In an era of accelerating ocean warming, understanding the drivers of microbial community composition is more urgent than ever. Long-term time-series studies are particularly powerful for this purpose. However, most previous work remains confined to the Northern Hemisphere and focuses solely on taxonomy, leaving the Southern Hemisphere underrepresented and microorganisms’ functional dimensions underexplored. Moreover, phenomena such as current-driven community shifts and microbial vulnerability to warming remain poorly understood. Here, we address these gaps by analyzing microbial communities over two years at the South Atlantic Microbial Observatory (SAMO), located off the coast of Uruguay within a Marine Protected Area. SAMO, situated under the contrasting influences of the Brazil and Malvinas currents and recognized as a global-warming hotspot, provides an ideal setting to study the temporal dynamics of marine microbial communities. Using shotgun metagenomics and 16S rRNA amplicon sequencing, we revealed strong seasonal shifts driven by environmental variability and the influence of these two ocean currents, resulting in two community states (summer–autumn vs winter–spring). These states exhibited contrasting composition, diversity, and assembly mechanisms. Further, our results show that taxonomic and functional diversity trends diverge between these periods. Crucially, our work suggests that the predicted tropicalization of Uruguay’s coast is likely to boost taxonomic richness but erode functional repertoires, while also increasing vulnerability to ocean warming, potentially undermining biogeochemical functioning.

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.