1932-6203},
mesh = {Biodiversity ; Biofilms ; Carbon/metabolism ; Carbon Cycle/*physiology ; Crenarchaeota/*genetics/*metabolism ; DNA, Archaeal/genetics ; Ecosystem ; Euryarchaeota/*genetics/*metabolism ; *Geologic Sediments ; Humic Substances ; *Lakes ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Tryptophan ; },
abstract = {Members of the phylum Bathyarchaeota and the class Thermoplasmata are widespread in marine and freshwater sediments where they have been recognized as key players in the carbon cycle. Here, we tested the responsiveness of archaeal communities on settled plant debris and sediment from a karstic lake to different organic carbon amendments (amino acids, plant-derived carbohydrates, and aromatics) using a lab-scale microcosm. Changes in the composition and abundance of sediment and biofilm archaeal communities in both DNA and RNA fractions were assessed by 16S rRNA gene amplicon sequencing and qPCR, respectively, after 7 and 30 days of incubation. Archaeal communities showed compositional changes in terms of alpha and beta diversity in relation to the type of carbon source (amino acids vs. plant-derived compounds), the nucleic acid fraction (DNA vs. RNA), and the incubation time (7 vs. 30 days). Distinct groups within the Bathyarchaeota (Bathy-15 and Bathy-6) and the Thermoplasmata (MBG-D) differently reacted to carbon supplements as deduced from the analysis of RNA libraries. Whereas Bathyarchaeota in biofilms showed a long-term positive response to humic acids, their counterparts in the sediment were mainly stimulated by the addition of tryptophan, suggesting the presence of different subpopulations in both habitats. Overall, our work presents an in vitro assessment of the versatility of archaea inhabiting freshwater sediments towards organic carbon and introduces settled leaf litter as a new habitat for the Bathyarchaeota and the Thermoplasmata.},
}
@article {pmid32247910,
year = {2020},
author = {Jin, D and Zhang, F and Shi, Y and Kong, X and Xie, Y and Du, X and Li, Y and Zhang, R},
title = {Diversity of bacteria and archaea in the groundwater contaminated by chlorinated solvents undergoing natural attenuation.},
journal = {Environmental research},
volume = {185},
number = {},
pages = {109457},
doi = {10.1016/j.envres.2020.109457},
pmid = {32247910},
issn = {1096-0953},
mesh = {*Archaea/genetics ; Bacteria/genetics ; *Groundwater ; RNA, Ribosomal, 16S/genetics ; Solvents ; },
abstract = {Chlorinated solvents (CS)-contaminated groundwater poses serious risks to the environment and public health. Microorganisms play a vital role in efficient remediation of CS. In this study, the microbial community (bacterial and archaeal) composition of three CS-contaminated groundwater wells located at an abandoned chemical factory which covers three orders of magnitude in concentration (0.02-16.15 mg/L) were investigated via 16S rRNA gene high-throughput sequencing. The results indicated that Proteobacteria and Thaumarchaeota were the most abundant bacterial and archaeal groups at the phylum level in groundwater, respectively. The major bacterial genera (Flavobacterium sp., Mycobacterium sp. and unclassified Parcubacteria taxa, etc.) and archaeal genera (Thaumarchaeota Group C3, Miscellaneous Crenarchaeotic Group and Miscellaneous Euryarchaeotic Group, etc.) might be involved in the dechlorination processes. In addition, Pearson's correlation analyses showed that alpha diversity of the bacterial community was not significantly correlated with CS concentration, while alpha diversity of archaeal community greatly decreased with the increased contamination of CS. Moreover, partial Mantel test indicated that oxidation-reduction potential, dissolved oxygen, temperature and methane concentration were major drivers of bacterial and archaeal community composition, whereas CS concentration had no significant impact, indicating that both indigenous bacterial and archaeal community compositions are capable of withstanding elevated CS contamination. This study improves our understanding of how the natural microbial community responds to high CS-contaminated groundwater.},
}
@article {pmid32232532,
year = {2020},
author = {Abril, AG and Rama, JLR and Sánchez-Pérez, A and Villa, TG},
title = {Prokaryotic sigma factors and their transcriptional counterparts in Archaea and Eukarya.},
journal = {Applied microbiology and biotechnology},
volume = {104},
number = {10},
pages = {4289-4302},
doi = {10.1007/s00253-020-10577-0},
pmid = {32232532},
issn = {1432-0614},
mesh = {Archaea/*genetics ; Bacteria/genetics/metabolism ; DNA, Archaeal/genetics ; DNA-Directed RNA Polymerases/genetics/metabolism ; Eukaryota/*genetics ; Gene Expression Regulation ; Promoter Regions, Genetic ; Sigma Factor/*genetics/metabolism ; Transcription Factors/*genetics ; Transcription Initiation, Genetic ; },
abstract = {RNA polymerases (RNAPs) carry out transcription in the three domains of life, Bacteria, Archaea, and Eukarya. Transcription initiation is highly regulated by a variety of transcription factors, whose number and subunit complexity increase during evolution. This process is regulated in Bacteria by the σ factor, while the three eukaryotic RNAPs require a complex set of transcription factors (TFs) and a TATA-binding protein (TBP). The archaeal transcription system appears to be an ancestral version of the eukaryotic RNAPII, requiring transcription factor B (TFB), TBP, and transcription factor E (TFE). The function of the bacterial sigma (σ) factor has been correlated to the roles played by the eukaryotic RNAP II and the archaeal RNAP. In addition, σ factors, TFB, and TFIIB all contain multiple DNA binding helix-turn-helix (HTH) structural motifs; although TFIIB and TFB display two HTH domains, while the bacterial σ factor spans 4 HTH motifs. The sequence similarities and structure alignments of the bacterial σ factor, eukaryotic TFIIB, and archaeal TFB evidence that these three proteins are homologs.Key Points• Transcription initiation is highly regulated by TFs.• Transcription is finely regulated in all domains of life by different sets of TFs.• Specific TFs in Bacteria, Eukarya and Archaea are homologs.},
}
@article {pmid32201928,
year = {2020},
author = {Cai, M and Liu, Y and Yin, X and Zhou, Z and Friedrich, MW and Richter-Heitmann, T and Nimzyk, R and Kulkarni, A and Wang, X and Li, W and Pan, J and Yang, Y and Gu, JD and Li, M},
title = {Diverse Asgard archaea including the novel phylum Gerdarchaeota participate in organic matter degradation.},
journal = {Science China. Life sciences},
volume = {63},
number = {6},
pages = {886-897},
pmid = {32201928},
issn = {1869-1889},
mesh = {Amino Acids/metabolism ; Archaea/*enzymology ; Carbon Cycle ; Ecosystem ; Fatty Acids/metabolism ; Genomics ; Geologic Sediments/*chemistry ; *Metagenome ; Peptides/metabolism ; *Phylogeny ; },
abstract = {Asgard is an archaeal superphylum that might hold the key to understand the origin of eukaryotes, but its diversity and ecological roles remain poorly understood. Here, we reconstructed 15 metagenomic-assembled genomes from coastal sediments covering most known Asgard archaea and a novel group, which is proposed as a new Asgard phylum named as the "Gerdarchaeota". Genomic analyses predict that Gerdarchaeota are facultative anaerobes in utilizing both organic and inorganic carbon. Unlike their closest relatives Heimdallarchaeota, Gerdarchaeota have genes encoding for cellulase and enzymes involved in the tetrahydromethanopterin-based Wood-Ljungdahl pathway. Transcriptomics showed that most of our identified Asgard archaea are capable of degrading organic matter, including peptides, amino acids and fatty acids, occupying ecological niches in different depths of layers of the sediments. Overall, this study broadens the diversity of the mysterious Asgard archaea and provides evidence for their ecological roles in coastal sediments.},
}
@article {pmid32156797,
year = {2020},
author = {Zhao, R and Dahle, H and Ramírez, GA and Jørgensen, SL},
title = {Indigenous Ammonia-Oxidizing Archaea in Oxic Subseafloor Oceanic Crust.},
journal = {mSystems},
volume = {5},
number = {2},
pages = {},
pmid = {32156797},
issn = {2379-5077},
abstract = {Oceanic ridge flank systems represent one of the largest and least-explored microbial habitats on Earth. Fundamental ecological questions regarding community activity, recruitment, and succession in this environment remain unanswered. Here, we investigated ammonia-oxidizing archaea (AOA) in the sediment-buried basalts on the oxic and young ridge flank at North Pond, a sediment-filled pond on the western flank of the Mid-Atlantic Ridge, and compared them with those in the overlying sediments and bottom seawater. Nitrification in the North Pond basement is thermodynamically favorable and is supported by a reaction-transport model simulating the dynamics of nitrate in the crustal fluids. Nitrification rate is estimated to account for 6% to 7% of oxygen consumption, which is similar to the ratios found in marine oxic sediments, suggesting that aerobic mineralization of organic matter is the major ammonium source for crustal nitrifiers. Using the archaeal 16S rRNA and amoA genes as phylogenetic markers, we show that AOA, composed solely of Nitrosopumilaceae, are the major archaeal dwellers at North Pond. Phylogenetic analysis reveals that the crustal AOA communities are distinct from those in the bottom seawater and the upper oxic sediments but are similar to those in the basal part of the overlying sediment column, suggesting either similar environmental selection or the dispersal of microbes across the sediment-basement interface. Additionally, quantitative abundance data suggest enrichment of the dominant Nitrosopumilaceae clade (Eta clade) in the basement compared to the seawater. This study explored AOA and their activity in the upper oceanic crust, and our results have ecological implications for the biogeochemical cycling of nitrogen in the crustal subsurface.IMPORTANCE Ridge flanks represent the major avenue of chemical and heat exchange between the Earth's oceans and the lithosphere and are thought to harbor an enormous and understudied biosphere. However, little is known about the diversity and functionality of the crustal biosphere. Here, we report an indigenous community of archaea specialized in ammonia oxidation (i.e., AOA) in the oxic oceanic crust at North Pond. These AOA are the dominant archaea and are likely responsible for most of the cycling taking place in the first step of nitrification, a feasible nitrogen cycling step in the oxic basement. The crustal AOA community structure significantly differs from that in deep ocean water but is similar to that of the community in the overlying sediments in close proximity. This report links the occurrence of AOA to their metabolic activity in the oxic subseafloor crust and suggests that ecological selection and in situ proliferation may shape the microbial community structure in the rocky subsurface.},
}
@article {pmid32148848,
year = {2020},
author = {Jeon, JH and Lee, HS and Shin, HC and Kwak, MJ and Kim, YG and Gruber, S and Oh, BH},
title = {Evidence for binary Smc complexes lacking kite subunits in archaea.},
journal = {IUCrJ},
volume = {7},
number = {Pt 2},
pages = {193-206},
pmid = {32148848},
issn = {2052-2525},
abstract = {SMC complexes play a central role in chromosome organization in all domains of life. The bacterial Smc-ScpAB complex is a three-subunit complex composed of Smc, ScpA and ScpB. ScpA bridges the two ATPase domains of the Smc homodimer, while ScpB, which belongs to the kite family of proteins, interacts with ScpA. The three subunits are known to be equally important for the function of Smc-ScpAB in bacteria. From crystallographic and biochemical studies, evidence is provided that six archaeal ScpA proteins are unable to interact with the only putative ScpB found in these species. Structure-based sequence alignment reveals that these archaeal ScpAs lack the ScpB-binding segment that is commonly present in the middle of bacterial ScpA sequences, which is thus responsible for their inability to interact with ScpB. ScpA proteins lacking the ScpB-binding segment are found to prevail in archaea. Moreover, two archaeal ScpA proteins with a longer middle region also failed to bind their putative ScpB partner. Furthermore, all or most species belonging to five out of 14 euryarchaeotal orders contain Smc and ScpA but not a detectable ScpB homologue. These data support the notion that archaeal Smc-based complexes generally function as a two-subunit complex composed of only Smc and ScpA.},
}
@article {pmid32126588,
year = {2020},
author = {Taylor, HB and Kurtz, HD},
title = {Composition, diversity, and activity of aerobic ammonia-oxidizing Bacteria and Archaea in the intertidal sands of a grand strand South Carolina beach.},
journal = {MicrobiologyOpen},
volume = {9},
number = {5},
pages = {e1011},
pmid = {32126588},
issn = {2045-8827},
mesh = {Ammonia/metabolism ; Archaea/*classification/metabolism ; Bacteria/*classification/metabolism ; Betaproteobacteria/classification ; Biodiversity ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Gammaproteobacteria/classification ; High-Throughput Nucleotide Sequencing ; Oxidation-Reduction ; Oxidoreductases/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sand/*microbiology ; *Soil Microbiology ; South Carolina ; },
abstract = {Aerobic ammonia oxidation to nitrite has been established as an important ecosystem process in regulating the level of nitrogen in marine ecosystems. This process is carried out by ammonia-oxidizing bacteria (AOB) within the classes Betaproteobacteria and Gammaproteobacteria and ammonia-oxidizing Archaea (AOA) from the phylum Thaumarchaeota, and the latter of which has been established as more prevalent in marine systems. This study investigated the presence, abundance, and activity of these groups of microbes at a beach near Springmaid Pier in Myrtle Beach, South Carolina, through the implementation of next generation sequencing, quantitative PCR (qPCR), and microcosm experiments to monitor activity. Sequencing analysis revealed a diverse community of ammonia-oxidizing microbes dominated by AOA classified within the family Nitrosopumilaceae, and qPCR revealed the abundance of AOA amoA genes over AOB by at least an order of magnitude in most samples. Microcosm studies indicate that the rates of potential ammonia oxidation in these communities satisfy Michaelis-Menten substrate kinetics and this process is more active at temperatures corresponding to summer months than winter. Potential rates in AOA medium were higher than that of AOB medium, indicating a potentially greater contribution of AOA to this process in this environment. In conclusion, this study provides further evidence of the dominance of AOA in these environments compared with AOB and highlights the overall efficiency of this process at turning over excess ammonium that may be present in these environments.},
}
@article {pmid32094586,
year = {2020},
author = {Sanders, TJ and Wenck, BR and Selan, JN and Barker, MP and Trimmer, SA and Walker, JE and Santangelo, TJ},
title = {FttA is a CPSF73 homologue that terminates transcription in Archaea.},
journal = {Nature microbiology},
volume = {5},
number = {4},
pages = {545-553},
pmid = {32094586},
issn = {2058-5276},
support = {R01 GM100329/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaeal Proteins/*chemistry/genetics/metabolism ; Bacteria/genetics/metabolism ; Biological Evolution ; Cleavage And Polyadenylation Specificity Factor/*chemistry/genetics/metabolism ; DNA-Directed RNA Polymerases/genetics/metabolism ; *Genome, Archaeal ; Humans ; Models, Molecular ; Protein Biosynthesis ; RNA, Messenger/genetics/metabolism ; Structural Homology, Protein ; Thermococcus/*genetics/metabolism ; Transcription Elongation, Genetic ; Transcription Factors/*chemistry/genetics/metabolism ; Transcription Initiation, Genetic ; *Transcription Termination, Genetic ; },
abstract = {Regulated gene expression is largely achieved by controlling the activities of essential, multisubunit RNA polymerase transcription elongation complexes (TECs). The extreme stability required of TECs to processively transcribe large genomic regions necessitates robust mechanisms to terminate transcription. Efficient transcription termination is particularly critical for gene-dense bacterial and archaeal genomes1-3 in which continued transcription would necessarily transcribe immediately adjacent genes and result in conflicts between the transcription and replication apparatuses4-6; the coupling of transcription and translation7,8 would permit the loading of ribosomes onto aberrant transcripts. Only select sequences or transcription termination factors can disrupt the otherwise extremely stable TEC and we demonstrate that one of the last universally conserved archaeal proteins with unknown biological function is the Factor that terminates transcription in Archaea (FttA). FttA resolves the dichotomy of a prokaryotic gene structure (operons and polarity) and eukaryotic molecular homology (general transcription apparatus) that is observed in Archaea. This missing link between prokaryotic and eukaryotic transcription regulation provides the most parsimonious link to the evolution of the processing activities involved in RNA 3'-end formation in Eukarya.},
}
@article {pmid32086308,
year = {2020},
author = {Wright, CL and Schatteman, A and Crombie, AT and Murrell, JC and Lehtovirta-Morley, LE},
title = {Inhibition of Ammonia Monooxygenase from Ammonia-Oxidizing Archaea by Linear and Aromatic Alkynes.},
journal = {Applied and environmental microbiology},
volume = {86},
number = {9},
pages = {},
pmid = {32086308},
issn = {1098-5336},
mesh = {Alkynes/*metabolism ; Ammonia/metabolism ; Archaea/*metabolism ; Oxidoreductases/*metabolism ; },
abstract = {Ammonia monooxygenase (AMO) is a key nitrogen-transforming enzyme belonging to the same copper-dependent membrane monooxygenase family (CuMMO) as the particulate methane monooxygenase (pMMO). The AMO from ammonia-oxidizing archaea (AOA) is very divergent from both the AMO of ammonia-oxidizing bacteria (AOB) and the pMMO from methanotrophs, and little is known about the structure or substrate range of the archaeal AMO. This study compares inhibition by C2 to C8 linear 1-alkynes of AMO from two phylogenetically distinct strains of AOA, "Candidatus Nitrosocosmicus franklandus" C13 and "Candidatus Nitrosotalea sinensis" Nd2, with AMO from Nitrosomonas europaea and pMMO from Methylococcus capsulatus (Bath). An increased sensitivity of the archaeal AMO to short-chain-length alkynes (≤C5) appeared to be conserved across AOA lineages. Similarities in C2 to C8 alkyne inhibition profiles between AMO from AOA and pMMO from M. capsulatus suggested that the archaeal AMO has a narrower substrate range than N. europaea AMO. Inhibition of AMO from "Ca Nitrosocosmicus franklandus" and N. europaea by the aromatic alkyne phenylacetylene was also investigated. Kinetic data revealed that the mechanisms by which phenylacetylene inhibits "Ca Nitrosocosmicus franklandus" and N. europaea are different, indicating differences in the AMO active site between AOA and AOB. Phenylacetylene was found to be a specific and irreversible inhibitor of AMO from "Ca Nitrosocosmicus franklandus," and it does not compete with NH3 for binding at the active site.IMPORTANCE Archaeal and bacterial ammonia oxidizers (AOA and AOB, respectively) initiate nitrification by oxidizing ammonia to hydroxylamine, a reaction catalyzed by ammonia monooxygenase (AMO). AMO enzyme is difficult to purify in its active form, and its structure and biochemistry remain largely unexplored. The bacterial AMO and the closely related particulate methane monooxygenase (pMMO) have a broad range of hydrocarbon cooxidation substrates. This study provides insights into the AMO of previously unstudied archaeal genera, by comparing the response of the archaeal AMO, a bacterial AMO, and pMMO to inhibition by linear 1-alkynes and the aromatic alkyne, phenylacetylene. Reduced sensitivity to inhibition by larger alkynes suggests that the archaeal AMO has a narrower hydrocarbon substrate range than the bacterial AMO, as previously reported for other genera of AOA. Phenylacetylene inhibited the archaeal and bacterial AMOs at different thresholds and by different mechanisms of inhibition, highlighting structural differences between the two forms of monooxygenase.},
}
@article {pmid32084690,
year = {2020},
author = {Yang, X and Ni, K and Shi, Y and Yi, X and Ji, L and Ma, L and Ruan, J},
title = {Heavy nitrogen application increases soil nitrification through ammonia-oxidizing bacteria rather than archaea in acidic tea (Camellia sinensis L.) plantation soil.},
journal = {The Science of the total environment},
volume = {717},
number = {},
pages = {137248},
doi = {10.1016/j.scitotenv.2020.137248},
pmid = {32084690},
issn = {1879-1026},
mesh = {Ammonia ; *Archaea ; Bacteria ; *Camellia sinensis ; Ecosystem ; Nitrification ; Nitrogen ; Oxidation-Reduction ; Phylogeny ; Soil ; Soil Microbiology ; Tea ; },
abstract = {Nitrogen (N) fertilizer is widely used in agricultural ecosystems and influences N transformation processes in the soil such as nitrification. However, whether nitrification is primarily dominated by ammonia-oxidizing bacteria (AOB) or archaea (AOA) under heavy N application is still under debate. In the present work, the effect of long-term (12 years) N fertilization on soil nitrification and the key influencing factors were investigated in acidic tea plantation soil that received four different rates of N application (0, 119, 285, and 569 kg N ha-1 yr-1). Nitrification potential was measured and partitioned using chemical inhibitors. The abundance of functional genes involved in ammonia oxidation was quantified using quantitative polymerase chain reaction (qPCR). Ammonia-oxidizing communities were identified by shotgun metagenome sequencing. Potential nitrification rate in tea plantation soil was mainly dominated by autotrophic nitrification (PNRA) (71-79%). PNRA and heterotrophic nitrification (PNRH) were both significantly increased by heavy N (569 kg ha-1) application. Moreover, PNRA was mainly due to the contribution of AOB (52-66%) in N-treated soils, and N569 significantly increased the AOB contribution without affecting the AOA contribution. N569 increased the functional gene abundance of AOB and TAO100 (a non-halophilic γ-AOB) but decreased that of AOA. The dominant AOB (Nitrosomonas, Nitrosospira, and Nitrosococcus), AOA (Nitrososphaera and Nitrosopumilus) and commamox (Nitrospira) groups were profoundly altered by long-term N application rates. Partial least squares regression showed that total nitrification (PNRT), PNRA, and PNRAOB were primarily explained by the functional gene abundance of nitrifiers whereas PNRH and PNRAOA were closely associated with soil and pruned litter properties. Moreover, structural equation modeling (SEM) revealed that long-term N application significantly and indirectly affected nitrification potential by directly influencing soil properties, pruned litter properties, and functional gene abundance. Understanding the relative contribution of AOA and AOB to nitrification may help to better regulate N fertilizer use in agricultural ecosystems.},
}
@article {pmid32073658,
year = {2020},
author = {Eckl, DB and Huber, H and Bäumler, W},
title = {First Report on Photodynamic Inactivation of Archaea Including a Novel Method for High-Throughput Reduction Measurement.},
journal = {Photochemistry and photobiology},
volume = {96},
number = {4},
pages = {883-889},
doi = {10.1111/php.13229},
pmid = {32073658},
issn = {1751-1097},
support = {415812443//Deutsche Forschungsgemeinschaft/International ; },
mesh = {Anti-Infective Agents/pharmacology ; Halobacterium salinarum/*drug effects ; Photosensitizing Agents/*pharmacology ; Porphyrins/*pharmacology ; },
abstract = {Archaea are considered third, independent domain of living organisms besides eukaryotic and bacterial cells. To date, no report is available of photodynamic inactivation (PDI) of any archaeal cells. Two commercially available photosensitizers (SAPYR and TMPyP) were used to investigate photodynamic inactivation of Halobacterium salinarum. In addition, a novel high-throughput method was tested to evaluate microbial reduction in vitro. Due to the high salt content of the culture medium, the physical and chemical properties of photosensitizers were analyzed via spectroscopy and fluorescence-based DPBF assays. Attachment or uptake of photosensitizers to or in archaeal cells was investigated. The photodynamic inactivation of Halobacterium salinarum was evaluated via growth curve method allowing a high throughput of samples. The presented results indicate that the photodynamic mechanisms are working even in high salt environments. Either photosensitizer inactivated the archaeal cells with a reduction of 99.9% at least. The growth curves provided a fast and precise measurement of cell viability. The results show for the first time that PDI can kill not only bacterial cells but also robust archaea. The novel method for generating high-throughput growth curves provides benefits for future research regarding antimicrobial substances in general.},
}
@article {pmid32071162,
year = {2020},
author = {Liechty, Z and Santos-Medellín, C and Edwards, J and Nguyen, B and Mikhail, D and Eason, S and Phillips, G and Sundaresan, V},
title = {Comparative Analysis of Root Microbiomes of Rice Cultivars with High and Low Methane Emissions Reveals Differences in Abundance of Methanogenic Archaea and Putative Upstream Fermenters.},
journal = {mSystems},
volume = {5},
number = {1},
pages = {},
pmid = {32071162},
issn = {2379-5077},
abstract = {Rice cultivation worldwide accounts for ∼7 to 17% of global methane emissions. Methane cycling in rice paddies is a microbial process not only involving methane producers (methanogens) and methane metabolizers (methanotrophs) but also other microbial taxa that affect upstream processes related to methane metabolism. Rice cultivars vary in their rates of methane emissions, but the influence of rice genotypes on methane cycling microbiota has been poorly characterized. Here, we profiled the rhizosphere, rhizoplane, and endosphere microbiomes of a high-methane-emitting cultivar (Sabine) and a low-methane-emitting cultivar (CLXL745) throughout the growing season to identify variations in the archaeal and bacterial communities relating to methane emissions. The rhizosphere of the high-emitting cultivar was enriched in methanogens compared to that in the low emitter, whereas the relative abundances of methanotrophs between the cultivars were not significantly different. Further analysis of cultivar-sensitive taxa identified families enriched in the high emitter that are associated with methanogenesis-related processes. The high emitter had greater relative abundances of sulfate-reducing and iron-reducing taxa which peak earlier in the season than methanogens and are necessary to lower soil oxidation reduction potential before methanogenesis can occur. The high emitter also had a greater abundance of fermentative taxa which produce methanogenesis precursors (acetate, CO2, and H2). Furthermore, the high emitter was enriched in taxa related to acetogenesis which compete with methanogens for CO2 and H2 These taxa were enriched in a spatio-specific manner and reveal a complex network of microbial interactions on which plant genotype-dependent factors can act to affect methanogenesis and methane emissions.IMPORTANCE Rice cultivation is a major source of anthropogenic emissions of methane, a greenhouse gas with a potentially severe impact on climate change. Emission variation between rice cultivars suggests the feasibility of breeding low-emission rice, but there is a limited understanding of how genotypes affect the microbiota involved in methane cycling. Here, we show that the root microbiome of the high-emitting cultivar is enriched both in methanogens and in taxa associated with fermentation, iron, and sulfate reduction and acetogenesis, processes that support methanogenesis. Understanding how cultivars affect microbes with methanogenesis-related functions is vital for understanding the genetic basis for methane emission in rice and can aid in the development of breeding programs that reduce the environmental impact of rice cultivation.},
}
@article {pmid32068866,
year = {2020},
author = {Badel, C and Da Cunha, V and Forterre, P and Oberto, J},
title = {Pervasive Suicidal Integrases in Deep-Sea Archaea.},
journal = {Molecular biology and evolution},
volume = {37},
number = {6},
pages = {1727-1743},
pmid = {32068866},
issn = {1537-1719},
mesh = {*Evolution, Molecular ; Hydrothermal Vents ; Integrases/genetics/*metabolism ; Interspersed Repetitive Sequences ; *Pseudogenes ; Thermococcus/*enzymology/genetics/isolation &amp; purification ; },
abstract = {Mobile genetic elements (MGEs) often encode integrases which catalyze the site-specific insertion of their genetic information into the host genome and the reverse reaction of excision. Hyperthermophilic archaea harbor integrases belonging to the SSV-family which carry the MGE recombination site within their open reading frame. Upon integration into the host genome, SSV integrases disrupt their own gene into two inactive pseudogenes and are termed suicidal for this reason. The evolutionary maintenance of suicidal integrases, concurring with the high prevalence and multiples recruitments of these recombinases by archaeal MGEs, is highly paradoxical. To elucidate this phenomenon, we analyzed the wide phylogenomic distribution of a prominent class of suicidal integrases which revealed a highly variable integration site specificity. Our results highlighted the remarkable hybrid nature of these enzymes encoded from the assembly of inactive pseudogenes of different origins. The characterization of the biological properties of one of these integrases, IntpT26-2 showed that this enzyme was active over a wide range of temperatures up to 99 °C and displayed a less-stringent site specificity requirement than comparable integrases. These observations concurred in explaining the pervasiveness of these suicidal integrases in the most hyperthermophilic organisms. The biochemical and phylogenomic data presented here revealed a target site switching system operating on highly thermostable integrases and suggested a new model for split gene reconstitution. By generating fast-evolving pseudogenes at high frequency, suicidal integrases constitute a powerful model to approach the molecular mechanisms involved in the generation of active genes variants by the recombination of proto-genes.},
}
@article {pmid32055827,
year = {2020},
author = {Tästensen, JB and Johnsen, U and Reinhardt, A and Ortjohann, M and Schönheit, P},
title = {D-galactose catabolism in archaea: operation of the DeLey-Doudoroff pathway in Haloferax volcanii.},
journal = {FEMS microbiology letters},
volume = {367},
number = {1},
pages = {},
doi = {10.1093/femsle/fnaa029},
pmid = {32055827},
issn = {1574-6968},
mesh = {Carbohydrate Metabolism/genetics ; Enzymes/genetics/metabolism ; Galactose/*metabolism ; Gene Knockout Techniques ; Genes, Archaeal/*genetics ; *Haloferax volcanii/enzymology/genetics ; Metabolic Networks and Pathways/*genetics ; },
abstract = {The haloarchaeon Haloferax volcanii was found to grow on D-galactose as carbon and energy source. Here we report a comprehensive analysis of D-galactose catabolism in H. volcanii. Genome analyses indicated a cluster of genes encoding putative enzymes of the DeLey-Doudoroff pathway for D-galactose degradation including galactose dehydrogenase, galactonate dehydratase, 2-keto-3-deoxygalactonate kinase and 2-keto-3-deoxy-6-phosphogalactonate (KDPGal) aldolase. The recombinant galactose dehydrogenase and galactonate dehydratase showed high specificity for D-galactose and galactonate, respectively, whereas KDPGal aldolase was promiscuous in utilizing KDPGal and also the C4 epimer 2-keto-3-deoxy-6-phosphogluconate as substrates. Growth studies with knock-out mutants indicated the functional involvement of galactose dehydrogenase, galactonate dehydratase and KDPGal aldolase in D-galactose degradation. Further, the transcriptional regulator GacR was identified, which was characterized as an activator of genes of the DeLey-Doudoroff pathway. Finally, genes were identified encoding components of an ABC transporter and a knock-out mutant of the substrate binding protein indicated the functional involvement of this transporter in D-galactose uptake. This is the first report of D-galactose degradation via the DeLey-Doudoroff pathway in the domain of archaea.},
}
@article {pmid32047285,
year = {2020},
author = {Roux, S and Krupovic, M and Daly, RA and Borges, AL and Nayfach, S and Schulz, F and Sharrar, A and Matheus Carnevali, PB and Cheng, JF and Ivanova, NN and Bondy-Denomy, J and Wrighton, KC and Woyke, T and Visel, A and Kyrpides, NC and Eloe-Fadrosh, EA},
title = {Author Correction: Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth's biomes.},
journal = {Nature microbiology},
volume = {5},
number = {3},
pages = {527},
doi = {10.1038/s41564-020-0681-5},
pmid = {32047285},
issn = {2058-5276},
abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.},
}
@article {pmid32041059,
year = {2020},
author = {Roy, D and McEvoy, J and Khan, E},
title = {Abundance and activity of ammonia oxidizing archaea and bacteria in bulk water and biofilm in water supply systems practicing chlorination and chloramination: Full and laboratory scale investigations.},
journal = {The Science of the total environment},
volume = {715},
number = {},
pages = {137043},
doi = {10.1016/j.scitotenv.2020.137043},
pmid = {32041059},
issn = {1879-1026},
mesh = {Ammonia ; *Archaea ; Bacteria ; *Biofilms ; Halogenation ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Soil Microbiology ; Water ; Water Supply ; },
abstract = {The abundance and nitrification activity of ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB) in bulk water and biofilm in chloraminated and chlorinated water supply systems were investigated. The abundance of AOB varied between cold and warm periods while that was the case for AOA only in biofilm. Lower ammonia concentrations favored the abundance of AOA over AOB. AOA and AOB were found more in distal zones of the distribution system (DS). Higher numbers of AOA and AOB were observed in DS associated with chloramination compared to those associated with chlorination. Significant positive correlations between ammonia-N in bulk water and AOA indicate a possibility of involvement of AOA in nitrification in DS. A separate laboratory-based experiment simulating DS condition was conducted to understand the effects of chlorine and chloramine dosages and temperature on AOA and AOB. AOA were inhibited less than AOB in the presence of lower concentrations of chlorine and chloramine (1.5 and 2.0 mg/L chlorine; 0.05-0.1 and 0.3-0.4 mg/L chloramine) while both of them were not detected at higher dosages (2.5 mg/L chlorine and 1.5-1.6 mg/L chloramine). At a low temperature (10-12 °C), chloramine and chlorine provided similar inhibition trends in which AOB were inhibited more than AOA. At a high temperature (25 °C), chloramine was less inhibitory to AOA and AOB than chlorine.},
}
@article {pmid32030412,
year = {2020},
author = {Phung, DK and Etienne, C and Batista, M and Langendijk-Genevaux, P and Moalic, Y and Laurent, S and Liuu, S and Morales, V and Jebbar, M and Fichant, G and Bouvier, M and Flament, D and Clouet-d'Orval, B},
title = {RNA processing machineries in Archaea: the 5'-3' exoribonuclease aRNase J of the β-CASP family is engaged specifically with the helicase ASH-Ski2 and the 3'-5' exoribonucleolytic RNA exosome machinery.},
journal = {Nucleic acids research},
volume = {48},
number = {7},
pages = {3832-3847},
pmid = {32030412},
issn = {1362-4962},
mesh = {Euryarchaeota/*enzymology ; Exoribonucleases/*metabolism ; Exosome Multienzyme Ribonuclease Complex/*metabolism ; Protein Interaction Mapping ; Pyrococcus abyssi/enzymology ; RNA Helicases/*metabolism ; *RNA Processing, Post-Transcriptional ; RNA, Archaeal/*metabolism ; Thermococcus/enzymology ; },
abstract = {A network of RNA helicases, endoribonucleases and exoribonucleases regulates the quantity and quality of cellular RNAs. To date, mechanistic studies focussed on bacterial and eukaryal systems due to the challenge of identifying the main drivers of RNA decay and processing in Archaea. Here, our data support that aRNase J, a 5'-3' exoribonuclease of the β-CASP family conserved in Euryarchaeota, engages specifically with a Ski2-like helicase and the RNA exosome to potentially exert control over RNA surveillance, at the vicinity of the ribosome. Proteomic landscapes and direct protein-protein interaction analyses, strengthened by comprehensive phylogenomic studies demonstrated that aRNase J interplay with ASH-Ski2 and a cap exosome subunit. Finally, Thermococcus barophilus whole-cell extract fractionation experiments provide evidences that an aRNase J/ASH-Ski2 complex might exist in vivo and hint at an association of aRNase J with the ribosome that is emphasised in absence of ASH-Ski2. Whilst aRNase J homologues are found among bacteria, the RNA exosome and the Ski2-like RNA helicase have eukaryotic homologues, underlining the mosaic aspect of archaeal RNA machines. Altogether, these results suggest a fundamental role of β-CASP RNase/helicase complex in archaeal RNA metabolism.},
}
@article {pmid32025518,
year = {2020},
author = {Lyubetsky, VA and Zverkov, OA and Rubanov, LI and Seliverstov, AV},
title = {Optimal Growth Temperature and Intergenic Distances in Bacteria, Archaea, and Plastids of Rhodophytic Branch.},
journal = {BioMed research international},
volume = {2020},
number = {},
pages = {3465380},
pmid = {32025518},
issn = {2314-6141},
