An analysis of Pseudomonas genomic diversity in take‐all infected wheat fields reveals the lasting impact of wheat cultivars on the soil microbiota

Abstract

SummaryManipulation of the soil microbiota associated with crop plants has huge promise for the control of crop pathogens. However, to fully realize this potential we need a better understanding of the relationship between the soil environment and the genes and phenotypes that enable microbes to colonize plants and contribute to biocontrol. A recent 2 years of investigation into the effect of wheat variety on second year crop yield in the context of take‐all fungal infection presented the opportunity to examine soil microbiomes under closely defined field conditions. Amplicon sequencing of second year soil samples showed that P seudomonas spp. were particularly affected by the wheat cultivar grown in year one. Consequently, 318 rhizosphere‐associated P seudomonas fluorescens strains were isolated and characterized across a variety of genetic and phenotypic traits. Again, the wheat variety grown in the first year of the study was shown to exert considerable selective pressure on both the extent and nature of P seudomonas genomic diversity. Furthermore, multiple significant correlations were identified within the phenotypic/genetic structure of the Pseudomonas population, and between individual genotypes and the external wheat field environment. The approach outlined here has considerable future potential for our understanding of plant–microbe interactions, and for the broader analysis of complex microbial communities.

Pan-genome analysis identifies intersecting roles for Pseudomonas specialized metabolites in potato pathogen inhibition

“…used transposon mutagenesis in the rhizobacterium P. fluorescens Pf.SS101 to show that auxin biosynthesis was linked to plant growth promotion and induced systemic resistance, but found no link with volatile or lipopeptide biosynthesis (6), while Mauchline et al . (18) also observed a negative correlation between genes for viscosin production and plant hormone manipulation pathways. It is also possible that irrigation enables Pseudomonas to out-compete S. scabies in the rhizosphere due to relative fitness in wet conditions.…”

“…To determine whether the strains and metabolites we identified specifically suppress S. scabies or have suppressive activity towards a range of plant pathogens, we investigated the ability of the potato field strain collection to suppress the growth of the destructive plant pathogens Phytophthora infestans , the oomycete that causes potato blight (75), and Gaeumannomyces graminis var. tritici , the fungus that causes take-all disease of cereal crops (18). Notably, this revealed strong positive correlations between suppressive phenotypes for each of the pathogens tested (a correlation coefficient of 0.55 between S. scabies and P. infestans inhibition, Figure S8).…”

Comparative Metatranscriptomics of Wheat Rhizosphere Microbiomes in Disease Suppressive and Non-suppressive Soils for Rhizoctonia solani AG8

“…in the non-suppressive soil, and thus probably involved in colonisation of the rhizosphere. This process requires flagella-dependent motility for migration into the root zone, followed by bacterial biofilm formation (Mauchline et al, 2015 ).…”

Functional and genomic insights into the pathogenesis of Burkholderia species to rice

“…Since only a limited number of isolates have currently been sequenced, the extent of genomic diversity of rice pathogenic Burkholderia in the environment is not known. Considerable genomic diversity can occur in soil dwelling plant‐associated microbes as revealed by recent studies of Pseudomonas fluorescens (Silby et al ., ; Loper et al ., ; Mauchline et al ., ).…”