uu.seUppsala University Publications
Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
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
National Category
Microbiology
Research subject
Biology with specialization in Microbiology
Identifiers
URN: urn:nbn:se:uu:diva-225114DOI: 10.1128/AEM.03108-09OAI: oai:DiVA.org:uu-225114DiVA: diva2:719904
Available from: 2014-05-27 Created: 2014-05-27 Last updated: 2017-12-05Bibliographically approved

Open Access in DiVA

fulltext(1625 kB)117 downloads
File information
File name FULLTEXT01.pdfFile size 1625 kBChecksum SHA-512
b4ccb7894e45c563d42c9241316ba5a5f7dc296a77207a07d0ae3cb54c9121b8b1ec46bc317feffdccac2b4a37debed7fd230b6e5f2acc17d48aa14367ae1709
Type fulltextMimetype application/pdf

Other links

Publisher's full texthttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC2976231/

Authority records BETA

Mondav, Rhiannon

Search in DiVA

By author/editor
Mondav, Rhiannon
By organisation
Limnology
In the same journal
Applied and Environmental Microbiology
Microbiology

Search outside of DiVA

GoogleGoogle Scholar
Total: 117 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

doi
urn-nbn

Altmetric score

doi
urn-nbn
Total: 459 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf