Ammonia-oxidizing archaea (AOA) play a key role in the aquatic nitrogen cycle. Their genetic diversity is viewed as the outcome of evolutionary processes that shaped ancestral transition from terrestrial to marine habitats. However, current genome-wide insights into AOA evolution rarely consider brackish and freshwater representatives or provide their divergence timeline in lacustrine systems. An unbiased global assessment of lacustrine AOA diversity is critical for understanding their origins, dispersal mechanisms, and ecosystem roles. Here, we leveraged continental-scale metagenomics to document that AOA species diversity in freshwater systems is remarkably low compared to marine environments. We show that the uncultured freshwater AOA, "Candidatus Nitrosopumilus limneticus," is ubiquitous and genotypically static in various large European lakes where it evolved 13 million years ago. We find that extensive proteome remodeling was a key innovation for freshwater colonization of AOA. These findings reveal the genetic diversity and adaptive mechanisms of a keystone species that has survived clonally in lakes for millennia.

Berlin Brandenburg Institute of Advanced Biodiversity Research Free University D 14195 Berlin Germany

Department of Biology University of Konstanz D 78457 Constance Germany

Department of Experimental Limnology Leibniz Institute for Freshwater Ecology and Inland Fisheries D 12587 Stechlin Germany

Department of Land Resources and Environmental Sciences Montana State University 334 Leon Johnson Hall Bozeman MT 59717 USA

Institute of Biochemistry and Biology Potsdam University D 14469 Potsdam Germany

Institute of Hydrobiology Biology Center CAS Na Sádkách 7 37005 České Budejovice Czech Republic

Institute of Microbiology Technical University of Braunschweig D 38108 Braunschweig Germany

Institute of Physics National Academy of Sciences of Kyrgyz Republic Chui Avenue 265 a Bishkek 720071 Kyrgyzstan

Leibniz Institute DSMZ German Collection of Cell Microorganisms and Cell Cultures GmbH D 38124 Braunschweig Germany

Microbial Evogenomics Lab Limnological Station Department of Plant and Microbial Biology University of Zurich Kilchberg Switzerland

State Key Laboratory of Lake Science and Environment Nanjing Institute of Geography and Limnology Chinese Academy of Sciences Nanjing China

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C. Brochier-Armanet, B. Boussau, S. Gribaldo, P. Forterre, Mesophilic crenarchaeota: Proposal for a third archaeal phylum, the Thaumarchaeota. Nat. Rev. Microbiol. 6, 245–252 (2008). PubMed

A. Oren, G. M. Garrity, Valid publication of the names of forty-two phyla of prokaryotes. Int. J. Syst. Evol. Micr. 71, (2021). PubMed

D. A. Stahl, J. R. de la Torre, Physiology and diversity of ammonia-oxidizing Archaea. Annu. Rev. Microbiol. 66, 83–101 (2012). PubMed

A. E. Santoro, R. A. Richter, C. L. Dupont, Planktonic marine Archaea. Annu. Rev. Mar. Sci. 11, 131–158 (2019). PubMed

T. B. Meador, N. Schoffelen, T. G. Ferdelman, O. Rebello, A. Khachikyan, M. Könneke, Carbon recycling efficiency and phosphate turnover by marine nitrifying archaea. Sci. Adv. 6, eaba1799 (2020). PubMed PMC

R. J. E. Alves, B. Q. Minh, T. Urich, A. von Haeseler, C. Schleper, Unifying the global phylogeny and environmental distribution of ammonia-oxidising archaea based on amoA genes. Nat. Commun. 9, 1517 (2018). PubMed PMC

T. H. Erguder, N. Boon, L. Wittebolle, M. Marzorati, W. Verstraete, Environmental factors shaping the ecological niches of ammonia-oxidizing archaea. FEMS Microbiol. Rev. 33, 855–869 (2009). PubMed

M. Ren, X. Feng, Y. Huang, H. Wang, Z. Hu, S. Clingenpeel, B. K. Swan, M. M. Fonseca, D. Posada, R. Stepanauskas, J. T. Hollibaugh, P. G. Foster, T. Woyke, H. Luo, Phylogenomics suggests oxygen availability as a driving force in Thaumarchaeota evolution. ISME J. 13, 2150–2161 (2019). PubMed PMC

P. O. Sheridan, S. Raguideau, C. Quince, J. Holden, L. Zhang, W. H. Gaze, J. Holden, A. Mead, S. Raguideau, C. Quince, A. C. Singer, E. M. H. Wellington, L. Zhang, T. A. Williams, C. Gubry-Rangin, Gene duplication drives genome expansion in a major lineage of Thaumarchaeota. Nat. Commun. 11, 5494 (2020). PubMed PMC

