Rice genes matter more than domestication in shaping plant microbiomes

(Press-News.org) Rice feeds more than half of the world’s population, but the tiny microbes living on and around rice plants may be just as important as the crop itself. A new study reveals that the specific genetic identity of a rice plant plays a stronger role than whether it is wild or domesticated in determining which microbes it hosts and how those microbes function.

The research, published in Agricultural Ecology and Environment, shows that differences among rice genotypes strongly shape microbial communities in both the soil surrounding roots, known as the rhizosphere, and on leaf surfaces, known as the phyllosphere. These microbes influence nutrient cycling, plant health, soil carbon storage, and responses to fertilizer use, all of which are critical for sustainable agriculture.

“Domestication has long been thought to be the dominant factor shaping crop microbiomes,” said lead author Yue Yin, a researcher specializing in plant–soil interactions. “Our results show that the genetic identity of individual rice varieties actually matters more. Even within the same species, different genotypes recruit very different microbial communities with distinct functions.”

The research team conducted a controlled greenhouse experiment using seven rice genotypes, including three widely cultivated varieties and four wild rice relatives. Plants were grown under low, moderate, and high nitrogen fertilization to test how genetics and management practices interact to influence plant-associated microbes.

Using advanced DNA sequencing and functional gene analysis, the scientists examined both bacterial and fungal communities in soil and on leaves. They also measured genes involved in carbon, nitrogen, phosphorus, and sulfur cycling, along with soil properties and plant traits.

Across nearly all measurements, rice genotype identity consistently explained more variation in microbial diversity and function than domestication status. This pattern held true for both belowground and aboveground microbiomes.

“In many cases, genotype differences outweighed the contrast between wild and cultivated rice,” said senior author Gui-Lan Duan. “This tells us that focusing only on domestication oversimplifies how crops interact with beneficial and harmful microbes.”

The study also found that nitrogen fertilization strongly influenced microbial communities, particularly in the rhizosphere. However, cultivated rice varieties were more sensitive to high nitrogen inputs than their wild relatives. In several cultivated genotypes, excessive nitrogen reduced microbial diversity and the abundance of genes involved in nutrient cycling.

“Wild rice showed a greater resilience to nitrogen enrichment,” Yin explained. “This suggests that traits lost during domestication may be important for stabilizing plant microbiomes under intensive fertilizer use.”

Beyond microbes, rice genotype identity also had a major influence on soil carbon storage and the elemental composition of rice leaves, including calcium, magnesium, zinc, and phosphorus. These chemical traits help shape which microbes can thrive on plant surfaces and in surrounding soils.

The findings have important implications for crop breeding and agricultural management. Rather than focusing only on yield or fertilizer responsiveness, breeders could select genotypes that naturally support beneficial microbial communities.

“Our results point to a new pathway for crop improvement,” said Duan. “By harnessing genetic diversity from both modern cultivars and wild rice, we can design crops that work together with their microbiomes to improve soil health, nutrient efficiency, and long-term sustainability.”

As agriculture faces growing pressure to reduce environmental impacts while feeding a rising global population, understanding how plant genetics shape microbial partners may offer a powerful tool. This study highlights that the future of sustainable rice production may lie not only in how crops are managed, but in which genes they carry.

 

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Journal Reference: Yin Y, Delgado-Baquerizo M, García-Palacios P, Zhang HM, Cheng WD, et al. 2025. Genotype identity overrides domestication status in shaping microbial diversity and functions in the rice rhizosphere and phyllosphere. Agricultural Ecology and Environment 1: e013  

https://www.maxapress.com/article/doi/10.48130/aee-0025-0013  

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About Agricultural Ecology and Environment: 

Agricultural Ecology and Environment (e-ISSN 3070-0639) is a multidisciplinary platform for communicating advances in fundamental and applied research on the agroecological environment, focusing on the interactions between agroecosystems and the environment. It is dedicated to advancing the understanding of the complex interactions between agricultural practices and ecological systems. The journal aims to provide a comprehensive and cutting-edge forum for researchers, practitioners, policymakers, and stakeholders from diverse fields such as agronomy, ecology, environmental science, soil science, and sustainable development. 

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