Comparative Analysis of Cranberry Fruit Rot Fungal Diversity in Massachusetts from Wild, Organic, and Conventional Ecosystems Using Multiplex PCR

Salisu Sulley¹Marty Sylvia¹Jyostna Devi Mura²Benjamin Cinget³Matteo Conti³Richard Belanger³Frank Caruso¹Leela Saisree Uppala^1*

• ¹Cranberry Station, University of Massachusetts Amherst, Amherst, United States
• ²Vegetable Crop Research Unit, Agricultural Research Service (USDA), Madison, Wisconsin, United States
• ³Department of Plant Science, Université Laval, Québec, Canada

Cranberry fruit rot (CFR) is a major disease complex that continues to challenge cranberry production by reducing fruit quality and yield, especially in Massachusetts and New Jersey. CFR is caused by a diverse assemblage of fungi whose dynamics can vary under different production systems. This study presents the first comprehensive assessment of CFR fungal population structure and persistence across wild, organic, and conventional cranberry bogs in southeastern Massachusetts. Using multiplex PCR, a high-throughput molecular diagnostic tool for simultaneous detection of multiple pathogens, we examined the prevalence and diversity of the 11 most commonly associated CFR fungi in 2021 and 2022. Surveys were conducted in 32 bogs (23 conventional, 4 organic, 5 wild) in 2021 and 50 bogs (40 conventional, 4 organic, 6 wild) in 2022. Significant differences in the detection and abundance of CFR fungi were observed among production systems. Fruit rot incidence in conventional bogs ranged from 2–42% in 2021 and 1–48% in 2022. Species richness was highest in wild bogs, with an average of 5.5 fungi per sample, compared to four fungi per sample in conventional and organic bogs. Organic bogs showed a notable decline in richness, from six fungi per sample in 2021 to two in 2022. All 11 target CFR fungi were detected across the ecosystems except Phomopsis vaccinii, which was not found in organic bogs in either year. Key species, including Coleophoma empetri, Allantophomopsis cytisporea, and Botryosphaeria vaccinii, were consistently detected across all systems and both years. Year-to-year comparisons indicated that wild bogs had higher fungal carryover, with eight of the 11 fungi persisting, compared to six in conventional and four in organic bogs. C. empetri showed the highest persistence, detected in 96% of conventional, 100% of organic, and 60% of wild bogs across both years. Colletotrichum spp. were less stable, with minimal carryover in wild and organic bogs. A general decrease in B. vaccinii and an increase in Physalospora vaccinii were observed across all bogs. These findings highlight the complex dynamics and persistence of CFR fungi across cranberry ecosystems and underscore the influence of management practices on pathogen diversity.