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

T H Mauchline,A Backhaus,S J Powers,J G Malone,J Burnell,P R Hirsch,N Greenaway,D Chedom‐Fotso,K E Hammond‐Kosack,V Mcmillan,G Chandra,G Canning,J Roworth,Z Mehrabi,I M Clark,T Samuels

doi:10.1111/1462-2920.13038

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.

Highlights

Manipulation and supplementation of the soil microbiota has significant potential for the development of natural treatments to control diseases such as take-all (Gaeumannomyces graminis var. tritici); an important fungal crop pathogen that affects around half of UK wheat crops and causes substantial yield losses, in temperate climates (Hornby and Bateman, 1998; Bateman et al, 2004)
The issue is further complicated by the extensive genetic diversity found within the Pseudomonas species group, with the core genome representing as little as 45% of an individual bacterial genome (Silby et al, 2009; Loper et al, 2012; Redondo-Nieto et al, 2012; Seaton and Silby, 2014)
Bacterial isolation and soil sampling took place from the Great Harpenden 2 field site at Rothamsted Research (Harpenden, UK) after a 2 year investigation into the effect of different take-all inoculum building wheat varieties on crop yield. This field experiment examined the effect of 16 different combinations of first- and second year wheat cultivar on take-all disease prevalence and is described at the following website http://www.wgin.org.uk/ stakeholders/newsletters.php

Summary

Introduction

Manipulation and supplementation of the soil microbiota has significant potential for the development of natural treatments to control diseases such as take-all (Gaeumannomyces graminis var. tritici); an important fungal crop pathogen that affects around half of UK wheat crops and causes substantial yield losses, in temperate climates (Hornby and Bateman, 1998; Bateman et al, 2004). Manipulation and supplementation of the soil microbiota has significant potential for the development of natural treatments to control diseases such as take-all The Gram-negative, soil-dwelling bacterium Pseudomonas fluorescens is an important biocontrol organism in numerous different plant–microbe systems (Naseby et al, 2001; Haas and Defago, 2005). The established role of P. fluorescens in take-all suppressive soils (Mazzola and Cook, 1991; Cook et al, 1995; Bergsma-Vlami et al, 2005; Yang et al, 2011; Kwak and Weller, 2013) makes this disease a highly attractive target for the development of Pseudomonas biocontrol agents. The effects of Pseudomonas biocontrol are currently somewhat inconsistent (Weller, 1988). The issue is further complicated by the extensive genetic diversity found within the Pseudomonas species group, with the core genome representing as little as 45% of an individual bacterial genome (Silby et al, 2009; Loper et al, 2012; Redondo-Nieto et al, 2012; Seaton and Silby, 2014)

Results

Discussion

Conclusion