Detection of Large Numbers of Novel Sequences in the Metatranscriptomes of Complex Marine Microbial Communities

Detection of Large Numbers of Novel Sequences in the Metatranscriptomes of Complex Marine Microbial Communities
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Journal Article
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Gilbert JA, Field D, Huang Y, Edwards R, Li W, Gilna P, Joint I

PLOS one
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mesocosm, pyrosequencing, microbial community, 11 m3, Bergen, Espegrend, Norway


Background: Sequencing the expressed genetic information of an ecosystem (metatranscriptome) can provide informationabout the response of organisms to varying environmental conditions. Until recently, metatranscriptomics has been limitedto microarray technology and random cloning methodologies. The application of high-throughput sequencing technologyis 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 randomwhole-community mRNA using the GS-FLX Pyrosequencing technology. Eight samples, four DNA and four mRNA, wereprocessed from two time points in a controlled coastal ocean mesocosm study (Bergen, Norway) involving an inducedphytoplankton bloom producing a total of 323,161,989 base pairs. Our study confirms the finding of the first publishedmetatranscriptomic studies of marine and soil environments that metatranscriptomics targets highly expressed sequenceswhich are frequently novel. Our alternative methodology increases the range of experimental options available forconducting 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 afar 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 microbialcommunities are not only feasible, but when paired with metagenomic data sets, offer an unprecedented opportunity toexplore both structure and function of microbial communities – if we can overcome the challenges of elucidating thefunctions of so many never-seen-before gene families

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