{ "abstract": "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 multiple putative 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 several sediment cores and depths (0–6 cm) at Vaxön (Stockholm archipelago, Sweden) as well as earlier isolates from this site and allopatric strains from surrounding locations obtained from both sediments and the water column. Using a reverse-ecology population genomics approach, we found unprecedented genomic diversification among sediment-associated strains, which form a species complex resolving into three cohesive evolutionary groups (G1, G2, and G3) with distinct signatures of metabolic specialization including sulfite respiration. While G1 consists predominantly of a single species (S. baltica) with high gene turnover, G2 and G3 comprise an array of divergent putative genospecies and previously reported species consistently recovered from sediments. Patterns of homologous recombination indicate that diversification of the lineages within G2 and G3 is primarily recombination-driven (‘sexual’) and is associated with specialization in sulfite reduction and utilization of certain carbon sources. The extent of diversity uncovered here far exceeds that reported for S. baltica from other environments, suggesting that a sediment-associated lifestyle promotes the emergence of novel genotypes. These findings expand the known limits of sympatric speciation in prokaryotes beyond subspecific ecotypes, demonstrating that bacterial species can diverge and persist as distinct lineages in the absence of spatial segregation and at microgeographic scales. Furthermore, our results suggest that collective interactions and ecological differentiation can structure sediment-associated bacterial populations strongly enough to drive divergence at the species level. Author summary: How new bacterial species arise remains one of the major questions in microbial evolution. Unlike plants and animals, bacteria exchange genes through homologous recombination, making it difficult to understand how genetically and ecologically distinct lineages can emerge while living together. We analyzed 112 genomes from Shewanella isolates collected from sediments at a site in the Baltic Sea, together with earlier local isolates and related strains from nearby sediment and water environments. We found that what was previously considered a single species, S. baltica, actually comprises three differentiated evolutionary groups occupying the same sediment habitat. Sediment-associated lineages appear to diversify through frequent homologous recombination while maintaining distinct evolutionary identities. These groups differ in their metabolic capabilities and patterns of gene exchange, suggesting that ecological specialization has contributed to their divergence. The remarkable diversity observed within a few centimeters of sediment greatly exceeds that reported for populations from other environments. Our findings show that bacterial populations can diversify into multiple species without geographic isolation, providing evidence that ecological differentiation and local interactions can promote speciation at extremely small spatial scales.", "abstract_shown": true, "affiliations": [ "Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden", "Unit of Medical Technology and Biological Function, Department of Medical Technology and Diagnostics, RISE Research Institutes of Sweden, Mölndal, Sweden", "Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden", "Culture Collection University of Gothenburg (CCUG), Sahlgrenska University Hospital and Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden" ], "article_type": "Research Article", "arxiv": null, "author_total": 4, "authors": [ { "affs": [ 0 ], "name": "Víctor Fernández-Juárez" }, { "affs": [ 1 ], "name": "Francisco Salvà-Serra" }, { "affs": [ 2 ], "name": "Guillem Seguí" }, { "affs": [ 3 ], "name": "Alberto J. Martín-Rodríguez" } ], "bibtex": "https://research.draconitic.com/paper/ft40z8k69wh56.bib", "cited_by": 0, "doi": "10.1371/journal.pgen.1012306", "fulltext_url": "https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1012306", "id": "ft40z8k69wh56", "issns": [ "1553-7404" ], "landing_url": "https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1012306", "language": null, "licence": "CC-BY-4.0", "licence_label": "CC BY 4.0", "licence_source": "journal", "licence_url": "https://creativecommons.org/licenses/by/4.0/", "metadata_licence": null, "native_subjects": [ [ "openalex", "2303|Microbial Community Ecology and Physiology" ], [ "plos", "/Biology and life sciences/Biochemistry/Nucleic acids/DNA/DNA recombination/Homologous recombination" ], [ "plos", "/Biology and life sciences/Computational biology/Genome analysis" ], [ "plos", "/Biology and life sciences/Evolutionary biology/Evolutionary processes/Speciation" ], [ "plos", "/Biology and life sciences/Evolutionary biology/Evolutionary systematics/Phylogenetics" ], [ "plos", "/Biology and life sciences/Evolutionary biology/Evolutionary systematics/Phylogenetics/Phylogenetic analysis" ], [ "plos", "/Biology and life sciences/Genetics/DNA/DNA recombination/Homologous recombination" ], [ "plos", "/Biology and life sciences/Genetics/Genomics" ], [ "plos", "/Biology and life sciences/Genetics/Genomics/Genome analysis" ], [ "plos", "/Biology and life sciences/Genetics/Genomics/Microbial genomics/Bacterial genomics" ], [ "plos", "/Biology and life sciences/Genetics/Microbial genetics/Bacterial genetics/Bacterial genomics" ], [ "plos", "/Biology and life sciences/Microbiology/Bacteriology/Bacterial genetics/Bacterial genomics" ], [ "plos", "/Biology and life sciences/Microbiology/Microbial genomics/Bacterial genomics" ], [ "plos", "/Biology and life sciences/Taxonomy/Evolutionary systematics/Phylogenetics" ], [ "plos", "/Biology and life sciences/Taxonomy/Evolutionary systematics/Phylogenetics/Phylogenetic analysis" ], [ "plos", "/Computer and information sciences/Data management/Taxonomy/Evolutionary systematics/Phylogenetics" ], [ "plos", "/Computer and information sciences/Data management/Taxonomy/Evolutionary systematics/Phylogenetics/Phylogenetic analysis" ], [ "plos", "/Earth sciences/Geology/Petrology/Sediment" ], [ "plos", "/Earth sciences/Geology/Sedimentary geology/Sediment" ] ], "openalex": "W7167885346", "pdf_url": "https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1012306&type=printable", "pmcid": null, "pmid": null, "published": "2026-09-11", "publisher": "Public Library of Science", "ris": "https://research.draconitic.com/paper/ft40z8k69wh56.ris", "sources": [ { "first_seen": "2026-10-30T12:17:56Z", "native_id": "10.1371/journal.pgen.1012306", "source": "plos", "url": "https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1012306" } ], "subjects": [ { "field": "biology", "origin": "plos:evolutionary biology", "subfield": "evolutionary-biology" }, { "field": "biology", "origin": "plos:genetics", "subfield": "genetics-genomics" } ], "title": "Life in sediments fosters ‘sexual’ speciation in the Shewanella baltica complex", "title_text": "Life in sediments fosters ‘sexual’ speciation in the Shewanella baltica complex", "type": "peer-reviewed", "updated_at": "2026-10-30T12:17:56Z", "url": "https://research.draconitic.com/paper/ft40z8k69wh56", "venue": "PLOS Genetics", "versions": [] }