The Blueberry Fruit Mycobiome Varies by Tissue Type and Fungicide Treatment

The microbial ecology of agricultural products may provide crucial insights into the management of postharvest fruit rots. To investigate postharvest microbial communities of highbush blueberry (Vaccinium corymbosum), five fungicide spray programs were evaluated for their influence on the mycobiome of fruit skin and within the fruit pulp. The mycobiome was characterized by sequencing amplicons of the internal transcribed spacer 1 (ITS1) region with primers ITS1f and ITS4 with the Illumina MiSeq 300bp v3 system. Two of the five programs utilized commercial biological fungicides, two utilized azoxystrobin, and one utilized a series of treatments to simulate a realistic disease management program. Fungicide applications reduced diversity of the fruit skin mycobiome (R2 = 0.409, P = 0.0001) and had a moderate impact on the pulp mycobiome (R2 = 0.233, P = 0.0001). The mycobiome of the fruit pulp was also more variable than the skin mycobiome. In comparison with the untreated controls, each fungicide treatment program had a strongly significant effect on the β diversity of the blueberry fruit skin mycobiome (R2 = 0.53 to 0.73, P = 0.0001). In the pulp, three of the five treatments had moderate but significant effects on β diversity in comparison with the control (R2 = 0.10 to 0.18, P = 0.0005 to 0.017). Most samples indicated that fungi belonging to genera Epicoccum, Papiliotrema, and Sporobolomyces were widely prevalent and abundant across treatments and tissues. Fruit pathogen Botrytis cinerea was particularly abundant in the pulp of three of the fungicide treatments. Results from this study provide a baseline for future exploration of postharvest rot pathology and provide a community context on how fungicides may alter fungal communities in agricultural systems