Beyond the Single Pathogen Paradigm in Citrus: A Pathobiome Perspective on Disease Complexes, Microbiome Dysbiosis, and Management

Abstract

Citrus diseases are commonly interpreted within a single pathogen framework, yet increasing evidence shows that disease outcomes can also be shaped by mixed infections, disease-associated microbiome restructuring, host responses, and interactions among multiple biotic agents. This review synthesizes current evidence on citrus disease complexes, disease-associated microbiome restructuring, and the mechanisms linking pathobiome dynamics to disease development. Particular attention is given to temporal- and compartment-specific microbiome changes, host physiological remodeling, immune reprogramming, and direct microbial interactions. We distinguish co-detection from functional interaction and emphasize the need to move from descriptive associations toward experimental and mechanistic validation. Across major citrus diseases, disease-associated microbiome restructuring emerges as a dynamic and context-dependent process rather than a uniform loss of microbial diversity. Management strategies based on microbiome restructuring, community preservation, functional biocontrol, and synthetic microbial communities further illustrate the potential of targeting pathogens, host responses, and resident microbiota simultaneously. A pathobiome perspective provides an integrative framework for deciphering and managing complex citrus diseases.