1932

Abstract

For more than 3.5 billion years, life experienced dramatic environmental extremes on Earth. These include shifts from oxygen-less to overoxygenated atmospheres and cycling between hothouse conditions and global glaciations. Meanwhile, an ecological revolution took place. Earth evolved from one dominated by microbial life to one containing the plants and animals that are most familiar today. Many key cellular features evolved early in the history of life, collectively defining the nature of our biosphere and underpinning human survival. Recent advances in molecular biology and bioinformatics have greatly improved our understanding of microbial evolution across deep time. However, the incorporation of molecular genetics, population biology, and evolutionary biology approaches into the study of Precambrian biota remains a significant challenge. This review synthesizes our current knowledge of early microbial life with an emphasis on ancient metabolisms. It also outlines the foundations of an emerging interdisciplinary area that integrates microbiology, paleobiology, and evolutionary synthetic biology to reconstruct ancient biological innovations.

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2024-11-20
2024-12-13
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Literature Cited

  1. 1.
    Adam PS, Kolyfetis GE, Bornemann TLV, Vorgias CE, Probst AJ. 2022.. Genomic remnants of ancestral methanogenesis and hydrogenotrophy in Archaea drive anaerobic carbon cycling. . Sci. Adv. 8::eabm9651
    [Crossref] [Google Scholar]
  2. 2.
    Adam ZR, Skidmore ML, Mogk DW, Butterfield NJ. 2017.. A Laurentian record of the earliest fossil eukaryotes. . Geology 45::38790
    [Crossref] [Google Scholar]
  3. 3.
    Alleon J, Summons RE. 2019.. Organic geochemical approaches to understanding early life. Free Radic. . Biol. Med. 140::10312
    [Google Scholar]
  4. 4.
    Amritkar K, Cuevas B, Kaçar B. 2024.. Ancestral structure prediction reveals the conformational impact of the RuBisCO small subunit across time. . bioRxiv 2024.06.06.597628. https://doi.org/10.1101/2024.06.06.597628
  5. 5.
    Anbar AD, Duan Y, Lyons TW, Arnold GL, Kendall B, et al. 2007.. A whiff of oxygen before the Great Oxidation Event?. Science 317::19036
    [Crossref] [Google Scholar]
  6. 6.
    Anbar AD, Knoll AH. 2002.. Proterozoic ocean chemistry and evolution: a bioinorganic bridge?. Science 297::113742
    [Crossref] [Google Scholar]
  7. 7.
    Bar-On YM, Milo R. 2019.. The global mass and average rate of rubisco. . PNAS 10::473843
    [Crossref] [Google Scholar]
  8. 8.
    Bar-On YM, Phillips R, Milo R. 2018.. The biomass distribution on Earth. . PNAS 115::650611
    [Crossref] [Google Scholar]
  9. 9.
    Battistuzzi FU, Feijao A, Hedges SB. 2004.. A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land. . BMC Evol. Biol. 4::44
    [Crossref] [Google Scholar]
  10. 10.
    Battistuzzi FU, Hedges SB. 2008.. A major clade of prokaryotes with ancient adaptations to life on land. . Mol. Biol. Evol. 26::33543
    [Crossref] [Google Scholar]
  11. 11.
    Belagaje R, Brown EL, Fritz HJ, Lees RG, Khorana HG. 1979.. Total synthesis of a tyrosine suppressor transfer RNA gene. XIV. Chemical synthesis of oligonucleotide segments corresponding to the terminal regions. . J. Biol. Chem. 254::576580
    [Crossref] [Google Scholar]
  12. 12.
    Bell EA, Boehnke P, Harrison TM, Mao WL. 2015.. Potentially biogenic carbon preserved in a 4.1 billion-year-old zircon. . PNAS 112::1451821
    [Crossref] [Google Scholar]
  13. 13.
    Benner S. 2017.. Uniting natural history with the molecular sciences. The ultimate multidisciplinarity. . Acc. Chem. Res. 50::498502
    [Crossref] [Google Scholar]
  14. 14.
    Bianchi TS, Cui X, Blair NE, Burdige DJ, Eglinton TI, Galy V. 2018.. Centers of organic carbon burial and oxidation at the land-ocean interface. . Org. Geochem. 115::13855
    [Crossref] [Google Scholar]
  15. 15.
    Blank CE. 2009.. Not so old Archaea – the antiquity of biogeochemical processes in the archaeal domain of life. . Geobiology 7::495514
    [Crossref] [Google Scholar]
  16. 16.
    Blank CE, Sánchez-Baracaldo P. 2010.. Timing of morphological and ecological innovations in the cyanobacteria—a key to understanding the rise in atmospheric oxygen. . Geobiology 8::123
    [Crossref] [Google Scholar]
  17. 17.
    Blankenship RE. 2002.. Molecular Mechanisms of Photosynthesis. Oxford, UK:: Blackwell Sci.
    [Google Scholar]
  18. 18.
    Blankenship RE, Sadekar S, Raymond J. 2007.. The evolutionary transition from anoxygenic to oxygenic photosynthesis. . In Evolution of Primary Producers in the Sea, ed. PG Falkowski, AH Knoll , pp. 2135. Cambridge, MA:: Academic
    [Google Scholar]
  19. 19.
    Blatt H, Jones RL. 1975.. Proportions of exposed igneous, metamorphic, and sedimentary rocks. . Geol. Soc. Am. Bull. 86::108588
    [Crossref] [Google Scholar]
  20. 20.
    Bloch K. 1991.. Cholesterol: evolution of structure and function. . New Compr. Biochem. 20::36381
    [Crossref] [Google Scholar]
  21. 21.
    Bloch K. 1992.. Sterol molecule: structure, biosynthesis, and function. . Steroids 57::37883
    [Crossref] [Google Scholar]
  22. 22.
    Bobrovskiy I, Hope JM, Ivantsov A, Nettersheim BJ, Hallmann C, Brocks JJ. 2018.. Ancient steroids establish the Ediacaran fossil Dickinsonia as one of the earliest animals. . Science 361::124649
    [Crossref] [Google Scholar]
  23. 23.
    Boden JS, Konhauser KO, Robbins LJ, Sánchez-Baracaldo P. 2021.. Timing the evolution of antioxidant enzymes in cyanobacteria. . Nat. Commun. 12::4742
    [Crossref] [Google Scholar]
  24. 24.
    Boller AJ, Thomas PJ, Cavanaugh CM, Scott KM. 2011.. Low stable carbon isotope fractionation by coccolithophore RubisCO. . Geochim. Cosmochim. Acta 75::72007
    [Crossref] [Google Scholar]
  25. 25.
    Bontognali TRR. 2019.. Anoxygenic phototrophs and the forgotten art of making dolomite. . Geology 47::59192
    [Crossref] [Google Scholar]
  26. 26.
    Boussau B, Gouy M. 2012.. What genomes have to say about the evolution of the Earth. . Gondwana Res. 21::48394
    [Crossref] [Google Scholar]
  27. 27.
    Boyd ES, Peters JW. 2013.. New insights into the evolutionary history of biological nitrogen fixation. . Front. Microbiol. 4::201
    [Google Scholar]
  28. 28.
    Braakman R. 2019.. Evolution of cellular metabolism and the rise of a globally productive biosphere. Free Radic. . Biol. Med. 140::17287
    [Google Scholar]
  29. 29.
