Microbial model communities reveal widespread auxotrophies in abundant bacteria

Microorganisms exist in complex communities shaped by intricate interactions. Here, we examined auxotrophies and metabolic interdependencies in microbial model communities established from Baltic Sea pelagic sample dilutions. We recovered 527 metagenome-assembled genomes (MAGs) from 204 microbial model communities, including some of the most abundant taxa such as Pelagibacterales. Combined with 1073 environmental MAGs, we created a genomic catalog of 701 species-clusters (95% average nucleotide identity - ANI). Our results show that more complex communities included microorganisms with smaller genome sizes and communities with more than three species exhibited lower average biosynthetic potential for amino acids and B vitamins. Furthermore, microorganisms with lower biosynthetic potential for those compounds are more abundant in the environment and have smaller estimated genome sizes. Overall, our results highlight the value of cultivating microorganisms in groups of naturally co-occurring microorganisms for unraveling ecological strategies such as auxotrophies and genomic streamlining which are widespread features of successful microorganisms.