Ecophysiology and global dispersal of the freshwater SAR11-IIIb clade

The freshwater SAR11-IIIb genus Allofontibacter (initially described as ‘Ca. Fonsibacter’ ) within the order Pelagibacterales is recognised for its ubiquitous presence in freshwater environments. However, it remains poorly understood due to cultivation limitations, with only one cultured genome published to data. As a result, its genetic diversity, metabolic capabilities and ecological roles remain largely unexplored, with most available data limited to lakes in the Northern Hemisphere. Here, we present seven new isolates representing two novel 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. Notably, we observed phylogeographic partitioning, including endemic species restricted to African lakes, quasi-endemic species confined to either the Northern or Southern Hemisphere, and the co-existence of cosmopolitan species alongside regionally constrained lineages. Furthermore, metabolic profiling and growth experiments uncovered species- and strain-specific adaptations for nutrient uptake, along with unique pathways for sulfur metabolism. These findings provide the first global-scale genomic and ecological overview for this lineage, raising key questions about dispersal barriers, priority effects, evolutionary trajectories, and mechanisms of niche adaptation in freshwater SAR11.