Cultivar-Dependent Variation of the Cotton Rhizosphere and Endosphere Microbiome Under Field Conditions

• Published in: Frontiers in plant science Vol. 10; p. 1659
• Main Authors: Wei, Feng, Zhao, Lihong, Xu, Xiangming, Feng, Hongjie, Shi, Yongqiang, Deakin, Greg, Feng, Zili, Zhu, Heqin
• Format: Journal Article
• Language: English
• Published: Switzerland Frontiers Media S.A 20.12.2019
• Subjects: cotton; Plant Science; rhizosphere microbiome; root endosphere; Verticillium dahliae; wilt resistance; root endosphere; cotton; Verticillium dahliae; wilt resistance; rhizosphere microbiome
• ISSN: 1664-462X; 1664-462X
• DOI: 10.3389/fpls.2019.01659

wilt caused by is a common soil-borne disease worldwide, affecting many economically important crop species. Soil microbes can influence plant disease development. We investigated rhizosphere and endosphere microbiomes in relation to cotton cultivars with differential susceptibility to wilt. Soil samples from nine cotton cultivars were assessed for the density of microsclerotia; plants were assessed for disease development. We used amplicon sequencing to profile both bacterial and fungal communities. Unlike wilt severity, wilt inoculum density did not differ significantly among resistant and susceptible cultivars. Overall, there were no significant association of alpha diversity indices with wilt susceptibility. In contrast, there were clear differences in the overall rhizosphere and endosphere microbial communities, particularly bacteria, between resistant and susceptible cultivars. Many rhizosphere and endosphere microbial groups differed in their relative abundance between resistant and susceptible cultivars. These operational taxonomic units included several well-known taxonomy groups containing beneficial microbes, such as Bacillales, Pseudomonadales, Rhizobiales, and , which were higher in their relative abundance in resistant cultivars. Greenhouse studies with sterilized soil supported that beneficial microbes in the rhizosphere contribute to reduced wilt development. These findings suggested that specific rhizosphere and endosphere microbes may contribute to cotton resistance to .