Wheat rhizosphere community selection reveals bacteria associated with reduced root disease

Authors: YIN, CHUNTAO - Washington State University; VARGAS, JUAN - Washington State University; Schlatter, Daniel; HAGERTY, CHRISTINA - Oregon State University; HULBERT, SCOT - Washington State University; Paulitz, Timothy

Submitted to: Microbiome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/29/2020
Publication Date: 4/9/2021
Citation: Yin, C., Vargas, J.M., Schlatter, D.C., Hagerty, C., Hulbert, S., Paulitz, T.C. 2021. Wheat rhizosphere community selection reveals bacteria associated with reduced root disease. Microbiome. 9. Article 86. https://doi.org/10.1186/s40168-020-00997-5.
DOI: https://doi.org/10.1186/s40168-020-00997-5

Interpretive Summary: Disease suppressive microbes in the rhizosphere of wheat can protect the roots against soilborne pathogens. However, the dynamics and composition of community selection as influenced by pathogen infection is largely unknown. We grew successive cycles of wheat in a soil inoculated with a fungal root pathogen, Rhizoctonia solani AG8. During each cycle, we washed microbes from the roots of healthier plants and sicker plants, and transferred them to the next cycling, to select for bacteria that would suppress disease, even when the pathogen was present. Our results demonstrated that successive wheat plantings and pathogen infection can shift the rhizosphere microbial communities and specifically accumulate a group of beneficial microbes.

Technical Abstract: Background: Disease suppressive microbes in the rhizosphere of wheat can protect the roots against soilborne pathogens. However, the dynamics and composition of community selection as influenced by pathogen infection is largely unknown. Results: In this study, we used a multi-cycle selection system and infection by the soilborne fungal pathogen Rhizoctonia solani AG8 to examine how plants impact the rhizobiome and recruit beneficial microorganisms to suppress pathogens in the rhizosphere and promote plant growth. Analysis of the soil microbial community using deep sequencing of the 16S rRNA revealed distinct bacterial community profiles assembled over successive wheat plantings. Moreover, the cluster of bacterial communities formed from the R. solani AG8-infected rhizosphere was distinct from those without AG8 infection. Interestingly, the bacterial communities from the rhizosphere soil with the lowest wheat root disease gradually separated from those with the highest wheat root disease over successive planting cycles. Successive monocultures and application of R. solani AG8 increased the abundance of some bacterial genera which have potential antagonistic activities, such as Chitinophaga, Pseudomonas, Chryseobacterium, and Flavobacterium, and a group of plant growth-promoting (PGP) microbes, including Caulobacter, Pedobacter, and Variovorax. Furthermore, a species of Janthinobacterium was isolated from the rhizosphere soil of wheat more tolerant to R. solani AG8 and exhibited broad antagonism against soilborne pathogens, Pythium ultimum, R. solani AG8, and R. oryzae in vitro, and suppressive activity to R. solani AG8 in soil. Conclusions: Our results demonstrated that successive wheat plantings and pathogen infection can shift the rhizosphere microbial communities and specifically accumulate a group of beneficial microbes.