    Braakman R, Smith E. 2012.. The emergence and early evolution of biological carbon-fixation. . PLOS Comput. Biol. 8::e1002455
    [Crossref] [Google Scholar]
  30. 30.
    Brocks JJ, Jarrett AJM, Sirantoine E, Hallmann C, Hoshino Y, Liyanage T. 2017.. The rise of algae in Cryogenian oceans and the emergence of animals. . Nature 548::57881
    [Crossref] [Google Scholar]
  31. 31.
    Brocks JJ, Love GD, Summons RE, Knoll AH, Logan GA, Bowden SA. 2005.. Biomarker evidence for green and purple sulphur bacteria in a stratified Palaeoproterozoic sea. . Nature 437::86670
    [Crossref] [Google Scholar]
  32. 32.
    Brocks JJ, Nettersheim BJ, Adam P, Schaeffer P, Jarrett AJM, et al. 2023.. Lost world of complex life and the late rise of the eukaryotic crown. . Nature 618::76773
    [Crossref] [Google Scholar]
  33. 33.
    Bryant DA, Frigaard N-U. 2006.. Prokaryotic photosynthesis and phototrophy illuminated. . Trends Microbiol. 14::48896
    [Crossref] [Google Scholar]
  34. 34.
    Butterfield NJ. 2000.. Bangiomorpha pubescens n. gen., n. sp.: implications for the evolution of sex, multicellularity, and the Mesoproterozoic/Neoproterozoic radiation of eukaryotes. . Paleobiology 26::386404
    [Crossref] [Google Scholar]
  35. 35.
    Butterfield NJ. 2004.. A vaucheriacean alga from the middle Neoproterozoic of Spitsbergen: implications for the evolution of Proterozoic eukaryotes and the Cambrian explosion. . Paleobiology 30::23152
    [Crossref] [Google Scholar]
  36. 36.
    Caforio A, Driessen AJM. 2017.. Archaeal phospholipids: structural properties and biosynthesis. . Biochim. Biophys. Acta Mol. Cell Biol. Lipids 1862::132539
    [Crossref] [Google Scholar]
  37. 37.
    Canfield DE, Farquhar J. 2009.. Animal evolution, bioturbation, and the sulfate concentration of the oceans. . PNAS 106::812327
    [Crossref] [Google Scholar]
  38. 38.
    Cantine MD, Fournier GP. 2017.. Environmental adaptation from the origin of life to the last universal common ancestor. . Origins Life Evol. Biospheres 48::3554
    [Crossref] [Google Scholar]
  39. 39.
    Cardona T. 2015.. A fresh look at the evolution and diversification of photochemical reaction centers. . Photosynth. Res. 126::11134
    [Crossref] [Google Scholar]
  40. 40.
    Cardona T. 2017.. Evolution of photosynthesis. . In Encyclopedia of Life Sciences, ed. M Cox , pp. 110. Hoboken, NJ:: Wiley
    [Google Scholar]
  41. 41.
    Cardona T. 2019.. Thinking twice about the evolution of photosynthesis. . Open Biol. 9::180246
    [Crossref] [Google Scholar]
  42. 42.
    Cardona T, Rutherford AW. 2019.. Evolution of photochemical reaction centres: more twists?. Trends Plant Sci. 24::100821
    [Crossref] [Google Scholar]
  43. 43.
    Catling DC, Zahnle KJ. 2020.. The Archean atmosphere. . Sci. Adv. 6::eaax1420
    [Crossref] [Google Scholar]
  44. 44.
    Cavosie AJ, Valley JW, Wilde SA. 2007.. The oldest terrestrial mineral record: a review of 4400 to 4000 Ma detrital zircons from Jack Hills, Western Australia. . Dev. Precambrian Geol. 15::91111
    [Crossref] [Google Scholar]
  45. 45.
    Chan MA, Hinman NW, Potter-McIntyre SL, Schubert KE, Gillams RJ, et al. 2019.. Deciphering biosignatures in planetary contexts. . Astrobiology 19::1075102
    [Crossref] [Google Scholar]
  46. 46.
    Chang BS, Jonsson K, Kazmi MA, Donoghue MJ, Sakmar TP. 2002.. Recreating a functional ancestral archosaur visual pigment. . Mol. Biol. Evol. 19::148389
    [Crossref] [Google Scholar]
  47. 47.
    Chatterjee R, Ludden PW, Shah VK. 1997.. Characterization of VNFG, the δ subunit of the vnf-encoded apodinitrogenase from Azotobacter vinelandii. Implications for its role in the formation of functional dinitrogenase 2. . J. Biol. Chem. 272::375865
    [Crossref] [Google Scholar]
  48. 48.
    Cicerone RJ, Oremland RS. 2012.. Biogeochemical aspects of atmospheric methane. . Global Biogeochem. Cycles 2::299327
    [Crossref] [Google Scholar]
  49. 49.
    Coleman GA, Davin AA, Mahendrarajah TA, Szantho LL, Spang A, et al. 2021.. A rooted phylogeny resolves early bacterial evolution. . Science 372::eabe0511
    [Crossref] [Google Scholar]
  50. 50.
    Crapitto AJ, Campbell A, Harris AJ, Goldman AD. 2022.. A consensus view of the proteome of the last universal common ancestor. . Ecol. Evol. 12::e8930
    [Crossref] [Google Scholar]
  51. 51.
    Cuevas-Zuviría B, Garcia AK, Rivier AJ, Rucker HR, Carruthers BM, Kaçar B. 2024.. Emergence of an orphan nitrogenase protein following atmospheric oxygenation. . Mol. Biol. Evol. 41::msae067
    [Crossref] [Google Scholar]
  52. 52.
    Dalai P, Sahai N. 2019.. A model protometabolic pathway across protocell membranes assisted by photocatalytic minerals. . J. Phys. Chem. C 124::146977
    [Crossref] [Google Scholar]
  53. 53.
    Daye M, Higgins J, Bosak T. 2019.. Formation of ordered dolomite in anaerobic photosynthetic biofilms. . Geology 47::50912
    [Crossref] [Google Scholar]
  54. 54.
    Dayhoff MO. 1965.. Computer aids to protein sequence determination. . J. Theor. Biol. 8::97112
    [Crossref] [Google Scholar]
  55. 55.
    Dayhoff MO. 1983.. Evolutionary connections of biological kingdoms based on protein and nucleic acid sequence evidence. . Precambrian Res. 20::299318
    [Crossref] [Google Scholar]
  56. 56.
    Demoulin CF, Lara YJ, Cornet L, François C, Baurain D, et al. 2019.. Cyanobacteria evolution: insight from the fossil record. Free Radic. . Biol. Med. 140::20623
    [Google Scholar]
  57. 57.
    Des Marais DJ. 1990.. Microbial mats and the early evolution of life. . Trends Ecol. Evol. 5::14044
    [Crossref] [Google Scholar]
  58. 58.
    Des Marais DJ. 2001.. Isotopic evolution of the biogeochemical carbon cycle during the Precambrian. . Rev. Mineral. Geochem. 43::55578
    [Crossref] [Google Scholar]
  59. 59.
    Desmond E, Gribaldo S. 2009.. Phylogenomics of sterol synthesis: insights into the origin, evolution, and diversity of a key eukaryotic feature. . Genome Biol. Evol. 1::36481
    [Crossref] [Google Scholar]
  60. 60.