mesh = {Archaea/*genetics/*growth &amp; development/metabolism ; Archaeal Proteins/genetics ; Bacteria/*genetics/*growth &amp; development/metabolism ; Bacterial Proteins/genetics ; Cell Culture Techniques ; Chloroplast Proteins/genetics ; Evolution, Molecular ; Genome, Archaeal ; Genome, Bacterial ; Genome, Plastid ; Linear Models ; Plastids/*genetics/metabolism/*physiology ; *Temperature ; },
abstract = {The lengths of intergenic regions between neighboring genes that are convergent, divergent, or unidirectional were calculated for plastids of the rhodophytic branch and complete archaeal and bacterial genomes. Statistically significant linear relationships between any pair of the medians of these three length types have been revealed in each genomic group. Exponential relationships between the optimal growth temperature and each of the three medians have been revealed as well. The leading coefficients of the regression equations relating all pairs of the medians as well as temperature and any of the medians have the same sign and order of magnitude. The results obtained for plastids, archaea, and bacteria are also similar at the qualitative level. For instance, the medians are always low at high temperatures. At low temperatures, the medians tend to statistically significant greater values and scattering. The original model was used to test our hypothesis that the intergenic distances are optimized in particular to decrease the competition of RNA polymerases within the locus that results in transcribing shortened RNAs. Overall, this points to an effect of temperature for both remote and close genomes.},
}
@article {pmid32014611,
year = {2020},
author = {Fusco, S and Aulitto, M and Iacobucci, I and Crocamo, G and Pucci, P and Bartolucci, S and Monti, M and Contursi, P},
title = {The interaction between the F55 virus-encoded transcription regulator and the RadA host recombinase reveals a common strategy in Archaea and Bacteria to sense the UV-induced damage to the host DNA.},
journal = {Biochimica et biophysica acta. Gene regulatory mechanisms},
volume = {1863},
number = {5},
pages = {194493},
doi = {10.1016/j.bbagrm.2020.194493},
pmid = {32014611},
issn = {1876-4320},
mesh = {Archaeal Proteins/*genetics/metabolism ; *DNA Damage ; DNA-Binding Proteins/*genetics/metabolism ; Escherichia coli/genetics/metabolism/radiation effects ; Escherichia coli Proteins/genetics/metabolism ; Fuselloviridae/genetics/metabolism/pathogenicity ; Promoter Regions, Genetic ; Protein Binding ; Rec A Recombinases/genetics/metabolism ; Sulfolobus/genetics/metabolism/radiation effects/virology ; Transcription Factors/genetics/*metabolism ; Ultraviolet Rays ; Viral Proteins/genetics/*metabolism ; },
abstract = {Sulfolobus spindle-shaped virus 1 is the only UV-inducible member of the virus family Fuselloviridae. Originally isolated from Saccharolobus shibatae B12, it can also infect Saccharolobus solfataricus. Like the CI repressor of the bacteriophage λ, the SSV1-encoded F55 transcription repressor acts as a key regulator for the maintenance of the SSV1 carrier state. In particular, F55 binds to tandem repeat sequences located within the promoters of the early and UV-inducible transcripts. Upon exposure to UV light, a temporally coordinated pattern of gene expression is triggered. In the case of the better characterized bacteriophage λ, the switch from lysogenic to lytic development is regulated by a crosstalk between the virus encoded CI repressor and the host RecA, which regulates also the SOS response. For SSV1, instead, the regulatory mechanisms governing the switch from the carrier to the induced state have not been completely unravelled. In this study we have applied an integrated biochemical approach based on a variant of the EMSA assay coupled to mass spectrometry analyses to identify the proteins associated with F55 when bound to its specific DNA promoter sequences. Among the putative F55 interactors, we identified RadA and showed that the archaeal molecular components F55 and RadA are functional homologs of bacteriophage λ (factor CI) and Escherichia coli (RecA) system.},
}
@article {pmid32013868,
year = {2020},
author = {Zhang, RY and Zou, B and Yan, YW and Jeon, CO and Li, M and Cai, M and Quan, ZX},
title = {Design of targeted primers based on 16S rRNA sequences in meta-transcriptomic datasets and identification of a novel taxonomic group in the Asgard archaea.},
journal = {BMC microbiology},
volume = {20},
number = {1},
pages = {25},
pmid = {32013868},
issn = {1471-2180},
support = {2018YFC0310600//the National Key R&amp;D Program of China/International ; 31870109//National Natural Science Foundation of China/International ; 31170114//National Natural Science Foundation of China/International ; },
mesh = {Archaea/*classification/genetics ; DNA Primers/*genetics ; DNA, Archaeal/genetics ; DNA, Ribosomal/genetics ; Databases, Genetic ; Gene Expression Profiling ; High-Throughput Nucleotide Sequencing ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, RNA/*methods ; },
abstract = {BACKGROUND: Amplification of small subunit (SSU) rRNA genes with universal primers is a common method used to assess microbial populations in various environmental samples. However, owing to limitations in coverage of these universal primers, some microorganisms remain unidentified. The present study aimed to establish a method for amplifying nearly full-length SSU rRNA gene sequences of previously unidentified prokaryotes, using newly designed targeted primers via primer evaluation in meta-transcriptomic datasets.<br><br>METHODS: Primer binding regions of universal primer 8F/Arch21F for bacteria or archaea were used for primer evaluation of SSU rRNA sequences in meta-transcriptomic datasets. Furthermore, targeted forward primers were designed based on SSU rRNA reads from unclassified groups unmatched with the universal primer 8F/Arch21F, and these primers were used to amplify nearly full-length special SSU rRNA gene sequences along with universal reverse primer 1492R. Similarity and phylogenetic analysis were used to confirm their novel status.<br><br>RESULTS: Using this method, we identified unclassified SSU rRNA sequences that were not matched with universal primer 8F and Arch21F. A new group within the Asgard superphylum was amplified by the newly designed specific primer based on these unclassified SSU rRNA sequences by using mudflat samples.<br><br>CONCLUSION: We showed that using specific primers designed based on universal primer evaluation from meta-transcriptomic datasets, identification of novel taxonomic groups from a specific environment is possible.},
}
@article {pmid32006018,
year = {2020},
author = {Menéndez-Serra, M and Ontiveros, VJ and Triadó-Margarit, X and Alonso, D and Casamayor, EO},
title = {Dynamics and ecological distributions of the Archaea microbiome from inland saline lakes (Monegros Desert, Spain).},
journal = {FEMS microbiology ecology},
volume = {96},
number = {3},
pages = {},
doi = {10.1093/femsec/fiaa019},
pmid = {32006018},
issn = {1574-6941},
mesh = {*Archaea/genetics ; Biodiversity ; Lakes ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Spain ; },
abstract = {We characterized the rich Archaea microbiome of shallow inland lakes (Monegros Desert, NE Spain) by 16S rRNA gene tag sequencing covering a wide salinity range (0.1%-40% w/v) along 3 years. Up to 990 operational taxonomic units (OTUs; >97% identity) were detected allocated in 14 major archaeal phyla and heterogeneously distributed along the salt gradient. Dynamics and idiosyncratic ecological distributions were uncovered for the different phyla. A high genetic richness was observed for Woesearchaeota and Pacearchaeota (>370 OTUs each), followed by Halobacteria (105), Nanohaloarchaeota (62) and Thermoplasmata (19). Overall, the distribution of genetic richness was strongly correlated with environmental niche amplitude, but not with occurrence. We unveiled high occurrence for a very rich Woesearchaeota assemblage, and an unexpected positive correlation of Pacearchaeota abundance with salinity at >15% dissolved salt content. The estimated dynamic behaviour (temporal 'turnover' rates of presence/absence data) unveiled Thaumarchaeota and Halobacteria as the most dynamic groups, and Aenigmarchaeota and Thermoplasmata as the most stable. The DPANN Pacearchaeota, Woesearchaeota, and Nanohaloarchaeota showed intermediate rates, suggesting higher resilience to environmental perturbations. A rich and dynamic Archaea microbiome was unveiled, including unseen ecological traits for relevant members of the still largely unknown DPANN group, supporting a strong ecological differentiation between Pacearchaeota and Woesearchaeota.},
}
@article {pmid31999377,
year = {2020},
author = {Roy, C and Kumar, R and Datta, S},
title = {Comparative studies on ion-pair energetic, distribution among three domains of life: Archaea, eubacteria, and eukarya.},
journal = {Proteins},
volume = {88},
number = {7},
pages = {865-873},
doi = {10.1002/prot.25878},
pmid = {31999377},
issn = {1097-0134},
mesh = {Archaea/*chemistry ; Archaeal Proteins/*chemistry ; Bacteria/*chemistry ; Bacterial Proteins/*chemistry ; Crystallography, X-Ray ; Datasets as Topic ; Eukaryota/*chemistry ; Models, Molecular ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Protein Interaction Domains and Motifs ; Protein Stability ; Static Electricity ; Thermodynamics ; },
abstract = {Salt-bridges play a unique role in the structural and functional stability of proteins, especially under harsh environments. How these salt-bridges contribute to the overall thermodynamic stability of protein structure and function across different domains of life is elusive still date. To address the issue, statistical analyses on the energies of salt-bridges, involved in proteins' structure and function, are performed across three domains of life, that is, archaea, eubacteria, and eukarya. Results show that although the majority of salt-bridges are stable and conserved, yet the stability of archaeal proteins (∆∆Gnet = -5.06 ± 3.8) is much more than that of eubacteria (∆∆Gnet = -3.7 ± 2.9) and eukarya (∆∆Gnet = -3.54 ± 3.1). Unlike earlier study with archaea, in eukarya and eubacteria, not all buried salt-bridge in our dataset are stable. Buried salt-bridges play surprising role in protein stability, whose variations are clearly observed among these domains. Greater desolvation penalty of buried salt-bridges is compensated by stable network of salt-bridges apart from equal contribution of bridge and background energy terms. On the basis proteins' secondary structure, topology, and evolution, our observation shows that salt-bridges when present closer to each other in sequence tend to form a greater number. Overall, our comparative study provides insight into the role of specific electrostatic interactions in proteins from different domains of life, which we hope, would be useful for protein engineering and bioinformatics study.},
}
@article {pmid31994760,
year = {2020},
author = {Eichler, J},
title = {Modifying Post-Translational Modifications: A Strategy Used by Archaea for Adapting to Changing Environments?: Manipulating the Extent, Position, or Content of Post-Translational Modifications May Help Archaea Adapt to Environmental Change.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {42},
number = {3},
pages = {e1900207},
doi = {10.1002/bies.201900207},
pmid = {31994760},
issn = {1521-1878},
support = {2193/16//ISF-NSFC joint research program/International ; },
mesh = {Adaptation, Physiological/*physiology ; Amino Acid Sequence ; Archaea/*growth &amp; development/*metabolism ; Archaeal Proteins/*metabolism ; *Environment ; Glycosylation ; Methylation ; Phosphorylation/physiology ; Protein Processing, Post-Translational/*physiology ; },
abstract = {In concert with the selective pressures affecting protein folding and function in the extreme environments in which they can exist, proteins in Archaea have evolved to present permanent molecular adaptations at the amino acid sequence level. Such adaptations may not, however, suffice when Archaea encounter transient changes in their surroundings. Post-translational modifications offer a rapid and reversible layer of adaptation for proteins to cope with such situations. Here, it is proposed that Archaea further augment their ability to survive changing growth conditions by modifying the extent, position, and, where relevant, the composition of different post-translational modifications, as a function of the environment. Support for this hypothesis comes from recent reports describing how patterns of protein glycosylation, methylation, and other post-translational modifications of archaeal proteins are altered in response to environmental change. Indeed, adjusting post-translational modifications as a means to cope with environmental variability may also hold true beyond the Archaea.},
}
@article {pmid31949227,
year = {2020},
author = {Guo, H and Ma, L and Liang, Y and Hou, Z and Min, W},
title = {Response of ammonia-oxidizing Bacteria and Archaea to long-term saline water irrigation in alluvial grey desert soils.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {489},
pmid = {31949227},
issn = {2045-2322},
support = {41661055//The National Natural Science Foundation of China/International ; },
mesh = {Agricultural Irrigation/*methods ; Ammonia/*chemistry ; Archaea/*metabolism ; Archaeal Proteins/genetics/metabolism ; Bacteria/*metabolism ; Bacterial Proteins/genetics/metabolism ; DNA Copy Number Variations ; Ecosystem ; *Nitrification ; Saline Waters/*chemistry ; *Soil Microbiology ; },
abstract = {Soil nitrification via ammonia oxidation is a key ecosystem process in terrestrial environments, but little is known of how increasing irrigation of farmland soils with saline waters effects these processes. We investigated the effects of long-term irrigation with saline water on the abundances and community structures of ammonia-oxidizing bacteria (AOB) and archaea (AOA). Irrigation with brackish or saline water increased soil salinity (EC1:5) and NH4-N compared to irrigation with freshwater, while NO3-N, potential nitrification rates (PNR) and amoA gene copy numbers of AOA and AOB decreased markedly under irrigation regimes with saline waters. Moreover, irrigation with brackish water lowered AOA/AOB ratios. PNR was positively correlated with AOA and AOB amoA gene copy numbers across treatments. Saline and brackish water irrigation significantly increased the diversity of AOA, as noted by Shannon index values, while saline water irrigation markedly reduced AOB diversity. In addition, irrigation with brackish or fresh waters resulted in higher proportions of unclassified taxa in the AOB communities. However, irrigation with saline water led to higher proportions of unclassified taxa in the AOA communities along with the Candidatus Nitrosocaldus genus, as compared to soils irrigated with freshwater. AOA community structures were closely associated with soil salinity, NO3-N, and pH, while AOB communities were only significantly associated with NO3-N and pH. These results suggest that salinity was the dominant factor affecting the growth of ammonia-oxidizing microorganisms and community structure. These results can provide a scientific basis for further exploring the response mechanism of ammonia-oxidizing microorganisms and their roles in nitrogen transformation in alluvial grey desert soils of arid areas.},
}
@article {pmid31942065,
year = {2020},
author = {},
title = {The life of archaea.},
journal = {Nature},
volume = {577},
number = {7790},
pages = {294},
doi = {10.1038/d41586-020-00087-4},
pmid = {31942065},
issn = {1476-4687},
mesh = {*Archaea ; *Eukaryota ; Phylogeny ; Prokaryotic Cells ; },
}
@article {pmid31941956,
year = {2020},
author = {Besseling, MA and Hopmans, EC and Bale, NJ and Schouten, S and Damsté, JSS and Villanueva, L},
title = {The absence of intact polar lipid-derived GDGTs in marine waters dominated by Marine Group II: Implications for lipid biosynthesis in Archaea.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {294},
pmid = {31941956},
issn = {2045-2322},
mesh = {Archaea/classification/genetics/*metabolism ; Atlantic Ocean ; Chromatography, High Pressure Liquid ; Euryarchaeota/classification/genetics/metabolism ; Glyceryl Ethers/analysis/metabolism ; Lipids/analysis/*biosynthesis/isolation &amp; purification ; Mass Spectrometry ; Phylogeny ; RNA, Ribosomal, 16S/chemistry/metabolism ; Solid Phase Extraction ; },
abstract = {The marine pelagic archaeal community is dominated by three major groups, the marine group I (MGI) Thaumarchaeota, and the marine groups II and III (MGII and MGIII) Euryarchaeota. Studies of both MGI cultures and the environment have shown that the MGI core membrane lipids are predominantly composed of glycerol dibiphytanyl glycerol tetraether (GDGT) lipids and the diether lipid archaeol. However, there are no cultured representatives of MGII and III archaea and, therefore, both their membrane lipid composition and potential contribution to the marine archaeal lipid pool remain unknown. Here, we show that GDGTs present in suspended particulate matter of the (sub)surface waters of the North Atlantic Ocean and the coastal North Sea are derived from MGI archaea, and that MGII archaea do not significantly contribute to the pool of GDGTs and archaeol. This implies, in contrast to previous suggestions, that their lipids do not affect the widely used sea surface temperature proxy TEX86. These findings also indicate that MGII archaea are not able to produce any known archaeal lipids, implying that our understanding of the evolution of membrane lipid biosynthesis in Archaea is far from complete.},
}
@article {pmid31937639,
year = {2020},
author = {Barco, RA and Garrity, GM and Scott, JJ and Amend, JP and Nealson, KH and Emerson, D},
title = {A Genus Definition for Bacteria and Archaea Based on a Standard Genome Relatedness Index.},
journal = {mBio},
volume = {11},
number = {1},
pages = {},
pmid = {31937639},
issn = {2150-7511},
mesh = {Archaea/*classification ; Bacteria/*classification ; Classification/*methods ; DNA, Bacterial/genetics ; *Genome, Archaeal ; *Genome, Bacterial ; Genomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {Genus assignment is fundamental in the characterization of microbes, yet there is currently no unambiguous way to demarcate genera solely using standard genomic relatedness indices. Here, we propose an approach to demarcate genera that relies on the combined use of the average nucleotide identity, genome alignment fraction, and the distinction between type- and non-type species. More than 3,500 genomes representing type strains of species from >850 genera of either bacterial or archaeal lineages were tested. Over 140 genera were analyzed in detail within the taxonomic context of order/family. Significant genomic differences between members of a genus and type species of other genera in the same order/family were conserved in 94% of the cases. Nearly 90% (92% if polyphyletic genera are excluded) of the type strains were classified in agreement with current taxonomy. The 448 type strains that need reclassification directly impact 33% of the genera analyzed in detail. The results provide a first line of evidence that the combination of genomic indices provides added resolution to effectively demarcate genera within the taxonomic framework that is currently based on the 16S rRNA gene. We also identify the emergence of natural breakpoints at the genome level that can further help in the circumscription of taxa, increasing the proportion of directly impacted genera to at least 43% and pointing at inaccuracies on the use of the 16S rRNA gene as a taxonomic marker, despite its precision. Altogether, these results suggest that genomic coherence is an emergent property of genera in Bacteria and Archaea IMPORTANCE In recent decades, the taxonomy of Bacteria and Archaea, and therefore genus designation, has been largely based on the use of a single ribosomal gene, the 16S rRNA gene, as a taxonomic marker. We propose an approach to delineate genera that excludes the direct use of the 16S rRNA gene and focuses on a standard genome relatedness index, the average nucleotide identity. Our findings are of importance to the microbiology community because the emergent properties of Bacteria and Archaea that are identified in this study will help assign genera with higher taxonomic resolution.},
}
@article {pmid31926374,
year = {2020},
author = {Wang, C and Tang, S and He, X and Ji, G},
title = {The abundance and community structure of active ammonia-oxidizing archaea and ammonia-oxidizing bacteria shape their activities and contributions in coastal wetlands.},
journal = {Water research},
volume = {171},
number = {},
pages = {115464},
doi = {10.1016/j.watres.2019.115464},
pmid = {31926374},
issn = {1879-2448},
mesh = {*Ammonia ; *Archaea ; Bacteria ; China ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Soil Microbiology ; Wetlands ; },
abstract = {Aerobic ammonia oxidation, an important part of the global nitrogen cycle, is thought to be jointly driven by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in coastal wetlands. However, the activities and contributions of AOA and AOB in coastal wetlands have remained largely unknown. Here, we investigated the oxidation capability of AOA and AOB in four types of typical coastal wetlands (paddy, estuary, shallow and reed wetland) in the Bohai region in China using DNA-based stable-isotope probing (DNA-SIP), quantitative PCR and high-throughput sequencing techniques. We found that the community structure of AOB varied substantially, and the AOA structure was more stable across different coastal wetlands. The rate of AOA was 0.12, 0.84, 0.45 and 0.93 μg N g-1 soil d-1 in paddy, estuary, shallow and reed wetlands, and the rate of AOB was 5.61, 10.72, 0.74 and 1.16 μg N g-1 soil d-1, respectively. We found that the contribution of AOA gradually increased from paddy to estuary to shallow wetland and finally to reed wetland, with values of 2.03%, 7.25%, 37.53% and 44.51%, respectively. Our results provide new insight into the mechanisms of the differences in activities and the contributions of AOA and AOB in different coastal wetlands, and our findings may contribute to further understanding of the global nitrogen cycle.},
}
@article {pmid31920997,
year = {2019},
author = {Dekas, AE and Parada, AE and Mayali, X and Fuhrman, JA and Wollard, J and Weber, PK and Pett-Ridge, J},
title = {Characterizing Chemoautotrophy and Heterotrophy in Marine Archaea and Bacteria With Single-Cell Multi-isotope NanoSIP.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2682},
pmid = {31920997},
issn = {1664-302X},
abstract = {Characterizing and quantifying in situ metabolisms remains both a central goal and challenge for environmental microbiology. Here, we used a single-cell, multi-isotope approach to investigate the anabolic activity of marine microorganisms, with an emphasis on natural populations of Thaumarchaeota. After incubating coastal Pacific Ocean water with 13C-bicarbonate and 15N-amino acids, we used nanoscale secondary ion mass spectrometry (nanoSIMS) to isotopically screen 1,501 individual cells, and 16S rRNA amplicon sequencing to assess community composition. We established isotopic enrichment thresholds for activity and metabolic classification, and with these determined the percentage of anabolically active cells, the distribution of activity across the whole community, and the metabolic lifestyle-chemoautotrophic or heterotrophic-of each cell. Most cells (>90%) were anabolically active during the incubation, and 4-17% were chemoautotrophic. When we inhibited bacteria with antibiotics, the fraction of chemoautotrophic cells detected via nanoSIMS increased, suggesting archaea dominated chemoautotrophy. With fluorescence in situ hybridization coupled to nanoSIMS (FISH-nanoSIMS), we confirmed that most Thaumarchaeota were living chemoautotrophically, while bacteria were not. FISH-nanoSIMS analysis of cells incubated with dual-labeled (13C,15N-) amino acids revealed that most Thaumarchaeota cells assimilated amino-acid-derived nitrogen but not carbon, while bacteria assimilated both. This indicates that some Thaumarchaeota do not assimilate intact amino acids, suggesting intra-phylum heterogeneity in organic carbon utilization, and potentially their use of amino acids for nitrification. Together, our results demonstrate the utility of multi-isotope nanoSIMS analysis for high-throughput metabolic screening, and shed light on the activity and metabolism of uncultured marine archaea and bacteria.},
}
@article {pmid31913316,
year = {2020},
author = {Maus, D and Heinz, J and Schirmack, J and Airo, A and Kounaves, SP and Wagner, D and Schulze-Makuch, D},
title = {Methanogenic Archaea Can Produce Methane in Deliquescence-Driven Mars Analog Environments.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {6},
pmid = {31913316},
issn = {2045-2322},
support = {339231//EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))/International ; },
mesh = {Chemoautotrophic Growth ; Exobiology/*methods ; *Extraterrestrial Environment ; *Mars ; Methane/analysis/*metabolism ; Methanosarcina/*physiology ; Salts/*chemistry ; Water/*chemistry ; },
abstract = {The current understanding of the Martian surface indicates that briny environments at the near-surface are temporarily possible, e.g. in the case of the presumably deliquescence-driven Recurring Slope Lineae (RSL). However, whether such dynamic environments are habitable for terrestrial organisms remains poorly understood. This hypothesis was tested by developing a Closed Deliquescence System (CDS) consisting of a mixture of desiccated Martian Regolith Analog (MRA) substrate, salts, and microbial cells, which over the course of days became wetted through deliquescence. The methane produced via metabolic activity for three methanogenic archaea: Methanosarcina mazei, M. barkeri and M. soligelidi, was measured after exposing them to three different MRA substrates using either NaCl or NaClO4 as a hygroscopic salt. Our experiments showed that (1) M. soligelidi rapidly produced methane at 4 °C, (2) M. barkeri produced methane at 28 °C though not at 4 °C, (3) M. mazei was not metabolically reactivated through deliquescence, (4) none of the species produced methane in the presence of perchlorate, and (5) all species were metabolically most active in the phyllosilicate-containing MRA. These results emphasize the importance of the substrate, microbial species, salt, and temperature used in the experiments. Furthermore, we show here for the first time that water provided by deliquescence alone is sufficient to rehydrate methanogenic archaea and to reactivate their metabolism under conditions roughly analogous to the near-subsurface Martian environment.},
}
@article {pmid31900730,
year = {2020},
author = {Cavalier-Smith, T and Chao, EE},
title = {Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria).},
journal = {Protoplasma},
volume = {257},
number = {3},
pages = {621-753},
pmid = {31900730},
issn = {1615-6102},
support = {NE/E004156/1//Natural Environment Research Council/ ; },
mesh = {Archaea/*chemistry ; Biological Evolution ; Eukaryota/*chemistry ; *Phylogeny ; Ribosomes/*chemistry ; },
abstract = {Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.},
}
@article {pmid31889259,
year = {2020},
author = {Knüppel, R and Fenk, M and Jüttner, M and Ferreira-Cerca, S},
title = {In Vivo RNA Chemical Footprinting Analysis in Archaea.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2106},
number = {},
pages = {193-208},
doi = {10.1007/978-1-0716-0231-7_12},
pmid = {31889259},
issn = {1940-6029},
mesh = {Archaea/chemistry/genetics ; Archaeal Proteins/chemistry/*metabolism ; *Molecular Probe Techniques ; *RNA Folding ; RNA, Archaeal/chemistry/genetics/*metabolism ; RNA-Binding Proteins/chemistry/*metabolism ; },
abstract = {RNA structural conformation and dynamics govern the functional properties of all RNA/RNP. Accordingly, defining changes of RNA structure and dynamics in various conditions may provide detailed insight into how RNA structural properties regulate the function of RNA/RNP. Traditional chemical footprinting analysis using chemical modifiers allows to sample the dynamics and conformation landscape of diverse RNA/RNP. However, many chemical modifiers are limited in their capacity to provide unbiased information reflecting the in vivo RNA/RNP structural landscape. In the recent years, the development of selective-2'-hydroxyl acylation analyzed by primer extension (SHAPE) methodology that uses powerful new chemical modifiers has significantly improved in vitro and in vivo structural probing of secondary and tertiary interactions of diverse RNA species at the single nucleotide level.Although the original discovery of Archaea as an independent domain of life is intimately linked to the technological development of RNA analysis, our understanding of in vivo RNA structural conformation and dynamics in this domain of life remains scarce.This protocol describes the in vivo use of SHAPE chemistry in two evolutionary divergent model Archaea, Sulfolobus acidocaldarius and Haloferax volcanii.},
}
@article {pmid31884971,
year = {2019},
author = {Coutinho, FH and Edwards, RA and Rodríguez-Valera, F},
title = {Charting the diversity of uncultured viruses of Archaea and Bacteria.},
journal = {BMC biology},
volume = {17},
number = {1},
pages = {109},
pmid = {31884971},
issn = {1741-7007},
mesh = {Archaea/*virology ; Bacteria/*virology ; Bacteriophages/*genetics ; *Genome, Viral ; *Microbiota ; Phylogeny ; },
abstract = {BACKGROUND: Viruses of Archaea and Bacteria are among the most abundant and diverse biological entities on Earth. Unraveling their biodiversity has been challenging due to methodological limitations. Recent advances in culture-independent techniques, such as metagenomics, shed light on the unknown viral diversity, revealing thousands of new viral nucleotide sequences at an unprecedented scale. However, these novel sequences have not been properly classified and the evolutionary associations between them were not resolved.<br><br>RESULTS: Here, we performed phylogenomic analysis of nearly 200,000 viral nucleotide sequences to establish GL-UVAB: Genomic Lineages of Uncultured Viruses of Archaea and Bacteria. The pan-genome content of the identified lineages shed light on some of their infection strategies, potential to modulate host physiology, and mechanisms to escape host resistance systems. Furthermore, using GL-UVAB as a reference database for annotating metagenomes revealed elusive habitat distribution patterns of viral lineages and environmental drivers of community composition.<br><br>CONCLUSIONS: These findings provide insights about the genomic diversity and ecology of viruses of prokaryotes. The source code used in these analyses is freely available at https://sourceforge.net/projects/gluvab/.},
}
@article {pmid31869713,
year = {2020},
author = {Li, M and Huang, Y and Yang, Y and Wang, H and Hu, L and Zhong, H and He, Z},
title = {Heavy metal ions removed from imitating acid mine drainages with a thermoacidophilic archaea: Acidianus manzaensis YN25.},
journal = {Ecotoxicology and environmental safety},
volume = {190},
number = {},
pages = {110084},
doi = {10.1016/j.ecoenv.2019.110084},
pmid = {31869713},
issn = {1090-2414},
mesh = {Acidianus/*physiology ; Adsorption ; Archaea/metabolism ; *Biodegradation, Environmental ; Heavy Ions ; Hydrogen-Ion Concentration ; Ions ; Metals, Heavy/analysis/metabolism ; *Mining ; Spectroscopy, Fourier Transform Infrared ; Water Pollutants, Chemical/analysis/*metabolism ; },
abstract = {Metals in acid mine drainages (AMD) have posed a great threat to environment, and in situ economic environment-friendly remediation technologies need to be developed. Moreover, the effects of acidophiles on biosorption and migrating behaviors of metals in AMD have not been previously reported. In this study, the extremely thermoacidophilic Archaea, Acidianus manzaensis YN25 (A. manzaensis YN25) was used as a bio-adsorbent to adsorb metals (Cu2+, Ni2+, Cd2+ and Zn2+) from acidic solutions which were taken to imitate AMD. The values of their maximum biosorption capacities at both high (1 mM) and low (0.1 mM) metal concentrations followed the order: Cu2+ > Ni2+ > Cd2+ > Zn2+. With the elevations of temperature and pH value, the adsorption amounts of metals increased. The results also indicated that A. manzaensis YN25 had the highest adsorption affinity to Cu2+ in coexisting system of quaternary metals. Acid-base titration data revealed that carboxyl and phosphoryl groups provided adsorption sites for metals via deprotonation. Fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS) further corroborated that amino played an important role in the biosorption process. The fitted Langmuir model illustrated monolayer adsorption occurring on cell surface. The possible adsorption mechanism of A. manzaensis YN25 mainly involved in electrostatic attraction and complexes formation. This study gives a profound insight into the biosorption behavior of heavy metals in acidic solution by thermoacidophilic Archaea and provides a probable novel strategy for in situ remediation of heavy metals pollution in AMD.},
}
@article {pmid31856202,
year = {2019},
author = {Hernandez-Guerrero, R and Galán-Vásquez, E and Pérez-Rueda, E},
title = {The protein architecture in Bacteria and Archaea identifies a set of promiscuous and ancient domains.},
journal = {PloS one},
volume = {14},
number = {12},
pages = {e0226604},
pmid = {31856202},
issn = {1932-6203},
mesh = {Archaea/genetics ; Archaeal Proteins/*chemistry/genetics/metabolism ; Bacteria/genetics ; Bacterial Proteins/*chemistry/genetics/metabolism ; Binding Sites ; Conserved Sequence ; *Evolution, Molecular ; Protein Binding ; Proteome ; },
abstract = {In this work, we describe a systematic comparative genomic analysis of promiscuous domains in genomes of Bacteria and Archaea. A quantitative measure of domain promiscuity, the weighted domain architecture score (WDAS), was used and applied to 1317 domains in 1320 genomes of Bacteria and Archaea. A functional analysis associated with the WDAS per genome showed that 18 of 50 functional categories were identified as significantly enriched in the promiscuous domains; in particular, small-molecule binding domains, transferases domains, DNA binding domains (transcription factors), and signal transduction domains were identified as promiscuous. In contrast, non-promiscuous domains were identified as associated with 6 of 50 functional categories, and the category Function unknown was enriched. In addition, the WDASs of 52 domains correlated with genome size, i.e., WDAS values decreased as the genome size increased, suggesting that the number of combinations at larger domains increases, including domains in the superfamilies Winged helix-turn-helix and P-loop-containing nucleoside triphosphate hydrolases. Finally, based on classification of the domains according to their ancestry, we determined that the set of 52 promiscuous domains are also ancient and abundant among all the genomes, in contrast to the non-promiscuous domains. In summary, we consider that the association between these two classes of protein domains (promiscuous and non-promiscuous) provides bacterial and archaeal cells with the ability to respond to diverse environmental challenges.},
}
@article {pmid31854886,
year = {2019},
author = {Bao, QL and Wang, FH and Bao, WK and Huang, YZ},
title = {[Effects of Rice Straw Addition on Methanogenic Archaea and Bacteria in Two Paddy Soils].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {40},
number = {9},
pages = {4202-4212},
doi = {10.13227/j.hjkx.201901195},
pmid = {31854886},
issn = {0250-3301},
mesh = {*Archaea ; Bacteria ; Methane ; *Oryza ; RNA, Ribosomal, 16S ; Soil ; *Soil Microbiology ; },
abstract = {Rice straw (RS) returning has an important effect on CH4 emission in rice paddy soil. In the present study, two paddy soil types from Jiangxi (JX) and Guangdong (GD), respectively, with different amounts of added RS were incubated through microcosmic anaerobic incubation experiments to investigate the responses of methanogenic archaea and bacteria communities after relatively long-term incubation. The different amounts of added RS affected methanogenic archaea community structures in the JX soil to some extent but did not affect the GD soil. The mcrA gene copy number increased with an increase in RS amount in both soils. Under the same amount of RS, the copy number of this gene in the JX soil was greater than that in the GD soil. In addition, significant positive correlations were shown between the RS amount and the copy number of the mcrA gene, and the response of the copy number was more sensitive to the RS amount in the JX soil. Obvious differences in methanogenic archaea community structures were shown between two soils. Methanosarcinaceae, Methanocellaceae, Methanomicrobiaceae, Methanobacteriaceae, and unknown microorganism (494 bp) were detected in the JX soil, and Methanobacteriaceae, Methanosarcinaceae, and Methanocellaceae were observed in the GD soil. The bacterial communities exhibited obvious differences between the two soil types after 180 days of incubation. The bacterial diversity in the GD soil was higher than that in the JX soil, although the amounts of dominant bacteria in the JX soil, including Bacillus, Desulfovirgula, Thermosporothrix, Acidobacteria/Gp1, Acidobacteria/Gp3, and Ktedonobacter, were higher than those of the GD soil, including Longilinea, Acidobacteria/Gp6, Bellilinea, and Thermosporothrix. RS application promoted the growth of methanogenic archaea as important substrates. Moreover, different structures of methanogens and bacteria were shown between the two soil types after relatively long-term incubation.},
}
@article {pmid31854584,
year = {2019},
author = {Guo, JL and Liu, Y and Wei, WX and Ge, TD and Wang, GJ},
title = {[Impact of Dicyandiamide (DCD) and 3,4-Dimethylpyrazole Phosphate (DMPP) on Ammonia-oxidizing Bacteria and Archaea in a Vegetable Planting Soil].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {40},
number = {11},
pages = {5142-5150},
doi = {10.13227/j.hjkx.201902031},
