The pathobiome concept applied to postharvest pathology and its implication on biocontrol strategies

Metagenomic sequencing and multi-omic technologies have greatly advanced our understanding of the microbiome of fruit crops and revealed the complex interactions that potentially occur between microbial communities and their host. Strong evidence exists for the involvement of multiple microorganisms in the onset and development of disease in plant hosts. A paradigm of postharvest pathology is that a single pathogen has the capacity to initiate and cause disease. New data on the fruit microbiome allows us to question the existing paradigm of a single pathogen-disease model and develop a more comprehensive understanding of the disease process. We suggest that a conceptual shift is needed and suggest that diseases in fruit crops originating from surface wounds are the result of complex interactions between a recognized pathogen and specific microorganisms occupying the wound site. We believe that the pathobiome concept should be applied to postharvest diseases and provide a more holistic view of disease development, involving complex assemblages of organisms. We present the wound-pathogen relationship as an interactive biological system in which the abundance and composition of specific resident microbial taxa in the wound are promoted in the early stages of infection. These shifts in the structure of the microbial community are potentially responsible for modulating pathogenicity/virulence factors in the pathogen and suppressing the activation of resistance responses in the host. The association of exo- and endo-bacteria with fungal pathogens and their role in the pathobiome is also discussed.