Study reveals beneficial microbes that can sustain yields in unfertilized fields

Despite rice being the staple food for more than half of the world’s population, its cultivation remains highly resource-intensive, requiring large amounts of water and chemical fertilizers. Even as environmental concerns pertaining to global food security and climate change continue to mount, there is a growing interest in finding more sustainable ways to grow this essential crop.

Microbes in plant roots are known to play a vital role in helping plants survive. It’s known that plants can survive in poor soils by recruiting helpful microbes and forming symbiotic relationships, but we still don’t fully understand how these microbial communities form and function in real paddy-grown rice.

Now, in a study published in Plant and Cell Physiology on June 9, 2025, researchers from the Nara Institute of Science and Technology (NAIST) explore how naturally occurring root microbes in rice can support plant growth, potentially reducing the need for synthetic fertilizers.

The research team was led by Professor Yusuke Saijo and 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 University of Tokyo, Takumi Murakami and Yuichi Hongoh from Tokyo Institute of Technology, Rina Shinjo from Nagoya University, and Kiwamu Minamisawa from Tohoku University, Japan.

To this end, the researchers studied rice (Oryza sativa ssp. japonica) grown in an experimental field that has produced healthy rice crops for over 70 years without the addition of fertilizer or pesticides. They compared the root microbiomes from this field with those from a nearby conventionally fertilized field.

Using 16S rRNA gene sequencing, the team analyzed microbial DNA in the roots of three Japanese rice cultivars (Nipponbare, Hinohikari, and Kinmaze), collecting samples every two to three weeks throughout the growing season, over a span of one to four years.

Their analysis revealed that microbial diversity in the rice roots increased as the plants matured. In high-yielding, unfertilized field soils, rice roots were enriched with nitrogen-fixing bacteria capable of converting atmospheric nitrogen into a usable form for plants, effectively compensating for the absence of fertilizers.

Furthermore, anaerobic bacteria were more dominant during the early vegetative stage, while aerobic and microaerophilic bacteria became more prevalent during the reproductive and maturation stages, likely reflecting the typical rice cultivation practice of draining water draining the developmental transition time.

These findings provide valuable insights into how beneficial microbes assemble and function in the roots of rice grown in nutrient-poor soils. Such microbes could be isolated and leveraged to support sustainable rice cultivation.

Commenting on the possibilities this study opens up, Saijo says, “Looking ahead, isolating these beneficial bacteria and utilizing them in customized microbial blends could pave the way for sustainable rice farming.”

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Resource

Title: Field Dynamics of the Root Endosphere Microbiome Assembly in Paddy Rice Cultivated under No Fertilizer Input

Authors: Asahi Adachi, John Jewish Dominguez, Yuniar Devi Utami, Masako Fuji, Sumire Kirita, Shunsuke Imai, Takumi Murakami, Yuichi Hongoh, Rina Shinjo, Takehiro Kamiya, Toru Fujiwara, Kiwamu Minamisawa, Naoaki Ono, Shigehiko Kanaya, and Yusuke Saijo

Journal: Plant and Cell Physiology

DOI: 10.1093/pcp/pcaf045

The study was conducted by the Laboratory of Plant Immunity at NAIST, which aims to improve sustainable agriculture by leveraging beneficial microbes and strengthening plant immunity without overreliance on chemicals: https://bsw3.naist.jp/saijo/en/home/   

About Nara Institute of Science and Technology (NAIST)

Established in 1991, Nara Institute of Science and Technology (NAIST) is a national university located in Kansai Science City, Japan. In 2018, NAIST underwent an organizational transformation to promote and continue interdisciplinary research in the fields of biological sciences, materials science, and information science. Known as one of the most prestigious research institutions in Japan, NAIST lays a strong emphasis on integrated research and collaborative co-creation with diverse stakeholders. NAIST envisions conducting cutting-edge research in frontier areas and training students to become tomorrow's leaders in science and technology.

Website: https://www.naist.jp/en/