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Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains
Arantxa Peña1, Hanno Teeling, Jaime Huerta-Cepas
1Departamento de Fisiología, Genética y Microbiología, and IMEM, Universidad de Alicante, Apartado 99, Alicante, Spain.
The ISME Journal
|February 19, 2010
Summary
Microbial genomes show extensive variation. This study reveals that genomic differences in Salinibacter ruber drive ecological divergence, suggesting micro-niche adaptation and viral predation shape bacterial evolution.
Area of Science:
- Microbial genomics and evolution
- Halophile biology
- Bacterial adaptation
Background:
- Microbial populations exhibit significant genomic variation, but its ecological and evolutionary implications are poorly understood.
- Microevolutionary studies, especially for non-pathogenic bacteria, are limited.
- Salinibacter ruber, a hyperhalophilic bacterium, offers a model to study microdiversity.
Purpose of the Study:
- To compare genomes, metabolomes, and ecological traits of two closely related Salinibacter ruber strains (M8 and M31).
- To investigate the genomic plasticity and evolutionary forces shaping microdiversity in S. ruber.
- To understand the ecological significance of genomic differences in bacteria.
Main Methods:
- Comparative genomics of S. ruber strains M8 and M31.
- Metabolomic profiling.
- Phage susceptibility assays and competition experiments.
- Analysis of ribosomal RNA (rRNA) gene and intergenic regions.
Main Results:
- S. ruber genomes display a mosaic structure with conserved and hypervariable regions (HVRs), alongside plasticity outside HVRs.
- Approximately 10% of genes differ between strains, with some likely acquired recently.
- Evidence of lateral gene transfer from Archaea predating strain divergence was found.
- Genomic differences significantly impact ecological traits, including competition and phage resistance.
Conclusions:
- Genomic microdiversity in S. ruber is not ecologically neutral.
- Micro-niche adaptation and viral predation are key drivers of microevolution in these bacteria.
- Bacterial functional diversity and adaptation extend beyond the resolution of standard 16S rRNA gene sequencing.
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