Soil bacteria can help farmers control crop diseases

A research-industry collaboration has developed an innovative and environmentally friendly method for combating a variety of severe crop diseases using native, beneficial soil bacteria. 

Plant infections and crop diseases are major agricultural issues that can decimate crop yields, and scientists are working to find sustainable solutions. Streptomyces scabies, a bacterial pathogen that produces potato scab, and Phytophthora infestans, an oomycete disease that causes potato blight, are major potato infections and were significant causes of the Great Famine in Ireland. 

The John Innes Centre team extracted and analyzed hundreds of Pseudomonas bacteria strains collected from the soil in a commercial potato field and conducted genome sequencing on 69 of them.

The researchers were able to uncover a crucial mechanism in some of the strains that protected the potato crop from hazardous disease-causing bacteria by comparing the genomes of those demonstrated to decrease pathogen activity with those that did not.

The agri-tech breakthrough aims to provide farmers with a means to lower the expense and reduce the environmental impact of chemical crop disease treatments that are widely used.

“The massive advantage of this approach is that we are using bacterial strains that are taken from the environment and put back in the same specific biological context in larger numbers so there is no ecological damage,” said study co-author Dr Jacob Malone.

Using a mix of chemistry, genetics, and plant infection experiments, the researchers demonstrated the creation of tiny molecules known as cyclic lipopeptides, which is vital in the control of potato scab. This particular bacterial disease causes significant losses in potato yields.

The lipopeptides are tiny compounds which have an antibiotic impact on the pathogenic bacteria that cause potato scab, and they aid in the movement and colonization of the plant roots by the protective Pseudomonas bacteria.

The study offers a strategy for screening the microbiome of nearly any crop site, taking into consideration different soil, agronomic, and environmental circumstances. 

“By identifying and validating mechanisms of potato pathogen suppression we hope that our study will accelerate the development of biological control agents to reduce the application of chemical treatments which are ecologically damaging.” said study first author Dr. Alba Pacheco-Moreno.

“The approach we describe should be applicable to a wide range of plant diseases because it is based on understanding the mechanisms of action that are important for biological control agents.”

The technique involves scanning the soil microbiome for therapeutic bacteria to determine which chemicals are being created to suppress pathogenic bacteria by utilizing breakthroughs in high-speed genetic sequencing. This method can also show how these beneficial soil bacteria are affected by agronomic factors such as soil type and irrigation.

According to the study, irrigation induces significant alterations in the genetically varied Pseudomonas population in the soil. The next step for the new approach is to put the beneficial bugs back into the same field in greater numbers or in cocktails of mixed strains as a soil microbiome boosting treatment.

The bacterial combinations could be introduced to the fields as seed coatings, as a spray, or by drip irrigation to improve the microbiome.

“In the future  it’s not the molecule produced by the bacteria that we would use, it would be the Pseudomonas strain itself,” said study co-author Dr. Andrew Truman.

“It offers a more sustainable route – we know these bacteria colonize the soil where potatoes grow, and they provide protection to the crop. Using a bacterium, you can easily grow and formulate it in an appropriate way and apply it to the field, and it is much greener than using a synthetic chemical.” 

The study is published in the journal eLife.

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By Ashikha Raoof, Earth.com Staff Writer