Development of an Environmental Functional Gene Microarray for Soil Microbial Communities
Mcgrath, Ken C. ; Mondav, Rhiannon LU
; Sintrajaya, Regina
; Slattery, Bill
; Schmidt, Susanne
and Schenk, Peer M.
(2010)
In Applied and Environmental Microbiology
76(21).
p.7161-7170
- 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... (More)
- 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. (Less)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/8f8b72c4-30e0-4352-ae5e-ea9865fc2e00
- author
- Mcgrath, Ken C.
; Mondav, Rhiannon
LU
; Sintrajaya, Regina
; Slattery, Bill
; Schmidt, Susanne
and Schenk, Peer M.
- publishing date
- 2010-11-01
- type
- Contribution to journal
- publication status
- published
- subject
- in
- Applied and Environmental Microbiology
- volume
- 76
- issue
- 21
- pages
- 7161 - 7170
- publisher
- American Society for Microbiology
- external identifiers
-
- scopus:78149428687
- ISSN
- 0099-2240
- DOI
- 10.1128/AEM.03108-09
- language
- English
- LU publication?
- no
- id
- 8f8b72c4-30e0-4352-ae5e-ea9865fc2e00
- date added to LUP
- 2023-06-05 15:49:20
- date last changed
- 2023-09-08 14:11:35
@article{8f8b72c4-30e0-4352-ae5e-ea9865fc2e00,
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.}},
author = {{Mcgrath, Ken C. and Mondav, Rhiannon and Sintrajaya, Regina and Slattery, Bill and Schmidt, Susanne and Schenk, Peer M.}},
issn = {{0099-2240}},
language = {{eng}},
month = {{11}},
number = {{21}},
pages = {{7161--7170}},
publisher = {{American Society for Microbiology}},
series = {{Applied and Environmental Microbiology}},
title = {{Development of an Environmental Functional Gene Microarray for Soil Microbial Communities}},
url = {{http://dx.doi.org/10.1128/AEM.03108-09}},
doi = {{10.1128/AEM.03108-09}},
volume = {{76}},
year = {{2010}},
}