Development and applications of functional gene microarrays in the analysis of the functional diversity, composition, and structure of microbial communities |
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Authors: | Zhili He Joy D Van Nostrand Ye Deng and Jizhong Zhou |
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Institution: | (1) Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, OK, USA;(2) Department of Environmental Science and Engineering, Tsinghua University, Beijing, China; |
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Abstract: | Functional gene arrays (FGAs) are a special type of microarrays containing probes for key genes involved in microbial functional
processes, such as biogeochemical cycling of carbon, nitrogen, sulfur, phosphorus, and metals, biodegradation of environmental
contaminants, energy processing, and stress responses. GeoChips are considered as the most comprehensive FGAs. Experimentally
established probe design criteria and a computational pipeline integrating sequence retrieval, probe design and verification,
array construction, data analysis, and automatic update are used to develop the GeoChip technology. GeoChip has been systematically
evaluated and demonstrated to be a powerful tool for rapid, specific, sensitive, and quantitative analysis of microbial communities
in a high-throughput manner. Several generations of GeoChip have been developed and applied to investigate the functional
diversity, composition, structure, function, and dynamics of a variety of microbial communities from different habitats, such
as water, soil, marine, bioreactor, human microbiome, and extreme ecosystems. GeoChip is able to address fundamental questions
related to global change, bioenergy, bioremediation, agricultural operation, land use, human health, environmental restoration,
and ecological theories and to link the microbial community structure to environmental factors and ecosystem functioning. |
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Keywords: | |
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