1932

Abstract

The discovery of the Archaea is a major scientific hallmark of the twentieth century. Since then, important features of their cell biology, physiology, ecology, and diversity have been revealed. Over the course of some 40 years, the diversity of known archaea has expanded from 2 to about 30 phyla comprising over 20,000 species. Most of this archaeal diversity has been revealed by environmental 16S rRNA gene amplicon sequencing surveys using a broad range of universal and targeted primers. Of the few primers that target a large fraction of known archaeal diversity, all display a bias against recently discovered lineages, which limits studies aiming to survey overall archaeal diversity. Induced by genomic exploration of archaeal diversity, and improved phylogenomics approaches, archaeal taxonomic classification has been frequently revised. Due to computational limitations and continued discovery of new lineages, a stable archaeal phylogeny is not yet within reach. Obtaining phylogenetic and taxonomic consensus of archaea should be a high priority for the archaeal research community.

Loading

Article metrics loading...

/content/journals/10.1146/annurev-micro-040921-050212
2021-10-08
2024-06-23
Loading full text...

Full text loading...

/deliver/fulltext/micro/75/1/annurev-micro-040921-050212.html?itemId=/content/journals/10.1146/annurev-micro-040921-050212&mimeType=html&fmt=ahah

Literature Cited

  1. 1. 
    Adam PS, Borrel G, Brochier-Armanet C, Gribaldo S. 2017. The growing tree of Archaea: new perspectives on their diversity, evolution and ecology. ISME J 11:2407–25
    [Google Scholar]
  2. 2. 
    Ahlgren NA, Fuchsman CA, Rocap G, Fuhrman JA. 2019. Discovery of several novel, widespread, and ecologically distinct marine Thaumarchaeota viruses that encode amoC nitrification genes. ISME J 13:618–31
    [Google Scholar]
  3. 3. 
    Baker BJ, Comolli LR, Dick GJ, Hauser LJ, Hyatt D et al. 2010. Enigmatic, ultrasmall, uncultivated Archaea. PNAS 107:8806–11
    [Google Scholar]
  4. 4. 
    Baker BJ, De Anda V, Seitz KW, Dombrowski N, Santoro AE, Lloyd KG. 2020. Diversity, ecology and evolution of Archaea. Nat. Microbiol. 5:887–900
    [Google Scholar]
  5. 5. 
    Baker BJ, Saw JH, Lind AE, Lazar CS, Hinrichs K-U et al. 2016. Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea. Nat. Microbiol 1:16002
    [Google Scholar]
  6. 6. 
    Baker BJ, Tyson GW, Webb RI, Flanagan J, Hugenholtz P et al. 2006. Lineages of acidophilic archaea revealed by community genomic analysis. Science 314:1933–35
    [Google Scholar]
  7. 7. 
    Balch WE, Magrum LJ, Fox GE, Wolfe RS, Woese CR. 1977. An ancient divergence among the bacteria. J. Mol. Evol. 9:305–11
    [Google Scholar]
  8. 8. 
    Barns SM, Delwiche CF, Palmer JD, Pace NR 1996. Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. PNAS 93:9188–93
    [Google Scholar]
  9. 9. 
    Berghuis BA, Yu FB, Schulz F, Blainey PC, Woyke T, Quake SR 2019. Hydrogenotrophic methanogenesis in archaeal phylum Verstraetearchaeota reveals the shared ancestry of all methanogens. PNAS 116:5037–44
    [Google Scholar]
  10. 10. 
    Biddle JF, Lipp JS, Lever MA, Lloyd KG, Sørensen KB et al. 2006. Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru. PNAS 103:3846–51
    [Google Scholar]
  11. 11. 
    Bontognali TRR, Sessions AL, Allwood AC, Fischer WW, Grotzinger JP et al. 2012. Sulfur isotopes of organic matter preserved in 3.45-billion-year-old stromatolites reveal microbial metabolism. PNAS 109:15146–51
    [Google Scholar]
  12. 12. 
    Boone D 2001. Class I. Methanobacteria class. nov. Bergey's Manual of Systematic Bacteriology D Boone, R Castenholz, G Garrity 213–35 New York: Springer
    [Google Scholar]
  13. 13. 
