Impacts of abiotic factors on the fungal communities of ‘Honeycrisp’ apples in Canada

Abstract

The maintenance of the beneficial plant microbiome to control plant pathogens is an emerging concept of disease management, and necessitates a clear understanding of these microbial communities and the environmental factors that affect their diversity and compositional structure. As such, studies investigating the microbiome of economically significant cultivars within each growing region are necessary to develop adequate disease management strategies. Here, we assessed the relative impacts of growing season, management strategy, and geographical location on the fungal microbiome of 'Honeycrisp' apples from seven different orchard locations in the Atlantic Maritime Ecozone for two consecutive growing years. Though apple fruit tissue was dominated by relatively few fungal genera, significant changes in their fungal communities were observed as a result of environmental factors, including shifts in genera with plant-associated lifestyles (symbionts and pathogens), such as Aureobasidium, Alternaria, Penicillium, Diplodia, and Mycosphaerella. Variation in fungal composition between different tissues of fruit was also observed. We demonstrate that growing season is the most significant factor affecting fungal community structure and diversity of apple fruit, suggesting that future microbiome studies should take place for multiple growing seasons to better represent the host-microbiome of perennial crops under different environmental conditions.

The effects of chemical fungicides and salicylic acid on the apple microbiome and fungal disease incidence under changing environmental conditions

“…When tissue-types are observed individually, growing season accounts for 67 and 74% of variations in the communities of core and peel tissues, respectively, providing further evidence that growing season impacts microbiome variation. On the whole, this corresponds to the observation in our previous study that the impact of the growing season was apparently greater on peel tissues than core tissues ( McLaughlin et al, 2023 ). Questions including how altering the macro-environmental conditions can impact tissue-specific micro-environments, and how these specific micro-environmental changes in turn are reflected in the microbiome, are likely important considerations if microbiome maintenance is to be seriously considered in disease management applications.…”

“…Further investigation of the factors influencing the fungal communities of specific fruit tissues will be necessary to identify the most relevant factors. In our previous studies we have observed similar trends of high microbial diversity in the core tissues compared to peel tissues ( Abdelfattah et al, 2021a ; McLaughlin et al, 2023 ).…”

“…To implement microbiome maintenance for disease control a thorough understanding of how the available treatment options impact the fruit microbiome is needed. Although the literature has found evidence of variation in apple fungal communities between conventional and organic management practices, the impact of exogenous plant defence elicitors on these communities has yet to be explored ( Abdelfattah et al, 2016 ; Bösch et al, 2021 ; Britt et al, 2021 ; McLaughlin et al, 2023 ). In addition to variation by treatment regime, spatial variation by tissue types and variations due to changes in environmental conditions between growing seasons have also been described ( Abdelfattah et al, 2016 ; Bösch et al, 2021 ; Abdelfattah et al, 2021a ).…”

“…While the rhizosphere and phyllosphere of apple have been extensively studied, the factors impacting the microbiome of apple fruit are not well understood ( Whitehead et al, 2021 ; Abdelfattah et al, 2021a ). Recently, we demonstrated that variations in environmental conditions between growing seasons had the greatest influence on the apple fruit microbiome compared to tissue type, management practice, and geographical location within a single ecozone ( McLaughlin et al, 2023 ). However, compelling evidence suggests that many factors—including geographical location, management practices, tissue type, cultivar., storage duration, and pre-storage treatments—can significantly impact the structure and diversity of the fungal microbiome of apple fruit ( Abdelfattah et al, 2016 ; Bösch et al, 2021 ; Britt et al, 2021 ; Abdelfattah et al, 2021a ).…”

The Impact of Abiotic and Biotic Factors on the Productivity of the Apple Cultivars (<i>Malus domestica</i>)

“…The maintenance of the beneficial plant microbiome to control plant pathogens is an emerging concept of disease management, and necessitates a clear understanding of these microbial communities and the environmental factors that affect their diversity and compositional structure. Growing season is the most significant factor affecting fungal community structure and diversity of apple fruit, suggesting that future microbiome studies should take place for multiple growing seasons to better represent the host-microbiome of perennial crops under different environmental conditions [15].…”