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High Oxygen Concentration Increases the Abundance and Activity of Bacterial Rather than Archaeal Nitrifiers in Rice Field Soil

  • Environmental Microbiology
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Abstract

Oxygen is considered as a limiting factor for nitrification in rice paddy soil. However, little is known about how the nitrifying microbial community responds to different oxygen concentrations at community and transcript level. In this study, soil and roots were harvested from 50-day-old rice microcosms and were incubated for up to 45 days under two oxygen concentrations: 2 % O2 and 20 % O2 (ambient air). Nitrification rates were measured from the accumulation of nitrite plus nitrate. The population dynamics of bacterial (AOB) and archaeal (AOA) ammonia oxidizers was determined from the abundance (using quantitative PCR (qPCR)) and composition (using terminal restriction fragment length polymorphism and cloning/sequencing) of their amoA genes, that of nitrite oxidizers (NOB) by quantifying the nxrA gene of Nitrobacter spp. and the 16S rRNA gene of Nitrospira spp. The activity of the nitrifiers was determined by quantifying the copy numbers of amoA and nxrA transcripts (using RT-qPCR). Different oxygen concentrations did not affect the community compositions of AOB, AOA, and NOB, which however were different between surface soil, bottom soil, and rice roots. However, nitrification rates were higher under ambient air than 2 % O2, and abundance and transcript activities of AOB, but not of AOA, were also higher. Abundance and transcript copy numbers of Nitrobacter were also higher at ambient air. These results indicate that AOB and NOB, but not AOA, were sensitive to oxygen availability.

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Acknowledgments

We thank the LOEWE Research Center “Synmicro,” the National High Technology Research and Development Program of China (863 program; grant no: 2012AA02A703), and the National Natural Science Foundation of China (grant no: 31400439) for financial support. We thank two anonymous reviewers for helpful comments.

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Authors and Affiliations

  1. Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China

    Xiubin Ke & Wei Lu

  2. Department Biogeochemistry, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse10, 35043, Marburg, Germany

    Xiubin Ke & Ralf Conrad

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  1. Xiubin Ke
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  2. Wei Lu
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Correspondence to Ralf Conrad.

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Ke, X., Lu, W. & Conrad, R. High Oxygen Concentration Increases the Abundance and Activity of Bacterial Rather than Archaeal Nitrifiers in Rice Field Soil. Microb Ecol 70, 961–970 (2015). https://doi.org/10.1007/s00248-015-0633-4

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