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

Y. Bösch, S. Perren, A. Naef, J.E. Frey, A. Bühlmann
Microbes are an integral part of the biome and interact in many ways with 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 cultivars 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 postharvest losses in the near future.
Bösch, Y., Perren, S., Naef, A., Frey, J.E. and Bühlmann, A. (2021). A metagenomic approach to assess Neofabraea infection and dynamics on stored apples. Acta Hortic. 1323, 119-126
DOI: 10.17660/ActaHortic.2021.1323.19
apple, Bull's eye rot, Neofabraea, microbiome, metagenomics

Acta Horticulturae