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The phyllosphere is colonized by a wide variety of microorganisms including epiphytes, plant-pathogenic fungus, bacteria, as well as human or animal pathogens. However, little is known about how microbial community composition changes with the development of angular leaf-spot of cucumber. Here, 18 mixed samples were collected based on the lesion coverage rate (LCR) of angular leaf-spot of cucumber from three disease severity groups (DM1: symptomatic-mild, DM2: symptomatic-moderate, DM3: symptomatic-severe). In our study, the microbial community structure and diversity were examined by Illumina MiSeq sequencing. A significant differences was observed in α diversity and community structure among three disease severity groups. The phyllosphere microbiota was observed to be dominated by bacterial populations from Proteobacteria, Actinobacteria, and Firmicutes, as well as fungal species from Ascomycota and Basidiomycota. In addition, some plant-specific microbe such as  Sphingomonas ,  Methylobacterium ,  Pseudomonas , and  Alternaria  showed significant changes in their relative abundance of population. The LCR was correlated negatively with  Sphingomonas ,  Methylobacterium ,  Quadrisphaera , and  Lactobacillus , whereas correlated positively with  Pseudomonas  and  Kineococcus  (p < 0.05). The LCR was negatively correlated with  Alternaria  and  Arthrinium  of the fungal communities (p < 0.05). Molecular ecological networks of the microbial communities were constructed to show the interactions among the OTUs. Our current results indicated that the competitive relationships among species were broken with the development of angular leaf-spot of cucumber. The microbial community composition changed over the development of angular leaf-spot of cucumber. The result of molecular ecological networks indicated that the overall bacterial community tends toward mutualism from the competition. The development of angular leaf-spot of cucumber affected the ecosystem functioning by disrupting the stability of the microbial community network. This work will help us to understand the host plant-specific microbial community structures and shows how these communities change throughout the development of angular leaf-spot of cucumber.   Electronic supplementary material  The online version of this article (10.1186/s13568-019-0800-y) contains supplementary material, which is available to authorized users.

Variations in phyllosphere microbial community along with the development of angular leaf-spot of cucumber