Response of the Endophytic Microbiome in Cotinus coggygria Roots to Verticillium Wilt Infection

Abstract

Verticillium wilt caused by Verticillium dahliae Kleb. is a lethal soil-borne fungal disease of Cotinus coggygria. The plant endophytic microbiome plays an important role in maintaining plant health and disease resistance, but it is unclear how the endophytic microbiome of C. coggygria roots varies in response to Verticillium wilt occurrence. In this study, the endophytic microbial diversity, community composition, dominant species, and co-occurrence network of C. coggygria under Verticillium wilt-affected and healthy conditions were assessed using Illumina sequencing. Compared with healthy plants, the bacterial alpha diversity indices of Verticillium wilt-affected plants decreased significantly, while the fungal alpha diversity indices showed obvious increases. The relative abundance of dominant taxa including Proteobacteria, Actinobacteriota, Ascomycota, and Basidiomycota at the phylum level, as well as Gammaproteobacteria, Thermoleophilia, Dothideomycetes, and Agaricomycetes at the class level, differed significantly between Verticillium wilt-affected and healthy plants. Co-occurrence networks revealed that the fungal network of Verticillium wilt-affected roots was denser with more negative interactions, which may be relevant to functional changes from reciprocity to competition in the microbial community, in response to V. dahliae infection. The results enhanced our understanding on the relationships between the endophytic microbiome and Verticillium wilt, which could provide information for the management of this disease in C. coggygria.

Keywords: Cotinus coggygria; Verticillium dahliae; community composition; endophytic microbiome; illumina sequencing.

Figure 1

The alpha diversity indices of the root endophytic microbiome in Verticillium wilt-affected and healthy C. coggygria plants. (A) Bacterial community; (B) fungal community. RP represents the Verticillium wilt-affected roots; RH represents healthy roots. * indicates significant differences at a certain significance level (for example, p < 0.05); ** indicates significant differences at a higher significance level (for example, p < 0.01); *** indicates significant differences at a very high significance level (for example, p < 0.001).

Figure 2

Community composition of the root endophytic microbiome in Verticillium wilt-affected and healthy C. coggygria. (A) Bacterial phylum level; (B) bacterial class level; (C) fungal phylum level; (D) fungal class level. RP represents the Verticillium wilt-affected roots; RH represents healthy roots.

Figure 3

PCA of the root endophytic microbiome in Verticillium wilt-affected and healthy C. coggygria at the OTU level. The PC coordinate axis in the principal component analysis (PCA) graph denoted the difference in microbial composition. (A) PCA of the bacterial community; (B) PCA of the fungal community. RP represents the Verticillium wilt-affected roots; RH represents healthy roots.

Figure 4

LEfSe analysis of the root endophytic bacterial of the Verticillium wilt-affected and healthy C. coggygria. The histogram of the LDA score calculates the differently abundant microbes among different health states, with a threshold of 3.5. Light yellow nodes represents microbial groups that show no significant differences among different groups or have no significant influence on the differences between groups. RP represents the Verticillium wilt-affected roots; RH represents healthy roots.

Figure 5

LEfSe analysis of the root endophytic fungal of the Verticillium wilt-affected and healthy C. coggygria. The histogram of the LDA score shows the differently abundant microbe among different health states, with a threshold of 3.0. Light yellow nodes represents microbial groups that show no significant differences among different groups or have no significant influence on the differences between groups. RP represents the Verticillium wilt-affected roots; RH represents healthy roots.

Figure 6

Co-occurrence networks of microbial communities of Verticillium wilt-affected and healthy C. coggygria at the genus level (Spearman > 0.8, p < 0.05). The size of the node shows the abundance of the genus, and the different colors indicate the corresponding taxonomic assignment at the phylum level. The edge color represents positive (red) and negative (green) correlations. (A) Bacterial networks from healthy plants, (B) bacterial networks from Verticillium wilt-affected plants, (C) fungal networks from healthy plants, and (D) fungal networks from Verticillium wilt-affected plants.