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N₂O is one of the major greenhouse gases, with a global warming potential 265 times greater than that of carbon dioxide. Agricultural activities that sustain human food supply account for approximately 60% of anthropogenic N₂O emissions (IPCC Fifth Assessment Report, 2013), with emissions from farmland representing a significant proportion. Nitrogen is an essential nutrient for plant growth; however, large quantities of nitrogen fertilizers applied to farmland, as well as unharvested crop residues, are known sources of N₂O emissions. Consequently, the development of technologies to reduce N₂O emissions from farmland has become a globally important challenge.

Rhizobia are soil microorganisms that establish symbiosis inside root nodules of leguminous plants such as soybean, supplying atmospheric nitrogen as a nutrient to the host plant. Furthermore, some rhizobia possess the ability to reduce N₂O to dinitrogen, a major component of the atmosphere that does not directly contribute to the greenhouse effect.

To this end, trials have been conducted to inoculate soybeans with N₂O-reducing rhizobia that possess high N₂O-reducing rhizobia and promote their symbiosis, thereby reducing the N₂O released during the decomposition of root nodules after harvest (Fig. 1). However, soils in farmland harbor diverse indigenous rhizobia, many of which either lack N₂O-reducing capacity or possess only weak capacity (Fig. 1). When soybeans are planted and inoculated with N₂O-reducing rhizobia, infection competition with indigenous rhizobia occurs, and the majority of nodules end up being colonized by the indigenous strains. Consequently, the proportion of nodules hosting N₂O-reducing rhizobia remains low, and the overall N₂O-reduction potential cannot be fully achieved (Fig. 2, left).

To overcome this limitation, the joint research group established a soybean-rhizobium symbiotic system that increases the proportion of nodules colonized by N₂O-reducing rhizobia by leveraging a phenomenon known as symbiotic incompatibility. This phenomenon occurs when soybeans carrying specific incompatibility genes recognize effector proteins secreted by certain rhizobia and block their infection. The research group developed soybean lines harboring two incompatibility genes and selected N₂O-reducing rhizobia that had naturally lost the ability to produce the effectors. Combining these enabled N₂O-reducing rhizobia to preferentially infect and form nodules with soybeans carrying incompatibility genes (Fig. 2, right).

Laboratory experiments showed that, in soybeans with incompatibility genes, more than 90% of nodules were colonized by N₂O-reducing rhizobia, and N₂O emissions from soil were reduced to 15% of that in soybeans lacking incompatibility genes. Furthermore, field trials demonstrated that nodule occupancy by N₂O-reducing rhizobia reached 64%, and N₂O emissions were reduced to 26% compared to uninoculated plots.

Soybean is cultivated worldwide as a source of food, feed, and oil. Soybean cultivation is inherently a low-emission food production system; however, the technology developed in this study enables a substantial reduction in N₂O emissions from soybean fields, facilitating more environmentally sustainable soybean production and contributing to global warming mitigation.

This study was published in the scientific journal Nature Communications on September 4, 2025.