The Archaea represent the so-called Third Domain of life, which has evolved in parallel with the Bacteria and which is implicated to have played a pivotal role in the emergence of the eukaryotic domain of life. Recent progress in genomic sequencing technologies and cultivation-independent methods has started to unearth a plethora of data of novel, uncultivated archaeal lineages. Here, we review how the availability of such genomic data has revealed several important insights into the diversity, ecological relevance, metabolic capacity, and the origin and evolution of the archaeal domain of life. 1. Introduction The description of the three (cellular) domains of life—Eukarya, Bacteria, and Archaea—by Carl Woese and George Fox [1] represents a milestone in the modern era of microbiology. In particular, using phylogenetic reconstructions of the small-subunit (16S or 18S) ribosomal RNA gene, Woese discovered that microscopically indistinguishable prokaryotes are not a homogeneous assemblage but are comprised of two fundamentally different groups of organisms: Eubacteria (later Bacteria) on one side and an additional life form referred to as Archaebacteria (later Archaea) on the other side [1]. Though not immediately accepted by the scientific community, this finding was early on supported by Wolfram Zillig through his studies on DNA-dependent RNA polymerases, as well as by Otto Kandler investigating “bacterial” cell walls [2]. Indeed, a subset of prokaryotic organisms subsequently assigned to Archaea was found to harbor DNA-dependent RNA polymerases that bore more similarity to those of eukaryotes, and to contain proteinaceous cell walls that lack peptidoglycan as well as cell membranes composed of L-glycerol ether lipids with isoprenoid chains instead of D-glycerol ester lipids with fatty acid chains [3–6]. Since then, further investigation of cellular characteristics of archaea has revealed that this domain of life contains eukaryotic-like information-processing machineries [7–14]. These findings were later supported by genome sequences and comparative analyses of genes coding for replication, transcription, and translation machineries as well as by protein crystal structures [15–21]. Additionally, some archaeal lineages were shown to contain homologs of eukaryotic cell division and cytoskeleton genes as well as histones and seem to express a chromatin architecture similar to eukaryotes [22–28]. In contrast to information-processing and cell division genes, archaeal operational systems (energy metabolism, biosynthesis pathways, and regulation) often
References
[1]
C. R. Woese and G. E. Fox, “Phylogenetic structure of the prokaryotic domain: the primary kingdoms,” Proceedings of the National Academy of Sciences of the United States of America, vol. 74, no. 11, pp. 5088–5090, 1977.
[2]
C. R. Woese, “The birth of the Archaea: a personal retrospective,” in Archaea, R. A. Garrett and H.-P. Klenk, Eds., Blackwell Publishing, 2007.
[3]
T. A. Langworthy, P. F. Smith, and W. R. Mayberry, “Lipids of Thermoplasma acidophilum,” Journal of Bacteriology, vol. 112, no. 3, pp. 1193–1200, 1972.
[4]
T. A. Langworthy, W. R. Mayberry, and P. F. Smith, “Long chain glycerol diether and polyol dialkyl glycerol triether lipids of Sulfolobus acidocaldarius,” Journal of Bacteriology, vol. 119, no. 1, pp. 106–116, 1974.
[5]
O. Kandler and H. Hippe, “Lack of peptidoglycan in the cell walls of Methanosarcina barkeri,” Archives of Microbiology, vol. 113, no. 1-2, pp. 57–60, 1977.
[6]
W. Zillig, K. O. Stetter, and D. Janekovic, “DNA-dependent RNA polymerase from the archaebacterium Sulfolobus acidocaldarius,” European Journal of Biochemistry, vol. 96, no. 3, pp. 597–604, 1979.
[7]
J. Huet, R. Schnabel, A. Sentenac, and W. Zillig, “Archaebacteria and eukaryotes possess DNA-dependent RNA polymerases of a common type,” EMBO Journal, vol. 2, no. 8, pp. 1291–1294, 1983.
[8]
J. A. Lake, “Ribosome evolution: the structural bases of protein synthesis in archaebacteria, eubacteria, and eukaryotes,” Progress in Nucleic Acid Research and Molecular Biology, vol. 30, pp. 163–194, 1983.
[9]
E. Henderson, M. Oakes, M. W. Clark, J. A. Lake, A. T. Matheson, and W. Zillig, “A new ribosome structure,” Science, vol. 225, no. 4661, pp. 510–512, 1984.
