archaea

Summary

Summary: One of the three domains of life (the others being BACTERIA and Eukarya), formerly called Archaebacteria under the taxon Bacteria, but now considered separate and distinct. They are characterized by: (1) the presence of characteristic tRNAs and ribosomal RNAs; (2) the absence of peptidoglycan cell walls; (3) the presence of ether-linked lipids built from branched-chain subunits; and (4) their occurrence in unusual habitats. While archaea resemble bacteria in morphology and genomic organization, they resemble eukarya in their method of genomic replication. The domain contains at least four kingdoms: CRENARCHAEOTA; EURYARCHAEOTA; NANOARCHAEOTA; and KORARCHAEOTA.

Top Publications

  1. Haroon M, Hu S, Shi Y, Imelfort M, Keller J, Hugenholtz P, et al. Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage. Nature. 2013;500:567-70 pubmed publisher
    ..manganese and sulphate reduction have been demonstrated in consortia containing anaerobic methanotrophic (ANME) archaea. More recently it has been shown that the bacterium Candidatus 'Methylomirabilis oxyfera' can couple AOM to ..
  2. Nürenberg E, Tampe R. Tying up loose ends: ribosome recycling in eukaryotes and archaea. Trends Biochem Sci. 2013;38:64-74 pubmed publisher
    Ribosome recycling is the final - or first - step of the cyclic process of mRNA translation. In eukaryotes and archaea, dissociation of the two ribosomal subunits proceeds in a fundamentally different way than in bacteria...
  3. Makarova K, Koonin E. Archaeology of eukaryotic DNA replication. Cold Spring Harb Perspect Biol. 2013;5:a012963 pubmed publisher
    ..It can be inferred that the archaeal ancestor of eukaryotes and even the last common ancestor of all extant archaea possessed replication machineries that were comparable in complexity to the eukaryotic replication system...
  4. Rinke C, Schwientek P, Sczyrba A, Ivanova N, Anderson I, Cheng J, et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature. 2013;499:431-7 pubmed publisher
    ..acid use for the opal stop codon, an archaeal-type purine synthesis in Bacteria and complete sigma factors in Archaea similar to those in Bacteria...
  5. Hong Y, Youshao W, Chen F. Archaea dominate ammonia oxidizers in the permian water ecosystem of midland basin. Microbes Environ. 2013;28:396-9 pubmed
    ..Molecular surveys targeting the amoA gene showed that only ammonia-oxidizing archaea (AOA) exist and have potential activity in this special environment...
  6. Farkas J, Picking J, Santangelo T. Genetic techniques for the archaea. Annu Rev Genet. 2013;47:539-61 pubmed publisher
    Genetic techniques for the Archaea have undergone a rapid expansion in complexity, resulting in increased exploration of the role of Archaea in the environment and detailed analyses of the molecular physiology and information-processing ..
  7. Meng J, Xu J, Qin D, He Y, Xiao X, Wang F. Genetic and functional properties of uncultivated MCG archaea assessed by metagenome and gene expression analyses. ISME J. 2014;8:650-9 pubmed publisher
    The Miscellaneous Crenarchaeota group (MCG) Archaea is one of the predominant archaeal groups in anoxic environments and may have significant roles in the global biogeochemical cycles...
  8. Fierer N, Ladau J, Clemente J, Leff J, Owens S, Pollard K, et al. Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States. Science. 2013;342:621-4 pubmed publisher
  9. Yilmaz P, Parfrey L, Yarza P, Gerken J, Pruesse E, Quast C, et al. The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks. Nucleic Acids Res. 2014;42:D643-8 pubmed publisher
    ..for up-to-date quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services...

More Information

Publications108 found, 100 shown here

  1. Forterre P. The common ancestor of archaea and eukarya was not an archaeon. Archaea. 2013;2013:372396 pubmed publisher
    It is often assumed that eukarya originated from archaea. This view has been recently supported by phylogenetic analyses in which eukarya are nested within archaea...
