Biological Control Agents: Environmental Manipulation and Suppressive Soils

Environmental manipulation is often used as an approach to achieve biological control against insect pests, such as the promotion of biodiverse crop margins to encourage predators, providing biological pest management under the title of Conservation Biological Control. This is used rather less against pathogens. Reduction in attack by pathogens can be achieved, in principle, by manipulating the habitat to encourage one or more BCA in the soil, or perhaps by using adjacent vegetation to encourage the right individual microorganisms or microbiomes. The use of elemental sulphur to lower the local pH and discourage Streptomyces scabies, causing scab on potato, is perhaps an example. Another example is watering potato plants during tuber formation to stimulate colonization of the new lenticels by antagonistic bacteria. Similarly, later in the season, damage from eyespot of wheat caused by Oculimacula spp. was—counterintuitively—reduced by ceasing straw burning. Compost and especially compost tea may provide a source of BCAs or alter the nutritional environment to favour BCAs, which are responsible for the activity of the compost tea. Biochar is hypothesized to provide increased surface area suitable for microbial growth and may interact desirably with compost teas. These approaches are a subject ripe for study, though reliability has been a major problem; metagenomic and community metabolism methods may improve this. Part of the effect of good cultural practices—though perhaps unconsciously—is likely to be the encouragement of microbial communities that either prime or induce plant defences, or act as direct BCAs.

Microbiota can increase natural soil suppressiveness against soilborne pathogens particularly when intensive cropping systems (with high inputs of synthetic chemicals, low soil organic matter accumulation, little humification and frequent soil tillage) are the primary reasons for soil depletion. Soil microbiota associated with biocontrol can be a key factor in the beneficial influence of agronomic practices on plant health. Next-generation sequencing often offers a deeper characterization of the soil microbial community during microbiome manipulation. This may allow a more mechanistic understanding of what is happening and the effect on crops in terms of soil suppressiveness, so helping to limit inconsistencies, drawbacks and failures related to soil microbiota disturbance. More generally, the omics sciences—through a combination of metagenomics, meta-transcriptomics, meta-proteomics and metabolomics approaches—should help in understanding the microbial activities as a whole and the potential of the plant-associated microbiota to suppress plant disease.