Recent studies have shown that the native microbiome plays an important role in biocontrol efficacy, but in comparison less is known about how the microbiome responds to conventional and natural product fungicides. This study investigated the effects of conventional fungicide fludioxonil, natural product fungicide natamycin, and scald inhibitor diphenylamine (DPA) on the microbiomes of ‘Fuji’ apples (Malus x domestica) from 1-28 days of cold storage and 7 days of room temperature after the cold storage. We hypothesized that fludioxonil would have a smaller effect on the microbiome than natamycin due to being more limited in targeting specific pathogens, and that antioxidant activity from DPA would shift the microbiome. DPA showed a strong effect on the fungal microbiome that increased with storage time, while natamycin resulted in modest fungal shifts and fludioxonil resulted in no observed shifts. While chemical treatment was not a predictor of bacterial microbiome variation, bacterial communities shifted throughout storage with many of the trends reversing when samples were removed and left at room temperature. Time in cold storage decreased the relative abundance of Pseudomonas and DPA application reduced the relative abundance of Aureobasidium, both notable biocontrol genera. These results highlight how chemical applications like DPA may have unintended effects on beneficial microbes that protect crops from pathogen infection.