  2. Chun J, Rainey F. Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea. Int J Syst Evol Microbiol. 2014;64:316-24 pubmed publisher
    The polyphasic approach used today in the taxonomy and systematics of the Bacteria and Archaea includes the use of phenotypic, chemotaxonomic and genotypic data...
  3. Emerson J, Andrade K, Thomas B, Norman A, Allen E, Heidelberg K, et al. Virus-host and CRISPR dynamics in Archaea-dominated hypersaline Lake Tyrrell, Victoria, Australia. Archaea. 2013;2013:370871 pubmed publisher
    ..All samples were dominated by Archaea (75-95%)...
  4. Lindås A, Bernander R. The cell cycle of archaea. Nat Rev Microbiol. 2013;11:627-38 pubmed publisher
    ..Recent findings have provided insight into the cell cycle of archaea, including the multiple-origin mode of DNA replication, the initial characterization of a genome segregation ..
  5. Oger P, Cario A. Adaptation of the membrane in Archaea. Biophys Chem. 2013;183:42-56 pubmed publisher
    ..We review here evidence for homeoviscous adaptation in Archaea, and discuss the limits of this strategy and our knowledge in this very peculiar domain of life.
  6. Wu D, Jospin G, Eisen J. Systematic identification of gene families for use as "markers" for phylogenetic and phylogeny-driven ecological studies of bacteria and archaea and their major subgroups. PLoS ONE. 2013;8:e77033 pubmed publisher
    ..here the identification of PhyEco markers for different taxonomic levels including 40 for "all bacteria and archaea", 114 for "all bacteria (greatly expanding on the ?30 commonly used), and 100 s to 1000 s for some of ..
  7. Raymann K, Forterre P, Brochier Armanet C, Gribaldo S. Global phylogenomic analysis disentangles the complex evolutionary history of DNA replication in archaea. Genome Biol Evol. 2014;6:192-212 pubmed publisher
    ..phylogenetic signal carried by DNA replication is highly consistent with that harbored by two other key informational machineries (translation and transcription), strengthening the existence of a robust organismal tree for the Archaea.
  8. Stieglmeier M, Mooshammer M, Kitzler B, Wanek W, Zechmeister Boltenstern S, Richter A, et al. Aerobic nitrous oxide production through N-nitrosating hybrid formation in ammonia-oxidizing archaea. ISME J. 2014;8:1135-46 pubmed publisher
    ..However, the contribution of the recently discovered ammonia-oxidizing archaea (AOA) to N2O production from soil is unclear as is the mechanism by which they produce it...
  9. Kennelly P. Protein Ser/Thr/Tyr phosphorylation in the Archaea. J Biol Chem. 2014;289:9480-7 pubmed publisher
    The third domain of life, the Archaea (formerly Archaebacteria), is populated by a physiologically diverse set of microorganisms, many of which reside at the ecological extremes of our global environment...
  10. Nakagawa T, Stahl D. Transcriptional response of the archaeal ammonia oxidizer Nitrosopumilus maritimus to low and environmentally relevant ammonia concentrations. Appl Environ Microbiol. 2013;79:6911-6 pubmed publisher
    The ability of chemoautotrophic ammonia-oxidizing archaea to compete for ammonia among marine microorganisms at low ambient concentrations has been in part attributed to their extremely high affinity for ammonia, but as yet there is no ..
  11. Forterre P. Why are there so many diverse replication machineries?. J Mol Biol. 2013;425:4714-26 pubmed publisher
    ..Comparison of DNA replication proteins in the three domains, Archaea, Bacteria, and Eukarya, have surprisingly revealed the existence of two distinct sets of non-homologous cellular ..
  12. Parte A. LPSN--list of prokaryotic names with standing in nomenclature. Nucleic Acids Res. 2014;42:D613-6 pubmed publisher
    ..bacterio.net) is a database that lists the names of prokaryotes (Bacteria and Archaea) that have been validly published in the International Journal of Systematic and Evolutionary Microbiology ..
