New Study Reveals Role of Root Bacteria in Rice Resilience

Despite being the primary food for more than half of the world's population, rice cultivation is very resource-intensive, necessitating vast amounts of water and artificial fertilizers. Even as environmental worries about global food security and climate change grow, there is an increasing interest in developing more sustainable ways to raise this vital commodity.

Image credit: FenlioQ/Shutterstock.com

Microbes found in plant roots are recognized to play an important role in plant survival. Plants can survive in poor soils by recruiting beneficial microbes and developing symbiotic partnerships, but how these microbial communities originate and function in actual paddy-grown rice is not yet understood.

In a study published in Plant and Cell Physiology on June 9^th, 2025, researchers from the Nara Institute of Science and Technology (NAIST) investigated how naturally existing root microbes in rice can boost plant growth, thereby eliminating the need for synthetic fertilizers.

Professor Yusuke Saijo led the research team, which included Asahi Adachi, John Jewish Dominguez, Masako Fuji, Yuniar Devi Utami, Sumire Kirita, Shunsuke Imai, Naoaki Ono, and Shigehiko Kanaya from NAIST, Takehiro Kamiya, and Toru Fujiwara from the University of Tokyo, Takumi Murakami and Yuichi Hongoh from the Tokyo Institute of Technology, Rina Shinjo from Nagoya University, and Kiwamu Minamisawa from Tohoku University in Japan.

Rice (Oryza sativa ssp. japonica) cultivated in an experimental field that has yielded nutritious rice harvests for more than 70 years without the use of fertilizer or pesticides was the subject of the study to achieve this goal. The root microbiomes from this field were compared with those from a routinely fertilized field nearby.

The researchers collected samples every two to three weeks during the growth season, spanning one to four years, and used 16S rRNA gene sequencing to study microbial DNA in the roots of three Japanese rice cultivars (Nipponbare, Hinohikari, and Kinmaze).

According to their investigation, as the plants grew older, the microbial diversity in the rice roots rose. Rice roots were enhanced with nitrogen-fixing bacteria in high-yielding, unfertilized field soils. These bacteria could transform atmospheric nitrogen into a form that plants could use, so making up for the lack of fertilizers.

Moreover, aerobic and microaerophilic bacteria became more common during the reproductive and maturation stages, whereas anaerobic bacteria were more common during the early vegetative stage. This is probably due to the common practice of draining water during the developmental transition period in rice cultivation.

These results shed important light on the assembly and activity of beneficial microbes in rice roots cultivated in nutrient-poor soils. These microorganisms might be separated and used to promote environmentally friendly rice farming.

Looking ahead, isolating these beneficial bacteria and utilizing them in customized microbial blends could pave the way for sustainable rice farming.

Rina Shinjo, Assistant Professor, Nagoya University