[10]
W. Zillig, R. Schnabel, and K. O. Stetter, “Archaebacteria and the origin of the eukaryotic cytoplasm,” Current Topics in Microbiology and Immunology, vol. 114, pp. 1–18, 1985.
[11]
G. Puhler, H. Leffers, F. Gropp et al., “Archaebacterial DNA-dependent RNA polymerase testify to the evolution of the eukaryotic nuclear genome,” Proceedings of the National Academy of Sciences of the United States of America, vol. 86, no. 12, pp. 4569–4573, 1989.
[12]
K. Sandman, J. A. Krzycki, B. Dobrinski, B. Lurz, and J. N. Reeve, “HMf, a DNA-binding protein isolated from the hyperthermophilic archaeon Methanothermus fervidus, is most closely related to histones,” Proceedings of the National Academy of Sciences of the United States of America, vol. 87, no. 15, pp. 5788–5791, 1990.
[13]
D. Langer, J. Hain, P. Thuriaux, and W. Zillig, “Transcription in archaea: similarity to that in eucarya,” Proceedings of the National Academy of Sciences of the United States of America, vol. 92, no. 13, pp. 5768–5772, 1995.
[14]
O. Kandler and H. K？nig, “Cell wall polymers in Archaea (Archaebacteria),” Cellular and Molecular Life Sciences, vol. 54, no. 4, pp. 305–308, 1998.
[15]
G. J. Olsen and C. R. Woese, “Lessons from an Archaeal genome: what are we learning from Methanococcus jannaschii?” Trends in Genetics, vol. 12, no. 10, pp. 377–379, 1996.
[16]
O. Lecompte, R. Ripp, J.-C. Thierry, D. Moras, and O. Poch, “Comparative analysis of ribosomal proteins in complete genomes: an example of reductive evolution at the domain scale,” Nucleic Acids Research, vol. 30, no. 24, pp. 5382–5390, 2002.
[17]
E. R. Barry and S. D. Bell, “DNA replication in the archaea,” Microbiology and Molecular Biology Reviews, vol. 70, no. 4, pp. 876–887, 2006.
[18]
S. Gribaldo and C. Brochier-Armanet, “The origin and evolution of Archaea: a state of the art,” Philosophical Transactions of the Royal Society B, vol. 361, no. 1470, pp. 1007–1022, 2006.
[19]
L. L. Grochowski, H. Xu, and R. H. White, “Methanocaldococcus jannaschii uses a modified mevalonate pathway for biosynthesis of isopentenyl diphosphate,” Journal of Bacteriology, vol. 188, no. 9, pp. 3192–3198, 2006.
[20]
M. Kwapisz, F. Beckou？t, and P. Thuriaux, “Early evolution of eukaryotic DNA-dependent RNA polymerases,” Trends in Genetics, vol. 24, no. 5, pp. 211–215, 2008.
[21]
F. Werner and D. Grohmann, “Evolution of multisubunit RNA polymerases in the three domains of life,” Nature Reviews Microbiology, vol. 9, no. 2, pp. 85–98, 2011.
[22]
S. L. Pereira and J. N. Reeve, “Histones and nucleosomes in Archaea and Eukarya: a comparative analysis,” Extremophiles, vol. 2, no. 3, pp. 141–148, 1998.
[23]
J. N. Reeve, K. A. Bailey, W.-T. Li, F. Marc, K. Sandman, and D. J. Soares, “Archaeal histones: structures, stability and DNA binding,” Biochemical Society Transactions, vol. 32, no. 2, pp. 227–230, 2004.
[24]
A.-C. Lind？s, E. A. Karlsson, M. T. Lindgren, T. J. G. Ettema, and R. Bernander, “A unique cell division machinery in the Archaea,” Proceedings of the National Academy of Sciences of the United States of America, vol. 105, no. 48, pp. 18942–18946, 2008.
[25]
R. Y. Samson, T. Obita, S. M. Freund, R. L. Williams, and S. D. Bell, “A role for the ESCRT system in cell division in archaea,” Science, vol. 322, no. 5908, pp. 1710–1713, 2008.
[26]
R. Bernander, A. E. Lind, and T. J. G. Ettema, “An archaeal origin for the actin cytoskeleton,” Communicative & Integrative Biology, vol. 4, pp. 664–667, 2011.