  13. Krupovic M, Quemin E, Bamford D, Forterre P, Prangishvili D. Unification of the globally distributed spindle-shaped viruses of the Archaea. J Virol. 2014;88:2354-8 pubmed publisher
    ..Our results illuminate the utility of structure-based virus classification and bring additional order to the virosphere. ..
  14. Wang F, Zhang Y, Chen Y, He Y, Qi J, Hinrichs K, et al. Methanotrophic archaea possessing diverging methane-oxidizing and electron-transporting pathways. ISME J. 2014;8:1069-78 pubmed publisher
    ..The process is thought to be mediated by three groups of uncultivated methane-oxidizing archaea (ANME-1, 2 and 3)...
  15. Pawlowski A, Rissanen I, Bamford J, Krupovic M, Jalasvuori M. Gammasphaerolipovirus, a newly proposed bacteriophage genus, unifies viruses of halophilic archaea and thermophilic bacteria within the novel family Sphaerolipoviridae. Arch Virol. 2014;159:1541-54 pubmed publisher
    ..Given the common features of these viruses, we propose to include the so far unclassified P23-77-like bacteriophages into a new genus, "Gammasphaerolipovirus", within the family Sphaerolipoviridae...
  16. Bräsen C, Esser D, Rauch B, Siebers B. Carbohydrate metabolism in Archaea: current insights into unusual enzymes and pathways and their regulation. Microbiol Mol Biol Rev. 2014;78:89-175 pubmed publisher
    The metabolism of Archaea, the third domain of life, resembles in its complexity those of Bacteria and lower Eukarya...
  17. Pinto A, Raskin L. PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets. PLoS ONE. 2012;7:e43093 pubmed publisher
    ..However, the greatest obstacle towards accurately evaluating community structure are the errors in estimated mean relative abundance of each detected OTU due to biases associated with multi-template PCR reactions. ..
  18. Li J, Zhou H, Peng X, Wu Z, Chen S, Fang J. Microbial diversity and biomineralization in low-temperature hydrothermal iron-silica-rich precipitates of the Lau Basin hydrothermal field. FEMS Microbiol Ecol. 2012;81:205-16 pubmed publisher
    ..analysis showed that the precipitates were dominated by the members of ?-proteobacteria and marine group I archaea. Ultrastructural analysis suggested the bacteriogenic origin of the iron-silica-rich deposits...
  19. Kozubal M, Romine M, Jennings R, Jay Z, Tringe S, Rusch D, et al. Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park. ISME J. 2013;7:622-34 pubmed publisher
    ..studies of acidic ferric iron mats from YNP have revealed considerable diversity of uncultivated and undescribed archaea. The goal of this study was to obtain replicate de novo genome assemblies for a dominant archaeal population ..
  20. Deatherage B, Cookson B. Membrane vesicle release in bacteria, eukaryotes, and archaea: a conserved yet underappreciated aspect of microbial life. Infect Immun. 2012;80:1948-57 pubmed publisher
    ..of bioactive membrane vesicles (MVs) from the cell surface is conserved across microbial life, in bacteria, archaea, fungi, and parasites...
  21. Milucka J, Ferdelman T, Polerecky L, Franzke D, Wegener G, Schmid M, et al. Zero-valent sulphur is a key intermediate in marine methane oxidation. Nature. 2012;491:541-6 pubmed publisher
    ..Sulphate-coupled AOM is believed to be mediated by a consortium of methanotrophic archaea (ANME) and sulphate-reducing Deltaproteobacteria but the underlying mechanism has not yet been resolved...
  22. Park S, Kim J, Jung M, Kim S, Cha I, Ghai R, et al. Draft genome sequence of an ammonia-oxidizing archaeon, "Candidatus Nitrosopumilus sediminis" AR2, from Svalbard in the Arctic Circle. J Bacteriol. 2012;194:6948-9 pubmed publisher
    Ammonia-oxidizing archaea (AOA) typically predominate over ammonia-oxidizing bacteria in marine sediments...
