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

  • Nasrin Sultana
  • Jun ZhaoEmail author
  • Yan Zheng
  • Yuanfeng Cai
  • Muhammad Faheem
  • Xianlong Peng
  • Weidong Wang
  • Zhongjun JiaEmail author
Original Paper


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.


Methanotrophs Cold-temperate paddy soil DNA-based stable isotope probing High-throughput sequencing 



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

Funding information

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).

Supplementary material

374_2018_1334_MOESM1_ESM.docx (1.2 mb)
ESM 1 (DOCX 1239 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil ScienceChinese Academy of SciencesJiangsu ProvincePeople’s Republic of China
  2. 2.University of Chinese Academy of SciencesBeijingChina
  3. 3.School of Food and BioengineeringZhengzhou University of Light IndustryZhengzhouChina
  4. 4.College of Resources and EnvironmentNortheast Agricultural UniversityHarbinChina
  5. 5.Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and BiotechnologyHeilongjiang Bayi Agricultural UniversityDaqingChina

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