Development of an environmental functional gene microarray for soil microbial communities

McGrath, Ken C., Mondav, Rhiannon, Sintrajaya, Regina, Slattery, Bill, Schmidt, Susanne and Schenk, Peer M. (2010) Development of an environmental functional gene microarray for soil microbial communities. Applied and Environmental Microbiology, 76 21: 7161-7170. doi:10.1128/AEM.03108-09

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Author McGrath, Ken C.
Mondav, Rhiannon
Sintrajaya, Regina
Slattery, Bill
Schmidt, Susanne
Schenk, Peer M.
Title Development of an environmental functional gene microarray for soil microbial communities
Journal name Applied and Environmental Microbiology   Check publisher's open access policy
ISSN 0099-2240
1098-5336
Publication date 2010-11
Sub-type Article (original research)
DOI 10.1128/AEM.03108-09
Open Access Status File (Publisher version)
Volume 76
Issue 21
Start page 7161
End page 7170
Total pages 10
Place of publication Washington, D.C., U. S.
Publisher American Society for Microbiology
Collection year 2011
Language eng
Abstract Functional attributes of microbial communities are difficult to study, and most current techniques rely on DNA- and rRNA-based profiling of taxa and genes, including microarrays containing sequences of known microorganisms. To quantify gene expression in environmental samples in a culture-independent manner, we constructed an environmental functional gene microarray (E-FGA) consisting of 13,056 mRNA-enriched anonymous microbial clones from diverse microbial communities to profile microbial gene transcripts. A new normalization method using internal spot standards was devised to overcome spotting and hybridization bias, enabling direct comparisons of microarrays. To evaluate potential applications of this metatranscriptomic approach for studying microbes in environmental samples, we tested the E-FGA by profiling the microbial activity of agricultural soils with a low or high flux of N2O. A total of 109 genes displayed expression that differed significantly between soils with low and high N2O emissions. We conclude that mRNA-based approaches such as the one presented here may complement existing techniques for assessing functional attributes of microbial communities. Copyright © 2010, American Society for Microbiology.
Keyword Nitrous-oxide Emission
Gradient Gel-electrophoresis
Ammonia-oxidizing Bacteria
16s Ribosomal-rna
Water-treatment
Diversity
Expression
Denitrification
Identification
Hybridization
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ
Additional Notes Received 23 December 2009/ Accepted 6 September 2010; Published ahead of print on 17 September 2010.

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2011 Collection
School of Biological Sciences Publications
 
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Created: Sun, 14 Nov 2010, 00:04:38 EST