S. S. Abby, M. Kerou, C. Schleper, Ancestral reconstructions decipher major adaptations of ammonia-oxidizing archaea upon radiation into moderate terrestrial and marine environments. mBio 11, 1–20 (2020). PubMed PMC

Y. Yang, C. Zhang, T. M. Lenton, X. Yan, M. Zhu, M. Zhou, J. Tao, T. J. Phelps, Z. Cao, The evolution pathway of ammonia-oxidizing archaea shaped by major geological events. Mol. Biol. Evol. 38, 3637–3648 (2021). PubMed PMC

B. Wang, W. Qin, Y. Ren, X. Zhou, M.-Y. Jung, P. Han, E. A. Eloe-Fadrosh, M. Li, Y. Zheng, L. Lu, X. Yan, J. Ji, Y. Liu, L. Liu, C. Heiner, R. Hall, W. Martens-Habbena, C. W. Herbold, S.-K. Rhee, D. H. Bartlett, L. Huang, A. E. Ingalls, M. Wagner, D. A. Stahl, Z. Jia, Expansion of Thaumarchaeota habitat range is correlated with horizontal transfer of ATPase operons. ISME J. 13, 3067–3079 (2019). PubMed PMC

M. Ren, J. Wang, Phylogenetic divergence and adaptation of Nitrososphaeria across lake depths and freshwater ecosystems. ISME J. 16, 1491–1501 (2022). PubMed PMC

N. R. Lovejoy, E. Bermingham, A. P. Martin, Marine incursion into South America. Nature 396, 421–422 (1998).

K. N. Kirchhoff, T. Hauffe, B. Stelbrink, C. Albrecht, T. Wilke, Evolutionary bottlenecks in brackish water habitats drive the colonization of fresh water by stingrays. J. Evol. Biol. 30, 1576–1591 (2017). PubMed

A. E. R. Soares, C. G. Schrago, The influence of taxon sampling on Bayesian divergence time inference under scenarios of rate heterogeneity among lineages. J. Theor. Biol. 364, 31–39 (2015). PubMed

M. Mehrshad, M. A. Amoozegar, R. Ghai, S. A. S. Fazeli, F. Rodriguez-Valera, Genome reconstruction from metagenomic data sets reveals novel microbes in the brackish waters of the Caspian Sea. Appl. Environ. Microbiol. 82, 1599–1612 (2016). PubMed PMC

S. Hiraoka, Y. Okazaki, M. Anda, A. Toyoda, S. I. Nakano, W. Iwasaki, Metaepigenomic analysis reveals the unexplored diversity of DNA methylation in an environmental prokaryotic community. Nat. Commun. 10, 159 (2019). PubMed PMC

Y. Okazaki, Y. Nishimura, T. Yoshida, H. Ogata, S. I. Nakano, Genome-resolved viral and cellular metagenomes revealed potential key virus-host interactions in a deep freshwater lake. Environ. Microbiol. 21, 4740–4754 (2019). PubMed

P. Xing, Y. Tao, J. Luo, L. Wang, B. Li, H. Li, Q. Wu, Stratification of microbiomes during the holomictic period of Lake Fuxian, an alpine monomictic lake. Limnol. Oceanogr. 65, S134–S148 (2020).

P. J. Cabello-Yeves, C. Callieri, A. Picazo, M. Mehrshad, J. M. Haro-Moreno, J. J. Roda-Garcia, N. Dzhembekova, V. Slabakova, N. Slabakova, S. Moncheva, F. Rodriguez-Valera, The microbiome of the Black Sea water column analyzed by shotgun and genome centric metagenomics. Environ. Microbiome 16, 5 (2021). PubMed PMC

L. Reji, C. A. Francis, Metagenome-assembled genomes reveal unique metabolic adaptations of a basal marine Thaumarchaeota lineage. ISME J. 14, 2105–2115 (2020). PubMed PMC

S. E. Hampton, S. McGowan, T. Ozersky, S. G. P. Virdis, T. T. Vu, T. L. Spanbauer, B. M. Kraemer, G. Swann, A. W. Mackay, S. M. Powers, M. F. Meyer, S. G. Labou, C. M. O’Reilly, M. DiCarlo, A. W. E. Galloway, S. C. Fritz, Recent ecological change in ancient lakes. Limnol. Oceanogr. 63, 2277–2304 (2018).

