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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.
Keywords
Fruit microbiome, Malus, holobiont, geographical location, niche specialization
Figure 1
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Figure 6
This is a list of supplementary files associated with this preprint. Click to download.
- Fig.S1.tif
Hierarchical clustering showing the similarity among apple fungal (a) and bacterial (b) communities composition collected from different countries i.e. Canada, Turkey, Israel, Italy, Uruguay, USA West, USA East, Switzerland, and Spain.
- Fig.S2.tif
A) a phylogenetic tree of the most prevalent Sphingomonas ASVs which were at least present with 0.1%. B) hierarchical clustering of Sphingomonas community. C) PCA ordination showing the variation in Sphingomonas (the core genus) community between fruit tissue types in all investigated orchards.
- Fig.S3.tif
Distribution of node-degree of core and none-core species in co-occurrence network. Most core species have multiple links (>13). Node degree of core species is significantly higher than non-core species (Wilcoxon p=0.0039).
- SupplementaryTable1.xlsx
A list summarizing the information about the apple samples included in the present study.
- SupplementaryTable2.xlsx
Taxonomy and relative abundance of the most prevalent fungal and bacterial taxa detected on apple fruit in each of the investigated countries (Canada, Turkey, Israel, Italy, Uruguay, USA West, USA East, Switzerland, and Spain).
- SupplementaryTable3.docx
Pairwise comparisons of the fungal and bacterial diversity (based on Shannon index) between the sampling locations (Canada, Turkey, Israel, Italy, Uruguay, USA West, USA East, Switzerland, and Spain) using Wilcox test and corrected using FDR method. P values less than 0.05 were considered significant.
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This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Research
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
History
CURRENT STATUS: Posted
View the published article at Environmental Microbiology.
Version 1
Posted 11 Jan, 2021
No community comments so far
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
General Microbiology
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published article at Environmental Microbiology.
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.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
This is a list of supplementary files associated with this preprint. Click to download.
- Fig.S1.tif
Hierarchical clustering showing the similarity among apple fungal (a) and bacterial (b) communities composition collected from different countries i.e. Canada, Turkey, Israel, Italy, Uruguay, USA West, USA East, Switzerland, and Spain.
- Fig.S2.tif
A) a phylogenetic tree of the most prevalent Sphingomonas ASVs which were at least present with 0.1%. B) hierarchical clustering of Sphingomonas community. C) PCA ordination showing the variation in Sphingomonas (the core genus) community between fruit tissue types in all investigated orchards.
- Fig.S3.tif
Distribution of node-degree of core and none-core species in co-occurrence network. Most core species have multiple links (>13). Node degree of core species is significantly higher than non-core species (Wilcoxon p=0.0039).
- SupplementaryTable1.xlsx
A list summarizing the information about the apple samples included in the present study.
- SupplementaryTable2.xlsx
Taxonomy and relative abundance of the most prevalent fungal and bacterial taxa detected on apple fruit in each of the investigated countries (Canada, Turkey, Israel, Italy, Uruguay, USA West, USA East, Switzerland, and Spain).
- SupplementaryTable3.docx
Pairwise comparisons of the fungal and bacterial diversity (based on Shannon index) between the sampling locations (Canada, Turkey, Israel, Italy, Uruguay, USA West, USA East, Switzerland, and Spain) using Wilcox test and corrected using FDR method. P values less than 0.05 were considered significant.
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