title: Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains.
abstract: Genomic and metagenomic data indicate a high degree of genomic variation within microbial populations, although the ecological and evolutive meaning of this microdiversity remains unknown. Microevolution analyses, including genomic and experimental approaches, are so far very scarce for non-pathogenic bacteria. In this study, we compare the genomes, metabolomes and selected ecological traits of the strains M8 and M31 of the hyperhalophilic bacterium Salinibacter ruber that contain ribosomal RNA (rRNA) gene and intergenic regions that are identical in sequence and were simultaneously isolated from a Mediterranean solar saltern. Comparative analyses indicate that S. ruber genomes present a mosaic structure with conserved and hypervariable regions (HVRs). The HVRs or genomic islands, are enriched in transposases, genes related to surface properties, strain-specific genes and highly divergent orthologous. However, the many indels outside the HVRs indicate that genome plasticity extends beyond them. Overall, 10% of the genes encoded in the M8 genome are absent from M31 and could stem from recent acquisitions. S. ruber genomes also harbor 34 genes located outside HVRs that are transcribed during standard growth and probably derive from lateral gene transfers with Archaea preceding the M8/M31 divergence. Metabolomic analyses, phage susceptibility and competition experiments indicate that these genomic differences cannot be considered neutral from an ecological perspective. The results point to the avoidance of competition by micro-niche adaptation and response to viral predation as putative major forces that drive microevolution within these Salinibacter strains. In addition, this work highlights the extent of bacterial functional diversity and environmental adaptation, beyond the resolution of the 16S rRNA and internal transcribed spacers regions.
authors.affiliation: Departamento de Fisiología, Genética y Microbiología, and IMEM, Universidad de Alicante, Apartado 99, Alicante, Spain.
authors.forename: Arantxa
authors.initials: A
authors.lastname: Peña
authors.forename: Hanno
authors.initials: H
authors.lastname: Teeling
authors.forename: Jaime
authors.initials: J
authors.lastname: Huerta-Cepas
authors.forename: Fernando
authors.initials: F
authors.lastname: Santos
authors.forename: Pablo
authors.initials: P
authors.lastname: Yarza
authors.forename: Jocelyn
authors.initials: J
authors.lastname: Brito-Echeverría
authors.forename: Marianna
authors.initials: M
authors.lastname: Lucio
authors.forename: Philippe
authors.initials: P
authors.lastname: Schmitt-Kopplin
authors.forename: Inmaculada
authors.initials: I
authors.lastname: Meseguer
authors.forename: Chantal
authors.initials: C
authors.lastname: Schenowitz
authors.forename: Carole
authors.initials: C
authors.lastname: Dossat
authors.forename: Valerie
authors.initials: V
authors.lastname: Barbe
authors.forename: Joaquín
authors.initials: J
authors.lastname: Dopazo
authors.forename: Ramon
authors.initials: R
authors.lastname: Rosselló-Mora
authors.forename: Margarete
authors.initials: M
authors.lastname: Schüler
authors.forename: Frank Oliver
authors.initials: FO
authors.lastname: Glöckner
authors.forename: Rudolf
authors.initials: R
authors.lastname: Amann
authors.forename: Toni
authors.initials: T
authors.lastname: Gabaldón
authors.forename: Josefa
authors.initials: J
authors.lastname: Antón
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D001435:Bacteriophages / Q000502:physiology; D041963:Bacteroidetes / Q000145:classification* / Q000235:genetics* / Q000254:growth & development / Q000821:virology; D017753:Ecosystem; D019143:Evolution, Molecular; D014644:Genetic Variation; D016680:Genome, Bacterial; D023281:Genomics; D008969:Molecular Sequence Data; D010641:Phenotype; D012623:Seawater / Q000382:microbiology*; D017422:Sequence Analysis, DNA; D012965:Sodium Chloride
chemical_list: D001426:Bacterial Proteins; D012965:Sodium Chloride