    Boone D 2001. Class II. Methanococci class. nov. Bergey's Manual of Systematic Bacteriology D Boone, R Castenholz, G Garrity 235–94 New York: Springer
    [Google Scholar]
  14. 14. 
    Borrel G, Brugère J-F, Gribaldo S, Schmitz RA, Moissl-Eichinger C. 2020. The host-associated archaeome. Nat. Rev. Microbiol. 18:11622–36
    [Google Scholar]
  15. 15. 
    Brochier-Armanet C, Boussau B, Gribaldo S, Forterre P. 2008. Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. Nat. Rev. Microbiol. 6:245–52
    [Google Scholar]
  16. 16. 
    Brock TD, Darland GK. 1970. Limits of microbial existence: temperature and pH. Science 169:1316–18
    [Google Scholar]
  17. 17. 
    Bulzu P-A, Andrei A-Ş, Salcher MM, Mehrshad M, Inoue K et al. 2019. Casting light on Asgardarchaeota metabolism in a sunlit microoxic niche. Nat. Microbiol. 4:1129–37
    [Google Scholar]
  18. 18. 
    Cai M, Liu Y, Yin X, Zhou Z, Friedrich MW et al. 2020. Diverse Asgard archaea including the novel phylum Gerdarchaeota participate in organic matter degradation. Sci. China Life Sci. 63:886–97
    [Google Scholar]
  19. 19. 
    Carr SA, Jungbluth SP, Eloe-Fadrosh EA, Stepanauskas R, Woyke T et al. 2019. Carboxydotrophy potential of uncultivated Hydrothermarchaeota from the subseafloor crustal biosphere. ISME J 13:1457–68
    [Google Scholar]
  20. 20. 
    Castelle CJ, Banfield JF. 2018. Major new microbial groups expand diversity and alter our understanding of the tree of life. Cell 172:1181–97
    [Google Scholar]
  21. 21. 
    Castelle CJ, Wrighton KC, Thomas BC, Hug LA, Brown CT et al. 2015. Genomic expansion of domain Archaea highlights roles for organisms from new phyla in anaerobic carbon cycling. Curr. Biol. 25:690–701
    [Google Scholar]
  22. 22. 
    Cavalier-Smith T. 1998. A revised six-kingdom system of life. Biol. Rev. 73:203–66
    [Google Scholar]
  23. 23. 
    Chatton E. 1938. Titres et travaux scientifiques (1906–1937) de Edouard Chatton Sète, France: Imprimerie Sottano
    [Google Scholar]
  24. 24. 
    Chuvochina M, Rinke C, Parks DH, Rappé MS, Tyson GW et al. 2019. The importance of designating type material for uncultured taxa. Syst. Appl. Microbiol. 42:15–21
    [Google Scholar]
  25. 25. 
    Copeland HF. 1938. The kingdoms of organisms. Q. Rev. Biol. 13:383–420
    [Google Scholar]
  26. 26. 
    Darland G, Brock TD, Samsonoff W, Conti SF. 1970. A thermophilic, acidophilic mycoplasma isolated from a coal refuse pile. Science 170:1416–18
    [Google Scholar]
  27. 27. 
    De Anda V, Chen L-X, Dombrowski N, Hua Z-S, Jiang H-C et al. 2021. Brockarchaeota, a novel archaeal phylum with unique and versatile carbon cycling pathways. Nat. Commun. 12:2404
    [Google Scholar]
  28. 28. 
    Delsuc F, Brinkmann H, Philippe H 2005. Phylogenomics and the reconstruction of the tree of life. Nat. Rev. Genet. 6:361–75
    [Google Scholar]
  29. 29. 
    Dombrowski N, Lee J-H, Williams TA, Offre P, Spang A. 2019. Genomic diversity, lifestyles and evolutionary origins of DPANN archaea. FEMS Microbiol. Lett. 366:2fnz008
    [Google Scholar]
  30. 30. 
    Dombrowski N, Williams TA, Sun J, Woodcroft BJ, Lee J-H et al. 2020. Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution. Nat. Commun. 11:3939
    [Google Scholar]
  31. 31. 
