A team led by scientists from the University of California, Riverside, set up experiments to answer these questions and better understand the competition process. The researchers used a native California nodule plant, Acmispon strigosus, and a set of eight compatible nitrogen fixing bacterial strains. They infected some plants with each of the eight strains to directly measure their ability to infect plants and provide benefits.
They then infected additional plants with pairs of bacterial strains to assess each strain’s competitive ability and effect on plant performance. The researchers found that competition between strains of beneficial bacteria in the soil degrades the service the bacteria provide to their hosts.
Joel Sachs, professor of evolution, ecology and organismal biology, who led the research team “More specifically, we found inter-strain competition that occurs in the soil before the bacteria infect the plant causes fewer bacteria to colonize the plant, resulting in the plant ultimately gaining less advantage, understand symbiosis, we often use sterile conditions where a single strain of bacteria is ‘inoculated’ or introduced into an otherwise sterile host. Our experiments show that a slightly more complex system simply by using two bacterial strains at once fundamentally shifts the balance of benefits that the hosts receive, reshaping our understanding of how symbiosis works.”
Acmispon strigosus form root nodules on legumes
Sachs explained that a major challenge in agriculture is harnessing the services that microbes can provide to crops by promoting growth in a sustainable way, without the environmental costs of chemical fertilizers. His lab studies rhizobia – bacteria that promote plant growth. Rhizobial competition is a long-standing problem in sustainable agriculture.
Rhizobia form root nodules on legumes in which the bacteria fix nitrogen for the plant in exchange for carbon from photosynthesis. Growers have long sought to use rhizobia to sustainably fertilize staple legumes such as soybeans, peanuts, peas and green beans.
“One might think that using rhizobia as inoculants should allow growers to minimize the use of chemical nitrogen that damages the environment,” said Sachs, who chairs the Department of Evolution, Ecology and Organismal Biology. “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 outcompete native rhizobia that are already in the soil and provide little or no benefit to the hosts.”
Sachs and his colleagues used bacterial strains whose genomes they had already sequenced in their experiments. They also characterized strains that ranged from highly beneficial to ineffective at fixing nitrogen to know exactly how beneficial they were to the target plant species. The researchers sequenced the contents of more than 1,100 nodules, each of which came from a plant that had been inoculated with one of 28 different combinations of strains.
Next, the researchers developed mathematical models to predict what benefit co-inoculated plants would receive based on expectations from plants that were “clonally infected” (infected with a single strain). This allowed the researchers to calculate the growth deficit that was specifically caused by interstrain competition.
“Our models showed that co-inoculated plants have a much lower benefit from symbiosis than would be expected from clonal infections,” said Arafat Rahman, a former graduate student in Sachs’ lab and first author of the research paper. “While beneficial bacteria work well in the lab, they get outcompeted in the natural environment. Ultimately, we want to find the strain of bacteria or set of bacteria that provides maximum benefit to the host plant and is competitive against the bacterial strains already in the soil.”
Acmispon strigosus discover and develop a bacterial strain
Sachs explained that to discover and develop a bacterial strain that is highly beneficial to plants, scientists must conduct experiments in 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. But in the field, that plant is covered in microbes, which complicates the story. In our experiments, we progressed from using a single strain to a pair of strains to see what effect that had on plant growth. Interestingly, with just two strains, many of our predictions fell apart.”
California nodule plant, Acmispon strigosus and a set of eight compatible nitrogen fixing bacterial strains
Rahman emphasized that while experiments are needed to determine how beneficial a bacterial strain is, experiments are also needed to test how competitive the strain is against a panel of other bacterial strains.
“Both steps are essential,” he said. “Our work found that some of the best strains can be highly beneficial for plant growth, but once you pair them with any other strain, that benefit is greatly reduced. Furthermore, it’s 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 for designing future experiments aimed at discovering strains that are better for cultivation.” Sachs said many current experimental designs emphasize the benefit to plants.