title: Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities.
abstract: 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.
  
  
  RESULTS
  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, approximately 91% of which were novel.
  
  
  CONCLUSIONS
  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.
authors: Plymouth Marine Laboratory, Prospect Place, Plymouth, United Kingdom. jagi@pml.ac.uk
authors: Jack A
authors: JA
authors: Gilbert
authors: Dawn
authors: D
authors: Field
authors: Ying
authors: Y
authors: Huang
authors: Rob
authors: R
authors: Edwards
authors: Weizhong
authors: W
authors: Li
authors: Paul
authors: P
authors: Gilna
authors: Ian
authors: I
authors: Joint
mesh_terms: D000818:Animals; D004247:DNA / Q000235:genetics; D018076:DNA, Complementary / Q000235:genetics; D017753:Ecosystem; D020869:Gene Expression Profiling; D009664:Norway; D016366:Open Reading Frames; D010933:Plankton / Q000235:genetics*; D016133:Polymerase Chain Reaction; D012333:RNA, Messenger / Q000235:genetics; D015203:Reproducibility of Results; D012623:Seawater; D014871:Water Microbiology
chemical_list: D018076:DNA, Complementary; D012333:RNA, Messenger; D004247:DNA