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Stable isotope probing of active methane oxidizers in rice field soils from cold regions

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Abstract

DNA-based stable isotope probing (DNA-SIP) was employed to establish direct link between methane oxidation activity and the taxonomic identity of active methanotrophs in three rice field soils from Jian-San-Jiang (one baijiang origin soil, JB and one meadow origin soil, JM) and Qing-An (meadow origin soil, QA) districts in Northeastern China. Following microcosm incubation under 1% v/v13CH4 condition, soil organic 13C atom percent significantly increased from background 1.08 to 1.21% in average, indicating the biomass synthesis supported by methanotrophy. Real-time PCR analysis of methanotroph-specific biomarker pmoA genes of the buoyant density for DNA gradient, following the ultracentrifugation of the total DNA extracted from SIP microcosms, indicated an enrichment of methanotroph genomes in 13C-labeled DNA. It suggested propagation of microbial methane oxidizers in soils. High-throughput sequencing of 16S rRNA and pmoA genes from 13C-labeled DNA further revealed a diverse guild of both type I and II methanotrophs in all three soils. Specifically, Methylobacter-affiliated type I methanotrophs dominated the methanotrophic activity in JB and JM soils, whereas Methylocystis-affiliated type II methanotrophs dominated QA soil. This implied the physiological diversification of soil methanotrophs that might be due to constant environmental fluctuations in paddies.

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Acknowledgments

Nasrin Sultana gratefully acknowledged the Organization for Women in Science for the Developing World (OWSD) for a PhD Fellowship program.

Funding

This study is financially supported by the National Science Foundation of P.R. China (41501276, 41701302, 91751204), the Open Foundation of the Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region (201714), and the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB15040000).

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Authors and Affiliations

  1. State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, Jiangsu Province, People’s Republic of China

    Nasrin Sultana, Jun Zhao, Yuanfeng Cai, Muhammad Faheem & Zhongjun Jia

  2. University of Chinese Academy of Sciences, Beijing, 100049, China

    Nasrin Sultana & Muhammad Faheem

  3. School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, 450002, Henan Province, China

    Yan Zheng

  4. College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China

    Xianlong Peng

  5. Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, China

    Weidong Wang

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  1. Nasrin Sultana
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  2. Jun Zhao
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Correspondence to Jun Zhao or Zhongjun Jia.

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Sultana, N., Zhao, J., Zheng, Y. et al. Stable isotope probing of active methane oxidizers in rice field soils from cold regions. Biol Fertil Soils 55, 243–250 (2019). https://doi.org/10.1007/s00374-018-01334-7

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  • DOI: https://doi.org/10.1007/s00374-018-01334-7

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