[27]
R. Ammar, D. Torti, K. Tsui et al., “Chromatin is an ancient innovation conserved between Archaea and Eukarya,” Elife, vol. 1, Article ID e00078, 2012.
[28]
N. Yutin and E. V. Koonin, “Archaeal origin of tubulin,” Biology Direct, vol. 7, article 10, 2012.
[29]
M. C. Rivera, R. Jain, J. E. Moore, and J. A. Lake, “Genomic evidence for two functionally distinct gene classes,” Proceedings of the National Academy of Sciences of the United States of America, vol. 95, no. 11, pp. 6239–6244, 1998.
[30]
C. R. Woese, O. Kandler, and M. L. Wheelis, “Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya,” Proceedings of the National Academy of Sciences of the United States of America, vol. 87, no. 12, pp. 4576–4579, 1990.
[31]
C. Schleper, G. Jurgens, and M. Jonuscheit, “Genomic studies of uncultivated archaea,” Nature Reviews Microbiology, vol. 3, no. 6, pp. 479–488, 2005.
[32]
A. Teske and K. B. S？rensen, “Uncultured archaea in deep marine subsurface sediments: have we caught them all?” The ISME Journal, vol. 2, no. 1, pp. 3–18, 2008.
[33]
C. Rinke, P. Schwientek, A. Sczyrba, et al., “Insights into the phylogeny and coding potential of microbial dark matter,” Nature, 2013.
[34]
J. O. McInerney, M. Wilkinson, J. W. Patching, T. M. Embley, and R. Powell, “Recovery and phylogenetic analysis of novel archaeal rRNA sequences from a deep-sea deposit feeder,” Applied and Environmental Microbiology, vol. 61, no. 4, pp. 1646–1648, 1995.
[35]
E. F. Delong, “Everything in moderation: Archaea as ‘non-extremophiles’,” Current Opinion in Genetics & Development, vol. 8, no. 6, pp. 649–654, 1998.
[36]
K. Takai and K. Horikoshi, “Genetic diversity of archaea in deep-sea hydrothermal vent environments,” Genetics, vol. 152, no. 4, pp. 1285–1297, 1999.
[37]
B. J. Baker, G. W. Tyson, R. I. Webb et al., “Lineages of acidophilic archaea revealed by community genomic analysis,” Science, vol. 314, no. 5807, pp. 1933–1935, 2006.
[38]
B. Chaban, S. Y. M. Ng, and K. F. Jarrell, “Archaeal habitats—from the extreme to the ordinary,” Canadian Journal of Microbiology, vol. 52, no. 2, pp. 73–116, 2006.
[39]
K. Kubo, K. G. Lloyd, J. F Biddle, R. Amann, A. Teske, and K. Knittel, “Archaea of the Miscellaneous Crenarchaeotal Group are abundant, diverse and widespread in marine sediments,” The ISME Journal, vol. 6, pp. 1949–1965, 2012.
[40]
S. M. Barns, C. F. Delwiche, J. D. Palmer, and N. R. Pace, “Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences,” Proceedings of the National Academy of Sciences of the United States of America, vol. 93, no. 17, pp. 9188–9193, 1996.
[41]
H. Huber, M. J. Hohn, R. Rachel, T. Fuchs, V. C. Wimmer, and K. O. Stetter, “A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont,” Nature, vol. 417, no. 6884, pp. 63–67, 2002.
[42]
C. Brochier-Armanet, B. Boussau, S. Gribaldo, and P. Forterre, “Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota,” Nature Reviews Microbiology, vol. 6, no. 3, pp. 245–252, 2008.
[43]
J. G. Elkins, M. Podar, D. E. Graham et al., “A korarchaeal genome reveals insights into the evolution of the Archaea,” Proceedings of the National Academy of Sciences of the United States of America, vol. 105, no. 23, pp. 8102–8107, 2008.
[44]
A. Spang, R. Hatzenpichler, C. Brochier-Armanet et al., “Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota,” Trends in Microbiology, vol. 18, no. 8, pp. 331–340, 2010.
[45]
T. Nunoura, Y. Takaki, J. Kakuta et al., “Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group,” Nucleic Acids Research, vol. 39, no. 8, pp. 3204–3223, 2011.
