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

Ahmed Abdelfattah,Shawkat Ali,Samir Droby,Silvana Vero,Pedro Mondino,Gabriele Berg,Ajay Kumar,Walid Ellouze,Antonio Biasi,Michael Wisniewski,Oleg Feygenberg,Awais Khan,Jia Liu,Shoshana Salim,V Yeka Zhimo,Andreas Buehlmann,Christopher Dardick,Erik Burchard,Shiri Freilich,Rotem Bartuv,Okan Özkaya ,Neus Teixidó ,D Spadaro ,Rosário Torres

doi:10.1111/1462-2920.15469

Abstract

SummaryWe present the first worldwide study on the apple (Malus × domestica) fruit microbiome that examines questions regarding the composition and the assembly of microbial communities on and in apple fruit. Results revealed that the composition and structure of the fungal and bacterial communities associated with apple fruit 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 suggests a potential link between location and the type and rate of postharvest diseases that develop in each country. The global core microbiome of apple fruit was represented by several beneficial microbial taxa and accounted for a large fraction of the fruit microbial community. The study provides 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.

Highlights

Developing a comprehensive understanding of the plant microbiome has identified as key for establishing a second green revolution (National Academies of Sciences E, Medicine, 2019)
The main objectives of the present study were to determine:(i) if the spatial differences in microbial composition previously reported exist on a global scale, irrespective of where the fruit is grown; (ii) how the structure of the fruit microbiome is affected by geographical location and general differences in climate and (iii) if a core microbiome could be identified and if so how do the members of the core microbiome interact as a network
The abundance distribution of the bacterial phyla was consistent across countries, except in Turkey where Firmicutes were more abundant than Proteobacteria compared with the other countries

Summary

Introduction

Developing a comprehensive understanding of the plant microbiome has identified as key for establishing a second green revolution (National Academies of Sciences E, Medicine, 2019) In this regard, the sequencing of plant and microbial genomes has provided a wealth of information for developing new opportunities for crop improvement. A growing body of information indicates that the plant microbiome is involved in many host functions, directly or indirectly affecting host physiology, biochemistry, growth, disease resistance, stress tolerance and quality, before and after harvest (Berg et al, 2016) This field of research has already provided new applications with the ‘microbiome factor’ being included in breeding strategies, seed production, preharvest disease control and the management of postharvest pathogens (Berg et al, 2016; Gopal and Gupta, 2016; Wei and Jousset, 2017). Studying the temporal changes in the assembly and composition of microbial communities on and in fruit during storage and marketing is essential for controlling postharvest diseases and reducing losses and waste along the supply chain

Objectives

Results

Discussion

Conclusion