Genetic and functional characterization of the bacterial community on fruit of three raspberry (Rubus idaeus) cultivars

BACKGROUND: Raspberry breeding programs allowed the development of highly yielding cultivars, but often resulted in a reduction of plant plasticity and resistance to abiotic and biotic stresses. The epiphytic bacterial community on leaves and fruit may play a crucial role in overcoming these shortcomings, influencing host performance and health status. OBJECTIVE: The bacterial community associated to two red-fleshed ("Imara" and "Regina") and one white-fleshed ("Anne") raspberry varieties was described. The bacterial community was functionally characterized to identify strains with plant growth promoting or plant protection traits. METHODS: Microbial community was assessed using both culture-independent and -dependent methods. Strains were tested for production of acetoin, siderophores, indoleacetic acid and ammonia, ACC deaminase activity, biofilm formation, biological control of Erwinia amylovora, Botrytis cinerea or Drosophila suzukii. RESULTS: The fruit bacterial community clearly differed between red- and white-fleshed raspberry. Thirteen isolates produced plant growth and resistance promoting substances, while twelve bacterial isolates were able to manipulate either auxin or ethylene metabolism. Five strains inhibited the growth of Erwinia amylovora and Botrytis cinerea, and one increased Drososphila suzukii mortality. CONCLUSIONS: This study offers new insights for the biotechnological exploitation of bacteria isolated from raspberry.