[46]
M. A. Kozubal, M. Romine, R. Jennings, et al., “Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park,” The ISME Journal, vol. 7, pp. 622–634, 2013.
[47]
P. Offre, A. Spang, and C. Schleper, “Archaea in biogeochemical cycles,” Annual Review of Microbiology, vol. 67, pp. 437–457, 2013.
[48]
M. K？nneke, A. E. Bernhard, J. R. de la Torre, C. B. Walker, J. B. Waterbury, and D. A. Stahl, “Isolation of an autotrophic ammonia-oxidizing marine archaeon,” Nature, vol. 437, no. 7058, pp. 543–546, 2005.
[49]
A. H. Treusch, S. Leininger, A. Kietzin, S. C. Schuster, H.-P. Klenk, and C. Schleper, “Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling,” Environmental Microbiology, vol. 7, no. 12, pp. 1985–1995, 2005.
[50]
K. Knittel and A. Boetius, “Anaerobic oxidation of methane: progress with an unknown process,” Annual Review of Microbiology, vol. 63, pp. 311–334, 2009.
[51]
P. López-Gar？ia and D. Moreira, “Metabolic symbiosis at the origin of eukaryotes,” Trends in Biochemical Sciences, vol. 24, pp. 88–93, 1999.
[52]
T. M. Embley and W. Martin, “Eukaryotic evolution, changes and challenges,” Nature, vol. 440, no. 7084, pp. 623–630, 2006.
[53]
N. Yutin, M. Y. Wolf, Y. I. Wolf, and E. V. Koonin, “The origins of phagocytosis and eukaryogenesis,” Biology Direct, vol. 4, article 9, 2009.
[54]
S. Gribaldo, A. M. Poole, V. Daubin, P. Forterre, and C. Brochier-Armanet, “The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse?” Nature Reviews Microbiology, vol. 8, no. 10, pp. 743–752, 2010.
[55]
L. Guy and T. J. G. Ettema, “The archaeal “TACK” superphylum and the origin of eukaryotes,” Trends in Microbiology, vol. 19, no. 12, pp. 580–587, 2011.
[56]
T. A. Williams, P. G. Foster, T. M. W. Nye, C. J. Cox, and T. M. Embley, “A congruent phylogenomic signal places eukaryotes within the Archaea,” Proceedings of the Royal Society B, vol. 279, no. 1749, pp. 4870–4879, 2012.
[57]
Y. I. Wolf, K. S. Makarova, N. Yutin, and E. V. Koonin, “Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer,” Biology Direct, vol. 7, article 46, 2012.
[58]
J. Martijn and J. G. Ettema Thijs, “From archaeon to eukaryote: the evolutionary dark ages of the eukaryotic cell,” Biochemical Society Transactions, vol. 41, pp. 451–457, 2013.
[59]
W. Martin, J. Baross, D. Kelley, and M. J. Russell, “Hydrothermal vents and the origin of life,” Nature Reviews Microbiology, vol. 6, no. 11, pp. 805–814, 2008.
[60]
N. Lane and W. F. Martin, “The origin of membrane bioenergetics,” Cell, vol. 151, pp. 1406–1416, 2012.
[61]
Y. Liu, L. L. Beer, and W. B. Whitman, “Methanogens: a window into ancient sulfur metabolism,” Trends in Microbiology, vol. 20, no. 5, pp. 251–258, 2012.
[62]
A. Poehlein, S. Schmidt, A.-K. Kaster et al., “An ancient pathway combining carbon dioxide fixation with the generation and utilization of a sodium ion gradient for ATP synthesis,” PLoS ONE, vol. 7, no. 3, Article ID e33439, 2012.
[63]
Y. Ueno, K. Yamada, N. Yoshida, S. Maruyama, and Y. Isozaki, “Evidence from fluid inclusions for microbial methanogenesis in the early Archaean era,” Nature, vol. 440, no. 7083, pp. 516–519, 2006.
[64]
C. Brochier-Armanet, P. Forterre, and S. Gribaldo, “Phylogeny and evolution of the Archaea: one hundred genomes later,” Current Opinion in Microbiology, vol. 14, no. 3, pp. 274–281, 2011.
[65]
N. Yutin, P. Puigbò, E. V. Koonin, and Y. I. Wolf, “Phylogenomics of prokaryotic ribosomal proteins,” PLoS ONE, vol. 7, no. 5, Article ID e36972, 2012.