  23. Fröls S. Archaeal biofilms: widespread and complex. Biochem Soc Trans. 2013;41:393-8 pubmed publisher
    ..Biofilm-forming archaea were identified in a broad range of extreme and moderate environments...
  24. Yutin N, Koonin E. Archaeal origin of tubulin. Biol Direct. 2012;7:10 pubmed publisher
    ..and are distantly related to the FtsZ GTPase that is involved in cell division in most bacteria and many archaea. Among prokaryotes, bona fide tubulins have been identified only in bacteria of the genus Prosthecobacter...
  25. Bai Y, Sun Q, Wen D, Tang X. Abundance of ammonia-oxidizing bacteria and archaea in industrial and domestic wastewater treatment systems. FEMS Microbiol Ecol. 2012;80:323-30 pubmed
    ..is performed in wastewater treatment by both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). Most previous studies focused on their distribution in natural environments...
  26. Hayden H, Mele P, Bougoure D, Allan C, Norng S, Piceno Y, et al. Changes in the microbial community structure of bacteria, archaea and fungi in response to elevated CO(2) and warming in an Australian native grassland soil. Environ Microbiol. 2012;14:3081-96 pubmed publisher
    The microbial community structure of bacteria, archaea and fungi is described in an Australian native grassland soil after more than 5 years exposure to different atmospheric CO2 concentrations ([CO2]) (ambient, +550 ppm) and ..
  27. Siam R, Mustafa G, Sharaf H, Moustafa A, Ramadan A, Antunes A, et al. Unique prokaryotic consortia in geochemically distinct sediments from Red Sea Atlantis II and discovery deep brine pools. PLoS ONE. 2012;7:e42872 pubmed publisher
    ..in the S-rich Atlantis II section are likely to play a dominant role in the cycling of methane and sulfur due to their phylogenetic affiliations with bacteria and archaea involved in anaerobic methane oxidation and sulfate reduction.
  28. Eichler J, Maupin Furlow J. Post-translation modification in Archaea: lessons from Haloferax volcanii and other haloarchaea. FEMS Microbiol Rev. 2013;37:583-606 pubmed publisher
    ..generating proteomic diversity are adopted by organisms across evolution, the responsible pathways and enzymes in Archaea are often less well described than are their eukaryotic and bacterial counterparts...
  29. Susanti D, Mukhopadhyay B. An intertwined evolutionary history of methanogenic archaea and sulfate reduction. PLoS ONE. 2012;7:e45313 pubmed publisher
    ..However, certain methanogenic archaea metabolize sulfite employing a deazaflavin cofactor (F(420))-dependent sulfite reductase (Fsr) where N- and C-..
  30. Williams T, Foster P, Nye T, Cox C, Embley T. A congruent phylogenomic signal places eukaryotes within the Archaea. Proc Biol Sci. 2012;279:4870-9 pubmed publisher
    ..In the textbook 'three domains' tree based on informational genes, eukaryotes and Archaea share a common ancestor to the exclusion of Bacteria...
  31. Abby S, Tannier E, Gouy M, Daubin V. Lateral gene transfer as a support for the tree of life. Proc Natl Acad Sci U S A. 2012;109:4962-7 pubmed publisher
  32. Munk B, Bauer C, Gronauer A, Lebuhn M. A metabolic quotient for methanogenic Archaea. Water Sci Technol. 2012;66:2311-7 pubmed publisher
    ..is a major bottleneck in the biogas process, the determination of the specific activity of methanogenic Archaea can be a good indicator of the process state...