    Di Rienzi SC, Sharon I, Wrighton KC, Koren O, Hug LA, et al. 2013.. The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria. . eLife 2::e01102
    [Crossref] [Google Scholar]
  61. 61.
    Dickerson RE. 1972.. The structure and history of an ancient protein. . Sci. Am. 226::5872
    [Crossref] [Google Scholar]
  62. 62.
    Dungan SZ, Chang BSW. 2022.. Ancient whale rhodopsin reconstructs dim-light vision over a major evolutionary transition: implications for ancestral diving behavior. . PNAS 119::e2118145119
    [Crossref] [Google Scholar]
  63. 63.
    Dupont CL, Neupane K, Shearer J, Palenik B. 2008.. Diversity, function and evolution of genes coding for putative Ni-containing superoxide dismutases. . Environ. Microbiol. 10::183143
    [Crossref] [Google Scholar]
  64. 64.
    Duve CD. 1998.. Clues from present-day biology: the thioester world. . In The Molecular Origins of Life: Assembling Pieces of the Puzzle, ed. A Brack , pp. 21936. Cambridge, UK:: Cambridge Univ. Press
    [Google Scholar]
  65. 65.
    Elser JJ, Bracken MES, Cleland EE, Gruner DS, Harpole WS, et al. 2007.. Global analysis of nitrogen and phosphorus limitation of primary producers in freshwater, marine and terrestrial ecosystems. . Ecol. Lett. 10::113542
    [Crossref] [Google Scholar]
  66. 66.
    Ernst OP, Lodowski DT, Elstner M, Hegemann P, Brown LS, Kandori H. 2013.. Microbial and animal rhodopsins: structures, functions, and molecular mechanisms. . Chem. Rev. 114::12663
    [Crossref] [Google Scholar]
  67. 67.
    Fakhraee M, Hancisse O, Canfield DE, Crowe SA, Katsev S. 2019.. Proterozoic seawater sulfate scarcity and the evolution of ocean–atmosphere chemistry. . Nat. Geosci. 12::37580
    [Crossref] [Google Scholar]
  68. 68.
    Falkowski P, Scholes RJ, Boyle E, Canadell J, Canfield D, et al. 2000.. The global carbon cycle: a test of our knowledge of Earth as a system. . Science 290::29196
    [Crossref] [Google Scholar]
  69. 69.
    Falkowski PG, Fenchel T, Delong EF. 2008.. The microbial engines that drive Earth's biogeochemical cycles. . Science 320::103439
    [Crossref] [Google Scholar]
  70. 70.
    Farquhar J. 2000.. Atmospheric influence of Earth's earliest sulfur cycle. . Science 289::75658
    [Crossref] [Google Scholar]
  71. 71.
    Fischer WW, Hemp J, Johnson JE. 2016.. Evolution of oxygenic photosynthesis. . Annu. Rev. Earth Planet. Sci. 44::64783
    [Crossref] [Google Scholar]
  72. 72.
    Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, et al. 1995.. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. . Science 269::496512
    [Crossref] [Google Scholar]
  73. 73.
    Fournier GP, Andam CP, Gogarten JP. 2015.. Ancient horizontal gene transfer and the last common ancestors. . BMC Evol. Biol. 15::70
    [Crossref] [Google Scholar]
  74. 74.
    Freeman KH, Hayes JM. 1992.. Fractionation of carbon isotopes by phytoplankton and estimates of ancient CO2 levels. . Global Biogeochem. Cycles 6::18598
    [Crossref] [Google Scholar]
  75. 75.
    Ganti T. 2003.. The Principles of Life. Oxford, UK:: Oxford Univ. Press
    [Google Scholar]
  76. 76.
    Garcia AK, Cavanaugh CM, Kacar B. 2021.. The curious consistency of carbon biosignatures over billions of years of Earth-life coevolution. . ISME J. 15:(8):218394
    [Crossref] [Google Scholar]
  77. 77.
    Garcia AK, Fer E, Sephus C, Kacar B. 2022.. An integrated method to reconstruct ancient proteins. . Methods Mol. Biol. 2569::26781
    [Crossref] [Google Scholar]
  78. 78.
    Garcia AK, Harris DF, Rivier AJ, Carruthers BM, Pinochet-Barros A, et al. 2023.. Nitrogenase resurrection and the evolution of a singular enzymatic mechanism. . eLife 12::e85003
    [Crossref] [Google Scholar]
  79. 79.
    Garcia AK, Kaçar B. 2019.. How to resurrect ancestral proteins as proxies for ancient biogeochemistry. Free Radic. . Biol. Med. 140::26069
    [Google Scholar]
  80. 80.
    Garcia AK, Kolaczkowski B, Kaçar B. 2022.. Reconstruction of nitrogenase predecessors suggests origin from maturase-like proteins. . Genome Biol. Evol. 14::evac031
    [Crossref] [Google Scholar]
  81. 81.
    Garcia AK, McShea H, Kolaczkowski B, Kaçar B. 2020.. Reconstructing the evolutionary history of nitrogenases: evidence for ancestral molybdenum-cofactor utilization. . Geobiology 18::394411
    [Crossref] [Google Scholar]
  82. 82.
    Geider RJ, Delucia EH, Falkowski PG, Finzi AC, Grime JP, et al. 2002.. Primary productivity of planet Earth: biological determinants and physical constraints in terrestrial and aquatic habitats. . Global Change Biol. 7::84982
    [Crossref] [Google Scholar]
  83. 83.
    Gibson TM, Shih PM, Cumming VM, Fischer WW, Crockford PW, et al. 2017.. Precise age of Bangiomorpha pubescens dates the origin of eukaryotic photosynthesis. . Geology 46::13538
    [Crossref] [Google Scholar]
  84. 84.
    Gil R, Silva FJ, Peretó J, Moya A. 2004.. Determination of the core of a minimal bacterial gene set. . Microbiol. Mol. Biol. Rev. 68::51837
    [Crossref] [Google Scholar]
  85. 85.
    Gilbert PUPA, Bergmann KD, Boekelheide N, Tambutté S, Mass T, et al. 2022.. Biomineralization: integrating mechanism and evolutionary history. . Sci. Adv. 8::eabl9653
    [Crossref] [Google Scholar]
  86. 86.
    Glass JB, Elbon CE, Williams LD. 2023.. Something old, something new, something borrowed, something blue: the anaerobic microbial ancestry of aerobic respiration. . Trends Microbiol. 31::13541
    [Crossref] [Google Scholar]
  87. 87.
    Glass JB, Wolfe-Simon F, Anbar AD. 2009.. Coevolution of metal availability and nitrogen assimilation in cyanobacteria and algae. . Geobiology 7::10023
    [Crossref] [Google Scholar]
  88. 88.
    Gold DA, Caron A, Fournier GP, Summons RE. 2017.. Paleoproterozoic sterol biosynthesis and the rise of oxygen. . Nature 543::42023
    [Crossref] [Google Scholar]
  89. 89.
    Goldford JE, Hartman H, Smith TF, Segre D. 2017.. Remnants of an ancient metabolism without phosphate. . Cell 168::112634
    [Crossref] [Google Scholar]
  90. 90.
    Goldman AD, Kacar B. 2021.. Cofactors are remnants of life's origin and early evolution. . J. Mol. Evol. 89::12733
    [Crossref] [Google Scholar]
  91. 91.
