Pine wilt disease as a holobiont disorder: microbiome assembly as a potential management target

David Pires , Margarida Espada, Diogo Proença, Cláudia S. L. Vicente

Pine wilt disease (PWD), caused by the pinewood nematode (PWN) Bursaphelenchus xylophilus, continues to expand globally despite decades of pathogen-focused management. Here, we propose that disruption of microbiome assembly within the pine holobiont may contribute to disease progression and help explain variation in disease outcomes and responses to microbial interventions. Drawing on recent advances in microbial ecology, multi-omics, and synthetic biology, we synthesize evidence of PWD-associated changes in host-associated microbial communities and examine how altered functional redundancy and pathobiome formation may contribute to disease progression. We propose that microbiome assembly, shaped by host traits, environmental filters, and biotic interactions, is a plausible and underexplored determinant of disease outcome. Building on this framework, we outline a shift from single-agent biocontrol toward assembly-informed microbiome engineering. To support reproducible design and future validation, we outline criteria for selecting candidate consortium members and assessing synthetic microbial community (SynCom) establishment, persistence and functional stability. We further propose experimentally testable strategies to compare assembly-informed versus conventional interventions and identify measurable indicators of microbiome stability and disease suppression. By reframing PWD as a problem of microbiome assembly and stability, this work provides a testable framework for developing durable, holobiont-level management strategies. Integrating ecological theory with applied microbiome engineering offers a path forward to move beyond inconsistent control outcomes and toward resilient forest health under ongoing environmental change.