A metagenomic approach to assess Neofabraea infection and dynamics on stored apples

Microbes are an integral part of the biome and interact in many ways with the plant products that humans produce for food. While the detrimental effect of postharvest pathogens on fresh produce can be characterized by classical microbiology, little is known about the infection dynamics of plant pathogens before symptoms appear. This holds especially true for Neofabraea spp. the causative agent of Bull’s eye rot on apple, which causes major losses on stored apples whereas important aspects about its life cycle and its infection dynamics are still unknown. Here, we aimed to characterize the infection levels of apples with Neofabraea spp. at the time of harvest and the dynamics thereof during storage in a controlled atmosphere facility by characterizing the apple skin microbiome using a metagenomic approach. While the classical microbiology approach consistently failed to detect Neofabraea spp. on asymptomatic apple skin tissue, the metagenomic approach was able to detect the occurrence of Neofabraea spp. before bull’s eye rot symptoms became visible. Furthermore, the quantification of Neofabraea spp. using the metagenomic approach correlated with the extent of post storage symptoms across two different apple varieties and across three different orchard management practices. Due to the inherent variability of fungal infection loads between locations and years, the experiment has to be repeated to gain a more robust insight. Nonetheless, the data provided here suggests that metagenomic data can serve as a monitoring tool to presymptomatically address the infection load of Neofabraea spp. and thus to assess the risk of developing bull’s eye rot symptoms during storage. Therefore metagenomic sequencing may provide a valuable tool to inform practitioners on disease risks and prevent post-harvest losses in the near future
Activity type
Publication in scientific journal (peer review)
Activity work package
Fruit quality; improvement of fruit handling/storage
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Activity contact
Andreas Bühlmann, e-mail: [email protected],
Tel.: +41 58 460 64 24, Fax: +41 58 460 63 41
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The EUFRUIT thematic network has received funding from the
European Union's Horizon 2020 research and innovation programme
under grant agreement No 696337.