    Elkins JG, Podar M, Graham DE, Makarova KS, Wolf Y et al. 2008. A korarchaeal genome reveals insights into the evolution of the Archaea. PNAS 105:8102–7
    [Google Scholar]
  32. 32. 
    Eme L, Spang A, Lombard J, Stairs CW, Ettema TJG. 2017. Archaea and the origin of eukaryotes. Nat. Rev. Microbiol. 15:711–23
    [Google Scholar]
  33. 33. 
    Farag IF, Zhao R, Biddle JF. 2021.. “ Sifarchaeota,” a novel Asgard phylum from Costa Rican sediment capable of polysaccharide degradation and anaerobic methylotrophy. Appl. Environ. Microbiol. 87:e02584-20
    [Google Scholar]
  34. 34. 
    Farlow WG. 1880. On the nature of the peculiar reddening of salted codfish during the summer season. Rep. Comm. 1878, Part VI, pp. 969–74, U. S. Comm. Fish Fisher., Washington, DC, Gov. Print. Off.
    [Google Scholar]
  35. 35. 
    Flemming H-C, Wuertz S. 2019. Bacteria and archaea on Earth and their abundance in biofilms. Nat. Rev. Microbiol. 17:247–60
    [Google Scholar]
  36. 36. 
    Fry JC, Parkes RJ, Cragg BA, Weightman AJ, Webster G. 2008. Prokaryotic biodiversity and activity in the deep subseafloor biosphere. FEMS Microbiol. Ecol. 66:181–96
    [Google Scholar]
  37. 37. 
    Galand PE, Casamayor EO, Kirchman DL, Lovejoy C 2009. Ecology of the rare microbial biosphere of the Arctic Ocean. PNAS 106:22427–32
    [Google Scholar]
  38. 38. 
    Garrity G, Bell J, Lilburn T. 2004. Taxonomic Outline of the Prokaryotes Release 5.0 Bergey's Manual® of Systematic Bacteriology New York: Springer-Verlag
    [Google Scholar]
  39. 39. 
    Garrity G, Holt J 2001. Class VI. Archaeoglobi class. nov. Bergey's Manual of Systematic Bacteriology D Boone, R Castenholz, G Garrity 349–53 New York: Springer
    [Google Scholar]
  40. 40. 
    Garrity G, Holt J 2001. Class VII. Methanopyri class. nov. Bergey's Manual of Systematic Bacteriology D Boone, R Castenholz, G Garrity 353–55 New York: Springer
    [Google Scholar]
  41. 41. 
    Ghai R, Pašić L, Fernández AB, Martin-Cuadrado A-B, Mizuno CM et al. 2011. New abundant microbial groups in aquatic hypersaline environments. Sci. Rep. 1:135
    [Google Scholar]
  42. 42. 
    Gilbert JA, Jansson JK, Knight R. 2014. The Earth Microbiome project: successes and aspirations. BMC Biol 12:69
    [Google Scholar]
  43. 43. 
    Golyshina OV, Toshchakov SV, Makarova KS, Gavrilov SN, Korzhenkov AA et al. 2017. ‘ARMAN’ archaea depend on association with euryarchaeal host in culture and in situ. Nat. Commun. 8:60
    [Google Scholar]
  44. 44. 
    Goodwin S, McPherson JD, McCombie WR. 2016. Coming of age: ten years of next-generation sequencing technologies. Nat. Rev. Genet. 17:333–51
    [Google Scholar]
  45. 45. 
    Grant W, Kamekura M, McGenity T, Ventosa A 2001. Class III. Halobacteria class. nov. Bergey's Manual of Systematic Bacteriology D Boone, R Castenholz, G Garrity 294–334 New York: Springer
    [Google Scholar]
  46. 46. 
    Guy L, Ettema TJG. 2011. The archaeal ‘TACK’ superphylum and the origin of eukaryotes. Trends Microbiol 19:580–87
    [Google Scholar]
  47. 47. 
    Hua Z-S, Qu Y-N, Zhu Q, Zhou E-M, Qi Y-L et al. 2018. Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota. Nat. Commun. 9:2832
    [Google Scholar]
  48. 48. 
    Hua Z-S, Wang Y-L, Evans PN, Qu Y-N, Goh KM et al. 2019. Insights into the ecological roles and evolution of methyl-coenzyme M reductase-containing hot spring Archaea. Nat. Commun. 10:4574
    [Google Scholar]
  49. 49. 
