GeoChip 4: a functional gene-array-based high-throughput environmental technology for microbial community analysis

Authors

  • Qichao Tu,

    1. Department of Microbiology and Plant Biology, Institute for Environmental Genomics (IEG), University of Oklahoma, Norman, OK, USA
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    • These two authors contributed equally to this work.
  • Hao Yu,

    1. Department of Microbiology and Plant Biology, Institute for Environmental Genomics (IEG), University of Oklahoma, Norman, OK, USA
    2. State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
    3. School of Environmental Science and Engineering, Liaoning Technical University, Fuxin, Liaoning, China
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    • These two authors contributed equally to this work.
  • Zhili He,

    1. Department of Microbiology and Plant Biology, Institute for Environmental Genomics (IEG), University of Oklahoma, Norman, OK, USA
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  • Ye Deng,

    1. Department of Microbiology and Plant Biology, Institute for Environmental Genomics (IEG), University of Oklahoma, Norman, OK, USA
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  • Liyou Wu,

    1. Department of Microbiology and Plant Biology, Institute for Environmental Genomics (IEG), University of Oklahoma, Norman, OK, USA
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  • Joy D. Van Nostrand,

    1. Department of Microbiology and Plant Biology, Institute for Environmental Genomics (IEG), University of Oklahoma, Norman, OK, USA
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  • Aifen Zhou,

    1. Department of Microbiology and Plant Biology, Institute for Environmental Genomics (IEG), University of Oklahoma, Norman, OK, USA
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  • James Voordeckers,

    1. Department of Microbiology and Plant Biology, Institute for Environmental Genomics (IEG), University of Oklahoma, Norman, OK, USA
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  • Yong-Jin Lee,

    1. Department of Microbiology and Plant Biology, Institute for Environmental Genomics (IEG), University of Oklahoma, Norman, OK, USA
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  • Yujia Qin,

    1. Department of Microbiology and Plant Biology, Institute for Environmental Genomics (IEG), University of Oklahoma, Norman, OK, USA
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  • Christopher L. Hemme,

    1. Department of Microbiology and Plant Biology, Institute for Environmental Genomics (IEG), University of Oklahoma, Norman, OK, USA
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  • Zhou Shi,

    1. Department of Microbiology and Plant Biology, Institute for Environmental Genomics (IEG), University of Oklahoma, Norman, OK, USA
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  • Kai Xue,

    1. Department of Microbiology and Plant Biology, Institute for Environmental Genomics (IEG), University of Oklahoma, Norman, OK, USA
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  • Tong Yuan,

    1. Department of Microbiology and Plant Biology, Institute for Environmental Genomics (IEG), University of Oklahoma, Norman, OK, USA
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  • Aijie Wang,

    1. Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
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  • Jizhong Zhou

    Corresponding author
    1. Department of Microbiology and Plant Biology, Institute for Environmental Genomics (IEG), University of Oklahoma, Norman, OK, USA
    2. State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
    3. Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
    • Correspondence: Jizhong Zhou, Fax: 405 325 7552; E-mail: jzhou@ou.edu

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Abstract

Micro-organisms play critical roles in many important biogeochemical processes in the Earth's biosphere. However, understanding and characterizing the functional capacity of microbial communities are still difficult due to the extremely diverse and often uncultivable nature of most micro-organisms. In this study, we developed a new functional gene array, GeoChip 4, for analysing the functional diversity, composition, structure, metabolic potential/activity and dynamics of microbial communities. GeoChip 4 contained approximately 82 000 probes covering 141 995 coding sequences from 410 functional gene families related to microbial carbon (C), nitrogen (N), sulphur (S), and phosphorus (P) cycling, energy metabolism, antibiotic resistance, metal resistance/reduction, organic remediation, stress responses, bacteriophage and virulence. A total of 173 archaeal, 4138 bacterial, 404 eukaryotic and 252 viral strains were targeted, providing the ability to analyse targeted functional gene families of micro-organisms included in all four domains. Experimental assessment using different amounts of DNA suggested that as little as 500 ng environmental DNA was required for good hybridization, and the signal intensities detected were well correlated with the DNA amount used. GeoChip 4 was then applied to study the effect of long-term warming on soil microbial communities at a Central Oklahoma site, with results indicating that microbial communities respond to long-term warming by enriching carbon degradation, nutrient cycling (nitrogen and phosphorous) and stress response gene families. To the best of our knowledge, GeoChip 4 is the most comprehensive functional gene array for microbial community analysis.

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