    Goldman AD, Kaçar B. 2022.. Very early evolution from the perspective of microbial ecology. . Environ. Microbiol. 25::510
    [Crossref] [Google Scholar]
  92. 92.
    Gould SJ. 1980.. G. G. Simpson, paleontology, and the modern synthesis. . In The Evolutionary Synthesis, ed. E Mayr, WB Provine , pp. 15372. Cambridge, MA:: Harvard Univ. Press
    [Google Scholar]
  93. 93.
    Gould SJ. 2016.. The promise of paleobiology as a nomothetic, evolutionary discipline. . Paleobiology 6::96118
    [Crossref] [Google Scholar]
  94. 94.
    Govorunova EG, Sineshchekov OA, Li H, Spudich JL. 2017.. Microbial rhodopsins: diversity, mechanisms, and optogenetic applications. . Annu. Rev. Biochem. 86::84572
    [Crossref] [Google Scholar]
  95. 95.
    Gull M, Mojica MA, Fernández FM, Gaul DA, Orlando TM, et al. 2015.. Nucleoside phosphorylation by the mineral schreibersite. . Sci. Rep. 5::17198
    [Crossref] [Google Scholar]
  96. 96.
    Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM. 1998.. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. . Chem. Biol. 5::R24549
    [Crossref] [Google Scholar]
  97. 97.
    Harris DF, Lukoyanov DA, Kallas H, Trncik C, Yang Z-Y, et al. 2019.. Mo-, V-, and Fe-nitrogenases use a universal eight-electron reductive-elimination mechanism to achieve N2 reduction. . Biochemistry 58::3293301
    [Crossref] [Google Scholar]
  98. 98.
    Harris DF, Rucker HR, Garcia AK, Yang Z-Y, Chang SD, et al. 2024.. Ancient nitrogenases are ATP dependent. . mBio 13::e0127124
    [Crossref] [Google Scholar]
  99. 99.
    Harrison TM, Bell EA, Boehnke P. 2017.. Hadean zircon petrochronology. . Rev. Mineral. Geochem. 83::32963
    [Crossref] [Google Scholar]
  100. 100.
    Hartman H, Smith TF. 2019.. Origin of the genetic code is found at the transition between a thioester world of peptides and the phosphoester world of polynucleotides. . Life 9::69
    [Crossref] [Google Scholar]
  101. 101.
    Havig JR, Hamilton TL, Bachan A, Kump LR. 2017.. Sulfur and carbon isotopic evidence for metabolic pathway evolution and a four-stepped Earth system progression across the Archean and Paleoproterozoic. . Earth-Sci. Rev. 174::121
    [Crossref] [Google Scholar]
  102. 102.
    He S, Linz AM, Stevens SLR, Tran PQ, Moya-Flores F, et al. 2023.. Diversity, distribution, and expression of opsin genes in freshwater lakes. . Mol. Ecol. 32::2798817
    [Crossref] [Google Scholar]
  103. 103.
    Hofer U. 2013.. Getting to the bottom of Cyanobacteria. . Nat. Rev. Microbiol. 11::81819
    [Crossref] [Google Scholar]
  104. 104.
    Hofmann HJ, Grey K, Hickman AH, Thorpe RI. 1999.. Origin of 3.45 Ga coniform stromatolites in Warrawoona Group, Western Australia. . Geol. Soc. Am. Bull. 111::125662
    [Crossref] [Google Scholar]
  105. 105.
    Hohmann-Marriott MF, Blankenship RE. 2011.. Evolution of photosynthesis. . Annu. Rev. Plant Biol. 62::51548
    [Crossref] [Google Scholar]
  106. 106.
    Holland SM. 2016.. The non-uniformity of fossil preservation. . Philos. Trans. R. Soc. B 371::20150130
    [Crossref] [Google Scholar]
  107. 107.
    Hoshino Y, Gaucher EA. 2021.. Evolution of bacterial steroid biosynthesis and its impact on eukaryogenesis. . PNAS 118::e2101276118
    [Crossref] [Google Scholar]
  108. 108.
    Hou J, Wang Y, Zhu P, Yang N, Liang L, et al. 2023.. Taxonomic and carbon metabolic diversification of Bathyarchaeia during its coevolution history with early Earth surface environment. . Sci. Adv. 9::eadf5069
    [Crossref] [Google Scholar]
  109. 109.
    Hurley SJ, Wing BA, Jasper CE, Hill NC, Cameron JC. 2021.. Carbon isotope evidence for the global physiology of Proterozoic cyanobacteria. . Sci. Adv. 7::eabc8998
    [Crossref] [Google Scholar]
  110. 110.
    Imhoff JF, Rahn T, Künzel S, Neulinger SC. 2019.. Phylogeny of anoxygenic photosynthesis based on sequences of photosynthetic reaction center proteins and a key enzyme in bacteriochlorophyll biosynthesis, the chlorophyllide reductase. . Microorganisms 7::576
    [Crossref] [Google Scholar]
  111. 111.
    Isson TT, Love GD, Dupont CL, Reinhard CT, Zumberge AJ, et al. 2018.. Tracking the rise of eukaryotes to ecological dominance with zinc isotopes. . Geobiology 16::34152
    [Crossref] [Google Scholar]
  112. 112.
    Jablonska J, Tawfik DS. 2021.. The evolution of oxygen-utilizing enzymes suggests early biosphere oxygenation. . Nat. Ecol. Evol. 5::44248
    [Crossref] [Google Scholar]
  113. 113.
    Javaux EJ. 2019.. Challenges in evidencing the earliest traces of life. . Nature 572::45160
    [Crossref] [Google Scholar]
  114. 114.
    Kacar B, Garmendia E, Tuncbag N, Andersson DI, Hughes D. 2017.. Functional constraints on replacing an essential gene with its ancient and modern homologs. . mBio 8::e01276-17
    [Crossref] [Google Scholar]
  115. 115.
    Kacar B, Ge X, Sanyal S, Gaucher EA. 2017.. Experimental evolution of Escherichia coli harboring an ancient translation protein. . J. Mol. Evol. 84::6984
    [Crossref] [Google Scholar]
  116. 116.
    Kacar B, Guy L, Smith E, Baross J. 2017.. Resurrecting ancestral genes in bacteria to interpret ancient biosignatures. . Philos. Trans. R. Soc. A 375::20160352
    [Crossref] [Google Scholar]
  117. 117.
    Kacar B, Hanson-Smith V, Adam ZR, Boekelheide N. 2017.. Constraining the timing of the Great Oxidation Event within the Rubisco phylogenetic tree. . Geobiology 15::62840
    [Crossref] [Google Scholar]
  118. 118.
    Karasuyama M, Inoue K, Nakamura R, Kandori H, Takeuchi I. 2018.. Understanding colour tuning rules and predicting absorption wavelengths of microbial rhodopsins by data-driven machine-learning approach. . Sci. Rep. 8::15580
    [Crossref] [Google Scholar]
  119. 119.
    Kasting JF. 2005.. Methane and climate during the Precambrian era. . Precambrian Res. 137::11929
    [Crossref] [Google Scholar]
  120. 120.
    Kasting JF, Siefert JL. 2002.. Life and the evolution of Earth's atmosphere. . Science 296::106668
    [Crossref] [Google Scholar]
  121. 121.