    Huang J-M, Baker BJ, Li J-T, Wang Y. 2019. New microbial lineages capable of carbon fixation and nutrient cycling in deep-sea sediments of the northern South China Sea. Appl. Environ. Microbiol. 85:e00523-19
    [Google Scholar]
  50. 50. 
    Huber H, Hohn MJ, Rachel R, Fuchs T, Wimmer VC, Stetter KO. 2002. A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature 417:63–67
    [Google Scholar]
  51. 51. 
    Hylemon PB, Wells JS, Krieg NR, Jannasch HW. 1973. The genus Spirillum: a taxonomic study. Int. J. Syst. Evol. Microbiol. 23:340–80
    [Google Scholar]
  52. 52. 
    Imachi H, Nobu MK, Nakahara N, Morono Y, Ogawara M et al. 2020. Isolation of an archaeon at the prokaryote–eukaryote interface. Nature 577:519–25
    [Google Scholar]
  53. 53. 
    Inagaki F, Suzuki M, Takai K, Oida H, Sakamoto T et al. 2003. Microbial communities associated with geological horizons in coastal subseafloor sediments from the Sea of Okhotsk. Appl. Environ. Microbiol. 69:7224–35
    [Google Scholar]
  54. 54. 
    Iverson V, Morris RM, Frazar CD, Berthiaume CT, Morales RL, Armbrust EV. 2012. Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota. Science 335:587–90
    [Google Scholar]
  55. 55. 
    Jay ZJ, Beam JP, Dlakić M, Rusch DB, Kozubal MA, Inskeep WP. 2018. Marsarchaeota are an aerobic archaeal lineage abundant in geothermal iron oxide microbial mats. Nat. Microbiol. 3:732–40
    [Google Scholar]
  56. 56. 
    Jungbluth SP, Amend JP, Rappé MS. 2017. Metagenome sequencing and 98 microbial genomes from Juan de Fuca Ridge flank subsurface fluids. Sci. Data 4:170037
    [Google Scholar]
  57. 57. 
    Karner MB, DeLong EF, Karl DM. 2001. Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature 409:507–10
    [Google Scholar]
  58. 58. 
    Karst SM, Dueholm MS, McIlroy SJ, Kirkegaard RH, Nielsen PH, Albertsen M. 2018. Retrieval of a million high-quality, full-length microbial 16S and 18S rRNA gene sequences without primer bias. Nat. Biotechnol. 36:190–95
    [Google Scholar]
  59. 59. 
    Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C et al. 2012. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res 41:e1
    [Google Scholar]
  60. 60. 
    Kluyver AJ, Schnellen CG. 1947. On the fermentation of carbon monoxide by pure cultures of methane bacteria. Arch. Biochem. 14:57–70
    [Google Scholar]
  61. 61. 
    Kluyver AJ, Van Niel CB. 1936. Prospects for a natural system of classification of bacteria. Zentralbl. Bakteriol. Parasitenkd. Infektionskr. Hyg. 94:369–403
    [Google Scholar]
  62. 62. 
    Kocur M, Hodgkiss W. 1973. Taxonomic status of the genus Halococcus Schoop. Int. J. Syst. Evol. Microbiol. 23:151–56
    [Google Scholar]
  63. 63. 
    Konstantinidis KT, Rosselló-Móra R, Amann R. 2017. Uncultivated microbes in need of their own taxonomy. ISME J 11:2399–406
    [Google Scholar]
  64. 64. 
    Koskinen K, Pausan MR, Perras AK, Beck M, Bang C et al. 2017. First insights into the diverse human archaeome: specific detection of archaea in the gastrointestinal tract, lung, and nose and on skin. mBio 8:e00824-17
    [Google Scholar]
  65. 65. 
    Krause S, Bremges A, Münch PC, McHardy AC, Gescher J. 2017. Characterisation of a stable laboratory co-culture of acidophilic nanoorganisms. Sci. Rep. 7:3289
    [Google Scholar]
  66. 66. 
