Amplicon sequencing and shotgun metagenomics reveal functional impacts of aminoethoxyvinylglycine-mediated ripening and cold storage on the microbiome of ‘NY1’ apples

Abstract

Understanding community-level microbial dynamics provides more holistic insight into the nature of pathogen infection and biocontrol in fruits and vegetables. We investigated the impact of preharvest sprays of aminoethoxyvinylglycine (AVG, 0.25 g L−1), an inhibitor of ethylene production of fruit, to assess the association between ethylene-mediated ripening and the microbiome at harvest and during storage. ‘NY1’ (Snapdragon®) apples were sprayed on the tree two weeks before first harvest and the microbiome of the fruit was assessed at harvest and at one-week intervals across four weeks. Fruit from harvests 1 and 4 were stored in air at 3 °C for up to 6 months. The bacterial communities changed over harvest time while fungal communities were affected by AVG treatment. In addition, both harvest time and AVG, as well as storage time, were associated with bacterial and fungal variation after 2–6 months of storage. Postharvest fungal microbiomes showed consistent responses to variations in fruit maturation, with the microbial communities of AVG-treated apples being similar to those of early harvested apples. Fungal microbiome variation was linked to the soluble solids concentration and IAD, revealing further links between microbial dynamics and apple quality. Bacterial shifts that occurred from harvest to 6 months of storage were characterized by metagenome changes that resulted in a lower abundance of biofilm formation pathways after cold storage, which may limit the ability of these bacterial communities to block colonization by fungal pathogens. These findings advance our understanding of how the microbiome is connected to fruit quality and functional metagenomics related to biocontrol.