    Kedzior M, Garcia AK, Li M, Taton A, Adam ZR, et al. 2022.. Resurrected Rubisco suggests uniform carbon isotope signatures over geologic time. . Cell Rep. 39::110726
    [Crossref] [Google Scholar]
  122. 122.
    Kipp MA. 2022.. A double-edged sword: the role of sulfate in anoxic marine phosphorus cycling through Earth history. . Geophys. Res. Lett. 49::e2022GL099817
    [Crossref] [Google Scholar]
  123. 123.
    Kipp MA, Stüeken EE. 2017.. Biomass recycling and Earth's early phosphorus cycle. . Sci. Adv. 3::eaao4795
    [Crossref] [Google Scholar]
  124. 124.
    Klein C, Beukes NJ, Schopf JW. 1987.. Filamentous microfossils in the Early Proterozoic transvaal supergroup: their morphology, significance, and paleoenvironmental setting. . Precambrian Res. 36::8194
    [Crossref] [Google Scholar]
  125. 125.
    Knoll AH. 1992.. The early evolution of eukaryotes: a geological perspective. . Science 256::62227
    [Crossref] [Google Scholar]
  126. 126.
    Knoll AH. 2014.. Paleobiological perspectives on early eukaryotic evolution. . Cold Spring Harb. Perspect. Biol. 6::a016121
    [Crossref] [Google Scholar]
  127. 127.
    Knoll AH. 2015.. Paleobiological perspectives on early microbial evolution. . Cold Spring Harb. Perspect. Biol. 7::a018093
    [Crossref] [Google Scholar]
  128. 128.
    Knoll AH, Nowak MA. 2017.. The timetable of evolution. . Sci. Adv. 3::e1603076
    [Crossref] [Google Scholar]
  129. 129.
    Knoll AH, Summons RE, Waldbauer JR, Zumberge JE. 2007.. The geological succession of primary producers in the oceans. . In Evolution of Primary Producers in the Sea, ed. PG Falkowski, AH Knoll , pp. 13363. Cambridge, MA:: Academic
    [Google Scholar]
  130. 130.
    Krissansen-Totton J, Buick R, Catling DC. 2015.. A statistical analysis of the carbon isotope record from the Archean to Phanerozoic and implications for the rise of oxygen. . Am. J. Sci. 315::275316
    [Crossref] [Google Scholar]
  131. 131.
    Laakso TA, Schrag DP. 2019.. Methane in the Precambrian atmosphere. . Earth Planet. Sci. Lett. 522::4854
    [Crossref] [Google Scholar]
  132. 132.
    Lindeman RL. 1942.. The trophic-dynamic aspect of ecology. . Ecology 23::399417
    [Crossref] [Google Scholar]
  133. 133.
    Lombard J, López-García P, Moreira D. 2012.. The early evolution of lipid membranes and the three domains of life. . Nat. Rev. Microbiol. 10::50715
    [Crossref] [Google Scholar]
  134. 134.
    López-García P, Moreira D. 2008.. Tracking microbial biodiversity through molecular and genomic ecology. . Res. Microbiol. 159::6773
    [Crossref] [Google Scholar]
  135. 135.
    Lyell C. 1837.. Principles of Geology. Book IV. London:: John Murray
    [Google Scholar]
  136. 136.
    Lyons TW, Fike DA, Zerkle A. 2015.. Emerging biogeochemical views of Earth's ancient microbial worlds. . Elements 11::41521
    [Crossref] [Google Scholar]
  137. 137.
    Lyons TW, Reinhard CT, Planavsky NJ. 2014.. The rise of oxygen in Earth's early ocean and atmosphere. . Nature 506::30715
    [Crossref] [Google Scholar]
  138. 138.
    Mackin KA, Roy RA, Theobald DL. 2014.. An empirical test of convergent evolution in rhodopsins. . Mol. Biol. Evol. 31::8595
    [Crossref] [Google Scholar]
  139. 139.
    Magnabosco C, Moore KR, Wolfe JM, Fournier GP. 2018.. Dating phototrophic microbial lineages with reticulate gene histories. . Geobiology 16::17989
    [Crossref] [Google Scholar]
  140. 140.
    Mahmoudi N, Steen AD, Halverson GP, Konhauser KO. 2023.. Biogeochemistry of Earth before exoenzymes. . Nat. Geosci. 16::84550
    [Crossref] [Google Scholar]
  141. 141.
    Marin J, Battistuzzi FU, Brown AC, Hedges SB. 2017.. The timetree of prokaryotes: new insights into their evolution and speciation. . Mol. Biol. Evol. 34::43746
    [Google Scholar]
  142. 142.
    Marshall B, Amritkar K, Wolfe M, Kaçar B, Landick R. 2023.. Evolutionary flexibility and rigidity in the bacterial methylerythritol phosphate (MEP) pathway. . Front. Microbiol. 14::1286626
    [Crossref] [Google Scholar]
  143. 143.
    Martin WF, Thauer RK. 2017.. Energy in ancient metabolism. . Cell 168::95355
    [Crossref] [Google Scholar]
  144. 144.
    Martinez-Gutierrez CA, Uyeda JC, Aylward FO. 2023.. A timeline of bacterial and archaeal diversification in the ocean. . eLife 12::RP88268
    [Crossref] [Google Scholar]
  145. 145.
    Matheus Carnevali PB, Schulz F, Castelle CJ, Kantor RS, Shih PM, et al. 2019.. Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria. . Nat. Commun. 10::463
    [Crossref] [Google Scholar]
  146. 146.
    McGlynn SE, Boyd ES, Peters JW, Orphan VJ. 2012.. Classifying the metal dependence of uncharacterized nitrogenases. . Front. Microbiol. 3::419
    [Google Scholar]
  147. 147.
    McKay CP. 2014.. Requirements and limits for life in the context of exoplanets. . PNAS 111::1262833
    [Crossref] [Google Scholar]
  148. 148.
    McKay LJ, Dlakić M, Fields MW, Delmont TO, Eren AM, et al. 2019.. Co-occurring genomic capacity for anaerobic methane and dissimilatory sulfur metabolisms discovered in the Korarchaeota. . Nat. Microbiol. 4::61422
    [Crossref] [Google Scholar]
  149. 149.
    Mix LJ, Haig D, Cavanaugh CM. 2005.. Phylogenetic analyses of the core antenna domain: investigating the origin of photosystem I. . J. Mol. Evol. 60::15363
    [Crossref] [Google Scholar]
  150. 150.
    Mojzsis SJ, Arrhenius G, McKeegan KD, Harrison TM, Nutman AP, Friend CRL. 1996.. Evidence for life on Earth before 3,800 million years ago. . Nature 384::5559
    [Crossref] [Google Scholar]
  151. 151.
    Mus F, Alleman AB, Pence N, Seefeldt LC, Peters JW. 2018.. Exploring the alternatives of biological nitrogen fixation. . Metallomics 10::52338
    [Crossref] [Google Scholar]
  152. 152.
    Navarro-González R, McKay CP, Mvondo DN. 2001.. A possible nitrogen crisis for Archaean life due to reduced nitrogen fixation by lightning. . Nature 412::6164
    [Crossref] [Google Scholar]
  153. 153.
    Nealson KH, Rye R. 2003.. Evolution of metabolism. . In Treatise on Geochemistry, ed. WH Schlesinger , pp. 4161. Amsterdam:: Elsevier
    [Google Scholar]
  154. 154.