    Kubo K, Lloyd KG, Biddle JF, Amann R, Teske A, Knittel K. 2012. Archaea of the Miscellaneous Crenarchaeotal Group are abundant, diverse and widespread in marine sediments. ISME J 6:1949–65
    [Google Scholar]
  67. 67. 
    Larsen H. 1986. Halophilic and halotolerant microorganisms—an overview and historical perspective. FEMS Microbiol. Rev. 2:3–7
    [Google Scholar]
  68. 68. 
    Lazar CS, Baker BJ, Seitz KW, Teske AP. 2017. Genomic reconstruction of multiple lineages of uncultured benthic archaea suggests distinct biogeochemical roles and ecological niches. ISME J 11:1118–29
    [Google Scholar]
  69. 69. 
    Lewis WH, Tahon G, Geesink P, Sousa DZ, Ettema TJG. 2021. Innovations to culturing the uncultured microbial majority. Nat. Rev. Microbiol. 19:4225–40
    [Google Scholar]
  70. 70. 
    Lloyd KG, Schreiber L, Petersen DG, Kjeldsen KU, Lever MA et al. 2013. Predominant archaea in marine sediments degrade detrital proteins. Nature 496:215–18
    [Google Scholar]
  71. 71. 
    Martijn J, Lind AE, Schön ME, Spiertz I, Juzokaite L et al. 2019. Confident phylogenetic identification of uncultured prokaryotes through long read amplicon sequencing of the 16S-ITS-23S rRNA operon. Environ. Microbiol. 21:2485–98
    [Google Scholar]
  72. 72. 
    Meng J, Xu J, Qin D, He Y, Xiao X, Wang F 2014. Genetic and functional properties of uncultivated MCG archaea assessed by metagenome and gene expression analyses. ISME J 8:650–59
    [Google Scholar]
  73. 73. 
    Müller OF, Fabricius O, Müller CF. 1786. Animalcula Infusoria Fluviatilia et Marina Copenhagen: Typis Nicolai Mölleri
    [Google Scholar]
  74. 74. 
    Murray AE, Freudenstein J, Gribaldo S, Hatzenpichler R, Hugenholtz P et al. 2020. Roadmap for naming uncultivated Archaea and Bacteria. Nat. Microbiol. 5:987–94
    [Google Scholar]
  75. 75. 
    Narasingarao P, Podell S, Ugalde JA, Brochier-Armanet C, Emerson JB et al. 2012. De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities. ISME J 6:81–93
    [Google Scholar]
  76. 76. 
    NCBI Res. Coord 2017. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 46:D8–13
    [Google Scholar]
  77. 77. 
    Nealson K 2008. A Korarchaeote yields to genome sequencing. PNAS 105:8805–6
    [Google Scholar]
  78. 78. 
    Needham DM, Fuhrman JA. 2016. Pronounced daily succession of phytoplankton, archaea and bacteria following a spring bloom. Nat. Microbiol. 1:16005
    [Google Scholar]
  79. 79. 
    Nunoura T, Takaki Y, Kakuta J, Nishi S, Sugahara J et al. 2010. Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group. Nucleic Acids Res 39:3204–23
    [Google Scholar]
  80. 80. 
    Orsi WD, Vuillemin A, Rodriguez P, Coskun ÖK, Gomez-Saez GV et al. 2020. Metabolic activity analyses demonstrate that Lokiarchaeon exhibits homoacetogenesis in sulfidic marine sediments. Nat. Microbiol. 5:248–55
    [Google Scholar]
  81. 81. 
    Parker CT, Tindall BJ, Garrity GM 2019. International Code of Nomenclature of Prokaryotes: Prokaryotic Code (2008) revision. Int. J. Syst. Evol. Microbiol. 69:1A)
    [Google Scholar]
  82. 82. 
    Parkes RJ, Webster G, Cragg BA, Weightman AJ, Newberry CJ et al. 2005. Deep sub-seafloor prokaryotes stimulated at interfaces over geological time. Nature 436:390–94
    [Google Scholar]
  83. 83. 
    Parks DH, Chuvochina M, Chaumeil P-A, Rinke C, Mussig AJ, Hugenholtz P. 2020. A complete domain-to-species taxonomy for Bacteria and Archaea. Nat. Biotechnol. 38:1079–86
    [Google Scholar]
  84. 84. 
    Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A et al. 2018. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat. Biotechnol. 36:996–1004
    [Google Scholar]
  85. 85. 
    Pausan MR, Csorba C, Singer G, Till H, Schöpf V et al. 2019. Exploring the archaeome: detection of archaeal signatures in the human body. Front. Microbiol. 10:2796
    [Google Scholar]
  86. 86. 
    Pester M, Schleper C, Wagner M. 2011. The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology. Curr. Opin. Microbiol. 14:300–6
    [Google Scholar]
  87. 87. 
    Preston CM, Wu KY, Molinski TF, DeLong EF 1996. A psychrophilic crenarchaeon inhabits a marine sponge: Cenarchaeum symbiosum gen. nov., sp. nov. PNAS 93:6241–46
    [Google Scholar]
  88. 88. 
    Probst AJ, Ladd B, Jarett JK, Geller-McGrath DE, Sieber CMK et al. 2018. Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface. Nat. Microbiol. 3:328–36
    [Google Scholar]
  89. 89. 
    Probst AJ, Weinmaier T, Raymann K, Perras A, Emerson JB et al. 2014. Biology of a widespread uncultivated archaeon that contributes to carbon fixation in the subsurface. Nat. Commun. 5:5497
    [Google Scholar]
  90. 90. 
    Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T et al. 2012. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41:D590–96
    [Google Scholar]
  91. 91. 
    Reimer LC, Vetcininova A, Carbasse JS, Söhngen C, Gleim D et al. 2018. BacDive in 2019: bacterial phenotypic data for high-throughput biodiversity analysis. Nucleic Acids Res 47:D631–36
    [Google Scholar]
  92. 92. 
    Reysenbach AL. 2001. Class IV. Thermoplasmata class. nov. Bergey's Manual of Systematic Bacteriology D Boone, R Castenholz, G Garrity 335–40 New York: Springer
    [Google Scholar]
  93. 93. 
    Rinke C, Chuvochina M, Mussig AJ, Chaumeil P-A, Davin AA et al. 2021. Resolving widespread incomplete and uneven archaeal classifications based on a rank-normalized genome-based taxonomy. bioRxiv 2020.03.01.972265. https://doi.org/10.1101/2020.03.01.972265
  94. 94. 
    Rinke C, Rubino F, Messer LF, Youssef N, Parks DH et al. 2019. A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.). ISME J 13:663–75 Correction. 2020. ISME J. 14:878
    [Google Scholar]
  95. 95. 
    Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ et al. 2013. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499:431–37
    [Google Scholar]
  96. 96. 
    Robertson CE, Harris JK, Spear JR, Pace NR. 2005. Phylogenetic diversity and ecology of environmental Archaea. Curr. Opin. Microbiol. 8:638–42
    [Google Scholar]
  97. 97. 
    Sanger F, Nicklen S, Coulson AR 1977. DNA sequencing with chain-terminating inhibitors. PNAS 74:5463–67
    [Google Scholar]
  98. 98. 
    Schnellen CGTP. 1947. Onderzoekingen over de methaangisting Doctoral Thesis, Tech. Univ. Delft Rotterdam, Neth:.
    [Google Scholar]
  99. 99. 
    Schopf JW. 2006. Fossil evidence of Archaean life. Philos. Trans. R. Soc. B 361:869–85
    [Google Scholar]
  100. 100. 
    Schrempf D, Lartillot N, Szöllősi G. 2020. Scalable empirical mixture models that account for across-site compositional heterogeneity. Mol. Biol. Evol. 37:123616–31
    [Google Scholar]
  101. 101. 
    Seitz KW, Dombrowski N, Eme L, Spang A, Lombard J et al. 2019. Asgard archaea capable of anaerobic hydrocarbon cycling. Nat. Commun. 10:1822
    [Google Scholar]
  102. 102. 
    Seitz KW, Lazar CS, Hinrichs K-U, Teske AP, Baker BJ. 2016. Genomic reconstruction of a novel, deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction. ISME J 10:1696–705
    [Google Scholar]
  103. 103. 
