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

doi:10.1007/s11783-011-0301-y

Front Envir Sci Eng Chin

2011, Vol. 5

Issue (1) : 1-20 https://doi.org/10.1007/s11783-011-0301-y

FEATURE ARTICLE

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

Zhili HE¹, Joy D. VAN NOSTRAND¹, Ye DENG¹, Jizhong ZHOU^1,2,3(

)

1. Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA; 2. Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; 3. Department of Environmental Science and Engineering, Tsinghua University, Beijing 100084, 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.

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

Corresponding Author(s): ZHOU Jizhong,Email:jzhou@ou.edu

Issue Date: 05 March 2011

Cite this article:

Joy D. VAN NOSTRAND,Ye DENG,Jizhong ZHOU, et al. Development and applications of functional gene microarrays in the analysis of the functional diversity, composition, and structure of microbial communities[J]. Front Envir Sci Eng Chin, 2011, 5(1): 1-20.

URL:

https://academic.hep.com.cn/fese/EN/10.1007/s11783-011-0301-y
https://academic.hep.com.cn/fese/EN/Y2011/V5/I1/1

Fig.1 Schematic presentation of GeoChip development and applications in analysis of microbial communities from a variety of habitats. A. GeoChip development; B. Target preparation; C. GeoChip data analysis. This figure is adapted from Fig. 1 by Zhou et al. []

Fig.2

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