Open Access Research article

Metagenomic islands of hyperhalophiles: the case of Salinibacter ruber

Lejla Pašić13, Beltran Rodriguez-Mueller2, Ana-Belen Martin-Cuadrado1, Alex Mira1, Forest Rohwer2 and Francisco Rodriguez-Valera1*

  • * Corresponding author: Francisco Rodriguez-Valera frvalera@umh.es

  • † Equal contributors

Author Affiliations

1 Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Apartado 18, San Juan 03550, Alicante, Spain

2 Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA

3 Department of Biology, University of Ljubljana, Večna pot 111, 1000 Ljubljana, Slovenia

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BMC Genomics 2009, 10:570  doi:10.1186/1471-2164-10-570

Published: 1 December 2009

Abstract

Background

Saturated brines are extreme environments of low diversity. Salinibacter ruber is the only bacterium that inhabits this environment in significant numbers. In order to establish the extent of genetic diversity in natural populations of this microbe, the genomic sequence of reference strain DSM 13855 was compared to metagenomic fragments recovered from climax saltern crystallizers and obtained with 454 sequencing technology. This kind of analysis reveals the presence of metagenomic islands, i.e. highly variable regions among the different lineages in the population.

Results

Three regions of the sequenced isolate were scarcely represented in the metagenome thus appearing to vary among co-occurring S. ruber cells. These metagenomic islands showed evidence of extensive genomic corruption with atypically low GC content, low coding density, high numbers of pseudogenes and short hypothetical proteins. A detailed analysis of island gene content showed that the genes in metagenomic island 1 code for cell surface polysaccharides. The strain-specific genes of metagenomic island 2 were found to be involved in biosynthesis of cell wall polysaccharide components. Finally, metagenomic island 3 was rich in DNA related enzymes.

Conclusion

The genomic organisation of S. ruber variable genomic regions showed a number of convergences with genomic islands of marine microbes studied, being largely involved in variable cell surface traits. This variation at the level of cell envelopes in an environment devoid of grazing pressure probably reflects a global strategy of bacteria to escape phage predation.