  33. Childs L, Held N, Young M, Whitaker R, Weitz J. Multiscale model of CRISPR-induced coevolutionary dynamics: diversification at the interface of Lamarck and Darwin. Evolution. 2012;66:2015-29 pubmed publisher
    ..Short Palindromic Repeats) system is a recently discovered type of adaptive immune defense in bacteria and archaea that functions via directed incorporation of viral and plasmid DNA into host genomes...
  34. Weinberger A, Wolf Y, Lobkovsky A, Gilmore M, Koonin E. Viral diversity threshold for adaptive immunity in prokaryotes. MBio. 2012;3:e00456-12 pubmed publisher
    Bacteria and archaea face continual onslaughts of rapidly diversifying viruses and plasmids...
  35. Offre P, Spang A, Schleper C. Archaea in biogeochemical cycles. Annu Rev Microbiol. 2013;67:437-57 pubmed publisher
    b>Archaea constitute a considerable fraction of the microbial biomass on Earth...
  36. Puigbò P, Wolf Y, Koonin E. Genome-wide comparative analysis of phylogenetic trees: the prokaryotic forest of life. Methods Mol Biol. 2012;856:53-79 pubmed publisher
    ..These results support the concept of the Tree of Life (TOL) as a central evolutionary trend in the FOL as opposed to the traditional view of the TOL as a "species tree." ..
  37. Fan L, Reynolds D, Liu M, Stark M, Kjelleberg S, Webster N, et al. Functional equivalence and evolutionary convergence in complex communities of microbial sponge symbionts. Proc Natl Acad Sci U S A. 2012;109:E1878-87 pubmed publisher
    ..Our data thus demonstrate evolutionary convergence in complex symbiont communities and reveal the details and mechanisms that underpin the process. ..
  38. Hatzenpichler R. Diversity, physiology, and niche differentiation of ammonia-oxidizing archaea. Appl Environ Microbiol. 2012;78:7501-10 pubmed publisher
    ..The cultivation of several ammonia-oxidizing archaea (AOA) as well as the discovery that archaeal ammonia monooxygenase (amo)-like gene sequences are nearly ..
  39. Bontognali T, Sessions A, Allwood A, Fischer W, Grotzinger J, Summons R, et al. Sulfur isotopes of organic matter preserved in 3.45-billion-year-old stromatolites reveal microbial metabolism. Proc Natl Acad Sci U S A. 2012;109:15146-51 pubmed
    ..Positive ?(33)S anomalies suggest that disproportionation of elemental sulfur would have been a prominent microbial process in these communities...
  40. Fernández Guerra A, Casamayor E. Habitat-associated phylogenetic community patterns of microbial ammonia oxidizers. PLoS ONE. 2012;7:e47330 pubmed publisher
    ..Bacteria and Archaea ammonia oxidizers (AOB and AOA, respectively) have colonized similar habitats worldwide...
  41. Probst A, Holman H, DeSantis T, Andersen G, Birarda G, Bechtel H, et al. Tackling the minority: sulfate-reducing bacteria in an archaea-dominated subsurface biofilm. ISME J. 2013;7:635-51 pubmed publisher
    b>Archaea are usually minor components of a microbial community and dominated by a large and diverse bacterial population...
  42. Abell G, Robert S, Frampton D, Volkman J, Rizwi F, Csontos J, et al. High-throughput analysis of ammonia oxidiser community composition via a novel, amoA-based functional gene array. PLoS ONE. 2012;7:e51542 pubmed publisher
  43. Pietilä M, Atanasova N, Manole V, Liljeroos L, Butcher S, Oksanen H, et al. Virion architecture unifies globally distributed pleolipoviruses infecting halophilic archaea. J Virol. 2012;86:5067-79 pubmed publisher
    Our understanding of the third domain of life, Archaea, has greatly increased since its establishment some 20 years ago. The increasing information on archaea has also brought their viruses into the limelight...
  44. Liu Y, Beer L, Whitman W. Sulfur metabolism in archaea reveals novel processes. Environ Microbiol. 2012;14:2632-44 pubmed publisher
    Studies on sulfur metabolism in archaea have revealed many novel enzymes and pathways and have advanced our understanding on metabolic processes, not only of the archaea, but of biology in general...