K. T. Konstantinidis, R. Rosselló-Móra, R. Amann, Uncultivated microbes in need of their own taxonomy. ISME J. 11, 2399–2406 (2017). PubMed PMC

F. Klotz, K. Kitzinger, D. K. Ngugi, P. Büsing, S. Littmann, M. M. M. Kuypers, B. Schink, M. Pester, Quantification of archaea-driven freshwater nitrification from single cell to ecosystem levels. ISME J. 16, 1647–1656 (2022). PubMed PMC

X. Didelot, D. J. Wilson, ClonalFrameML: Efficient inference of recombination in whole bacterial genomes. PLOS Comput. Biol. 11, e1004041 (2015). PubMed PMC

J. Alneberg, C. M. G. Karlsson, A.-M. Divne, C. Bergin, F. Homa, M. V. Lindh, L. W. Hugerth, T. J. G. Ettema, S. Bertilsson, A. F. Andersson, J. Pinhassi, Genomes from uncultivated prokaryotes: A comparison of metagenome-assembled and single-amplified genomes. Microbiome 6, 173 (2018). PubMed PMC

J. Herber, F. Klotz, B. Frommeyer, S. Weis, D. Straile, A. Kolar, J. Sikorski, M. Egert, M. Dannenmann, M. Pester, A single Thaumarchaeon drives nitrification in deep oligotrophic Lake Constance. Environ. Microbiol. 22, 212–228 (2020). PubMed

K. T. Konstantinidis, E. F. DeLong, Genomic patterns of recombination, clonal divergence and environment in marine microbial populations. ISME J. 2, 1052–1065 (2008). PubMed

A. Peña-Gonzalez, M. J. Soto-Girón, S. Smith, J. Sistrunk, L. Montero, M. Páez, E. Ortega, J. K. Hatt, W. Cevallos, G. Trueba, K. Levy, K. T. Konstantinidis, Metagenomic signatures of gut infections caused by different Escherichia coli pathotypes. Appl. Environ. Microbiol. 85, e01820-19 (2019). PubMed PMC

W. P. Hanage, B. G. Spratt, K. M. E. Turner, C. Fraser, Modelling bacterial speciation. Philos. Trans. R. Soc. Lond. B Biol. Sci. 361, 2039–2044 (2006). PubMed PMC

C. Fraser, W. P. Hanage, B. G. Spratt, Recombination and the nature of bacterial speciation. Science 315, 476–480 (2007). PubMed PMC

K. Zaremba-Niedzwiedzka, J. Viklund, W. Zhao, J. Ast, A. Sczyrba, T. Woyke, K. McMahon, S. Bertilsson, R. Stepanauskas, S. G. E. Andersson, Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade. Genome Biol. 14, R130 (2013). PubMed PMC

M. Vos, X. Didelot, A comparison of homologous recombination rates in bacteria and archaea. ISME J. 3, 199–208 (2009). PubMed

M. L. Bendall, S. L. Stevens, L.-K. Chan, S. Malfatti, P. Schwientek, J. Tremblay, W. Schackwitz, J. Martin, A. Pati, B. Bushnell, J. Froula, D. Kang, S. G. Tringe, S. Bertilsson, M. A. Moran, A. Shade, R. J. Newton, K. D. McMahon, R. R. Malmstrom, Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations. ISME J. 10, 1589–1601 (2016). PubMed PMC

M. Groussin, M. Gouy, Adaptation to environmental temperature is a major determinant of molecular evolutionary rates in Archaea. Mol. Biol. Evol. 28, 2661–2674 (2011). PubMed

R. I. Woolway, C. J. Merchant, Worldwide alteration of lake mixing regimes in response to climate change. Nat. Geosci. 12, 271–276 (2019).

W. Qin, K. R. Heal, R. Ramdasi, J. N. Kobelt, W. Martens-Habbena, A. D. Bertagnolli, S. A. Amin, C. B. Walker, H. Urakawa, M. Könneke, A. H. Devol, J. W. Moffett, E. V. Armbrust, G. J. Jensen, A. E. Ingalls, D. A. Stahl, Nitrosopumilus maritimus gen. nov., sp. nov., Nitrosopumilus cobalaminigenes sp. nov., Nitrosopumilus oxyclinae sp. nov., and Nitrosopumilus ureiphilus sp. nov., four marine ammonia-oxidizing archaea of the phylum Thaumarchaeota. Int. J. Syst. Evol. Microbiol. 67, 5067–5079 (2017). PubMed

T. I. Gossmann, A. Shanmugasundram, S. Börno, L. Duvaux, C. Lemaire, H. Kuhl, S. Klages, L. D. Roberts, S. Schade, J. M. Gostner, F. Hildebrand, J. Vowinckel, C. Bichet, M. Mülleder, E. Calvani, A. Zelezniak, J. L. Griffin, P. Bork, D. Allaine, A. Cohas, J. J. Welch, B. Timmermann, M. Ralser, Ice-age climate adaptations trap the Alpine Marmot in a state of low genetic diversity. Curr. Biol. 29, 1712–1720.e7 (2019). PubMed PMC

