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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