  45. Sasaki K, Morita M, Sasaki D, Ohmura N, Igarashi Y. The membraneless bioelectrochemical reactor stimulates hydrogen fermentation by inhibiting methanogenic archaea. Appl Microbiol Biotechnol. 2013;97:7005-13 pubmed publisher
    ..6 ± 1.7 mM) at pHout 5.0 ± 0.1. Methanogenic archaea were not detected in the Ml-BER and anode-BER. However, Methanosarcina sp. and Methanobacterium sp...
  46. Syed M, Levesque C. Chromosomal bacterial type II toxin-antitoxin systems. Can J Microbiol. 2012;58:553-62 pubmed publisher
    ..Type II TA systems are widely distributed throughout the chromosomes of almost all free-living bacteria and archaea. The vast majority of type II toxins are mRNA-specific endonucleases arresting cell growth through the mechanism ..
  47. Matarazzo F, Ribeiro A, Faveri M, Taddei C, Martinez M, Mayer M. The domain Archaea in human mucosal surfaces. Clin Microbiol Infect. 2012;18:834-40 pubmed publisher
    b>Archaea present distinct features from bacteria and eukaryotes, and thus constitute one of the branches of the phylogenetic tree of life...
  48. Prosser J, Nicol G. Archaeal and bacterial ammonia-oxidisers in soil: the quest for niche specialisation and differentiation. Trends Microbiol. 2012;20:523-31 pubmed publisher
  49. Ziegler S, Dolch K, Geiger K, Krause S, Asskamp M, Eusterhues K, et al. Oxygen-dependent niche formation of a pyrite-dependent acidophilic consortium built by archaea and bacteria. ISME J. 2013;7:1725-37 pubmed publisher
    ..Interestingly, archaea were identified only in the anoxic parts of the biofilm...
  50. Horz H, Seyfarth I, Conrads G. McrA and 16S rRNA gene analysis suggests a novel lineage of Archaea phylogenetically affiliated with Thermoplasmatales in human subgingival plaque. Anaerobe. 2012;18:373-7 pubmed publisher
    ..on the molecular analysis of human subgingival plaque samples from 30 periodontitis patients a novel lineage of Archaea within the phylogenetic radiation of Thermoplasmatales was identified in 10% of cases...
  51. Baker B, Lesniewski R, Dick G. Genome-enabled transcriptomics reveals archaeal populations that drive nitrification in a deep-sea hydrothermal plume. ISME J. 2012;6:2269-79 pubmed publisher
    Ammonia-oxidizing Archaea (AOA) are among the most abundant microorganisms in the oceans and have crucial roles in biogeochemical cycling of nitrogen and carbon...
  52. Lane N, Martin W. The origin of membrane bioenergetics. Cell. 2012;151:1406-16 pubmed publisher
    ..Our hypothesis accounts for the Na(+)/H(+) promiscuity of bioenergetic proteins, as well as the deep divergence between bacteria and archaea.
  53. Catão E, Castro A, Barreto C, Krüger R, Kyaw C. Diversity of Archaea in Brazilian savanna soils. Arch Microbiol. 2013;195:507-12 pubmed publisher
    ..a dense subtype of sensu strict (cerrado denso) and riverbank forest (mata de galeria), was used to amplify Archaea-specific 16S rRNA gene...
  54. Lasek Nesselquist E, Gogarten J. The effects of model choice and mitigating bias on the ribosomal tree of life. Mol Phylogenet Evol. 2013;69:17-38 pubmed publisher
    Deep-level relationships within Bacteria, Archaea, and Eukarya as well as the relationships of these three domains to each other require resolution...
  55. Kandiba L, Eichler J. Analysis of putative nonulosonic acid biosynthesis pathways in Archaea reveals a complex evolutionary history. FEMS Microbiol Lett. 2013;345:110-20 pubmed publisher
    ..Yet, despite the prevalence of N-glycosylation in Archaea and the variety of sugars recruited for the archaeal version of this post-translational modification, only a ..
