The SAR11-IIIb genus Fontibacterium within the order 'Ca. Pelagibacterales' is recognized for its ubiquitous presence in freshwater environments. However, cultivation limitations have hampered deeper ecophysiological understanding of this genus, with most data limited to lakes in the Northern Hemisphere. Here we present seven isolates representing two previously undescribed species, along with 93 high-quality metagenome-assembled genomes (MAGs) derived from a global survey across five continents. Phylogenomic analysis revealed 16 species forming nine distinct biogeographic clusters, indicating speciation patterns linked to water temperature and latitude. We observed endemic species restricted to African lakes, and quasi-endemic species confined to the Northern or Southern Hemisphere, which co-exist alongside cosmopolitan species. Metabolic profiling and growth experiments uncovered species- and strain-specific adaptations for nutrient uptake, along with unique pathways for sulfur metabolism. These findings provide a global-scale genomic and ecological overview for this underexplored lineage of freshwater SAR11.

Australian Rivers Institute Griffith University Queensland Australia

Center for Ecological Research Kyoto University Kyoto Japan

Centro Universitario de la Región Este Universidad de la República Rocha Uruguay

Department of Fisheries Lilongwe Malawi

Department of Fisheries Oceanography and Marine Ecology National Marine Fisheries Research Institute Gdynia Poland

Faculty of Science University of South Bohemia Ceske Budejovice Czech Republic

Institute for Chemical Research Kyoto University Kyoto Japan

Institute of Biochemistry and Biology Potsdam University Potsdam Germany

Institute of Hydrobiology Biology Centre CAS Ceske Budejovice Czech Republic

Leibniz Institute of Freshwater Ecology and Inland Fisheries Stechlin Germany

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Giovannoni, S. J. SAR11 bacteria: the most abundant plankton in the oceans. Annu. Rev. Mar. Sci. 9, 231–255 (2017). DOI

Henson, M. W., Lanclos, V. C., Faircloth, B. C. & Thrash, J. C. Cultivation and genomics of the first freshwater SAR11 (LD12) isolate. ISME J. 12, 1846–1860 (2018). PubMed DOI PMC

Salcher, M. M., Pernthaler, J. & Posch, T. Seasonal bloom dynamics and ecophysiology of the freshwater sister clade of SAR11 bacteria ‘that rule the waves’ (LD12). ISME J. 5, 1242–1252 (2011). PubMed DOI PMC

Giovannoni, S. J., Cameron Thrash, J. & Temperton, B. Implications of streamlining theory for microbial ecology. ISME J. 8, 1553–1565 (2014). PubMed DOI PMC

Haro-Moreno, J. M. et al. Ecogenomics of the SAR11 clade. Environ. Microbiol. 22, 1748–1763 (2020). PubMed DOI

Grote, J. et al. Streamlining and core genome conservation among highly divergent members of the SAR11 clade. mBio 3, e00252-12 (2012). PubMed DOI PMC

López-Pérez, M., Haro-Moreno, J. M., Coutinho, F. H., Martinez-Garcia, M. & Rodriguez-Valera, F. The evolutionary success of the marine bacterium SAR11 analyzed through a metagenomic perspective. mSystems 5, e00605–e00620 (2020). PubMed DOI PMC

Chiriac, M.-C., Haber, M. & Salcher, M. M. Adaptive genetic traits in pelagic freshwater microbes. Environ. Microbiol. 25, 606–641 (2023). PubMed DOI

Tsementzi, D. et al. Ecogenomic characterization of widespread, closely-related SAR11 clades of the freshwater genus ‘Candidatus Fonsibacter’ and proposal of Ca. Fonsibacter lacus sp. nov. Syst. Appl. Microbiol. 42, 495–505 (2019). PubMed DOI

Morris, J. J., Lenski, R. E. & Zinser, E. R. The Black Queen Hypothesis: evolution of dependencies through adaptive gene loss. mBio 3, e00036-12 (2012). PubMed DOI PMC

Carini, P. et al. Discovery of a SAR11 growth requirement for thiamin’s pyrimidine precursor and its distribution in the Sargasso Sea. ISME J. 8, 1727–1738 (2014). PubMed DOI PMC

