Genes 2010, 1(3), 371-384; doi:10.3390/genes1030371
Article

Identification of Carbohydrate Metabolism Genes in the Metagenome of a Marine Biofilm Community Shown to Be Dominated by Gammaproteobacteria and Bacteroidetes

1 Microbiology Research Group, School of Biological Sciences, BioSciences Building, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK 2 Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH, UK
* Author to whom correspondence should be addressed.
Received: 21 September 2010; in revised form: 5 October 2010 / Accepted: 11 October 2010 / Published: 26 October 2010
(This article belongs to the Special Issue Next Generation DNA Sequencing)
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Abstract: Polysaccharides are an important source of organic carbon in the marine environment and degradation of the insoluble and globally abundant cellulose is a major component of the marine carbon cycle. Although a number of species of cultured bacteria are known to degrade crystalline cellulose, little is known of the polysaccharide hydrolases expressed by cellulose-degrading microbial communities, particularly in the marine environment. Next generation 454 Pyrosequencing was applied to analyze the microbial community that colonizes and degrades insoluble polysaccharides in situ in the Irish Sea. The bioinformatics tool MG-RAST was used to examine the randomly sampled data for taxonomic markers and functional genes, and showed that the community was dominated by members of the Gammaproteobacteria and Bacteroidetes. Furthermore, the identification of 211 gene sequences matched to a custom-made database comprising the members of nine glycoside hydrolase families revealed an extensive repertoire of functional genes predicted to be involved in cellulose utilization. This demonstrates that the use of an in situ cellulose baiting method yielded a marine microbial metagenome considerably enriched in functional genes involved in polysaccharide degradation. The research reported here is the first designed to specifically address the bacterial communities that colonize and degrade cellulose in the marine environment and to evaluate the glycoside hydrolase (cellulase and chitinase) gene repertoire of that community, in the absence of the biases associated with PCR-based molecular techniques.
Keywords: 454 pyrosequencing; next generation sequencing; marine polysaccharide degradation; glycoside hydrolases; metagenomics; marine bacteria; cellulose biofilm

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MDPI and ACS Style

Edwards, J.L.; Smith, D.L.; Connolly, J.; McDonald, J.E.; Cox, M.J.; Joint, I.; Edwards, C.; McCarthy, A.J. Identification of Carbohydrate Metabolism Genes in the Metagenome of a Marine Biofilm Community Shown to Be Dominated by Gammaproteobacteria and Bacteroidetes. Genes 2010, 1, 371-384.

AMA Style

Edwards JL, Smith DL, Connolly J, McDonald JE, Cox MJ, Joint I, Edwards C, McCarthy AJ. Identification of Carbohydrate Metabolism Genes in the Metagenome of a Marine Biofilm Community Shown to Be Dominated by Gammaproteobacteria and Bacteroidetes. Genes. 2010; 1(3):371-384.

Chicago/Turabian Style

Edwards, Jennifer L.; Smith, Darren L.; Connolly, John; McDonald, James E.; Cox, Michael J.; Joint, Ian; Edwards, Clive; McCarthy, Alan J. 2010. "Identification of Carbohydrate Metabolism Genes in the Metagenome of a Marine Biofilm Community Shown to Be Dominated by Gammaproteobacteria and Bacteroidetes." Genes 1, no. 3: 371-384.

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