Microorganisms in aquatic environments live in complex communities governed by environmental gradients, ecological interactions, and evolutionary processes. Although many bacteria and archaea lack complete biosynthetic pathways for essential metabolites, how the resulting metabolic dependencies are organized in natural communities remains unclear. This thesis examines metabolic dependencies among free-living microorganisms in the Baltic Sea and how biosynthetic potential is distributed across levels of microbial organization, from natural microbial cohorts and experimentally cultivated communities (microbial model communities) to genomic variation within an abundant microbial population.

The thesis combines genome-resolved metagenomics, co-occurrence network analysis, cultivated model communities, and population-level analyses. Chapter I shows that microbial communities can be organized into recurring groups of microorganisms, here referred to as microbial cohorts. These represent an intermediate level between taxa and whole communities for studying community structure and associations.

Chapter II applies cohort analysis to the Baltic Sea using BalticMAG. Across 701 species-representative genomes and 112 metagenomes, microbial cohorts were associated with gradients such as salinity, oxygen, and temperature, and differed in metabolic potential. Amino acid biosynthesis pathways were generally more complete, whereas B-vitamin pathways were more often incomplete or patchy, suggesting that potential metabolic dependencies are tied to the ecological context shaping the cohorts.

Chapter III examines cultivated microbial model communities established from a Baltic Sea sample using a dilution-to-extinction approach. From 204 communities, we recovered 527 metagenome-assembled genomes (MAGs) representing 72 species-clusters. Many recovered taxa were previously uncultivated and appeared only in multi-species communities. Microorganisms in communities with more than three species tended to have lower biosynthetic potential for amino acids and B-vitamins, while different species often encoded different steps of the same pathways. These results suggest that naturally derived model communities can reveal metabolic interdependencies difficult to observe in pure culture.

Chapter IV focuses on an abundant Nitrosopumilus population from the Baltic Sea that retained complete or near-complete pathways for vitamins B₁, B₇, and B₁₂ despite its small genome. Analyses revealed genetic structure across environmental gradients, and B-vitamin biosynthesis genes showed stronger purifying selection than the genomic background. These genes were widely retained across ammonia-oxidizing archaea (AOA), while measurements in the cultivated relative Nitrosopumilus maritimus detected B-vitamins and precursors in both intracellular and extracellular fractions. These results suggest that biosynthetic functions may be retained in streamlined genomes under particular ecological or evolutionary conditions.

Overall, this thesis brings together recurring microbial cohorts, growth in cultivated communities, and retention of specific pathways within populations to understand biosynthetic potential and metabolic dependencies. This genome-resolved view shows how biosynthetic potential is distributed among Baltic Sea microorganisms and why metabolic dependencies must be interpreted in relation to ecological context, cultivation, and genome evolution.