Tripp, H. J. et al. SAR11 marine bacteria require exogenous reduced sulphur for growth. Nature 452, 741–744 (2008). PubMed DOI

Zaremba-Niedzwiedzka, K. et al. Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade. Genome Biol. 14, R130 (2013). PubMed DOI PMC

Rodriguez-Valera, F., Martin-Cuadrado, A.-B. & López-Pérez, M. Flexible genomic islands as drivers of genome evolution. Curr. Opin. Microbiol. 31, 154–160 (2016). PubMed DOI

Rodriguez-Valera, F. et al. Explaining microbial population genomics through phage predation. Nat. Rev. Microbiol. 7, 828–836 (2009). PubMed DOI

Okazaki, Y. et al. Microdiversity and phylogeographic diversification of bacterioplankton in pelagic freshwater systems revealed through long-read amplicon sequencing. Microbiome 9, 24 (2021). PubMed DOI PMC

Brown, M. V. et al. Global biogeography of SAR11 marine bacteria. Mol. Syst. Biol. 8, 595 (2012).

Delmont, T. O. et al. Single-amino acid variants reveal evolutionary processes that shape the biogeography of a global SAR11 subclade. eLife 8, e46497 (2019). PubMed DOI PMC

Louca, S. The rates of global bacterial and archaeal dispersal. ISME J. 16, 159–167 (2021). PubMed DOI PMC

Garcia, S. L. et al. Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations. ISME J. 12, 742–755 (2018). PubMed DOI

Neuenschwander, S. M., Ghai, R., Pernthaler, J. & Salcher, M. M. Microdiversification in genome-streamlined ubiquitous freshwater Actinobacteria. ISME J. 12, 185–198 (2018). PubMed DOI

Newton, R. J., Jones, S. E., Eiler, A., McMahon, K. D. & Bertilsson, S. A guide to the natural history of freshwater lake bacteria. Microbiol. Mol. Biol. Rev. 75, 14–49 (2011). PubMed DOI PMC

Salcher, M. M., Schaefle, D., Kaspar, M., Neuenschwander, S. M. & Ghai, R. Evolution in action: habitat transition from sediment to the pelagial leads to genome streamlining in Methylophilaceae. ISME J. 13, 2764–2777 (2019). PubMed DOI PMC

Hoetzinger, M., Pitt, A., Huemer, A. & Hahn, M. W. Continental-scale gene flow prevents allopatric divergence of pelagic freshwater bacteria. Genome Biol. Evol. 13, evab019 (2021). PubMed DOI PMC

Mehrshad, M. et al. Hidden in plain sight—highly abundant and diverse planktonic freshwater Chloroflexi. Microbiome 6, 176 (2018). PubMed DOI PMC

Hoetzinger, M. et al. Geographic population structure and distinct intra-population dynamics of globally abundant freshwater bacteria. ISME J. https://doi.org/10.1093/ismejo/wrae113 (2024).

Buck, M. et al. Comprehensive dataset of shotgun metagenomes from oxygen stratified freshwater lakes and ponds. Sci. Data 8, 131 (2021). PubMed DOI PMC

Garner, R. E. et al. A genome catalogue of lake bacterial diversity and its drivers at continental scale. Nat. Microbiol. https://doi.org/10.1038/s41564-023-01435-6 (2023).

Hedlund, B. P. et al. SeqCode: a nomenclatural code for prokaryotes described from sequence data. Nat. Microbiol. 7, 1702–1708 (2022). PubMed PMC

Cabello-Yeves, P. J. et al. Genomes of novel microbial lineages assembled from the sub-ice waters of Lake Baikal. Appl. Environ. Microbiol. 84, e02132-17 (2018). PubMed DOI

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

Zhao, J. et al. Promiscuous and genome-wide recombination underlies the sequence-discrete species of the SAR11 lineage in the deep ocean. ISME J. https://doi.org/10.1093/ismejo/wraf072 (2025).

Salcher, M. M. et al. Bringing the uncultivated microbial majority of freshwater ecosystems into culture. Nat. Commun. (in the press).

