Life in sediments fosters 'sexual' speciation in Shewanella baltica

Understanding how intra- and interspecific differentiation arises in natural microbial populations is central to explaining the processes that drive bacterial evolution. Motivated by the co-occurrence of several genospecies closely related to Shewanella baltica in Baltic Sea sediments, we investigated the genomic structure of this species complex across fine spatial scales. We analyzed 112 genome sequences from strains collected across multiple sediment cores and depths (0-6 cm) at Vaxon (Stockholm archipelago, Sweden), including sympatric isolates from this site as well as earlier isolates and allopatric strains from other locations in the Stockholm region obtained from both sediments and the water column. Using a reverse-ecology population genomics approach, we found that these strains form a species complex that resolves into three cohesive evolutionary lineages (G1, G2, and G3). Each lineage is characterized by extensive gene turnover, driven largely by horizontal gene transfer (HGT), and displays distinct genomic signatures of metabolic specialization. While G1 consists predominantly of a single species (S. baltica), G2 and G3 comprise a diverse set of divergent genospecies, many of which are repeatedly recovered from sediment samples. Patterns of homologous recombination indicate that speciation within G2 and G3 is primarily recombination-driven ( sexual), and that both groups derive from a common ancestor. Together, these results capture a snapshot of early-stage speciation within a shared ecosystem and provide insight into the mechanisms that diversify sympatric, recombining bacterial populations, with a sediment-associated lifestyle likely promoting this process.