Chapter 14 : Monitoring Microbial Activity with GeoChip

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This chapter focuses on functional gene arrays (FGAs). Researchers have designed an array containing oligonucleotide probes for 59 / genes to study methanotrophs. This array was later expanded to cover 68 genes and was used to study methanotrophic communities from simulated landfills using DNA and mRNA. The utility of microarrays was further expanded when microarrays were tested and used to study microbial communities. The latest version of the GeoChip is version 3.0, which covers 56,990 sequences from 292 gene families. The signal intensity of the common oligo reference standard (CORS) probe is then used to normalize the signal intensity of the sample and allows a comparison of hybridization results among different samples. A computational pipeline has also been developed for GeoChip probe design and data analysis. Methods commonly used for descriptive and exploratory data analysis include unconstrained ordination, hierarchical cluster analysis, and neural network analysis. While GeoChip is generally used to examine the presence of functional genes in the environment, some studies have examined microbial activity. While many advances have been made in FGA technology in the past decade, there are still challenges that need to be addressed in the future. FGAs, specifically, the GeoChips, are powerful tools in linking microbial function to ecosystem processes and are able to provide sensitive, specific, and potentially quantitative information. This technology is expected to transform the field of microbial ecology and the study of microbial community functional structure and dynamics.

Citation: Van Nostrand J, Kang S, Deng Y, Liang Y, He Z, Zhou J. 2011. Monitoring Microbial Activity with GeoChip, p 261-281. In Stolz J, Oremland R (ed), Microbial Metal and Metalloid Metabolism. ASM Press, Washington, DC. doi: 10.1128/9781555817190.ch14

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CCA and VPA results of metal resistance and reduction microbial communities. CCA model was most significant ( = 0.017). 10.1128/9781555817190.ch14.f1

Citation: Van Nostrand J, Kang S, Deng Y, Liang Y, He Z, Zhou J. 2011. Monitoring Microbial Activity with GeoChip, p 261-281. In Stolz J, Oremland R (ed), Microbial Metal and Metalloid Metabolism. ASM Press, Washington, DC. doi: 10.1128/9781555817190.ch14
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