Bacteria that demonstrate positive effects on plants in the lab often can’t compete in field conditions
Some soil microbes set up shop in the root nodules of plants, providing nutrients and water while getting access to carbon produced by their hosts. Some of these bacteria are better tenants, but they must compete for space.
Researchers at the University of California, Riverside, recently explored if the competition between different microbe strains for plant access, inhibited how bacteria provide beneficial services to plants.
“For bacteria, the plant is home,” said Joel Sachs, associate professor and vice-chair of biology at the university. “But while a plant is picky about which strains of bacteria it lets in, it only has partial control over that. Bacteria compete for a plant’s resources. We wanted to understand that. How does that play out? It’s an old concept that has been highlighted for decades and described as the rhizobia competition problem.”
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Sachs’ laboratory studies rhizobia, the bacteria that infect legume roots and promote plant growth. A core challenge, he said, is getting those bacteria to promote growth in a sustainable way without chemical fertilizers and then getting it to perform in fields where it faces competition from strains better adapted the conditions.
“It starts as a simple problem,” said Sachs. “Under controlled conditions we can have different strains of these bacteria. We can isolate a strain, grow it on a plate in the lab, take the strain and inoculate a plant that is sterile and has nothing else.
“The procedure shows that when a plant gets this one strain, it gets a huge benefit compared to plants that don’t get that strain. I can take other strains and show that some are more beneficial compared to others. But the more complicated part is what happens when we take that good strain and use it in realistic conditions. We find that it generally doesn’t work and that’s because of interactions among the many different strains in a natural setting.
“When we try to apply a strain under field conditions, the strains that are already adapted to those conditions are more competitive. That’s the theory.”
His research team used a native plant called hairy lotus, a species of legume also known as strigose bird’s-foot trefoil, and a set of eight bacterial strains whose genomes had been sequenced. They characterized the strains from highly beneficial to ineffective at fixing nitrogen in order to have a profile for how valuable they were for the target plant species.
They sequenced the contents of more than 1,100 nodules, each of which was from a plant inoculated with one of the 28 different strain combinations.
Plants were infected with each of the eight strains to monitor how well they infected the plants and the benefits they provided. Then they infected other plants with pairs of bacteria to measure their competitive ability and the effect of each strain on plant performance.
They developed mathematical models to predict how much benefit co-inoculated plants would receive based on expectations from plants that were infected with just one strain. This allowed them to calculate any growth deficit caused by competition between the two strains. Results showed competition between the pairs of bacteria degraded benefits they provided to host plants.
“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, a former graduate student in Sachs’ lab. “While beneficial bacteria work well in the lab, they get out-competed in the natural environment.”
If this result happens in a lab experiment, what happens in a field trial?
“Researchers have gone into a field and isolated bacteria from nodules of crops that have been inoculated with different strains,” said Sachs. Study after study has shown that rarely have those strains provided benefits. Sometimes they are completely absent. They have disappeared.”
The goal is to find a strain, or several strains, of bacteria that offer maximum benefit to the host crop and can successfully compete against local bacterial strains already in the soil.
Researchers have also turned their attention to selective breeding and how that affects plant symbionts.
“Theories have held that when you domesticate a crop, you are focusing on specific traits like production or rapid growth. It might cause you to lose other traits you weren’t focusing on. One thought was that symbionts were overlooked.”
Farmers have been co-operating with Sachs’ studies, planting fields with different crops and the researchers gathered soil samples to study the microbe communities.
“We took the soil back to the lab and inoculated all the different crops to explore the microbial benefits. Now we’re doing genome sequencing of the bacteria from those soils to figure out in what way they are affected. We want to know if they are travelling from field to field, are there epidemic strains, are they beneficial, can we move strains from place to place, can they adapt to different soils.”
Climate change and its effects are complicating the research.
“There has been some nice work on bacterial behaviour post-fire, post-drought, and how microbial communities have changed. How do these changed communities affect plants? For growers, their land has changed for what they can reliably or economically grow and that is going to affect the soil health as well.
“For sustainable agriculture, this will require moving past polluting methods, such as adding huge amounts of nitrogen to soil. Understanding how to efficiently deliver beneficial microbes to a target host is a central challenge in medicine, agriculture, and livestock science.”
The research was published in the journal Current Biology.