[66]
M. Groussin and M. Gouy, “Adaptation to environmental temperature is a major determinant of molecular evolutionary rates in archaea,” Molecular Biology and Evolution, vol. 28, no. 9, pp. 2661–2674, 2011.
[67]
C. Brochier, P. Forterre, and S. Gribaldo, “Archaeal phylogeny based on proteins of the transcription and translation machineries: tackling the Methanopyrus kandleri paradox,” Genome Biology, vol. 5, no. 3, p. R17, 2004.
[68]
K. S. Makarova, A. V. Sorokin, P. S. Novichkov, Y. I. Wolf, and E. V. Koonin, “Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea,” Biology Direct, vol. 2, article 33, 2007.
[69]
S. Kelly, B. Wickstead, and K. Gull, “Archaeal phylogenomics provides evidence in support of a methanogenic origin of the Archaea and a thaumarchaeal origin for the eukaryotes,” Proceedings of the Royal Society B, vol. 278, no. 1708, pp. 1009–1018, 2011.
[70]
L. Guy, J. H. Saw, and T. J. G. Ettema, “The archaeal legacy of eukaryotes: a phylogenomic perspective,” Cold Spring Harbor Perspectives in Biology. In press.
[71]
N. Lartillot, T. Lepage, and S. Blanquart, “PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating,” Bioinformatics, vol. 25, no. 17, pp. 2286–2288, 2009.
[72]
J. G. Ferry, “How to make a living by exhaling methane,” Annual Review of Microbiology, vol. 64, pp. 453–473, 2010.
[73]
O. Matte-Tailliez, C. Brochier, P. Forterre, and H. Philippe, “Archaeal phylogeny based on ribosomal proteins,” Molecular Biology and Evolution, vol. 19, no. 5, pp. 631–639, 2002.
[74]
B. Dridi, M.-L. Fardeau, B. Ollivier, D. Raoult, and M. Drancourt, “Methanomassiliicoccus luminyensis gen. nov., sp. nov., a methanogenic archaeon isolated from human faeces,” International Journal of Systematic and Evolutionary Microbiology, vol. 62, pp. 1902–1907, 2012.
[75]
K. Paul, J. O. Nonoh, L. Mikulski, and A. Brune, “‘Methanoplasmatales,’ Thermoplasmatales-related archaea in termite guts and other environments, are the seventh order of methanogens,” Applied and Environmental Microbiology, vol. 78, pp. 8245–8253, 2012.
[76]
G. Borrel, P. W. O'Toole, H. M. B. Harris, P. Peyret, J.-F. Brugère, and S. Gribaldo, “Phylogenomic data support a seventh order of methylotrophic methanogens and provide insights into the evolution of methanogenesis,” Genome Biology and Evolution, 2013.
[77]
S. Nelson-Sathi, T. Dagan, G. Landan, et al., “Acquisition of 1, 000 eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea,” Proceedings of the National Academy of Sciences, vol. 109, pp. 20537–20542, 2012.
[78]
B. Schworer, J. Breitung, A. R. Klein, K. O. Stetter, and R. K. Thauer, “Formylmethanofuran: tetrahydromethanopterin formyltransferase and N5,N10-methylenetetrahydromethanopterin dehydrogenase from the sulfate-reducing Archaeoglobus fulgidus: similarities with the enzymes from methanogenic Archaea,” Archives of Microbiology, vol. 159, no. 3, pp. 225–232, 1993.
[79]
E. Waters, M. J. Hohn, I. Ahel et al., “The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism,” Proceedings of the National Academy of Sciences of the United States of America, vol. 100, no. 22, pp. 12984–12988, 2003.
[80]
M. Di Giulio, “Formal proof that the split genes of tRNAs of nanoarchaeum equitans are an ancestral character,” Journal of Molecular Evolution, vol. 69, no. 5, pp. 505–511, 2009.
[81]
C. Brochier, S. Gribaldo, Y. Zivanovic, F. Confalonieri, and P. Forterre, “Nanoarchaea: representatives of a novel archaeal phylum or a fast-evolving euryarchaeal lineage related to Thermococcales?” Genome Biology, vol. 6, no. 5, p. R42, 2005.
