Clever soil bacteria offer farmers an eco-friendly way to control crop diseases
Effects of John Innes central irrigation on microbial populations in potato fields.(A) VOOM was used to determine the population difference of 26 species in one or more sampling sites, and the error detection rate was 0.05.The data is displayed as a heat map of logarithmic 2-fold variation relative to the total mean count per million in a given order.Sample A1a was omitted from the analysis due to possible contamination resulting in atypical bacterial populations (FIG. 1 – FIG. 1 supplement).(B) The overall mean population for each sample shows the 10 most abundant bacterial sequences from all samples.(C) Populations of eight bacterial species were determined to differ significantly between irrigated and non-irrigated sites, expressed in counts per million reads.The error bar represents the standard deviation of the three data pieces.An innovative approach to control a range of devastating crop diseases using beneficial native soil bacteria has emerged in a research-industry collaboration.The agricultural technology innovation hopes to provide farmers with a way to reduce the cost and environmental damage caused by chemical treatments currently used to control crop diseases.The team at The John Innes Center isolated and tested hundreds of pseudomonas strains from soil in a commercial potato field, then sequenced the genomes of 69 of them.By comparing the genomes of those strains that showed activity against pathogens with those that did not, the team was able to identify key mechanisms in some of the strains that protect potato crops from harmful disease-causing bacteria.Then, in combination with chemical, genetic and plant infection experiments, they showed that the production of a small molecule called a cyclic lipopeptide is important for controlling potato scab, a bacterial disease that wreaks havoc on potato harvests.These small molecules have an antibacterial effect on the bacteria that cause potato scab, helping the protective pseudomonas bacteria move around and take root in plant roots.Irrigation also caused significant changes in the genetic diversity of pseudomonas in soil.”By identifying and validating the mechanisms of potato pathogen inhibition, we hope that our research will accelerate the development of biological control agents to reduce the application of chemical treatments, which are ecologically damaging,” said Dr Alba Pacheco-Moreno, lead author of the study.”The approach we describe should be applicable to a wide range of plant diseases because it is based on an understanding of the important mechanisms of action of biological control agents,” she added.The study, published in the journal eLife, suggests a method by which researchers can screen microbiota at almost any crop site, taking into account different soil, agronomic and environmental conditions.By taking advantage of advances in high-speed gene sequencing technology, the method can screen the soil microbiome of therapeutic bacteria and identify the molecules that produce inhibiting pathogenic bacteria.They can also show how these beneficial bacteria are affected by agronomic factors such as soil type and irrigation.The next step in the new method is to put beneficial bacteria back into the same fields in larger numbers, or into a mixture of mixed strains as a treatment to boost the soil microbiome.Dr. Jacob Malone, head of the John Innes Center and co-corresponding author of the study explained the benefits, “The great advantage of this approach is that we use strains from the environment and put back the same specific organisms in large quantities in the environment so there is no ecological damage.”Potential methods of using microbiome promoters include applying bacterial mixtures to seed coating, spray or drip irrigation.Dr. Andrew Truman, leader of the John Innes Center and corresponding author of the study, told us about the long-term vision of this approach: “In the future, instead of using molecules produced by bacteria, we’ll be using pseudomonas strains themselves.It offers a more sustainable route — we know that these bacteria thrive in the soil where potatoes grow and provide protection for crops.Using a bacterium, you can easily grow it and synthesize it in a proper way and apply it to the field, and it’s much greener than using synthetic chemicals.”Plant disease is an agricultural problem that causes significant losses to crops such as potatoes.Important potato pathogens include Streptomyces scabies, a bacterial pathogen that causes potato scab, and Phytophthora infestans, an oocytic pathogen that causes potato blight, a major cause of the Irish Famine.Pseudomonas are usually associated with plants and have been widely studied as biological control agents because of the natural products they secrete that promote plant growth and inhibit pathogens.However, their use in the past has been hampered by inconsistencies.The inhibition of potato fusarium head blight showed that pseudomonas has potential biological control effect.However, progress is hampered by a lack of mechanical knowledge.Irrigation is known to suppress Streptomyces scabies infection, and now this study suggests it’s because of the effects of water on microbial populations.”Pan-genomic analysis identifies the crossover role of specific metabolites of Pseudomonas in potato pathogen inhibition” appears in eLife.