N. Lartillot, T. Lepage, S. Blanquart, PhyloBayes 3: A Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics 25, 2286–2288 (2009). PubMed

S.-C. Chen, G.-X. Sun, Y. Yan, K. T. Konstantinidis, S.-Y. Zhang, Y. Deng, X.-M. Li, H.-L. Cui, F. Musat, D. Popp, B. P. Rosen, Y.-G. Zhu, The great oxidation event expanded the genetic repertoire of arsenic metabolism and cycling. Proc. Natl. Acad. Sci. U.S.A. 117, 10414–10421 (2020). PubMed PMC

B. K. Kim, M.-Y. Jung, D. S. Yu, S.-J. Park, T. K. Oh, S.-K. Rhee, J. F. Kim, Genome sequence of an ammonia-oxidizing soil archaeon, “Candidatus Nitrosoarchaeum koreensis” MY1. J. Bacteriol. 193, 5539–5540 (2011). PubMed PMC

B. Bayer, J. Vojvoda, T. Reinthaler, C. Reyes, M. Pinto, G. J. Herndl, Nitrosopumilus adriaticus sp. nov. and Nitrosopumilus piranensis sp. nov., two ammonia-oxidizing archaea from the Adriatic Sea and members of the class Nitrososphaeria. IJSEM 69, 1892–1902 (2019). PubMed

A. E. Santoro, C. L. Dupont, R. A. Richter, M. T. Craig, P. Carini, M. R. McIlvin, Y. Yang, W. D. Orsi, D. M. Moran, M. A. Saito, Genomic and proteomic characterization of “Candidatus Nitrosopelagicus brevis”: An ammonia-oxidizing archaeon from the open ocean. Proc. Natl. Acad. Sci. U.S.A. 112, 1173–1178 (2015). PubMed PMC

D. K. Ngugi, J. Blom, I. Alam, M. Rashid, W. Ba-Alawi, G. Zhang, T. Hikmawan, Y. Guan, A. Antunes, R. Siam, H. E. Dorry, V. Bajic, U. Stingl, Comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the Red Sea. ISME J. 9, 396–411 (2015). PubMed PMC

P. F. Hoffman, D. S. Abbot, Y. Ashkenazy, D. I. Benn, J. J. Brocks, P. A. Cohen, G. M. Cox, J. R. Creveling, Y. Donnadieu, D. H. Erwin, I. J. Fairchild, D. Ferreira, J. C. Goodman, G. P. Halverson, M. F. Jansen, G. L. Hir, G. D. Love, F. A. Macdonald, A. C. Maloof, C. A. Partin, G. Ramstein, B. E. J. Rose, C. V. Rose, P. M. Sadler, E. Tziperman, A. Voigt, S. G. Warren, Snowball Earth climate dynamics and Cryogenian geology-geobiology. Sci. Adv. 3, e1600983 (2017). PubMed PMC

T. W. Lyons, C. T. Reinhard, N. J. Planavsky, The rise of oxygen in Earth’s early ocean and atmosphere. Nature 506, 307–315 (2014). PubMed

I. P. Montañez, C. J. Poulsen, The late paleozoic ice age: An evolving paradigm. Annu. Rev. Earth Planet. Sci. 41, 629–656 (2013).

Z.-Q. Chen, M. J. Benton, The timing and pattern of biotic recovery following the end-Permian mass extinction. Nat. Geosci. 5, 375–383 (2012).

E. Cavaliere, H. M. Baulch, Winter nitrification in ice-covered lakes. PLOS ONE 14, e0224864 (2019). PubMed PMC

T. M. Butler, A.-C. Wilhelm, A. C. Dwyer, P. N. Webb, A. L. Baldwin, S. M. Techtmann, Microbial community dynamics during lake ice freezing. Sci. Rep. 9, 6231 (2019). PubMed PMC

B. Kraft, N. Jehmlich, M. Larsen, L. A. Bristow, M. Könneke, B. Thamdrup, D. E. Canfield, Oxygen and nitrogen production by an ammonia-oxidizing archaeon. Science 375, 97–100 (2022). PubMed

A. Milanese, D. R. Mende, L. Paoli, G. Salazar, H.-J. Ruscheweyh, M. Cuenca, P. Hingamp, R. Alves, P. I. Costea, L. P. Coelho, T. S. B. Schmidt, A. Almeida, A. L. Mitchell, R. D. Finn, J. Huerta-Cepas, P. Bork, G. Zeller, S. Sunagawa, Microbial abundance, activity and population genomic profiling with mOTUs2. Nat. Commun. 10, 1014 (2019). PubMed PMC

C. Callieri, S. Hernández-Avilés, M. M. Salcher, D. Fontaneto, R. Bertoni, Distribution patterns and environmental correlates of Thaumarchaeota abundance in six deep subalpine lakes. Aquat. Sci. 78, 215–225 (2015).

