It is well known that soil microbes affect plant growth. But the extent of these interactions is not well understood. Using Acmispon strigosus (a native California plant with nodules) and a set of eight nitrogen-fixing bacterial strains, researchers unpacked some of the questions that surround interstrain competition.

Researchers infected plants with each of the eight Bradyrhizobium strains, individually, to measure their ability to provide benefits. The strains, which vary in their capacity to fix nitrogen symbiotically the host plant, were also tested in full-factorial coinoculation experiments involving 28 pairwise strain combinations and the effect on plant performance was measured. In doing so, the researchers found that competition between strains of beneficial bacteria in the soil diminishes the benefits bacteria provide to their hosts.

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The paper’s authors are seen here in the field along with colleagues. [Sachs lab, UC Riverside.]

“More specifically, we found interstrain competition that occurs in the soil before the bacteria infect the plant causes fewer of the bacteria to colonize the plant, resulting in the plant gaining smaller benefits in the end,” said Joel Sachs, PhD, associate professor of evolution, ecology, and organismal biology at University of California, Riverside. “To understand symbiosis, we often use sterile conditions where one strain of bacteria is ‘inoculated’ or introduced into an otherwise sterile host. Our experiments show that making that system slightly more complex—simply by using two bacterial strains at a time— fundamentally shifts the balance of benefits that the hosts receive, reshaping our understanding of how symbiosis works.”

This work is published in Current Biology in the paper, “Competitive interference among rhizobia reduces benefits to hosts.”

Rhizobial competition is a longstanding problem for sustainable agriculture. Rhizobia form root nodules on legumes, within which the bacteria fix nitrogen for the plant in exchange for carbon from photosynthesis. Growers have long sought to leverage rhizobia to sustainably fertilize staple legume crops such as soybean, peanuts, peas, and green beans.

“One might think using rhizobia as inoculants should allow growers to minimize the use of chemical nitrogen, which is environmentally damaging,” said Sachs. “But such rhizobial inoculation is rarely successful. When growers inoculate their crops with high-quality rhizobia—strains that fix a lot of nitrogen—these ‘elite’ strains get outcompeted by indigenous rhizobia that are already in the soil and provide little or no benefit to hosts.”

The authors note that, “more than one thousand root nodules of coinoculated plants were genotyped to quantify strain occupancy, and the Bradyrhizobium strain genome sequences were analyzed to uncover the genetic bases of interstrain competition outcomes.”

The researchers developed mathematical models to predict how much benefit co-inoculated plants would gain based on expectations from plants that were “clonally infected” (infected with one strain). This allowed the researchers to calculate the growth deficit that was specifically caused by interstrain competition.

“Our models showed that co-inoculated plants got much lower benefits from symbiosis than what could be expected from the clonal infections,” said Arafat Rahman, PhD, a former graduate student in Sachs’ lab who is starting a postdoc at Oregon State University.

“While beneficial bacteria work well in the lab, they get out-competed in the natural environment. Ultimately, we want to find a strain of bacteria—or a set of them—that gives maximum benefit to the host plant and is competitive against bacterial strains that are already in the soil.”

Sachs explained that to discover and develop a bacterial strain that is highly beneficial to plants, scientists need to conduct experiments under very clean conditions.

“Ultimately, we want to use beneficial bacteria in agriculture,” he said. “To identify these bacteria, we would, typically, add one bacterial strain to a plant in the lab and show that the plant grows much better with the strain than without. In the field, however, that plant is covered in microbes, complicating the story. In our experiments, we advanced from using one strain to a pair of strains to see what impact that has on plant growth. Interestingly, with just two strains, many of our predictions fell apart.”

Rahman stressed that while experiments are needed to ascertain how beneficial a bacterial strain is, experiments that test how competitive the strain is against a panel of other bacterial strains are also needed.“Both steps are crucial,” he said. “Our work found some of the best strains can be highly beneficial to plant growth but as soon as you pair them with any other strain, that benefit is greatly reduced. Further, it is important to know at which stage the interstrain competition takes place: before the bacteria interact with the plant or after? Our work suggests it’s the former and provides a useful guide to designing future experiments aimed at discovering strains that are better for delivery in crops.”

According to Sachs and Rahman, sustainable growth practices need to be a critical aspect of new agriculture to feed a growing population on a limited resource base.

“This will require moving past polluting methods such as adding huge amounts of chemical nitrogen to soil,” Sachs said. “Understanding how to efficiently deliver beneficial microbes to a target host is a central challenge in medicine, agriculture, and livestock science. By revealing that interstrain dynamics can reduce the benefits of symbiosis, our work has opened new avenues of research to improve sustainable agricultural practices.”

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