Microorganisms thrive in complex communities shaped by intricate interactions, yet the extent and ecological implications of biosynthetic dependencies in natural communities remain underexplored. Here, we used a dilution approach to cultivate 204 microbial model communities from the Baltic Sea and recovered 527 metagenome-assembled genomes (MAGs) that dereplicated into 72 species-clusters (>95% average nucleotide identity, ANI). Of these species, at least 70% represent previously uncultivated lineages. Combined with 1073 MAGs from Baltic Sea metagenomes, we generated a genomic catalog of 701 species-clusters. Our results show that cultures with more than three species included microorganisms with smaller genome sizes, lower biosynthetic potential for amino acids and B vitamins, and higher prevalence and abundance in the environment. Moreover, the taxa found together in the same model communities had complementary biosynthetic gene repertoires. Our results demonstrate that cultivating bacteria in dilution model communities facilitates access to previously uncultivated but abundant species that likely depend on metabolic partners for survival. Together, our findings highlight the value of community-based cultivation for unraveling ecological strategies. Finally, we confirm that metabolic interdependencies and genome streamlining are widespread features of successful environmental microorganisms.

Vitamin B₁₂ (B₁₂) is an essential cofactor for vital metabolic processes in both prokaryotes and eukaryotes. De novo B₁₂ biosynthesis is exclusively carried out by a modicum of prokaryotes, although being required by most organisms. Recently, it has been demonstrated that not all B₁₂-prototrophic bacteria voluntarily share this vital cofactor and, therefore, are termed B₁₂-retainers. Consequently, low biosynthesis potential and limited voluntary release lead to a large discrepancy between availability and demand for B₁₂ in the ocean, indicating that release of B₁₂ may be an important control. Hence, in this study, we examined a specific release process, cell lysis after phage infection. We isolated bacteriophages specific for the B₁₂-prototrophic, yet B₁₂-retainer bacterium Sulfitobacter sp. M39. The addition of the bacteriophages to a Sulfitobacter sp. M39 mono-culture led to a significant increase in virus-like particles, reduced bacterial growth, and quantifiable extracellular dissolved B₁₂. When introducing bacteriophages to a co-culture comprising the host bacterium and the B₁₂-auxotrophic diatom Thalassiosira pseudonana, we observed rapid response in the form of microalgal growth. Our results indicate that B₁₂ is released as a result of bacteriophage-mediated cell lysis of Sulfitobacter sp. M39, enabling the growth of T. pseudonana in co-culture and possibly other microbes in nature. Therefore, we propose that bacteriophage-mediated cell lysis is a key mechanism for the release of essential metabolites, including vitamins, and given the estimated bacteriophage infection rates in the ocean, it plays a crucial role in the B-vitamin cycle in the marine environment.

Genome size is known to reflect the eco-evolutionary history of prokaryotic species, including their lifestyle, environmental preferences, and habitat breadth. However, it remains uncertain how strongly genome size is linked to prokaryotic prevalence, relative abundance and co-occurrence. To address this gap, we present a systematic and global-scale evaluation of the relationship between genome size, relative abundance and prevalence in freshwater ecosystems. Our study includes 80,561 medium-to-high quality genomes, from which we identified 9,028 species (ANI > 95%) present in a manually curated dataset of 636 freshwater metagenomes. Our results show that prokaryotes with reduced genomes exhibited higher prevalence and relative abundance, suggesting that genome streamlining may promote cosmopolitanism. Furthermore, network analyses revealed that the most prevalent prokaryotes have streamlined genomes that are found in co-occurrent cohorts potentially sustained by metabolic dependencies. Overall, species in these groups possess a diminished capacity for synthesizing different essential metabolites such as vitamins, amino acids and nucleotides, potentially fostering metabolic complementarities within the community. Moreover, we found the presence of the essential biosynthetic functions to be usage-dependent: nucleotide and amino acids biosynthesis are the most complete, whereas vitamin biosynthesis is most incomplete. Our results underscore genome streamlining as a central eco-evolutionary strategy that both shapes and is shaped by community dynamics, ultimately fostering interdependences among prokaryotes.