Identification of helper strains from apple fruit epiphytic microbiome to increase P. anomala strain K efficacy against B. cinerea on postharvest apples

Apple fruit epiphytic microbiota has been the source of the majority of biocontrol agents (BCAs) and can influence the fruit quality during storage. However, the use of BCA in commercial application is limited by low or non-reliable efficacies in comparison to chemical fungicides. Indeed, once applied on the fruit surface, a BCA faces a complex microbiota where ecological interactions (parasitism, mutualism, commensalism) occur, thus affecting its efficacy. To address this concern, Massart et al. (2015) suggested the use of microbiota to improve BCA efficacy by the selection of helper strains. Apple fruit samples of fifteen varieties grown in four disease management practices (DMP) (never treated, light organic, organic and conventional) were collected in Belgium. Their epiphytic microbiota were harvested and their efficacy to raise the biocontrol of Pichia anomala strain K against Botrytis cinerea were tested. Amplicon (V3-V4 region of 16s rRNA gene and ITS1 region) high throughput sequencing allowed to decipher the bacterial and fungal populations of the microbiota. Results of the taxonomic profiling reveal significant differential abundances of microorganisms (FDR-p < 0.05), influenced by DMP (ADONIS test p < 0,05). The core microbiota (OTUs shared in 90% of our samples), showed a diversified profile including 60 bacterial OTUs and 26 fungal OTUs at genera level. Results of the biological assay disclosed that apple microbiota can either raise up to 100%, or reduce at 17% the biocontrol of the strain K against B. cinerea. Co-clustering analysis of the correlation between the biological assays and the amplicon sequencing, have help to detect 81 interesting genera being isolated for their ability to significantly raise the efficacy of strain K.