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

Genes

Jennifer L. Edwards¹  Darren L. Smith¹  John Connolly¹  James E. McDonald¹  Michael J. Cox¹  Ian Joint²  Clive Edwards¹ 

[1] Microbiology Research Group, School of Biological Sciences, BioSciences Building, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK; E-Mails:;Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH, UK;E-Mail:

关键词: 454 pyrosequencing;    next generation sequencing;    marine polysaccharide degradation;    glycoside hydrolases;    metagenomics;    marine bacteria;    cellulose biofilm;   

DOI  :  10.3390/genes1030371

来源: mdpi

【 摘 要 】

Polysaccharides are an important source of organic carbon in the marine environment, degradation of the insoluble, 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, 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, functional genes,, showed that the community was dominated by members of the Gammaproteobacteria, 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, degrade cellulose in the marine environment, to evaluate the glycoside hydrolase (cellulase, chitinase) gene repertoire of that community, in the absence of the biases associated with PCR-based molecular techniques.

【 授权许可】

CC BY   
© 2010 by the authors; licensee MDPI, Basel, Switzerland