Apple Blossoms from a Swiss Orchard with Low-Input Plant Protection Regime Reveal High Abundance of Potential Fire Blight Antagonists

Erwinia amylovora causes fire blight, a serious disease of Rosaceae plants, including apple and pear. A predominant path of bacterial infection is entry through nectartodes after multiplication on the stigma. Depending on the inhibitory abilities of the native blossom microbiota, it may control the outbreak of fire blight and, therefore, may bar potential plant protection with reduced input of synthetic chemicals. Blossoms of five apple varieties in a low-input orchard, which had no fire blight history despite disease outbreaks in close proximity, were analyzed to assess bacterial and fungal communities. Metabarcoding indicated low microbial diversity and the presence of a few dominant operational taxonomic units (OTUs), including known fire blight antagonists such as Metschnikowia pulcherrima and Aureobasidium pullulans. The most dominant bacterial taxon (bOTU_01) was classified as Erwinia spp. To resolve sequences of species within bOTU_01, we used analyses of sequence variants and DNA signatures (i.e., nucleotide polymorphisms that are indicative for different species or species groups). These analyses revealed that >94.5% of the sequences of bOTU_01 derived from E. tasmaniensis, a potential E. amylovora antagonist. The latter was represented by up to 0.006% of the sequences. Cultivation-based analyses confirmed the prevalence of E. tasmaniensis. The high abundance of native potential E. amylovora antagonists likely indicates that this special set of native apple blossom microbiota counteracted the establishment of E. amylovora in this low-input orchard. This may allow for a new approach to assess possible components of synthetic apple blossom communities to mitigate fire blight infections.