In the soil where plants grow, they form alliances with bacteria. For example, legumes benefit from a symbiotic relationship with microorganisms that live in nodules in their roots and “fix” atmospheric nitrogen to make it available for legume growth. But do microbes benefit plants in general? Or does competition between strains for access to plants reduce the function the bacteria ultimately provide?
To find out the answers to these questions and to better understand the competitive process, a team of scientists from the University of California, Riverside, conducted experiments. The researchers used Acmispon strigosus, a nodule native to California, and a collection of eight compatible nitrogen-fixing bacterial strains. They infected some plants with each of the eight strains to assess the ability of each to infect and benefit the plants.
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, a professor of evolution. ecology and organismal biology says “More specifically, we found that interstrain 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”.
Rhizobia – bacteria that promote plant growth
The results of the study appear in the journal Current Biology. 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”.
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 perform well in the laboratory, in the natural environment they thrive on competition. Ultimately, we want to find the bacterial strain or set of bacteria that provides maximum benefit to the host plant and is competitive with the bacterial strains already in the soil.”
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.” However, in the field, this plant is covered in microbes, which complicates the whole story. In our experiments, we progressed from using a single strain to a pair of strains to see what effect this had on plant growth. Interestingly, with only two tribes, many of our predictions fell apart.”
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 very beneficial to plant growth, but once you pair them with any other strain, that benefit is greatly reduced. Furthermore, it is important to know at which stage the interstrain competition occurs: before the bacteria interact with the plant or after?
Sachs said many current experimental designs emphasize the benefit to plants. “But it’s important to remember that bacteria are shaped by natural selection,” he said. “Some of them can be highly competitive in entering the nodule to infect the plant, but they’re not very beneficial to the plant, and that could be a winning trait in nature.” If we are to exploit microbial communities for the services they can provide to plants and animals, we need to understand the inter-species dynamics in these communities.
