Rethinking Cranberry Fruit Rot Management: Insights into Fungal Community Shifts and Infection Timing

Cranberry fruit rot (CFR) is the most economically damaging disease in cranberry production, yet its management remains challenging due to its complex etiology involving up to 15 fungal species. Management relies heavily on fungicide applications during bloom and early fruit set, yet our findings challenge this long-standing approach. Using culture-based and metagenomic analyses, we found that CFR-associated fungi were nearly absent in flowers and early fruit, which instead harbored an abundance of endophytic fungi ( >85%). Fungal diversity declined sharply after fruit set (χ², p < 0.001), while well-known pathogens such as Colletotrichum and Phyllosticta became dominant in mature fruit. Principal Coordinates Analysis revealed distinct shifts in fungal composition by phenological stage (PERMANOVA, p < 0.001), suggesting a temporal shift in pathogen presence. Metagenomic sequencing further confirmed that CFR fungi were present in both symptomatic and asymptomatic mature berries, with differential abundance as the primary distinguishing factor. These findings contradict the assumption that CFR infection originates during bloom and instead suggest that pathogen establishment occurs later in fruit development. A reevaluation of fungicide application timing could improve disease management by targeting CFR fungi when they are most active, rather than during early stages when they are largely absent.