NARO develops soybean-rhizobia symbiosis system with enhanced agricultural greenhouse gas reduction effects

A research group led by Group Leader Haruko Imaizumi-Anraku and Researcher Hanna Nishida from the Division of Plant Molecular Regulation Research at the Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), in collaboration with Tohoku University, Obihiro University of Agriculture and Veterinary Medicine, and RIKEN, announced on September 5 that they have developed a soybean-rhizobia symbiosis system. In this system, N₂O-reducing rhizobia (rhizobia with high N₂O (a greenhouse gas) decomposition capability) establish symbiosis at high dominance rates. Field cultivation tests confirmed that this symbiosis system reduced N₂O emissions after soybean harvest to approximately 26% of the control plot levels. These research findings are expected to lead to soybean cultivation with reduced environmental impact and were published in Nature Communications on September 4.

N₂O is a greenhouse gas with approximately 265 times the global warming potential of CO₂, and it must be reduced to prevent global warming. The IPCC Fifth Assessment Report indicates that agricultural N₂O accounts for approximately 60% of anthropogenic N₂O emissions.

Soybeans form symbiotic relationships with rhizobia in the soil, where rhizobia live within nodules formed on the roots and fix atmospheric nitrogen to provide it to the soybeans. Because soybeans can obtain atmospheric nitrogen as a nutrient source through nodule symbiosis, they have lower dependence on nitrogen fertilizers compared with other crops. On the other hand, it is known that N₂O is generated during the process of nodule aging and decomposition after soybean harvest.

Some rhizobia possess N₂O reductase genes and have the ability to decompose N₂O into nitrogen. Therefore, attempts have been made to reduce the N₂O released during nodule decomposition after the soybean harvest by inoculating and symbiosing soybeans with N₂O-reducing rhizobia that have high N₂O decomposition capability. However, many indigenous rhizobia in field soils either lack N₂O decomposition capability or have only weak capability. Therefore, when soybeans are planted in fields and inoculated with N₂O-reducing rhizobia, infection competition with indigenous rhizobia occurs, and the majority of nodules are colonized by indigenous rhizobia, resulting in a low proportion of nodules colonized by N₂O-reducing rhizobia and insufficient expression of N₂O reduction capability. Therefore, the joint research group developed a soybean symbiosis system that increases the proportion of nodules colonized by N₂O-reducing rhizobia by utilizing the "symbiotic incompatibility phenomenon" observed in nodule symbiosis.

The incompatibility phenomenon is known as a phenomenon where soybeans with specific "incompatibility genes" recognize proteins called "effectors" secreted by specific rhizobia, block the infection of those rhizobia, and prevent nodule formation. It was previously known that infection by rhizobia carrying the effector NopP122 is blocked by the soybean Rj2 gene, and that infection by rhizobia carrying the effectors NopP6 and NopP110 is blocked by the GmNNL1 gene. The research team created soybeans carrying both incompatibility genes Rj2 and GmNNL1, and selected N₂O-reducing rhizobia that no longer produce the effector NopP recognized by these incompatibility genes due to natural mutations. Since most indigenous bacteria carry NopP6, 110, and 122 type effectors, they cannot infect soybeans that have accumulated incompatibility genes. On the other hand, N₂O-reducing rhizobia that do not produce NopP effectors are thought to be able to establish dominant symbiosis with soybeans carrying incompatibility genes (Image).

The group verified the effectiveness of combining incompatibility gene-accumulating soybeans with N₂O-reducing rhizobia that do not produce NopP effectors. Equal amounts of competing rhizobia that produce effectors and N₂O-reducing rhizobia that do not produce effectors were mixed and inoculated into incompatibility gene-accumulating soybeans and soybean lines without incompatibility genes. As a result, in soybeans with incompatibility genes, the nodule occupancy rate of N₂O-reducing rhizobia exceeded 90%, and N₂O emissions from soil decreased to 15% of that from soybeans without incompatibility genes. Furthermore, in field trials, the nodule occupancy rate of N₂O-reducing rhizobia in incompatibility gene-accumulating soybeans was 64%, and N₂O emissions decreased to 26% of the test plots not inoculated with N₂O-reducing rhizobia.

Soybeans are widely cultivated around the world as food, feed, and oilseed crops. Compared with other crops, soybean cultivation is a food production system with lower levels of greenhouse gas emissions. However, the technology developed during this research can reduce the amount of N₂O released from these fields, enabling soybean production with reduced environmental impact and contributing to global warming mitigation.

This achievement was published in the scientific journal Nature Communications (September 4, 2025).

Imaizumi-Anraku commented: "While we were considering the relationship between incompatibility genes and effectors, we thought, 'Wouldn't it be nice if the rhizobia we want to make dominant didn't have effectors,' and that became the starting point of this research."

Nishida commented: "Soybeans are widely cultivated around the world, and their cultivation area is increasing with growing demand. We believe that by utilizing the results of this research in the future, we can reduce greenhouse gas emissions from soybean fields and contribute to global warming mitigation."

Journal Information
Publication: Nature Communications
Title: Genetic design of soybean hosts and bradyrhizobial endosymbionts reduces N₂O emissions from soybean rhizosphere
DOI: 10.1038/s41467-025-63223-6