pmid = {31854584},
issn = {0250-3301},
mesh = {Ammonia ; *Archaea ; Bacteria ; Guanidines ; Nitrification ; Oxidation-Reduction ; Phosphates ; Phylogeny ; *Pyrazoles ; *Soil ; *Soil Microbiology ; *Vegetables ; },
abstract = {Nitrification inhibitors (NIs) dicyandiamide (DCD) and 3,4-dimethylpyrazole phosphate (DMPP) showed significant effects in the inhibition of nitrification and the improvement of the utilization efficiency of nitrogen fertilizer in agricultural soils. However, the effects of different NIs on ammonia-oxidizing bacteria (AOB) and archaea (AOA) is still unclear. To verify the inhibitory effect of DCD and DMPP on AOB and AOA, a pot experiment was performed, including Urea, Urea+DCD, and Urea+DMPP treatments. The dynamics of NH4+-N and NO3--N and nitrification potential among different treatments were measured. In addition, real-time PCR and high-throughput sequencing approaches were applied to investigate the changes in the AOB and AOA population abundance and composition. The results revealed that the concentrations of NH4+-N in Urea+DCD and Urea+DMPP treatments were 213% and 675% higher than that in the CK treatment, respectively. However, the concentrations of NO3--N and the nitrification potentials were 13.3% and 37.2%, and 20.4% and 82.4% lower than that in CK treatment, respectively; Furthermore, the copy numbers of the bacterial and archaeal amoA gene were 51.2% and 56.5%, and 6.0% and 27.0% lower than that in the CK treatment, respectively. However, the diversity indexes of AOB and AOA communities, including evenness and richness, exhibited no significant differences after addition of DCD and DMPP. The nork-environmental-samples, unclassified-Nitrosomonadaceae, unclassified-Bacteria, and Nitrosospira, were the predominant genera of the AOB community. The no rank-Crenarchaeota, no rank-environmental-samples and Nitrososphaera were the predominant groups in the AOA community. Summarily, application of DCD and DMPP significantly delayed the transformation of NH4+-N, decreased the formation of NO3--N, inhibited the abundance and changed the composition of AOB and AOA communities. DMPP had a stronger inhibitory effect on nitrification, and on AOB and AOA than DCD. Therefore, compared with DCD, DMPP had a better application prospect regarding the improvement of the nitrogen utilization efficiency in vegetable soil.},
}
@article {pmid31836857,
year = {2020},
author = {Gribaldo, S and Brochier-Armanet, C},
title = {Evolutionary relationships between archaea and eukaryotes.},
journal = {Nature ecology &amp; evolution},
volume = {4},
number = {1},
pages = {20-21},
pmid = {31836857},
issn = {2397-334X},
mesh = {*Archaea ; Biological Evolution ; *Eukaryota ; Evolution, Molecular ; Phylogeny ; },
}
@article {pmid31828323,
year = {2020},
author = {Jüttner, M and Weiß, M and Ostheimer, N and Reglin, C and Kern, M and Knüppel, R and Ferreira-Cerca, S},
title = {A versatile cis-acting element reporter system to study the function, maturation and stability of ribosomal RNA mutants in archaea.},
journal = {Nucleic acids research},
volume = {48},
number = {4},
pages = {2073-2090},
pmid = {31828323},
issn = {1362-4962},
mesh = {Gene Regulatory Networks/*genetics ; Haloferax volcanii/genetics ; Mutation/genetics ; Phylogeny ; RNA Precursors/genetics ; RNA Processing, Post-Transcriptional/*genetics ; RNA Stability/genetics ; RNA, Archaeal/genetics ; RNA, Ribosomal/*genetics ; Ribosomes/*genetics ; },
abstract = {General molecular principles of ribosome biogenesis have been well explored in bacteria and eukaryotes. Collectively, these studies have revealed important functional differences and few similarities between these processes. Phylogenetic studies suggest that the information processing machineries from archaea and eukaryotes are evolutionary more closely related than their bacterial counterparts. These observations raise the question of how ribosome synthesis in archaea may proceed in vivo. In this study, we describe a versatile plasmid-based cis-acting reporter system allowing to analyze in vivo the consequences of ribosomal RNA mutations in the model archaeon Haloferax volcanii. Applying this system, we provide evidence that the bulge-helix-bulge motif enclosed within the ribosomal RNA processing stems is required for the formation of archaeal-specific circular-pre-rRNA intermediates and mature rRNAs. In addition, we have collected evidences suggesting functional coordination of the early steps of ribosome synthesis in H. volcanii. Together our investigation describes a versatile platform allowing to generate and functionally analyze the fate of diverse rRNA variants, thereby paving the way to better understand the cis-acting molecular determinants necessary for archaeal ribosome synthesis, maturation, stability and function.},
}
@article {pmid31827386,
year = {2019},
author = {Zheng, P and Wang, C and Zhang, X and Gong, J},
title = {Community Structure and Abundance of Archaea in a Zostera marina Meadow: A Comparison between Seagrass-Colonized and Bare Sediment Sites.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2019},
number = {},
pages = {5108012},
pmid = {31827386},
issn = {1472-3654},
mesh = {Archaea/classification/genetics/*growth &amp; development/*isolation &amp; purification ; Biodiversity ; Genes, Archaeal ; Genes, rRNA ; Geologic Sediments/*microbiology ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Zosteraceae/*growth &amp; development ; },
abstract = {Seagrass colonization alters sediment physicochemical properties by depositing seagrass fibers and releasing organic carbon and oxygen from the roots. How this seagrass colonization-induced spatial heterogeneity affects archaeal community structure and abundance remains unclear. In this study, we investigated archaeal abundance, diversity, and composition in both vegetated and adjacent bare surface sediments of a Zostera marina meadow. High-throughput sequencing of 16S rDNA showed that Woesearchaeota, Bathyarchaeota, and Thaumarchaeota were the most abundant phyla across all samples, accounting for approximately 42%, 21%, and 17% of the total archaeal communities, respectively. In terms of relative abundance, Woesearchaeota and Bathyarchaeota were not significantly different between these two niches; however, specific subclades (Woese-3, Woese-21, Bathy-6, Bathy-18) were significantly enriched in vegetated sediments (P < 0.05), while Thaumarchaeota was favored in unvegetated sites (P = 0.02). The quantification of archaeal 16S rRNA genes showed that the absolute abundance of the whole archaeal community, Bathyarchaeota, and Woese-3, Woese-10, Woese-13, and Woese-21 was significantly more abundant in vegetated sediments than in bare sediments (P < 0.05). Our study expands the available knowledge of the distribution patterns and niche preferences of archaea in seagrass systems, especially for the different subclades of Woesearchaeota and Bathyarchaeota, in terms of both relative proportions and absolute quantities.},
}
@article {pmid31819085,
year = {2019},
author = {Togo, AH and Grine, G and Khelaifia, S and des Robert, C and Brevaut, V and Caputo, A and Baptiste, E and Bonnet, M and Levasseur, A and Drancourt, M and Million, M and Raoult, D},
title = {Culture of Methanogenic Archaea from Human Colostrum and Milk.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {18653},
pmid = {31819085},
issn = {2045-2322},
mesh = {Animals ; Body Mass Index ; Breast Feeding/*adverse effects ; Chemoautotrophic Growth/genetics ; Colostrum/*microbiology ; DNA, Archaeal/genetics/isolation &amp; purification ; Euryarchaeota/genetics/pathogenicity ; Feces/microbiology ; Female ; Humans ; Infant ; Methanobrevibacter/genetics/*isolation &amp; purification/pathogenicity ; Microbiota/genetics ; Milk, Human/*microbiology ; Mothers ; Pregnancy ; },
abstract = {Archaeal sequences have been detected in human colostrum and milk, but no studies have determined whether living archaea are present in either of these fluids. Methanogenic archaea are neglected since they are not detected by usual molecular and culture methods. By using improved DNA detection protocols and microbial culture techniques associated with antioxidants previously developed in our center, we investigated the presence of methanogenic archaea using culture and specific Methanobrevibacter smithii and Methanobrevibacter oralis real-time PCR in human colostrum and milk. M. smithii was isolated from 3 colostrum and 5 milk (day 10) samples. M. oralis was isolated from 1 milk sample. For 2 strains, the genome was sequenced, and the rhizome was similar to that of strains previously isolated from the human mouth and gut. M. smithii was detected in the colostrum or milk of 5/13 (38%) and 37/127 (29%) mothers by culture and qPCR, respectively. The different distribution of maternal body mass index according to the detection of M. smithii suggested an association with maternal metabolic phenotype. M. oralis was not detected by molecular methods. Our results suggest that breastfeeding may contribute to the vertical transmission of these microorganisms and may be essential to seed the infant's microbiota with these neglected critical commensals from the first hour of life.},
}
@article {pmid31801875,
year = {2019},
author = {Prakash, D and Iyer, PR and Suharti, S and Walters, KA and Santiago-Martinez, MG and Golbeck, JH and Murakami, KS and Ferry, JG},
title = {Structure and function of an unusual flavodoxin from the domain Archaea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {116},
number = {51},
pages = {25917-25922},
pmid = {31801875},
issn = {1091-6490},
support = {P41 GM103485/GM/NIGMS NIH HHS/United States ; R01 GM087350/GM/NIGMS NIH HHS/United States ; },
mesh = {Acetates/metabolism ; Bacterial Proteins/chemistry ; Binding Sites ; Cloning, Molecular ; Crystallography, X-Ray ; Ferredoxins/chemistry/metabolism ; Flavin Mononucleotide/chemistry ; Flavodoxin/*chemistry/genetics/isolation &amp; purification/*metabolism ; Flavoproteins/chemistry ; Global Warming ; Hydroquinones ; Methane/metabolism ; Methanosarcina/*metabolism ; Models, Molecular ; Oxidation-Reduction ; Protein Conformation ; },
abstract = {Flavodoxins, electron transfer proteins essential for diverse metabolisms in microbes from the domain Bacteria, are extensively characterized. Remarkably, although genomic annotations of flavodoxins are widespread in microbes from the domain Archaea, none have been isolated and characterized. Herein is described the structural, biochemical, and physiological characterization of an unusual flavodoxin (FldA) from Methanosarcina acetivorans, an acetate-utilizing methane-producing microbe of the domain Archaea In contrast to all flavodoxins, FldA is homodimeric, markedly less acidic, and stabilizes an anionic semiquinone. The crystal structure reveals an flavin mononucleotide (FMN) binding site unique from all other flavodoxins that provides a rationale for stabilization of the anionic semiquinone and a remarkably low reduction potentials for both the oxidized/semiquinone (-301 mV) and semiquinone/hydroquinone couples (-464 mV). FldA is up-regulated in acetate-grown versus methanol-grown cells and shown here to substitute for ferredoxin in mediating the transfer of low potential electrons from the carbonyl of acetate to the membrane-bound electron transport chain that generates ion gradients driving ATP synthesis. FldA offers potential advantages over ferredoxin by (i) sparing iron for abundant iron-sulfur proteins essential for acetotrophic growth and (ii) resilience to oxidative damage.},
}
@article {pmid31792218,
year = {2019},
author = {Zhu, Q and Mai, U and Pfeiffer, W and Janssen, S and Asnicar, F and Sanders, JG and Belda-Ferre, P and Al-Ghalith, GA and Kopylova, E and McDonald, D and Kosciolek, T and Yin, JB and Huang, S and Salam, N and Jiao, JY and Wu, Z and Xu, ZZ and Cantrell, K and Yang, Y and Sayyari, E and Rabiee, M and Morton, JT and Podell, S and Knights, D and Li, WJ and Huttenhower, C and Segata, N and Smarr, L and Mirarab, S and Knight, R},
title = {Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {5477},
pmid = {31792218},
issn = {2041-1723},
support = {P30 MH062512/MH/NIMH NIH HHS/United States ; },
mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; *Evolution, Molecular ; *Genome, Archaeal ; *Genome, Bacterial ; *Phylogeny ; },
abstract = {Rapid growth of genome data provides opportunities for updating microbial evolutionary relationships, but this is challenged by the discordant evolution of individual genes. Here we build a reference phylogeny of 10,575 evenly-sampled bacterial and archaeal genomes, based on a comprehensive set of 381 markers, using multiple strategies. Our trees indicate remarkably closer evolutionary proximity between Archaea and Bacteria than previous estimates that were limited to fewer "core" genes, such as the ribosomal proteins. The robustness of the results was tested with respect to several variables, including taxon and site sampling, amino acid substitution heterogeneity and saturation, non-vertical evolution, and the impact of exclusion of candidate phyla radiation (CPR) taxa. Our results provide an updated view of domain-level relationships.},
}
@article {pmid31787176,
year = {2019},
author = {Islam, GM and Vi, P and Gilbride, KA},
title = {Functional relationship between ammonia-oxidizing bacteria and ammonia-oxidizing archaea populations in the secondary treatment system of a full-scale municipal wastewater treatment plant.},
journal = {Journal of environmental sciences (China)},
volume = {86},
number = {},
pages = {120-130},
doi = {10.1016/j.jes.2019.04.031},
pmid = {31787176},
issn = {1001-0742},
mesh = {Ammonia/*metabolism ; Archaea/*genetics ; Bacteria/genetics ; Denaturing Gradient Gel Electrophoresis ; Sewage/*microbiology ; Waste Disposal, Fluid/*methods ; Waste Water/*microbiology ; Water Pollutants, Chemical/*metabolism ; },
abstract = {The abundance of ammonia-oxidizing bacteria and archaea and their amoA genes from the aerobic activated sludge tanks, recycled sludge and anaerobic digesters of a full-scale wastewater treatment plant (WWTP) was determined. Polymerase chain reaction and denaturing gradient gel electrophoresis were used to generate diversity profiles, which showed that each population had a consistent profile although the abundance of individual members varied. In the aerobic tanks, the ammonia-oxidizing bacterial (AOB) population was more than 350 times more abundant than the ammonia-oxidizing archaeal (AOA) population, however in the digesters, the AOA population was more than 10 times more abundant. Measuring the activity of the amoA gene expression of the two populations using RT-PCR also showed that the AOA amoA gene was more active in the digesters than in the activated sludge tanks. Using batch reactors and ddPCR, amoA activity could be measured and it was found that when the AOB amoA activity was inhibited in the anoxic reactors, the expression of the AOA amoA gene increased fourfold. This suggests that these two populations may have a cooperative relationship for the oxidation of ammonia.},
}
@article {pmid31754204,
year = {2020},
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 = {Correction: A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.).},
journal = {The ISME journal},
volume = {14},
number = {3},
pages = {878},
doi = {10.1038/s41396-019-0556-z},
pmid = {31754204},
issn = {1751-7370},
abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.},
}
@article {pmid31745137,
year = {2019},
author = {Paula, FS and Chin, JP and Schnürer, A and Müller, B and Manesiotis, P and Waters, N and Macintosh, KA and Quinn, JP and Connolly, J and Abram, F and McGrath, JW and O'Flaherty, V},
title = {The potential for polyphosphate metabolism in Archaea and anaerobic polyphosphate formation in Methanosarcina mazei.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {17101},
pmid = {31745137},
issn = {2045-2322},
mesh = {Anaerobiosis ; Archaeal Proteins/genetics/*metabolism ; Methanosarcina/*growth &amp; development/*metabolism ; Phosphotransferases (Phosphate Group Acceptor)/*metabolism ; Polyphosphates/*metabolism ; },
abstract = {Inorganic polyphosphate (polyP) is ubiquitous across all forms of life, but the study of its metabolism has been mainly confined to bacteria and yeasts. Few reports detail the presence and accumulation of polyP in Archaea, and little information is available on its functions and regulation. Here, we report that homologs of bacterial polyP metabolism proteins are present across the major taxa in the Archaea, suggesting that archaeal populations may have a greater contribution to global phosphorus cycling than has previously been recognised. We also demonstrate that polyP accumulation can be induced under strictly anaerobic conditions, in response to changes in phosphate (Pi) availability, i.e. Pi starvation, followed by incubation in Pi replete media (overplus), in cells of the methanogenic archaeon Methanosarcina mazei. Pi-starved M. mazei cells increased transcript abundance of the alkaline phosphatase (phoA) gene and of the high-affinity phosphate transport (pstSCAB-phoU) operon: no increase in polyphosphate kinase 1 (ppk1) transcript abundance was observed. Subsequent incubation of Pi-starved M. mazei cells under Pi replete conditions, led to a 237% increase in intracellular polyphosphate content and a > 5.7-fold increase in ppk1 gene transcripts. Ppk1 expression in M. mazei thus appears not to be under classical phosphate starvation control.},
}
@article {pmid31739075,
year = {2020},
author = {Dame-Teixeira, N and de Cena, JA and Côrtes, DA and Belmok, A and Dos Anjos Borges, LG and Marconatto, L and Giongo, A and Kyaw, CM},
title = {Presence of Archaea in dental caries biofilms.},
journal = {Archives of oral biology},
volume = {110},
number = {},
pages = {104606},
doi = {10.1016/j.archoralbio.2019.104606},
pmid = {31739075},
issn = {1879-1506},
mesh = {*Archaea/genetics/isolation &amp; purification ; Bacteria ; *Biofilms ; *DNA, Bacterial/analysis ; *Dental Caries/microbiology ; Humans ; Phylogeny ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; },
abstract = {OBJECTIVE: Although the prevalence and functions associated with members of Bacteria are well known in dental caries, the role of Archaea in cariogenic biofilms has not been studied yet.<br><br>DESIGN: To detect the presence of Archaea in dental caries, a triplicate of carious dentine samples and duplicate of supragingival biofilms were collected, total microbial DNA was extracted and the composition of the microbiota was investigated. Total DNA was submitted to 16S rRNA gene amplification using universal prokaryotic primers; amplicons were sequenced by high-throughput DNA sequencing. As a second strategy to detect Archaea, a representative sample of caries was chosen and other PCR reactions were performed using specific primers targeting the archaeal 16S rRNA gene; amplicons were cloned and sequenced. Annotation of sequences was performed using SILVA database and the relative abundance of genus level OTUs was calculated.<br><br>RESULTS: The high-throughput sequencing method detected archaeal sequences in all samples (identified as group I.1c of the phylum Thaumarchaeota), although in a very low abundance (≤0.03 % of the total sequences). For the second strategy, 14 archaeal clones were detected, with an OTU affiliated to Methanocella clade, and another one affiliated to group I.1b of the phylum Thaumarchaeota.<br><br>CONCLUSIONS: Archaeal sequences were detected in dental caries and biofilms from surfaces without caries lesions. DNA sequences of Thaumarchaeota were also identified, showing that overall archaeal diversity in the human oral cavity could be currently underestimated and not restricted to methanogens.},
}
@article {pmid31712737,
year = {2020},
author = {Brewer, TE and Albertsen, M and Edwards, A and Kirkegaard, RH and Rocha, EPC and Fierer, N},
title = {Unlinked rRNA genes are widespread among bacteria and archaea.},
journal = {The ISME journal},
volume = {14},
number = {2},
pages = {597-608},
pmid = {31712737},
issn = {1751-7370},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; Environmental Microbiology ; Gastrointestinal Microbiome ; Genes, rRNA ; Humans ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S ; rRNA Operon/*genetics ; },
abstract = {Ribosomes are essential to cellular life and the genes for their RNA components are the most conserved and transcribed genes in bacteria and archaea. Ribosomal RNA genes are typically organized into a single operon, an arrangement thought to facilitate gene regulation. In reality, some bacteria and archaea do not share this canonical rRNA arrangement-their 16S and 23S rRNA genes are separated across the genome and referred to as "unlinked". This rearrangement has previously been treated as an anomaly or a byproduct of genome degradation in intracellular bacteria. Here, we leverage complete genome and long-read metagenomic data to show that unlinked 16S and 23S rRNA genes are more common than previously thought. Unlinked rRNA genes occur in many phyla, most significantly within Deinococcus-Thermus, Chloroflexi, and Planctomycetes, and occur in differential frequencies across natural environments. We found that up to 41% of rRNA genes in soil were unlinked, in contrast to the human gut, where all sequenced rRNA genes were linked. The frequency of unlinked rRNA genes may reflect meaningful life history traits, as they tend to be associated with a mix of slow-growing free-living species and intracellular species. We speculate that unlinked rRNA genes may confer selective advantages in some environments, though the specific nature of these advantages remains undetermined and worthy of further investigation. More generally, the prevalence of unlinked rRNA genes in poorly-studied taxa serves as a reminder that paradigms derived from model organisms do not necessarily extend to the broader diversity of bacteria and archaea.},
}
@article {pmid31712277,
year = {2020},
author = {Johnsen, U and Sutter, JM and Reinhardt, A and Pickl, A and Wang, R and Xiang, H and Schönheit, P},
title = {d-Ribose Catabolism in Archaea: Discovery of a Novel Oxidative Pathway in Haloarcula Species.},
journal = {Journal of bacteriology},
volume = {202},
number = {3},
pages = {},
pmid = {31712277},
issn = {1098-5530},
mesh = {Arabinose/metabolism ; Archaea/*metabolism ; Haloarcula/*metabolism ; Oxidation-Reduction ; Ribose/*metabolism ; Xylose/metabolism ; },
abstract = {The Haloarcula species H. marismortui and H. hispanica were found to grow on d-ribose, d-xylose, and l-arabinose. Here, we report the discovery of a novel promiscuous oxidative pathway of pentose degradation based on genome analysis, identification and characterization of enzymes, transcriptional analysis, and growth experiments with knockout mutants. Together, the data indicate that in Haloarcula spp., d-ribose, d-xylose, and l-arabinose were degraded to α-ketoglutarate involving the following enzymes: (i) a promiscuous pentose dehydrogenase that catalyzed the oxidation of d-ribose, d-xylose, and l-arabinose; (ii) a promiscuous pentonolactonase that was involved in the hydrolysis of ribonolactone, xylonolactone, and arabinolactone; (iii) a highly specific dehydratase, ribonate dehydratase, which catalyzed the dehydration of ribonate, and a second enzyme, a promiscuous xylonate/gluconate dehydratase, which was involved in the conversion of xylonate, arabinonate, and gluconate. Phylogenetic analysis indicated that the highly specific ribonate dehydratase constitutes a novel sugar acid dehydratase family within the enolase superfamily; and (iv) finally, 2-keto-3-deoxypentanonate dehydratase and α-ketoglutarate semialdehyde dehydrogenase catalyzed the conversion of 2-keto-3-deoxypentanonate to α-ketoglutarate via α-ketoglutarate semialdehyde. We conclude that the expanded substrate specificities of the pentose dehydrogenase and pentonolactonase toward d-ribose and ribonolactone, respectively, and the presence of a highly specific ribonate dehydratase are prerequisites of the oxidative degradation of d-ribose in Haloarcula spp. This is the first characterization of an oxidative degradation pathway of d-ribose to α-ketoglutarate in archaea.IMPORTANCE The utilization and degradation of d-ribose in archaea, the third domain of life, have not been analyzed so far. We show that Haloarcula species utilize d-ribose, which is degraded to α-ketoglutarate via a novel oxidative pathway. Evidence is presented that the oxidative degradation of d-ribose involves novel promiscuous enzymes, pentose dehydrogenase and pentonolactonase, and a novel sugar acid dehydratase highly specific for ribonate. This is the first report of an oxidative degradation pathway of d-ribose in archaea, which differs from the canonical nonoxidative pathway of d-ribose degradation reported for most bacteria. The data contribute to our understanding of the unusual sugar degradation pathways and enzymes in archaea.},
}
@article {pmid31709520,
year = {2020},
author = {Zhao, C and Lyu, Z and Long, F and Akinyemi, T and Manakongtreecheep, K and Söll, D and Whitman, WB and Vinyard, DJ and Liu, Y},
title = {The Nbp35/ApbC homolog acts as a nonessential [4Fe-4S] transfer protein in methanogenic archaea.},
journal = {FEBS letters},
volume = {594},
number = {5},
pages = {924-932},
doi = {10.1002/1873-3468.13673},
pmid = {31709520},
issn = {1873-3468},
mesh = {Archaeal Proteins/genetics/metabolism ; Cell Nucleus/metabolism ; Cytosol/metabolism ; Gene Deletion ; Iron-Sulfur Proteins/genetics/*metabolism ; Methanococcus/genetics/*growth &amp; development/metabolism ; Phylogeny ; },
abstract = {The nucleotide binding protein 35 (Nbp35)/cytosolic Fe-S cluster deficient 1 (Cfd1)/alternative pyrimidine biosynthetic protein C (ApbC) protein homologs have been identified in all three domains of life. In eukaryotes, the Nbp35/Cfd1 heterocomplex is an essential Fe-S cluster assembly scaffold required for the maturation of Fe-S proteins in the cytosol and nucleus, whereas the bacterial ApbC is an Fe-S cluster transfer protein only involved in the maturation of a specific target protein. Here, we show that the Nbp35/ApbC homolog MMP0704 purified from its native archaeal host Methanococcus maripaludis contains a [4Fe-4S] cluster that can be transferred to a [4Fe-4S] apoprotein. Deletion of mmp0704 from M. maripaludis does not cause growth deficiency under our tested conditions. Our data indicate that Nbp35/ApbC is a nonessential [4Fe-4S] cluster transfer protein in methanogenic archaea.},
}
@article {pmid31705614,
year = {2020},
author = {Kubatova, N and Pyper, DJ and Jonker, HRA and Saxena, K and Remmel, L and Richter, C and Brantl, S and Evguenieva-Hackenberg, E and Hess, WR and Klug, G and Marchfelder, A and Soppa, J and Streit, W and Mayzel, M and Orekhov, VY and Fuxreiter, M and Schmitz, RA and Schwalbe, H},
title = {Rapid Biophysical Characterization and NMR Spectroscopy Structural Analysis of Small Proteins from Bacteria and Archaea.},
journal = {Chembiochem : a European journal of chemical biology},
volume = {21},
number = {8},
pages = {1178-1187},
pmid = {31705614},
issn = {1439-7633},
mesh = {Archaea/*metabolism ; Archaeal Proteins/*chemistry ; Bacteria/*metabolism ; Bacterial Proteins/*chemistry ; Computational Biology/*methods ; Nuclear Magnetic Resonance, Biomolecular/*methods ; Open Reading Frames ; Protein Conformation ; *Protein Folding ; },
abstract = {Proteins encoded by small open reading frames (sORFs) have a widespread occurrence in diverse microorganisms and can be of high functional importance. However, due to annotation biases and their technically challenging direct detection, these small proteins have been overlooked for a long time and were only recently rediscovered. The currently rapidly growing number of such proteins requires efficient methods to investigate their structure-function relationship. Herein, a method is presented for fast determination of the conformational properties of small proteins. Their small size makes them perfectly amenable for solution-state NMR spectroscopy. NMR spectroscopy can provide detailed information about their conformational states (folded, partially folded, and unstructured). In the context of the priority program on small proteins funded by the German research foundation (SPP2002), 27 small proteins from 9 different bacterial and archaeal organisms have been investigated. It is found that most of these small proteins are unstructured or partially folded. Bioinformatics tools predict that some of these unstructured proteins can potentially fold upon complex formation. A protocol for fast NMR spectroscopy structure elucidation is described for the small proteins that adopt a persistently folded structure by implementation of new NMR technologies, including automated resonance assignment and nonuniform sampling in combination with targeted acquisition.},
}
@article {pmid31704973,
year = {2019},
author = {Chénard, C and Wijaya, W and Vaulot, D and Lopes Dos Santos, A and Martin, P and Kaur, A and Lauro, FM},
title = {Temporal and spatial dynamics of Bacteria, Archaea and protists in equatorial coastal waters.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {16390},
pmid = {31704973},
issn = {2045-2322},
mesh = {Archaea/genetics/isolation &amp; purification ; Bacteria/classification/genetics/isolation &amp; purification ; Biodiversity ; Eukaryota/genetics/isolation &amp; purification ; *Microbiota/genetics ; Seasons ; Seawater/*microbiology ; Singapore ; Spatio-Temporal Analysis ; Wind ; },
abstract = {Singapore, an equatorial island in South East Asia, is influenced by a bi-annual reversal of wind directions which defines two monsoon seasons. We characterized the dynamics of the microbial communities of Singapore coastal waters by collecting monthly samples between February 2017 and July 2018 at four sites located across two straits with different trophic status, and sequencing the V6-V8 region of the small sub-unit ribosomal RNA gene (rRNA gene) of Bacteria, Archaea, and Eukaryota. Johor Strait, which is subjected to wider environmental fluctuations from anthropogenic activities, presented a higher abundance of copiotrophic microbes, including Cellvibrionales and Rhodobacterales. The mesotrophic Singapore Strait, where the seasonal variability is caused by changes in the oceanographic conditions, harboured a higher proportion of typically marine microbe groups such as Synechococcales, Nitrosupumilales, SAR11, SAR86, Marine Group II Archaea and Radiolaria. In addition, we observed seasonal variability of the microbial communities in the Singapore Strait, which was possibly influenced by the alternating monsoon regime, while no seasonal pattern was detected in the Johor Strait.},
}
@article {pmid31690001,
year = {2019},
author = {Mukhtar, H and Lin, YP and Lin, CM and Lin, YR},
title = {Relative Abundance of Ammonia Oxidizing Archaea and Bacteria Influences Soil Nitrification Responses to Temperature.},
journal = {Microorganisms},
volume = {7},
number = {11},
pages = {},
pmid = {31690001},
issn = {2076-2607},
abstract = {Ammonia oxidizing archaea (AOA) and bacteria (AOB) are thought to contribute differently to soil nitrification, yet the extent to which their relative abundances influence the temperature response of nitrification is poorly understood. Here, we investigated the impact of different AOA to AOB ratios on soil nitrification potential (NP) across a temperature gradient from 4 °C to 40 °C in twenty different organic and inorganic fertilized soils. The temperature responses of different relative abundance of ammonia oxidizers for nitrification were modeled using square rate theory (SQRT) and macromolecular rate theory (MMRT) models. We found that the proportional nitrification rates at different temperatures varied among AOA to AOB ratios. Predicted by both models, an optimum temperature (Topt) for nitrification in AOA dominated soils was significantly higher than for soils where AOA and AOB abundances are within the same order of magnitude. Moreover, the change in heat capacity (Δ C P ‡) associated with the temperature dependence of nitrification was positively correlated with Topt and significantly varied among the AOA to AOB ratios. The temperature ranges for NP decreased with increasing AOA abundance for both organic and inorganic fertilized soils. These results challenge the widely accepted approach of comparing NP rates in different soils at a fixed temperature. We conclude that a shift in AOA to AOB ratio in soils exhibits distinguished temperature-dependent characteristics that have an important impact on nitrification responses across the temperature gradient. The proposed approach benefits the accurate discernment of the true contribution of fertilized soils to nitrification for improvement of nitrogen management.},
}
@article {pmid31683078,
year = {2020},
author = {Magdalena, JA and González-Fernández, C},
title = {Archaea inhibition: Strategies for the enhancement of volatile fatty acids production from microalgae.},
journal = {Waste management (New York, N.Y.)},
volume = {102},
number = {},
pages = {222-230},
doi = {10.1016/j.wasman.2019.10.044},
pmid = {31683078},
issn = {1879-2456},
mesh = {Anaerobiosis ; Archaea ; Fatty Acids, Volatile ; Fermentation ; *Microalgae ; Sewage ; },
abstract = {In the present study, anaerobic sludge was subjected to thermal and chemical pretreatments to favour VFAs production from a protein-rich waste (i.e. microalgae biomass). Sludge pretreatments have been previously used in hydrogen production; however, information about how they can affect VFAs production from microalgae is still lacking. Thermal pretreatment was studied at: (i) 80 °C for 10 and 30 min; (ii) 120 °C for 10 and 30 min; and (iii) 100 °C for 20 min. 2-bromoethanesulfonate (BES) at 10 mM and 30 mM was used as chemical pretreatment. Besides, a combination of both pretreatment methods (80 °C and 120 °C at 10 mM and 30 mM BES) was also tested. Thermal pretreatment increased organic matter conversions into VFAs (up to 71% COD-VFAs/CODin) when compared to control values (40% in the untreated anaerobic sludge). Acetic acid was the most abundant VFAs at high temperatures (120 °C) and when BES was employed (up to 60% and 40%, respectively, in terms of COD). On the other hand, propionic acid was the most abundant product at low temperatures and in the untreated anaerobic sludge (up to 60% in terms of COD). This research work might set guidelines in order to choose a suitable sludge pretreatment for VFAs production from microalgae.},
}
@article {pmid31681249,
year = {2019},
author = {He, H and Fu, L and Liu, Q and Fu, L and Bi, N and Yang, Z and Zhen, Y},
title = {Community Structure, Abundance and Potential Functions of Bacteria and Archaea in the Sansha Yongle Blue Hole, Xisha, South China Sea.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2404},
pmid = {31681249},
issn = {1664-302X},
abstract = {The Sansha Yongle Blue Hole is the deepest blue hole in the world and exhibits unique environmental characteristics. In this paper, Illumina sequencing and qPCR analysis were conducted to obtain the microbial information in this special ecosystem. The results showed that the richness and diversity of bacterial communities in the hole was greater than those of archaeal communities, and bacterial and archaeal communities were dominated by Proteobacteria and Euryarchaeota, respectively. Temperature and nitrate concentration significantly contributed to the heterogeneous distribution of major bacterial clades; salinity explained most variations of the archaeal communities, but not significant. A sudden increase of bacterial 16S rRNA, archaeal 16S rRNA, ANAMMOX 16S rRNA, nirS and dsrB gene was noticed from 90 to 100 m in the hole probably due to more phytoplankton at this depth. Sulfur oxidation and nitrate reduction were the most abundant predicted ecological functions in the hole, while lots of archaea were predicted to be involved in aerobic ammonia oxidation and methanogenesis. The co-occurrence network analysis illustrated that a synergistic effect between sulfate reduction and sulfur oxidation, and between nitrogen fixation and denitrification, a certain degree of coupling between sulfur and nitrogen cycle was also observed in the hole. The comparisons of bacterial and archaeal communities between the hole and other caves in the world (or other areas of the South China Sea) suggest that similar conditions are hypothesized to give rise to similar microbial communities, and environmental conditions may contribute significantly to the bacterial and archaeal communities.},
}
@article {pmid31669955,
year = {2019},
author = {Tu, R and Jin, W and Han, SF and Zhou, X and Wang, T and Gao, SH and Wang, Q and Chen, C and Xie, GJ and Wang, Q},
title = {Rapid enrichment and ammonia oxidation performance of ammonia-oxidizing archaea from an urban polluted river of China.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {255},
number = {Pt 2},
pages = {113258},
doi = {10.1016/j.envpol.2019.113258},
pmid = {31669955},
issn = {1873-6424},
mesh = {Ammonia/*metabolism ; Archaea/*metabolism ; Bacteria/genetics ; Betaproteobacteria ; *Biodegradation, Environmental ; China ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Rivers/microbiology ; Soil Microbiology ; Water Pollutants, Chemical/*metabolism ; },
abstract = {Ammonia oxidation is the rate-limiting step in nitrification process and dominated by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). In the present study, a highly enriched culture of AOA was obtained from urban polluted water in Shahe River, Shenzhen, China. The optimum growth conditions were identified by orthogonal analysis as 37 °C, with pH 7.0 and initial ammonia concentration of 1.0 mM. Under these conditions, the highest abundance of AOA was obtained as 4.6 × 107 copies/ng DNA. Growth of AOA in polluted river water showed significant reduction in ammonia concentration in AOA-enriched cultures without antibiotics after 10 days of incubation, while synchronous increase in nitrate concentration was up to 12.7 mg/L. However, AOA-enriched by antibiotic showed insignificant changes in ammonia or nitrite concentration. This study showed that AOB play an important role in ammonia oxidation of polluted river water, and AOA alone showed insignificant changes in ammonia or nitrite concentrations. Therefore, the ammonia oxidation performance of natural water could not be improved by adding high concentration AOA bacterial liquid.},
