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

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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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Authors and Affiliations

  1. Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, OK, 73019, USA

    Zhili He, Joy D. Van Nostrand, Ye Deng & Jizhong Zhou

  2. Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA

    Jizhong Zhou

  3. Department of Environmental Science and Engineering, Tsinghua University, Beijing, 100084, China

    Jizhong Zhou

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  1. Zhili He
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  2. Joy D. Van Nostrand
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  3. Ye Deng
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  4. Jizhong Zhou
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Correspondence to Jizhong Zhou.

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Jizhong Zhou is a Presidential Professor in the Department of Botany and Microbiology and Director for the Institute for Environmental Genomics, University of Oklahoma, Norman, OK, Adjunct Senior Scientist at Lawrence Berkeley National Laboratory, and Adjunct Professor at Tsinghua University, Beijing, China. He received a B.S. in Plant Pathology and Entomology in 1981, an M.S. in Insect Mathematical Ecology in 1984 from Hunan Agricultural University, China, and a Ph.D. in Molecular Genetics and Cell Biology in 1993 from Washington State University. He studied theoretical ecology and ecosystem modeling for three years at the Eco-Environmental Research Center, Chinese Academy of Sciences, Beijing, China. He worked at the Center for Microbial Ecology, Michigan State University, from 1993 to 1995 as a Postdoctoral Research Associate with James Tiedje. Before moving to OU in 2005, he worked at Oak Ridge National Laboratory as a Staff Scientist, Senior Staff Scientist, and then Distinguished Staff Scientist for 10 years. His expertise is in molecular biology, microbial genomics, microbial ecology, molecular evolution, theoretical ecology and genomic technologies. His laboratory has pioneered the development and use of genomic technologies for environmental studies in which GeoChip was awarded a 2009 R&D100 Award. He received a Presidential Early Career Award for Scientists and Engineers in 2001.

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He, Z., Van Nostrand, J.D., Deng, Y. et al. Development and applications of functional gene microarrays in the analysis of the functional diversity, composition, and structure of microbial communities. Front. Environ. Sci. Eng. China 5, 1–20 (2011). https://doi.org/10.1007/s11783-011-0301-y

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