Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column

Shi, Yanmei, Tyson, Gene W. and DeLong, Edward F. (2009) Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column. Nature, 459 7244: 266-269. doi:10.1038/nature08055


Author Shi, Yanmei
Tyson, Gene W.
DeLong, Edward F.
Title Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column
Journal name Nature   Check publisher's open access policy
ISSN 0028-0836
Publication date 2009-05-14
Year available 2009
Sub-type Article (original research)
DOI 10.1038/nature08055
Open Access Status Not yet assessed
Volume 459
Issue 7244
Start page 266
End page 269
Total pages 4
Editor Philip Campbell
Nick Campbell
Place of publication United Kingdom
Publisher Nature Publishing Group
Language eng
Subject C1
Abstract Microbial gene expression in the environment has recently been assessed via pyrosequencing of total RNA extracted directly from natural microbial assemblages. Several such 'metatranscriptomic' studies1, 2 have reported that many complementary DNA sequences shared no significant homology with known peptide sequences, and so might represent transcripts from uncharacterized proteins. Here we report that a large fraction of cDNA sequences detected in microbial metatranscriptomic data sets are comprised of well-known small RNAs (sRNAs)3, as well as new groups of previously unrecognized putative sRNAs (psRNAs). These psRNAs mapped specifically to intergenic regions of microbial genomes recovered from similar habitats, displayed characteristic conserved secondary structures and were frequently flanked by genes that indicated potential regulatory functions. Depth-dependent variation of psRNAs generally reflected known depth distributions of broad taxonomic groups4, but fine-scale differences in the psRNAs within closely related populations indicated potential roles in niche adaptation. Genome-specific mapping of a subset of psRNAs derived from predominant planktonic species such as Pelagibacter revealed recently discovered as well as potentially new regulatory elements. Our analyses show that metatranscriptomic data sets can reveal new information about the diversity, taxonomic distribution and abundance of sRNAs in naturally occurring microbial communities, and indicate their involvement in environmentally relevant processes including carbon metabolism and nutrient acquisition.
Keyword metatranscriptomics
microbial
RNAs
genome
bacterioplankton
IGRs
pelagibacter
Q-Index Code C1
Q-Index Status Confirmed Code
Grant ID HTCC7211
MCB-0348001
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: 2010 Higher Education Research Data Collection
Advanced Water Management Centre Publications
 
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Citation counts: TR Web of Science Citation Count  Cited 152 times in Thomson Reuters Web of Science Article | Citations
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Created: Wed, 14 Apr 2010, 19:24:49 EST by Hong Lee on behalf of Advanced Water Management Centre