Sat, 26 Jul 2008 17:26:58 BST CiteULike: vrich Zhou http://www.citeulike.org/user/vrich/author/Zhou CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/vrich/article/2802979 <i>Appl. Environ. Microbiol., Vol. 72, No. 7. (1 July 2006), pp. 4931-4941.</i><br /><br />Microarray technology provides the opportunity to identify thousands of microbial genes or populations simultaneously, but low microbial biomass often prevents application of this technology to many natural microbial communities. We developed a whole-community genome amplification-assisted microarray detection approach based on multiple displacement amplification. The representativeness of amplification was evaluated using several types of microarrays and quantitative indexes. Representative detection of individual genes or genomes was obtained with 1 to 100 ng DNA from individual or mixed genomes, in equal or unequal abundance, and with 1 to 500 ng community DNAs from groundwater. Lower concentrations of DNA (as low as 10 fg) could be detected, but the lower template concentrations affected the representativeness of amplification. Robust quantitative detection was also observed by significant linear relationships between signal intensities and initial DNA concentrations ranging from (i) 0.04 to 125 ng (r2 = 0.65 to 0.99) for DNA from pure cultures as detected by whole-genome open reading frame arrays, (ii) 0.1 to 1,000 ng (r2 = 0.91) for genomic DNA using community genome arrays, and (iii) 0.01 to 250 ng (r2 = 0.96 to 0.98) for community DNAs from ethanol-amended groundwater using 50-mer functional gene arrays. This method allowed us to investigate the oligotrophic microbial communities in groundwater contaminated with uranium and other metals. The results indicated that microorganisms containing genes involved in contaminant degradation and immobilization are present in these communities, that their spatial distribution is heterogeneous, and that microbial diversity is greatly reduced in the highly contaminated environment. 10.1128/AEM.02738-05 Microarray-Based Analysis of Subnanogram Quantities of Microbial Community DNAs by Using Whole-Community Genome Amplification Liyou Wu Xueduan Liu Christopher Schadt Jizhong Zhou doi:10.1128/AEM.02738-05 Appl. Environ. Microbiol., Vol. 72, No. 7. (1 July 2006), pp. 4931-4941. 2008-05-15T23:34:38-00:00 2006 Appl. Environ. Microbiol. 72 7 4931 4941 geochip mda microarray http://www.citeulike.org/user/vrich/article/2802959 <i>Appl. Environ. Microbiol., Vol. 73, No. 2. (1 January 2007), pp. 563-571.</i><br /><br />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. 10.1128/AEM.01771-06 Microarray-Based Analysis of Microbial Community RNAs by Whole-Community RNA Amplification Haichun Gao Zamin Yang Terry Gentry Liyou Wu Christopher Schadt Jizhong Zhou doi:10.1128/AEM.01771-06 Appl. Environ. Microbiol., Vol. 73, No. 2. (1 January 2007), pp. 563-571. 2008-05-15T23:32:04-00:00 2007 Appl. Environ. Microbiol. 73 2 563 571 geochip microarray http://www.citeulike.org/user/vrich/article/1429519 <i>Microbial Ecology, Vol. 53, No. 3. (April 2007), pp. 498-506.</i> Unravelling Microbial Communities with DNA-Microarrays: Challenges and Future Directions Wagner Michael Smidt Hauke Loy Alexander Zhou Jizhong doi:10.1007/s00248-006-9197-7 Microbial Ecology, Vol. 53, No. 3. (April 2007), pp. 498-506. 2007-07-02T21:31:41-00:00 2007 Microbial Ecology 0095-3628 53 3 498 506 Springer arrays