Genetic design of soybean hosts and bradyrhizobial endosymbionts reduces N2O emissions from soybean rhizosphere

Hanna Nishida, Manabu Itakura, Khin Thuzar Win, Feng Li, Kaori Kakizaki, Atsuo Suzuki, Satoshi Ohkubo, Luong Van Duc, Masayuki Sugawara, Koji Takahashi, Matthew Shenton, Sachiko Masuda, Arisa Shibata, Ken Shirasu, Yukiko Fujisawa, Misa Tsubokura, Hiroko Akiyama, Yoshikazu Shimoda, Kiwamu Minamisawa () and Haruko Imaizumi-Anraku ()
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Hanna Nishida: National Agriculture and Food Research Organization (NARO)
Manabu Itakura: Tohoku University
Khin Thuzar Win: National Agriculture and Food Research Organization (NARO)
Feng Li: National Agriculture and Food Research Organization (NARO)
Kaori Kakizaki: Tohoku University
Atsuo Suzuki: Tohoku University
Satoshi Ohkubo: Tohoku University
Luong Van Duc: Tohoku University
Masayuki Sugawara: Obihiro University of Agriculture and Veterinary Medicine
Koji Takahashi: National Agriculture and Food Research Organization (NARO)
Matthew Shenton: National Agriculture and Food Research Organization (NARO)
Sachiko Masuda: RIKEN Center for Sustainable Resource Science
Arisa Shibata: RIKEN Center for Sustainable Resource Science
Ken Shirasu: RIKEN Center for Sustainable Resource Science
Yukiko Fujisawa: National Agriculture and Food Research Organization (NARO)
Misa Tsubokura: National Agriculture and Food Research Organization (NARO)
Hiroko Akiyama: National Agriculture and Food Research Organization (NARO)
Yoshikazu Shimoda: National Agriculture and Food Research Organization (NARO)
Kiwamu Minamisawa: Tohoku University
Haruko Imaizumi-Anraku: National Agriculture and Food Research Organization (NARO)

Nature Communications, 2025, vol. 16, issue 1, 1-13

Abstract: Abstract Soybeans fix atmospheric N2 through symbiosis with rhizobia. The relationship between rhizobia and soybeans, particularly those with high nitrous oxide (N2O)-reducing (N2OR) activities, can be leveraged to reduce N2O emissions from agricultural soils. However, inoculating soybeans with these rhizobia under field conditions often fails because of the competition from indigenous rhizobia that possess low or no N2OR activity. In this work, we utilize natural incompatibility systems between soybean and rhizobia to address this challenge. Specifically, Rj2 and GmNNL1 inhibit certain rhizobial infections in response to NopP, an effector protein. By combining a soybean line with a hybrid accumulation of the Rj2 and GmNNL1 genes and bradyrhizobia lacking the nopP gene, we develop a soybean-bradyrhizobial symbiosis system in which strains with high N2OR activity predominantly infect. Our optimize symbiotic system substantially reduces N2O emissions in field and laboratory tests, presenting a promising approach for sustainable agricultural practices.

Date: 2025
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DOI: 10.1038/s41467-025-63223-6

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