Scientists on a global hunt discover endemicity in freshwater bacteria

SAR11 (Pelagibacterales) are the most abundant microbes on Earth, dominating marine ecosystems and serving as model system for genome-streamlined oligotrophs (low-nutrient-adapted). The freshwater SAR11-IIIb genus Fontibacterium is among the most common bacterial genera in lakes worldwide, yet its biology has remained poorly understood due to cultivation challenges. Like their marine relatives, Fontibacterium have small, streamlined genomes and are well adapted to life in low-nutrient (oligotrophic) conditions. “These bacteria are small, slow-growing, and require specific low-nutrient conditions, which makes them very difficult to cultivate. It is therefore not surprising that, until now, only one strain has been isolated and it took us several years to get stable cultures” explains Michaela Salcher, head of the Laboratory of Microbial Cultivation and Ecogenomics at the Biology Centre CAS and senior author of the study.

Her team used high-throughput dilution-to-extinction techniques and defined media that closely mimic natural lake chemistry and succeeded in isolating seven strains belonging to two new Fontibacterium species (F. abundans and F. medardense, the latter named after Lake Medard in northern Czechia). “These newly cultured strains provide rare opportunities for experimental work on freshwater oligotrophs, microbes that are often abundant in nature but severely underrepresented in laboratory studies and culture collections” adds Clafy Fernandes, a PhD student at the University of South Bohemia and first author of the study. Genomic analyses and growth assays with the axenic strains revealed metabolic adaptations such as sulfur metabolism pathways and temperature preferences, helping to explain how these bacteria thrive in different lake environments.

Global sampling: Lake Samsonvale (Australia), Laguna Negra (Uruguay), Lake Wabby (Australia), Lake Inawashiro (Japan), Lake Malawi, field lab in Japan. Photos: Michaela Salcher, Jan Svatoš.

The team also conducted a global sampling campaign, collecting water from freshwater and brackish lakes across Europe, Asia, Australia, South America, and Africa - most notably the African Great Lakes. Special focus was given to under-sampled regions in the Southern Hemisphere. By combining short- and long-read DNA sequencing, the researchers recovered numerous high-quality metagenome-assembled genomes (MAGs), many representing previously unknown species.

Lake Malawi, one of the Great African Lakes with endemic Fontibacterium species. Photo: Michaela Salcher.

Phylogenomic analysis revealed clear biogeographic patterns. Some Fontibacterium species appear to be globally distributed, while others are restricted to specific regions or even single lakes. This includes endemic lineages found only in the African Great Lakes and quasi-endemic taxa restricted to either the Northern or Southern Hemisphere. “These findings suggest that although Fontibacterium is broadly adapted to freshwater environments, local environmental conditions play an important role in shaping the global distribution of different Fontibacterium species” explains Clafy Fernandes.

This study not only opens the door for using Fontibacterium as a model organism in freshwater microbial ecology, but also offers a valuable resource for studying the evolution of oligotrophic bacteria more broadly.

Reference:

Fernandes, C., M. Haber, P. Layoun, M.-C. Chiriac, P.-A. Bulzu, R. Ghai, V. Kasalický, T. Shabarova, H.-P. Grossart, J. Woodhouse, K. Piwosz, C. Alonso, J. Zanetti, D. P. Hamilton, M. Ngochera, S.-i. Nakano, Y. Okazaki and M. M. Salcher (2025). Ecophysiology and global dispersal of the freshwater SAR11-IIIb genus Fontibacterium. Nature Microbiology. doi: 10.1038/s41564-025-02091-8. https://www.nature.com/articles/s41564-025-02091-8

Behind the paper blog article: https://go.nature.com/4lgEJie

Contact: Michaela Salcher, michaelasalcher@gmail.com