Pathobiomes and biotic interactions in plant disease

Studies on bacterial plant diseases have thus far been focused on single bacterial species causing the disease, with little or no attention given to the many other microorganisms present in the microbiome. Plant microbiome studies clearly indicate that plants host and live in association with complex bacterial communities that are thought to play important roles in plant health. However, how and whether the entire plant microbial community is capable of affecting/interacting positively or negatively pathogen establishment remains still largely unknown. Recently, the discovery of complex diseases involving more than one pathogen and the growing perception that the microbiome contributes to disease formation and severity has led to the introduction of the term pathobiome. In this study, the microbiome of healthy rice plants and the pathobiome of rice foot rot diseased caused by Dickeya zeae from the same location were determined with the aim to provide insight on potential commensal/resident bacteria that can cooperate with the pathogen and take part in the pathosystem. Interestingly, our results showed that the microbial diversity and complexity is significantly reduced upon invasion by the pathogen and it is accompanied by an increase/domination of certain microbial species that are believed to be synergistically involved in the disease process. In addition, isolation and in planta infection studies of bacterial members of the pathobiome indicates that they benefit from the presence of the pathogen. It is necessary to begin to shift from a pathogen-focused stance towards a more ecological perception considering the effect of the entire microbial community.