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Development of an environmental functional gene microarray for soil microbial communities
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.ORCID iD: 538928
2010 (English)In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 76, no 21, 7161-7170 p.Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
American Society for Microbiology , 2010. Vol. 76, no 21, 7161-7170 p.
Keyword [en]
nitrogen cycle, microarray, gene expression, microbial ecology, agriculture, DNA, Bacterial genetics, Nitrogen Fixation, Oligonucleotide Array Sequence Analysis, RNA, Soil Microbiology
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Research subject
Biology with specialization in Microbiology
URN: urn:nbn:se:uu:diva-225114DOI: 10.1128/AEM.03108-09OAI: diva2:719904
Available from: 2014-05-27 Created: 2014-05-27 Last updated: 2014-05-27Bibliographically approved

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Mondav, Rhiannon
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