Abstract
Rhizosphere microbial communities are known to be related to plant health; using such an association for crop management requires a better understanding of this relationship. We investigated rhizosphere microbiomes associated with Verticillium wilt symptoms in two cotton cultivars. Microbial communities were profiled by amplicon sequencing, with the total bacterial and fungal DNA quantified by quantitative polymerase chain reaction based on the respective 16S and internal transcribed spacer primers. Although the level of V. dahliae inoculum was higher in the rhizosphere of diseased plants than in the healthy plants, such a difference explained only a small proportion of variation in wilt severities. Compared to healthy plants, the diseased plants had much higher total fungal/bacterial biomass ratio, as represented by quantified total fungal or bacterial DNA. The variability in the fungal/bacterial biomass ratio was much smaller than variability in either fungal or bacterial total biomass among samples within diseased or healthy plants. Diseased plants generally had lower bacterial alpha diversity in their rhizosphere, but such differences in the fungal alpha diversity depended on cultivars. There were large differences in both fungal and bacterial communities between diseased and healthy plants. Many rhizosphere microbial groups differed in their abundance between healthy and diseased plants. There was a decrease in arbuscular mycorrhizal fungi and an increase in several plant pathogen and saprophyte guilds in diseased plants. These findings suggested that V. dahliae infection of roots led to considerable changes in rhizosphere microbial communities, with large increases in saprophytic fungi and reduction in bacterial community.
Highlights
Cotton (Gossypium hirsutum L.) is an important fiber crop
The overall bacterial and fungal abundances in the rhizosphere soil were estimated with the quantitative polymerase chain reaction (qPCR) technique
The density of V. dahliae microsclerotia in soil quantified with the wet-sieving method increased with wilt severity (P < 0.05) independent of cultivars, but this relationship accounted for only limited variation in the wilt severity (Supplementary Figure 1)
Summary
Cotton (Gossypium hirsutum L.) is an important fiber crop. Cotton Verticillium wilt, caused by Verticillium dahliae, is one of the most devastating plant diseases worldwide (Klosterman et al, 2009). The pathogen can survive in the soil as resting microsclerotia without a host plant for more than 14 years. In China, its hosts include a number of economically important crops. Controlling Verticillium wilt is difficult because of the inaccessibility of the pathogen during infection, longterm survival of microsclerotia in soil, and its broad host range (Klosterman et al, 2009). In Xinjiang, the main cotton production region in China, crop rotation with non-hosts of V. dahliae has not been adopted because of the difficulties in changing cropping systems and saline–alkali soils. Several remaining fumigants, such as chloropicrin and dazomet, can be used to manage wilt, farmers in China are reluctant to use them in cotton production because of their limited economic benefits
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