Endophytic bacterial communities in apple leaves are minimally impacted by streptomycin use for fire blight management

Authors: WALLIS, ANNA - Cornell University; Gu, Ganyu; RAMACHANDRAN, OADMINI - Food And Drug Administration(FDA); REED, ELIZABETH - Food And Drug Administration(FDA); OTTESEN, ANDREA - Food And Drug Administration(FDA); Nou, Xiangwu; COX, KERIK - Cornell University

Submitted to: Phytobiomes Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/18/2021
Publication Date: 4/16/2021
Citation: Wallis, A., Gu, G., Ramachandran, O., Reed, E., Ottesen, A., Nou, X., Cox, K. 2021. Endophytic bacterial communities in apple leaves are minimally impacted by streptomycin use for fire blight management. Phytobiomes Journal. https://doi.org/10.1094/PBIOMES-11-20-0081-R.
DOI: https://doi.org/10.1094/PBIOMES-11-20-0081-R

Interpretive Summary: Antibiotic (streptomycin) is commonly used to control apple fire blight disease, which is caused by a bacterium Erwinia amylovora. However, the impact of antibiotic application on the microbial population residing inside the plant tissue (endophytes) and the downstream effects on the apple trees and orchard environment are unclear. In this study, ARS scientists assisted researchers from Cornell University for assessing the cumulative effects of different disease management programs, including multiple applications of streptomycin, on the abundance and diversity of endophyte communities and on selection of antibiotic resistant bacteria, using conventional culture-dependent and DNA sequencing based methods. Researchers determined that these management programs did not greatly affect the endophyte microbial communities and did not lead to an increase of antibiotic resistant endophites. Findings from this study can help apple growers in selecting more sustainable management programs, and provide insights for understanding the endophites including potential foodborne pathogens on food crops.

Technical Abstract: Fire blight, caused by the bacteria Erwinia amylovora, is a devastating disease of apples routinely managed by commercial growers using the antibiotic streptomycin. Both E. amylovora, which moves systemically via the vascular tissue, and streptomycin, which is locally systemic, interact with endophytic bacterial communities, which are increasingly being recognized for their complex roles and valuable services to plant hosts. Diminishing or altering these communities may have profound downstream implications for plant health and selection for streptomycin resistance. In this study, we investigated the impact of multiple streptomycin applications (1, 3, or 9 post-bloom sprays) on endophytic bacterial communities in apple leaves in two orchards, using both culture-dependent and independent methods. Streptomycin programs were compared to untreated trees and two programs approved for organic production. Culture-dependent methods did not impact abundance of culturable endophytic bacteria or select for streptomycin resistance, as indicated by colony forming units (CFU) ml-1 on Luria-Bertani media. Culture-independent methods, using 16S rDNA high-throughput sequencing to identify endophytic communities, generally did not detect a significant difference in bacterial abundance (alpha diversity) or community composition (beta diversity) between treatments. A greater difference was observed in community composition between the two orchards investigated, indicating a strong selection by 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 parasites of arthropods, which could indicate horizontal transfer of these endosymbionts between insect and plant hosts. Our results provide evidence that antibiotic applications in apple orchards have minimal effect on endophytic bacterial communities, adding to the growing body of evidence that current commercial practices are sustainable solutions for fire blight management.