[82]
B. J. Baker, L. R. Comolli, G. J. Dick et al., “Enigmatic, ultrasmall, uncultivated Archaea,” Proceedings of the National Academy of Sciences of the United States of America, vol. 107, no. 19, pp. 8806–8811, 2010.
[83]
M. Podar, K. S. Makarova, D. E. Graham, Y. I. Wolf, E. V. Koonin, and A.-L. Reysenbach, “Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park,” Biology Direct, vol. 8, article 9, 2013.
[84]
P. Narasingarao, S. Podell, J. A. Ugalde et al., “De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities,” The ISME Journal, vol. 6, no. 1, pp. 81–93, 2012.
[85]
C. Brochier-Armanet, S. Gribaldo, and P. Forterre, “A DNA topoisomerase IB in Thaumarchaeota testifies for the presence of this enzyme in the last common ancestor of Archaea and Eucarya,” Biology Direct, vol. 3, article 54, 2008.
[86]
R. S. Gupta and A. Shami, “Molecular signatures for the Crenarchaeota and the Thaumarchaeota,” Antonie van Leeuwenhoek, vol. 99, no. 2, pp. 133–157, 2011.
[87]
M. Pester, C. Schleper, and M. Wagner, “The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology,” Current Opinion in Microbiology, vol. 14, no. 3, pp. 300–306, 2011.
[88]
C. J. Cox, P. G. Foster, R. P. Hirt, S. R. Harris, and T. M. Embley, “The archaebacterial origin of eukaryotes,” Proceedings of the National Academy of Sciences of the United States of America, vol. 105, no. 51, pp. 20356–20361, 2008.
[89]
T. Nunoura, H. Hirayama, H. Takami et al., “Genetic and functional properties of uncultivated thermophilic crenarchaeotes from a subsurface gold mine as revealed by analysis of genome fragments,” Environmental Microbiology, vol. 7, no. 12, pp. 1967–1984, 2005.
[90]
T. Nunoura, H. Oida, M. Nakaseama et al., “Archaeal diversity and distribution along thermal and geochemical gradients in hydrothermal sediments at the yonaguni knoll IV hydrothermal field in the Southern Okinawa Trough,” Applied and Environmental Microbiology, vol. 76, no. 4, pp. 1198–1211, 2010.
[91]
C. Brochier-Armanet, S. Gribaldo, and P. Forterre, “Spotlight on the Thaumarchaeota,” The ISME Journal, vol. 6, no. 2, pp. 227–230, 2012.
[92]
S. Gribaldo and C. Brochier-Armanet, “Time for order in microbial systematics,” Trends in Microbiology, vol. 20, no. 5, pp. 209–210, 2012.
[93]
L. Margulis, M. Chapman, R. Guerrero, and J. Hall, “The last eukaryotic common ancestor (LECA): acquisition of cytoskeletal motility from aerotolerant spirochetes in the Proterozoic Eon,” Proceedings of the National Academy of Sciences of the United States of America, vol. 103, no. 35, pp. 13080–13085, 2006.
[94]
D. Moreira and P. López-García, “Symbiosis between methanogenic archaea and δ-proteobacteria as the origin of eukaryotes: the syntrophic hypothesis,” Journal of Molecular Evolution, vol. 47, no. 5, pp. 517–530, 1998.
[95]
W. Martin and M. Müller, “The hydrogen hypothesis for the first eukaryote,” Nature, vol. 392, no. 6671, pp. 37–41, 1998.
[96]
J. A. Lake, “Origin of the eukaryotic nucleus determined by rate-invariant analysis of rRNA sequences,” Nature, vol. 331, no. 6152, pp. 184–186, 1988.
[97]
K. G. Lloyd, L. Schreiber, D. G. Petersen, et al., “Predominant archaea in marine sediments degrade detrital proteins,” Nature, vol. 496, pp. 215–218, 2013.
[98]
M. A. Kozubal, R. E. Macur, Z. J. Jay, et al., “Microbial iron cycling in acidic geothermal springs of yellowstone national park: integrating molecular surveys, geochemical processes, and isolation of novel fe-active microorganisms,” Frontiers in Microbiology, vol. 3, article 109, 2012.
[99]
J. P. Gogarten, H. Kibak, P. Dittrich et al., “Evolution of the vacuolar H+-ATPase: implications for the origin of eukaryotes,” Proceedings of the National Academy of Sciences of the United States of America, vol. 86, no. 17, pp. 6661–6665, 1989.
