Endophytic Bacterial Communities in Apple Leaves Are Minimally Impacted by Streptomycin Use for Fire Blight Management

Abstract

In apple fruit, streptomycin is routinely used to manage fire blight, a devastating disease that greatly affects commercial apple production. Applications of streptomycin may affect the endophytic bacterial communities, which are increasingly recognized for their valuable roles in plant hosts. Altering these communities may have implications for plant health and selection for streptomycin resistance in off-target bacteria. In a previous study, we found rapid selection of streptomycin-resistant epiphytes following season-long streptomycin use, and now sought to investigate the season-long impact of streptomycin applications (one, three, or nine postbloom applications) on endophytic bacterial communities. Studies were conducted in two orchards, and both culture-dependent and independent methods were used to assess the bacterial endophytic community. Streptomycin programs were compared with untreated trees and two programs approved for organic production. Treatments minimally affected abundance of culturable endophytic bacteria as determined by culture-dependent methods. Similarly, there were no significant differences in relative bacterial abundance or community composition between treatments as determined by 16S ribosomal RNA high-throughput sequencing (culture independent). There were greater differences between orchards than between treatments, suggesting a stronger influence of locality. Communities were dominated by the families Pseudomonadaceae, Enterobacteriaceae, Desulfovibrionaceae, Bacillaceae, and Burkholderiaceae, which are commonly described in other investigations of microbial communities of apple orchards. In addition, we found a high abundance of Amoebophiliaceae, a family dominated by arthropod parasites. Our results provide evidence that season-long applications of streptomycin in apple orchards have minimal impact on endophytic bacterial communities, which is in contrast to some reports on epiphytic communities.