Biology subjects

Milke, F.

Publications and source records attributed to Milke, F..

2 recordsLinked to original sources

bioRxiv2026

Baltic Sea microbial cohorts exhibit catabolic specialization and anabolic interdependencies across environmental gradients

Microbial communities are structured by environmental gradients and metabolic interactions, yet the genomic characteristics and metabolic functions of co-occurring populations remain underexplored. Here, we investigated co-occurring microbial cohorts across the Baltic Sea, a system characterized by strong salinity, temperature, and oxygen gradients. For this, we used a genomic catalog consisting of 701 species-representative genomes to recruit reads from 112 metagenomes and infer cohort structure, environmental distributions, and metabolic potential. We identified nine microbial cohorts that showed strong associations with environmental gradients, indicating deterministic assembly. Cohorts differed markedly in genomic traits, with the most abundant and prevalent taxa associated with smaller, streamlined genomes, while a low-oxygen cohort with larger genomes contributed disproportionately to nitrogen and sulfur transformations. Across cohorts, biosynthetic potential was unevenly distributed. Amino acid biosynthesis pathways were frequently complete, whereas B-vitamin pathways were typically incomplete and rarely encoded in full by individual genomes. Metabolites with low pathway completeness showed consistent taxonomic partitioning, with biosynthetic capabilities distributed across taxa rather than collectively encoded within cohorts. Together, these results show that Baltic Sea microbial cohorts are ecologically structured assemblages whose genomic repertoires reflect catabolic specialization and anabolic interdependencies. Our findings highlight microbial cohorts as a useful framework for linking environmental gradients, genome traits, and the organization of metabolic functions in natural microbial communities.

microbiology↗

bioRxiv2025

The ecological success of freshwater microorganisms is mediated by streamlining and biotic interactions

Genome size is known to reflect aspects of 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 microbial prevalence, relative abundance and co-occurrence in the environment. 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, including 80,561 medium-to-high quality genomes. We identified 9,028 species (defined by ANI >95%) across a manually curated dataset of 636 freshwater metagenomes and calculated their relative abundance. Our results show that prokaryotes with reduced genomes exhibited higher prevalence and relative abundance, and a greater prevalence than expected based on their mean abundance, suggesting that genome streamlining may promote cosmopolitanism. Furthermore, our network analysis revealed that prokaryotes with reduced genomes are found in co-occurrent groups comprising up to 295 species. The species in these groups potentially possess a diminished capacity for synthesizing essential metabolites such as vitamins, amino acids and nucleotides, which may foster complex metabolic interdependencies within the community. Moreover, the fitness advantage of losing biosynthetic functions appears to be frequency dependent: while nucleotide biosynthesis is the most retained biosynthetic function, amino acid and then vitamin biosynthesis are more frequently lost. Our study finds that genome size is linked to microbial community structure and ecological adaptation to freshwaters. Our results underscore genome streamlining as a central ecological and evolutionary strategy that both shapes and is shaped by community dynamics, ultimately fostering interdependences among prokaryotes.

microbiology↗