    Nealson KH, Zeki S, Conrad PG. 1999.. Life: past, present and future. . Philos. Trans. R. Soc. B 354::192339
    [Crossref] [Google Scholar]
  155. 155.
    Nemchin AA, Whitehouse MJ, Menneken M, Geisler T, Pidgeon RT, Wilde SA. 2008.. A light carbon reservoir recorded in zircon-hosted diamond from the Jack Hills. . Nature 454::9295
    [Crossref] [Google Scholar]
  156. 156.
    Newman DK, Banfield JF. 2002.. Geomicrobiology: how molecular-scale interactions underpin biogeochemical systems. . Science 296::107177
    [Crossref] [Google Scholar]
  157. 157.
    Nutman AP, Bennett VC, Friend CR, Van Kranendonk MJ, Chivas AR. 2016.. Rapid emergence of life shown by discovery of 3,700-million-year-old microbial structures. . Nature 537::53538
    [Crossref] [Google Scholar]
  158. 158.
    Oehler DZ, Walsh MM, Sugitani K, Liu M-C, House CH. 2017.. Large and robust lenticular microorganisms on the young Earth. . Precambrian Res. 296::11219
    [Crossref] [Google Scholar]
  159. 159.
    Oliver T, Kim TD, Trinugroho JP, Cordón-Preciado V, Wijayatilake N, et al. 2023.. The evolution and evolvability of photosystem II. . Annu. Rev. Plant Biol. 74::22557
    [Crossref] [Google Scholar]
  160. 160.
    Oliver T, Sánchez-Baracaldo P, Larkum AW, Rutherford AW, Cardona T. 2021.. Time-resolved comparative molecular evolution of oxygenic photosynthesis. . Biochim. Biophys. Acta Bioenerg. 1862::148400
    [Crossref] [Google Scholar]
  161. 161.
    Onstott TC, Moser DP, Pfiffner SM, Fredrickson JK, Brockman FJ, et al. 2003.. Indigenous and contaminant microbes in ultradeep mines. . Environ. Microbiol. 5::116891
    [Crossref] [Google Scholar]
  162. 162.
    Pace NR. 1996.. New Perspective on the Natural Microbial World: Molecular Microbial Ecology. Washington, DC:: Am. Soc. Microbiol.
    [Google Scholar]
  163. 163.
    Parfrey LW, Lahr DJ, Knoll AH, Katz LA. 2011.. Estimating the timing of early eukaryotic diversification with multigene molecular clocks. . PNAS 108::1362429
    [Crossref] [Google Scholar]
  164. 164.
    Parsons C, Stüeken EE, Rosen CJ, Mateos K, Anderson RE. 2020.. Radiation of nitrogen-metabolizing enzymes across the tree of life tracks environmental transitions in Earth history. . Geobiology 19::1834
    [Crossref] [Google Scholar]
  165. 165.
    Pasek MA, Sampson JM, Atlas Z. 2014.. Redox chemistry in the phosphorus biogeochemical cycle. . PNAS 111::1546873
    [Crossref] [Google Scholar]
  166. 166.
    Pauling L, Zuckerkandl E. 1963.. Chemical paleogenetics molecular restoration studies of extinct forms of life. . Acta Chem. Scand. 17::916
    [Crossref] [Google Scholar]
  167. 167.
    Pawlowska MM, Butterfield NJ, Brocks JJ. 2013.. Lipid taphonomy in the Proterozoic and the effect of microbial mats on biomarker preservation. . Geology 41::1036
    [Crossref] [Google Scholar]
  168. 168.
    Peterson KJ, Butterfield NJ. 2005.. Origin of the Eumetazoa: testing ecological predictions of molecular clocks against the Proterozoic fossil record. . PNAS 102::954752
    [Crossref] [Google Scholar]
  169. 169.
    Pinhassi J, DeLong EF, Béjà O, González JM, Pedrós-Alió C. 2016.. Marine bacterial and archaeal ion-pumping rhodopsins: genetic diversity, physiology, and ecology. . Microbiol. Mol. Biol. Rev. 80::92954
    [Crossref] [Google Scholar]
  170. 170.
    Pinna S, Kunz C, Halpern A, Harrison SA, Jordan SF, et al. 2022.. A prebiotic basis for ATP as the universal energy currency. . PLOS Biol. 20::e3001437
    [Crossref] [Google Scholar]
  171. 171.
    Planavsky N, Partin C, Bekker A. 2011.. Carbon isotopes as a geochemical tracer. . In Encyclopedia of Astrobiology, ed. M Gargaud, R Amils, JC Quintanilla, HJ Cleaves, WM Irvine , et al. pp. 24145. Berlin:: Springer
    [Google Scholar]
  172. 172.
    Priya B, Premanandh J, Dhanalakshmi RT, Seethalakshmi T, Uma L, et al. 2007.. Comparative analysis of cyanobacterial superoxide dismutases to discriminate canonical forms. . BMC Genom. 8::435
    [Crossref] [Google Scholar]
  173. 173.
    Ramirez MD, Pairett AN, Pankey MS, Serb JM, Speiser DI, et al. 2016.. The last common ancestor of most bilaterian animals possessed at least 9 opsins. . Genome Biol. Evol. 8:(12):364052
    [Google Scholar]
  174. 174.
    Reinhard CT, Planavsky NJ, Gill BC, Ozaki K, Robbins LJ, et al. 2017.. Evolution of the global phosphorus cycle. . Nature 541::38689
    [Crossref] [Google Scholar]
  175. 175.
    Rothman DH, Fournier GP, French KL, Alm EJ, Boyle EA, et al. 2014.. Methanogenic burst in the end-Permian carbon cycle. . PNAS 111::546267
    [Crossref] [Google Scholar]
  176. 176.
    Rozi MFAM, Rahman RNZRA, Leow ATC, Ali MSM. 2022.. Ancestral sequence reconstruction of ancient lipase from family I.3 bacterial lipolytic enzymes. . Mol. Phylogenet. Evol. 168::107381
    [Crossref] [Google Scholar]
  177. 177.
    Rucker HR, Kaçar B. 2024.. Enigmatic evolution of microbial nitrogen fixation: insights from Earth's past. . Trends Microbiol. 32::55464
    [Crossref] [Google Scholar]
  178. 178.
    Ruiz-González MX, Marín I. 2004.. New insights into the evolutionary history of type 1 rhodopsins. . J. Mol. Evol. 58::34858
    [Crossref] [Google Scholar]
  179. 179.
    Sachse D, Billault I, Bowen GJ, Chikaraishi Y, Dawson TE, et al. 2012.. Molecular paleohydrology: interpreting the hydrogen-isotopic composition of lipid biomarkers from photosynthesizing organisms. . Annu. Rev. Earth Planet. Sci. 40::22149
    [Crossref] [Google Scholar]
  180. 180.
    Sagan L. 1967.. On the origin of mitosing cells. . J. Theor. Biol. 14::25574
    [Crossref] [Google Scholar]
  181. 181.
    Sage RF, Coleman JR. 2001.. Effects of low atmospheric CO2 on plants: more than a thing of the past. . Trends Plant Sci. 6::1824
    [Crossref] [Google Scholar]
  182. 182.
    Sánchez-Baracaldo P, Cardona T. 2020.. On the origin of oxygenic photosynthesis and Cyanobacteria. . New Phytol. 225::144046
    [Crossref] [Google Scholar]
  183. 183.