    Sorokin DY, Makarova KS, Abbas B, Ferrer M, Golyshin PN et al. 2017. Discovery of extremely halophilic, methyl-reducing euryarchaea provides insights into the evolutionary origin of methanogenesis. Nat. Microbiol. 2:17081
    [Google Scholar]
  104. 104. 
    Sorokin DY, Merkel AY, Abbas B, Makarova KS, Rijpstra WIC et al. 2018. Methanonatronarchaeum thermophilum gen. nov., sp. nov. and ‘Candidatus Methanohalarchaeum thermophilum’, extremely halo(natrono)philic methyl-reducing methanogens from hypersaline lakes comprising a new euryarchaeal class Methanonatronarchaeia classis nov. Int. J. Syst. Evol. Microbiol. 68:2199–208
    [Google Scholar]
  105. 105. 
    Sousa FL, Neukirchen S, Allen JF, Lane N, Martin WF. 2016. Lokiarchaeon is hydrogen dependent. Nat. Microbiol. 1:16034
    [Google Scholar]
  106. 106. 
    Spang A, Caceres EF, Ettema TJG. 2017. Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life. Science 357:eaaf3883
    [Google Scholar]
  107. 107. 
    Spang A, Saw JH, Jørgensen SL, Zaremba-Niedzwiedzka K, Martijn J et al. 2015. Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature 521:173–79
    [Google Scholar]
  108. 108. 
    Spang A, Stairs CW, Dombrowski N, Eme L, Lombard J et al. 2019. Proposal of the reverse flow model for the origin of the eukaryotic cell based on comparative analyses of Asgard archaeal metabolism. Nat. Microbiol. 4:1138–48
    [Google Scholar]
  109. 109. 
    Spear JR, Walker JJ, McCollom TM, Pace NR 2005. Hydrogen and bioenergetics in the Yellowstone geothermal ecosystem. PNAS 102:2555–60
    [Google Scholar]
  110. 110. 
    St. John E, Liu Y, Podar M, Stott MB, Meneghin J et al. 2019. A new symbiotic nanoarchaeote (Candidatus Nanoclepta minutus) and its host (Zestosphaera tikiterensis gen. nov., sp. nov.) from a New Zealand hot spring. Syst. Appl. Microbiol. 42:94–106
    [Google Scholar]
  111. 111. 
    Stetter KO, Lauerer G, Thomm M, Neuner A. 1987. Isolation of extremely thermophilic sulfate reducers: evidence for a novel branch of archaebacteria. Science 236:822–24
    [Google Scholar]
  112. 112. 
    Stieglmeier M, Alves RJE, Schleper C 2014. The phylum Thaumarchaeota. The Prokaryotes: Other Major Lineages of Bacteria and the Archaea E Rosenberg, EF DeLong, S Lory, E Stackebrandt, F Thompson 347–62 Berlin: Springer
    [Google Scholar]
  113. 113. 
    Takai K, Horikoshi K. 1999. Genetic diversity of archaea in deep-sea hydrothermal vent environments. Genetics 152:1285–97
    [Google Scholar]
  114. 114. 
    Teske A, Sørensen KB. 2008. Uncultured archaea in deep marine subsurface sediments: have we caught them all?. ISME J 2:3–18
    [Google Scholar]
  115. 115. 
    Tully BJ, Graham ED, Heidelberg JF. 2018. The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans. Sci. Data 5:170203
    [Google Scholar]
  116. 116. 
    Vanwonterghem I, Evans PN, Parks DH, Jensen PD, Woodcroft BJ et al. 2016. Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota. Nat. Microbiol. 1:16170
    [Google Scholar]
  117. 117. 
    Vetriani C, Jannasch HW, MacGregor BJ, Stahl DA, Reysenbach AL. 1999. Population structure and phylogenetic characterization of marine benthic Archaea in deep-sea sediments. Appl. Environ. Microbiol. 65:4375–84
    [Google Scholar]
  118. 118. 
    Vetriani C, Reysenbach A-L, Doré J. 1998. Recovery and phylogenetic analysis of archaeal rRNA sequences from continental shelf sediments. FEMS Microbiol. Lett. 161:83–88
    [Google Scholar]
  119. 119. 
    Wang B, Qin W, Ren Y, Zhou X, Jung M-Y et al. 2019. Expansion of Thaumarchaeota habitat range is correlated with horizontal transfer of ATPase operons. ISME J 13:3067–79
    [Google Scholar]
  120. 120. 