}
@article {pmid31666740,
year = {2019},
author = {Belilla, J and Moreira, D and Jardillier, L and Reboul, G and Benzerara, K and López-García, JM and Bertolino, P and López-Archilla, AI and López-García, P},
title = {Hyperdiverse archaea near life limits at the polyextreme geothermal Dallol area.},
journal = {Nature ecology &amp; evolution},
volume = {3},
number = {11},
pages = {1552-1561},
pmid = {31666740},
issn = {2397-334X},
support = {322669/ERC_/European Research Council/International ; },
mesh = {*Archaea ; *Bacteria ; Phylogeny ; RNA, Ribosomal, 16S ; },
abstract = {Microbial life has adapted to various individual extreme conditions; yet, organisms simultaneously adapted to very low pH, high salt and high temperature are unknown. We combined environmental 16S/18S ribosomal RNA gene metabarcoding, cultural approaches, fluorescence-activated cell sorting, scanning electron microscopy and chemical analyses to study samples along such unique polyextreme gradients in the Dallol-Danakil area in Ethiopia. We identified two physicochemical barriers to life in the presence of surface liquid water defined by (1) high chaotropicity-low water activity in Mg2+/Ca2+-dominated brines and (2) hyperacidity-salt combinations (pH ~0/NaCl-dominated salt saturation). When detected, life was dominated by highly diverse ultrasmall archaea that were widely distributed across phyla with and without previously known halophilic members. We hypothesize that a high cytoplasmic K+-level was an original archaeal adaptation to hyperthermophily, subsequently exapted during several transitions to extreme halophily. We detect active silica encrustment/fossilization of cells but also abiotic biomorphs of varied chemistry. Our work helps circumscribing habitability and calls for cautionary interpretations of morphological biosignatures on Earth and beyond.},
}
@article {pmid31654454,
year = {2020},
author = {Xu, S and Lu, W and Mustafa, MF and Liu, Y and Wang, H},
title = {Presence of diverse nitrate-dependent anaerobic methane oxidizing archaea in sewage sludge.},
journal = {Journal of applied microbiology},
volume = {128},
number = {3},
pages = {775-783},
doi = {10.1111/jam.14502},
pmid = {31654454},
issn = {1365-2672},
support = {BK20190481//Natural Science Foundation of Jiangsu Province/ ; 30919011212//Fundamental Research Funds for the Central Universities/ ; },
mesh = {Anaerobiosis ; Archaea/classification/genetics/*isolation &amp; purification/*metabolism ; China ; Methane/*metabolism ; Methanosarcinales/classification/genetics/isolation &amp; purification/metabolism ; Microbiota ; Nitrates/*metabolism ; Oxidation-Reduction ; Phylogeny ; Seasons ; Sewage/chemistry/*microbiology ; },
abstract = {AIM: The aim of this study was to explore the community diversity and abundance of nitrate-dependent anaerobic methane oxidizing archaea, Candidatus Methanoperedens nitroreducens, in sewage sludge from wastewater treatment plants.<br><br>METHODS AND RESULTS: Seasonal sampling of the sewage sludge was carried out from two wastewater treatment plants (WWTPs) located in the northern and southern parts of China. Through amplicon sequencing using our newly designed primers, a large number of Candidatus Methanoperedens nitroreducens-like (M. nitroreducens) archaeal sequences (638 743) were generated. These sequences were assigned into 742 operational protein units (OPUs) at 90% cut-off level and classified as Group B member of M. nitroreducens archaea in the phylogenetic tree. More than 80% of the OPUs were not shared between these two WWTPs, showing the M. nitroreducens-like archaeal community in each WWTP was unique. Quantitative PCR assays also confirmed the presence of M. nitroreducens-like archaea and revealed a higher abundance in autumn and winter than other seasons, indicating that the environmental attributes in these seasons might favour the growth of this archaea. Further redundancy analysis revealed that volatile solid and pH were the significant environmental attributes (P < 0·05) in shaping the M. nitroreducens-like archaeal community based on variance inflation factor selection and Monte Carlo permutation test.<br><br>CONCLUSIONS: The results confirmed the presence of diverse M. nitroreducens-like archaea in sewage sludge using Illumina-based mcrA gene sequencing and quantitative PCR assays.<br><br>The results of this study revealed the ecological characteristics of M. nitroreducens-like archaea in sewage sludge that improved our understanding of nitrate-dependent anaerobic methane oxidation process and may be the basis for future application of M. nitroreducens-like archaea for new nitrogen removal in WWTPs.},
}
@article {pmid31637140,
year = {2019},
author = {Yuan, M and Liu, S and Wang, Z and Wang, L and Xue, B and Zou, H and Tian, G and Cai, J and Peng, Q},
title = {Effects of particle size of ground alfalfa hay on caecal bacteria and archaea populations of rabbits.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e7910},
pmid = {31637140},
issn = {2167-8359},
abstract = {This work was aimed to investigate the effects of the different particle size of ground alfalfa hay on caecal microbial and archeal communities of rabbits. One hundred-twenty New Zealand rabbits (950.3 ± 8.82 g) were allocated into four treatments, with five replicates in each treatment and six rabbits in each replicate. The particle sizes of the alfalfa meal in the four treatment diets were 2,500, 1,000, 100 and 10 µm respectively, while the other ingredients were ground through a 2.5 mm sieve. High-throughput sequencing technology was applied to examine the differences in bacteria and methanogenic archaea diversity in the caecum of the four treatment groups of rabbits. A total of 745,946 bacterial sequences (a mean of 31,081 ± 13,901 sequences per sample) and 539,227 archaeal sequences (a mean of 22,468 ± 2,443 sequences per sample) were recovered from twenty-four caecal samples, and were clustered into 9,953 and 2,246 OTUs respectively. A total of 26 bacterial phyla with 465 genera and three archaeal phyla with 10 genera were identified after taxonomic summarization. Bioinformatic analyses illustrated that Firmicutes (58.69% ∼ 68.50%) and Bacteroidetes (23.96% ∼ 36.05%) were the two most predominant bacterial phyla and Euryarchaeota (over 99.9%) was the most predominant archaeal phyla in the caecum of all rabbits. At genus level, as the particle size of alfalfa decreased from 2,500 to 10 µm, the relative abundances of Ruminococcaceae UCG-014 (P < 0.001) and Lactobacillus (P = 0.043) were increased and Ruminococcaceae UCG-005 (P = 0.012) was increased first and then decreased when the alfalfa particle size decreased, while Lachnospiraceae NK4A136 group (P = 0.016), Ruminococcaceae NK4A214 (P = 0.044), Christensenellaceae R-7 group (P = 0.019), Lachnospiraceae other (Family) (P = 0.011) and Ruminococcaceae UCG-013 (P = 0.021) were decreased. The relative abundance of Methanobrevibacter was increased from 62.48% to 90.40% (P < 0.001), whereas the relative abundance of Methanosphaera was reduced from 35.47% to 8.62% (P < 0.001). In conclusion, as the particle size of alfalfa meal decreased, both the bacterial and archaeal population in the caecum of rabbit experienced alterations, however archaea response earlier than bacteria to the decrease of alfalfa meal particle size.},
}
@article {pmid31618850,
year = {2019},
author = {Lu, Y and Xia, X and Cheung, S and Jing, H and Liu, H},
title = {Differential Distribution and Determinants of Ammonia Oxidizing Archaea Sublineages in the Oxygen Minimum Zone off Costa Rica.},
journal = {Microorganisms},
volume = {7},
number = {10},
pages = {},
pmid = {31618850},
issn = {2076-2607},
support = {2015CB954003//Ministry of Science and Technology of the People's Republic of China/ ; N-HKUST609/15//Research Grants Council, University Grants Committee/ ; 16128416//Research Grants Council, University Grants Committee/ ; 16101318//Research Grants Council, University Grants Committee/ ; Y8SL031001//CAS Pioneer Hundred Talents Program, the South China Sea Institute of Oceanography/ ; Y9YB021001//CAS Pioneer Hundred Talents Program, the South China Sea Institute of Oceanography/ ; 31971501//National Natural Science Foundation of China/ ; },
abstract = {Ammonia oxidizing archaea (AOA) are microbes that are widely distributed in the ocean that convert ammonia to nitrite for energy acquisition in the presence of oxygen. Recent study has unraveled highly diverse sublineages within the previously defined AOA ecotypes (i.e., water column A (WCA) and water column B (WCB)), although the eco-physiology and environmental determinants of WCB subclades remain largely unclear. In this study, we examined the AOA communities along the water columns (40-3000 m depth) in the Costa Rica Dome (CRD) upwelling region in the eastern tropical North Pacific Ocean. Highly diverse AOA communities that were significantly different from those in oxygenated water layers were observed in the core layer of the oxygen minimum zone (OMZ), where the dissolved oxygen (DO) concentration was < 2μM. Moreover, a number of AOA phylotypes were found to be enriched in the OMZ core. Most of them were negatively correlated with DO and were also detected in other OMZs in the Arabian Sea and Gulf of California, which suggests low oxygen adaptation. This study provided the first insight into the differential niche partitioning and environmental determinants of various subclades within the ecotype WCB. Our results indicated that the ecotype WCB did indeed consist of various sublineages with different eco-physiologies, which should be further explored.},
}
@article {pmid31614851,
year = {2019},
author = {Odelade, KA and Babalola, OO},
title = {Bacteria, Fungi and Archaea Domains in Rhizospheric Soil and Their Effects in Enhancing Agricultural Productivity.},
journal = {International journal of environmental research and public health},
volume = {16},
number = {20},
pages = {},
pmid = {31614851},
issn = {1660-4601},
mesh = {Agriculture/*statistics &amp; numerical data ; Archaea/*metabolism ; Bacteria/*metabolism ; Fungi/*metabolism ; *Microbiota ; Plant Roots/*metabolism ; *Rhizosphere ; Soil Microbiology ; },
abstract = {The persistent and undiscriminating application of chemicals as means to improve crop growth, development and yields for several years has become problematic to agricultural sustainability because of the adverse effects these chemicals have on the produce, consumers and beneficial microbes in the ecosystem. Therefore, for agricultural productivity to be sustained there are needs for better and suitable preferences which would be friendly to the ecosystem. The use of microbial metabolites has become an attractive and more feasible preference because they are versatile, degradable and ecofriendly, unlike chemicals. In order to achieve this aim, it is then imperative to explore microbes that are very close to the root of a plant, especially where they are more concentrated and have efficient activities called the rhizosphere. Extensive varieties of bacteria, archaea, fungi and other microbes are found inhabiting the rhizosphere with various interactions with the plant host. Therefore, this review explores various beneficial microbes such as bacteria, fungi and archaea and their roles in the environment in terms of acquisition of nutrients for plants for the purposes of plant growth and health. It also discusses the effect of root exudate on the rhizosphere microbiome and compares the three domains at molecular levels.},
}
@article {pmid31605529,
year = {2019},
author = {Farley, KR and Metcalf, WW},
title = {The streptothricin acetyltransferase (sat) gene as a positive selectable marker for methanogenic archaea.},
journal = {FEMS microbiology letters},
volume = {366},
number = {17},
pages = {},
pmid = {31605529},
issn = {1574-6968},
support = {R21 AI122019/AI/NIAID NIH HHS/United States ; },
mesh = {Acetyltransferases/*genetics ; Anti-Infective Agents/pharmacology ; Archaea/drug effects/*genetics ; Drug Resistance, Microbial ; *Evolution, Molecular ; Genes, Archaeal ; Humans ; Microbial Sensitivity Tests ; Mutation ; *Selection, Genetic ; Sequence Deletion ; },
abstract = {A repertoire of sophisticated genetic tools has significantly enhanced studies of Methanosarcina genera, yet the lack of multiple positive selectable markers has limited the types of genetic experiments that can be performed. In this study, we report the development of an additional positive selection system for Methanosarcina that utilizes the antibiotic nourseothricin and the Streptomyces rochei streptothricin acetyltransferase (sat) gene, which may be broadly applicable to other groups of methanogenic archaea. Nourseothricin was found to inhibit growth of four different methanogen species at concentrations ≤300 μg/ml in liquid or on solid media. Selection of nourseothricin resistant transformants was possible in two genetically tractable Methanosarcina species, M. acetivorans and M. barkeri, using the sat gene as a positive selectable marker. Additionally, the sat marker was useful for constructing a gene deletion mutant strain of M. acetivorans, emphasizing its utility as a second positive selectable marker for genetic analyses of Methanosarcina genera. Interestingly, two human gut-associated methanogens Methanobrevibacter smithii and Methanomassillicoccus luminyensis were more sensitive to nourseothricin than either Methanosarcina species, suggesting the nourseothricin-sat gene pair may provide a robust positive selection system for development of genetic tools in these and other methanogens.},
}
@article {pmid31594929,
year = {2019},
author = {Hua, ZS and Wang, YL and Evans, PN and Qu, YN and Goh, KM and Rao, YZ and Qi, YL and Li, YX and Huang, MJ and Jiao, JY and Chen, YT and Mao, YP and Shu, WS and Hozzein, W and Hedlund, BP and Tyson, GW and Zhang, T and Li, WJ},
title = {Insights into the ecological roles and evolution of methyl-coenzyme M reductase-containing hot spring Archaea.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {4574},
pmid = {31594929},
issn = {2041-1723},
mesh = {Alkanes/metabolism ; Archaea/enzymology/*genetics/isolation &amp; purification ; *Biological Evolution ; China ; Computational Biology ; Genome, Archaeal ; Hot Springs/*microbiology ; Hot Temperature ; Metabolic Networks and Pathways/genetics ; *Metagenome ; Methane/metabolism ; Multigene Family/genetics ; Oxidoreductases/*genetics/metabolism ; Phylogeny ; },
abstract = {Several recent studies have shown the presence of genes for the key enzyme associated with archaeal methane/alkane metabolism, methyl-coenzyme M reductase (Mcr), in metagenome-assembled genomes (MAGs) divergent to existing archaeal lineages. Here, we study the mcr-containing archaeal MAGs from several hot springs, which reveal further expansion in the diversity of archaeal organisms performing methane/alkane metabolism. Significantly, an MAG basal to organisms from the phylum Thaumarchaeota that contains mcr genes, but not those for ammonia oxidation or aerobic metabolism, is identified. Together, our phylogenetic analyses and ancestral state reconstructions suggest a mostly vertical evolution of mcrABG genes among methanogens and methanotrophs, along with frequent horizontal gene transfer of mcr genes between alkanotrophs. Analysis of all mcr-containing archaeal MAGs/genomes suggests a hydrothermal origin for these microorganisms based on optimal growth temperature predictions. These results also suggest methane/alkane oxidation or methanogenesis at high temperature likely existed in a common archaeal ancestor.},
}
@article {pmid31587640,
year = {2019},
author = {Santoro, AE and Kellom, M and Laperriere, SM},
title = {Contributions of single-cell genomics to our understanding of planktonic marine archaea.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {374},
number = {1786},
pages = {20190096},
pmid = {31587640},
issn = {1471-2970},
mesh = {Archaea/*genetics ; *Genome, Archaeal ; *Genomics ; Plankton/*genetics ; *Single-Cell Analysis ; },
abstract = {Single-cell genomics has transformed many fields of biology, marine microbiology included. Here, we consider the impact of single-cell genomics on a specific group of marine microbes-the planktonic marine archaea. Despite single-cell enabled discoveries of novel metabolic function in the marine thaumarchaea, population-level investigations are hindered by an overall lower than expected recovery of thaumarchaea in single-cell studies. Metagenome-assembled genomes have so far been a more useful method for accessing genome-resolved insights into the Marine Group II euryarchaea. Future progress in the application of single-cell genomics to archaeal biology in the ocean would benefit from more targeted sorting approaches, and a more systematic investigation of potential biases against archaea in single-cell workflows including cell lysis, genome amplification and genome screening. This article is part of a discussion meeting issue 'Single cell ecology'.},
}
@article {pmid31582767,
year = {2019},
author = {Loth, K and Largillière, J and Coste, F and Culard, F and Landon, C and Castaing, B and Delmas, AF and Paquet, F},
title = {New protein-DNA complexes in archaea: a small monomeric protein induces a sharp V-turn DNA structure.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {14253},
pmid = {31582767},
issn = {2045-2322},
mesh = {Archaeal Proteins/chemistry/*metabolism ; DNA, Archaeal/chemistry/*metabolism ; DNA-Binding Proteins/chemistry/*metabolism ; Methanosarcina/chemistry/*metabolism ; Models, Molecular ; Nuclear Magnetic Resonance, Biomolecular ; Nucleic Acid Conformation ; Protein Binding ; Protein Conformation ; Ribonucleoproteins/chemistry/*metabolism ; },
abstract = {MC1, a monomeric nucleoid-associated protein (NAP), is structurally unrelated to other DNA-binding proteins. The protein participates in the genome organization of several Euryarchaea species through an atypical compaction mechanism. It is also involved in DNA transcription and cellular division through unknown mechanisms. We determined the 3D solution structure of a new DNA-protein complex formed by MC1 and a strongly distorted 15 base pairs DNA. While the protein just needs to adapt its conformation slightly, the DNA undergoes a dramatic curvature (the first two bend angles of 55° and 70°, respectively) and an impressive torsional stress (dihedral angle of 106°) due to several kinks upon binding of MC1 to its concave side. Thus, it adopts a V-turn structure. For longer DNAs, MC1 stabilizes multiple V-turn conformations in a flexible and dynamic manner. The existence of such V-turn conformations of the MC1-DNA complexes leads us to propose two binding modes of the protein, as a bender (primary binding mode) and as a wrapper (secondary binding mode). Moreover, it opens up new opportunities for studying and understanding the repair, replication and transcription molecular machineries of Archaea.},
}
@article {pmid31568679,
year = {2020},
author = {Ding, J and Ma, M and Jiang, X and Liu, Y and Zhang, J and Suo, L and Wang, L and Wei, D and Li, J},
title = {Effects of applying inorganic fertilizer and organic manure for 35 years on the structure and diversity of ammonia-oxidizing archaea communities in a Chinese Mollisols field.},
journal = {MicrobiologyOpen},
volume = {9},
number = {1},
pages = {e00942},
pmid = {31568679},
issn = {2045-8827},
mesh = {Ammonia/*metabolism ; Archaea/*classification/growth &amp; development/*metabolism ; China ; Fertilizers/*analysis ; Nitrogen Compounds/analysis ; Oxidation-Reduction ; Phosphorus/analysis ; Potassium/analysis ; Soil/*chemistry ; Soil Microbiology ; Soybeans/growth &amp; development ; },
abstract = {In this study, we investigated the physicochemical properties of soil, and the diversity and structure of the soil ammonia-oxidizing archaea (AOA) community, when subjected to fertilizer treatments for over 35 years. We collected soil samples from a black soil fertilization trial in northeast China. Four treatments were tested: no fertilization (CK); manure (M); nitrogen (N), phosphorus (P), and potassium (K) chemical fertilizer (NPK); and N, P, and K plus M (MNPK). We employed 454 high-throughput pyrosequencing to measure the response of the soil AOA community to the long-term fertilization. The fertilization treatments had different impacts on the shifts in the soil properties and AOA community. The utilization of manure alleviated soil acidification and enhanced the soybean yield. The soil AOA abundance was increased greatly by inorganic and organic fertilizers. In addition, the community Chao1 and ACE were highest in the MNPK treatment. In terms of the AOA community composition, Thaumarchaeota and Crenarchaeota were the main AOA phyla in all samples. Compared with CK and M, the abundances of Thaumarchaeota were remarkably lower in the MNPK and NPK treatments. There were distinct shifts in the compositions of the AOA operational taxonomic units (OTUs) under different fertilization management practices. OTU51 was the dominant OTU in all treatments, except for NPK. OTU79 and OTU11 were relatively abundant OTUs in NPK. Only Nitrososphaera AOA were tracked from the black soil. Redundancy analysis indicated that the soil pH and soil available P were the two main factors that affected the AOA community structure. The abundances of AOA were positively correlated with the total N and available P concentrations, and negatively correlated with the soil pH.},
}
@article {pmid31552452,
year = {2019},
author = {He, S and Tan, J and Hu, W and Mo, C},
title = {Diversity of Archaea and Its Correlation with Environmental Factors in the Ebinur Lake Wetland.},
journal = {Current microbiology},
volume = {76},
number = {12},
pages = {1417-1424},
pmid = {31552452},
issn = {1432-0991},
support = {31160026//National Natural Science Foundation of China/ ; },
mesh = {Archaea/*classification/genetics/isolation &amp; purification ; *Biodiversity ; China ; DNA, Archaeal/genetics ; Lakes ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; *Wetlands ; },
abstract = {The diversity and community composition of archaea in soil samples from three wetlands (SP1, SP2, and SP3) of Ebinur Lake were studied by constructing 16S rDNA cloning library. The correlation between the diversity of archaea and soil environmental factors was analyzed by CANOCO software. The aim of this study was to reveal the differences of community structures of archaea in different sample sites, to provide a theoretical basis for further study on degradation and restoration of Ebinur Lake wetland. The results showed that Euryarchaeota accounted for 57.1% was the most dominant phylum observed, followed by Thaumarchaeota and Crenarchaeota for the three wetland soil analyzed. Compared with SP3 site, the proportions of Euryarchaeota were decreased by 16.70% and 31.78%, while Thaumarchaeota increased by 7.26% and 17.64% in the SP1 and SP2, respectively. Crenarchaeota was found only in SP3. Shannon-wiener diversity indices in SP1, SP2, and SP3 sites were 3.44, 3.87, and 3.94, respectively, indicating that the diversity of archaea in three plots was: SP3 > SP2 > SP1. Redundancy analysis (RDA) showed that electrical conductivity (EC), soil moisture (SM), hydrogen potential (pH), and soil organic matter content (SOM) may affect archaeal communities. Compared to EC and pH, SM and SOM may have a greater impact on the community composition of archaea.},
}
@article {pmid31533962,
year = {2019},
author = {Mand, TD and Metcalf, WW},
title = {Energy Conservation and Hydrogenase Function in Methanogenic Archaea, in Particular the Genus Methanosarcina.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {83},
number = {4},
pages = {},
pmid = {31533962},
issn = {1098-5557},
mesh = {Cytochromes/metabolism ; *Energy Metabolism ; Hydrogen/metabolism ; Hydrogenase/*metabolism ; Methane/metabolism ; Methanosarcina/*enzymology ; Phylogeny ; },
abstract = {The biological production of methane is vital to the global carbon cycle and accounts for ca. 74% of total methane emissions. The organisms that facilitate this process, methanogenic archaea, belong to a large and phylogenetically diverse group that thrives in a wide range of anaerobic environments. Two main subgroups exist within methanogenic archaea: those with and those without cytochromes. Although a variety of metabolisms exist within this group, the reduction of growth substrates to methane using electrons from molecular hydrogen is, in a phylogenetic sense, the most widespread methanogenic pathway. Methanogens without cytochromes typically generate methane by the reduction of CO2 with electrons derived from H2, formate, or secondary alcohols, generating a transmembrane ion gradient for ATP production via an Na+-translocating methyltransferase (Mtr). These organisms also conserve energy with a novel flavin-based electron bifurcation mechanism, wherein the endergonic reduction of ferredoxin is facilitated by the exergonic reduction of a disulfide terminal electron acceptor coupled to either H2 or formate oxidation. Methanogens that utilize cytochromes have a broader substrate range, and can convert acetate and methylated compounds to methane, in addition to the ability to reduce CO2 Cytochrome-containing methanogens are able to supplement the ion motive force generated by Mtr with an H+-translocating electron transport system. In both groups, enzymes known as hydrogenases, which reversibly interconvert protons and electrons to molecular hydrogen, play a central role in the methanogenic process. This review discusses recent insight into methanogen metabolism and energy conservation mechanisms with a particular focus on the genus Methanosarcina.},
}
@article {pmid31522353,
year = {2019},
author = {Sereme, Y and Mezouar, S and Grine, G and Mege, JL and Drancourt, M and Corbeau, P and Vitte, J},
title = {Methanogenic Archaea: Emerging Partners in the Field of Allergic Diseases.},
journal = {Clinical reviews in allergy &amp; immunology},
volume = {57},
number = {3},
pages = {456-466},
pmid = {31522353},
issn = {1559-0267},
support = {10-IAHU-03//Agence Nationale de la Recherche/ ; PhD//Fondation Méditerranée Infection/ ; post-doctoral//Fondation Méditerranée Infection/ ; PhD//Fondation Méditerranée Infection/ ; },
mesh = {Allergens/*immunology ; Animals ; Archaea/*immunology ; Disease Susceptibility ; Host-Pathogen Interactions/immunology ; Humans ; Hypersensitivity/diagnosis/*etiology ; Microbiota/immunology ; },
abstract = {Archaea, which form one of four domains of life alongside Eukarya, Bacteria, and giant viruses, have long been neglected as components of the human microbiota and potential opportunistic infectious pathogens. In this review, we focus on methanogenic Archaea, which rely on hydrogen for their metabolism and growth. On one hand, methanogenic Archaea in the gut are functional associates of the fermentative digestion of dietary fibers, favoring the production of beneficial short-chain fatty acids and likely contributing to the weaning reaction during the neonatal window of opportunity. On the other hand, methanogenic Archaea trigger the activation of innate and adaptive responses and the generation of specific T and B cells in animals and humans. In mouse models, lung hypersensitivity reactions can be induced by inhaled methanogenic Archaea mimicking human professional exposure to organic dust. Changes in methanogenic Archaea of the microbiota are detected in an array of dysimmune conditions comprising inflammatory bowel disease, obesity, malnutrition, anorexia, colorectal cancer, and diverticulosis. At the subcellular level, methanogenic Archaea are activators of the TLR8-dependent NLRP3 inflammasome, modulate the release of antimicrobial peptides and drive the production of proinflammatory, Th-1, Th-2, and Th-17 cytokines. Our objective was to introduce the most recent and major pieces of evidence supporting the involvement of Archaea in the balance between health and dysimmune diseases, with a particular focus on atopic and allergic conditions.},
}
@article {pmid31520950,
year = {2019},
author = {Pal, S and Sar, A and Dam, B},
title = {Moderate halophilic bacteria, but not extreme halophilic archaea can alleviate the toxicity of short-alkyl side chain imidazolium-based ionic liquids.},
journal = {Ecotoxicology and environmental safety},
volume = {184},
number = {},
pages = {109634},
doi = {10.1016/j.ecoenv.2019.109634},
pmid = {31520950},
issn = {1090-2414},
mesh = {Geologic Sediments/chemistry/microbiology ; Halobacteriaceae/*drug effects ; Halomonas/*drug effects ; Imidazoles/*toxicity ; India ; Ionic Liquids/*toxicity ; Lakes/chemistry/microbiology ; Salinity ; Salt Tolerance ; },
abstract = {Imidazolium-based ionic liquids (IL) with short-alkyl side chain such as 1-ethyl-3-methyl-imidazolium chloride ([Emim]Cl) and 1-butyl-3-methyl-imidazolium chloride ([Bmim]Cl) has immense application potential including in lignocellulosic bioenergy production. But they are toxic to most microorganisms, and those isolated from different environments as IL-tolerant have salt tolerance capabilities. This study evaluates the relationship between salt and [Emim]Cl tolerance of microorganisms using different salinity sediments (2-19%) and brines (35%) of India's largest inland hypersaline lake, Sambhar in Rajasthan as the model system. While samples with 2% and 35% salinities do not yield any [Emim]Cl (100 mM) tolerant colonies, others have 6-50% colonies tolerant to the IL. Similar trend was observed with 50 mM [Bmim]Cl. Moderate halophilic isolates of genera Halomonas and Bacillus (growth in 0.7-3.0 M NaCl) isolated from the sediments could grow in as high as 375 mM [Emim]Cl, or 125 mM [Bmim]Cl facilitated by higher synthesis, and uptake of organic osmolytes; and up to 1.7-fold increased activity of active efflux pumps. [Bmim]Cl was more toxic than [Emim]Cl in all performed experiments. [Emim]Cl-adapted cells could trounce IL-induced stress. Interestingly, enrichment with 100 mM [Emim]Cl resulted in increase of IL-tolerant colonies in all sediments including the one with 2% salinity. However, the salt saturated brines (35%) do not yield any such colony even after repeated incubations. Extreme halophilic archaea, Natronomonas (growth in 3.0-4.0 M NaCl) isolated from such brines, were exceedingly sensitive to even 5 mM [Emim]Cl, or 1 mM [Bmim]Cl. Two additional extremophilic archaea, namely Haloferax and Haladaptatus were also sensitive to the tested ILs. Archaeal sensitivity is possibly due to the competitive interaction of [Emim]+ with their acidic proteome (15.4-17.5% aspartic and glutamic acids, against 10.7-12.9% in bacteria) that they maintain to stabilize the high amount of K+ ion accumulated by salt-in strategy. Thus, general salt adaptation strategies of moderate halophilic bacteria help them to restrain toxicity of these ILs, but extremophilic archaea are highly sensitive and demands meticulous use of these solvents to prevent environmental contamination.},
}
@article {pmid31505830,
year = {2019},
author = {Salvador-Castell, M and Tourte, M and Oger, PM},
title = {In Search for the Membrane Regulators of Archaea.},
journal = {International journal of molecular sciences},
volume = {20},
number = {18},
pages = {},
pmid = {31505830},
issn = {1422-0067},
support = {ANR 17-CE11-0012-01//Agence Nationale de la Recherche/ ; Origines "ReseArch"//Centre National de la Recherche Scientifique/ ; },
mesh = {*Adaptation, Physiological ; Archaea/*physiology ; Cell Membrane/*metabolism ; Membrane Lipids/*metabolism ; },
abstract = {Membrane regulators such as sterols and hopanoids play a major role in the physiological and physicochemical adaptation of the different plasmic membranes in Eukarya and Bacteria. They are key to the functionalization and the spatialization of the membrane, and therefore indispensable for the cell cycle. No archaeon has been found to be able to synthesize sterols or hopanoids to date. They also lack homologs of the genes responsible for the synthesis of these membrane regulators. Due to their divergent membrane lipid composition, the question whether archaea require membrane regulators, and if so, what is their nature, remains open. In this review, we review evidence for the existence of membrane regulators in Archaea, and propose tentative location and biological functions. It is likely that no membrane regulator is shared by all archaea, but that they may use different polyterpenes, such as carotenoids, polyprenols, quinones and apolar polyisoprenoids, in response to specific stressors or physiological needs.},
}
@article {pmid31504156,
year = {2019},
author = {Bønløkke, JH and Duchaine, C and Schlünssen, V and Sigsgaard, T and Veillette, M and Basinas, I},
title = {Archaea and Bacteria Exposure in Danish Livestock Farmers.},
journal = {Annals of work exposures and health},
volume = {63},
number = {9},
pages = {965-974},
pmid = {31504156},
issn = {2398-7316},
mesh = {*Agriculture ; Air Pollutants, Occupational/*analysis ; Animal Husbandry/*statistics &amp; numerical data ; Animals ; Archaea/*isolation &amp; purification ; Bacteria/*isolation &amp; purification ; Denmark ; Dust/analysis ; Endotoxins/analysis ; Environmental Monitoring/methods ; Humans ; Inhalation Exposure/*analysis ; Livestock ; Occupational Exposure/*analysis ; RNA, Ribosomal, 16S/analysis ; Ventilation ; },
abstract = {OBJECTIVES: Methanogenic archaea have been found to make up part of the bioaerosols in pig, cattle, and poultry farms. So far no attempts have been made to determine how season, farm type, and farm characteristics may affect workers' exposure to archaea.<br><br>METHODS: Personal filter samples from 327 farmers working on 89 Danish farms were analysed for the number of 16S rRNA gene copies from archaea and bacteria and for their dust and endotoxin content. The farms were visited during summer and winter. Information on farm type and stable characteristics were collected using self-reported activity diaries and walk-through surveys. Differences in archaea and bacteria levels with farm type and stable characteristics and correlations with dust and endotoxin levels were examined.<br><br>RESULTS: Personal archaea exposure was documented in all farm types including, for the first time, during mink farming. At 7.3*104 gene copies m-3 the archaea levels were around two orders of magnitude lower than bacteria levels at 5.7*106 gene copies m-3. At 1.7*105 gene copies m-3 among pig farmers and 1.9*104 gene copies m-3 among cattle farmers the archaea levels differed with farm type (P < 0.0005). The archaea and bacteria levels correlated weakly with a Pearson correlation coefficient of 0.17. Neither archaea nor bacteria levels differed by season. In pig farms the archaea levels differed by type of ventilation and by wetness of the floor.<br><br>CONCLUSIONS: Archaea levels were not neglible and appeared to vary greatly between farm types. In pig farms they varied with some farm characteristics. Archaea levels appeared to depend on factors that differed from those of bacteria.},
}
@article {pmid31488843,
year = {2019},
author = {Huber, M and Faure, G and Laass, S and Kolbe, E and Seitz, K and Wehrheim, C and Wolf, YI and Koonin, EV and Soppa, J},
title = {Translational coupling via termination-reinitiation in archaea and bacteria.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {4006},
pmid = {31488843},
issn = {2041-1723},
mesh = {Archaea/*genetics/metabolism ; Bacteria/*genetics/metabolism ; Base Sequence ; Codon, Initiator ; Escherichia coli/genetics ; Genes, Archaeal/*genetics ; Genes, Bacterial/*genetics ; Genes, Overlapping ; Genes, Reporter ; Open Reading Frames/genetics ; Peptide Chain Initiation, Translational/*physiology ; Peptide Chain Termination, Translational/*physiology ; Protein Biosynthesis/*physiology ; RNA, Messenger ; Terminator Regions, Genetic ; },
abstract = {The genomes of many prokaryotes contain substantial fractions of gene pairs with overlapping stop and start codons (ATGA or TGATG). A potential benefit of overlapping gene pairs is translational coupling. In 720 genomes of archaea and bacteria representing all major phyla, we identify substantial, albeit highly variable, fractions of co-directed overlapping gene pairs. Various patterns are observed for the utilization of the SD motif for de novo initiation at upstream genes versus reinitiation at overlapping gene pairs. We experimentally test the predicted coupling in 9 gene pairs from the archaeon Haloferax volcanii and 5 gene pairs from the bacterium Escherichia coli. In 13 of 14 cases, translation of both genes is strictly coupled. Mutational analysis of SD motifs located upstream of the downstream genes indicate that the contribution of the SD to translational coupling widely varies from gene to gene. The nearly universal, abundant occurrence of overlapping gene pairs suggests that tight translational coupling is widespread in archaea and bacteria.},
}
@article {pmid31437442,
year = {2019},
author = {Hackley, RK and Schmid, AK},
title = {Global Transcriptional Programs in Archaea Share Features with the Eukaryotic Environmental Stress Response.},
journal = {Journal of molecular biology},
volume = {431},
number = {20},
pages = {4147-4166},
pmid = {31437442},
issn = {1089-8638},
support = {T32 GM007754/GM/NIGMS NIH HHS/United States ; },
mesh = {*Adaptation, Physiological ; Fungi/genetics ; Gene Expression Profiling ; *Gene Expression Regulation, Archaeal ; Halobacterium salinarum/*genetics ; *Stress, Physiological ; *Transcription, Genetic ; },