S. N. Merbt, D. A. Stahl, E. O. Casamayor, E. Martí, G. W. Nicol, J. I. Prosser, Differential photoinhibition of bacterial and archaeal ammonia oxidation. FEMS Microbiol. Lett. 327, 41–46 (2012). PubMed

J.-G. Kim, S.-J. Park, J. S. S. Damsté, S. Schouten, W. I. C. Rijpstra, M.-Y. Jung, S.-J. Kim, J.-H. Gwak, H. Hong, O.-J. Si, S. Lee, E. L. Madsen, S.-K. Rhee, Hydrogen peroxide detoxification is a key mechanism for growth of ammonia-oxidizing archaea. Proc. Natl. Acad. Sci. U.S.A. 113, 7888–7893 (2016). PubMed PMC

C. M. Duarte, D. K. Ngugi, I. Alam, J. Pearman, A. Kamau, V. M. Eguiluz, T. Gojobori, S. G. Acinas, J. M. Gasol, V. Bajic, X. Irigoien, Sequencing effort dictates gene discovery in marine microbial metagenomes. Environ. Microbiol. 22, 4589–4603 (2020). PubMed PMC

D. Dudgeon, A. H. Arthington, M. O. Gessner, Z. Kawabata, D. J. Knowler, C. Lévêque, R. J. Naiman, A. Prieur-Richard, D. Soto, M. L. J. Stiassny, C. A. Sullivan, Freshwater biodiversity: Importance, threats, status and conservation challenges. Biol. Rev. 81, 163–182 (2006). PubMed

S. F. Paver, R. J. Newton, M. L. Coleman, Microbial communities of the Laurentian Great Lakes reflect connectivity and local biogeochemistry. Environ. Microbiol. 22, 433–446 (2020). PubMed PMC

P. Q. Tran, S. C. Bachand, P. B. McIntyre, B. M. Kraemer, Y. Vadeboncoeur, I. A. Kimirei, R. Tamatamah, K. D. McMahon, K. Anantharaman, Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika. ISME J. 15, 1971–1986 (2021). PubMed PMC

D. M. Emms, S. Kelly, OrthoFinder: Phylogenetic orthology inference for comparative genomics. Genome Biol. 20, 238 (2019). PubMed PMC

C. L. Dupont, J. Larsson, S. Yooseph, K. Ininbergs, J. Goll, J. Asplund-Samuelsson, J. P. McCrow, N. Celepli, L. Z. Allen, M. Ekman, A. J. Lucas, Å. Hagström, M. Thiagarajan, B. Brindefalk, A. R. Richter, A. F. Andersson, A. Tenney, D. Lundin, A. Tovchigrechko, J. A. A. Nylander, D. Brami, J. H. Badger, A. E. Allen, D. B. Rusch, J. Hoffman, E. Norrby, R. Friedman, J. Pinhassi, J. C. Venter, B. Bergman, Functional tradeoffs underpin salinity-driven divergence in microbial community composition. PLOS ONE 9, e89549 (2014). PubMed PMC

K. Julenius, A. G. Pedersen, Protein evolution is faster outside the cell. Mol. Biol. Evol. 23, 2039–2048 (2006). PubMed

R. Logares, J. Bråte, S. Bertilsson, J. L. Clasen, K. Shalchian-Tabrizi, K. Rengefors, Infrequent marine-freshwater transitions in the microbial world. Trends Microbiol. 17, 414–422 (2009). PubMed

G. Salazar, L. Paoli, A. Alberti, J. Huerta-Cepas, H.-J. Ruscheweyh, M. Cuenca, C. M. Field, L. P. Coelho, C. Cruaud, S. Engelen, A. C. Gregory, K. Labadie, C. Marec, E. Pelletier, M. Royo-Llonch, S. Roux, P. Sánchez, H. Uehara, A. A. Zayed, G. Zeller, M. Carmichael, C. Dimier, J. Ferland, S. Kandels, M. Picheral, S. Pisarev, J. Poulain, T. O. Coordinators, S. G. Acinas, M. Babin, P. Bork, C. Bowler, C. de Vargas, L. Guidi, P. Hingamp, D. Iudicone, L. Karp-Boss, E. Karsenti, H. Ogata, S. Pesant, S. Speich, M. B. Sullivan, P. Wincker, S. Sunagawa, Gene expression changes and community turnover differentially shape the global ocean metatranscriptome. Cell 179, 1068–1083.e21 (2019). PubMed PMC

