Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities

Gilbert, Jack A.; Field, Dawn; Huang, Ying; Edwards, Rob; Li, Weizhong; Gilna, Paul; Joint, Ian. 2008 Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. PLoS ONE, 3 (8), e3042. 10.1371/journal.pone.0003042

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Abstract/Summary

Background Sequencing the expressed genetic information of an ecosystem (metatranscriptome) can provide information about the response of organisms to varying environmental conditions. Until recently, metatranscriptomics has been limited to microarray technology and random cloning methodologies. The application of high-throughput sequencing technology is now enabling access to both known and previously unknown transcripts in natural communities. Methodology/Principal Findings We present a study of a complex marine metatranscriptome obtained from random whole-community mRNA using the GS-FLX Pyrosequencing technology. Eight samples, four DNA and four mRNA, were processed from two time points in a controlled coastal ocean mesocosm study (Bergen, Norway) involving an induced phytoplankton bloom producing a total of 323,161,989 base pairs. Our study confirms the finding of the first published metatranscriptomic studies of marine and soil environments that metatranscriptomics targets highly expressed sequences which are frequently novel. Our alternative methodology increases the range of experimental options available for conducting such studies and is characterized by an exceptional enrichment of mRNA (99.92%) versus ribosomal RNA. Analysis of corresponding metagenomes confirms much higher levels of assembly in the metatranscriptomic samples and a far higher yield of large gene families with >100 members, ~91% of which were novel. Conclusions/Significance This study provides further evidence that metatranscriptomic studies of natural microbial communities are not only feasible, but when paired with metagenomic data sets, offer an unprecedented opportunity to explore both structure and function of microbial communities – if we can overcome the challenges of elucidating the functions of so many never-seen-before gene families.

Item Type:	Publication - Article
Digital Object Identifier (DOI):	10.1371/journal.pone.0003042
Programmes:	CEH Programmes pre-2009 publications > Biodiversity
UKCEH and CEH Sections/Science Areas:	Hails
ISSN:	19326203
Additional Information. Not used in RCUK Gateway to Research.:	PLoS ONE is an open access journal
NORA Subject Terms:	Biology and Microbiology Ecology and Environment Data and Information
Date made live:	12 Feb 2009 15:31 +0 (UTC)
URI:	https://nora.nerc.ac.uk/id/eprint/5486

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