Tran, P. Q. et al. Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika. ISME J. 15, 1971–1986 (2021). PubMed DOI PMC

Okazaki, Y., Nakano, S.-i, Toyoda, A. & Tamaki, H. Long-read-resolved, ecosystem-wide exploration of nucleotide and structural microdiversity of lake bacterioplankton genomes. mSystems 7, e00433-22 (2022). PubMed DOI PMC

Layoun, P. et al. Flexible genomic island conservation across freshwater and marine Methylophilaceae. ISME J. 18, wrad036 (2024). PubMed DOI PMC

Linz, A. M. et al. Freshwater carbon and nutrient cycles revealed through reconstructed population genomes. PeerJ 6, e6075 (2018). PubMed DOI PMC

Heinrich, F., Eiler, A. & Bertilsson, S. Seasonality and environmental control of freshwater SAR11 (LD12) in a temperate lake (Lake Erken, Sweden). Aquat. Microb. Ecol. 70, 33–44 (2013). DOI

Carlson, C. A. et al. Seasonal dynamics of SAR11 populations in the euphotic and mesopelagic zones of the northwestern Sargasso Sea. ISME J. 3, 283–295 (2008). PubMed DOI

Eiler, A., Hayakawa, D. H., Church, M. J., Karl, D. M. & Rappé, M. S. Dynamics of the SAR11 bacterioplankton lineage in relation to environmental conditions in the oligotrophic North Pacific subtropical gyre. Environ. Microbiol. 11, 2291–2300 (2009). PubMed DOI

Vergin, K. L. et al. High-resolution SAR11 ecotype dynamics at the Bermuda Atlantic Time-series Study site by phylogenetic placement of pyrosequences. ISME J. 7, 1322–1332 (2013). PubMed DOI PMC

Rappé, M. S., Connon, S. A., Vergin, K. L. & Giovannoni, S. J. Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418, 630–633 (2002). PubMed DOI

Tripp, H. J. The unique metabolism of SAR11 aquatic bacteria. J. Microbiol. 51, 147–153 (2013). PubMed DOI

Molina-Pardines, C., Haro-Moreno, J. M., Rodriguez-Valera, F. & López-Pérez, M. Extensive paralogism in the environmental pangenome: a key factor in the ecological success of natural SAR11 populations. Microbiome 13, 41 (2025). PubMed DOI PMC

Borisov, V. B., Gennis, R. B., Hemp, J. & Verkhovsky, M. I. The cytochrome bd respiratory oxygen reductases. Biochim. Biophys. Acta 1807, 1398–1413 (2011). PubMed DOI PMC

Tanaka, Y. et al. Crystal structure of a YeeE/YedE family protein engaged in thiosulfate uptake. Sci. Adv. 6, eaba7637 (2020). PubMed DOI PMC

Liu, Y.-K., Kuo, H.-C., Lai, C.-H. & Chou, C.-C. Single amino acid utilization for bacterial categorization. Sci. Rep. 10, 12686 (2020). PubMed DOI PMC

Kim, S., Kang, I., Seo, J.-H. & Cho, J.-C. Culturing the ubiquitous freshwater actinobacterial acI lineage by supplying a biochemical ‘helper’ catalase. ISME J. 13, 2252–2263 (2019). PubMed DOI PMC

Ruiz-Perez, C. A. et al. Description of Candidatus Mesopelagibacter carboxydoxydans and Candidatus Anoxipelagibacter denitrificans: nitrate-reducing SAR11 genera that dominate mesopelagic and anoxic marine zones. Syst. Appl. Microbiol. 44, 126185 (2021). PubMed DOI

Tsementzi, D. et al. SAR11 bacteria linked to ocean anoxia and nitrogen loss. Nature 536, 179–183 (2016). PubMed DOI PMC

Moore, L. R., Post, A. F., Rocap, G. & Chisholm, S. W. Utilization of different nitrogen sources by the marine cyanobacteria Prochlorococcus and Synechococcus. Limnol. Oceanogr. 47, 989–996 (2002). DOI

Wiedenbeck, J. & Cohan, F. M. Origins of bacterial diversity through horizontal genetic transfer and adaptation to new ecological niches. FEMS Microbiol. Rev. 35, 957–976 (2011). PubMed DOI

Arnold, B. J., Huang, I. T. & Hanage, W. P. Horizontal gene transfer and adaptive evolution in bacteria. Nat. Rev. Microbiol. 20, 206–218 (2022). PubMed DOI

