Deciphering the Cape Gooseberry Fruits Mycobiome for Further Safety Improvement Postharvest

Abstract

Cape gooseberries are exquisitely flavored fruits; their rapid deterioration reduces their shelf life. Understanding the unique mycobiome of fruit peels is an essential step in identifying the taxa causing postharvest loss. The current study proposes to analyze the fungal communities of cape gooseberry peels collected from an organic orchard at unripe and ripe stages and purchased from open-air market sites, using the ITS2 region metabarcoding. According to the Kruskal-Wallis test, there were no statistically significant differences found in either the phylogenetic or non-phylogenetic alpha diversity indices. Significant differences in fungal communities were observed between the market and orchard groups based on beta diversity results. Ascomycota (85.72-96.76%), Basidiomycota (3.21-13.91%), and Chytridiomycota (0.07-9.35%) were the most common fungal phyla, their abundance varying with the ripening stage and origin. Dothideomycetes in the orchard group and Saccharomycetes in the market group were the two most prevalent classes. Furthermore, we investigate which taxa showed a significant difference in abundance between the two conditions (market vs. orchard) using the analysis of compositions of microbiomes with bias correction (ANCOM-BC) test. Regardless of the phase, the orchard samples exhibited a notable increase in the mean absolute abundance of various beneficial fungal taxa, including Tilletiopsis washingtonensis and Articulospora proliferata, whereas the market samples demonstrated a high abundance of harmful yeasts and molds such as Meyerozyma guilliermondii, Candida railenensis, and Botrytis caroliniana. Although it is unclear how these microorganisms augment at the market sites and might impact the fruit quality after harvest, from a fruit safety perspective, it is essential to comprehend the diversity and variation of the mycobiome composition at different ripening stages to further develop strategies to improve food safety postharvest.

Keywords: Botrytis caroliniana; Candida railenensis; ITS2 metabarcoding; Meyerozyma guilliermondii; cape gooseberry; organic management system.

Figure 1

Box and whisker plots of alpha diversity values of fungal communities analyzed. (A) Pielou’s evenness; (B) Faith PD (phylogenetic diversity); (C) Shannon diversity index; (D) observed features. Legend: Two: fruits collected from the orchard phase two; Four: fruits collected from the orchard phase four; Market: fruits purchased from the market sites. Each box’s middle line aligns with the mean, and its upper and lower bounds are spaced one standard deviation apart from the mean. The highest and lowest values of each group are reached by the whiskers that extend above and below the box. The significance was determined Kruskal–Wallis; the values were considered significant when p < 0.05.

Figure 2

Principal coordinate analysis (PCoA) plots. (A) Bray–Curtis dissimilarity indices; (B) Jaccard distance; (C) unweighted UniFrac distance; (D) weighted UniFrac distance. Statistics were calculated using pairwise PERMANOVA with 999 permutations. Legend: Two: fruits collected from the orchard phase two; Four: fruits collected from the orchard phase four; Market: fruits purchased from the market sites.

Figure 3

Fungal relative abundance (%) at the class and family levels across the samples (A,C) and groups (B,D). The stacked bar plots were constructed based on the relative abundance of the top 10 fungal classes/families, while “Other” category was defined as the sum of all classifications with less than 0.50% abundance. Legend: U2L1–U2L6: fruits collected from the organic orchard ripe phase two; U4FL1–U4FL6: fruits collected from the organic orchard ripe phase four; UP1–UP6: fruits purchased from the market sites.

Figure 4

Fungal genera relative abundance (%) across the samples (A) and among the groups (B). The stacked bar plots were constructed based on the relative abundance of the top 10 fungal genera, while “Other” category was defined as the sum of all classifications with less than 0.50% abundance. Legend: U2L1–U2L6: fruits collected from the organic orchard ripe phase two; U4FL1–U4FL6: fruits collected from the organic orchard ripe phase four; UP1–UP6: fruits purchased from the market sites.

Figure 5

Differential abundance relative to the reference group (market) using ANCOM-BC test. (A) Phase two; (B) phase four. Y-axis (Feature ID): lists the identifiers of the features (taxa) being compared. X-axis (log fold change, LFC): shows the LFC in abundance of each feature between the groups being compared. A positive value indicates that the feature is more enriched (more abundant) in the group of interest, while a negative value indicates that it is more depleted (less abundant). Error bars: indicate variability or uncertainty in the log fold change estimate. Smaller error bars suggest a more precise estimate.

Figure 6

Heatmap and hierarchical clustering of the most abundant fungi at the genus level. On the X-axis are the experimental conditions that are being compared (groups); Y-axis contains the microbial genus that has been identified in the group; blue intense color: low abundance, red color: high abundance.