The decay and fungal succession of apples with bitter rot across a vegetation diversity gradient

Bitter rot is a disease of apple caused by fungi in the genus Colletotrichum. Management begins with removal of infected twigs and fruits from tree canopies to reduce overwintering inoculum. Infected apples are usually tossed to the orchard floor, which is generally managed as herbicide-treated weed-free tree rows, separated by grass drive rows. We monitored decay rates and succession of fungi of apples with bitter rot in tree canopies, and on the soil surface in tree rows, grass drive rows, and nearby diverse plant communities. We hypothesized that decay would occur most rapidly within diverse plant communities, which would provide a more diverse array of potential fungal decomposers. Apples in tree canopies became dry and mummified and had more Colletotrichum gene marker copies the following growing season than did apples on the soil surface. Of the soil surface samples, those in grass drive rows and diverse plant communities had higher moisture, faster decay rates, and sharper decreases in Colletotrichum gene marker copies than apples in tree rows. Fungal composition across all decaying apples was dominated by yeasts, with higher genus-level richness, diversity, and evenness in apples from tree canopies than those on the soil surface. In soil surface apples, we observed clear successional waves of Pichia, Kregervanrija, and [Candida] yeasts, with similar but distinctly diverging fungal composition. Our results show that orchard floor management can influence fungal succession in apples with bitter rot, but suggests that bitter rot management should primarily focus on removing infected apples from tree canopies.