Host phenology drives directional assembly of the fruit endophytic mycobiome and precedes disease-associated community dominance in cranberry
- 1Department of Plant Pathology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI 53706 USA
- 2Department of Plant and Environmental Sciences, Clemson University, Clemson, USA
Abstract
Background: Plant disease complexes are difficult to resolve because disease progression can be correlated among multiple microbial taxa within the same host environment rather than arising from a single causal agent. Cranberry fruit rot (CFR), one of the most economically important diseases in cranberry production, has been associated with up to 15 fungal species. Current disease etiology describes an initial floral infection followed by a persistent latent period until disease development in mature fruits. However, this model has not been demonstrated, and it is still unknown whether it is applicable to all fungal species. We conducted a two-year field study of the cranberry fruit endophytic mycobiome across successive phenological stages. Combining ITS2 amplicon sequencing with detection-probability modeling and quantitative PCR–based estimates of fungal biomass and species-specific detection, we evaluated mycobiome dynamics with a particular focus on disease-associated species.
Results: Host phenology explained most of the variation in fungal richness and community composition. CFR-associated fungi were infrequently detected during flowering and fruit set and occurred at very low biomass, but their prevalence and abundance increased markedly during fruit maturation. These taxa became dominant in asymptomatic ripe berries and were further enriched in rotten fruit. Targeted qPCR assays corroborated the near absence of major CFR-associated fungi at early developmental stages, inconsistent with the widely proposed model of flowering-time infection.
Conclusions: Our data support a framework in which disease emergence is linked to a phenology-dependent reorganization of the resident mycobiome accompanied by a strong increase in fungal biomass. This shift in community structure revises the current view of CFR epidemiology and underscores the role of host developmental filtering in structuring pathogen-complex dynamics in perennial crops. In addition, this pathosystem could serve as a model system for testing community-based models of pathogenesis in perennial crops.
Graphical abstract:
Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1186/s40793-026-00942-3.
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BibTeX
@article{pozasrodriguez2026host,
title = {{Host phenology drives directional assembly of the fruit endophytic mycobiome and precedes disease-associated community dominance in cranberry}},
author = {Eithan A. Pozas-Rodriguez and Fabian Rodriguez Bonilla and Leslie A. Holland},
journal = {Environmental Microbiome},
year = {2026},
month = aug,
doi = {10.1186/s40793-026-00942-3},
url = {https://doi.org/10.1186/s40793-026-00942-3},
note = {CC BY-NC-ND 4.0},
}
RIS
TY - JOUR
TI - Host phenology drives directional assembly of the fruit endophytic mycobiome and precedes disease-associated community dominance in cranberry
AU - Eithan A. Pozas-Rodriguez
AU - Fabian Rodriguez Bonilla
AU - Leslie A. Holland
PY - 2026
DA - 2026/08/08
JO - Environmental Microbiome
DO - 10.1186/s40793-026-00942-3
UR - https://doi.org/10.1186/s40793-026-00942-3
AB - Background: Plant disease complexes are difficult to resolve because disease progression can be correlated among multiple microbial taxa within the same host environment rather than arising from a single causal agent. Cranberry fruit rot (CFR), one of the most economically important diseases in cranberry production, has been associated with up to 15 fungal species. Current disease etiology describes an initial floral infection followed by a persistent latent period until disease development in mature fruits. However, this model has not been demonstrated, and it is still unknown whether it is applicable to all fungal species. We conducted a two-year field study of the cranberry fruit endophytic mycobiome across successive phenological stages. Combining ITS2 amplicon sequencing with detection-probability modeling and quantitative PCR–based estimates of fungal biomass and species-specific detection, we evaluated mycobiome dynamics with a particular focus on disease-associated species. Results: Host phenology explained most of the variation in fungal richness and community composition. CFR-associated fungi were infrequently detected during flowering and fruit set and occurred at very low biomass, but their prevalence and abundance increased markedly during fruit maturation. These taxa became dominant in asymptomatic ripe berries and were further enriched in rotten fruit. Targeted qPCR assays corroborated the near absence of major CFR-associated fungi at early developmental stages, inconsistent with the widely proposed model of flowering-time infection. Conclusions: Our data support a framework in which disease emergence is linked to a phenology-dependent reorganization of the resident mycobiome accompanied by a strong increase in fungal biomass. This shift in community structure revises the current view of CFR epidemiology and underscores the role of host developmental filtering in structuring pathogen-complex dynamics in perennial crops. In addition, this pathosystem could serve as a model system for testing community-based models of pathogenesis in perennial crops. Graphical abstract: Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1186/s40793-026-00942-3.
SN - 2524-6372
ER -