  56. Yutin N, Puigbò P, Koonin E, Wolf Y. Phylogenomics of prokaryotic ribosomal proteins. PLoS ONE. 2012;7:e36972 pubmed publisher
    ..than 50 proteins, including 34 that are universally conserved in the three domains of cellular life (bacteria, archaea, and eukaryotes)...
  57. Bower Phipps K, Taylor D, Wang H, Baserga S. The box C/D sRNP dimeric architecture is conserved across domain Archaea. RNA. 2012;18:1527-40 pubmed publisher
    ..Our results span three distantly related archaeal species--Sulfolobus solfataricus, Pyrococcus abyssi, and Archaeoglobus fulgidus--indicating that the di-sRNP architecture is broadly conserved across the entire archaeal domain. ..
  58. Park S, Kim J, Jung M, Kim S, Cha I, Kwon K, et al. Draft genome sequence of an ammonia-oxidizing archaeon, "Candidatus Nitrosopumilus koreensis" AR1, from marine sediment. J Bacteriol. 2012;194:6940-1 pubmed publisher
    Ammonia-oxidizing archaea (AOA) are ubiquitous in various marine environments and play important roles in the global nitrogen and carbon cycles...
  59. Vajrala N, Martens Habbena W, Sayavedra Soto L, Schauer A, Bottomley P, Stahl D, et al. Hydroxylamine as an intermediate in ammonia oxidation by globally abundant marine archaea. Proc Natl Acad Sci U S A. 2013;110:1006-11 pubmed publisher
    The ammonia-oxidizing archaea have recently been recognized as a significant component of many microbial communities in the biosphere...
  60. Cao H, Auguet J, Gu J. Global ecological pattern of ammonia-oxidizing archaea. PLoS ONE. 2013;8:e52853 pubmed publisher
    The global distribution of ammonia-oxidizing archaea (AOA), which play a pivotal role in the nitrification process, has been confirmed through numerous ecological studies...
  61. Mosier A, Allen E, Kim M, Ferriera S, Francis C. Genome sequence of "Candidatus Nitrosopumilus salaria" BD31, an ammonia-oxidizing archaeon from the San Francisco Bay estuary. J Bacteriol. 2012;194:2121-2 pubmed publisher
    Ammonia-oxidizing archaea (AOA) play important roles in nitrogen and carbon cycling in marine and terrestrial ecosystems...
  62. Kim J, Jung M, Park S, Rijpstra W, Sinninghe Damsté J, Madsen E, et al. Cultivation of a highly enriched ammonia-oxidizing archaeon of thaumarchaeotal group I.1b from an agricultural soil. Environ Microbiol. 2012;14:1528-43 pubmed publisher
    ..The first step of nitrification, ammonia oxidation, is mediated by Archaea as well as Bacteria...
  63. Lesniewski R, Jain S, Anantharaman K, Schloss P, Dick G. The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs. ISME J. 2012;6:2257-68 pubmed publisher
    ..De novo metagenomic assembly was used to reconstruct genomes of abundant populations, including Marine Group I archaea, Methylococcaceae, SAR324 Deltaproteobacteria and SUP05 Gammaproteobacteria...
  64. Sambasiva Rao K, Srinivasa Rao D. A comparative-based phylogenetic study in the evolution of 16S rRNA and rad a genes in Archaea. Int J Data Min Bioinform. 2012;6:396-405 pubmed
    b>Archaea are ubiquitous in their presence and abundant not only in extreme environments, but also in soil, oceans and freshwater, where they may fulfil a key role in the biogeochemical cycles of the earth...
  65. Hoffmann C, Dollive S, Grunberg S, Chen J, Li H, Wu G, et al. Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents. PLoS ONE. 2013;8:e66019 pubmed publisher
    ..Diet was quantified using inventories scoring both long-term and recent diet, and archaea and fungi were characterized by deep sequencing of marker genes in DNA purified from stool...