abstract = {The environmental stress response (ESR), a global transcriptional program originally identified in yeast, is characterized by a rapid and transient transcriptional response composed of large, oppositely regulated gene clusters. Genes induced during the ESR encode core components of stress tolerance, macromolecular repair, and maintenance of homeostasis. In this review, we investigate the possibility for conservation of the ESR across the eukaryotic and archaeal domains of life. We first re-analyze existing transcriptomics data sets to illustrate that a similar transcriptional response is identifiable in Halobacterium salinarum, an archaeal model organism. To substantiate the archaeal ESR, we calculated gene-by-gene correlations, gene function enrichment, and comparison of temporal dynamics. We note reported examples of variation in the ESR across fungi, then synthesize high-level trends present in expression data of other archaeal species. In particular, we emphasize the need for additional high-throughput time series expression data to further characterize stress-responsive transcriptional programs in the Archaea. Together, this review explores an open question regarding features of global transcriptional stress response programs shared across domains of life.},
}
@article {pmid31435153,
year = {2019},
author = {Bandyopadhyay, AK and Islam, RNU and Mitra, D and Banerjee, S and Goswami, A},
title = {Structural insights from water-ferredoxin interaction in mesophilic algae and halophilic archaea.},
journal = {Bioinformation},
volume = {15},
number = {2},
pages = {79-89},
pmid = {31435153},
issn = {0973-2063},
abstract = {We analyzed the water-ferredoxin interaction in mesophilic (moderate temperature) algae (PDB ID: 1AWD) and halophilic (salt-tolerant) archaea (PDB ID: 1DOI) using POWAIND version 2.0 (a protein-water interactions calculation program). It is found that the shell water (SW) is 2.5 fold greater in halophilic ferredoxin than mesophilic ferredoxin. Water-ferredoxin interactions in the core and cavity are the signature of stability. The normalized frequency of such interactions is less in halophilic relative to mesophilic ferredoxin and the halophilic signature for stability by such interactions is negligible. However, the surface dominated with such interactions seems to be important for ferredoxin and oxido-reductase recognition.},
}
@article {pmid31432245,
year = {2020},
author = {Sun, Y and Liu, Y and Pan, J and Wang, F and Li, M},
title = {Perspectives on Cultivation Strategies of Archaea.},
journal = {Microbial ecology},
volume = {79},
number = {3},
pages = {770-784},
pmid = {31432245},
issn = {1432-184X},
support = {31622002//NSFC/ ; 91851105//NSFC/ ; },
mesh = {Archaea/*growth &amp; development ; Bacteriological Techniques/instrumentation/*methods ; },
abstract = {Archaea have been recognized as a major domain of life since the 1970s and occupy a key position in the tree of life. Recent advances in culture-independent approaches have greatly accelerated the research son Archaea. However, many hypotheses concerning the diversity, physiology, and evolution of archaea are waiting to be confirmed by culture-base experiments. Consequently, archaeal isolates are in great demand. On the other hand, traditional approaches of archaeal cultivation are rarely successful and require urgent improvement. Here, we review the current practices and applicable microbial cultivation techniques, to inform on potential strategies that could improve archaeal cultivation in the future. We first summarize the current knowledge on archaeal diversity, with an emphasis on cultivated and uncultivated lineages pertinent to future research. Possible causes for the low success rate of the current cultivation practices are then discussed to propose future improvements. Finally, innovative insights for archaeal cultivation are described, including (1) medium refinement for selective cultivation based on the genetic and transcriptional information; (2) consideration of the up-to-date archaeal culturing skills; and (3) application of multiple cultivation techniques, such as co-culture, direct interspecies electron transfer (DIET), single-cell isolation, high-throughput culturing (HTC), and simulation of the natural habitat. Improved cultivation efforts should allow successful isolation of as yet uncultured archaea, contributing to the much-needed physiological investigation of archaea.},
}
@article {pmid31416876,
year = {2019},
author = {DasSarma, P and Anton, BP and DasSarma, SL and Martinez, FL and Guzman, D and Roberts, RJ and DasSarma, S},
title = {Genome Sequences and Methylation Patterns of Natrinema versiforme BOL5-4 and Natrinema pallidum BOL6-1, Two Extremely Halophilic Archaea from a Bolivian Salt Mine.},
journal = {Microbiology resource announcements},
volume = {8},
number = {33},
pages = {},
pmid = {31416876},
issn = {2576-098X},
abstract = {Two extremely halophilic archaea, namely, Natrinema versiforme BOL5-4 and Natrinema pallidum BOL6-1, were isolated from a Bolivian salt mine and their genomes sequenced using single-molecule real-time sequencing. The GC-rich genomes of BOL5-4 and BOL6-1 were 4.6 and 3.8 Mbp, respectively, with large chromosomes and multiple megaplasmids. Genome annotation was incorporated into HaloWeb and methylation patterns incorporated into REBASE.},
}
@article {pmid31411686,
year = {2019},
author = {Tang, Z and Chen, S and Chen, A and He, B and Zhou, Y and Chai, G and Guo, F and Huang, J},
title = {CasPDB: an integrated and annotated database for Cas proteins from bacteria and archaea.},
journal = {Database : the journal of biological databases and curation},
volume = {2019},
number = {},
pages = {},
pmid = {31411686},
issn = {1758-0463},
mesh = {Archaea/*genetics ; Archaeal Proteins/*genetics ; Bacteria/*genetics ; Bacterial Proteins/*genetics ; CRISPR-Associated Proteins/*genetics ; *CRISPR-Cas Systems ; *Databases, Protein ; },
abstract = {Clustered regularly interspaced short palindromic repeats (CRISPR) and associated proteins (Cas) constitute CRISPR-Cas systems, which are antiphage immune systems present in numerous bacterial and most archaeal species. In recent years, CRISPR-Cas systems have been developed into reliable and powerful genome editing tools. Nevertheless, finding similar or better tools from bacteria or archaea remains crucial. This requires the exploration of different CRISPR systems, identification and characterization new Cas proteins. Archives tailored for Cas proteins are urgently needed and necessitate the prediction and grouping of Cas proteins into an information center with all available experimental evidence. Here, we constructed Cas Protein Data Bank (CasPDB), an integrated and annotated online database for Cas proteins from bacteria and archaea. The CasPDB database contains 287 reviewed Cas proteins, 257 745 putative Cas proteins and 3593 Cas operons from 32 023 bacteria species and 1802 archaea species. The database can be freely browsed and searched. The CasPDB web interface also represents all the 3593 putative Cas operons and its components. Among these operons, 328 are members of the type II CRISPR-Cas system.},
}
@article {pmid31407306,
year = {2019},
author = {Yin, X and Kulkarni, AC and Friedrich, MW},
title = {DNA and RNA Stable Isotope Probing of Methylotrophic Methanogenic Archaea.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2046},
number = {},
pages = {189-206},
doi = {10.1007/978-1-4939-9721-3_15},
pmid = {31407306},
issn = {1940-6029},
mesh = {Archaea/*genetics ; Carbon/metabolism ; Carbon Isotopes/*analysis/chemistry ; Centrifugation, Density Gradient ; DNA Probes ; DNA, Archaeal/analysis/isolation &amp; purification/*metabolism ; Geologic Sediments/analysis/chemistry/microbiology ; Isotope Labeling/*methods ; Methane/metabolism ; Methanol ; Phylogeny ; RNA Probes ; RNA, Archaeal/analysis/isolation &amp; purification/*metabolism ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Methylotrophic methanogenic archaea are an integral part of the carbon cycle in various anaerobic environments. Different from methylotrophic bacteria, methylotrophic methanogens assimilate both, the methyl compound and dissolved inorganic carbon. Here, we present DNA- and RNA-stable isotope probing (SIP) methods involving an effective labeling strategy using 13C-labeled dissolved inorganic carbon (DIC) as carbon source along with methanol as dissimilatory substrate.},
}
@article {pmid31397430,
year = {2019},
author = {Khlebodarova, TM and Likhoshvai, VA},
title = {[Molecular Mechanisms of Non-Inherited Antibiotic Tolerance in Bacteria and Archaea].},
journal = {Molekuliarnaia biologiia},
volume = {53},
number = {4},
pages = {531-540},
doi = {10.1134/S0026898419040050},
pmid = {31397430},
issn = {0026-8984},
mesh = {Anti-Bacterial Agents/*pharmacology ; Archaea/cytology/*drug effects ; Bacteria/cytology/*drug effects ; *Drug Tolerance ; Toxin-Antitoxin Systems ; },
abstract = {The phenomenon of bacterial persistence, also known as non-inherited antibiotic tolerance in a part of bacterial populations, was described more than 70 years ago. This type of tolerance contributes to the chronization of infectious diseases, including tuberculosis. Currently, the emergence of persistent cells in bacterial populations is associated with the functioning of some stress-induced molecular triggers, including toxin-antitoxin systems. In the presented review, genetic and metabolic peculiarities of persistent cells are considered and the mechanisms of their occurrence are discussed. The hypothesis of the origin of persister cells based on bistability, arising due to the non-linear properties of a coupled transcription-translation system, was proposed. Within this hypothesis, the phenomenon of the bacterial persistence of modern cells is considered as a result of the genetic fixation of the phenotypic multiplicity that emerged in primitive cells in the process of neutrally coupled co-evolution (genetic drift of multiple neutrally coupled mutations). Our hypothesis explains the properties of persister cells, as well as their origin and "ineradicable" nature.},
}
@article {pmid31388130,
year = {2019},
author = {Steen, AD and Crits-Christoph, A and Carini, P and DeAngelis, KM and Fierer, N and Lloyd, KG and Cameron Thrash, J},
title = {High proportions of bacteria and archaea across most biomes remain uncultured.},
journal = {The ISME journal},
volume = {13},
number = {12},
pages = {3126-3130},
pmid = {31388130},
issn = {1751-7370},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; Ecosystem ; Phylogeny ; RNA, Ribosomal, 16S ; },
abstract = {A recent paper by Martiny argues that "high proportions" of bacteria in diverse Earth environments have been cultured. Here we reanalyze a portion of the data in that paper, and argue that the conclusion is based on several technical errors, most notably a calculation of sequence similarity that does not account for sequence gaps, and the reliance on 16S rRNA gene amplicons that are known to be biased towards cultured organisms. We further argue that the paper is also based on a conceptual error: namely, that sequence similarity cannot be used to infer "culturability" because one cannot infer physiology from 16S rRNA gene sequences. Combined with other recent, more reliable studies, the evidence supports the conclusion that most bacterial and archaeal taxa remain uncultured.},
}
@article {pmid31384725,
year = {2019},
author = {Blum, P and Payne, S},
title = {Evidence of an Epigenetics System in Archaea.},
journal = {Epigenetics insights},
volume = {12},
number = {},
pages = {2516865719865280},
pmid = {31384725},
issn = {2516-8657},
abstract = {Changes in the phenotype of a cell or organism that are heritable but do not involve changes in DNA sequence are referred to as epigenetic. They occur primarily through the gain or loss of chemical modification of chromatin protein or DNA. Epigenetics is therefore a non-Mendelian process. The study of epigenetics in eukaryotes is expanding with advances in knowledge about the relationship between mechanism and phenotype and as a requirement for multicellularity and cancer. However, life also includes other groups or domains, notably the bacteria and archaea. The occurrence of epigenetics in these deep lineages is an emerging topic accompanied by controversy. In these non-eukaryotic organisms, epigenetics is critically important because it stimulates new evolutionary theory and refines perspective about biological action.},
}
@article {pmid31384702,
year = {2019},
author = {MacLeod, F and Kindler, GS and Wong, HL and Chen, R and Burns, BP},
title = {Asgard archaea: Diversity, function, and evolutionary implications in a range of microbiomes.},
journal = {AIMS microbiology},
volume = {5},
number = {1},
pages = {48-61},
pmid = {31384702},
issn = {2471-1888},
abstract = {Elucidating the diversity of the Archaea has many important ecological and evolutionary implications. The Asgard superphylum of the archaea, described recently from metagenomic data, has reignited the decades-old debate surrounding the topology of the tree of life. This review synthesizes recent findings through publicly available genomes and literature to describe the current ecological and evolutionary significance of the Asgard superphylum. Asgard archaea have been found in a diverse range of microbiomes across the globe, primarily from sedimentary environments. Within these environments, positive correlations between specific members of the Asgard archaea and Candidate Division TA06 bacteria have been observed, opening up the possibility of symbiotic interactions between the groupings. Asgard archaeal genomes encode functionally diverse metabolic pathways, including the Wood-Ljungdahl pathway as a carbon-fixation strategy, putative nucleotide salvaging pathways, and novel mechanisms of phototrophy including new rhodopsins. Asgard archaea also appear to be active in nitrogen cycling. Asgard archaea encode genes involved in both dissimilatory nitrate reduction and denitrification, and for the potential to use atmospheric nitrogen or nitrite as nitrogen sources. Asgard archaea also may be involved in the transformation of sulfur compounds, indicating a putative role in sulfur cycling. To date, all Asgard archaeal genomes identified were described as obligately anaerobic. The Asgard archaea also appear to have important evolutionary implications. The presence of eukaryotic signature proteins and the affiliation of Asgard archaea in phylogenetic analyses appears to support two-domain topologies of the tree of life with eukaryotes emerging from within the domain of archaea, as opposed to the eukaryotes being a separate domain of life. Thus far, Heimdallarchaeota appears as the closest archaeal relative of eukaryotes.},
}
@article {pmid31377507,
year = {2019},
author = {Pan, KL and Gao, JF and Li, DC and Fan, XY},
title = {The dominance of non-halophilic archaea in autotrophic ammonia oxidation of activated sludge under salt stress: A DNA-based stable isotope probing study.},
journal = {Bioresource technology},
volume = {291},
number = {},
pages = {121914},
doi = {10.1016/j.biortech.2019.121914},
pmid = {31377507},
issn = {1873-2976},
mesh = {*Ammonia ; Archaea ; DNA ; Isotopes ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Salt Stress ; *Sewage ; Soil Microbiology ; },
abstract = {Dynamics of nitrification activity, ammonia-oxidizing archaea (AOA) and bacteria (AOB) abundance and active ammonia oxidizers of activated sludge were explored under different salinities. Results showed that specific ammonium oxidation rates were significantly negative with increasing salinity. The responses of AOA and AOB populations to salt stress were distinct. AOA abundance decreased at moderate salinities (2.5, 5 and 7 g L-1) and increased at high salinities (10, 15, 20 and 30 g L-1), while AOB abundance showed opposite tendency. DNA-based stable isotope probing assays indicated AOA exclusively dominated active ammonia oxidation of test samples under different salinities. The active AOA communities retrieved were all non-halophilic and regulated by salinities. Candidatus Nitrosocosmicus exaquare and Ca. Nitrosocosmicus franklandus were the predominantly active AOA in both salt-free and salt-containing microcosms, while 13C-labeled Nitrososphaera viennensis and Ca. Nitrososphaera gargensis were only retrieved from the microcosms amended with 0 and 30 g L-1 salinity, respectively.},
}
@article {pmid31364272,
year = {2019},
author = {Bird, LR and Dawson, KS and Chadwick, GL and Fulton, JM and Orphan, VJ and Freeman, KH},
title = {Carbon isotopic heterogeneity of coenzyme F430 and membrane lipids in methane-oxidizing archaea.},
journal = {Geobiology},
volume = {17},
number = {6},
pages = {611-627},
doi = {10.1111/gbi.12354},
pmid = {31364272},
issn = {1472-4669},
mesh = {Archaea/*chemistry ; California ; Carbon Isotopes/*analysis ; Geologic Sediments/microbiology ; Membrane Lipids/*chemistry ; Metalloporphyrins/*chemistry ; Methane/metabolism ; Oregon ; Oxidation-Reduction ; Pacific Ocean ; },
abstract = {Archaeal ANaerobic MEthanotrophs (ANME) facilitate the anaerobic oxidation of methane (AOM), a process that is believed to proceed via the reversal of the methanogenesis pathway. Carbon isotopic composition studies indicate that ANME are metabolically diverse and able to assimilate metabolites including methane, methanol, acetate, and dissolved inorganic carbon (DIC). Our data support the interpretation that ANME in marine sediments at methane seeps assimilate both methane and DIC, and the carbon isotopic compositions of the tetrapyrrole coenzyme F430 and the membrane lipids archaeol and hydroxy-archaeol reflect their relative proportions of carbon from these substrates. Methane is assimilated via the methyl group of CH3 -tetrahydromethanopterin (H4 MPT) and DIC from carboxylation reactions that incorporate free intracellular DIC. F430 was enriched in 13 C (mean δ13 C = -27‰ for Hydrate Ridge and -80‰ for the Santa Monica Basin) compared to the archaeal lipids (mean δ13 C = -97‰ for Hydrate Ridge and -122‰ for the Santa Monica Basin). We propose that depending on the side of the tricarboxylic acid (TCA) cycle used to synthesize F430, its carbon was derived from 76% DIC and 24% methane via the reductive side or 57% DIC and 43% methane via the oxidative side. ANME lipids are predicted to contain 42% DIC and 58% methane, reflecting the amount of each assimilated into acetyl-CoA. With isotope models that include variable fractionation during biosynthesis for different carbon substrates, we show the estimated amounts of DIC and methane can result in carbon isotopic compositions of - 73‰ to - 77‰ for F430 and - 105‰ for archaeal lipids, values close to those for Santa Monica Basin. The F430 δ13 C value for Hydrate Ridge was 13 C-enriched compared with the modeled value, suggesting there is divergence from the predicted two carbon source models.},
}
@article {pmid31363851,
year = {2019},
author = {Beyer, HM and Mikula, KM and Kudling, TV and Iwaï, H},
title = {Crystal structures of CDC21-1 inteins from hyperthermophilic archaea reveal the selection mechanism for the highly conserved homing endonuclease insertion site.},
journal = {Extremophiles : life under extreme conditions},
volume = {23},
number = {6},
pages = {669-679},
pmid = {31363851},
issn = {1433-4909},
support = {131413//Biotieteiden ja Ympäristön Tutkimuksen Toimikunta/ ; 137995//Biotieteiden ja Ympäristön Tutkimuksen Toimikunta/ ; 277335//Biotieteiden ja Ympäristön Tutkimuksen Toimikunta/ ; NNF17OC0025402//Novo Nordisk Foundation/ ; NNF17OC0027550//Novo Nordisk Foundation/ ; },
mesh = {Archaeal Proteins/*chemistry/genetics ; Endonucleases/*chemistry/genetics ; Enzyme Stability ; Hot Temperature ; *Inteins ; Protein Domains ; Pyrococcus abyssi/*enzymology/genetics ; Pyrococcus horikoshii/*enzymology/genetics ; },
abstract = {Self-splicing inteins are mobile genetic elements invading host genes via nested homing endonuclease (HEN) domains. All HEN domains residing within inteins are inserted at a highly conserved insertion site. A purifying selection mechanism directing the location of the HEN insertion site has not yet been identified. In this work, we solved the three-dimensional crystal structures of two inteins inserted in the cell division control protein 21 of the hyperthermophilic archaea Pyrococcus abyssi and Pyrococcus horikoshii. A comparison between the structures provides the structural basis for the thermo-stabilization mechanism of inteins that have lost the HEN domain during evolution. The presence of an entire extein domain in the intein structure from Pyrococcus horikoshii suggests the selection mechanism for the highly conserved HEN insertion point.},
}
@article {pmid31341668,
year = {2019},
author = {Taffner, J and Cernava, T and Erlacher, A and Berg, G},
title = {Novel insights into plant-associated archaea and their functioning in arugula (Eruca sativa Mill.).},
journal = {Journal of advanced research},
volume = {19},
number = {},
pages = {39-48},
pmid = {31341668},
issn = {2090-1232},
abstract = {A plant's microbiota has various implications for the plant's health and performance; however, the roles of many microbial lineages, particularly Archaea, have not been explored in detail. In the present study, analysis of archaea-specific 16S rRNA gene fragments and shotgun-sequenced metagenomes was combined with visualization techniques to obtain the first insights into the archaeome of a common salad plant, arugula (Eruca sativa Mill.). The archaeal communities associated with the soil, rhizosphere and phyllosphere were distinct, but a high proportion of community members were shared among all analysed habitats. Soil habitats exhibited the highest diversity of Archaea, followed by the rhizosphere and the phyllosphere. The archaeal community was dominated by Thaumarchaeota and Euryarchaeota, with the most abundant taxa assigned to Candidatus Nitrosocosmicus, species of the 'Soil Crenarchaeotic Group' and, interestingly, Methanosarcina. Moreover, a large number of archaea-assigned sequences remained unassigned at lower taxonomic levels. Overall, analysis of shotgun-sequenced total-community DNA revealed a more diverse archaeome. Differences were evident at the class level and at higher taxonomic resolutions when compared to results from the 16S rRNA gene fragment amplicon library. Functional assessments primarily revealed archaeal genes related to response to stress (especially oxidative stress), CO2 fixation, and glycogen degradation. Microscopic visualizations of fluorescently labelled archaea in the phyllosphere revealed small scattered colonies, while archaea in the rhizosphere were found to be embedded within large bacterial biofilms. Altogether, Archaea were identified as a rather small but niche-specific component of the microbiomes of the widespread leafy green plant arugula.},
}
@article {pmid31337720,
year = {2019},
author = {Shimosaka, T and Makarova, KS and Koonin, EV and Atomi, H},
title = {Identification of Dephospho-Coenzyme A (Dephospho-CoA) Kinase in Thermococcus kodakarensis and Elucidation of the Entire CoA Biosynthesis Pathway in Archaea.},
journal = {mBio},
volume = {10},
number = {4},
pages = {},
pmid = {31337720},
issn = {2150-7511},
mesh = {Biosynthetic Pathways ; Coenzyme A/*biosynthesis/metabolism ; Computational Biology ; Peptide Synthases/metabolism ; Phosphorylation ; Phosphotransferases (Alcohol Group Acceptor)/*genetics/*metabolism ; Thermococcus/*enzymology/*genetics ; },
abstract = {Dephospho-coenzyme A (dephospho-CoA) kinase (DPCK) catalyzes the ATP-dependent phosphorylation of dephospho-CoA, the final step in coenzyme A (CoA) biosynthesis. DPCK has been identified and characterized in bacteria and eukaryotes but not in archaea. The hyperthermophilic archaeon Thermococcus kodakarensis encodes two homologs of bacterial DPCK and the DPCK domain of eukaryotic CoA synthase, TK1334 and TK2192. We purified the recombinant TK1334 and TK2192 proteins and found that they lacked DPCK activity. Bioinformatic analyses showed that, in several archaea, the uncharacterized gene from arCOG04076 protein is fused with the gene for phosphopantetheine adenylyltransferase (PPAT), which catalyzes the reaction upstream of the DPCK reaction in CoA biosynthesis. This observation suggested that members of arCOG04076, both fused to PPAT and standalone, could be the missing archaeal DPCKs. We purified the recombinant TK1697 protein, a standalone member of arCOG04076 from T. kodakarensis, and demonstrated its GTP-dependent DPCK activity. Disruption of the TK1697 resulted in CoA auxotrophy, indicating that TK1697 encodes a DPCK that contributes to CoA biosynthesis in T. kodakarensis TK1697 homologs are widely distributed in archaea, suggesting that the arCOG04076 protein represents a novel family of DPCK that is not homologous to bacterial and eukaryotic DPCKs but is distantly related to bacterial and eukaryotic thiamine pyrophosphokinases. We also constructed and characterized gene disruption strains of TK0517 and TK2128, homologs of bifunctional phosphopantothenoylcysteine synthetase-phosphopantothenoylcysteine decarboxylase and PPAT, respectively. Both strains displayed CoA auxotrophy, indicating their contribution to CoA biosynthesis. Taken together with previous studies, the results experimentally validate the entire CoA biosynthesis pathway in T. kodakarensis IMPORTANCE CoA is utilized in a wide range of metabolic pathways, and its biosynthesis is essential for all life. Pathways for CoA biosynthesis in bacteria and eukaryotes have been established. In archaea, however, the enzyme that catalyzes the final step in CoA biosynthesis, dephospho-CoA kinase (DPCK), had not been identified. In the present study, bioinformatic analyses identified a candidate for the DPCK in archaea, which was biochemically and genetically confirmed in the hyperthermophilic archaeon Thermococcus kodakarensis Genetic analyses on genes presumed to encode bifunctional phosphopantothenoylcysteine synthetase-phosphopantothenoylcysteine decarboxylase and phosphopantetheine adenylyltransferase confirmed their involvement in CoA biosynthesis. Taken together with previous studies, the results reveal the entire pathway for CoA biosynthesis in a single archaeon and provide insight into the different mechanisms of CoA biosynthesis and their distribution in nature.},
}
@article {pmid31336026,
year = {2019},
author = {Bayer, B and Hansman, RL and Bittner, MJ and Noriega-Ortega, BE and Niggemann, J and Dittmar, T and Herndl, GJ},
title = {Ammonia-oxidizing archaea release a suite of organic compounds potentially fueling prokaryotic heterotrophy in the ocean.},
journal = {Environmental microbiology},
volume = {21},
number = {11},
pages = {4062-4075},
pmid = {31336026},
issn = {1462-2920},
support = {P28781-B21//Austrian Science Fund/International ; W1257-B20//Austrian Science Fund/International ; },
mesh = {Ammonia/*metabolism ; Archaea/*metabolism ; Carbon/metabolism ; Chemoautotrophic Growth/physiology ; Heterotrophic Processes/*physiology ; Oceans and Seas ; Organic Chemicals/*metabolism ; Oxidation-Reduction ; Phylogeny ; },
abstract = {Ammonia-oxidizing archaea (AOA) constitute a considerable fraction of microbial biomass in the global ocean, comprising 20%-40% of the ocean's prokaryotic plankton. However, it remains enigmatic to what extent these chemolithoautotrophic archaea release dissolved organic carbon (DOC). A combination of targeted and untargeted metabolomics was used to characterize the exometabolomes of three model AOA strains of the Nitrosopumilus genus. Our results indicate that marine AOA exude a suite of organic compounds with potentially varying reactivities, dominated by nitrogen-containing compounds. A significant fraction of the released dissolved organic matter (DOM) consists of labile compounds, which typically limit prokaryotic heterotrophic activity in open ocean waters, including amino acids, thymidine and B vitamins. Amino acid release rates corresponded with ammonia oxidation activity and the three Nitrosopumilus strains predominantly released hydrophobic amino acids, potentially as a result of passive diffusion. Despite the low contribution of DOC released by AOA (~0.08%-1.05%) to the heterotrophic prokaryotic carbon demand, the release of physiologically relevant metabolites could be crucial for microbes that are auxotrophic for some of these compounds, including members of the globally abundant and ubiquitous SAR11 clade.},
}
@article {pmid31332386,
year = {2019},
author = {Roux, S and Krupovic, M and Daly, RA and Borges, AL and Nayfach, S and Schulz, F and Sharrar, A and Matheus Carnevali, PB and Cheng, JF and Ivanova, NN and Bondy-Denomy, J and Wrighton, KC and Woyke, T and Visel, A and Kyrpides, NC and Eloe-Fadrosh, EA},
title = {Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth's biomes.},
journal = {Nature microbiology},
volume = {4},
number = {11},
pages = {1895-1906},
pmid = {31332386},
issn = {2058-5276},
support = {DP5 OD021344/OD/NIH HHS/United States ; R01 GM127489/GM/NIGMS NIH HHS/United States ; T32 AI060537/AI/NIAID NIH HHS/United States ; },
mesh = {Archaea/*virology ; Archaeal Viruses/classification/genetics ; Bacteria/*virology ; Bacteriophages/classification/genetics ; Computational Biology/*methods ; Genome, Viral ; Inoviridae/*classification/genetics ; Machine Learning ; Phylogeny ; },
abstract = {Bacteriophages from the Inoviridae family (inoviruses) are characterized by their unique morphology, genome content and infection cycle. One of the most striking features of inoviruses is their ability to establish a chronic infection whereby the viral genome resides within the cell in either an exclusively episomal state or integrated into the host chromosome and virions are continuously released without killing the host. To date, a relatively small number of inovirus isolates have been extensively studied, either for biotechnological applications, such as phage display, or because of their effect on the toxicity of known bacterial pathogens including Vibrio cholerae and Neisseria meningitidis. Here, we show that the current 56 members of the Inoviridae family represent a minute fraction of a highly diverse group of inoviruses. Using a machine learning approach leveraging a combination of marker gene and genome features, we identified 10,295 inovirus-like sequences from microbial genomes and metagenomes. Collectively, our results call for reclassification of the current Inoviridae family into a viral order including six distinct proposed families associated with nearly all bacterial phyla across virtually every ecosystem. Putative inoviruses were also detected in several archaeal genomes, suggesting that, collectively, members of this supergroup infect hosts across the domains Bacteria and Archaea. Finally, we identified an expansive diversity of inovirus-encoded toxin-antitoxin and gene expression modulation systems, alongside evidence of both synergistic (CRISPR evasion) and antagonistic (superinfection exclusion) interactions with co-infecting viruses, which we experimentally validated in a Pseudomonas model. Capturing this previously obscured component of the global virosphere may spark new avenues for microbial manipulation approaches and innovative biotechnological applications.},
}
@article {pmid31320751,
year = {2019},
author = {Eloe-Fadrosh, EA},
title = {Genome gazing in ammonia-oxidizing archaea.},
journal = {Nature reviews. Microbiology},
volume = {17},
number = {9},
pages = {531},
doi = {10.1038/s41579-019-0248-8},
pmid = {31320751},
issn = {1740-1534},
mesh = {Ammonia/metabolism ; Archaea/*genetics/metabolism/virology ; *Genome, Archaeal ; *Interspersed Repetitive Sequences ; Metabolic Networks and Pathways/*genetics ; Oxidation-Reduction ; Viruses/genetics ; },
}
@article {pmid31314099,
year = {2019},
author = {Liu, TT and Yang, H},
title = {An RNA-based quantitative and compositional study of ammonium-oxidizing bacteria and archaea in Lake Taihu, a eutrophic freshwater lake.},
journal = {FEMS microbiology ecology},
volume = {95},
number = {9},
pages = {},
doi = {10.1093/femsec/fiz117},
pmid = {31314099},
issn = {1574-6941},
mesh = {Ammonium Compounds/*metabolism ; Archaea/classification/genetics/growth &amp; development/*metabolism ; Bacteria/classification/genetics/growth &amp; development/*metabolism ; Biodiversity ; Geologic Sediments/microbiology ; Lakes/chemistry/*microbiology ; Microbiota ; Nitrification ; Oxidation-Reduction ; Phylogeny ; RNA, Bacterial/genetics ; },
abstract = {Ammonium-oxidizing archaea (AOA) and bacteria (AOB) play crucial roles in ammonium oxidation in freshwater lake sediment. However, previous reports on the predominance of AOA and AOB in the surface sediment of Lake Taihu have been based on DNA levels, detecting the total abundance of microbiota (including inactive cells), and have resulted in numerous contradictory conclusions. Existing RNA-level studies detecting active transcription are very limited. The current study, using RNA-based real-time quantification and clone library analysis, demonstrated that the amoA gene abundance of active AOB was higher than that of active AOA, despite conflicting results at the DNA level. Further exploration revealed a significant positive correlation between the potential nitrification rate (PNR) and the abundance of AOA and AOB at the RNA level, with irregular or contradictory correlation found at the DNA level. Ultimately, using quantitative analysis of RNA levels, we show AOB to be the active dominant contributor to ammonium oxidation. Our investigations also indicated that AOB were more diverse in high-ammonium lake regions, with Nitrosomonas being the active and dominating cluster, but that AOA had an advantage in the low-ammonium lake regions.},
}
@article {pmid31312729,
year = {2019},
author = {DeMott, MS and Dedon, PC},
title = {The road less traveled: A new phosphorothioate antiviral defense mechanism discovered in Archaea.},
journal = {Synthetic and systems biotechnology},
volume = {4},
number = {3},
pages = {132-133},
pmid = {31312729},
issn = {2405-805X},
}
@article {pmid31283101,
year = {2019},
author = {Schwarz, TS and Wäber, NB and Feyh, R and Weidenbach, K and Schmitz, RA and Marchfelder, A and Hartmann, RK},
title = {Homologs of aquifex aeolicus protein-only RNase P are not the major RNase P activities in the archaea haloferax volcanii and methanosarcina mazei.},
journal = {IUBMB life},
volume = {71},
number = {8},
pages = {1109-1116},
doi = {10.1002/iub.2122},
pmid = {31283101},
issn = {1521-6551},
mesh = {Aquifex ; Bacteria/*enzymology ; Catalysis ; Circular Dichroism ; Escherichia coli/metabolism ; Gene Deletion ; Genetic Complementation Test ; Haloferax volcanii/*enzymology ; Methanosarcina/*enzymology ; Nucleic Acid Conformation ; Phenotype ; Plasmids/genetics ; RNA, Transfer/genetics ; Recombinant Proteins/metabolism ; Ribonuclease P/*metabolism ; Species Specificity ; Temperature ; Thermus thermophilus/enzymology ; },
abstract = {The mature 5'-ends of tRNAs are generated by RNase P in all domains of life. The ancient form of the enzyme is a ribonucleoprotein consisting of a catalytic RNA and one or more protein subunits. However, in the hyperthermophilic bacterium Aquifex aeolicus and close relatives, RNase P is a protein-only enzyme consisting of a single type of polypeptide (Aq_880, ~23 kDa). In many archaea, homologs of Aq_880 were identified (termed HARPs for Homologs of Aquifex RNase P) in addition to the RNA-based RNase P, raising the question about the functions of HARP and the classical RNase P in these archaea. Here we investigated HARPs from two euryarchaeotes, Haloferax volcanii and Methanosarcina mazei. Archaeal strains with HARP gene knockouts showed no growth phenotypes under standard conditions, temperature and salt stress (H. volcanii) or nitrogen deficiency (M. mazei). Recombinant H. volcanii and M. mazei HARPs were basically able to catalyse specific tRNA 5'-end maturation in vitro. Furthermore, M. mazei HARP was able to rescue growth of an Escherichia coli RNase P depletion strain with comparable efficiency as Aq_880, while H. volcanii HARP was unable to do so. In conclusion, both archaeal HARPs showed the capacity (in at least one functional assay) to act as RNases P. However, the ease to obtain knockouts of the singular HARP genes and the lack of growth phenotypes upon HARP gene deletion contrasts with the findings that the canonical RNase P RNA gene cannot be deleted in H. volcanii, and a knockdown of RNase P RNA in H. volcanii results in severe tRNA processing defects. We conclude that archaeal HARPs do not make a major contribution to global tRNA 5'-end maturation in archaea, but may well exert a specialised, yet unknown function in (t)RNA metabolism. © 2019 IUBMB Life, 2019 © 2019 IUBMB Life, 71(8):1109-1116, 2019.},
}
@article {pmid31270201,
year = {2019},
author = {DasSarma, S and Fomenkov, A and DasSarma, SL and Vincze, T and DasSarma, P and Roberts, RJ},
title = {Methylomes of Two Extremely Halophilic Archaea Species, Haloarcula marismortui and Haloferax mediterranei.},
journal = {Microbiology resource announcements},
volume = {8},
number = {27},
pages = {},
pmid = {31270201},
issn = {2576-098X},
abstract = {The genomes of two extremely halophilic Archaea species, Haloarcula marismortui and Haloferax mediterranei, were sequenced using single-molecule real-time sequencing. The ∼4-Mbp genomes are GC rich with multiple large plasmids and two 4-methyl-cytosine patterns. Methyl transferases were incorporated into the Restriction Enzymes Database (REBASE), and gene annotation was incorporated into the Haloarchaeal Genomes Database (HaloWeb).},
}
@article {pmid31264806,
year = {2019},
author = {Pereira, O and Hochart, C and Auguet, JC and Debroas, D and Galand, PE},
title = {Genomic ecology of Marine Group II, the most common marine planktonic Archaea across the surface ocean.},
journal = {MicrobiologyOpen},
volume = {8},
number = {9},
pages = {e00852},
pmid = {31264806},
issn = {2045-8827},
mesh = {Aquatic Organisms/*classification/*genetics ; Euryarchaeota/*classification/*genetics ; Metabolic Networks and Pathways/genetics ; Metagenomics ; *Microbiota ; *Oceans and Seas ; Phylogeny ; Rhodopsins, Microbial/genetics ; Seawater/*microbiology ; },
