An innovative method of combating crop diseases using local beneficial soil bacteria has emerged from the collaboration between science and industry.
A team of scientists from the John Innes Center (UK) isolated and tested hundreds of strains of Pseudomonas bacteria from soil collected from farm sites, and then sequenced the genomes of 69 of them.
By comparing the genomes of those strains that inhibit pathogen activity with those that do not, the team was able to identify a key mechanism for protecting the potato crop from harmful bacteria.
Then, using a combination of chemistry and genetics and a series of experiments, the scientists showed that the production of small molecules called cyclic lipopeptides is important in controlling potato scab (a bacterial disease that causes significant damage to the potato crop). These small molecules have an antibacterial effect on pathogenic scab-causing bacteria and help the beneficial Pseudomonas bacteria to migrate and colonize plant roots.
Experiments have also shown that irrigation causes significant changes in the genetically diverse population of Pseudomonas in the soil.
The study, published in eLife, offers a method by which scientists can study the microbiome of virtually any area of a field and take into account different soil, agrochemical and environmental conditions.
Using advances in high-speed genetic sequencing, scientists can test the soil microbiome for beneficial bacteria and determine which molecules are produced to suppress pathogens. The next step is to propagate and return beneficial microorganisms to the same field.
Potential applications for microbiome enhancers include applying bacterial cocktails to the surface of tubers as a spray or directly into the soil using drip irrigation.