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28 Sep 2021 at 01:30
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Bibliography on: Archaea


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RJR: Recommended Bibliography 28 Sep 2021 at 01:30 Created: 


In 1977, Carl Woese and George Fox applied molecular techniques to biodiversity and discovered that life on Earth consisted of three, not two (prokaryotes and eukaryotes), major lineages, tracing back nearly to the very origin of life on Earth. The third lineage has come to be known as the Archaea. Organisms now considered Archaea were originally thought to be a kind of prokaryote, but Woese and Fox showed that they were as different from prokaryotes as they were from eukaryotes. To understand life on Earth one must also understand the Archaea .

Created with PubMed® Query: archaea[TITLE] OR archaebacteria[TITLE] NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)


RevDate: 2021-09-20

Weidenbach K, Gutt M, Cassidy L, et al (2021)

Small proteins in Archaea, a mainly unexplored world.

Journal of bacteriology [Epub ahead of print].

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.

RevDate: 2021-09-20

Blombach F, Fouqueau T, Matelska D, et al (2021)

Promoter-proximal elongation regulates transcription in archaea.

Nature communications, 12(1):5524.

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.

RevDate: 2021-09-18

Lin T, Zhang L, Wu M, et al (2021)

Repair of Hypoxanthine in DNA Revealed by DNA Glycosylases and Endonucleases From Hyperthermophilic Archaea.

Frontiers in microbiology, 12:736915.

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.

RevDate: 2021-09-17

Franke JD, Fuerst JA, AM Poole (2021)

Editorial: Structure, Function and Evolution of Complex Cellular Organization in Bacteria and Archaea.

Frontiers in microbiology, 12:751416.

RevDate: 2021-09-15
CmpDate: 2021-09-15

Pallen MJ (2021)

The status Candidatus for uncultured taxa of Bacteria and Archaea: SWOT analysis.

International journal of systematic and evolutionary microbiology, 71(9):.

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.

RevDate: 2021-09-12

Kumar V, Singh B, van Belkum MJ, et al (2021)

Halocins, natural antimicrobials of Archaea: Exotic or special or both?.

Biotechnology advances pii:S0734-9750(21)00140-3 [Epub ahead of print].

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.

RevDate: 2021-09-07

Li L, Zhang W, Zhang S, et al (2021)

Bacteria and Archaea Synergistically Convert Glycine Betaine to Biogenic Methane in the Formosa Cold Seep of the South China Sea.

mSystems [Epub ahead of print].

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.

RevDate: 2021-09-08

Hu D, Yang J, Qi Y, et al (2021)

Metagenomic Analysis of Fecal Archaea, Bacteria, Eukaryota, and Virus in Przewalski's Horses Following Anthelmintic Treatment.

Frontiers in veterinary science, 8:708512.

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.

RevDate: 2021-09-08

Makarova KS, Wolf YI, Karamycheva S, et al (2021)

A Unique Gene Module in Thermococcales Archaea Centered on a Hypervariable Protein Containing Immunoglobulin Domains.

Frontiers in microbiology, 12:721392.

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.

RevDate: 2021-09-15

Haiming T, Chao L, Kaikai C, et al (2021)

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 of applied microbiology [Epub ahead of print].

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.

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.

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.

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.

RevDate: 2021-09-06

Cai M, Yin X, Tang X, et al (2021)

Metatranscriptomics reveals different features of methanogenic archaea among global vegetated coastal ecosystems.

The Science of the total environment, 802:149848 pii:S0048-9697(21)04923-8 [Epub ahead of print].

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.

RevDate: 2021-08-31

Koirala A, VS Brözel (2021)

Phylogeny of Nitrogenase Structural and Assembly Components Reveals New Insights into the Origin and Distribution of Nitrogen Fixation across Bacteria and Archaea.

Microorganisms, 9(8):.

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.

RevDate: 2021-08-26

Martinez-Gutierrez CA, FO Aylward (2021)

Phylogenetic Signal, Congruence, and Uncertainty across Bacteria and Archaea.

Molecular biology and evolution pii:6358142 [Epub ahead of print].

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 multi-domain phylogenetic trees of bacteria and archaea, and present a set of marker genes that performs best for multi-domain trees constructed from concatenated alignments. We use recently-developed Tree Certainty (TC) 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 multi-domain 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 artefact caused by biased sequence composition. Our findings provide a robust and standardized framework for multi-domain phylogenetic reconstruction that can be used to evaluate inter-phylum relationships and assess uncertainty in conflicting topologies of the Tree of Life.

