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Development of a whole community genome amplification-assisted DNA microarray method to detect functional genes involved in the nitrogen cycle

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Abstract

A novel DNA microarray analysis targeting key functional genes involved in most nitrogen cycling reactions was developed to comprehensively analyze microbial populations associated with the nitrogen cycle. The developed microarray contained 876 oligonucleotide probes based on the nucleotide sequences of the nif, amo, hao/hzo, nap, nar, nirK, nirS, nrf, cnor, qnor and nos genes. An analytical method combining detection by the designed microarray with whole community genome amplification was then applied to monitor the nitrogen cycling microorganisms in river water and wastewater treatment sludge samples. The developed method revealed that nitrogen cycling microorganisms in river water appeared to become less diverse in response to input of effluent from municipal wastewater treatment plants. Additionally, the nitrogen cycling community associated with anaerobic ammonium oxidation and partial nitrification reactors could be reasonably analyzed by the developed method. However, the results obtained for two activated sludge samples from municipal wastewater treatment plants with almost equivalent wastewater treatment performance differed greatly from each other. These results suggested that the developed method is useful for comprehensive analysis of nitrogen cycling microorganisms, although its applicability to complex samples with abundant untargeted populations should be further examined.

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Acknowledgments

This study was partly supported by the Global COE Program, “Evaluation of Research and Education on Integrated River Basin Management in Asian Region” of the University of Yamanashi, which was sponsored by the Japan Society for the Promotion of Science (JSPS) and by a grant from the Kurita Water Environment Foundation, Japan. We thank Dr. Kazuichi Isaka from Hitachi Plant Technologies, Ltd., Japan (Presently, Hitachi, Ltd., Japan) for kindly providing the partial nitrification sludge samples.

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Authors and Affiliations

  1. Department of Health Science, Kitasato University, 1-15-1 Kitasato, Sagamihara-Minami, Kanagawa, 252-0373, Japan

    Daisuke Inoue & Kazunari Sei

  2. Division of Sustainable Energy and Environmental Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan

    Daisuke Inoue, Junqin Pang, Masami Matsuda, Kazunari Sei & Michihiko Ike

  3. International Research Centre for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi, 400-8511, Japan

    Kei Nishida

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  1. Daisuke Inoue
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  2. Junqin Pang
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  3. Masami Matsuda
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  4. Kazunari Sei
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  5. Kei Nishida
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  6. Michihiko Ike
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Correspondence to Michihiko Ike.

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Inoue, D., Pang, J., Matsuda, M. et al. Development of a whole community genome amplification-assisted DNA microarray method to detect functional genes involved in the nitrogen cycle. World J Microbiol Biotechnol 30, 2907–2915 (2014). https://doi.org/10.1007/s11274-014-1718-9

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  • DOI: https://doi.org/10.1007/s11274-014-1718-9

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