abstract = {Planktonic Archaea have been detected in all the world's oceans and are found from surface waters to the deep sea. The two most common Archaea phyla are Thaumarchaeota and Euryarchaeota. Euryarchaeota are generally more common in surface waters, but very little is known about their ecology and their potential metabolisms. In this study, we explore the genomic ecology of the Marine Group II (MGII), the main marine planktonic Euryarchaeota, and test if it is composed of different ecologically relevant units. We re-analyzed Tara Oceans metagenomes from the photic layer and the deep ocean by annotating sequences against a custom MGII database and by mapping gene co-occurrences. Our data provide a global view of the distribution of Euryarchaeota, and more specifically of MGII subgroups, and reveal their association to a number of gene-coding sequences. In particular, we show that MGII proteorhodopsins were detected in both the surface and the deep chlorophyll maximum layer and that different clusters of these light harvesting proteins were present. Our approach helped describing the set of genes found together with specific MGII subgroups. We could thus define genomic environments that could theoretically describe ecologically meaningful units and the ecological niche that they occupy.},
}
@article {pmid31249623,
year = {2019},
author = {Zhao, X and Li, X and Li, Y and Sun, Y and Zhang, X and Weng, L and Ren, T and Li, Y},
title = {Shifting interactions among bacteria, fungi and archaea enhance removal of antibiotics and antibiotic resistance genes in the soil bioelectrochemical remediation.},
journal = {Biotechnology for biofuels},
volume = {12},
number = {},
pages = {160},
pmid = {31249623},
issn = {1754-6834},
abstract = {BACKGROUND: Antibiotics and antibiotic resistance genes (ARGs) are two pollutants in soil, especially ARGs as one of the top three threats to human health. The performance of soil microbial fuel cells (MFCs) fuelled with antibiotics was investigated.<br><br>RESULTS: In this study, soil MFCs spiked with tetracycline exhibited optimal bioelectricity generation, which was 25% and 733% higher than those of MFCs spiked with sulfadiazine and control, respectively. Compared with the non-electrode treatment, not only did functional micro-organisms change in open- and closed-circuit treatments, but also the microbial affinities, respectively, increased by 50% and 340% to adapt to higher removal of antibiotics. For the open-circuit treatment, the ineffective interspecific relation of micro-organisms was reduced to assist the removal efficiency of antibiotics by 7-27%. For the closed-circuit treatment, an intensive metabolic network capable of bioelectricity generation, degradation and nitrogen transformation was established, which led to 10-35% higher removal of antibiotics. Importantly, the abundances of ARGs and mobile genetic element (MGE) genes decreased after the introduction of electrodes; especially in the closed-circuit treatment, the highest reduction of 47% and 53% was observed, respectively.<br><br>CONCLUSIONS: Soil MFCs possess advantages for the elimination of antibiotics and ARGs with sevenfold to eightfold higher electricity generation than that of the control treatment. Compared with sulphonamides, the enhancement removal of tetracycline is higher, while both potential ARG propagation risk is reduced in soil MFCs. This study firstly synchronously reveals the relationships among bacteria, fungi and archaea and with ARGs and MGE genes in soil bioelectrochemical systems.},
}
@article {pmid31249390,
year = {2019},
author = {Trivedi, C and Reich, PB and Maestre, FT and Hu, HW and Singh, BK and Delgado-Baquerizo, M},
title = {Plant-driven niche differentiation of ammonia-oxidizing bacteria and archaea in global drylands.},
journal = {The ISME journal},
volume = {13},
number = {11},
pages = {2727-2736},
pmid = {31249390},
issn = {1751-7370},
mesh = {Ammonia/*metabolism ; Archaea/genetics/*metabolism ; Bacteria/classification/genetics/*metabolism ; Betaproteobacteria/metabolism ; Climate ; Ecosystem ; Environment ; Nitrification ; Oxidation-Reduction ; Phylogeny ; *Soil Microbiology ; },
abstract = {Under controlled laboratory conditions, high and low ammonium availability are known to favor soil ammonia-oxidizing bacteria (AOB) and archaea (AOA) communities, respectively. However, whether this niche segregation is maintained under field conditions in terrestrial ecosystems remains unresolved, particularly at the global scale. We hypothesized that perennial vegetation might favor AOB vs. AOA communities compared with adjacent open areas devoid of perennial vegetation (i.e., bare soil) via several mechanisms, including increasing the amount of ammonium in soil. To test this niche-differentiation hypothesis, we conducted a global field survey including 80 drylands from 6 continents. Data supported our hypothesis, as soils collected under plant canopies had higher levels of ammonium, as well as higher richness (number of terminal restriction fragments; T-RFs) and abundance (qPCR amoA genes) of AOB, and lower richness and abundance of AOA, than those collected in open areas located between plant canopies. Some of the reported associations between plant canopies and AOA and AOB communities can be a consequence of the higher organic matter and available N contents found under plant canopies. Other aspects of soils associated with vegetation including shading and microclimatic conditions might also help explain our results. Our findings provide strong evidence for niche differentiation between AOA and AOB communities in drylands worldwide, advancing our understanding of their ecology and biogeography at the global scale.},
}
@article {pmid31249385,
year = {2019},
author = {Zhang, H and Sun, H and Zhou, S and Bai, N and Zheng, X and Li, S and Zhang, J and Lv, W},
title = {Effect of Straw and Straw Biochar on the Community Structure and Diversity of Ammonia-oxidizing Bacteria and Archaea in Rice-wheat Rotation Ecosystems.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {9367},
pmid = {31249385},
issn = {2045-2322},
mesh = {Agriculture/methods ; *Ammonia/metabolism ; *Archaea/classification/genetics/metabolism ; *Bacteria/classification/genetics/metabolism ; Crops, Agricultural ; *Ecosystem ; Fertilizers ; Nitrification ; *Oryza/growth &amp; development ; *Oxidation-Reduction ; Soil/chemistry ; *Soil Microbiology ; *Triticum/growth &amp; development ; },
abstract = {Ammonia oxidation is the first and rate-limiting step of nitrification, driven by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). Straw and straw biochar retention are the popular ways to utilize the agricultural by-products in China, but their long-term effects on AOB and AOA still remain poorly understood. Based on a 7-year plot experiment, which had 4 fertilization regimes: no fertilizer (CK), regular fertilization (RT), straw retention (SR) and straw biochar retention (SB), the abundance and the composition of AOB and AOA was investigated before both the harvest of rice and wheat season by quantitative PCR and 454 high-throughput pyrosequencing, respectively. (1) Compared to RT, straw and straw biochar increased AOB abundance and diversity significantly only in wheat season (P < 0.05), and they both ranked as SB > SR > RT. Among fertilized treatments, a significant difference between SR and RT was found in AOB community composition of the winter season (R value = 0.58, P value = 0.02); (2) In contrast, AOA was almost not responsive to organic addition, except the significant enhancement of abundance by biochar in wheat season; (3) After straw and straw biochar addition, soil potential nitrification rates (PNR) was positive correlated to AOB abundance in both rice and wheat season (P < 0.01), not to AOA abundance (P = 0.211 and 0.068, respectively). This study provides scientific support for the potential of straw utilization to improve nitrification in rice-wheat rotation system with respect to soil ammonia oxidation microorganism.},
}
@article {pmid31239395,
year = {2019},
author = {Bayer, B and Pelikan, C and Bittner, MJ and Reinthaler, T and Könneke, M and Herndl, GJ and Offre, P},
title = {Proteomic Response of Three Marine Ammonia-Oxidizing Archaea to Hydrogen Peroxide and Their Metabolic Interactions with a Heterotrophic Alphaproteobacterium.},
journal = {mSystems},
volume = {4},
number = {4},
pages = {},
pmid = {31239395},
issn = {2379-5077},
abstract = {Ammonia-oxidizing archaea (AOA) play an important role in the nitrogen cycle and account for a considerable fraction of the prokaryotic plankton in the ocean. Most AOA lack the hydrogen peroxide (H2O2)-detoxifying enzyme catalase, and some AOA have been shown to grow poorly under conditions of exposure to H2O2 However, differences in the degrees of H2O2 sensitivity of different AOA strains, the physiological status of AOA cells exposed to H2O2, and their molecular response to H2O2 remain poorly characterized. Further, AOA might rely on heterotrophic bacteria to detoxify H2O2, and yet the extent and variety of costs and benefits involved in these interactions remain unclear. Here, we used a proteomics approach to compare the protein profiles of three Nitrosopumilus strains grown in the presence and absence of catalase and in coculture with the heterotrophic alphaproteobacterium Oceanicaulis alexandrii We observed that most proteins detected at a higher relative abundance in H2O2-exposed Nitrosopumilus cells had no known function in oxidative stress defense. Instead, these proteins were putatively involved in the remodeling of the extracellular matrix, which we hypothesize to be a strategy limiting the influx of H2O2 into the cells. Using RNA-stable isotope probing, we confirmed that O. alexandrii cells growing in coculture with the Nitrosopumilus strains assimilated Nitrosopumilus-derived organic carbon, suggesting that AOA could recruit H2O2-detoxifying bacteria through the release of labile organic matter. Our results contribute new insights into the response of AOA to H2O2 and highlight the potential ecological importance of their interactions with heterotrophic free-living bacteria in marine environments.IMPORTANCE Ammonia-oxidizing archaea (AOA) are the most abundant chemolithoautotrophic microorganisms in the oxygenated water column of the global ocean. Although H2O2 appears to be a universal by-product of aerobic metabolism, genes encoding the hydrogen peroxide (H2O2)-detoxifying enzyme catalase are largely absent in genomes of marine AOA. Here, we provide evidence that closely related marine AOA have different degrees of sensitivity to H2O2, which may contribute to niche differentiation between these organisms. Furthermore, our results suggest that marine AOA rely on H2O2 detoxification during periods of high metabolic activity and release organic compounds, thereby potentially attracting heterotrophic prokaryotes that provide this missing function. In summary, this report provides insights into the metabolic interactions between AOA and heterotrophic bacteria in marine environments and suggests that AOA play an important role in the biogeochemical carbon cycle by making organic carbon available for heterotrophic microorganisms.},
}
@article {pmid31237975,
year = {2019},
author = {Horai, S and Yamauchi, N and Naraoka, H},
title = {Simultaneous total analysis of core and polar membrane lipids in archaea by high-performance liquid chromatography/high-resolution mass spectrometry coupled with heated electrospray ionization.},
journal = {Rapid communications in mass spectrometry : RCM},
volume = {33},
number = {20},
pages = {1571-1577},
doi = {10.1002/rcm.8506},
pmid = {31237975},
issn = {1097-0231},
support = {KAKENHI Grant JP15H05749//Japan Society for the Promotion of Science/ ; },
abstract = {RATIONALE: Archaea have characteristic membrane lipids including diether and/or tetraether isoprenoidal core lipids with various polar head groups. Since the polar group is removed soon after the end of archaeal activity, the occurrences of core and polar lipids are regarded as dead and active signals, respectively. The core and polar lipids have generally been analyzed separately using atmospheric pressure chemical ionization (APCI) and electrospray ionization (ESI), respectively, coupled with mass spectrometry.<br><br>METHODS: In this study, simultaneous analyses of core and polar archaeal lipids have been examined using heated electrospray ionization (HESI) by high-performance liquid chromatography/high-resolution mass spectrometry (HPLC/HRMS).<br><br>RESULTS: Both core and intact polar lipids can be analyzed simultaneously by HESI with good sensitivity (sub ng to 100 ng) and separation using a semi-bore diol column by normal-phase chromatography. The core lipids eluted firstly to separate archeaol, then glycerol dibiphytanyl glycerol tetraethers (GDGTs), followed by the polar lipids with glycosides and glycophosphates. The relative GDGT composition is identical between HESI and APCI methods.<br><br>CONCLUSIONS: The simultaneous analysis has the benefit of minimizing sample amount and elution solvent as well as preparation work. The method can also be applied to a compound class fractionation for compound-specific carbon and hydrogen isotope analysis.},
}
@article {pmid31223656,
year = {2019},
author = {Vuillemin, A and Wankel, SD and Coskun, ÖK and Magritsch, T and Vargas, S and Estes, ER and Spivack, AJ and Smith, DC and Pockalny, R and Murray, RW and D'Hondt, S and Orsi, WD},
title = {Archaea dominate oxic subseafloor communities over multimillion-year time scales.},
journal = {Science advances},
volume = {5},
number = {6},
pages = {eaaw4108},
pmid = {31223656},
issn = {2375-2548},
mesh = {Ammonia/metabolism ; Archaea/*metabolism/*physiology ; Carbon Cycle/physiology ; Geologic Sediments/microbiology ; Microbiota/physiology ; Nitrogen/metabolism ; Nitrogen Cycle/physiology ; Oxidation-Reduction ; Water Microbiology ; },
abstract = {Ammonia-oxidizing archaea (AOA) dominate microbial communities throughout oxic subseafloor sediment deposited over millions of years in the North Atlantic Ocean. Rates of nitrification correlated with the abundance of these dominant AOA populations, whose metabolism is characterized by ammonia oxidation, mixotrophic utilization of organic nitrogen, deamination, and the energetically efficient chemolithoautotrophic hydroxypropionate/hydroxybutyrate carbon fixation cycle. These AOA thus have the potential to couple mixotrophic and chemolithoautotrophic metabolism via mixotrophic deamination of organic nitrogen, followed by oxidation of the regenerated ammonia for additional energy to fuel carbon fixation. This metabolic feature likely reduces energy loss and improves AOA fitness under energy-starved, oxic conditions, thereby allowing them to outcompete other taxa for millions of years.},
}
@article {pmid31212151,
year = {2019},
author = {Zhang, X and Duan, P and Wu, Z and Xiong, Z},
title = {Aged biochar stimulated ammonia-oxidizing archaea and bacteria-derived N2O and NO production in an acidic vegetable soil.},
journal = {The Science of the total environment},
volume = {687},
number = {},
pages = {433-440},
doi = {10.1016/j.scitotenv.2019.06.128},
pmid = {31212151},
issn = {1879-1026},
mesh = {Agriculture ; Ammonia/*metabolism ; Archaea ; Bacteria ; Charcoal/*chemistry ; Nitrogen Oxides/analysis/*metabolism ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {Both nitrous oxide (N2O) and nitric oxide (NO) emissions are typically high in greenhouse-based high N input vegetable soils. Biochar amendment has been widely recommended for mitigating soil N2O emissions in agriculture. However, knowledge of the regulatory mechanisms of fresh and aged biochar for both N2O and NO production during ammonia oxidation is lacking. Two vegetable soils with different pH values were used in aerobic incubation experiments with 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO), 1-octyne and acetylene. The relative importance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) to N2O and NO production was investigated as influenced by fresh and aged biochar amendments. The results showed that AOA dominated N2O production in acidic soil, while AOB dominated N2O production in alkaline soil. Aged biochar stimulated both AOA- and AOB-derived N2O and NO production by 84.8 and 340%, respectively, in acidic soil but only increased AOA-derived N2O and NO production in alkaline soil. Fresh biochar amendment increased AOA- and AOB-derived NO in acidic soil and AOA-derived NO in alkaline soil but had negligible effects on AOA- and AOB-derived N2O in both soils. Fresh biochar decreased AOA-amoA but increased AOB-amoA gene abundances in acidic soil, whereas aged biochar increased AOA- and AOB-amoA gene abundances in both soils. These findings improved our understanding of N2O and NO production mechanisms under different biochar amendments in alkaline and acidic vegetable soils.},
}
@article {pmid31196534,
year = {2019},
author = {Kırtel, O and Lescrinier, E and Van den Ende, W and Toksoy Öner, E},
title = {Discovery of fructans in Archaea.},
journal = {Carbohydrate polymers},
volume = {220},
number = {},
pages = {149-156},
doi = {10.1016/j.carbpol.2019.05.064},
pmid = {31196534},
issn = {1879-1344},
mesh = {Evolution, Molecular ; *Fructans/chemistry/metabolism ; *Halobacteriaceae/classification/metabolism ; *Inulin/chemistry/metabolism ; Lakes/*microbiology ; Salinity ; Turkey ; Water Microbiology ; },
abstract = {Fructans are fructose-based oligo- and polysaccharides derived from sucrose that occur in a plethora of Eubacteria and plants. While fructan-producing (fructanogenic) Eubacteria are abundant in hypersaline environments, fructan production by Archaea has never been reported before. Exopolysaccharides accumulated by various Archaea from the Halobacteria class (belonging to the genera of Halomicrobium, Haloferax and Natronococcus) originating from different locations on Earth were structurally characterized as either levans or inulins with varying branching degrees (10%-16%). Thus, we show for the first time in the literature that fructans are produced in all three domains of life, including Archaea. This proof of concept will not only provide insight into Archaeal glycans and evolution but it may also open new frontiers for innovative strategies to overcome the ever-increasing threat of excessive salinization.},
}
@article {pmid31195017,
year = {2019},
author = {Lemmens, L and Maklad, HR and Bervoets, I and Peeters, E},
title = {Transcription Regulators in Archaea: Homologies and Differences with Bacterial Regulators.},
journal = {Journal of molecular biology},
volume = {431},
number = {20},
pages = {4132-4146},
doi = {10.1016/j.jmb.2019.05.045},
pmid = {31195017},
issn = {1089-8638},
mesh = {Archaea/*genetics/metabolism ; Evolution, Molecular ; Gene Expression Regulation, Archaeal ; Transcription Factors/genetics/*metabolism ; *Transcription, Genetic ; },
abstract = {The fitness and survival of prokaryotic microorganisms depends on their ability to adequately respond to environmental changes, sudden stress conditions and metabolic shifts. An important mechanism underlying this response is the regulation of gene expression mediated by transcription factors that are responsive to small-molecule ligands or other intracellular signals. Despite constituting a distinct domain of life from bacteria and harboring a eukaryotic-like basal transcription apparatus, it is well established that archaea have similar transcription factors pointing to the existence of shared ancestral proteins and to the occurrence of inter-domain horizontal gene transfer events. However, while global structural features of bacterial and archaeal transcription factors are indeed similar, other characteristics imply that archaeal regulators have undergone independent evolution. Here, we discuss the characteristics of Lrp/AsnC, MarR, ArsR/SmtB and TrmB families of transcription factors, which are the dominant families that constitute the transcription factor repertoire in archaea. We exemplify the evolutionary expansion of these families in archaeal lineages by emphasizing homologies and differences with bacterial counterparts in terms of ligand or signal response, physiological functions and mechanistic principles of regulation. As such, we aim to define future research approaches that enable further characterization of the functions and mechanisms of archaeal transcription factors.},
}
@article {pmid31189733,
year = {2019},
author = {Ludt, K and Soppa, J},
title = {Polyploidy in halophilic archaea: regulation, evolutionary advantages, and gene conversion.},
journal = {Biochemical Society transactions},
volume = {47},
number = {3},
pages = {933-944},
doi = {10.1042/BST20190256},
pmid = {31189733},
issn = {1470-8752},
mesh = {Archaea/*genetics ; Chromosomes, Archaeal ; *Evolution, Molecular ; *Gene Conversion ; *Genes, Archaeal ; *Polyploidy ; Replication Origin ; },
abstract = {All analyzed haloarachea are polyploid. In addition, haloarchaea contain more than one type of chromosome, and thus the gene dosage can be regulated independently on different replicons. Haloarchaea and several additional archaea have more than one replication origin on their major chromosome, in stark contrast with bacteria, which have a single replication origin. Two of these replication origins of Haloferax volcanii have been studied in detail and turned out to have very different properties. The chromosome copy number appears to be regulated in response to growth phases and environmental factors. Archaea typically contain about two Origin Recognition Complex (ORC) proteins, which are homologous to eukaryotic ORC proteins. However, haloarchaea are the only archaeal group that contains a multitude of ORC proteins. All 16 ORC protein paralogs from H. volcanii are involved in chromosome copy number regulation. Polyploidy has many evolutionary advantages for haloarchaea, e.g. a high resistance to desiccation, survival over geological times, and the relaxation of cell cycle-specific replication control. A further advantage is the ability to grow in the absence of external phosphate while using the many genome copies as internal phosphate storage polymers. Very efficient gene conversion operates in haloarchaea and results in the unification of genome copies. Taken together, haloarchaea are excellent models to study many aspects of genome biology in prokaryotes, exhibiting properties that have not been found in bacteria.},
}
@article {pmid31184586,
year = {2019},
author = {Killelea, T and Palud, A and Akcha, F and Lemor, M and L'haridon, S and Godfroy, A and Henneke, G},
title = {The interplay at the replisome mitigates the impact of oxidative damage on the genetic integrity of hyperthermophilic Archaea.},
journal = {eLife},
volume = {8},
number = {},
pages = {},
pmid = {31184586},
issn = {2050-084X},
support = {ANR-10-JCJC-1501-01//Agence Nationale de la Recherche/International ; },
mesh = {8-Hydroxy-2'-Deoxyguanosine/*metabolism ; Archaea/*genetics/metabolism ; *DNA Damage ; DNA Repair ; DNA Replication/*genetics ; DNA, Archaeal/*genetics/metabolism ; DNA-Directed DNA Polymerase/genetics/metabolism ; Genome, Archaeal/*genetics ; Models, Genetic ; Mutation ; Oxidative Stress ; Protein Biosynthesis/genetics ; },
abstract = {8-oxodeoxyguanosine (8-oxodG), a major oxidised base modification, has been investigated to study its impact on DNA replication in hyperthermophilic Archaea. Here we show that 8-oxodG is formed in the genome of growing cells, with elevated levels following exposure to oxidative stress. Functional characterisation of cell-free extracts and the DNA polymerisation enzymes, PolB, PolD, and the p41/p46 complex, alone or in the presence of accessory factors (PCNA and RPA) indicates that translesion synthesis occurs under replicative conditions. One of the major polymerisation effects was stalling, but each of the individual proteins could insert and extend past 8-oxodG with differing efficiencies. The introduction of RPA and PCNA influenced PolB and PolD in similar ways, yet provided a cumulative enhancement to the polymerisation performance of p41/p46. Overall, 8-oxodG translesion synthesis was seen to be potentially mutagenic leading to errors that are reminiscent of dA:8-oxodG base pairing.},
}
@article {pmid31170597,
year = {2019},
author = {Wang, W and Su, Y and Wang, B and Wang, Y and Zhuang, L and Zhu, G},
title = {Spatiotemporal shifts of ammonia-oxidizing archaea abundance and structure during the restoration of a multiple pond and plant-bed/ditch wetland.},
journal = {The Science of the total environment},
volume = {684},
number = {},
pages = {629-640},
doi = {10.1016/j.scitotenv.2019.04.415},
pmid = {31170597},
issn = {1879-1026},
mesh = {Ammonia/metabolism ; Archaea/classification/*physiology ; *Conservation of Natural Resources ; *Microbiota ; Oxidation-Reduction ; Population Dynamics ; Spatio-Temporal Analysis ; *Wetlands ; },
abstract = {Ammonia-oxidizing archaea (AOA) microorganisms have been increasingly found in aquatic and terrestrial environments. These microorganisms make vital contributions to ammonia oxidation in such systems. However, their community succession characteristics in man-made wetland ecosystems have scarcely been reported. We assessed the AOA's spatiotemporal shifts in the sediments of a constructed wetland (CW) - the Shijiuyang constructed wetland (SJY-CW) - in China from the third year (2011) to the fifth year (2013) of the CW operation. The SJY-CW is composed of a pretreatment pond, a multiple plant-bed/ditch system, and a post-treatment pond. Results showed that AOA abundance in the pre- and post-treatment ponds remained invariant through 2011-2012 and decreased in 2013, while the abundance in the plant-bed/ditch system decreased gradually with wetland operation. The AOA abundance in 2013 was one order of magnitude lower than that through 2011-2012, and the AOA abundance in the plant-bed/ditch system was generally higher than that in the pre- and post-treatment ponds from 2011 to 2013. AOA diversity showed little temporal differentiation with a slightly decreasing trend for community richness index Chao1 and diversity index Shannon H' from 2011 to 2013. The AOA community was dominated by the Nitrososphaera cluster accompanied by an increasing Nitrosopumilus cluster and Nitrososphaera sister cluster within the wetland operation. Hierarchical clustering and redundancy analysis verified the horizontal shifts of AOA communities. The shifts occurred preferentially in the central plant-bed/ditch system. The operational duration of the wetland became a key factor influencing AOA abundance and community shift in SJY-CW sediments.},
}
@article {pmid31150759,
year = {2020},
author = {Stachler, AE and Schwarz, TS and Schreiber, S and Marchfelder, A},
title = {CRISPRi as an efficient tool for gene repression in archaea.},
journal = {Methods (San Diego, Calif.)},
volume = {172},
number = {},
pages = {76-85},
doi = {10.1016/j.ymeth.2019.05.023},
pmid = {31150759},
issn = {1095-9130},
mesh = {CRISPR-Cas Systems/*genetics ; Chromosomes, Archaeal/genetics ; Gene Editing/*methods ; *Gene Expression Regulation, Archaeal ; Gene Knockdown Techniques/methods ; Genes, Archaeal/genetics ; Genes, Essential/genetics ; Haloferax volcanii/*genetics ; Plasmids/genetics ; },
abstract = {In the years following its discovery and characterization, the CRISPR-Cas system has been modified and converted into a multitude of applications for eukaryotes and bacteria, such as genome editing and gene regulation. Since no such method has been available for archaea, we developed a tool for gene repression in the haloarchaeon Haloferax volcanii by repurposing its endogenous type I-B CRISPR-Cas system. Here, we present the two possible approaches for gene repression as well as our workflow to achieve and assess gene knockdown, offer recommendations on protospacer selection and give some examples of genes we have successfully silenced.},
}
@article {pmid31150548,
year = {2019},
author = {Kurth, JM and Smit, NT and Berger, S and Schouten, S and Jetten, MSM and Welte, CU},
title = {Anaerobic methanotrophic archaea of the ANME-2d clade feature lipid composition that differs from other ANME archaea.},
journal = {FEMS microbiology ecology},
volume = {95},
number = {7},
pages = {},
pmid = {31150548},
issn = {1574-6941},
support = {339880/ERC_/European Research Council/International ; },
mesh = {Anaerobiosis ; Archaea/*chemistry/classification/*metabolism ; Carbon/metabolism ; Lipids/biosynthesis/*chemistry ; Methane/*metabolism ; Nitrates/metabolism ; Oxidation-Reduction ; Seawater/chemistry/*microbiology ; },
abstract = {The anaerobic oxidation of methane (AOM) is a microbial process present in marine and freshwater environments. AOM is important for reducing the emission of the second most important greenhouse gas methane. In marine environments anaerobic methanotrophic archaea (ANME) are involved in sulfate-reducing AOM. In contrast, Ca. Methanoperedens of the ANME-2d cluster carries out nitrate AOM in freshwater ecosystems. Despite the importance of those organisms for AOM in non-marine environments little is known about their lipid composition or carbon sources. To close this gap, we analysed the lipid composition of ANME-2d archaea and found that they mainly synthesise archaeol and hydroxyarchaeol as well as different (hydroxy-) glycerol dialkyl glycerol tetraethers, albeit in much lower amounts. Abundant lipid headgroups were dihexose, monomethyl-phosphatidyl ethanolamine and phosphatidyl hexose. Moreover, a monopentose was detected as a lipid headgroup that is rare among microorganisms. Batch incubations with 13C labelled bicarbonate and methane showed that methane is the main carbon source of ANME-2d archaea varying from ANME-1 archaea that primarily assimilate dissolved inorganic carbon (DIC). ANME-2d archaea also assimilate DIC, but to a lower extent than methane. The lipid characterisation and analysis of the carbon source of Ca. Methanoperedens facilitates distinction between ANME-2d and other ANMEs.},
}
@article {pmid31147749,
year = {2019},
author = {Ijichi, M and Itoh, H and Hamasaki, K},
title = {Vertical distribution of particle-associated and free-living ammonia-oxidizing archaea in Suruga Bay, a deep coastal embayment of Japan.},
journal = {Archives of microbiology},
volume = {201},
number = {8},
pages = {1141-1146},
doi = {10.1007/s00203-019-01680-6},
pmid = {31147749},
issn = {1432-072X},
support = {JP24121004//Japan Society for the Promotion of Science/ ; },
mesh = {Ammonia/*metabolism ; Archaea/*genetics/*metabolism ; Bays/*microbiology ; Japan ; Oxidation-Reduction ; Oxidoreductases/*genetics ; Phylogeny ; Seawater/microbiology ; },
abstract = {We analyzed the vertical distributions of ammonia-oxidizing archaea (AOA) in terms of abundance in Suruga Bay, Japan. We distinguished particle-associated (PA) from free-living (FL) assemblages. According to quantitative PCR measurements of the ammonia monooxygenase subunit A gene (amoA), most marine AOA were in an FL state. The vertical distributions of PA AOA ecotypes differed from the general trend; the Shallow Marine clade was dominant in both the surface and deep layers. Thus, although PA AOA account for a small percentage of AOA abundance, they have a community structure distinct from that of FL AOA in planktonic environments. Marine particles should be investigated further as an unexplored niche of AOA in the ocean.},
}
@article {pmid32625030,
year = {2019},
author = {Pappenreiter, PA and Zwirtmayr, S and Mauerhofer, LM and Rittmann, SKR and Paulik, C},
title = {Development of a simultaneous bioreactor system for characterization of gas production kinetics of methanogenic archaea at high pressure.},
journal = {Engineering in life sciences},
volume = {19},
number = {7},
pages = {537-544},
pmid = {32625030},
issn = {1618-0240},
abstract = {Cultivation of methanogens under high pressure offers a great opportunity in biotechnological processes, one of which is the improvement of the gas-liquid transfer of substrate gases into the medium broth. This article describes a newly developed simultaneous bioreactor system consisting of four identical cultivation vessels suitable for investigation of microbial activity at pressures up to 50 bar and temperatures up to 145°C. Initial pressure studies at 10 and 50 bar of the autotrophic and hydrogenotrophic methanogens Methanothermobacter marburgensis, Methanobacterium palustre, and Methanobacterium thermaggregans were performed to evaluate the reproducibility of the system as well as to test the productivity of these strains. The strains were compared with respect to gas conversion (%), methane evolution rate (MER) (mmol L-1 h-1), turnover rate (h-1), and maximum conversion rate (k min) (bar h-1). A pressure drop that can be explained by the reaction stoichiometry showed that all tested strains were active under pressurized conditions. Our study sheds light on the production kinetics of methanogenic strains under high-pressure conditions. In addition, the simultaneous bioreactor system is a suitable first step screening system for analyzing the substrate uptake and/or production kinetics of gas conversion and/or gas production processes for barophilic or barotolerant microbes.},
}
@article {pmid31136034,
year = {2019},
author = {Walsh, JC and Angstmann, CN and Bisson-Filho, AW and Garner, EC and Duggin, IG and Curmi, PMG},
title = {Division plane placement in pleomorphic archaea is dynamically coupled to cell shape.},
journal = {Molecular microbiology},
volume = {112},
number = {3},
pages = {785-799},
pmid = {31136034},
issn = {1365-2958},
support = {DP2 AI117923/AI/NIAID NIH HHS/United States ; 203276/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Archaeal Proteins/genetics/metabolism ; *Cell Division ; Cell Shape ; Haloferax/cytology/genetics/metabolism ; Haloferax volcanii/*cytology/genetics/*metabolism ; },
abstract = {One mechanism for achieving accurate placement of the cell division machinery is via Turing patterns, where nonlinear molecular interactions spontaneously produce spatiotemporal concentration gradients. The resulting patterns are dictated by cell shape. For example, the Min system of Escherichia coli shows spatiotemporal oscillation between cell poles, leaving a mid-cell zone for division. The universality of pattern-forming mechanisms in divisome placement is currently unclear. We examined the location of the division plane in two pleomorphic archaea, Haloferax volcanii and Haloarcula japonica, and showed that it correlates with the predictions of Turing patterning. Time-lapse analysis of H. volcanii shows that divisome locations after successive rounds of division are dynamically determined by daughter cell shape. For H. volcanii, we show that the location of DNA does not influence division plane location, ruling out nucleoid occlusion. Triangular cells provide a stringent test for Turing patterning, where there is a bifurcation in division plane orientation. For the two archaea examined, most triangular cells divide as predicted by a Turing mechanism; however, in some cases multiple division planes are observed resulting in cells dividing into three viable progeny. Our results suggest that the division site placement is consistent with a Turing patterning system in these archaea.},
}
@article {pmid31133998,
year = {2019},
author = {Zhang, R and Neu, TR and Li, Q and Blanchard, V and Zhang, Y and Schippers, A and Sand, W},
title = {Insight Into Interactions of Thermoacidophilic Archaea With Elemental Sulfur: Biofilm Dynamics and EPS Analysis.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {896},
pmid = {31133998},
issn = {1664-302X},
abstract = {Biooxidation of reduced inorganic sulfur compounds (RISCs) by thermoacidophiles is of particular interest for the biomining industry and for environmental issues, e.g., formation of acid mine drainage (AMD). Up to now, interfacial interactions of acidophiles with elemental sulfur as well as the mechanisms of sulfur oxidation by acidophiles, especially thermoacidophiles, are not yet fully clear. This work focused on how a crenarchaeal isolate Acidianus sp. DSM 29099 interacts with elemental sulfur. Analysis by Confocal laser scanning microscopy (CLSM) and Atomic force microscopy (AFM) in combination with Epifluorescence microscopy (EFM) shows that biofilms on elemental sulfur are characterized by single colonies and a monolayer in first stage and later on 3-D structures with a diameter of up to 100 μm. The analysis of extracellular polymeric substances (EPS) by a non-destructive lectin approach (fluorescence lectin-barcoding analysis) using several fluorochromes shows that intial attachment was featured by footprints rich in biofilm cells that were embedded in an EPS matrix consisting of various glycoconjugates. Wet chemistry data indicate that carbohydrates, proteins, lipids and uronic acids are the main components. Attenuated reflectance (ATR)-Fourier transformation infrared spectroscopy (FTIR) and high-performance anion exchange chromatography with pulsed amperometric detection (HPAE-PAD) indicate glucose and mannose as the main monosaccharides in EPS polysaccharides. EPS composition as well as sugar types in EPS vary according to substrate (sulfur or tetrathionate) and lifestyle (biofilms and planktonic cells). This study provides information on the building blocks/make up as well as dynamics of biofilms of thermoacidophilic archaea in extremely acidic environments.},
}
@article {pmid31121445,
year = {2019},
author = {Zhang, L and Dong, H and Zhang, J and Chen, Y and Zeng, G and Yuan, Y and Cao, W and Fang, W and Hou, K and Wang, B and Li, L},
title = {Influence of FeONPs amendment on nitrogen conservation and microbial community succession during composting of agricultural waste: Relative contributions of ammonia-oxidizing bacteria and archaea to nitrogen conservation.},
journal = {Bioresource technology},
volume = {287},
number = {},
pages = {121463},
doi = {10.1016/j.biortech.2019.121463},