L. C. Vitorino, L. A. Bessa, Microbial diversity: The gap between the estimated and the known. Diversity 10, 46 (2018).

E. French, J. A. Kozlowski, M. Mukherjee, G. Bullerjahn, A. Bollmann, Ecophysiological characterization of ammonia-oxidizing archaea and bacteria from freshwater. Appl. Environ. Microbiol. 78, 5773–5780 (2012). PubMed PMC

S. Nurk, D. Meleshko, A. Korobeynikov, P. A. Pevzner, metaSPAdes: A new versatile metagenomic assembler. Genome Res. 27, 824–834 (2017). PubMed PMC

D. Li, C.-M. Liu, R. Luo, K. Sadakane, T.-W. Lam, MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31, 1674–1676 (2015). PubMed

D. D. Kang, J. Froula, R. Egan, Z. Wang, MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ 3, e1165 (2015). PubMed PMC

D. H. Parks, M. Imelfort, C. T. Skennerton, P. Hugenholtz, G. W. Tyson, CheckM: Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25, 1043–1055 (2015). PubMed PMC

P.-A. Chaumeil, A. J. Mussig, P. Hugenholtz, D. H. Parks, GTDB-Tk: A toolkit to classify genomes with the genome taxonomy database. Bioinformatics 36, 1925–1927 (2019). PubMed PMC

L.-T. Nguyen, H. A. Schmidt, A. von Haeseler, B. Q. Minh, IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268–274 (2015). PubMed PMC

L. J. Revell, phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol. 3, 217–223 (2012).

R. M. Bowers, N. C. Kyrpides, R. Stepanauskas, M. Harmon-Smith, D. Doud, T. B. K. Reddy, F. Schulz, J. Jarett, A. R. Rivers, E. A. Eloe-Fadrosh, S. G. Tringe, N. N. Ivanova, A. Copeland, A. Clum, E. D. Becraft, R. R. Malmstrom, B. Birren, M. Podar, P. Bork, G. M. Weinstock, G. M. Garrity, J. A. Dodsworth, S. Yooseph, G. Sutton, F. O. Glöckner, J. A. Gilbert, W. C. Nelson, S. J. Hallam, S. P. Jungbluth, T. J. G. Ettema, S. Tighe, K. T. Konstantinidis, W.-T. Liu, B. J. Baker, T. Rattei, J. A. Eisen, B. Hedlund, K. D. McMahon, N. Fierer, G. Cochrane, I. Karsch-Mizrachi, G. W. Tyson, C. Rinke, F. Meyer, R. Knight, R. Finn, A. Lapidus, P. Yilmaz, D. H. Parks, A. M. Eren, L. Schriml, J. F. Banfield, P. Hugenholtz, T. Woyke, Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat. Biotechnol. 35, 725–731 (2017). PubMed PMC

N. Lartillot, N. Rodrigue, D. Stubbs, J. Richer, PhyloBayes MPI: Phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment. Syst. Biol. 62, 611–615 (2013). PubMed

K. Katoh, D. M. Standley, MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013). PubMed PMC

S. Capella-Gutiérrez, J. M. Silla-Martínez, T. Gabaldón, trimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973 (2009). PubMed PMC

Q. Tao, K. Tamura, F. U. Battistuzzi, S. Kumar, A machine learning method for detecting autocorrelation of evolutionary rates in large phylogenies. Mol. Biol. Evol. 36, 811–824 (2019). PubMed PMC

J. M. Wolfe, G. P. Fournier, Horizontal gene transfer constrains the timing of methanogen evolution. Nat. Ecol. Evol. 2, 897–903 (2018). PubMed

C. E. Blank, An expansion of age constraints for microbial clades that lack a conventional fossil record using phylogenomic dating. J. Mol. Evol. 73, 188–208 (2011). PubMed

A. Bekker, H. D. Holland, P.-L. Wang, D. Rumble, H. J. Stein, J. L. Hannah, L. L. Coetzee, N. J. Beukes, Dating the rise of atmospheric oxygen. Nature 427, 117–120 (2004). PubMed

G. Luo, S. Ono, N. J. Beukes, D. T. Wang, S. Xie, R. E. Summons, Rapid oxygenation of Earth’s atmosphere 2.33 billion years ago. Sci. Adv. 2, e1600134 (2016). PubMed PMC

C. E. Blank, Phylogenomic dating—A method of constraining the age of microbial taxa that lack a conventional fossil record. Astrobiology 9, 173–191 (2009). PubMed

A. E. Darling, B. Mau, N. T. Perna, progressiveMauve: Multiple genome alignment with gene gain, loss and rearrangement. PLOS ONE 5, e11147 (2010). PubMed PMC