Beier, S. et al. The transcriptional regulation of the glyoxylate cycle in SAR11 in response to iron fertilization in the Southern Ocean. Environ. Microbiol. Rep. 7, 427–434 (2015). PubMed DOI

Vrede, T. & Tranvik, L. J. Iron constraints on planktonic primary production in oligotrophic lakes. Ecosystems 9, 1094–1105 (2006). DOI

Swan, B. K. et al. Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean. Proc. Natl Acad. Sci. USA 110, 11463–11468 (2013). PubMed DOI PMC

Herbold, C. W., Lee, C. K., McDonald, I. R. & Cary, S. C. Evidence of global-scale aeolian dispersal and endemism in isolated geothermal microbial communities of Antarctica. Nat. Commun. 5, 3875 (2014). PubMed DOI

Schultze, M. et al. Localization of cytochrome b6f complexes implies an incomplete respiratory chain in cytoplasmic membranes of the cyanobacterium Synechocystis sp. PCC 6803. Biochim. Biophys. Acta 1787, 1479–1485 (2009). PubMed DOI

Kozhov, M. Biology of Lake Baikal (Publishing House of the USSR Acad. Sci., 1962).

Salzburger, W., Van Bocxlaer, B. & Cohen, A. S. Ecology and evolution of the African Great Lakes and their faunas. Annu. Rev. Ecol. Syst. 45, 519–545 (2014). DOI

Cabello-Yeves, P. J. et al. Microbiome of the deep Lake Baikal, a unique oxic bathypelagic habitat. Limnol. Oceanogr. 65, 1471–1488 (2020). DOI

De Meester, L., Gómez, A., Okamura, B. & Schwenk, K. The Monopolization Hypothesis and the dispersal–gene flow paradox in aquatic organisms. Acta Oecol. 23, 121–135 (2002). DOI

Jezbera, J., Jezberová, J., Brandt, U. & Hahn, M. W. Ubiquity of Polynucleobacter necessarius subspecies asymbioticus results from ecological diversification. Environ. Microbiol. 13, 922–931 (2011). PubMed DOI PMC

Baas-Becking, L. G. M. Geobiologie of Inleiding tot de Milieukunde (WP Van Stockum & Zoon NV, 1934).

Chiriac, M.-C. et al. Ecogenomics sheds light on diverse lifestyle strategies in freshwater CPR. Microbiome 10, 84 (2022). PubMed DOI PMC

Šimek, K. et al. A finely tuned symphony of factors modulates the microbial food web of a freshwater reservoir in spring. Limnol. Oceanogr. 59, 1477–1492 (2014). DOI

Zotina, T., Köster, O. & Jüttner, F. Photoheterotrophy and light-dependent uptake of organic and organic nitrogenous compounds by Planktothrix rubescens under low irradiance. Freshw. Biol. 48, 1859–1872 (2003). DOI

Salcher, M. M., Neuenschwander, S. M., Posch, T. & Pernthaler, J. The ecology of pelagic freshwater methylotrophs assessed by a high-resolution monitoring and isolation campaign. ISME J. 9, 2442–2453 (2015). PubMed DOI PMC

Li, H. Fast construction of FM-index for long sequence reads. Bioinformatics 30, 3274–3275 (2014). PubMed DOI PMC

Bonenfant, Q., Noé, L. & Touzet, H. Porechop_ABI: discovering unknown adapters in Oxford Nanopore Technology sequencing reads for downstream trimming. Bioinform. Adv. 3, vbac085 (2022). PubMed DOI PMC

Mak, Q. X. C., Wick, R. R., Holt, J. M. & Wang, J. R. Polishing de novo Nanopore assemblies of bacteria and eukaryotes with FMLRC2. Mol. Biol. Evol. 40, msad048 (2023). PubMed DOI PMC

Kolmogorov, M. et al. metaFlye: scalable long-read metagenome assembly using repeat graphs. Nat. Methods 17, 1103–1110 (2020). PubMed DOI PMC

Sieber, C. M. K. et al. Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy. Nat. Microbiol. 3, 836–843 (2018). PubMed DOI PMC