  66. Murina V, Nikulin A. RNA-binding Sm-like proteins of bacteria and archaea. similarity and difference in structure and function. Biochemistry (Mosc). 2011;76:1434-49 pubmed publisher
    ..The presence of these proteins in bacteria, archaea, and eukaryotes emphasizes their biological significance...
  67. Grzymski J, Riesenfeld C, Williams T, Dussaq A, Ducklow H, Erickson M, et al. A metagenomic assessment of winter and summer bacterioplankton from Antarctica Peninsula coastal surface waters. ISME J. 2012;6:1901-15 pubmed publisher
    ..If chemolithoautotrophy is widespread in the Southern Ocean in winter, this process may be a previously unaccounted carbon sink and may help account for the unexplained anomalies in surface inorganic nitrogen content...
  68. Borrel G, Lehours A, Crouzet O, Jézéquel D, Rockne K, Kulczak A, et al. Stratification of Archaea in the deep sediments of a freshwater meromictic lake: vertical shift from methanogenic to uncultured archaeal lineages. PLoS ONE. 2012;7:e43346 pubmed publisher
    As for lineages of known methanogens, several lineages of uncultured archaea were recurrently retrieved in freshwater sediments. However, knowledge is missing about how these lineages might be affected and structured according to depth...
  69. Hoeppner M, Poole A. Comparative genomics of eukaryotic small nucleolar RNAs reveals deep evolutionary ancestry amidst ongoing intragenomic mobility. BMC Evol Biol. 2012;12:183 pubmed publisher
    ..Their presence in both eukaryotes and archaea indicates that snoRNAs are evolutionarily ancient...
  70. Cobucci Ponzano B, Rossi M, Moracci M. Translational recoding in archaea. Extremophiles. 2012;16:793-803 pubmed publisher
    ..In archaea, in which translational recoding regulates the decoding of the 21st and the 22nd amino acids selenocysteine and ..
  71. Makarova K, Anantharaman V, Aravind L, Koonin E. Live virus-free or die: coupling of antivirus immunity and programmed suicide or dormancy in prokaryotes. Biol Direct. 2012;7:40 pubmed publisher
    The virus-host arms race is a major theater for evolutionary innovation. Archaea and bacteria have evolved diverse, elaborate antivirus defense systems that function on two general principles: i) immune systems that discriminate self DNA ..
  72. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590-6 pubmed publisher
    ..for up to date, quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services...
  73. Lu L, Jia Z. Urease gene-containing Archaea dominate autotrophic ammonia oxidation in two acid soils. Environ Microbiol. 2013;15:1795-809 pubmed publisher
    The metabolic traits of ammonia-oxidizing archaea (AOA) and bacteria (AOB) interacting with their environment determine the nitrogen cycle at the global scale...
  74. Blainey P. The future is now: single-cell genomics of bacteria and archaea. FEMS Microbiol Rev. 2013;37:407-27 pubmed publisher
  75. Hugoni M, Etien S, Bourges A, Lepère C, Domaizon I, Mallet C, et al. Dynamics of ammonia-oxidizing Archaea and Bacteria in contrasted freshwater ecosystems. Res Microbiol. 2013;164:360-70 pubmed publisher
    ..However, little is known about the role of ammonia-oxidizing Archaea (AOA) and Bacteria (AOB) in lacustrine ecosystems...
  76. Bertram S, Blumenberg M, Michaelis W, Siegert M, Krüger M, Seifert R. Methanogenic capabilities of ANME-archaea deduced from (13) C-labelling approaches. Environ Microbiol. 2013;15:2384-93 pubmed publisher
    Anaerobic methanotrophic archaea (ANME) are ubiquitous in marine sediments where sulfate dependent anaerobic oxidation of methane (AOM) occurs...
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