[100]
N. Iwabe, K. Kuma, M. Hasegawa, S. Osawa, and T. Miyata, “Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes,” Proceedings of the National Academy of Sciences of the United States of America, vol. 86, no. 23, pp. 9355–9359, 1989.
[101]
S. Gribaldo and P. Cammarano, “The root of the universal tree of life inferred from anciently duplicated genes encoding components of the protein-targeting machinery,” Journal of Molecular Evolution, vol. 47, no. 5, pp. 508–516, 1998.
[102]
O. Zhaxybayeva, P. Lapierre, and J. P. Gogarten, “Ancient gene duplications and the root(s) of the tree of life,” Protoplasma, vol. 227, no. 1, pp. 53–64, 2005.
[103]
B. Boussau, S. Blanquart, A. Necsulea, N. Lartillot, and M. Gouy, “Parallel adaptations to high temperatures in the Archaean eon,” Nature, vol. 456, no. 7224, pp. 942–945, 2008.
[104]
T. Dagan, M. Roettger, D. Bryant, and W. Martin, “Genome networks root the tree of life between prokaryotic domains,” Genome Biology and Evolution, vol. 2, no. 1, pp. 379–392, 2010.
[105]
T. Cavalier-Smith, “Rooting the tree of life by transition analyses,” Biology Direct, vol. 1, article 19, 2006.
[106]
J. A. Lake, R. G. Skophammer, C. W. Herbold, and J. A. Servin, “Genome beginnings: rooting the tree of life,” Philosophical Transactions of the Royal Society B, vol. 364, no. 1527, pp. 2177–2185, 2009.
[107]
T. Cavalier-Smith, “Deep phylogeny, ancestral groups and the four ages of life,” Philosophical Transactions of the Royal Society B, vol. 365, pp. 111–132, 2010.
[108]
M. Di Giulio, “The tree of life might be rooted in the branch leading to Nanoarchaeota,” Gene, vol. 401, no. 1-2, pp. 108–113, 2007.
[109]
K. M. Kim and G. Caetano-Anollés, “The evolutionary history of protein fold families and proteomes confirms that the archaeal ancestor is more ancient than the ancestors of other superkingdoms,” BMC Evolutionary Biology, vol. 12, no. 1, article 13, 2012.
[110]
C. G. Kurland, L. J. Collins, and D. Penny, “Genomics and the irreducible nature of eukaryote cells,” Science, vol. 312, no. 5776, pp. 1011–1014, 2006.
[111]
N. Glansdorff, Y. Xu, and B. Labedan, “The Last Universal Common Ancestor: emergence, constitution and genetic legacy of an elusive forerunner,” Biology Direct, vol. 3, article 29, 2008.
[112]
T. Cavalier-Smith, “Molecular phylogeny. Archaebacteria and Archezoa,” Nature, vol. 339, no. 6220, pp. l00–01, 1989.
[113]
A. M. Poole and D. Penny, “Evaluating hypotheses for the origin of eukaryotes,” BioEssays, vol. 29, no. 1, pp. 74–84, 2007.
[114]
T. Cavalier-Smith, “The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification,” International Journal of Systematic and Evolutionary Microbiology, vol. 52, no. 1, pp. 7–76, 2002.
[115]
D. P. Devos and E. G. Reynaud, “Evolution. Intermediate steps,” Science, vol. 330, no. 6008, pp. 1187–1188, 2010.
[116]
P. Forterre and S. Gribaldo, “Bacteria with a eukaryotic touch: a glimpse of ancient evolution?” Proceedings of the National Academy of Sciences of the United States of America, vol. 107, no. 29, pp. 12739–12740, 2010.
[117]
P. Forterre, “A new fusion hypothesis for the origin of Eukarya: better than previous ones, but probably also wrong,” Research in Microbiology, vol. 162, no. 1, pp. 77–91, 2011.
[118]
E. G. Reynaud and D. P. Devos, “Transitional forms between the three domains of life and evolutionary implications,” Proceedings of the Royal Society B, vol. 278, no. 1723, pp. 3321–3328, 2011.
[119]
P. J. Livingstone Bell, “Viral eukaryogenesis: was the ancestor of the nucleus a complex DNA virus?” Journal of Molecular Evolution, vol. 53, no. 3, pp. 251–256, 2001.