pmid = {31121445},
issn = {1873-2976},
mesh = {Ammonia ; Archaea ; Bacteria ; *Composting ; *Microbiota ; Nitrogen ; Oxidation-Reduction ; Soil ; Soil Microbiology ; },
abstract = {Composting amended with iron oxide nanoparticles (FeONPs, α-Fe2O3 and Fe3O4 NPs) were conducted to study the impacts of FeONPs on nitrogen conservation and microbial community. It was found that amendment of FeONPs, especially α-Fe2O3 NPs, reduced total nitrogen (TN) loss, and reserved more NH4+-N and mineral N. Pearson correlation analysis revealed that decrease of ammonia-oxidizing bacteria (AOB) in FeONPs treatments played more important role than ammonia-oxidizing archaea (AOA) in reserving more NH4+-N and mineral N, and reducing TN loss. Bacterial community composition at phylum level did not shift with addition of FeONPs. Firmicutes, Actinobacteria, and Proteobacteria were the three most dominant phyla in all treatments. Overall, this study provides a method to reduce TN loss and improve mineral N reservation during composting, and gives a deep insight into the role of AOB and AOA in nitrogen transformation.},
}
@article {pmid31089359,
year = {2019},
author = {Safarpour, A and Ebrahimi, M and Shahzadeh Fazeli, SA and Amoozegar, MA},
title = {Supernatant Metabolites from Halophilic Archaea to Reduce Tumorigenesis in Prostate Cancer In-vitro and In-vivo.},
journal = {Iranian journal of pharmaceutical research : IJPR},
volume = {18},
number = {1},
pages = {241-253},
pmid = {31089359},
issn = {1735-0328},
abstract = {Halophilic archaea are known as the novel producers of natural products and their supernatant metabolites could have cytotoxic effects on cancer cells. In the present study, we screened the anticancer potential of supernatant metabolites from eight native haloarchaeal strains obtained from a culture collection in Iran. Five human cancer cell lines including breast, lung, prostate and also human fibroblast cells as the normal control were used in the present study. Moreover, to evaluate the anti-tumor effect of the selected supernatant, inhibition of sphere formation and tumor development was assessed in-vitro and in-vivo, respectively. Among all strains, supernatant metabolites from Halobacterium salinarum IBRC M10715 had the most potent cytotoxic effect on prostate cancer cell lines (IC50 = 0.5 mg/mL) without any effects on normal cells. It significantly increased both early and late apoptosis (about 11% and 9%, respectively) in the androgen-dependent PC3 cell line, reduced sphere formation ability of DU145 and PC3 cells with down-regulation of SOX2 gene expression. Furthermore, our results revealed that tumors developed in nude mice significantly shrank post intratumor injection of metabolites of the haloarchaeal strain. In conclusion, we suggested here for the first time that supernatant metabolites from Halobacterium salinarum IBRC M10715 could be a novel component against prostate cancer in-vitro and in-vivo with remarkable reduction in stem-like properties of tumor.},
}
@article {pmid31085691,
year = {2019},
author = {Hepowit, NL and Maupin-Furlow, JA},
title = {Rhodanese-Like Domain Protein UbaC and Its Role in Ubiquitin-Like Protein Modification and Sulfur Mobilization in Archaea.},
journal = {Journal of bacteriology},
volume = {201},
number = {15},
pages = {},
pmid = {31085691},
issn = {1098-5530},
support = {R01 GM057498/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaeal Proteins/chemistry/genetics/*metabolism ; Haloferax volcanii/chemistry/*enzymology/genetics/metabolism ; Protein Domains ; Sulfur/*metabolism ; Sulfurtransferases/genetics/metabolism ; Thiosulfate Sulfurtransferase ; Ubiquitin/metabolism ; Ubiquitins/metabolism ; },
abstract = {Ubiquitin-like protein (Ubl) modification targets proteins for transient inactivation and/or proteasome-mediated degradation in archaea. Here the rhodanese-like domain (RHD) protein UbaC (HVO_1947) was found to copurify with the E1-like enzyme (UbaA) of the Ubl modification machinery in the archaeon Haloferax volcanii UbaC was shown to be important for Ubl ligation, particularly for the attachment of the Ubl SAMP2/3s to protein targets after exposure to oxidants (NaOCl, dimethyl sulfoxide [DMSO], and methionine sulfoxide [MetO]) and the proteasome inhibitor bortezomib. While UbaC was needed for ligation of the Ubl SAMP1 to MoaE (the large subunit of molybdopterin synthase), it was not important in the formation of oxidant-induced SAMP1 protein conjugates. Indicative of defects in sulfur relay, mutation of ubaC impaired molybdenum cofactor (Moco)-dependent DMSO reductase activity and cell survival at elevated temperature, suggesting a correlation with defects in the 2-thiolated state of wobble uridine tRNA. Overall, the archaeal stand-alone RHD UbaC has an important function in Ubl ligation and is associated with sulfur relay processes.IMPORTANCE Canonical E2 Ub/Ubl-conjugating enzymes are not conserved in the dual-function Ubl systems associated with protein modification and sulfur relay. Instead, the C-terminal RHDs of E1-RHD fusion proteins are the apparent E2 modules of these systems in eukaryotes. E1s that lack an RHD are common in archaea. Here we identified an RHD (UbaC) that serves as an apparent E2 analog with the E1-like UbaA in the dual-function Ubl sampylation system of archaea. Unlike the eukaryotic E1-RHD fusion, the archaeal RHD is a stand-alone protein. This new insight suggests that E1 function in Ubl pathways could be influenced by shifts in RHD abundance and/or competition with other protein partners in the cell.},
}
@article {pmid31069963,
year = {2019},
author = {Lu, S and Zhang, X and Chen, K and Chen, Z and Li, Y and Qi, Z and Shen, Y and Li, Z},
title = {The small subunit of DNA polymerase D (DP1) associates with GINS-GAN complex of the thermophilic archaea in Thermococcus sp. 4557.},
journal = {MicrobiologyOpen},
volume = {8},
number = {9},
pages = {e00848},
pmid = {31069963},
issn = {2045-8827},
mesh = {Archaeal Proteins/*metabolism ; DNA Replication ; *Protein Interaction Maps ; *Protein Multimerization ; Thermococcus/*enzymology ; Transcription Factor DP1/*metabolism ; },
abstract = {The eukaryotic GINS, Cdc45, and minichromosome maintenance proteins form an essential complex that moves with the DNA replication fork. The GINS protein complex has also been reported to associate with DNA polymerase. In archaea, the third domain of life, DNA polymerase D (PolD) is essential for DNA replication, and the genes encoding PolDs exist only in the genomes of archaea. The archaeal GAN (GINS-associated nuclease) is believed to be a homolog of the eukaryotic Cdc45. In this study, we found that the Thermococcus sp. 4557 DP1 (small subunit of PolD) interacted with GINS15 in vitro, and the 3'-5' exonuclease activity of DP1 was inhibited by GINS15. We also demonstrated that the GAN, GINS15, and DP1 proteins interact to form a complex adapting a GAN-GINS15-DP1 order. The results of this study imply that the complex constitutes a core of the DNA replisome in archaea.},
}
@article {pmid31064832,
year = {2019},
author = {Makarova, KS and Wolf, YI and Karamycheva, S and Zhang, D and Aravind, L and Koonin, EV},
title = {Antimicrobial Peptides, Polymorphic Toxins, and Self-Nonself Recognition Systems in Archaea: an Untapped Armory for Intermicrobial Conflicts.},
journal = {mBio},
volume = {10},
number = {3},
pages = {},
pmid = {31064832},
issn = {2150-7511},
mesh = {Amino Acid Sequence ; Antimicrobial Cationic Peptides/*genetics ; Archaea/*genetics ; Archaeal Proteins/*genetics ; Bacterial Proteins/genetics ; Evolution, Molecular ; *Genome, Archaeal ; Genome, Bacterial ; Genomics ; Microbial Interactions ; Toxins, Biological/*genetics ; },
abstract = {Numerous, diverse, highly variable defense and offense genetic systems are encoded in most bacterial genomes and are involved in various forms of conflict among competing microbes or their eukaryotic hosts. Here we focus on the offense and self-versus-nonself discrimination systems encoded by archaeal genomes that so far have remained largely uncharacterized and unannotated. Specifically, we analyze archaeal genomic loci encoding polymorphic and related toxin systems and ribosomally synthesized antimicrobial peptides. Using sensitive methods for sequence comparison and the "guilt by association" approach, we identified such systems in 141 archaeal genomes. These toxins can be classified into four major groups based on the structure of the components involved in the toxin delivery. The toxin domains are often shared between and within each system. We revisit halocin families and substantially expand the halocin C8 family, which was identified in diverse archaeal genomes and also certain bacteria. Finally, we employ features of protein sequences and genomic locus organization characteristic of archaeocins and polymorphic toxins to identify candidates for analogous but not necessarily homologous systems among uncharacterized protein families. This work confidently predicts that more than 1,600 archaeal proteins, currently annotated as "hypothetical" in public databases, are components of conflict and self-versus-nonself discrimination systems.IMPORTANCE Diverse and highly variable systems involved in biological conflicts and self-versus-nonself discrimination are ubiquitous in bacteria but much less studied in archaea. We performed comprehensive comparative genomic analyses of the archaeal systems that share components with analogous bacterial systems and propose an approach to identify new systems that could be involved in these functions. We predict polymorphic toxin systems in 141 archaeal genomes and identify new, archaea-specific toxin and immunity protein families. These systems are widely represented in archaea and are predicted to play major roles in interactions between species and in intermicrobial conflicts. This work is expected to stimulate experimental research to advance the understanding of poorly characterized major aspects of archaeal biology.},
}
@article {pmid31064826,
year = {2019},
author = {Li, Z and Kinosita, Y and Rodriguez-Franco, M and Nußbaum, P and Braun, F and Delpech, F and Quax, TEF and Albers, SV},
title = {Positioning of the Motility Machinery in Halophilic Archaea.},
journal = {mBio},
volume = {10},
number = {3},
pages = {},
pmid = {31064826},
issn = {2150-7511},
mesh = {Archaeal Proteins/*chemistry ; *Cell Polarity ; *Chemotaxis ; Cytoplasm/chemistry ; Flagella/physiology ; Haloferax volcanii/*physiology/ultrastructure ; Microscopy, Electron ; Time-Lapse Imaging ; },
abstract = {Bacteria and archaea exhibit tactical behavior and can move up and down chemical gradients. This tactical behavior relies on a motility structure, which is guided by a chemosensory system. Environmental signals are sensed by membrane-inserted chemosensory receptors that are organized in large ordered arrays. While the cellular positioning of the chemotaxis machinery and that of the flagellum have been studied in detail in bacteria, we have little knowledge about the localization of such macromolecular assemblies in archaea. Although the archaeal motility structure, the archaellum, is fundamentally different from the flagellum, archaea have received the chemosensory machinery from bacteria and have connected this system with the archaellum. Here, we applied a combination of time-lapse imaging and fluorescence and electron microscopy using the model euryarchaeon Haloferax volcanii and found that archaella were specifically present at the cell poles of actively dividing rod-shaped cells. The chemosensory arrays also had a polar preference, but in addition, several smaller arrays moved freely in the lateral membranes. In the stationary phase, rod-shaped cells became round and chemosensory arrays were disassembled. The positioning of archaella and that of chemosensory arrays are not interdependent and likely require an independent form of positioning machinery. This work showed that, in the rod-shaped haloarchaeal cells, the positioning of the archaellum and of the chemosensory arrays is regulated in time and in space. These insights into the cellular organization of H. volcanii suggest the presence of an active mechanism responsible for the positioning of macromolecular protein complexes in archaea.IMPORTANCE Archaea are ubiquitous single cellular microorganisms that play important ecological roles in nature. The intracellular organization of archaeal cells is among the unresolved mysteries of archaeal biology. With this work, we show that cells of haloarchaea are polarized. The cellular positioning of proteins involved in chemotaxis and motility is spatially and temporally organized in these cells. This suggests the presence of a specific mechanism responsible for the positioning of macromolecular protein complexes in archaea.},
}
@article {pmid31058146,
year = {2019},
author = {Isupov, MN and Boyko, KM and Sutter, JM and James, P and Sayer, C and Schmidt, M and Schönheit, P and Nikolaeva, AY and Stekhanova, TN and Mardanov, AV and Ravin, NV and Bezsudnova, EY and Popov, VO and Littlechild, JA},
title = {Corrigendum: Thermostable Branched-Chain Amino Acid Transaminases From the Archaea Geoglobus acetivorans and Archaeoglobus fulgidus: Biochemical and Structural Characterization.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {7},
number = {},
pages = {79},
doi = {10.3389/fbioe.2019.00079},
pmid = {31058146},
issn = {2296-4185},
abstract = {[This corrects the article DOI: 10.3389/fbioe.2019.00007.].},
}
@article {pmid31048384,
year = {2019},
author = {Webster, G and Mullins, AJ and Watkins, AJ and Cunningham-Oakes, E and Weightman, AJ and Mahenthiralingam, E and Sass, H},
title = {Genome Sequences of Two Choline-Utilizing Methanogenic Archaea, Methanococcoides spp., Isolated from Marine Sediments.},
journal = {Microbiology resource announcements},
volume = {8},
number = {18},
pages = {},
pmid = {31048384},
issn = {2576-098X},
support = {//Wellcome Trust/United Kingdom ; MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; },
abstract = {The genomes of two Methanococcoides spp. that were isolated from marine sediments and are capable of carrying out methanogenesis from choline and other methylotrophic substrates were sequenced. The average nucleotide identity and in silico DNA-DNA hybridization analyses demonstrate that they represent species different from those previously described.},
}
@article {pmid31020937,
year = {2019},
author = {Gupta, A and Swati, D},
title = {Riboswitches in Archaea.},
journal = {Combinatorial chemistry &amp; high throughput screening},
volume = {22},
number = {2},
pages = {135-149},
doi = {10.2174/1386207322666190425143301},
pmid = {31020937},
issn = {1875-5402},
mesh = {5' Untranslated Regions ; Archaea/genetics/*metabolism ; Databases, Genetic ; Genes, Archaeal ; *Riboswitch ; },
abstract = {BACKGROUND: Riboswitches are cis-acting, non-coding RNA elements found in the 5'UTR of bacterial mRNA and 3' UTR of eukaryotic mRNA, that fold in a complex manner to act as receptors for specific metabolites hence altering their conformation in response to the change in concentrations of a ligand or metabolite. Riboswitches function as gene regulators in numerous bacteria, archaea, fungi, algae and plants.<br><br>AIM AND OBJECTIVE: This study identifies different classes of riboswitches in the Archaeal domain of life. Previous studies have suggested that riboswitches carry a conserved aptameric domain in different domains of life. Since Archaea are considered to be the most idiosyncratic organisms it was interesting to look for the conservation pattern of riboswitches in these obviously strange microorganisms.<br><br>MATERIALS AND METHODS: Completely sequenced Archaeal Genomes present in the NCBI repository were used for studying riboswitches and other ncRNAs. The sequence files in FASTA format were downloaded from NCBI Genome database and information related to these genomes was retrieved from GenBank. Three bioinformatics approaches were used namely, ab initio, consensus structure prediction and statistical model-based prediction for identifying riboswitches.<br><br>RESULTS: Archaeal genomes have a sporadic distribution of putative riboswitches like the TPP, FMN, Guanidine, Lysine and c-di-AMP riboswitches, which are known to occur in bacteria. Also, a class of riboswitch sensing c-di-GMP, a second messenger, has been identified in a few Archaeal organisms.<br><br>CONCLUSION: This study clearly reveals that bioinformatics methods are likely to play a major role in identifying conserved riboswitches and in establishing how widespread these classes are in all domains of life, even though the final confirmation may come from wet lab methods.},
}
@article {pmid31016969,
year = {2019},
author = {Cândido, ES and Cardoso, MH and Chan, LY and Torres, MDT and Oshiro, KGN and Porto, WF and Ribeiro, SM and Haney, EF and Hancock, REW and Lu, TK and de la Fuente-Nunez, C and Craik, DJ and Franco, OL},
title = {Short Cationic Peptide Derived from Archaea with Dual Antibacterial Properties and Anti-Infective Potential.},
journal = {ACS infectious diseases},
volume = {5},
number = {7},
pages = {1081-1086},
doi = {10.1021/acsinfecdis.9b00073},
pmid = {31016969},
issn = {2373-8227},
mesh = {Amino Acid Sequence ; Animals ; Antimicrobial Cationic Peptides/chemistry/*pharmacology ; Archaeal Proteins/chemistry ; Biofilms/drug effects/growth &amp; development ; Disease Models, Animal ; Humans ; Mice ; Microbial Sensitivity Tests ; Protein Structure, Secondary ; Pseudomonas Infections/*drug therapy ; Pseudomonas aeruginosa/*drug effects/physiology ; Pyrobaculum/*metabolism ; Ribosomal Proteins/*chemistry ; },
abstract = {Bacterial biofilms and associated infections represent one of the biggest challenges in the clinic, and as an alternative to counter bacterial infections, antimicrobial peptides have attracted great attention in the past decade. Here, ten short cationic antimicrobial peptides were generated through a sliding-window strategy on the basis of the 19-amino acid residue peptide, derived from a Pyrobaculum aerophilum ribosomal protein. PaDBS1R6F10 exhibited anti-infective potential as it decreased the bacterial burden in murine Pseudomonas aeruginosa cutaneous infections by more than 1000-fold. Adverse cytotoxic and hemolytic effects were not detected against mammalian cells. The peptide demonstrated structural plasticity in terms of its secondary structure in the different environments tested. PaDBS1R6F10 represents a promising antimicrobial agent against bacteria infections, without harming human cells.},
}
@article {pmid31015799,
year = {2019},
author = {Wemheuer, F and von Hoyningen-Huene, AJE and Pohlner, M and Degenhardt, J and Engelen, B and Daniel, R and Wemheuer, B},
title = {Primary Production in the Water Column as Major Structuring Element of the Biogeographical Distribution and Function of Archaea in Deep-Sea Sediments of the Central Pacific Ocean.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2019},
number = {},
pages = {3717239},
pmid = {31015799},
issn = {1472-3654},
mesh = {Archaea/classification/genetics/*physiology ; Chlorophyll/analysis ; Ferric Compounds/analysis ; Geography ; Geologic Sediments/chemistry/*microbiology ; *Microbiota ; Pacific Ocean ; RNA, Archaeal/genetics ; RNA, Ribosomal, 16S/genetics ; Seawater/chemistry/*microbiology ; },
abstract = {Information on environmental conditions shaping archaeal communities thriving at the seafloor of the central Pacific Ocean is limited. The present study was conducted to investigate the diversity, composition, and function of both entire and potentially active archaeal communities within Pacific deep-sea sediments. For this purpose, sediment samples were taken along the 180° meridian of the central Pacific Ocean. Community composition and diversity were assessed by Illumina tag sequencing targeting archaeal 16S rRNA genes and transcripts. Archaeal communities were dominated by Candidatus Nitrosopumilus (Thaumarchaeota) and other members of the Nitrosopumilaceae (Thaumarchaeota), but higher relative abundances of the Marine Group II (Euryarchaeota) were observed in the active compared to the entire archaeal community. The composition of the entire and the active archaeal communities was strongly linked to primary production (chlorophyll content), explaining more than 40% of the variance. Furthermore, we found a strong correlation of the entire archaeal community composition to latitude and silicic acid content, while the active community was significantly correlated with primary production and ferric oxide content. We predicted functional profiles from 16S rRNA data to assess archaeal community functions. Latitude was significantly correlated with functional profiles of the entire community, whereas those of the active community were significantly correlated with nitrate and chlorophyll content. The results of the present study provide first insights into benthic archaeal communities in the Pacific Ocean and environmental conditions shaping their diversity, distribution, and function. Additionally, they might serve as a template for further studies investigating archaea colonizing deep-sea sediments.},
}
@article {pmid31015394,
year = {2019},
author = {Seitz, KW and Dombrowski, N and Eme, L and Spang, A and Lombard, J and Sieber, JR and Teske, AP and Ettema, TJG and Baker, BJ},
title = {Asgard archaea capable of anaerobic hydrocarbon cycling.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {1822},
pmid = {31015394},
issn = {2041-1723},
support = {OCE-0647633//National Science Foundation/International ; OCE-1357238//National Science Foundation/International ; DE-AC02-05CH11231//US Department of Energy/International ; },
mesh = {Anaerobiosis ; Archaea/genetics/*metabolism ; Archaeal Proteins/genetics/*metabolism ; Genome, Archaeal/*genetics ; Geologic Sediments/microbiology ; Hydrocarbons/*metabolism ; Hydrothermal Vents/microbiology ; Metabolic Networks and Pathways/genetics ; Metagenomics ; Oceans and Seas ; Oxidoreductases/genetics/*metabolism ; Phylogeny ; },
abstract = {Large reservoirs of natural gas in the oceanic subsurface sustain complex communities of anaerobic microbes, including archaeal lineages with potential to mediate oxidation of hydrocarbons such as methane and butane. Here we describe a previously unknown archaeal phylum, Helarchaeota, belonging to the Asgard superphylum and with the potential for hydrocarbon oxidation. We reconstruct Helarchaeota genomes from metagenomic data derived from hydrothermal deep-sea sediments in the hydrocarbon-rich Guaymas Basin. The genomes encode methyl-CoM reductase-like enzymes that are similar to those found in butane-oxidizing archaea, as well as several enzymes potentially involved in alkyl-CoA oxidation and the Wood-Ljungdahl pathway. We suggest that members of the Helarchaeota have the potential to activate and subsequently anaerobically oxidize hydrothermally generated short-chain hydrocarbons.},
}
@article {pmid31000700,
year = {2019},
author = {Dong, X and Greening, C and Rattray, JE and Chakraborty, A and Chuvochina, M and Mayumi, D and Dolfing, J and Li, C and Brooks, JM and Bernard, BB and Groves, RA and Lewis, IA and Hubert, CRJ},
title = {Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {1816},
pmid = {31000700},
issn = {2041-1723},
mesh = {Acetates/metabolism ; Archaea/genetics/isolation &amp; purification/*metabolism ; Bacteria/genetics/isolation &amp; purification/*metabolism ; Geologic Sediments/chemistry/*microbiology ; Hydrocarbons/metabolism ; Hydrogen/metabolism ; Metagenome ; Metagenomics/methods ; Mexico ; Microbial Interactions/physiology ; Microbiota/*physiology ; Petroleum/*metabolism ; },
abstract = {The lack of microbial genomes and isolates from the deep seabed means that very little is known about the ecology of this vast habitat. Here, we investigate energy and carbon acquisition strategies of microbial communities from three deep seabed petroleum seeps (3 km water depth) in the Eastern Gulf of Mexico. Shotgun metagenomic analysis reveals that each sediment harbors diverse communities of chemoheterotrophs and chemolithotrophs. We recovered 82 metagenome-assembled genomes affiliated with 21 different archaeal and bacterial phyla. Multiple genomes encode enzymes for anaerobic oxidation of aliphatic and aromatic compounds, including those of candidate phyla Aerophobetes, Aminicenantes, TA06 and Bathyarchaeota. Microbial interactions are predicted to be driven by acetate and molecular hydrogen. These findings are supported by sediment geochemistry, metabolomics, and thermodynamic modelling. Overall, we infer that deep-sea sediments experiencing thermogenic hydrocarbon inputs harbor phylogenetically and functionally diverse communities potentially sustained through anaerobic hydrocarbon, acetate and hydrogen metabolism.},
}
@article {pmid30997302,
year = {2019},
author = {Verma, S and Kumar, R and Meghwanshi, GK},
title = {Identification of new members of alkaliphilic lipases in archaea and metagenome database using reconstruction of ancestral sequences.},
journal = {3 Biotech},
volume = {9},
number = {5},
pages = {165},
pmid = {30997302},
issn = {2190-572X},
abstract = {The application of bioinformatics in lipase research has the potential to discover robust members from different genomic/metagenomic databses. In this study, we explored the diversity and distribution of alkaliphilic lipases in archaea domain and metagenome data sets through phylogenetic survey. Reconstructed ancestral sequence of alkaphilic lipase was used to search the homologous alkaliphilic lipases among the archaea and metagenome public databases. Our investigation revealed a total 21 unique sequences of new alkaliphilic lipases in the archaeal and environmental metagenomic protein databases that shared significant sequence similarity to the bacterial alkaliphilic lipases. Most of the identified new members of alkaliphilic lipases belong to class Haloarchaea. The searched list of homologs also comprised of one characterized lipase from alkalohyperthermophilic Archaeoglobus fulgidus. All the newly identified alkaliphilic lipase members showed conserved pentapeptide [X-His-Ser-X-Gly] motif, a key feature of lipase family. Furthermore, detailed analysis of all these new sequences showed homology either with thermostable or alkalophilic lipases. The reconstructed ancestral sequence-based searches increased the sensitivity and efficacies to detect remotely homologous sequences. We hypothesize that this study can enrich our current knowledge on lipases in designing more potential thermo-alkaliphilic lipases for industrial applications.},
}
@article {pmid30995692,
year = {2019},
author = {Langer, SG and Gabris, C and Einfalt, D and Wemheuer, B and Kazda, M and Bengelsdorf, FR},
title = {Different response of bacteria, archaea and fungi to process parameters in nine full-scale anaerobic digesters.},
journal = {Microbial biotechnology},
volume = {12},
number = {6},
pages = {1210-1225},
pmid = {30995692},
issn = {1751-7915},
mesh = {Anaerobiosis ; Archaea/classification/genetics/*growth &amp; development ; Bacteria, Anaerobic/classification/genetics/*growth &amp; development ; Biofuels ; Bioreactors/*microbiology ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Fungi/classification/genetics/*growth &amp; development ; Manure/*microbiology ; Metagenomics ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 28S/genetics ; Sequence Analysis, DNA ; },
abstract = {Biogas production is a biotechnological process realized by complex bacterial, archaeal and likely fungal communities. Their composition was assessed in nine full-scale biogas plants with distinctly differing feedstock input and process parameters. This study investigated the actually active microbial community members by using a comprehensive sequencing approach based on ribosomal 16S and 28S rRNA fragments. The prevailing taxonomical units of each respective community were subsequently linked to process parameters. Ribosomal rRNA of bacteria, archaea and fungi, respectively, showed different compositions with respect to process parameters and supplied feedstocks: (i) bacterial communities were affected by the key factors temperature and ammonium concentration; (ii) composition of archaea was mainly related to process temperature; and (iii) relative abundance of fungi was linked to feedstocks supplied to the digesters. Anaerobic digesters with a high methane yield showed remarkably similar bacterial communities regarding identified taxonomic families. Although archaeal communities differed strongly on genus level from each other, the respective digesters still showed high methane yields. Functional redundancy of the archaeal communities may explain this effect. 28S rRNA sequences of fungi in all nine full-scale anaerobic digesters were primarily classified as facultative anaerobic Ascomycota and Basidiomycota. Since the presence of ribosomal 28S rRNA indicates that fungi may be active in the biogas digesters, further research should be carried out to examine to which extent they are important players in anaerobic digestion processes.},
}
@article {pmid30994930,
year = {2019},
author = {Gomes-Filho, JV and Randau, L},
title = {RNA stabilization in hyperthermophilic archaea.},
journal = {Annals of the New York Academy of Sciences},
volume = {1447},
number = {1},
pages = {88-96},
doi = {10.1111/nyas.14060},
pmid = {30994930},
issn = {1749-6632},
support = {RA 2169/3-1//Deutsche Forschungsgemeinschaft/International ; },
mesh = {Animals ; Archaea/*chemistry/*genetics ; Humans ; Proteolysis ; RNA Stability/*genetics ; RNA, Archaeal/*chemistry/*genetics ; },
abstract = {Analyses of the RNA metabolism of hyperthermophilic archaea highlight the efficiency of regulatory RNAs and RNA-guided processes at extreme temperatures. These organisms must overcome the intrinsic thermolability of RNAs. Elevated levels of RNA modifications and structured GC-rich regions are observed for many universal noncoding RNA families. Guide RNAs are often protected from degradation by their presence within ribonucleoprotein complexes. Modification and ligation of RNA termini can be employed to impair exonucleolytic degradation. Finally, antisense strand transcription promotes the formation of RNA duplexes and can be used to stabilize RNA regions. In our review, we provide examples of these RNA stabilization mechanisms that have been observed in hyperthermophilic archaeal model organisms.},
}
@article {pmid30991941,
year = {2019},
author = {Santos-Zavaleta, A and Pérez-Rueda, E and Sánchez-Pérez, M and Velázquez-Ramírez, DA and Collado-Vides, J},
title = {Tracing the phylogenetic history of the Crl regulon through the Bacteria and Archaea genomes.},
journal = {BMC genomics},
volume = {20},
number = {1},
pages = {299},
pmid = {30991941},
issn = {1471-2164},
support = {R01GM110597//Foundation for the National Institutes of Health/ ; PAPIIT IN-201117//Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México (MX)/ ; R01 GM110597/GM/NIGMS NIH HHS/United States ; U24GM077678//Foundation for the National Institutes of Health/ ; U24 GM077678/GM/NIGMS NIH HHS/United States ; },
mesh = {Evolution, Molecular ; Genome, Archaeal/*genetics ; Genome, Bacterial/*genetics ; *Phylogeny ; Regulon/*genetics ; },
abstract = {BACKGROUND: Crl, identified for curli production, is a small transcription factor that stimulates the association of the σS factor (RpoS) with the RNA polymerase core through direct and specific interactions, increasing the transcription rate of genes during the transition from exponential to stationary phase at low temperatures, using indole as an effector molecule. The lack of a comprehensive collection of information on the Crl regulon makes it difficult to identify a dominant function of Crl and to generate any hypotheses concerning its taxonomical distribution in archaeal and bacterial organisms.<br><br>RESULTS: In this work, based on a systematic literature review, we identified the first comprehensive dataset of 86 genes under the control of Crl in the bacterium Escherichia coli K-12; those genes correspond to 40% of the σS regulon in this bacterium. Based on an analysis of orthologs in 18 archaeal and 69 bacterial taxonomical divisions and using E. coli K-12 as a framework, we suggest three main events that resulted in this regulon's actual form: (i) in a first step, rpoS, a gene widely distributed in bacteria and archaea cellular domains, was recruited to regulate genes involved in ancient metabolic processes, such as those associated with glycolysis and the tricarboxylic acid cycle; (ii) in a second step, the regulon recruited those genes involved in metabolic processes, which are mainly taxonomically constrained to Proteobacteria, with some secondary losses, such as those genes involved in responses to stress or starvation and cell adhesion, among others; and (iii) in a posterior step, Crl might have been recruited in Enterobacteriaceae; because its taxonomical pattern constrained to this bacterial order, however further analysis are necessary.<br><br>CONCLUSIONS: Therefore, we suggest that the regulon Crl is highly flexible for phenotypic adaptation, probably as consequence of the diverse growth environments associated with all organisms in which members of this regulatory network are present.},
}
@article {pmid30991368,
year = {2019},
author = {Eggenberger, OM and Leriche, G and Koyanagi, T and Ying, C and Houghtaling, J and Schroeder, TBH and Yang, J and Li, J and Hall, A and Mayer, M},
title = {Fluid surface coatings for solid-state nanopores: comparison of phospholipid bilayers and archaea-inspired lipid monolayers.},
journal = {Nanotechnology},
volume = {30},
number = {32},
pages = {325504},
doi = {10.1088/1361-6528/ab19e6},
pmid = {30991368},
issn = {1361-6528},
mesh = {Archaea/*metabolism ; Diffusion ; Lipid Bilayers/*chemistry ; *Nanopores ; Phosphatidylcholines/chemistry ; Phospholipids/chemistry ; Surface Properties ; Unilamellar Liposomes/*chemistry ; },
abstract = {In the context of sensing and characterizing single proteins with synthetic nanopores, lipid bilayer coatings provide at least four benefits: first, they minimize unwanted protein adhesion to the pore walls by exposing a zwitterionic, fluid surface. Second, they can slow down protein translocation and rotation by the opportunity to tether proteins with a lipid anchor to the fluid bilayer coating. Third, they provide the possibility to impart analyte specificity by including lipid anchors with a specific receptor or ligand in the coating. Fourth, they offer a method for tuning nanopore diameters by choice of the length of the lipid's acyl chains. The work presented here compares four properties of various lipid compositions with regard to their suitability as nanopore coatings for protein sensing experiments: (1) electrical noise during current recordings through solid-state nanopores before and after lipid coating, (2) long-term stability of the recorded current baseline and, by inference, of the coating, (3) viscosity of the coating as quantified by the lateral diffusion coefficient of lipids in the coating, and (4) the success rate of generating a suitable coating for quantitative nanopore-based resistive pulse recordings. We surveyed lipid coatings prepared from bolaamphiphilic, monolayer-forming lipids inspired by extremophile archaea and compared them to typical bilayer-forming phosphatidylcholine lipids containing various fractions of curvature-inducing lipids or cholesterol. We found that coatings from archaea-inspired lipids provide several advantages compared to conventional phospholipids; the stable, low noise baseline qualities and high viscosity make these membranes especially suitable for analysis that estimates physical protein parameters such as the net charge of proteins as they enable translocation events with sufficiently long duration to time-resolve dwell time distributions completely. The work presented here reveals that the ease or difficulty of coating a nanopore with lipid membranes did not depend significantly on the composition of the lipid mixture, but rather on the geometry and surface chemistry of the nanopore in the solid state substrate. In particular, annealing substrates containing the nanopore increased the success rate of generating stable lipid coatings.},
}
@article {pmid30975999,
year = {2019},
author = {Xiong, L and Liu, S and Chen, S and Xiao, Y and Zhu, B and Gao, Y and Zhang, Y and Chen, B and Luo, J and Deng, Z and Chen, X and Wang, L and Chen, S},
title = {A new type of DNA phosphorothioation-based antiviral system in archaea.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {1688},
pmid = {30975999},
issn = {2041-1723},
mesh = {Archaea/*physiology/virology ; Archaeal Proteins/genetics/immunology/*metabolism ; Archaeal Viruses/*genetics/pathogenicity ; DNA Replication/immunology ; DNA, Viral/*metabolism ; Gene Transfer, Horizontal/immunology ; Host Microbial Interactions/*genetics ; Immunity, Innate/genetics/immunology ; Phosphorothioate Oligonucleotides/metabolism ; RNA, Archaeal/genetics/isolation &amp; purification ; Sequence Analysis, DNA ; },
abstract = {Archaea and Bacteria have evolved different defence strategies that target virtually all steps of the viral life cycle. The diversified virion morphotypes and genome contents of archaeal viruses result in a highly complex array of archaea-virus interactions. However, our understanding of archaeal antiviral activities lags far behind our knowledges of those in bacteria. Here we report a new archaeal defence system that involves DndCDEA-specific DNA phosphorothioate (PT) modification and the PbeABCD-mediated halt of virus propagation via inhibition of DNA replication. In contrast to the breakage of invasive DNA by DndFGH in bacteria, DndCDEA-PbeABCD does not degrade or cleave viral DNA. The PbeABCD-mediated PT defence system is widespread and exhibits extensive interdomain and intradomain gene transfer events. Our results suggest that DndCDEA-PbeABCD is a new type of PT-based virus resistance system, expanding the known arsenal of defence systems as well as our understanding of host-virus interactions.},
