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The first In vivo co-occurrence evidence of methane oxidation-nitrogen fixation in a single methanotrophic bacterial cell in rice root

Figure 1. A hypothetical scheme for the ecological interactions of type II methanotrophs-plant host-other soil bacteria in the methane oxidation and nitrogen fixation.

Methanotrophic bacteria are capable of removing greenhouse gas CH4 by methane oxidation; moreover, type II methanotrophic bacteria (a group of Alphaproteobacteria) can also fix nitrogen according to genomic analysis and pure bacterial cultivation-dependent studies. However, methane oxidation requires oxygen but nitrogen fixation occurs in anoxygenic condition. Whether these two “conflict” metabolisms in oxygen requirement can co-occur in a single methanotrophic bacterial cell in the nature environment that lacks no direct evidence.

Dr. Kiwamu Minamisawa at Graduate School of Life Science, Tohoku University, Japan, cooperated with Dr. Sen-Lin Tang at Biodiversity Research Center, Academia Sinica, and the core facility nanometer-scale secondary ion mass spectrometry (NanoSIMS) maintained by Institute of Astronomy and Astrophysics and Institute of Earth Science, Academia Sinica to search for the direct evidence of the co-occurrence mechanism of methane oxidation and nitrogen fixation. We applied techniques of next-generation sequencing, fluorescence in situ hybridization (FISH) and stable isotope probing to this study. We successfully identified type II methanotrophs that were dominantly responsible for both methane oxidation and nitrogen fixation in rice root. Moreover, in the single bacterial cells, our results proved that type II methanotrophs can perform two metabolic metabolisms simultaneously and showed their metabolic coupling relationship. In the 42 hours culture experiment, methane oxidation activity for each single type II methanotrophic cell exponentially increased. However, nitrogen fixation activity in some of type II methanotrophs slowed down after 23-hours incubation. That suggests the bacteria started sharing fixed nitrogen to the plant host. Our findings revealed the coupling between methane oxidation and nitrogen fixation in more details which may benefit in designing better sustainable management of rice field, especially on the aspect of reduction of greenhouse gas methane in rice paddy.


Our findings have been published on a prestigious journal of American Society for Microbiology, mBio.


Paper source:


Contributors for the paper:

  • Kiwamu Minamisawa’s Lab: Dr. Shintaro Hara (Co-first author), Dr. Meng Zhang (Co-author), Dr. Zhihua Bao (Co-author), Dr. Kiwamu Minamisawa (Co-corresponding author)
  • Sen-Lin Tang’s Lab: Dr. Naoshia Wada (Co-first author) and Dr. Sen-Lin Tang (Co-corresponding author)
  • The NanoSIMS Core Lab: Dr. Sliver Sung-Yun Hsiao (Co-corresponding author) and Dr. Der-Chuen Lee (Co-author, Leader of the Core Lab)
  • Lab of Electron Probe Microanalysis: Dr. Yoshiyuki Iizuka (Co-author)


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