ArticleApplied and environmental microbiology2007
Microarray-based analysis of microbial community RNAs by whole-community RNA amplification.
Article in Applied and environmental microbiology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Functional Gene Array-Based Ultrasensitive and Quantitative Detection of Microbial Populations in Complex Communities.mSystems · 2019Article
- Nitrogen Cycle Evaluation (NiCE) Chip for Simultaneous Analysis of Multiple N Cycle-Associated Genes.Applied and environmental microbiology · 2018Article
- Warming Alters Expressions of Microbial Functional Genes Important to Ecosystem Functioning.Frontiers in microbiology · 2016Article
- Review
- Lessons learned and unlearned in periodontal microbiology.Periodontology 2000 · 2013Review
- Mislocalization of Rieske protein PetA predominantly accounts for the aerobic growth defect of Tat mutants in Shewanella oneidensis.PloS one · 2013Article
- The Hydrogenase Chip: a tiling oligonucleotide DNA microarray technique for characterizing hydrogen-producing and -consuming microbes in microbial communities.The ISME journal · 2012Article
- Use of functional gene arrays for elucidating in situ biodegradation.Frontiers in microbiology · 2012Article
- Extraction of bacterial RNA from soil: challenges and solutions.Microbes and environments · 2012Review
- Design and verification of a pangenome microarray oligonucleotide probe set for Dehalococcoides spp.Applied and environmental microbiology · 2011Article
- Amplification of viral RNA from drinking water using TransPlex™ whole-transcriptome amplification.Journal of applied microbiology · 2011Article
- Using DNA microarrays to assay part function.Methods in enzymology · 2011Article
- Development of an environmental functional gene microarray for soil microbial communities.Applied and environmental microbiology · 2010Article
- Detecting variants with Metabolic Design, a new software tool to design probes for explorative functional DNA microarray development.BMC bioinformatics · 2010Article
- Technical considerations in using DNA microarrays to define regulons.Methods (San Diego, Calif.) · 2009Article
- Microbial Diagnostic Array Workstation (MDAW): a web server for diagnostic array data storage, sharing and analysis.Source code for biology and medicine · 2008Article
- Advances in monitoring of catabolic genes during bioremediation.Indian journal of microbiology · 2008Article
- Detection of viable but nonculturable Escherichia coli O157:H7 bacteria in drinking water and river water.Applied and environmental microbiology · 2008Article
- Microarray analysis of defined Mycobacterium tuberculosis populations using RNA amplification strategies.BMC genomics · 2008Article
- Prokaryotic lifestyles in deep sea habitats.Extremophiles : life under extreme conditions · 2008Review
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A new approach, termed whole-community RNA amplification (WCRA), was developed to provide sufficient amounts of mRNAs from environmental samples for microarray analysis. This method employs fusion primers (six to nine random nucleotides with an attached T7 promoter) for the first-strand synthesis. The shortest primer (T7N6S) gave the best results in terms of the yield and representativeness of amplification. About 1,200- to 1,800-fold amplification was obtained with amounts of the RNA templates ranging from 10 to 100 ng, and very representative detection was obtained with 50 to 100 ng total RNA. Evaluation with a Shewanella oneidensis Deltafur strain revealed that the amplification method which we developed could preserve the original abundance relationships of mRNAs. In addition, to determine whether representative detection of RNAs can be achieved with mixed community samples, amplification biases were evaluated with a mixture containing equal quantities of RNAs (100 ng each) from four bacterial species, and representative amplification was also obtained. Finally, the method which we developed was applied to the active microbial populations in a denitrifying fluidized bed reactor used for denitrification of contaminated groundwater and ethanol-stimulated groundwater samples for uranium reduction. The genes expressed were consistent with the expected functions of the bioreactor and groundwater system, suggesting that this approach is useful for analyzing the functional activities of microbial communities. This is one of the first demonstrations that microarray-based technology can be used to successfully detect the activities of microbial communities from real environmental samples in a high-throughput fashion.
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