Harnessing agricultural microbiomes for human pathogen control

Plant microbial communities comprise a complex network of microorganisms present on surface and internal tissues, which interact with the host plant and the environment. Each plant compartment represents a microhabitat characterised by specific conditions that support distinct microbial communities. Whilst the plant microbiota is predominately beneficial or benign in nature, plant pathogens and, to a lesser extent, human pathogens, can be naturally present in the microbiome or become incorporated into the community. For edible crops, human pathogens represent a health risk and are increasingly responsible for foodborne disease, with fresh produce accounting for over 1/3 of all foodborne outbreaks in some countries. Growing evidence that certain human pathogens are well adapted to occupying plant niches necessitates a shift in thinking regarding their ecological range and should be incorporated within control strategies. In this article we argue that it is possible, through agricultural management practices, to enhance suppression of human pathogens by microbiota associated with horticultural crops. We examine the environmental fitness of these pathogens and the ecology of suppressive interactions, explore the knowledge gaps and approaches needed to fill these, and provide our perspectives on the potential to harness agricultural microbiomes to reduce the risk of disease transmission into the food-chain.