Development and applications of functional gene microarrays in the analysis of the functional diversity, composition, and structure of microbial communities

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.

Keywords

functional gene arrays (FGAs) / GeoChip / microbial communities / functional diversity/composition/structure / environmental factor / ecosystem functioning

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Acknowledgments

This work has been partially supported through contracts DE-SC0004601 and DE-AC02-05CH11231 (as part of ENIGMA, a Scientific Focus Area) by the U.S. Department of Energy, Office of Science, Office of Biologic and Environmental Research, Genomics: GTL Foundational Science and Environmental Remediation Science Program (ERSP) Programs, and Oklahoma Applied Research Support (OARS), Oklahoma Center for the Advancement of Science and Technology (OCAST), the Oklahoma Bioenergy Center (OBC), and the State of Oklahoma through the Project AR062-034.

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