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Detection and Diversity of the Nitrite Oxidoreductase Alpha Subunit (nxrA) Gene of Nitrospina in Marine Sediments

  • Environmental Microbiology
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Abstract

Nitrite-oxidizing bacteria (NOB) are chemolithoautotrophs that catalyze the oxidation of nitrite to nitrate, which is the second step of aerobic nitrification. In marine ecosystems, Nitrospina is assumed to be a major contributor to nitrification. To date, two strains of Nitrospina have been isolated from marine environments. Despite their ecological relevance, their ecophysiology and environmental distribution are understudied owing to fastidious cultivation techniques and the lack of a sufficient functional gene marker. To estimate the abundance, diversity, and distribution of Nitrospina in various marine sediments, we used nxrA, which encodes the alpha subunit of nitrite oxidoreductase, as a functional and phylogenetic marker. We observed that Nitrospina diversity in polar sediments was significantly lower than that of non-polar samples. Moreover, nxrA-like sequences revealed an unexpected diversity of Nitrospina, with approximately 41,000 different sequences based on a 95% similarity cutoff from six marine sediments. We detected nxrA gene copy numbers of up to 3.57 × 104 per gram of marine sediment sample. The results of this study provide insight into the distribution and diversity of Nitrospina, which is fundamentally important for understanding their contribution to the nitrogen cycle in marine sediments.

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Acknowledgments

This work was supported by a National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIP) (no. 2015R1C1A1A01053750) and the C1 Gas Refinery Program through the NRF funded by the Ministry of Science, ICT & Future Planning (no. 2015M3D3A1A01064881). We thank the editor and two anonymous reviewers for their constructive and scientific comments, which helped us to improve the manuscript.

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  1. Department of Biology, Jeju National University, 102 Jejudaehak-ro, Jeju, 63243, Republic of Korea

    Sundas Rani, Hyeon-Woo Koh & Soo-Je Park

  2. Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Cheongju, 28644, Republic of Korea

    Sung-Keun Rhee

  3. Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan

    Hirotsugu Fujitani

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  1. Sundas Rani
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Correspondence to Hirotsugu Fujitani or Soo-Je Park.

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Rani, S., Koh, HW., Rhee, SK. et al. Detection and Diversity of the Nitrite Oxidoreductase Alpha Subunit (nxrA) Gene of Nitrospina in Marine Sediments. Microb Ecol 73, 111–122 (2017). https://doi.org/10.1007/s00248-016-0897-3

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