Fighting bacteria favor speed over service

In findings published today in Current Biology, scientists from the University of California, Riverside report that plants’ relationships with their nitrogen-fixing rhizobacteria are far more complex than previously realized, or rather, the relationships among those bacteria complicate them.

The research team infected initially bacteria-free Acmispon strigosus with eight different strains of nitrogen-fixing microbes from the genus Bradyrhizobium and then exposed them to other bacteria to determine which would establish themselves in the plant roots. All eight of the initial bacterial strains used in this study had fully sequenced genomes, and they ranged in effectiveness from highly beneficial to no improvement. The team established 28 different bacterial combinations and evaluated over 1000 of the nodules that formed on the plants in an experiment lasting more than five months.

The research team found that the bacteria that grew the fastest colonized the plants to the greatest extent, even if they offered the host less benefit. The best results, the team found, were found on plants colonized with only one, highly effective strain that had no other bacteria to compete against.

“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 team leader Joel Sachs.

In agriculture, optimizing the benefits offered by industrious microbes can render farms and farmers less dependent on chemical fertilizers, which have their own (literally) downstream environmental consequences. Sachs warns that sustainable agriculture must move away from adding large amounts of nitrogen to soil artificially. But many efforts to deliberately introduce rhizobacteria to real-world farms have failed, and this inter-microbe competition may be part of the reason why.

“Our models showed that co-inoculated plants got much lower benefits from symbiosis than what could be expected from the clonal infections,” said first author Arafat Rahman. He went on to say that the bacteria that are most beneficial under laboratory conditions may be out-competed in the wild. “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.”

One major conclusion drawn in the work is that engineering rhizobacteria for optimal crop growth will be a highly involved challenge. In order to evaluate bacteria, scientists must work in sterile conditions and introduce new factors—such as competing bacteria—one at a time. The fact that the bacteria’ strains competitive traits appear to be controlled by multiple genes adds another layer.

The National Science Foundation and United States Department of Agriculture both helped fund this study.

Read the full study in Current Biology.

Rahman A, Manci M, Nadon C, Perez IA, Farsamin WF, Lampe MT, Le TH, Torres Martínez L, Weisberg AJ, Chang JH, Sachs JL. Competitive interference among rhizobia reduces benefits to hosts. July 24, 2023. Current Biology. 33(14). P2988-3001.e4. doi: 10.1016/j.cub.2023.06.081.