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Logo of bmcgenoBioMed Centralsearchsubmit a manuscriptregisterthis articleBMC Genomics
 
BMC Genomics. 2009; 10: 570.
Published online Dec 1, 2009. doi:  10.1186/1471-2164-10-570
PMCID: PMC2800850
Metagenomic islands of hyperhalophiles: the case of Salinibacter ruber
Lejla Pašić,#1,3 Beltran Rodriguez-Mueller,#2 Ana-Belen Martin-Cuadrado,1 Alex Mira,1 Forest Rohwer,2 and Francisco Rodriguez-Valeracorresponding author1
1Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Apartado 18, San Juan 03550, Alicante, Spain
2Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
3Department of Biology, University of Ljubljana, Večna pot 111, 1000 Ljubljana, Slovenia
corresponding authorCorresponding author.
#Contributed equally.
Lejla Pašić: lejla.pasic/at/bf.uni-lj.si; Beltran Rodriguez-Mueller: beltran.rodriguez-brito/at/gmail.com; Ana-Belen Martin-Cuadrado: amartin/at/umh.es; Alex Mira: mira.ale/at/gva.es; Forest Rohwer: forest/at/sunstroke.sdsu.edu; Francisco Rodriguez-Valera: frvalera/at/umh.es
Received June 12, 2009; Accepted December 1, 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.
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