}
@article {pmid30938665,
year = {2019},
author = {Bayer, B and Vojvoda, J and Reinthaler, T and Reyes, C and Pinto, M and Herndl, GJ},
title = {Nitrosopumilus adriaticus sp. nov. and Nitrosopumilus piranensis sp. nov., two ammonia-oxidizing archaea from the Adriatic Sea and members of the class Nitrososphaeria.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {69},
number = {7},
pages = {1892-1902},
doi = {10.1099/ijsem.0.003360},
pmid = {30938665},
issn = {1466-5034},
mesh = {Ammonia/*metabolism ; Archaea/*classification/isolation &amp; purification ; Base Composition ; DNA, Archaeal/genetics ; Glyceryl Ethers/chemistry ; Hydrogen Peroxide ; Oceans and Seas ; Oxidation-Reduction ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Vitamin K 2/analogs &amp; derivatives/chemistry ; },
abstract = {Two mesophilic, neutrophilic and aerobic marine ammonia-oxidizing archaea, designated strains NF5T and D3CT, were isolated from coastal surface water of the Northern Adriatic Sea. Cells were straight small rods 0.20-0.25 µm wide and 0.49-2.00 µm long. Strain NF5T possessed archaella as cell appendages. Glycerol dibiphytanyl glycerol tetraethers with zero to four cyclopentane moieties (GDGT-0 to GDGT-4) and crenarchaeol were the major core lipids. Menaquinone MK6 : 0 was the major respiratory quinone. Both isolates gained energy by oxidizing ammonia (NH3) to nitrite (NO2-) and used bicarbonate as a carbon source. Strain D3CT was able use urea as a source of ammonia for energy production and growth. Addition of hydrogen peroxide (H2O2) scavengers (catalase or α-keto acids) was required to sustain growth. Optimal growth occurred between 30 and 32 °C, pH 7.1 and 7.3 and between 34 and 37‰ salinity. The cellular metal abundance ranking of both strains was Fe>Zn>Cu>Mn>Co. The genomes of strains NF5T and D3CT have a DNA G+C content of 33.4 and 33.8 mol%, respectively. Phylogenetic analyses of 16S rRNA gene sequences revealed that both strains are affiliated with the class Nitrososphaeria, sharing ~85 % 16S rRNA gene sequence identity with Nitrososphaera viennensis EN76T. The two isolates are separated by phenotypic and genotypic characteristics and are assigned to distinct species within the genus Nitrosopumilus gen. nov. according to average nucleotide identity thresholds of their closed genomes. Isolates NF5T (=JCM 32270T =NCIMB 15114T) and D3CT (=JCM 32271T =DSM 106147T =NCIMB 15115T) are type strains of the species Nitrosopumilusadriaticus sp. nov. and Nitrosopumiluspiranensis sp. nov., respectively.},
}
@article {pmid30936420,
year = {2019},
author = {Straka, LL and Meinhardt, KA and Bollmann, A and Stahl, DA and Winkler, MH},
title = {Affinity informs environmental cooperation between ammonia-oxidizing archaea (AOA) and anaerobic ammonia-oxidizing (Anammox) bacteria.},
journal = {The ISME journal},
volume = {13},
number = {8},
pages = {1997-2004},
pmid = {30936420},
issn = {1751-7370},
mesh = {Ammonia/chemistry/metabolism ; Anaerobiosis ; Archaea/chemistry/classification/isolation &amp; purification/*metabolism ; Bacteria/chemistry/classification/isolation &amp; purification/*metabolism ; Kinetics ; Lakes/microbiology ; Oxidation-Reduction ; Oxygen/metabolism ; Phylogeny ; Soil/chemistry ; Soil Microbiology ; },
abstract = {Anaerobic ammonia-oxidizing (Anammox) bacteria (AnAOB) rely on nitrite supplied by ammonia-oxidizing bacteria (AOB) and archaea (AOA). Affinities for ammonia and oxygen play a crucial role in AOA/AOB competition and their association with AnAOB. In this work we measured the affinity constants for ammonia and oxygen (half-saturation; km) of two freshwater AOA enrichments, an AOA soil isolate (N. viennensis), and a freshwater AnAOB enrichment. The AOA enrichments had similar kinetics (μmax ≈ 0.36 d-1, km,NH4 ≈ 0.78 µM, and km,O2 ≈ 2.9 µM), whereas N. viennensis had similar km values but lower μmax (0.23 d-1). In agreement with the current paradigm, these AOA strains showed a higher affinity for ammonia (lower km,NH4; 0.34-1.27 µM) than published AOB measurements (>20 µM). The slower growing AnAOB (μmax ≈ 0.16 d-1) had much higher km values (km,NH4 ≈ 132 µM, km,NO2 ≈ 48 µM) and were inhibited by oxygen at low levels (half-oxygen inhibition; ki,O2 ≈ 0.092 µM). The higher affinity of AOA for ammonia relative to AnAOB, suggests AOA/AnAOB cooperation is only possible where AOA do not outcompete AnAOB for ammonia. Using a biofilm model, we show that environments of ammonia/oxygen counter diffusion, such as stratified lakes, favors this cooperation.},
}
@article {pmid30924222,
year = {2019},
author = {Zou, D and Li, Y and Kao, SJ and Liu, H and Li, M},
title = {Genomic adaptation to eutrophication of ammonia-oxidizing archaea in the Pearl River estuary.},
journal = {Environmental microbiology},
volume = {21},
number = {7},
pages = {2320-2332},
doi = {10.1111/1462-2920.14613},
pmid = {30924222},
issn = {1462-2920},
support = {JCYJ20170818091727570//Science and Technology Innovation Committee of Shenzhen/International ; 91851105，31622002//National Natural Science Foundation of China/International ; //State Key Laboratory of Marine Pollution/International ; //Research Grants Council of the Hong Kong Special Administrative Region/International ; },
mesh = {Ammonia/*metabolism ; Archaea/*genetics/*physiology ; California ; China ; Ecosystem ; Estuaries ; Eutrophication/*physiology ; Genome, Archaeal/genetics ; Genomics ; Geologic Sediments/microbiology ; Metals, Heavy/metabolism ; Nitrification ; Oxidation-Reduction ; Oxidoreductases/*genetics ; Phosphate Transport Proteins/genetics ; Phylogeny ; Rivers/microbiology ; },
abstract = {Ammonia-oxidizing archaea (AOA) are ubiquitous in natural ecosystems, and they are responsible for a significant fraction of ammonia oxidation globally. Since the first AOA isolate was established a decade ago, molecular surveys of their environmental distribution [based primarily on amplicon sequencing of the amoA, which codes for the alpha subunit of ammonia monooxygenase (AMO)], show that their habitats are believed to range from marine to terrestrial environments. However, the mechanisms of adaptation underpinning to their habitat expansion remain poorly understood. Here, we report that AOA accounts for almost all of the ammonia oxidizers in the shelf water adjacent to the Pearl River estuary (PRE), with the Nitrosopumilus maritimus SCM1-like (SCM1-like) being the main amoA genotype. Using a metagenomic approach, seven high-quality AOA genomes were reconstructed from the PRE. Phylogenetic analysis indicated that four of these genomes with high completeness were closely affiliated with the Nitrosomatrinus catalina strain SPOT01, which was originally isolated off the coast of California. Genomic comparison revealed that the PRE AOA genomes encoded genes functioning in amino acid synthesis, xenobiotic biodegradation metabolism and transportation of inorganic phosphate and heavy metals. This illustrates the different adaptations of AOA in one of the largest estuaries in China, which is strongly influenced by anthropogenic input. Overall, this study provides additional genomic information about estuarine AOA and highlights the importance of their contribution to nitrification in eutrophic coastal environments.},
}
@article {pmid30923872,
year = {2019},
author = {Wu, RN and Meng, H and Wang, YF and Gu, JD},
title = {Functional dominance and community compositions of ammonia-oxidizing archaea in extremely acidic soils of natural forests.},
journal = {Applied microbiology and biotechnology},
volume = {103},
number = {10},
pages = {4229-4240},
doi = {10.1007/s00253-019-09721-2},
pmid = {30923872},
issn = {1432-0614},
support = {31470562//National Natural Science Foundation of China/ ; },
mesh = {Ammonia/*metabolism ; Archaea/*classification/enzymology/genetics/*metabolism ; *Forests ; Hydrogen-Ion Concentration ; *Microbiota ; Oxidation-Reduction ; Oxidoreductases/analysis/genetics ; RNA, Messenger/analysis/genetics ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {Extremely acidic soils of natural forests in Nanling National Nature Reserve have been previously investigated and revisited in two successive years to reveal the active ammonia oxidizers. Ammonia-oxidizing archaea (AOA) rather than ammonia-oxidizing bacteria (AOB) were found more functionally important in the extremely acidic soils of the natural forests in Nanling National Nature Reserve. The relative abundances of Nitrosotalea, Nitrososphaera sister group, and Nitrososphaera lineages recovered by ammonia monooxygenase subunit A (amoA) transcripts were reassessed and compared to AOA communities formerly detected by genomic DNA. Nitrosotalea, previously found the most abundant AOA, were the second-most-active lineage after Nitrososphaera sister group. Our field study results, therefore, propose the acidophilic AOA, Nitrosotalea, can better reside in extremely acidic soils while they may not contribute to nitrification proportionately according to their abundances or they are less functionally active. In contrast, the functional importance of Nitrososphaera sister group may be previously underestimated and the functional dominance further extends their ecological distribution as little has been reported. Nitrososphaera gargensis-like AOA, the third abundant lineage, were more active in summer. The analyses of AOA community composition and its correlation with environmental parameters support the previous observations of the potential impact of organic matter on AOA composition. Al3+, however, did not show a strong adverse correlation with the abundances of functional AOA unlike in the DNA-based study. The new data further emphasize the functional dominance of AOA in extremely acidic soils, and unveil the relative contributions of AOA lineages to nitrification and their community transitions under the environmental influences.},
}
@article {pmid30918404,
year = {2019},
author = {Chen, SC and Musat, N and Lechtenfeld, OJ and Paschke, H and Schmidt, M and Said, N and Popp, D and Calabrese, F and Stryhanyuk, H and Jaekel, U and Zhu, YG and Joye, SB and Richnow, HH and Widdel, F and Musat, F},
title = {Anaerobic oxidation of ethane by archaea from a marine hydrocarbon seep.},
journal = {Nature},
volume = {568},
number = {7750},
pages = {108-111},
pmid = {30918404},
issn = {1476-4687},
mesh = {Anaerobiosis ; Aquatic Organisms/*metabolism ; Archaea/classification/enzymology/genetics/*metabolism ; Deltaproteobacteria/metabolism ; Ethane/chemistry/*metabolism ; Gases/chemistry/metabolism ; Gulf of Mexico ; Methane/biosynthesis ; Oxidation-Reduction ; Oxidoreductases/genetics/isolation &amp; purification/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sulfates/metabolism ; Sulfides/metabolism ; },
abstract = {Ethane is the second most abundant component of natural gas in addition to methane, and-similar to methane-is chemically unreactive. The biological consumption of ethane under anoxic conditions was suggested by geochemical profiles at marine hydrocarbon seeps1-3, and through ethane-dependent sulfate reduction in slurries4-7. Nevertheless, the microorganisms and reactions that catalyse this process have to date remained unknown8. Here we describe ethane-oxidizing archaea that were obtained by specific enrichment over ten years, and analyse these archaea using phylogeny-based fluorescence analyses, proteogenomics and metabolite studies. The co-culture, which oxidized ethane completely while reducing sulfate to sulfide, was dominated by an archaeon that we name 'Candidatus Argoarchaeum ethanivorans'; other members were sulfate-reducing Deltaproteobacteria. The genome of Ca. Argoarchaeum contains all of the genes that are necessary for a functional methyl-coenzyme M reductase, and all subunits were detected in protein extracts. Accordingly, ethyl-coenzyme M (ethyl-CoM) was identified as an intermediate by liquid chromatography-tandem mass spectrometry. This indicated that Ca. Argoarchaeum initiates ethane oxidation by ethyl-CoM formation, analogous to the recently described butane activation by 'Candidatus Syntrophoarchaeum'9. Proteogenomics further suggests that oxidation of intermediary acetyl-CoA to CO2 occurs through the oxidative Wood-Ljungdahl pathway. The identification of an archaeon that uses ethane (C2H6) fills a gap in our knowledge of microorganisms that specifically oxidize members of the homologous alkane series (CnH2n+2) without oxygen. Detection of phylogenetic and functional gene markers related to those of Ca. Argoarchaeum at deep-sea gas seeps10-12 suggests that archaea that are able to oxidize ethane through ethyl-CoM are widespread members of the local communities fostered by venting gaseous alkanes around these seeps.},
}
@article {pmid30915060,
year = {2019},
author = {Qiu, X and Yao, Y and Wang, H and Shen, A and Zhang, J},
title = {Halophilic Archaea Mediate the Formation of Proto-Dolomite in Solutions With Various Sulfate Concentrations and Salinities.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {480},
pmid = {30915060},
issn = {1664-302X},
abstract = {In the past several decades, sulfate concentration and salinity have been considered to be the two essential hydrochemical factors in the formation of dolomite, yet arguments against this hypothesis have existed simultaneously. To clarify the effects of sulfate concentration and salinity in the mineralization of dolomite, we conducted experiments on dolomite precipitation mediated by a halophilic archaeon, Natrinema sp. J7-1 with various sulfate concentrations and salinities. This strain was cultured in a series of modified growth media (MGM) with salinities of 140, 200, and 280‰. Cells in the post-log phase were harvested and used to mediate the formation of dolomite in solutions with various sulfate concentrations of 0, 3, 29.8, and 100 mM and salinities of 140, 200, and 280‰. X-ray diffraction (XRD) spectra showed that proto-dolomite, monohydrocalcite, and aragonite formed in samples with cells, yet only aragonite was detected in samples without cells. Proto-dolomite was found in all biotic samples, regardless of the variation in salinity and sulfate concentration. Moreover, the relative abundances of proto-dolomite in the precipitates were positively correlated with the salinities of the media but were uncorrelated with the sulfate concentrations of the solutions. Scanning electronic microscopy (SEM) and energy dispersive spectroscopy (EDS) results showed that all the proto-dolomites were sphere or sphere aggregates with a mole ratio of Mg/Ca close to 1.0. No obvious variations in morphology and Mg/Ca were found among samples with various sulfate concentrations or salinities. This work reveals that a variation of sulfate concentration in solution (from 0 to 100 mM) does not affect the formation of dolomite mediated by halophilic archaea, but an increase of salinity (from 140 to 280‰) enhances this process. Our results indicate that under natural conditions, an increase in salinity may be more significant than the decrease of sulfates in microbe-mediated dolomite formation.},
}
@article {pmid30910020,
year = {2019},
author = {Fu, X and Adams, Z and Maupin-Furlow, J},
title = {Assays for ubiquitin-like protein ligation and proteasome function in archaea.},
journal = {Methods in enzymology},
volume = {619},
number = {},
pages = {161-178},
pmid = {30910020},
issn = {1557-7988},
support = {R01 GM057498/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaeal Proteins/*metabolism ; Enzyme Assays/methods ; Haloferax volcanii/*metabolism ; Immunoblotting/methods ; Proteasome Endopeptidase Complex/*metabolism ; Ubiquitins/*metabolism ; },
abstract = {Ubiquitin-like protein (Ubl) ligation is common to diverse archaea and targets many cellular pathways, including those associated with sulfur mobilization, and also tags proteins as substrates for degradation by the proteasome. Here we highlight protocols to assay proteasome function and Ubl ligation in archaea. A chase assay is described to monitor the impact of proteasome function on the stability of Ubl-modified proteins in the cell. A method to reconstitute Ubl ligation using a purified E1-like enzyme (UbaA), Ubl (SAMP2), methionine sulfoxide reductase A (MsrA), and cell lysate of an ΔmsrA ΔubaA Δsamp1-3 mutant is also described. MsrA is found to have the surprising ability to stimulate the formation of Ubl bonds. Haloferax volcanii, a halophilic archaeon originally isolated from the Dead Sea, serves as the model organism for these protocols.},
}
@article {pmid30886840,
year = {2019},
author = {Sogodogo, E and Fellag, M and Loukil, A and Nkamga, VD and Michel, J and Dessi, P and Fournier, PE and Drancourt, M},
title = {Nine Cases of Methanogenic Archaea in Refractory Sinusitis, an Emerging Clinical Entity.},
journal = {Frontiers in public health},
volume = {7},
number = {},
pages = {38},
pmid = {30886840},
issn = {2296-2565},
abstract = {The authors report the cases of 9 patients eventually diagnosed with methanogenic archaea refractory or recalcitrant chronic rhinosinusitis, a condition known to involve various anaerobic bacteria but in which the role of methanogenic archaea is unknown. The authors retrospectively searched these microorganisms by PCR in surgically-collected sinusal pus specimens from patients diagnosed with refractory sinusitis, defined by the persistance of sinus inflammation and related-symptoms for more than 12 weeks despite appropriate treatment. Of the 116 tested sinus surgical specimens, 12 (10.3%) from 9 patients (six females, three males; aged 20-71 years) were PCR-positive. These specimens were further investigated by fluorescence in-situ hybridization, PCR amplicon-sequencing and culture. Methanobrevibacter smithii was documented in four patients and Methanobrevibacter oralis in another four, one of whom was also culture-positive. They were associated with a mixed flora including Gram-positive and Gram-negative bacteria. In the latter patient, "Methanobrevibacter massiliense" was the sole microorganism detected. These results highlight methanogenic archaea as being part of a mixed anaerobic flora involved in refractory sinusitis, and suggest that the treatment of this condition should include an antibiotic active against methanogens, notably a nitroimidazole derivative.},
}
@article {pmid30884174,
year = {2019},
author = {Braun, F and Thomalla, L and van der Does, C and Quax, TEF and Allers, T and Kaever, V and Albers, SV},
title = {Cyclic nucleotides in archaea: Cyclic di-AMP in the archaeon Haloferax volcanii and its putative role.},
journal = {MicrobiologyOpen},
volume = {8},
number = {9},
pages = {e00829},
pmid = {30884174},
issn = {2045-8827},
mesh = {Adenylyl Cyclases/genetics ; Dinucleoside Phosphates/*metabolism ; Gene Expression Regulation, Archaeal ; Genes, Essential ; Genome, Bacterial ; Haloferax volcanii/enzymology/genetics/*metabolism ; Osmoregulation ; Signal Transduction ; },
abstract = {The role of cyclic nucleotides as second messengers for intracellular signal transduction has been well described in bacteria. One recently discovered bacterial second messenger is cyclic di-adenylate monophosphate (c-di-AMP), which has been demonstrated to be essential in bacteria. Compared to bacteria, significantly less is known about second messengers in archaea. This study presents the first evidence of in vivo presence of c-di-AMP in an archaeon. The model organism Haloferax volcanii was demonstrated to produce c-di-AMP. Its genome encodes one diadenylate cyclase (DacZ) which was shown to produce c-di-AMP in vitro. Similar to bacteria, the dacZ gene is essential and homologous overexpression of DacZ leads to cell death, suggesting the need for tight regulation of c-di-AMP levels. Such tight regulation often indicates the control of important regulatory processes. A central target of c-di-AMP signaling in bacteria is cellular osmohomeostasis. The results presented here suggest a comparable function in H. volcanii. A strain with decreased c-di-AMP levels exhibited an increased cell area in hypo-salt medium, implying impaired osmoregulation. In summary, this study expands the field of research on c-di-AMP and its physiological function to archaea and indicates that osmoregulation is likely to be a common function of c-di-AMP in bacteria and archaea.},
}
@article {pmid30859290,
year = {2019},
author = {Du, Y and Shu, K and Guo, X and Pengjin, Z},
title = {Moderate Grazing Promotes Grassland Nitrous Oxide Emission by Increasing Ammonia-Oxidizing Archaea Abundance on the Tibetan Plateau.},
journal = {Current microbiology},
volume = {76},
number = {5},
pages = {620-625},
pmid = {30859290},
issn = {1432-0991},
support = {31770532//National Natural Science Foundation of China/ ; },
mesh = {Ammonia/*metabolism ; Animals ; Archaea/*metabolism ; Fertilizers/analysis ; *Grassland ; *Herbivory ; Nitrous Oxide/*analysis ; Oxidation-Reduction ; Sheep ; Soil ; Tibet ; },
abstract = {Grasslands are suffering from long-term overgrazing because of the population inflation. Furthermore, nitrous oxide (N2O) is a major greenhouse gas that also depletes stratospheric ozone. However, the emission rate of grassland N2O and underlying mechanisms remained unclear under different grazing intensities. We conducted a field manipulation under four grazing intensities to compare its N2O fluxes and main affected factors. It was indicated that alpine meadow N2O emission rates increased from 39.7 ± 3.1 to 47.8 ± 2.3 μg m-2 h-1 (p < 0.05), then decreased to 43.4 ± 4.1 and 32.9 ± 1.4 μg m-2 h-1 with grazing intensity increasing from 4 to 8, 12 and 16 sheep ha-1, respectively. Multiple-stepwise regression analysis indicated that the predominant affected soil factors were separately TN and BD, pH and BD, also pH and BD, SOC and BD. Simple linear regression models revealed that ammonia-oxidizing archaea (AOA) contributed much to N2O emission (R2 = 0.77). Additionally, the R2 coefficient of linear regression was 0.87 between nosZ genes and N2O emission rates in alpine meadow. Much attention should be paid to protecting alpine meadow from degradation to mitigate N2O emission source on the Tibetan Plateau.},
}
@article {pmid30837306,
year = {2019},
author = {He, D and Piergentili, C and Ross, J and Tarrant, E and Tuck, LR and Mackay, CL and McIver, Z and Waldron, KJ and Clarke, DJ and Marles-Wright, J},
title = {Conservation of the structural and functional architecture of encapsulated ferritins in bacteria and archaea.},
journal = {The Biochemical journal},
volume = {476},
number = {6},
pages = {975-989},
doi = {10.1042/BCJ20180922},
pmid = {30837306},
issn = {1470-8728},
support = {BB/N005570/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M010996/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 098375/Z/12/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Archaeal Proteins/*chemistry ; Bacterial Proteins/*chemistry ; Ferritins/*chemistry ; Myxococcales/*chemistry ; Protein Domains ; Pyrococcus furiosus/*chemistry ; Rhodospirillum rubrum/*chemistry ; Structural Homology, Protein ; Structure-Activity Relationship ; },
abstract = {Ferritins are a large family of intracellular proteins that protect the cell from oxidative stress by catalytically converting Fe(II) into less toxic Fe(III) and storing iron minerals within their core. Encapsulated ferritins (EncFtn) are a sub-family of ferritin-like proteins, which are widely distributed in all bacterial and archaeal phyla. The recently characterized Rhodospirillum rubrum EncFtn displays an unusual structure when compared with classical ferritins, with an open decameric structure that is enzymatically active, but unable to store iron. This EncFtn must be associated with an encapsulin nanocage in order to act as an iron store. Given the wide distribution of the EncFtn family in organisms with diverse environmental niches, a question arises as to whether this unusual structure is conserved across the family. Here, we characterize EncFtn proteins from the halophile Haliangium ochraceum and the thermophile Pyrococcus furiosus, which show the conserved annular pentamer of dimers topology. Key structural differences are apparent between the homologues, particularly in the centre of the ring and the secondary metal-binding site, which is not conserved across the homologues. Solution and native mass spectrometry analyses highlight that the stability of the protein quaternary structure differs between EncFtn proteins from different species. The ferroxidase activity of EncFtn proteins was confirmed, and we show that while the quaternary structure around the ferroxidase centre is distinct from classical ferritins, the ferroxidase activity is still inhibited by Zn(II). Our results highlight the common structural organization and activity of EncFtn proteins, despite diverse host environments and contexts within encapsulins.},
}
@article {pmid30833729,
year = {2019},
author = {Borrel, G and Adam, PS and McKay, LJ and Chen, LX and Sierra-García, IN and Sieber, CMK and Letourneur, Q and Ghozlane, A and Andersen, GL and Li, WJ and Hallam, SJ and Muyzer, G and de Oliveira, VM and Inskeep, WP and Banfield, JF and Gribaldo, S},
title = {Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea.},
journal = {Nature microbiology},
volume = {4},
number = {4},
pages = {603-613},
pmid = {30833729},
issn = {2058-5276},
mesh = {Alkanes/*chemistry/metabolism ; Archaea/classification/genetics/growth &amp; development/*metabolism ; *Biodiversity ; DNA, Archaeal ; Metagenome ; Methane/chemistry/*metabolism ; Oxidation-Reduction ; Phylogeny ; },
abstract = {Methanogenesis is an ancient metabolism of key ecological relevance, with direct impact on the evolution of Earth's climate. Recent results suggest that the diversity of methane metabolisms and their derivations have probably been vastly underestimated. Here, by probing thousands of publicly available metagenomes for homologues of methyl-coenzyme M reductase complex (MCR), we have obtained ten metagenome-assembled genomes (MAGs) belonging to potential methanogenic, anaerobic methanotrophic and short-chain alkane-oxidizing archaea. Five of these MAGs represent under-sampled (Verstraetearchaeota, Methanonatronarchaeia, ANME-1 and GoM-Arc1) or previously genomically undescribed (ANME-2c) archaeal lineages. The remaining five MAGs correspond to lineages that are only distantly related to previously known methanogens and span the entire archaeal phylogeny. Comprehensive comparative annotation substantially expands the metabolic diversity and energy conservation systems of MCR-bearing archaea. It also suggests the potential existence of a yet uncharacterized type of methanogenesis linked to short-chain alkane/fatty acid oxidation in a previously undescribed class of archaea ('Candidatus Methanoliparia'). We redefine a common core of marker genes specific to methanogenic, anaerobic methanotrophic and short-chain alkane-oxidizing archaea, and propose a possible scenario for the evolutionary and functional transitions that led to the emergence of such metabolic diversity.},
}
@article {pmid30833728,
year = {2019},
author = {Wang, Y and Wegener, G and Hou, J and Wang, F and Xiao, X},
title = {Expanding anaerobic alkane metabolism in the domain of Archaea.},
journal = {Nature microbiology},
volume = {4},
number = {4},
pages = {595-602},
pmid = {30833728},
issn = {2058-5276},
mesh = {Alkanes/chemistry/*metabolism ; Archaea/chemistry/*classification/genetics/*metabolism ; Archaeal Proteins/genetics/metabolism ; Methane/metabolism ; Phylogeny ; },
abstract = {Methanogenesis and anaerobic methane oxidation through methyl-coenzyme M reductase (MCR) as a key enzyme have been suggested to be basal pathways of archaea1. How widespread MCR-based alkane metabolism is among archaea, where it occurs and how it evolved remain elusive. Here, we performed a global survey of MCR-encoding genomes based on metagenomic data from various environments. Eleven high-quality mcr-containing metagenomic-assembled genomes were obtained belonging to the Archaeoglobi in the Euryarchaeota, Hadesarchaeota and different TACK superphylum archaea, including the Nezhaarchaeota, Korarchaeota and Verstraetearchaeota. Archaeoglobi WYZ-LMO1 and WYZ-LMO3 and Korarchaeota WYZ-LMO9 encode both the (reverse) methanogenesis and the dissimilatory sulfate reduction pathway, suggesting that they have the genomic potential to couple both pathways in individual organisms. The Hadesarchaeota WYZ-LMO4-6 and Archaeoglobi JdFR-42 encode highly divergent MCRs, enzymes that may enable them to thrive on non-methane alkanes. The occurrence of mcr genes in different archaeal phyla indicates that MCR-based alkane metabolism is common in the domain of Archaea.},
}
@article {pmid30810807,
year = {2019},
author = {Lopes-Dos-Santos, RMA and De Troch, M and Bossier, P and Van Stappen, G},
title = {Labelling halophilic Archaea using 13C and 15N stable isotopes: a potential tool to investigate haloarchaea consumption by metazoans.},
journal = {Extremophiles : life under extreme conditions},
volume = {23},
number = {3},
pages = {359-365},
pmid = {30810807},
issn = {1433-4909},
support = {BOF/01N01615//Universiteit Gent, Special Research Fund (BOF)/ ; },
mesh = {Animals ; *Biomass ; Carbon Isotopes/*chemistry ; *Food Chain ; Halobacteriales/*growth &amp; development ; Isotope Labeling/*methods ; Nitrogen Isotopes/*chemistry ; },
abstract = {The use of stable isotope (SI) labelling and tracing of live diets is currently considered one of the most comprehensive tools to detect their uptake and assimilation by aquatic organisms. These techniques are indeed widely used in nutritional studies to follow the fate of specific microbial dietary components, unraveling trophic interactions. Nevertheless, to the current date our understanding of aquatic trophic relationships has yet to include a whole domain of life, the Archaea. The aim of the present research was, therefore, to describe a halophilic Archaea (haloarchaea) labelling procedure, using the SI 13C and 15N, to enable the application of SI tracing in future studies of haloarchaea consumption by aquatic metazoans. To this end, three 13C enriched carbon sources and two 15N enriched nitrogen sources were tested as potential labels to enrich cells of three haloarchaea strains when supplemented to the culture medium. Our overall results indicate 13C-glycerol as the most effective carbon source to achieve an efficient 13C enrichment in haloarchaea cells, with Δδ13C values above 5000‰ in all tested haloarchaea strains. As for 15N enriched nitrogen sources, both (15NH4)2SO4 and 15NH4Cl seem to be readily assimilated, also resulting in efficient 15N enrichment in haloarchaea cells, with Δδ15N values higher than 20,000‰. We believe that the proposed methodology will allow for the use of SI labelled haloarchaea biomass in feeding tests, potentially providing unambiguous confirmation of the assimilation of haloarchaea biomass by aquatic metazoans.},
}
@article {pmid30808005,
year = {2019},
author = {Díaz-Perales, A and Quesada, V and Peinado, JR and Ugalde, AP and Álvarez, J and Suárez, MF and Gomis-Rüth, FX and López-Otín, C},
title = {Withdrawal: Identification and characterization of human archaemetzincin-1 and -2, two novel members of a family of metalloproteases widely distributed in Archaea.},
journal = {The Journal of biological chemistry},
volume = {294},
number = {4},
pages = {1434},
doi = {10.1074/jbc.W118.007328},
pmid = {30808005},
issn = {1083-351X},
}
@article {pmid30806656,
year = {2019},
author = {Rissanen, AJ and Peura, S and Mpamah, PA and Taipale, S and Tiirola, M and Biasi, C and Mäki, A and Nykänen, H},
title = {Vertical stratification of bacteria and archaea in sediments of a small boreal humic lake.},
journal = {FEMS microbiology letters},
volume = {366},
number = {5},
pages = {},
pmid = {30806656},
issn = {1574-6968},
mesh = {Archaea/*classification/genetics/isolation &amp; purification ; Bacteria/*classification/genetics/isolation &amp; purification ; Biodiversity ; Biomass ; DNA Restriction Enzymes/genetics ; Geologic Sediments/chemistry/*microbiology ; Humic Substances/analysis ; Lakes/chemistry/*microbiology ; Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Water Microbiology ; },
abstract = {Although sediments of small boreal humic lakes are important carbon stores and greenhouse gas sources, the composition and structuring mechanisms of their microbial communities have remained understudied. We analyzed the vertical profiles of microbial biomass indicators (PLFAs, DNA and RNA) and the bacterial and archaeal community composition (sequencing of 16S rRNA gene amplicons and qPCR of mcrA) in sediment cores collected from a typical small boreal lake. While microbial biomass decreased with sediment depth, viable microbes (RNA and PLFA) were present all through the profiles. The vertical stratification patterns of the bacterial and archaeal communities resembled those in marine sediments with well-characterized groups (e.g. Methanomicrobia, Proteobacteria, Cyanobacteria, Bacteroidetes) dominating in the surface sediment and being replaced by poorly-known groups (e.g. Bathyarchaeota, Aminicenantes and Caldiserica) in the deeper layers. The results also suggested that, similar to marine systems, the deep bacterial and archaeal communities were predominantly assembled by selective survival of taxa able to persist in the low energy conditions. Methanotrophs were rare, further corroborating the role of these methanogen-rich sediments as important methane emitters. Based on their taxonomy, the deep-dwelling groups were putatively organo-heterotrophic, organo-autotrophic and/or acetogenic and thus may contribute to changes in the lake sediment carbon storage.},
}
@article {pmid30796982,
year = {2019},
author = {Barnett, DJM and Mommers, M and Penders, J and Arts, ICW and Thijs, C},
title = {Intestinal archaea inversely associated with childhood asthma.},
journal = {The Journal of allergy and clinical immunology},
volume = {143},
number = {6},
pages = {2305-2307},
doi = {10.1016/j.jaci.2019.02.009},
pmid = {30796982},
issn = {1097-6825},
mesh = {Allergens/immunology ; *Archaea ; Asthma/immunology/*microbiology ; Child ; Eczema/immunology/microbiology ; Feces/microbiology ; Female ; Food Hypersensitivity/immunology/microbiology ; Humans ; Immunoglobulin E/blood ; Intestines/*microbiology ; Male ; },
}
@article {pmid30796347,
year = {2019},
author = {Wang, L and Li, K and Sheng, R and Li, Z and Wei, W},
title = {Remarkable N2O emissions by draining fallow paddy soil and close link to the ammonium-oxidizing archaea communities.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {2550},
pmid = {30796347},
issn = {2045-2322},
mesh = {Ammonium Compounds/*metabolism ; Archaea/genetics/*metabolism ; Floods ; Nitrification ; Nitrous Oxide/*analysis ; Soil/*chemistry ; Soil Microbiology ; },
abstract = {Fallow paddies experience natural flooding and draining water status due to rainfall and evaporation, which could induce considerable nitrous oxide (N2O) emissions and need to be studied specially. In this study, intact soil columns were collected from a fallow paddy field and the flooding-draining process was simulated in a microcosm experiment. The results showed that both N2O concentrations in the soil and N2O emission rates were negligible during flooding period, which were greatly elevated by draining the fallow paddy soil. The remarkable N2O concentrations in the soil and N2O emission/h during draining both had significant relationships with the Arch-amoA gene (P < 0.01) but not the Bac-amoA, narG, nirK, nirS, and nosZ genes, indicating that the ammonium-oxidizing archaea (AOA) might be the important players in soil N2O net production and emissions after draining. Moreover, we observed that N2O concentrations in the upper soil layers (0-10 cm) were not significantly different from that in the 10-20 cm layer under draining condition (P > 0.05). However, the number of AOA and the nitrification substrate (NH4+-N) in the 0-10 cm layer were significantly higher than in the 10-20 cm layer (P < 0.01), indicating N2O production in the 0-10 cm layer might be higher than the measured concentration and would contribute considerably to N2O emissions as shorter distance of gas diffusion to the soil surface.},
}
@article {pmid30790413,
year = {2019},
author = {Wang, Y and Feng, X and Natarajan, VP and Xiao, X and Wang, F},
title = {Diverse anaerobic methane- and multi-carbon alkane-metabolizing archaea coexist and show activity in Guaymas Basin hydrothermal sediment.},
journal = {Environmental microbiology},
volume = {21},
number = {4},
pages = {1344-1355},
doi = {10.1111/1462-2920.14568},
pmid = {30790413},
issn = {1462-2920},
support = {2018T110390//China Postdoctoral Science Foundation Grant/International ; 41525011//National Natural Science Foundation of China/International ; 91428308//National Natural Science Foundation of China/International ; 91751205//National Natural Science Foundation of China/International ; 2018YFC0310800//State Key R&amp;D Project of China/International ; 2016YFA0601102//State Key R&amp;D Project of China/International ; 2018T110390//China Postdoctoral Science Foundation/International ; 91428308//Natural Science Foundation of China/International ; 91751205//Natural Science Foundation of China/International ; 41525011//Natural Science Foundation of China/International ; },
mesh = {Alkanes/*metabolism ; Anaerobiosis/genetics ; Archaea/*classification/*genetics ; Carbon/metabolism ; Ecosystem ; Genes, Archaeal/genetics ; Geologic Sediments/*microbiology ; Hydrothermal Vents ; Metagenome ; Methane/*metabolism ; Oxidation-Reduction ; Phylogeny ; },
abstract = {Anaerobic oxidation of methane greatly contributes to global carbon cycling, yet the anaerobic oxidation of non-methane alkanes by archaea was only recently detected in lab enrichments. The distribution and activity of these archaea in natural environments are not yet reported and understood. Here, a combination of metagenomic and metatranscriptomic approaches was utilized to understand the ecological roles and metabolic potentials of methyl-coenzyme M reductase (MCR)-based alka