RevDate: 2021-08-17

Kostygov AY, Alves JMP, V Yurchenko (2021)

Editorial: Symbioses Between Protists and Bacteria/Archaea.

Frontiers in microbiology, 12:709184.

RevDate: 2021-09-26

Moghimipour E, Abedishirehjin S, Baghbadorani MA, et al (2021)

Bacteria and Archaea: A new era of cancer therapy.

Journal of controlled release : official journal of the Controlled Release Society, 338:1-7 pii:S0168-3659(21)00425-9 [Epub ahead of print].

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.

RevDate: 2021-08-14

Acharya S, Dahal A, HK Bhattarai (2021)

Evolution and origin of sliding clamp in bacteria, archaea and eukarya.

PloS one, 16(8):e0241093.

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.

RevDate: 2021-08-11

Xie R, Wang Y, Huang D, et al (2021)

Expanding Asgard members in the domain of Archaea sheds new light on the origin of eukaryotes.

Science China. Life sciences [Epub ahead of print].

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.

RevDate: 2021-08-10

Wu D, Zhao C, Bai H, et al (2021)

Characteristics and metabolic patterns of soil methanogenic archaea communities in the high-latitude natural forested wetlands of China.

Ecology and evolution, 11(15):10396-10408.

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.

RevDate: 2021-08-10

Londei P, S Ferreira-Cerca (2021)

Ribosome Biogenesis in Archaea.

Frontiers in microbiology, 12:686977.

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.

RevDate: 2021-08-20

Xiao L, Liu G, Gong F, et al (2021)

The reductive carboxylation activity of heterotetrameric pyruvate synthases from hyperthermophilic archaea.

Biochemical and biophysical research communications, 572:151-156.

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.

RevDate: 2021-08-09

Deng F, Li Y, Peng Y, et al (2021)

The Diversity, Composition, and Metabolic Pathways of Archaea in Pigs.

Animals : an open access journal from MDPI, 11(7):.

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.

RevDate: 2021-08-09

Clark IM, Hughes DJ, Fu Q, et al (2021)

Metagenomic approaches reveal differences in genetic diversity and relative abundance of nitrifying bacteria and archaea in contrasting soils.

Scientific reports, 11(1):15905.

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.

RevDate: 2021-08-05

Wakai M, Hayashi S, Chiba Y, et al (2021)

Growth and morphologic response of rumen methanogenic archaea and bacteria to cashew nut shell liquid and its alkylphenol components.

Animal science journal = Nihon chikusan Gakkaiho, 92(1):e13598.

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.

RevDate: 2021-08-04

French E, Kozlowski JA, A Bollmann (2021)

Competition of Ammonia-Oxidizing Archaea and Bacteria from Freshwater Environments.

Applied and environmental microbiology [Epub ahead of print].

In the environment, nutrients are rarely available in constant supply. Therefore, microorganisms require strategies to compete for limiting nutrients. In freshwater systems, ammonia-oxidizing archaea (AOA) and 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 an AOA (AOA-AC1) and an 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. 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 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 AOB when the ammonium availability increases. These results will help to predict potential shifts in community composition of ammonia oxidizers in the environment due to changes in ammonium availability.

RevDate: 2021-08-04

Santos MVD, Goes RHTB, Takiya CS, et al (2021)

Effect of increasing doses of chitosan to grazing beef steers on the relative population and transcript abundance of Archaea and cellulolytic and amylolytic bacterias.

Animal biotechnology [Epub ahead of print].

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.

RevDate: 2021-08-24

Zhu J, Yan X, Zhou L, et al (2021)

Insight of bacteria and archaea in Feammox community enriched from different soils.

Environmental research, 203:111802 pii:S0013-9351(21)01096-3 [Epub ahead of print].

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.

RevDate: 2021-08-08

Li C, Hambright KD, Bowen HG, et al (2021)

Global co-occurrence of methanogenic archaea and methanotrophic bacteria in Microcystis aggregates.

Environmental microbiology [Epub ahead of print].

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.

RevDate: 2021-07-28

Jung MY, Sedlacek CJ, Kits KD, et al (2021)

Ammonia-oxidizing archaea possess a wide range of cellular ammonia affinities.

The ISME journal [Epub ahead of print].

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.