    Sánchez-Baracaldo P, Ridgwell A, Raven JA. 2014.. A Neoproterozoic transition in the marine nitrogen cycle. . Curr. Biol. 24::65257
    [Crossref] [Google Scholar]
  184. 184.
    Schidlowski M. 1983.. Evolution of photoautotrophy and early atmospheric oxygen levels. . Precambrian Res. 20::31935
    [Crossref] [Google Scholar]
  185. 185.
    Schidlowski M. 2001.. Carbon isotopes as biogeochemical recorders of life over 3.8 Ga of Earth history: evolution of a concept. . Precambrian Res. 106::11734
    [Crossref] [Google Scholar]
  186. 186.
    Schirrmeister BE, de Vos JM, Antonelli A, Bagheri HC. 2013.. Evolution of multicellularity coincided with increased diversification of cyanobacteria and the Great Oxidation Event. . PNAS 110::179196
    [Crossref] [Google Scholar]
  187. 187.
    Schirrmeister BE, Sanchez-Baracaldo P, Wacey D. 2016.. Cyanobacterial evolution during the Precambrian. . Int. J. Astrobiol. 15::187204
    [Crossref] [Google Scholar]
  188. 188.
    Schmidt FV, Schulz L, Zarzycki J, Prinz S, Oehlmann NN, et al. 2024.. Structural insights into the iron nitrogenase complex. . Nat. Struct. Mol. Biol. 31:(1):15058
    [Crossref] [Google Scholar]
  189. 189.
    Schopf JW. 1993.. Microfossils of the Early Archean Apex Chert: new evidence of the antiquity of life. . Science 260::64046
    [Crossref] [Google Scholar]
  190. 190.
    Schopf JW. 1999.. Cradle of Life. Princeton, NJ:: Princeton Univ. Press
    [Google Scholar]
  191. 191.
    Schopf JW. 2000.. Solution to Darwin's dilemma: discovery of the missing Precambrian record of life. . PNAS 97::694753
    [Crossref] [Google Scholar]
  192. 192.
    Schopf JW. 2011.. The paleobiological record of photosynthesis. . Photosynth. Res. 107::87101
    [Crossref] [Google Scholar]
  193. 193.
    Schubert W-D, Klukas O, Saenger W, Witt HT, Fromme P, Krauß N. 1998.. A common ancestor for oxygenic and anoxygenic photosynthetic systems. . J. Mol. Biol. 280::297314
    [Crossref] [Google Scholar]
  194. 194.
    Schulz L, Guo Z, Zarzycki J, Steinchen W, Schuller JM, et al. 2022.. Evolution of increased complexity and specificity at the dawn of form I Rubiscos. . Science 378::15560
    [Crossref] [Google Scholar]
  195. 195.
    Sendra KM, Barwinska-Sendra A, Mackenzie ES, Baslé A, Kehl-Fie TE, Waldron KJ. 2023.. An ancient metalloenzyme evolves through metal preference modulation. . Nat. Ecol. Evol. 7::73244
    [Crossref] [Google Scholar]
  196. 196.
    Sephus CD, Fer E, Garcia AK, Adam ZR, Schwieterman EW, Kacar B. 2022.. Earliest photic zone niches probed by ancestral microbial rhodopsins. . Mol. Biol. Evol. 39::msac100
    [Crossref] [Google Scholar]
  197. 197.
    Sepkoski D. 2005.. Stephen Jay Gould, Jack Sepkoski, and the ‘quantitative revolution’ in American paleobiology. . J. Hist. Biol. 38::20937
    [Crossref] [Google Scholar]
  198. 198.
    Sepkoski D. 2009.. The emergence of paleobiology. . In The Paleobiological Revolution, ed. D Sepkoski, M Ruse , pp. 1542. Chicago:: Univ. Chicago Press
    [Google Scholar]
  199. 199.
    Sepkoski D. 2018.. The unfinished synthesis? Paleontology and evolutionary biology in the 20th century. . J. Hist. Biol. 52::687703
    [Crossref] [Google Scholar]
  200. 200.
    Sepkoski JJ. 2015.. Biodiversity: past, present, and future. . J. Paleontol. 71::53339
    [Crossref] [Google Scholar]
  201. 201.
    Shalaeva DN, Galperin MY, Mulkidjanian AY. 2015.. Eukaryotic G protein-coupled receptors as descendants of prokaryotic sodium-translocating rhodopsins. . Biol. Direct 10::63
    [Crossref] [Google Scholar]
  202. 202.
    Shang H, Rothman DH, Fournier GP. 2022.. Oxidative metabolisms catalyzed Earth's oxygenation. . Nat. Commun. 13::1328
    [Crossref] [Google Scholar]
  203. 203.
    Sharma AK, Spudich JL, Doolittle WF. 2006.. Microbial rhodopsins: functional versatility and genetic mobility. . Trends Microbiol. 14::46369
    [Crossref] [Google Scholar]
  204. 204.
    Sheridan PP, Freeman KH, Brenchley JE. 2003.. Estimated minimal divergence times of the major bacterial and archaeal phyla. . Geomicrobiol. J. 20::114
    [Crossref] [Google Scholar]
  205. 205.
    Shih PM, Hemp J, Ward LM, Matzke NJ, Fischer WW. 2016.. Crown group Oxyphotobacteria postdate the rise of oxygen. . Geobiology 15::1929
    [Crossref] [Google Scholar]
  206. 206.
    Shih PM, Occhialini A, Cameron JC, Andralojc PJ, Parry MA, Kerfeld CA. 2016.. Biochemical characterization of predicted Precambrian RuBisCO. . Nat. Commun. 7::10382
    [Crossref] [Google Scholar]
  207. 207.
    Simpson GG. 1984.. Tempo and Mode in Evolution. New York:: Columbia Univ. Press
    [Google Scholar]
  208. 208.
    Slotznick SP, Johnson JE, Rasmussen B, Raub TD, Webb SM, et al. 2022.. Reexamination of 2.5-Ga “whiff” of oxygen interval points to anoxic ocean before GOE. . Sci. Adv. 8::eabj7190
    [Crossref] [Google Scholar]
  209. 209.
    Snel B, Plachetzki DC, Degnan BM, Oakley TH. 2007.. The origins of novel protein interactions during animal opsin evolution. . PLOS ONE 2::e1054
    [Crossref] [Google Scholar]
  210. 210.
    Soo RM, Skennerton CT, Sekiguchi Y, Imelfort M, Paech SJ, et al. 2014.. An expanded genomic representation of the phylum Cyanobacteria. . Genome Biol. Evol. 6::103145
    [Crossref] [Google Scholar]
  211. 211.
    Stackhouse J, Presnell SR, McGeehan GM, Nambiar KP, Benner SA. 1990.. The ribonuclease from an extinct bovid ruminant. . FEBS Lett. 262::1046
    [Crossref] [Google Scholar]
  212. 212.
    Stein JL, Marsh TL, Wu KY, Shizuya H, DeLong EF. 1996.. Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon. . J. Bacteriol. 178::59199
    [Crossref] [Google Scholar]
  213. 213.
    Stüeken EE. 2013.. A test of the nitrogen-limitation hypothesis for retarded eukaryote radiation: nitrogen isotopes across a Mesoproterozoic basinal profile. . Geochim. Cosmochim. Acta 120::12139
    [Crossref] [Google Scholar]
  214. 214.
