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

  • Zhili He
  • Joy D. Van Nostrand
  • Ye Deng
  • Jizhong Zhou
Feature Article

DOI: 10.1007/s11783-011-0301-y

Cite this article as:
He, Z., Van Nostrand, J.D., Deng, Y. et al. Front. Environ. Sci. Eng. China (2011) 5: 1. doi:10.1007/s11783-011-0301-y

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)GeoChipmicrobial communitiesfunctional diversity/composition/structureenvironmental factorecosystem functioning

Copyright information

© Higher Education Press and Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • Zhili He
    • 1
  • Joy D. Van Nostrand
    • 1
  • Ye Deng
    • 1
  • Jizhong Zhou
    • 1
    • 2
    • 3
  1. 1.Institute for Environmental Genomics, Department of Botany and MicrobiologyUniversity of OklahomaNormanUSA
  2. 2.Earth Sciences DivisionLawrence Berkeley National LaboratoryBerkeleyUSA
  3. 3.Department of Environmental Science and EngineeringTsinghua UniversityBeijingChina