Global analysis of the apple fruit microbiome: are all apples the same

Authors: ABDELFATTAH, AHMED - Universitat Graz; FREILICH, SHIRI - Israel Agricultural Research Organization (ARO); BARTUV, ROTEM - Hebrew University Of Jerusalem; ZHIMO, YEKA - Volcani Center (ARO); KUMAR, AJAY - Volcani Center (ARO); BIASI, ANTONIO - Volcani Center (ARO); SALIM, SHOSHANA - Volcani Center (ARO); FEYGENBERG, OLEG - Volcani Center (ARO); Burchard, Erik; Dardick, Christopher - Chris; LIU, JIA - Chongqing University; KHAN, AWAIS - Cornell University; AMIRI, ACHOUR - Washington State University; ELLOUZE, QUALID (WALID) - Agriculture And Agri-Food Canada; ALI, SHAWKAT - Agriculture And Agri-Food Canada; SPADARO, DAVIDE - University Of Torino; TORRES, ROSARIO - Institute De Recerca I Tecnologia Agroalimentaries (IRTA); TEIXIDO, NEUS - Institute De Recerca I Tecnologia Agroalimentaries (IRTA); OZKAYA, OKAN - Cukurova University; BUEHLMANN, ANDREAS - Agroscope; VERO, SILVANA - Universidad De La República; BERG, GABRIELE - Universitat Graz; WHITEHEAD, SUSAN - Virginia Polytechnic Institution & State University; WISNIEWSKI, MICHAEL - Virginia Polytechnic Institution & State University; DROBY, SAMIR - Agricultural Research Organization, Volcani Center

Submitted to: Environmental Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/16/2021
Publication Date: 3/18/2021
Citation: Abdelfattah, A., Freilich, S., Bartuv, R., Zhimo, Y., Kumar, A., Biasi, A., Salim, S., Feygenberg, O., Burchard, E.A., Dardick, C.D., Liu, J., Khan, A., Amiri, A., Ellouze, Q., Ali, S., Spadaro, D., Torres, R., Teixido, N., Ozkaya, O., Buehlmann, A., Vero, S., Berg, G., Whitehead, S., Wisniewski, M., Droby, S. 2021. Global analysis of the apple fruit microbiome: are all apples the same. Environmental Microbiology. https://doi.org/10.1111/1462-2920.15469.
DOI: https://doi.org/10.1111/1462-2920.15469

Interpretive Summary: Fruit contain numerous bacteria and fungi, collectively referred to as the microbiome. Previously, it has been shown that these microbes play important roles in fruit quality, post-harvest diseases, as well as food safety. Here, we analyzed the microbiomes of apple fruit collected worldwide. The results showed that the apple microbiome substantially varies depending on geographic location. Changes in the apple microbiome were associated with susceptibility to post-harvest diseases. A common set of microbes were identified in all apple fruit that represent the ‘core’ apple microbiome. This information provides a foundation for understanding how fruit microbiomes impact fruit quality and safety as well as the management of post-harvest diseases.

Technical Abstract: Background: Apple is one of the most highly consumed fruits worldwide and is the largest fruit crop produced in temperate regions. Fruit quality, safety and long-term storage are issues that are important to growers, distributors, and consumers. We present the first worldwide study on the apple fruit microbiome that examines questions regarding the composition and the assembly of microbial communities on and in apple fruit. Results: Results revealed that the composition and structure of the fungal and bacterial communities associated with ‘Royal Gala’ apple fruit at harvest maturity vary and are highly dependent on geographical location. The study also confirmed that the spatial variation in the fungal and bacterial composition of different fruit tissues exists at a global level. Fungal diversity varied significantly in fruit harvested in different geographical locations and suggest a potential link between location and the type and rate of postharvest diseases that develop in each country. Although the geography, climatic conditions, and management practices may have a significant impact on the composition of fruit microbial communities, we were able to identify a 'core' microbiome that is shared in fruit across the globe. Conclusions: Results of this study provide foundational information about the apple fruit microbiome that can be utilized for the development of novel approaches for the management of fruit quality and safety, as well as for reducing losses due to the establishment and proliferation of postharvest pathogens. It also lays the groundwork for studying the complex microbial interactions that occur on apple fruit surfaces.