    Stüeken EE, Buick R, Guy BM, Koehler MC. 2015.. Isotopic evidence for biological nitrogen fixation by molybdenum-nitrogenase from 3.2 Gyr. . Nature 520::66669
    [Crossref] [Google Scholar]
  215. 215.
    Stüeken EE, Kipp MA, Koehler MC, Buick R. 2016.. The evolution of Earth's biogeochemical nitrogen cycle. . Earth-Sci. Rev. 160::22039
    [Crossref] [Google Scholar]
  216. 216.
    Sugitani K, Mimura K, Nagaoka T, Lepot K, Takeuchi M. 2013.. Microfossil assemblage from the 3400Ma Strelley Pool Formation in the Pilbara Craton, Western Australia: Results form a new locality. . Precambrian Res. 226::5974
    [Crossref] [Google Scholar]
  217. 217.
    Summons RE, Jahnke LL, Hope JM, Logan GA. 1999.. 2-Methylhopanoids as biomarkers for cyanobacterial oxygenic photosynthesis. . Nature 400::55457
    [Crossref] [Google Scholar]
  218. 218.
    Summons RE, Jahnke LL, Roksandic Z. 1994.. Carbon isotopic fractionation in lipids from methanotrophic bacteria: relevance for interpretation of the geochemical record of biomarkers. . Geochim. Cosmochim. Acta 58::285363
    [Crossref] [Google Scholar]
  219. 219.
    Summons RE, Welander PV, Gold DA. 2021.. Lipid biomarkers: molecular tools for illuminating the history of microbial life. . Nat. Rev. Microbiol. 20::17485
    [Crossref] [Google Scholar]
  220. 220.
    Sumner DY. 2002.. Biology and geology: a necessary symbiosis. . Palaios 17::3078
    [Crossref] [Google Scholar]
  221. 221.
    Tashiro T, Ishida A, Hori M, Igisu M, Koike M, et al. 2017.. Early trace of life from 3.95 Ga sedimentary rocks in Labrador, Canada. . Nature 549::51618
    [Crossref] [Google Scholar]
  222. 222.
    Todd ZR. 2022.. Sources of nitrogen-, sulfur-, and phosphorus-containing feedstocks for prebiotic chemistry in the planetary environment. . Life 12::1268
    [Crossref] [Google Scholar]
  223. 223.
    Tyrrell T. 1999.. The relative influences of nitrogen and phosphorus on oceanic primary production. . Nature 400::52531
    [Crossref] [Google Scholar]
  224. 224.
    Ueno Y, Yamada K, Yoshida N, Maruyama S, Isozaki Y. 2006.. Evidence from fluid inclusions for microbial methanogenesis in the early Archaean era. . Nature 440::51619
    [Crossref] [Google Scholar]
  225. 225.
    Valenti R, Jabłońska J, Tawfik DS. 2022.. Characterization of ancestral Fe/Mn superoxide dismutases indicates their cambialistic origin. . Protein Sci. 31::e4423
    [Crossref] [Google Scholar]
  226. 226.
    Valentine JW. 2009.. The infusion of biology into paleontological research. . In The Paleobiological Revolution, ed. D Sepkoski, M Ruse , pp. 38597. Chicago:: Univ. Chicago Press
    [Google Scholar]
  227. 227.
    Valley JW, Peck WH, King EM, Wilde SA. 2002.. A cool early Earth. . Geology 30::35154
    [Crossref] [Google Scholar]
  228. 228.
    Van Nynatten A, Castiglione GM, de A Gutierrez E, Lovejoy NR, Chang BSW, Kim Y. 2021.. Recreated ancestral opsin associated with marine to freshwater croaker invasion reveals kinetic and spectral adaptation. . Mol. Biol. Evol. 38::207687
    [Crossref] [Google Scholar]
  229. 229.
    Vieth A, Wilkes H. 2010.. Stable isotopes in understanding origin and degradation processes of petroleum. . In Handbook of Hydrocarbon and Lipid Microbiology, ed. KN Timmis , pp. 97111. Berlin:: Springer
    [Google Scholar]
  230. 230.
    Walter MR, Buick R, Dunlop JSR. 1980.. Stromatolites 3,400–3,500 Myr old from the North Pole area, Western Australia. . Nature 284::44345
    [Crossref] [Google Scholar]
  231. 231.
    Wang RZ, Liu AK, Banda DM, Fischer WW, Shih PM. 2023.. A bacterial Form I′ Rubisco has a smaller carbon isotope fractionation than its Form I counterpart. . Biomolecules 13::596
    [Crossref] [Google Scholar]
  232. 232.
    Wang RZ, Nichols RJ, Liu AK, Flamholz AI, Artier J, et al. 2023.. Carbon isotope fractionation by an ancestral rubisco suggests that biological proxies for CO2 through geologic time should be reevaluated. . PNAS 120::e2300466120
    [Crossref] [Google Scholar]
  233. 233.
    Ward LM, Cardona T, Holland-Moritz H. 2019.. Evolutionary implications of anoxygenic phototrophy in the bacterial phylum Candidatus Eremiobacterota (WPS-2). . Front. Microbiol. 10::1658
    [Crossref] [Google Scholar]
  234. 234.
    Wei JH, Yin X, Welander PV. 2016.. Sterol synthesis in diverse bacteria. . Front. Microbiol. 7::990
    [Google Scholar]
  235. 235.
    Weiss MC, Preiner M, Xavier JC, Zimorski V, Martin WF. 2018.. The last universal common ancestor between ancient Earth chemistry and the onset of genetics. . PLOS Genet. 14::e1007518
    [Crossref] [Google Scholar]
  236. 236.
    Weiss MC, Sousa FL, Mrnjavac N, Neukirchen S, Roettger M, et al. 2016.. The physiology and habitat of the last universal common ancestor. . Nat. Microbiol. 1::16116
    [Crossref] [Google Scholar]
  237. 237.
    Whicher A, Camprubi E, Pinna S, Herschy B, Lane N. 2018.. Acetyl phosphate as a primordial energy currency at the origin of life. . Origins Life Evol. Biosph. 48::15979
    [Crossref] [Google Scholar]
  238. 238.
    Woese CR, Kandler O, Wheelis ML. 1990.. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. . PNAS 87::457679
    [Crossref] [Google Scholar]
  239. 239.
    Wolfe JM, Fournier GP. 2018.. Horizontal gene transfer constrains the timing of methanogen evolution. . Nat. Ecol. Evol. 2::897903
    [Crossref] [Google Scholar]
  240. 240.
    Xavier JC, Hordijk W, Kauffman S, Steel M, Martin WF. 2020.. Autocatalytic chemical networks at the origin of metabolism. . Proc. R. Soc. B 287::20192377
    [Crossref] [Google Scholar]
  241. 241.
    Yutin N, Koonin EV. 2012.. Proteorhodopsin genes in giant viruses. . Biol. Direct 7::34
    [Crossref] [Google Scholar]
  242. 242.
    Zumberge JA, Love GD, Cardenas P, Sperling EA, Gunasekera S, et al. 2018.. Demosponge steroid biomarker 26-methylstigmastane provides evidence for Neoproterozoic animals. . Nat. Ecol. Evol. 2::170914
    [Crossref] [Google Scholar]
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