[120]
M. Takemura, “Poxviruses and the origin of the eukaryotic nucleus,” Journal of Molecular Evolution, vol. 52, no. 5, pp. 419–425, 2001.
[121]
P. Forterre, “The two ages of the RNA world, and the transition to the DNA world: a story of viruses and cells,” Biochimie, vol. 87, no. 9-10, pp. 793–803, 2005.
[122]
P. Forterre, “Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: a hypothesis for the origin of cellular domain,” Proceedings of the National Academy of Sciences of the United States of America, vol. 103, no. 10, pp. 3669–3674, 2006.
[123]
T. M. Embley, “Multiple secondary origins of the anaerobic lifestyle in eukaryotes,” Philosophical Transactions of the Royal Society B, vol. 361, no. 1470, pp. 1055–1067, 2006.
[124]
J. A. Lake, E. Henderson, M. Oakes, and M. W. Clark, “Eocytes: a new ribosome structure indicates a kingdom with a close relationship to eukaryotes,” Proceedings of the National Academy of Sciences of the United States of America, vol. 81, no. 12, pp. 3786–3790, 1984.
[125]
S. L. Baldauf, J. D. Palmer, and W. F. Doolittle, “The root of the universal tree and the origin of eukaryotes based on elongation factor phylogeny,” Proceedings of the National Academy of Sciences of the United States of America, vol. 93, no. 15, pp. 7749–7754, 1996.
[126]
T. Hashimoto and M. Hasegawa, “Origin and early evolution of eukaryotes inferred from the amino acid sequences of translation elongation factors 1α/Tu and 2/G,” Advances in Biophysics, vol. 32, pp. 73–120, 1996.
[127]
E. Lasek-Nesselquist and J. P. Gogarten, “The effects of model choice and mitigating bias on the ribosomal tree of life,” Molecular Phylogenetics and Evolution, vol. 69, pp. 17–38, 2013.
[128]
P. G. Foster, C. J. Cox, and T. Martin Embley, “The primary divisions of life: a phylogenomic approach employing composition-heterogeneous methods,” Philosophical Transactions of the Royal Society B, vol. 364, no. 1527, pp. 2197–2207, 2009.
[129]
D. Alvarez-Ponce, P. Lopez, E. Bapteste, and J. O. McInerney, “Gene similarity networks provide tools for understanding eukaryote origins and evolution,” Proceedings of the National Academy of Sciences of the United States of America, vol. 110, pp. 1594–1603, 2013.
[130]
T. J. G. Ettema, A.-C. Lind？s, and R. Bernander, “An actin-based cytoskeleton in archaea,” Molecular Microbiology, vol. 80, no. 4, pp. 1052–1061, 2011.
[131]
T. J. G. Ettema and R. Bernander, “Cell division and the ESCRT complex: a surprise from the archaea,” Communicative and Integrative Biology, vol. 2, no. 2, pp. 86–88, 2009.
[132]
B. K. Kim, M.-Y. Jung, D. S. Yu et al., “Genome sequence of an ammonia-oxidizing soil archaeon, “Candidatus Nitrosoarchaeum koreensis” MY1,” Journal of Bacteriology, vol. 193, no. 19, pp. 5539–5540, 2011.
[133]
A. Spang, A. Poehlein, P. Offre, et al., “The genome of the ammonia-oxidizing Candidatus Nitrososphaera gargensis: insights into metabolic versatility and environmental adaptations,” Environmental Microbiology, vol. 14, pp. 3122–3145, 2012.
[134]
S. J. Hallam, K. T. Konstantinidis, N. Putnam et al., “Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum,” Proceedings of the National Academy of Sciences of the United States of America, vol. 103, no. 48, pp. 18296–18301, 2006.
[135]
V. Iverson, R. M. Morris, C. D. Frazar, C. T. Berthiaume, R. L. Morales, and E. V. Armbrust, “Untangling genomes from metagenomes: revealing an uncultured class of marine euryarchaeota,” Science, vol. 335, no. 6068, pp. 587–590, 2012.
[136]
P. C. Blainey, A. C. Mosier, A. Potanina, C. A. Francis, and S. R. Quake, “Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis,” PLoS ONE, vol. 6, no. 2, Article ID e16626, 2011.