Chaumeil, P.-A., Mussig, A. J., Hugenholtz, P. & Parks, D. H. GTDB-Tk v2: memory friendly classification with the genome taxonomy database. Bioinformatics 38, 5315–5316 (2022). PubMed DOI PMC

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

Chklovski, A., Parks, D. H., Woodcroft, B. J. & Tyson, G. W. CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Nat. Methods 20, 1203–1212 (2023). PubMed DOI

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

Lowe, T. M. & Eddy, S. R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955–964 (1997). PubMed DOI PMC

Eddy, S. R. Accelerated profile HMM searches. PLoS Comput. Biol. 7, e1002195 (2011). PubMed DOI PMC

Jones, P. et al. InterProScan 5: genome-scale protein function classification. Bioinformatics 30, 1236–1240 (2014). PubMed DOI PMC

Tatusov, R. L. et al. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 29, 22–28 (2001). PubMed DOI PMC

Haft, D. H. et al. TIGRFAMs: a protein family resource for the functional identification of proteins. Nucleic Acids Res. 29, 41–43 (2001). PubMed DOI PMC

Kanehisa, M., Furumichi, M., Sato, Y., Matsuura, Y. & Ishiguro-Watanabe, M. KEGG: biological systems database as a model of the real world. Nucleic Acids Res. 53, D672–D677 (2024). DOI PMC

Löytynoja, A. in Multiple Sequence Alignment: Methods and Protocols (ed Katoh, K.) 17–37 (Springer, 2021).

Minh, B. Q. et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37, 1530–1534 (2020). PubMed DOI PMC

Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K. F., von Haeseler, A. & Jermiin, L. S. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat. Methods 14, 587–589 (2017). PubMed DOI PMC

Getz, E. W. et al. The AEGEAN-169 clade of bacterioplankton is synonymous with SAR11 subclade V (HIMB59) and metabolically distinct. mSystems 8, e00179-23 (2023). PubMed DOI PMC

Goris, J. et al. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int. J. Syst. Evol. Microbiol. 57, 81–91 (2007). PubMed DOI

Palmer, M., Steenkamp, E. T., Blom, J., Hedlund, B. P. & Venter, S. N. All ANIs are not created equal: implications for prokaryotic species boundaries and integration of ANIs into polyphasic taxonomy. Int. J. Syst. Evol. Microbiol. 70, 2937–2948 (2020). PubMed DOI

Olm, M. R., Brown, C. T., Brooks, B. & Banfield, J. F. 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 DOI PMC

Rissman, A. I. et al. Reordering contigs of draft genomes using the Mauve Aligner. Bioinformatics 25, 2071–2073 (2009). PubMed DOI PMC

Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119 (2010). PubMed DOI PMC

Steinegger, M. & Söding, J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat. Biotechnol. 35, 1026–1028 (2017). PubMed DOI

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

Kavagutti, V. S., Andrei, A.-Ş., Mehrshad, M., Salcher, M. M. & Ghai, R. Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics. Microbiome 7, 135 (2019). PubMed DOI PMC

Kavagutti, V. S. et al. High-resolution metagenomic reconstruction of the freshwater spring bloom. Microbiome 11, 15 (2023). PubMed DOI PMC

Cheng, C. & Thrash, J. C. sparse-growth-curve: a computational pipeline for parsing cellular growth curves with low temporal resolution. Microbiol. Resour. Announc. 10, e00296-21 (2021). PubMed DOI PMC

Giorgi, F. M., Ceraolo, C. & Mercatelli, D. The R language: an engine for bioinformatics and data science. Life 12, 648 (2022). PubMed DOI PMC

Oksanen, J. et al. Community ecology package. R package Version 2 (2013).

Maechler, M. Cluster: cluster analysis basics and extensions. R package version 2.0 (2018).

Kruskal, W. H. & Wallis, W. A. Use of ranks in one-criterion variance analysis. J. Am. Stat. Assoc. 47, 583–621 (1952). DOI

Revelle, W. psych: Procedures for Personality and Psychological Research. R package version 1.5.1 (2015).

Wickham, H. ggplot2. WIREs Comput. Stat. 3, 180–185 (2011). DOI

Gu, Z. Complex heatmap visualization. Imeta 1, e43 (2022). PubMed DOI PMC

Bringing the uncultivated microbial majority of freshwater ecosystems into culture