The Distinguished Microbiome: Differentiating Microbial Dysbiosis and the Pathobiome of Banana Fusarium Tropical Race 4

Microbial interkingdom interactions are key to the successful infection of soil-borne pathogens, as pathogen success is not solely dependent on a susceptible host but also on a conducive microbiome. The emerging concept of the pathobiome encompasses the pathogen and associated microorganisms, including pathobionts, which can potentially aid in pathogen survival, persistence and/or virulence. However, technical limitations pose a challenge in distinguishing the pathobionts from those involved in microbial dysbiosis. In this study, Fusarium oxysporum f. sp. cubense tropical race 4 pathobionts were identified and differentiated from microbiota under dysbiosis during the infection. The microbial community structures of three microniches (healthy tissue, diseased tissue, and FOC hyphosphere) were compared using near full-length 16S rRNA metabarcoding using ONT v14 chemistry. The results indicated a high similarity in microbiota in hyphosphere and disease tissue. The correlation networks suggest a possible conflict between the pathogen's deterministic influence on microbial recruitment and the increasing role of stochastic processes within the endosphere microbiota. Functional analysis using EcoPlate revealed the potential roles of the pathobionts in synergistically infecting the plant host. Thus, our results show a clear distinction between the pathobiome and functions that differentiate from a dysbiotic community within the same endosphere niche. These functions may involve bacterial-fungal recruitment and the regulation of virulence factors, which were found to be significantly utilized by Fusarium in conjunction with its hyphosphere pathobionts, compared to when Fusarium is alone. Our findings reveal a clear distinction between the pathobiome and its potential functions, which distinguish it from the dysbiotic community.