New insights into the microbiome of apple fruit surface “cv. Pinova” through metagenomics

Plant microbial communities (microbiota) living at the surface of fruit have been the source of the majority of biocontrol agents (BCAs) but their role as a community has been poorly studied so far. A pioneering assay using highthroughput sequencing (HTS) has been carried out to get insight into the microbiota of apple surface through metagenome sequencing. Apple from cv. Pinova were sampled in Belgium during Autumn 2013 and then the microbiota was isolated. After DNA extraction, the HTS assay generated 14.5 Gbases which were assembled in 133,888 contigs. These contigs provided useful information on taxonomic composition of the microbiota. Our results demonstrated high fungal and bacterial diversity on conventionally treated apple cv. Pinova. A total of 1398 bacterial species and 397 fungal species have been identified. Among the detected fungi, the phylum Ascomycota prevailed on the surface of fruits whilst Bacteroides were dominant in the bacterial population. Some contigs appear to be closely related to apple pathogenic fungi like Aspergillus spp., Botrytis spp., Sclerotinia spp. and Penicilium spp. and apple associated pathogenic bacteria like Erwinia spp. and Agrobacterium spp. Others were assigned to species of known BCA strains like Cryptococcus spp., Talaromyces spp, Candida spp., Saccharomyces spp., Bacillus spp. and Enterobacter spp. These results underline a very diverse microbial community whose role needs to be characterized