Summary: We 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.

The contribution of the apple microbiome to the production chain of apple was so far largely unknown. Here, we describe the apple fruit microbiome and influences on its composition by parameters such as storage season, storage duration, storage technology, apple variety, and plant protection schemes. A combined culturing and metabarcoding approach revealed significant differences in the abundance, composition, and diversity of the apple fruit microbiome. We showed that relatively few genera contribute a large portion of the microbiome on fruit and that the fruit microbiome changes during the storage season depending on the storage conditions. In addition, we show that the plant protection regime has an influence on the diversity of the fruit microbiome and on the dynamics of pathogenic fungal genera during the storage season. For the genus Neofabraea, the quantitative results from the metabarcoding approach were validated with real-time PCR. In conclusion, we identified key parameters determining the composition and temporal changes of the apple fruit microbiome, and the main abiotic driving factors of microbiome diversity on apple fruit were characterized.

The yeast Metschnikowia pulcherrima is frequently isolated from environmental samples and has often been reported to exhibit strong antagonistic activity against plant pathogens. In order to assess the potential of this species for its development into a plant protection product, the survival during formulation and storage were quantified and field efficacy was assessed over a period of five years. Freeze dried and liquid M. pulcherrima formulations (i.e., with skim milk powder (SMP), sucrose, glycerol, xanthan, without additives) were prepared and the number of viable cells was quantified during storage at different temperatures. Field trials against apple postharvest diseases (Neofabreae) were performed with different dry formulations. M. pulcherrima proved exceptionally stable for many months and even years. Five years of field trials with the yeast revealed variable effects, but reduced Neofabreae infections of stored apples were observed in some years. M. pulcherrima applications after prior fungicide treatments repeatedly showed an additive effect as compared to the fungicide treatments alone. In summary, M. pulcherrima exhibited highly advantageous storage properties and encouraging activity against apple postharvest rots. Further studies to identify the factors responsible for antagonistic activity in the field and survival during storage are expected to lay the foundation for the future development of a plant protection product.

The unintentional movement of agronomic pests and pathogens is steadily increasing due to the intensification of global trade. Being able to identify accurately and rapidly early stages of an invasion is critical for developing successful eradication or management strategies. For most invasive organisms, molecular diagnostics is today the method of choice for species identification. However, the currently implemented tools are often developed for certain taxa and need to be adapted for new species, making them ill-suited to cope with the current constant increase in new invasive species. To alleviate this impediment, we developed a fast and accurate sequencing tool allowing to modularly obtain genetic information at different taxonomical levels. Using whole genome amplification (WGA) followed by Oxford nanopore MinION sequencing, our workflow does not require any a priori knowledge on the investigated species and its classification. While mainly focusing on harmful plant pathogenic insects, we also demonstrate the suitability of our workflow for the molecular identification of bacteria (Erwinia amylovora and Escherichia coli), fungi (Cladosporium herbarum, Colletotrichum salicis, Neofabraea alba) and nematodes (Globodera rostochiensis). On average, the pairwise identity between the generated consensus sequences and best GenBank BLAST matches was 99.6 ± 0.6%. Additionally, assessing the generated insect genomic dataset, the potential power of the workflow to detect pesticide resistance genes, as well as arthropod-infecting viruses and endosymbiotic bacteria is demonstrated.

Superficial scald is a physiological disorder that develops during cold storage affecting apples and causes substantial market losses. Malus × domestica cv. Ladina, a new scab resistant and fire blight tolerant variety, commercialized in 2012, shows a physiological disorder similar to superficial scald after storage. Here, we used different pre- and postharvest approaches to characterize the occurrence of these superficial scald symptoms in Malus × domestica cv. Ladina. Over a period of seven years, fruits from multiple orchards were stored for five to seven months and the occurrence of superficial scald was assessed in fruits after cold storage and controlled atmosphere (CA) storage. Apples picked at different stages of ripeness within the same year differed in superficial scald development. Additionally, superficial scald differed significantly between years and locations, strongly suggesting that maturity at harvest, weather during the growing season, and orchard management play important roles in scald occurrence. Treatment with 1-methylcyclopropene (1-MCP) after harvest, and storage in a dynamically controlled atmosphere (DCA) significantly reduced the occurrence of superficial scald, whereas storage under ultralow oxygen concentrations (ULO) showed mild but not significant effects. Low calcium concentrations in the fruit flesh and peel were associated with stronger superficial scald occurrence.

Core collections (CCs) constitute a key tool for the characterization and management of genetic resources (GR). When the institutions involved in GR preservation decide to define a CC, they frequently prefer to select accessions based not only on strictly objective criteria, but also to add others following expert knowledge considerations (popularity, prestige, role in breeding history, or presence of phenotypic features of interest). The aim of this study was to evaluate the implications of approaches that combine formal analytical procedures and expert knowledge on the efficiency of CC definition through a case study to establish a pear CC from the Swiss National Pear Inventory. The CC had to represent a maximum of the genetic diversity, not to exceed 150 accessions, and required to include a priority set (SPPS) with 86 genotypes selected based on expert knowledge. In total, nine strategies were evaluated, resulting of combining compositions of the dataset sampled, sampling sizes and methods. The CCs sampled by mixed approaches provided similar scores, irrespective of the approach considered, and obtained similar efficiency in optimizing the genetic diversity retained. Therefore, mixed approaches can be an appropriate choice for applications involving genetic conservation in tree germplasm collections.