RevDate: 2021-07-22

Coutinho FH, Zaragoza-Solas A, López-Pérez M, et al (2021)

RaFAH: Host prediction for viruses of Bacteria and Archaea based on protein content.

Patterns (New York, N.Y.), 2(7):100274.

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/.

RevDate: 2021-07-21

Yu H, Skennerton CT, Chadwick GL, et al (2021)

Sulfate differentially stimulates but is not respired by diverse anaerobic methanotrophic archaea.

The ISME journal [Epub ahead of print].

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.

RevDate: 2021-09-10

Umbach AK, Stegelmeier AA, JD Neufeld (2021)

Archaea Are Rare and Uncommon Members of the Mammalian Skin Microbiome.

mSystems, 6(4):e0064221.

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.

RevDate: 2021-07-20

Dong Y, Shan Y, Xia K, et al (2021)

The Proposed Molecular Mechanisms Used by Archaea for Fe(III) Reduction and Fe(II) Oxidation.

Frontiers in microbiology, 12:690918.

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.

RevDate: 2021-07-20

Wang L, D Huang (2021)

Soil ammonia-oxidizing archaea in a paddy field with different irrigation and fertilization managements.

Scientific reports, 11(1):14563.

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.

RevDate: 2021-07-13

Jørgensen BB (2021)

Do methanogenic archaea cause reductive pyrite dissolution in subsurface sediments?.

The ISME journal [Epub ahead of print].

RevDate: 2021-07-13

Christakis CA, Barkay T, ES Boyd (2021)

Expanded Diversity and Phylogeny of mer Genes Broadens Mercury Resistance Paradigms and Reveals an Origin for MerA Among Thermophilic Archaea.

Frontiers in microbiology, 12:682605.

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.

RevDate: 2021-08-01

Wang S, Narsing Rao MP, Wei D, et al (2021)

Complete genome sequencing and comparative genome analysis of the extremely halophilic archaea, Haloterrigena daqingensis.

Biotechnology and applied biochemistry [Epub ahead of print].

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.

RevDate: 2021-07-08

Kakuk B, Wirth R, Maróti G, et al (2021)

Early response of methanogenic archaea to H2 as evaluated by metagenomics and metatranscriptomics.

Microbial cell factories, 20(1):127.

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.

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.

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.

RevDate: 2021-07-26
CmpDate: 2021-07-26

Wang X, He Z, Li X, et al (2020)

[Comparison of pretreatment methods in lipid analysis and ultra-performance liquid chromatography-mass spectrometry analysis of archaea].

Se pu = Chinese journal of chromatography, 38(8):914-922.

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.

RevDate: 2021-07-14

Abellan-Schneyder I, Siebert A, Hofmann K, et al (2021)

Full-Length SSU rRNA Gene Sequencing Allows Species-Level Detection of Bacteria, Archaea, and Yeasts Present in Milk.

Microorganisms, 9(6):.

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.

RevDate: 2021-07-27

Pfeiffer F, M Dyall-Smith (2021)

Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea.

Genes, 12(7):.

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.

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.

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.

RevDate: 2021-07-14

Tamisier M, Schmidt M, Vogt C, et al (2021)

Iron corrosion by methanogenic archaea characterized by stable isotope effects and crust mineralogy.

Environmental microbiology [Epub ahead of print].

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.

RevDate: 2021-06-23

Zhao R, Mogollón JM, Roerdink DL, et al (2021)

Ammonia-oxidizing archaea have similar power requirements in diverse marine oxic sediments.

The ISME journal [Epub ahead of print].

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.

RevDate: 2021-08-05
CmpDate: 2021-08-05

Chen Z, Liu WS, Zhong X, et al (2021)

Genome- and community-level interaction insights into the ecological role of archaea in rare earth element mine drainage in South China.

Water research, 201:117331.

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.

RevDate: 2021-08-19

Ziegler CA, PL Freddolino (2021)

The leucine-responsive regulatory proteins/feast-famine regulatory proteins: an ancient and complex class of transcriptional regulators in bacteria and archaea.

Critical reviews in biochemistry and molecular biology, 56(4):373-400.

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.

RevDate: 2021-06-22

De Lise F, Strazzulli A, Iacono R, et al (2021)

Programmed Deviations of Ribosomes From Standard Decoding in Archaea.

Frontiers in microbiology, 12:688061.

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.

