Characterization of apple metagenome in Belgium

Microbial communities (microbiota) living at the surface of fruit have been the source of most of biocontrol agents. Despite this interest, their role as a community has been poorly studied due to the lack of techniques to survey the holistic microbiota and their evolution. Thanks to high-throughput sequencing, their holistic study is now possible. In this study, we characterized apple fruit surface bacterial microbiome in Belgium. Seventeen apple varieties grown in four disease management practices [no phytosanitary treatment (conservation orchard), light-organic, organic and conventional] were harvested and their microbiota collected for DNA extraction and Illumina sequencing. The sequencing (2x250 nucleotides) targeted the V3-V4 16s ribosomal DNA and bioinformatic analysis were carried out with QIIME1.9.0. A total of 3,302,088 filtered high-quality sequences were assigned into 13,507 Operational Taxonomic Units (OTUs). Proteobacteria (64%) and Bacteriodetes (22%) were by far the dominant phyla. A total of 60 OTUs were present in 90% of samples, and they can be considered as a bacterial core microbiota. No significant difference (Bonferroni probability > 0,05) of Kruskall-Wallis was identified between tested varieties of Golden, Jonagold and Elstar for conventional and organic treatment as well as varieties of conservation orchard. The overall analysis (without varieties) of alpha diversity (Observed-OTUs, Shannon, Simpson and phylogenetic diversity) and beta diversity show differences among not treated, organic and conventional apples. These results
underline not only a diverse microbiota whose role needs to be characterized, but also a diversity of apple microbiota that was reduced across the time by modern agriculture.