S. Guindon, J.-F. Dufayard, V. Lefort, M. Anisimova, W. Hordijk, O. Gascuel, New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0. Syst. Biol. 59, 307–321 (2010). PubMed

C. Sjöqvist, L. F. Delgado, J. Alneberg, A. F. Andersson, Ecologically coherent population structure of uncultivated bacterioplankton. ISME J. 15, 3034–3049 (2021). PubMed PMC

D. L. Rabosky, Automatic detection of key innovations, rate shifts, and diversity-dependence on phylogenetic trees. PLOS ONE 9, e89543 (2014). PubMed PMC

D. L. Rabosky, M. Grundler, C. Anderson, P. Title, J. J. Shi, J. W. Brown, H. Huang, J. G. Larson, BAMMtools: An R package for the analysis of evolutionary dynamics on phylogenetic trees. Methods Ecol. Evol. 5, 701–707 (2014).

A.-Ş. Andrei, M. M. Salcher, M. Mehrshad, P. Rychtecký, P. Znachor, R. Ghai, Niche-directed evolution modulates genome architecture in freshwater Planctomycetes. ISME J. 13, 1056–1071 (2019). PubMed PMC

I. Mukherjee, M. M. Salcher, A.-Ş. Andrei, V. S. Kavagutti, T. Shabarova, V. Grujčić, M. Haber, P. Layoun, Y. Hodoki, S.-I. Nakano, K. Šimek, R. Ghai, A freshwater radiation of diplonemids. Environ. Microbiol. 22, 4658–4668 (2020). PubMed

K. Rojas-Jimenez, A. Araya-Lobo, F. Quesada-Perez, J. Akerman-Sanchez, B. Delgado-Duran, L. Ganzert, P. O. Zavialov, S. Alymkulov, G. Kirillin, H.-P. Grossart, Variation of bacterial communities along the vertical gradient in Lake Issyk Kul, Kyrgyzstan. Env. Microbiol. Rep. 13, 337–347 (2021). PubMed

K. Rojas-Jimenez, C. Wurzbacher, E. C. Bourne, A. Chiuchiolo, J. C. Priscu, H.-P. Grossart, Early diverging lineages within Cryptomycota and Chytridiomycota dominate the fungal communities in ice-covered lakes of the McMurdo Dry Valleys, Antarctica. Sci. Rep. 7, 15348 (2017). PubMed PMC

A. M. Bolger, A. M. Bolger, M. Lohse, M. Lohse, B. Usadel, B. Usadel, Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014). PubMed PMC

B. Brian, BBMap: A fast, accurate, splice-aware aligner, in Proceedings of the 9th Annual Genomics of Energy & Environment Meeting (2014);www.osti.gov/biblio/1241166.

S. Andrews, FastQC: A quality control tool for high throughput sequence data (2010);www.bioinformatics.babraham.ac.uk/projects/fastqc.

D. Hyatt, G.-L. Chen, P. F. Locascio, M. L. Land, F. W. Larimer, L. J. Hauser, Prodigal: Prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119 (2010). PubMed PMC

M. Steinegger, J. Söding, Clustering huge protein sequence sets in linear time. Nat. Commun. 9, 2542 (2018). PubMed PMC

S. Sunagawa, D. R. Mende, G. Zeller, F. Izquierdo-Carrasco, S. A. Berger, J. R. Kultima, L. P. Coelho, M. Arumugam, J. Tap, H. B. Nielsen, S. Rasmussen, S. Brunak, O. Pedersen, F. Guarner, W. M. de Vos, J. Wang, J. Li, J. Doré, S. D. Ehrlich, A. Stamatakis, P. Bork, Metagenomic species profiling using universal phylogenetic marker genes. Nat. Methods 10, 1196–1199 (2013). PubMed

T. Kahlke, P. J. Ralph, BASTA—Taxonomic classification of sequences and sequence bins using last common ancestor estimations. Methods Ecol. Evol. 10, 100–103 (2018).

B. Buchfink, C. Xie, D. H. Huson, Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12, 59–60 (2017). PubMed

R. C. Edgar, MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004). PubMed PMC

H. Wickham, ggplot2, Elegant Graphics for Data Analysis (Springer, 2009), vol. 8.

E. Kopylova, L. Noé, H. Touzet, SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics 28, 3211–3217 (2012). PubMed

M. G. Grabherr, B. J. Haas, M. Yassour, J. Z. Levin, D. A. Thompson, I. Amit, X. Adiconis, L. Fan, R. Raychowdhury, Q. Zeng, Z. Chen, E. Mauceli, N. Hacohen, A. Gnirke, N. Rhind, F. D. Palma, B. W. Birren, C. Nusbaum, K. Lindblad-Toh, N. Friedman, A. Regev, Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29, 644–652 (2011). PubMed PMC