RevDate: 2021-06-19

Kurth JM, Nobu MK, Tamaki H, et al (2021)

Methanogenic archaea use a bacteria-like methyltransferase system to demethoxylate aromatic compounds.

The ISME journal [Epub ahead of print].

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.

RevDate: 2021-06-19

Murali R, Gennis RB, J Hemp (2021)

Evolution of the cytochrome bd oxygen reductase superfamily and the function of CydAA' in Archaea.

The ISME journal [Epub ahead of print].

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.

RevDate: 2021-07-24

Takemata N, SD Bell (2021)

Chromosome conformation capture assay combined with biotin enrichment for hyperthermophilic archaea.

STAR protocols, 2(2):100576.

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).

RevDate: 2021-06-19

Castelle CJ, Méheust R, Jaffe AL, et al (2021)

Protein Family Content Uncovers Lineage Relationships and Bacterial Pathway Maintenance Mechanisms in DPANN Archaea.

Frontiers in microbiology, 12:660052.

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.

RevDate: 2021-09-23

Schulze S, Pfeiffer F, Garcia BA, et al (2021)

Comprehensive glycoproteomics shines new light on the complexity and extent of glycosylation in archaea.

PLoS biology, 19(6):e3001277.

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.

RevDate: 2021-08-25
CmpDate: 2021-08-25

Shen LD, Yang YL, Liu JQ, et al (2021)

Different responses of ammonia-oxidizing archaea and bacteria in paddy soils to elevated CO2 concentration.

Environmental pollution (Barking, Essex : 1987), 286:117558.

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.

RevDate: 2021-07-24

Takemata N, SD Bell (2021)

High-resolution analysis of chromosome conformation in hyperthermophilic archaea.

STAR protocols, 2(2):100562.

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).

RevDate: 2021-06-12

Garnier F, Couturier M, Débat H, et al (2021)

Archaea: A Gold Mine for Topoisomerase Diversity.

Frontiers in microbiology, 12:661411.

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.

RevDate: 2021-06-11

Payne D, Spietz RL, ES Boyd (2021)

Reductive dissolution of pyrite by methanogenic archaea.

The ISME journal [Epub ahead of print].

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.

RevDate: 2021-08-11
CmpDate: 2021-08-11

Watanabe S, Murase Y, Watanabe Y, et al (2021)

Crystal structures of aconitase X enzymes from bacteria and archaea provide insights into the molecular evolution of the aconitase superfamily.

Communications biology, 4(1):687.

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.

RevDate: 2021-06-10
CmpDate: 2021-06-10

Pende N, Sogues A, Megrian D, et al (2021)

SepF is the FtsZ anchor in archaea, with features of an ancestral cell division system.

Nature communications, 12(1):3214.

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.

RevDate: 2021-06-15

Vázquez-Madrigal AS, Barbachano-Torres A, Arellano-Plaza M, et al (2021)

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.

Microorganisms, 9(5):.

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.

RevDate: 2021-08-03

McNichol J, Berube PM, Biller SJ, et al (2021)

Evaluating and Improving Small Subunit rRNA PCR Primer Coverage for Bacteria, Archaea, and Eukaryotes Using Metagenomes from Global Ocean Surveys.

mSystems, 6(3):e0056521.

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.

RevDate: 2021-05-26

Cockram C, Thierry A, R Koszul (2021)

Generation of gene-level resolution chromosome contact maps in bacteria and archaea.

STAR protocols, 2(2):100512.

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).

RevDate: 2021-05-26

Inkinen J, Siponen S, Jayaprakash B, et al (2021)

Diverse and active archaea communities occur in non-disinfected drinking water systems-Less activity revealed in disinfected and hot water systems.

Water research X, 12:100101.

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&B use artificially recharged non-disinfected groundwater (ARG), the other DWDS's supplied water disinfected by using ultraviolet (UV) light and chlorine compounds, C&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.

RevDate: 2021-05-26

Bomberg M, H Miettinen (2020)

Data on the optimization of an archaea-specific probe-based qPCR assay.

Data in brief, 33:106610.

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).

RevDate: 2021-05-26

Lei L, ZF Burton (2021)

Early Evolution of Transcription Systems and Divergence of Archaea and Bacteria.

Frontiers in molecular biosciences, 8:651134.

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.

RevDate: 2021-07-23
CmpDate: 2021-06-22

Naitam MG, R Kaushik (2021)

Archaea: An Agro-Ecological Perspective.

Current microbiology, 78(7):2510-2521.

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.

