Harvested aquatic microbes from a controlled environment

In a groundbreaking study, an international team of researchers has successfully cultivated 627 isolates from 72 genera of slow-growing oligotrophic microorganisms, largely unexplored until now. This collection, published in Nature Communications under the title "Bringing the uncultivated microbial majority of freshwater ecosystems into culture", offers a foundational resource for researchers investigating various aspects of freshwater ecosystems.

The researchers analysed over 460 publicly available freshwater metagenomes from six continents and confirmed that many of these taxa are globally distributed. The new strain collection includes strains from 15 of the 30 most common freshwater bacterial genera, accounting for up to 72% (on average 40%) of the genera detected in environmental samples.

The collection includes previously uncultivated taxa from classical freshwater phyla, such as Actinomycetota, Pseudomonadota, Verrucomicrobiota, Bacteroidota, and Armatimonadota. Among the cultivated strains are representatives of the freshwater SAR11 genus Fontibacterium, the methylotrophic Methylopumilus, and freshwater specialists like Planktophila.

Small genome sizes leading to energy savings and reduced metabolic flexibility are often found in common taxa like Fontibacterium and Planktophila, adapted to nutrient-poor environments. Some strains in the collection appear capable of providing crucial vitamins like cobalamin (vitamin B12) to the surrounding freshwater community.

The team, led by Thomas R. Neu from the Helmholtz Centre for Environmental Research (UFZ), used a high-throughput dilution approach with specially designed media that mimic natural lake water and support the growth of oligotrophs. The research involved an international team of researchers from multiple institutions.

Whole-genome sequencing of 87 of the cultivated strains revealed two new families, nine new genera, and 41 new species. The new cultures provide access to model organisms that are abundant in nature but rarely cultivated in the lab, enabling controlled experiments to answer fundamental ecological and evolutionary questions.

Strains in the collection utilise proton-pumping rhodopsins or aerobic anoxygenic photosynthesis to harvest light energy. The new strain collection and genomes are publicly accessible, serving as a valuable resource for researchers investigating carbon and nutrient cycling, water quality, ecosystem resilience, and more.

Metagenomic sequencing of the same lake samples showed that the cultivated strains largely match the genomes assembled from metagenomes (MAGs), validating the relevance of the cultures for natural microbial communities. The publication's DOI is 10.1038/s41467-025-63266-9.

The research includes the first free-living freshwater representative of the Armatimonadota. The new cultures cover a wide range of ecological functions, including sulfur and nitrogen metabolism, vitamin biosynthesis, and carbohydrate degradation. This breakthrough in cultivating slow-growing oligotrophic microorganisms promises to open new avenues for understanding the intricate workings of freshwater ecosystems.