Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains
Autor: | Frank Oliver Glöckner, Arantxa Peña, Philippe Schmitt-Kopplin, Valérie Barbe, Hanno Teeling, Fernando Santos, Jocelyn Brito-Echeverría, Inmaculada Meseguer, Chantal Schenowitz, Jaime Huerta-Cepas, Pablo Yarza, Ramon Rosselló-Móra, Toni Gabaldón, Marianna Lucio, Margarete Schüler, Rudolf Amann, Joaquín Dopazo, Josefa Antón, Carole Dossat |
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Rok vydání: | 2010 |
Předmět: |
Bacteroidetes
Ecology Molecular Sequence Data Genetic Variation Microevolution Genomics Sequence Analysis DNA Sodium Chloride Biology Ribosomal RNA Microbiology Genome Hypervariable region Evolution Molecular Phenotype Intergenic region Bacterial Proteins Metagenomics Bacteriophages Seawater Adaptation Gene Ecosystem Genome Bacterial Ecology Evolution Behavior and Systematics |
Zdroj: | Digital.CSIC. Repositorio Institucional del CSIC instname |
ISSN: | 1751-7370 1751-7362 |
DOI: | 10.1038/ismej.2010.6 |
Popis: | 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. This work was funded by projects CGL2006-12714-CO2-01 and 02 from de Spanish Ministry of Science (to JA and RRM). J Dopazo thanks the National Institute of Bioinformatics (www.inab.org), that is a platform of Genoma España. This work was financially supported by the Max Plank Society within the projects Marine Genomics and EnviTools. |
Databáze: | OpenAIRE |
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