Microbiome succession during apple fruit development: Healthy and pathological microbial assemblages

The surface and internal tissues of fruits host diverse microbial communities but the functional role of this microflora, outside of pathogenic species, in fruit health and quality are largely unknown. The recent use of universal primer sets and advanced sequencing technologies, however, has greatly increased our understanding of these microbial communities without the need to culture them. This is fostering a paradigm shift that views an organism and its microbiota as a single entity (metaorganism). We present our current understanding of the microbiome assembly in apple fruit and its implication on postharvest pathology. We first describe the initial microbial colonization and establishment in flowers, as well as the spatial and temporal community dynamics during fruit development. We then elucidate the patterns of succession that take place in the fruit microbiome as it develops and matures in the field, and subsequently after harvest and during cold storage. Next, we discuss the crucial need to identify species comprising the core microbiome and the need to conduct functional analysis of networks and the cross-talk between microbial components. We then discuss the utilization of this information for the practical development of targeted and precise biological control strategies against postharvest diseases and highlight the opportunities and challenges that exist for designing and manipulating the fruit microbiome. Lastly, topics of research that will enable a paradigm shift in fruit management are discussed in which a fruit and its dynamic microbiota are viewed as one biological entity.