Organic fungicides and diphenylamine shift microbiomes of 'Fuji' apples during storage

The native microbiome plays an important role in biocontrol efficacy, but less is known about how the microbiome responds to conventional and organic natural product fungicides. This study investigated the effects of the conventional fungicide fludioxonil and the organic fungicide natamycin, with and without the superficial scald inhibitor diphenylamine (DPA) on the microbiomes of 'Fuji' apples from 1 to 28 d of storage at 0.5 degrees C plus 7 d at 20 degrees C. We hypothesized that fungicide applications would shift the microbiome, with a more pronounced effect from natamycin due to the target specificity of fludioxonil. We also predicted that the antioxidant properties of DPA would shift both bacterial and fungal microbiomes. We found that natamycin resulted in modest fungal shifts and fludioxonil resulted in no observed shifts, while DPA strongly affected the fungal microbiome over time. Chemical treatment was not a predictor of bacterial microbiome variation, but bacterial communities shifted throughout storage. However, many of the trends that occurred during storage were reversed during the 7-d shelf life period at 20 degrees C after storage. Time in cold storage decreased the relative abundance of Pseudomonas, while DPA application reduced the relative abundance of Aureobasidium, both notable biocontrol genera. These results highlight how chemical applications such as DPA may have unintended effects on beneficial microbes that protect fruit from pathogen infection.