RevDate: 2021-05-21

Graham F (2021)

Daily briefing: Enigmatic archaea might be key to complex life.

RevDate: 2021-05-18

Clemmons BA, Schneider LG, Melchior EA, et al (2021)

The effects of feeding ferric citrate on ruminal bacteria, methanogenic archaea and methane production in growing beef steers.

Access microbiology, 3(1):acmi000180.

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.

RevDate: 2021-05-18

Weixlbaumer A, Grünberger F, Werner F, et al (2021)

Coupling of Transcription and Translation in Archaea: Cues From the Bacterial World.

Frontiers in microbiology, 12:661827.

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.

RevDate: 2021-09-15

Yang Y, Zhang C, Lenton TM, et al (2021)

The Evolution Pathway of Ammonia-Oxidizing Archaea Shaped by Major Geological Events.

Molecular biology and evolution, 38(9):3637-3648.

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.

RevDate: 2021-05-14

Westoby M, Nielsen DA, Gillings MR, et al (2021)

Cell size, genome size, and maximum growth rate are near-independent dimensions of ecological variation across bacteria and archaea.

Ecology and evolution, 11(9):3956-3976.

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.

RevDate: 2021-07-14
CmpDate: 2021-07-14

Mikhaylina AO, Nikonova EY, Kostareva OS, et al (2021)

Characterization of Regulatory Elements of L11 and L1 Operons in Thermophilic Bacteria and Archaea.

Biochemistry. Biokhimiia, 86(4):397-408.

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.

RevDate: 2021-05-04

Schnakenberg A, Aromokeye DA, Kulkarni A, et al (2021)

Electron Acceptor Availability Shapes Anaerobically Methane Oxidizing Archaea (ANME) Communities in South Georgia Sediments.

Frontiers in microbiology, 12:617280.

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.

RevDate: 2021-05-26

Liu Y, Makarova KS, Huang WC, et al (2021)

Expanded diversity of Asgard archaea and their relationships with eukaryotes.

Nature, 593(7860):553-557.

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.

RevDate: 2021-07-05
CmpDate: 2021-07-05

Kitamura R, Kozaki T, Ishii K, et al (2021)

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.

Microbes and environments, 36(2):.

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.

RevDate: 2021-09-23

Płaza G, Jałowiecki Ł, Głowacka D, et al (2021)

Insights into the microbial diversity and structure in a full-scale municipal wastewater treatment plant with particular regard to Archaea.

PloS one, 16(4):e0250514.

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.

RevDate: 2021-06-15
CmpDate: 2021-06-15

Westoby M, Gillings MR, Madin JS, et al (2021)

Trait dimensions in bacteria and archaea compared to vascular plants.

Ecology letters, 24(7):1487-1504.

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.

RevDate: 2021-05-24
CmpDate: 2021-05-24

Thema M, Weidlich T, Kaul A, et al (2021)

Optimized biological CO2-methanation with a pure culture of thermophilic methanogenic archaea in a trickle-bed reactor.

Bioresource technology, 333:125135.

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.

RevDate: 2021-04-14

Grinter R, C Greening (2021)

Cofactor F420: an expanded view of its distribution, biosynthesis, and roles in bacteria and archaea.

FEMS microbiology reviews pii:6225804 [Epub ahead of print].

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 five 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. Fifty years since its discovery, multiple paradigms associated with F420 have shifted, and new F420-dependent organisms and processes continue to be discovered.

RevDate: 2021-06-18
CmpDate: 2021-06-18

Taib N, Gribaldo S, SA MacNeill (2021)

Single-Stranded DNA-Binding Proteins in the Archaea.

Methods in molecular biology (Clifton, N.J.), 2281:23-47.

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.

RevDate: 2021-04-09

Gao K, Y Lu (2021)

Putative Extracellular Electron Transfer in Methanogenic Archaea.

Frontiers in microbiology, 12:611739.

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.

RevDate: 2021-04-06

Chuphal N, Singha KP, Sardar P, et al (2021)

Scope of Archaea in Fish Feed: a New Chapter in Aquafeed Probiotics?.

Probiotics and antimicrobial proteins [Epub ahead of print].

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.

RevDate: 2021-04-08

Gonzalez-Bosquet J, Pedra-Nobre S, Devor EJ, et al (2021)

Bacterial, Archaea, and Viral Transcripts (BAVT) Expression in Gynecological Cancers and Correlation with Regulatory Regions of the Genome.

