Biological control in the microbiome era: Challenges and opportunities

Biocontrol research has long been focused on the study of single strains of biocontrol agents (BCAs) and on their interaction with pathogens and host plants. Further focus on plant-associated microbial communities was suggested several years ago, but significant advances only occurred recently. The advent of high-throughput sequencing (or next-generation sequencing – NGS) technologies is now driving a paradigm change that allows researchers to integrate microbial community studies into the traditional biocontrol approach. This integration could answer old scientific questions, and will raise new biocontrol hypotheses. Microbial communities could impact disease control through their interaction with host plants, pathogens, and BCAs. A better understanding of these interactions will provide unexpected opportunities to develop innovative biocontrol methods against plant pathogens. For example, formulation or timing of BCA application can be improved, “helper” microbial strains can be selected, or molecules driving the microbiota to a pathogen-resistant composition (“prebiotic” approach) can be developed. The five main challenges of microbiome implementation in biocontrol research are also described, i.e. (i) the management of technical errors and biases, (ii) the growing importance of bioinformatics, (iii) the adaptation of experimental schemes, (iv) the appropriate interplay between NGS and other technologies, and (v) the need to complete current genome databases.