Isolation and analysis of mRNA from environmental microbial communities

McGrath, K., Thomas-Hall, S. R., Cheng, C.T., Leo, L., Alexa, A., Schmidt, Susanne and Schenk, Peer M.P. (2008) Isolation and analysis of mRNA from environmental microbial communities. Journal of Microbiological Methods, 75 2: 172-176. doi:10.1016/j.mimet.2008.05.019


Author McGrath, K.
Thomas-Hall, S. R.
Cheng, C.T.
Leo, L.
Alexa, A.
Schmidt, Susanne
Schenk, Peer M.P.
Title Isolation and analysis of mRNA from environmental microbial communities
Journal name Journal of Microbiological Methods   Check publisher's open access policy
ISSN 1872-8359
Publication date 2008-10-01
Sub-type Article (original research)
DOI 10.1016/j.mimet.2008.05.019
Volume 75
Issue 2
Start page 172
End page 176
Total pages 5
Place of publication Netherlands
Publisher Elsevier BV
Collection year 2009
Language eng
Subject C1
829802 Management of Greenhouse Gas Emissions from Plant Production
060504 Microbial Ecology
Abstract The advent of metagenomics has revealed that our planet harbors millions of previously undiscovered microbial species. However, functional insights into the activities of microbial communities cannot easily be obtained using metagenomics. Using transcriptional analyses to study microbial gene functions is currently problematic due to difficulties working with unstable microbial mRNA as a small fraction of total cellular RNA. Current techniques can be expensive and time consuming, and still result in significant levels of rRNA contamination. We have adapted techniques to rapidly isolate high high-quality RNA from environmental samples and developed a simple method for specific isolation of mRNA by size separation. This new technique was evaluated by constructing cDNA libraries directly from uncultured environmental microbial communities, including agricultural soil samples, aquatic flocculants, organic composts, mammalian oral and faecal samples, and wastewater sludge. The sequencing of a fraction of these cDNA clones revealed a high degree of novelty, demonstrating the potential of this approach to capture a large number of unique transcripts directly from the environment. To our knowledge, this is the first study that uses gel electrophoresis to isolate mRNA from microbial communities. We conclude that this method could be used to provide insights into the microbial ‘metatranscriptome’ of entire microbial communities. Coupled with high-throughput sequencing or the construction of cDNA microarrays, this approach will provide a useful tool to study the transcriptional activities of microorganisms, including those of entire microbial communities and of non-culturable microorganisms.
Q-Index Code C1
Q-Index Status Confirmed Code

Document type: Journal Article
Sub-type: Article (original research)
Collections: 2009 Higher Education Research Data Collection
School of Biological Sciences Publications
Ecology Centre Publications
 
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Created: Fri, 16 Jan 2009, 03:29:13 EST by Gail Walter on behalf of School of Biological Sciences