Cancers, 13(5):.

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.

RevDate: 2021-05-28
CmpDate: 2021-05-28

Fan C, Zhang W, Chen X, et al (2021)

Residual effects of four-year amendments of organic material on N2O production driven by ammonia-oxidizing archaea and bacteria in a tropical vegetable soil.

The Science of the total environment, 781:146746.

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.

RevDate: 2021-05-07

Liu J, Cvirkaite-Krupovic V, Baquero DP, et al (2021)

Virus-induced cell gigantism and asymmetric cell division in archaea.

Proceedings of the National Academy of Sciences of the United States of America, 118(15):.

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.

RevDate: 2021-03-30

Teske A, Amils R, Ramírez GA, et al (2021)

Editorial: Archaea in the Environment: Views on Archaeal Distribution, Activity, and Biogeography.

Frontiers in microbiology, 12:667596.

RevDate: 2021-03-30

Czekay DP, U Kothe (2021)

H/ACA Small Ribonucleoproteins: Structural and Functional Comparison Between Archaea and Eukaryotes.

Frontiers in microbiology, 12:654370.

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.

RevDate: 2021-09-24
CmpDate: 2021-09-24

Orona-Navar A, Aguilar-Hernández I, Nigam KDP, et al (2021)

Alternative sources of natural pigments for dye-sensitized solar cells: Algae, cyanobacteria, bacteria, archaea and fungi.

Journal of biotechnology, 332:29-53.

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.

RevDate: 2021-05-19

Galperin MY, Wolf YI, Garushyants SK, et al (2021)

Non-essential ribosomal proteins in bacteria and archaea identified using COGs.

Journal of bacteriology [Epub ahead of print].

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.

RevDate: 2021-05-19
CmpDate: 2021-05-19

Bize A, Midoux C, Mariadassou M, et al (2021)

Exploring short k-mer profiles in cells and mobile elements from Archaea highlights the major influence of both the ecological niche and evolutionary history.

BMC genomics, 22(1):186.

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.

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.

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.

RevDate: 2021-04-21
CmpDate: 2021-04-21

Zhang C, Meckenstock RU, Weng S, et al (2021)

Marine sediments harbor diverse archaea and bacteria with the potential for anaerobic hydrocarbon degradation via fumarate addition.

FEMS microbiology ecology, 97(5):.

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.

RevDate: 2021-08-18
CmpDate: 2021-08-18

Jain A, KP Krishnan (2021)

Marine Group-II archaea dominate particle-attached as well as free-living archaeal assemblages in the surface waters of Kongsfjorden, Svalbard, Arctic Ocean.

Antonie van Leeuwenhoek, 114(5):633-647.

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.

RevDate: 2021-08-10
CmpDate: 2021-08-10

Mauerhofer LM, Zwirtmayr S, Pappenreiter P, et al (2021)

Hyperthermophilic methanogenic archaea act as high-pressure CH4 cell factories.

Communications biology, 4(1):289.

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.

RevDate: 2021-03-02
CmpDate: 2021-03-02

Zheng M, He S, Feng Y, et al (2021)

Active ammonia-oxidizing bacteria and archaea in wastewater treatment systems.

Journal of environmental sciences (China), 102:273-282.

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.

RevDate: 2021-08-20
CmpDate: 2021-08-20

Kim JG, Gazi KS, Awala SI, et al (2021)

Ammonia-oxidizing archaea in biological interactions.

Journal of microbiology (Seoul, Korea), 59(3):298-310.

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.

RevDate: 2021-04-27
CmpDate: 2021-04-27

Sorokin DY, Roman P, TV Kolganova (2021)

Halo(natrono)archaea from hypersaline lakes can utilize sulfoxides other than DMSO as electron acceptors for anaerobic respiration.

Extremophiles : life under extreme conditions, 25(2):173-180.

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.

RevDate: 2021-05-13
CmpDate: 2021-04-30

Cai R, Zhang J, Liu R, et al (2021)

Metagenomic Insights into the Metabolic and Ecological Functions of Abundant Deep-Sea Hydrothermal Vent DPANN Archaea.

Applied and environmental microbiology, 87(9):.

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.

RevDate: 2021-02-15

Distaso MA, Bargiela R, Brailsford FL, et al (2021)

Corrigendum: High Representation of Archaea Across All Depths in Oxic and Low-pH Sediment Layers Underlying an Acidic Stream.