M. R. Olm, C. T. Brown, B. Brooks, J. F. Banfield, dRep: A tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J. 11, 2864–2868 (2017). PubMed PMC

M. Richter, R. Rosselló-Móra, Shifting the genomic gold standard for the prokaryotic species definition. Proc. Natl. Acad. Sci. U.S.A. 106, 19126–19131 (2009). PubMed PMC

T. Seemann, Prokka: Rapid prokaryotic genome annotation. Bioinformatics 30, 2068–2069 (2014). PubMed

B. Contreras-Moreira, P. Vinuesa, GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis. Appl. Environ. Microbiol. 79, 7696–7701 (2013). PubMed PMC

F. Boyer, C. Mercier, A. Bonin, Y. L. Bras, P. Taberlet, E. Coissac, obitools: A unix-inspired software package for DNA metabarcoding. Mol. Ecol. Resour. 16, 176–182 (2016). PubMed

J. Huerta-Cepas, D. Szklarczyk, K. Forslund, H. Cook, D. Heller, M. C. Walter, T. Rattei, D. R. Mende, S. Sunagawa, M. Kuhn, L. J. Jensen, C. von Mering, P. Bork, eggNOG 4.5: A hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res. 44, D286–D293 (2016). PubMed PMC

M. L. Borowiec, AMAS: A fast tool for alignment manipulation and computing of summary statistics. PeerJ 4, e1660 (2016). PubMed PMC

J. T. Osvatic, L. G. E. Wilkins, L. Leibrecht, M. Leray, S. Zauner, J. Polzin, Y. Camacho, O. Gros, J. A. van Gils, J. A. Eisen, J. M. Petersen, B. Yuen, Global biogeography of chemosynthetic symbionts reveals both localized and globally distributed symbiont groups. Proc. Natl. Acad. Sci. U.S.A. 118, e2104378118 (2021). PubMed PMC

A. Crits-Christoph, M. R. Olm, S. Diamond, K. Bouma-Gregson, J. F. Banfield, Soil bacterial populations are shaped by recombination and gene-specific selection across a grassland meadow. ISME J 14, 1834–1846 (2020). PubMed PMC

Z. Chen, X. Wang, Y. Song, Q. Zeng, Y. Zhang, H. Luo, Prochlorococcus have low global mutation rate and small effective population size. Nat. Ecol. Evol. 6, 183–194 (2022). PubMed

C. Gawad, W. Koh, S. R. Quake, Single-cell genome sequencing: Current state of the science. Nat. Rev. Microbiol. 17, 175–188 (2016). PubMed

M. L. Reno, N. L. Held, C. J. Fields, P. V. Burke, R. J. Whitaker, Biogeography of the Sulfolobus islandicus pan-genome. Proc. Natl. Acad. Sci. U.S.A. 106, 8605–8610 (2009). PubMed PMC

N. J. Croucher, A. J. Page, T. R. Connor, A. J. Delaney, J. A. Keane, S. D. Bentley, J. Parkhill, S. R. Harris, Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. Nucleic Acids Res. 43, e15 (2015). PubMed PMC

M. Lynch, Evolution of the mutation rate. Trends Genet. 26, 345–352 (2010). PubMed PMC

J. W. Drake, Avoiding dangerous missense: Thermophiles display especially low mutation rates. PLOS Genet. 5, e1000520 (2009). PubMed PMC

G. E. A. Swann, V. N. Panizzo, S. Piccolroaz, V. Pashley, M. S. A. Horstwood, S. Roberts, E. Vologina, N. Piotrowska, M. Sturm, A. Zhdanov, N. Granin, C. Norman, S. McGowan, A. W. Mackay, Changing nutrient cycling in Lake Baikal, the world’s oldest lake. Proc. Natl. Acad. Sci. U.S.A. 117, 27211–27217 (2020). PubMed PMC

J. Quehenberger, L. Shen, S.-V. Albers, B. Siebers, O. Spadiut, Sulfolobus—A potential key organism in future biotechnology. Front. Microbiol. 8, 2474 (2017). PubMed PMC

A.-M. Waldvogel, M. Pfenninger, Temperature dependence of spontaneous mutation rates. Genome Res. 31, 1582–1589 (2021). PubMed PMC

R. F. Weiss, E. C. C. Carmack, V. M. Koropalov, Deep-water renewal and biological production in Lake Baikal. Nature 349, 665–669 (1991).

C. H. Wellman, P. L. Osterloff, U. Mohiuddin, Fragments of the earliest land plants. Nature 425, 282–285 (2003). PubMed

Freshwater genome-reduced bacteria exhibit pervasive episodes of adaptive stasis