    Wang H-C, Hickey DA. 2002. Evidence for strong selective constraint acting on the nucleotide composition of 16S ribosomal RNA genes. Nucleic Acids Res 30:2501–7
    [Google Scholar]
  121. 121. 
    Wang H-C, Minh BQ, Susko E, Roger AJ. 2017. Modeling site heterogeneity with posterior mean site frequency profiles accelerates accurate phylogenomic estimation. Syst. Biol. 67:216–35
    [Google Scholar]
  122. 122. 
    Wang Y, Wegener G, Hou J, Wang F, Xiao X 2019. Expanding anaerobic alkane metabolism in the domain of Archaea. Nat. Microbiol. 4:595–602
    [Google Scholar]
  123. 123. 
    Watson JD, Crick FHC. 1953. Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid. Nature 171:737–38
    [Google Scholar]
  124. 124. 
    Whitman WB. 2016. Modest proposals to expand the type material for naming of prokaryotes. Int. J. Syst. Evol. Microbiol. 66:2108–12
    [Google Scholar]
  125. 125. 
    Whittaker RH. 1969. New concepts of kingdoms of organisms. Science 163:150–60
    [Google Scholar]
  126. 126. 
    Williams MA, Rittenberg SC. 1957. A taxonomic study of the genus Spirillum Ehrenberg. Int. J. Syst. Evol. Microbiol. 7:49–112
    [Google Scholar]
  127. 127. 
    Williams TA, Foster PG, Cox CJ, Embley TM. 2013. An archaeal origin of eukaryotes supports only two primary domains of life. Nature 504:231–36
    [Google Scholar]
  128. 128. 
    Woese CR, Fox GE 1977. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. PNAS 74:5088–90
    [Google Scholar]
  129. 129. 
    Woese CR, Kandler O, Wheelis ML 1990. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. PNAS 87:4576–79
    [Google Scholar]
  130. 130. 
    Woese CR, Magrum LJ, Fox GE. 1978. Archaebacteria. J. Mol. Evol. 11:245–52
    [Google Scholar]
  131. 131. 
    Wurch L, Giannone RJ, Belisle BS, Swift C, Utturkar S et al. 2016. Genomics-informed isolation and characterization of a symbiotic Nanoarchaeota system from a terrestrial geothermal environment. Nat. Commun. 7:12115
    [Google Scholar]
  132. 132. 
    Zallen DT. 2003. Despite Franklin's work, Wilkins earned his Nobel. Nature 425:15
    [Google Scholar]
  133. 133. 
    Zaremba-Niedzwiedzka K, Caceres EF, Saw JH, Bäckström D, Juzokaite L et al. 2017. Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature 541:353–58
    [Google Scholar]
  134. 134. 
    Zhang J-W, Dong H-P, Hou L-J, Liu Y, Ou Y-F et al. 2021. Newly discovered Asgard archaea Hermodarchaeota potentially degrade alkanes and aromatics via alkyl/benzyl-succinate synthase and benzoyl-CoA pathway. ISME J 15:61826–43
    [Google Scholar]
  135. 135. 
    Zhou Z, Pan J, Wang F, Gu J-D, Li M 2018. Bathyarchaeota: globally distributed metabolic generalists in anoxic environments. FEMS Microbiol. Rev. 42:639–55
    [Google Scholar]
  136. 136. 
    Zillig W, Holz I, Janekovic D, Schäfer W, Reiter WD. 1983. The Archaebacterium Thermococcus celer represents, a novel genus within the thermophilic branch of the Archaebacteria. Syst. Appl. Microbiol. 4:88–94
    [Google Scholar]
  137. 137. 
    Zillig W, Reysenbach AL 2001. Class V. Thermococci class. nov. Bergey's Manual of Systematic Bacteriology D Boone, R Castenholz, G Garrity 341–48 New York: Springer
    [Google Scholar]
/content/journals/10.1146/annurev-micro-040921-050212
Loading
/content/journals/10.1146/annurev-micro-040921-050212
Loading

Data & Media loading...

Supplementary Data

  • Article Type: Review Article
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error