Frontiers in microbiology, 12:633015.

[This corrects the article DOI: 10.3389/fmicb.2020.576520.].

RevDate: 2021-06-18
CmpDate: 2021-06-18

Starke R, Siles JA, Fernandes MLP, et al (2021)

The structure and function of soil archaea across biomes.

Journal of proteomics, 237:104147.

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.

RevDate: 2021-06-07

Shalvarjian KE, DD Nayak (2021)

Transcriptional regulation of methanogenic metabolism in archaea.

Current opinion in microbiology, 60:8-15.

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.

RevDate: 2021-09-24
CmpDate: 2021-08-10

Kuprat T, Ortjohann M, Johnsen U, et al (2021)

Glucose Metabolism and Acetate Switch in Archaea: the Enzymes in Haloferax volcanii.

Journal of bacteriology, 203(8):.

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.

RevDate: 2021-05-12
CmpDate: 2021-05-12

Du H, Sun T, Liu Y, et al (2021)

Bacteria and archaea involved in anaerobic mercury methylation and methane oxidation in anaerobic sulfate-rich reactors.

Chemosphere, 274:129773.

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.

RevDate: 2021-09-07
CmpDate: 2021-09-07

Makarova KS, Wolf YI, Shmakov SA, et al (2020)

Unprecedented Diversity of Unique CRISPR-Cas-Related Systems and Cas1 Homologs in Asgard Archaea.

The CRISPR journal, 3(3):156-163.

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.


RJR Experience and Expertise


Robbins holds BS, MS, and PhD degrees in the life sciences. He served as a tenured faculty member in the Zoology and Biological Science departments at Michigan State University. He is currently exploring the intersection between genomics, microbial ecology, and biodiversity — an area that promises to transform our understanding of the biosphere.


Robbins has extensive experience in college-level education: At MSU he taught introductory biology, genetics, and population genetics. At JHU, he was an instructor for a special course on biological database design. At FHCRC, he team-taught a graduate-level course on the history of genetics. At Bellevue College he taught medical informatics.


Robbins has been involved in science administration at both the federal and the institutional levels. At NSF he was a program officer for database activities in the life sciences, at DOE he was a program officer for information infrastructure in the human genome project. At the Fred Hutchinson Cancer Research Center, he served as a vice president for fifteen years.


Robbins has been involved with information technology since writing his first Fortran program as a college student. At NSF he was the first program officer for database activities in the life sciences. At JHU he held an appointment in the CS department and served as director of the informatics core for the Genome Data Base. At the FHCRC he was VP for Information Technology.


While still at Michigan State, Robbins started his first publishing venture, founding a small company that addressed the short-run publishing needs of instructors in very large undergraduate classes. For more than 20 years, Robbins has been operating The Electronic Scholarly Publishing Project, a web site dedicated to the digital publishing of critical works in science, especially classical genetics.


Robbins is well-known for his speaking abilities and is often called upon to provide keynote or plenary addresses at international meetings. For example, in July, 2012, he gave a well-received keynote address at the Global Biodiversity Informatics Congress, sponsored by GBIF and held in Copenhagen. The slides from that talk can be seen HERE.


Robbins is a skilled meeting facilitator. He prefers a participatory approach, with part of the meeting involving dynamic breakout groups, created by the participants in real time: (1) individuals propose breakout groups; (2) everyone signs up for one (or more) groups; (3) the groups with the most interested parties then meet, with reports from each group presented and discussed in a subsequent plenary session.


Robbins has been engaged with photography and design since the 1960s, when he worked for a professional photography laboratory. He now prefers digital photography and tools for their precision and reproducibility. He designed his first web site more than 20 years ago and he personally designed and implemented this web site. He engages in graphic design as a hobby.

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E-mail: RJR8222@gmail.com

Collection of publications by R J Robbins

Reprints and preprints of publications, slide presentations, instructional materials, and data compilations written or prepared by Robert Robbins. Most papers deal with computational biology, genome informatics, using information technology to support biomedical research, and related matters.

Research Gate page for R J Robbins

ResearchGate is a social networking site for scientists and researchers to share papers, ask and answer questions, and find collaborators. According to a study by Nature and an article in Times Higher Education , it is the largest academic social network in terms of active users.

Curriculum Vitae for R J Robbins

short personal version

Curriculum Vitae for R J Robbins

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RJR Picks from Around the Web (updated 11 MAY 2018 )