Untangling the Effects of Plant Genotype and Soil Conditions on the Assembly of Bacterial and Fungal Communities in the Rhizosphere of the Wild Andean Blueberry (Vaccinium floribundum Kunth)

Abstract

Microbial communities in the rhizosphere influence nutrient acquisition and stress tolerance. How abiotic and biotic factors impact the plant microbiome in the wild has not been thoroughly addressed. We studied how plant genotype and soil affect the rhizosphere microbiome of Vaccinium floribundum, an endemic species of the Andean region that has not been domesticated or cultivated. Using high-throughput sequencing of the 16S rRNA and ITS region, we characterized 39 rhizosphere samples of V. floribundum from four plant genetic clusters in two soil regions from the Ecuadorian Highlands. Our results showed that Proteobacteria and Acidobacteria were the most abundant bacterial phyla and that fungal communities were not dominated by any specific taxa. Soil region was the main predictor for bacterial alpha diversity, phosphorous and lead being the most interesting edaphic factors explaining this diversity. The interaction of plant genotype and altitude was the most significant factor associated with fungal diversity. This study highlights how different factors govern the assembly of the rhizosphere microbiome of a wild plant. Bacterial communities depend more on the soil and its mineral content, while plant genetics influence the fungal community makeup. Our work illustrates plant-microbe associations and the drivers of their variation in a unique unexplored ecosystem from the Ecuadorian Andes.

Keywords: Ecuadorian Highland; Vaccinium floribundum; edaphic factors; microbiome; plant genotype; rhizosphere.

Figure 1

Sampling distribution of V. floribundum along the Ecuadorian Highlands.

Figure 2

Bacteria and fungi rhizosphere microbiome analysis of the Andean Blueberry from the northern and southern Highlands. Microbiome composition for bacteria (a) and fungi (b). Boxplot of the entropy (Shannon Diversity Index) for bacteria (c) and fungi (d). * represents significant differences using t-Student test (p value < 0.001). Principal Coordinate Analysis based on Bray–Curtis dissimilarities between bacterial (e) and fungal (f) communities across Highland soil regions. The variance explained (R²) and the significance (p-value) are shown for a PERMANOVA model.

Figure 3

Plant genotype effect over bacterial and fungal communities from the Andean Blueberry rhizosphere. Microbiome composition for bacteria (a) and fungi (b). Boxplot of the entropy (Shannon Diversity Index) for bacteria (c) and fungi (d). Letters represent the results of the Tukey HSD post hoc test for one-way ANOVA. Principal Coordinate Analysis based on Bray–Curtis dissimilarities between bacterial (e) and fungal (f) communities across plant genotype clusters. The variance explained (R²) and the significance (p-value) are shown for a PERMANOVA model.

Figure 4

Phosphorous and lead drive relationship between Shannon diversity index of the bacterial rhizosphere and soil regions. Dispersion graph and regression analysis of Shannon diversity index versus phosphorous (a) and lead (b). Regression coefficient (R²) and the significance (p-value) are presented for each factor. Boxplot of phosphorous (c) and lead (d) concentration found in the three soil regions. * represents significant differences using t-Student test (p-value < 0.001).