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Chapter 83 : Functional Gene Arrays for Microbial Community Analysis
The major advantage of microarrays is that attachment to the solid surface confers the ability to print an enormous number of different probes (thousands to hundreds of thousands per square centimeter) on an individual array. The authors proposed that microarrays of potential use for environmental samples can be divided into three or more major groups based on the type of nucleic acid probes arrayed including (i) phylogenetic oligonucleotide arrays (POAs), (ii) community genome arrays (CGAs), and (iii) functional gene arrays (FGAs). Due to the analytical versatility of FGAs, this chapter focuses on their development, application, and use in characterizing functional genes involved in biogeochemical processes and bioremediation. Along with the size and sequence of the FGA probes, the temperature and composition of the hybridization solution control the stringency of hybridization. It is preferable to use highly specific hybridization conditions for FGAs because of the potential for many similar sequences to be present. Researchers have successfully used FGAs to examine microbial involvement in several environmental processes including nitrogen fixation, nitrification, denitrification, and sulfate reduction in freshwater and marine systems; degradation of organic contaminants including polychlorinated biphenyls and polycyclic aromatic hydrocarbons in soils and sediments; and methane-oxidizing capacity and diversity in landfill-simulating soil. Development of prokaryotic mRNA amplification methods will likely broaden the range of samples for which FGA analysis of microbial activity is possible.
Freely available programs for oligonucleotide probe design