Alternaria Brown Spot Alters the Bacteriome with Alternaria–Bacteria Interactions in Mature Citrus Fruits

Alternaria brown spot is an important fungal disease in citrus. The infection of young citrus organs usually coincides with strong rainfall, which causes low efficiency of fungicides and the outbreak of this disease. Here, the microbiomes of the asymptomatic peels, the spot edge, and the center of citrus fruits were compared to reveal the commensal microbes as alternative control methods for the Alternaria pathogen. As the disease severity increased from the asymptomatic peels to the spot edge and the center, the bacterial communities were more severely changed than the fungal communities. Both the bacterial diversity, represented by the Shannon diversity index, and the bacterial composition and structure significantly decreased and altered, respectively. Increased Alternaria, in relative abundance, correlated positively with bacterial genera like Massilia and Sphingomonas, while negatively correlating with bacterial genera like Delftia and Pantoea. In addition, Alternaria fASV1 positively correlated with several top ASVs of 1174_901_12 and Sphingomonas. These results suggest that the bacterial communities respond to Alternaria brown spot by Alternaria–bacteria cross-kingdom interactions; these responsive bacteria are worth testing experimentally.