Metagenomics analysis of belowground microbial communities using microarrays
Joy D. Van Nostrand, Zhili He and Jizhong Zhou
from: Metagenomics: Current Innovations and Future Trends (Edited by: Diana Marco). Caister Academic Press, U.K. (2011)
The use of microarrays has revolutionized the field of microbiology. While many types of microarrays are available, the functional gene arrays (FGAs) afford a way to link environmental processes with microbial communities. FGAs probe for a wide range of genes involved in functional activities of interest to microbial ecology (e.g. carbon degradation, N2-fixation, metal resistance) from many different microorganisms, cultured and uncultured. The most comprehensive FGA reported to date are the GeoChip arrays. GeoChip 3.0 targets tens of thousands of genes involved in the geochemical cycling of carbon, nitrogen, phosphorus, and sulphur, metal resistance and reduction, energy processing, antibiotic resistance and contaminant degradation as well as phylogenetic information (gyrB). This technology has been used successfully to examine the effects of global climate change on microbial communities. This chapter provides an overview of FGA development with a focus on the GeoChip. Several GeoChip studies, which have established the GeoChip's worth as a rapid, sensitive and specific tool for the examination of microbial communities, will be highlighted read more ...