Pseudomonas spp. Enriched in Endophytic Community of Healthy Cotton Plants Inhibit Cotton Verticillium Wilt

Abstract

The plant microbiome plays a fundamental role in plant growth and health. However, detailed information regarding the plant endophytic microbiome during the infection period of a pathogen is largely unknown. Here, we investigated the microbial community of healthy and diseased cotton plants and the root exudate profiles of susceptible and resistant cultivars utilizing high-throughput sequencing and metabolomics. The results showed that the pathogen infection reduced bacterial diversity and significantly affected the bacterial community composition. The microbiome assembly is shaped predominantly by cultivars. The endophytic microbiome of the infected plants showed greater complexity than the healthy plants in network analysis. The results displayed that a total of 76 compounds were significantly different in the two groups, with 18 compounds showing a higher relative abundance in the resistant cultivars and 58 compounds in the susceptible cultivars. Pathway enrichment analysis showed that pathways related to plant hormone signal transduction, biosynthesis of various secondary metabolites, and biosynthesis and metabolism of amino acids were prominently altered. We also demonstrate that plants inoculated with Pseudomonas sp. strains showed increased resistance to the cotton Verticillium wilt compared with the control plants in pot experiments. Overall, it showed that the pathogen infection affected the community composition, and healthy plants displayed an enriched beneficial microbiome to combat the plant disease. These findings significantly advance our understanding of the endophytic microbiome assembly under the pathogen infection and develop microbiome-based solutions for sustainable crop production systems.

Keywords: bacterial community; beneficial microbe; cotton Verticillium wilt; endophytic; microbiome assembly.

FIGURE 1

The alpha-diversity measurements based on the bacterial endophytic bacterial community. (A) For different healthy conditions. (B) For different cultivars.

FIGURE 2

Network visualization of the interaction architecture in bacterial community of healthy and diseased cotton plants.

FIGURE 3

Comparative analysis of the endophytic bacterial community under different healthy conditions. (A) Unconstrained principal coordinate analysis (PCoA) of beta-diversity using Bray-Curtis distances of the bacterial community in healthy and diseased samples. (B) Venn diagrams showing the shared and specific bacterial OTUs among the healthy and diseased samples of different cultivars. (C) Relative abundance of the abundant bacterial taxa in healthy and diseased cotton plants. (D) Differential abundance analysis of bacterial OTUs in healthy and diseased samples, and Welch’s test was performed to calculate the significance of differences at the family level. (E) The biomarker taxa of bacterial communities among healthy and diseased cotton plants. Only the top five most specific biomarker taxonomies are displayed.

FIGURE 4

Analysis of exudation profiles between resistant and susceptible cotton cultivars. (A) PCA plot of the root exudate profiles of two cotton cultivars. (B) The comparison of volcano plots of differentially expressed metabolites between the resistant and susceptible cultivars. (C) Heatmap of identified differentially expressed metabolites from resistant and susceptible samples. (D) Pathway enrichment analysis of differential metabolites from resistant and susceptible cultivars. XZ is the resistant cultivar and JM is the susceptible cultivar.

FIGURE 5

Effect of Pseudomonas sp. on the cotton wilt disease. (A) Effect of single bacterial strain (N1 and L4) on the Verticillium wilt of cotton. (B) Diameter of inhibition zone of single bacteria strain (N1 and L4). Error bars indicate ± SD of three replicates. (C) The phenotypes of cotton inoculated with single bacteria after 40 days of growth in a growth chamber. Effect of the single bacteria (N1 and L4) on the disease index (D) and the height of cotton plants (E). *** Represents obvious differences at P < 0.001 compared with the control.