Compared the differences between the shoot surface and interior-living bacteria and investigated their responses to chlorothalonil and propiconazole fungicides

Phyllosphere bacterial communities play important roles in plant fitness and growth. The objective of this study was to characterize the epiphytic and endophytic bacterial communities of boxwood shoots and determine how they may respond to commonly-used fungicides. In early summer and early fall, shoot samples were collected immediately before and then 1, 7, and 14 days after spray treatments with three fungicides containing chlorothalonil and/or propiconazole. DNA from shoot surface washings and from washed and surface-sterilized shoots were used as template for 16S rRNA metabarcoding, and the amplicons were sequenced on a Nanopore MinION® sequencer to characterize epiphytic and endophytic communities. Overall, 1,491 bacterial genera or 36 phyla were identified from the epiphyte communities, and 438 bacterial genera or 30 phyla from the endophyte communities. The epiphytic and endophytic communities had different compositions and were dominated by Methylobacterium and Brevundimonas, respectively. Further, 124 identified epiphytes and 30 endophytes were predicted to have plant growth- and health-promoting or other beneficial activities. Fungicide treatments containing the contact fungicide chlorothalonil impacted the diversity and composition of the epiphytic communities but did not significantly affect endophytic communities. Among the affected epiphytes, for example, Pantoea spp. and Burkholderia spp. were enhanced while Nocardioides spp. were suppressed by the contact fungicides containing chlorothalonil, while propiconazole treatment did not show a similar effect. These results are foundational for integrating microbiome considerations into integrated pest management and developing a systems approach for maintaining boxwood health.