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

Abstract

Erwinia amylovora causes fire blight, a serious disease of Rosaceae plants including apples and pears. 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 bare 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 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 more than 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.

Priority Effects in the Apple Flower Determine If the Siderophore Desferrioxamine Is a Virulence Factor for Erwinia amylovora CFBP1430

“…Bacterial DNA from apple flowers was extracted by transferring 0.5 mL of the 1 mL flower resuspension to sterile 1.5 mL reaction tubes followed by centrifugation for 1 min at 12.100 × g in an Eppendorf mini centrifuge. The pellet was stored at −20°C until DNA was extracted using the BioSprint 96 DNA Plant kit (Qiagen) as described previously ( 39 ).…”

A Synoptic Review of Plant Disease Epidemics and Outbreaks Published in 2021

“…Biological control of the fire blight pathogen has been proposed as an environmentally benign alternative to antibiotics such as streptomycin, now banned in Switzerland (Gschwend et al, 2021), with the increased availability of DNA sequencing in plant microbiome studies opening-up new areas of research. Blossom samples were taken in a lowinput apple orchard and subjected to standard DNA-based methods to estimate microbial diversity.…”

Site and land-use associations of soil bacteria and fungi define core and indicative taxa

“…Gschwend et al . 2021a ), or due to missing reference sequences. To elucidate the unknown microbial diversity and describe consistently occurring OTUs, several attempts have been made to identify the most common taxa, which could constitute a core of soil microbial communities (Delgado-Baquerizo et al .…”