Plant genes influence bacterial evolution in legume-bacteria partnership

UNIVERSITY PARK, Pa. — Legumes like soybeans, alfalfa, peas, beans, peanuts and many more have a remarkable ability: They can partner with soil bacteria called rhizobia to capture nitrogen from the air in a biological process called nitrogen fixation. It is a mutualistic relationship — both the plant and bacteria benefit — that provides nitrogen in an accessible form that is essential for plant growth and sustainable agriculture.

Not just any rhizobia will do, however, as specific rhizobia match with specific plants for the best crop outcome, according to a team led by Penn State researchers, who wanted to learn how specific plant genes determine which rhizobia can form relationships. In a study published in The ISME Journal, they describe the complex relationship between plant host genes and rhizobial genes, and how plant genes strongly influence which rhizobial strains plants chose from a diverse mixture.

“We identified a core set of rhizobial genes that altered bacterial strain success when plant genes were disrupted,” said study senior author and team leader Liana Burghardt, assistant professor in Penn State’s College of Agricultural Sciences. “Our results reveal how genetic mutations in plant hosts alter which genes are important for bacterial strain success, setting the stage for scientists to develop improved rhizobial strains for agricultural inoculants and breed legume hosts better adapted to field environments where many strains coexist.”

Rhizobia live inside specialized structures on plant roots called nodules, where they convert atmospheric nitrogen into a form the plant can use, explained study first author Sohini Guha, postdoctoral scholar in the Department of Plant Science. In return, the plant provides rhizobia with nutrients and a safe place to live. Like any complex biological phenomenon, this partnership is heavily moderated by interactions between the partners.

The outcome of the interaction depends not just on the legume or rhizobial genetic makeup alone, but on the specific combination of both, Guha noted, and different hosts can favor or suppress different rhizobial strains, leading to variation in performance across pairings. In nature, legumes encounter dozens of rhizobial strains at a time, each having a slightly different genetic makeup.

“When a legume plant puts out its roots, it isn't just reaching for water and nutrients — it is sending out chemical invitations to bacteria in the soil,” she said. “These bacteria — rhizobia — can take up residence in root nodules and fix atmospheric nitrogen for the plant, acting as a built-in fertilizer. But the plant doesn't let just any bacterium in. It screens candidates, and the outcome of that screening depends heavily on the plant's own genes.”

In this study, Guha added, the researchers asked a pointed question: What happens to that bacterial screening process when specific plant genes are broken? To find out, they grew legume plants with defined genetic mutations — plants missing particular genes involved in the interaction with the bacteria — and exposed them to a controlled community of rhizobial strains. Then they watched to see which bacteria ended up winning out inside which plants.

To see how plant genes affect the selection of soil bacteria, the researchers studied a well-known plant-bacteria partnership involving a plant commonly called barrel medic — a small, annual, clover-like legume closely related to alfalfa — and a rhizobial strain called Sinorhizobium. Native to the Mediterranean region, the relationship is widely used as a model for legume biology, nitrogen fixation and symbiotic relationships.

The researchers introduced a mixture of 86 Sinorhizobium bacterial strains to 18 barrel medic plant hosts that had mutated — or altered — genes known to be important for forming root nodules, to see which strains thrived and which struggled. They found that bacterial success was not consistent. Some strains of bacteria did better in certain mutants; others did worse. This suggests that plant genes direct bacterial evolutionary trajectories by changing which strains reproduce the most, the researchers said.

When plant genes are disrupted, they alter the selective environment that the rhizobia experience, and strains that were previously at equal fitness behave differently following gene disruption, Guha explained.

“We wanted to see how individual host genes influence rhizobial fitness, an important metric for maintaining stable populations of nitrogen-fixing bacterial strains in soil and also identify the potential candidate genes in rhizobia that were responsible for negotiating root nodule formation,” she said. “This study presents a bird’s-eye view of the selection landscape of the Sinorhizobium genome in the absence of host genes that underlie effective symbiosis.”

This research was completed using computing resources provided by the Penn State Institute for Computational and Data Science, and genome sequencing was performed by the Huck Genomics Core Facility.

The study was supported by a U.S. National Science Foundation Plant Genome Research grant and represents a multi-institutional collaboration between researchers at Penn State, North Dakota State University, the Stowers Institute for Medical Research and the University of Minnesota.

Co-authors on the study at Penn State were Regina Bledsoe, former lab technician in the Burghardt lab; Jeremy Sutherland, former postdoctoral researcher in the Burghardt lab; Gwendolyn Fry, undergraduate student majoring in biology and in anthropology; and Alejandra Gil-Polo, doctoral degree candidate in plant biology. Other co-authors included Brendan Epstein, postdoctoral scholar, University of Minnesota College of Biological Sciences; Vikram Venugopal and Siva Sankari, Stowers Institute for Medical Research; Garrett Levin, microbiology doctoral student, North Dakota State University; Barney Geddes, assistant professor, North Dakota State University; Nevin Young, Distinguished McKnight Professor, University of Minnesota, Department of Plant Pathology; and Peter Tiffin, professor, plant and microbial biology, University of Minnesota.

This work was also supported by the U.S. Department of Agriculture’s National Institute of Food and Agriculture and Penn State College of Agricultural Sciences startup funds.