Species-Specific Pathogens Drive Distinct Structural and Inter-Kingdom Dynamics in the Mulberry Leaf Microbiome

A plant pathogen is a deterministic factor affecting the plant microbiome. However, whether the influence of different pathogen species on the plant microbiome is consistent is not well-known. In this study, mulberry leaves with similar spots caused by two diseases—mulberry brown spot (MBS, caused by Neophloeospora maculans) and mulberry snags rotten leaves disease (MSRL, caused by Boeremia exigua var. mori)—along with asymptomatic leaves, were collected. Their endophytic fungal and bacterial communities were sequenced. The occurrence of MSRL reduced leaf fungal richness and diversity (observed species from 329 to 203; Shannon diversity index from 3.6 to 2.6, p < 0.05; phylogenetic diversity index from 45.8 to 20.6, p < 0.05), along with leaf bacterial diversity; in contrast, the occurrence of MBS had little effect on both fungal and bacterial richness and diversity. Both diseases significantly altered the composition and structure of leaf fungal communities, whereas only MBS did so for bacterial communities. For the dominant genera, the fungal genera, except Cercospora, were differently affected by the occurrence of MBS and MSRL, while the bacterial genera Pseudomonas (from 8.3% to 30.6%, p < 0.05 for MBS; from 23.1% to 28.1% for MSRL), Massilia (0.2% to 7.7%, p < 0.05; 2.1% to 6.1%), Chryseobacterium (0.1% to 0.3%; 2.7% to 7%), Pantoea (2.6% to 3.7%; 0.4% to 1%), and Aureimonas (0.7% to 1.4%; 1.3% to 1.7%) were consistently enriched by both diseases. In addition, Chryseobacterium (LDA score = 4.6, p < 0.01) was detected as a biomarker after the occurrence of MSRL. Intriguingly, there were four times more significant fungi–bacteria positive associations induced by the occurrence of MSRL compared to MBS (10.2% to 2.5%). Taken together, the responses of mulberry leaf microbiome to pathogen infection vary in response to the pathogen species; although several bacterial genera were consistently enriched, whether their enrichment reflects their antagonistic roles in fungal—bacterial inter-kingdom interactions remains to be determined and should be interpreted with further experimental tests.