Fig 1.
(A) Bacterial samples from tolerant and susceptible varieties under insecticide and netting treatments. (B) Fungal samples from tolerant and susceptible varieties under insecticide and netting treatments. (C) Bacterial samples from tolerant and susceptible varieties under healthy and infected berry treatments. (D) Fungal samples from tolerant and susceptible varieties under healthy and infected berry treatments. The vertical gray line indicates the subsampling depth at which maximum diversity was captured and most samples were retained. The y-axis represents the number of species (OTUs) in each sample while the x-axis represents the number of sequences sampled.
Fig 2.
Alpha diversity measures of microbiota communities.
(A) Bacterial communities under insecticide treatment for the tolerant variety. (B) Bacterial communities under insecticide treatment for the susceptible variety. (C) Fungal communities under insecticide treatment for the tolerant variety. (D) Fungal communities under insecticide treatment for the susceptible variety. (E) Bacterial communities under netting treatment for the tolerant variety. (F) Bacterial communities under netting treatment for the susceptible variety. (G) Fungal communities under netting treatment for the tolerant variety; and (H) Fungal communities under netting treatment for the susceptible variety.
Table 1.
Analysis of variance among different treatments on two experimental varieties of Vitis vinifera.
Fig 3.
Relative abundances of recovered OTUs.
(A) Bacterial phyla in the tolerant and susceptible varieties. (B) Fungal phyla in the tolerant and susceptible varieties. (C) Bacterial genera from insecticide treatments between the tolerant and susceptible varieties. (D) Bacterial genera from bagging treatments between the tolerant and susceptible varieties. (E) Fungal genera from insecticide treatments between the tolerant and susceptible varieties; and (F) Fungal genera from bagging treatments between the tolerant and susceptible varieties.
Fig 4.
Healthy CF and VB samples showed varied differences in microbial community composition.
(A–B) Bacterial community clusters between +Max/-Max for tolerant and susceptible varieties. (C–D) Bacterial community clusters between +Net/-Net for tolerant and susceptible varieties. (E–F) Fungal community clusters between +Max/-Max for tolerant and susceptible varieties. (G–H) Fungal community clusters between +Net/-Net for tolerant and susceptible varieties. (I) NMDS for bacteria between varieties based on Bray-Curtis distances. (J) NMDS for fungi between varieties based on Bray-Curtis distances. (K) Distinct fungal OTUs between varieties; and (L) LEfSe plots showing fungal OTUs responsible for the observed differences in community composition between varieties. The bars represent the effect size (LDA) for a particular taxon in a certain treatment group. The length of the bar represents a log10 transformed LDA score and the colors illustrate which group that taxon was found to be more abundant compared to the other group.
Table 2.
Permutational multivariate analysis of variance for bacteria and fungi between tolerant and susceptible Vitis vinifera varieties.
Table 3.
Linear discriminant analysis results showing significantly different fungal taxa among two grape varieties under different treatments.
Fig 5.
Microbial community diversity and OTU abundance differed between healthy and infected grape berries.
(A) Bacterial diversity between healthy and infected berries. (B) Fungal diversity between healthy and infected berries. (C) Abundance of bacterial phyla between berry types. (D) Abundance of bacterial genera based on berry status (E) Abundance of fungal phyla between berry types; and (F) Abundance of fungal genera based on berry status.
Table 4.
Analysis of variance among different healthy and infected berries of Vitis vinifera.
Fig 6.
Microbiota community composition differed significantly between healthy and infected grape berries.
(A) NMDS showing two clusters of bacteria communities between healthy and infected berries based on Bray-Curtis distances. (B) NMDS showing two distinct clusters of fungal communities between healthy and infected berries based on Bray-Curtis distances. (C) Distribution of bacterial OTUs between samples. (D) Distribution of fungal OTUs between samples. Linear discriminant analysis of significantly abundant (E) bacteria between healthy and infected berries; and (F) fungi between healthy and infected berries.
Table 5.
Permutational multivariate analysis of variance for bacteria and fungi between healthy and sour rot-affected Vitis vinifera berries.
Table 6.
Linear discriminant analysis results showing significantly different taxa among healthy and infected grape berries.
Fig 7.
Culturable bacteria and fungi from healthy and infected grape berries.
(A) Bacteria, fungi, and yeast obtained from culturing (counts represent the number of isolates cultured). (B) Abundance of cultured bacteria in healthy and infected berries; and (C) Abundance of cultured fungi in healthy and infected berries.
Table 7.
Bacterial and fungal species from cultural studies indicating berry status from which they were isolated.
Empty cells (in gray color) indicate zero abundance for bacteria or fungi in healthy and infected berries.
Fig 8.
Core microbiomes associated with sour-affected grapes.
(A) Core bacterial community members; and (B) Core fungal community members. Note: abundance/dominance is indicated by the color of the bands on the heatmap. Darker bands indicate higher dominance.