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Vol. 76, No. 21, 2010; Pages: 6920-6927

Development of an Environmental Functional Gene Microarray for Soil Microbial Communities

Ken C. McGrath,1 Rhiannon Mondav,1 Regina Sintrajaya,1 Bill Slattery,2 Susanne Schmidt,1 and Peer M. Schenk1*

School of Biological Sciences, University of Queensland, St. Lucia, Queensland 4072, Australia.


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.

Keywords:functional gene microarray;microbial gene transcripts;microbes;Microarray for Soil Microbial Communities;soil fertility.

Corresponding author: Tel 61-7-3365 8817, Fax 61-7-3365 1699.

E-mail: p.schenk@uq.edu.au


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