A Novel 'Population Genomics' Approach to Analysing Pseudomonas Diversity in Take-All Infected Wheat Fields.. Analysing microbial diversity in field environments.

Take-all (G. graminis var. tritici) is an important fungal crop pathogen that affects around half of UK wheat crops and causes substantial yield losses. Soil Pseudomonas spp. have great potential for development as biocontrol supplements for the control of take-all and other crop diseases, but their effects are currently somewhat inconsistent. A major reason for this is an incomplete understanding of the phenotypic characteristics important for colonisation and biocontrol in different plant environments. By using a combination of microbiology, genome sequencing and statistical analysis, we have established a novel ‘population genomics’ approach to examine the associations between genes and phenotypes, and the selective pressures exerted by the environment on the Pseudomonas population in take-all infected wheat fields. 318 Pseudomonas isolates were collected from wheat plants following a two-year investigation into the effect of different take-all inoculum building wheat varieties on second-year crop yield. These strains were subjected to a combination of phenotypic and genetic assays, genome sequencing, and statistical analysis to examine the distribution of a wide range of different phenotypes/genotypes across the field population. The wheat Pseudomonas population was shown to be highly variable, with the diversity within one field only slightly lower than that recorded for all currently annotated P. fluorescens strains. Furthermore, a number of significant correlations were identified within the data, both in terms of the phenotypic/genomic structure of the population and between individual genotypes and the planted wheat varieties. Selective pressure from wheat variety on the Pseudomonas genome was shown to arise predominantly as a consequence of the wheat planted in year one. This study sheds light both on the internal structure of soil Pseudomonas genomes and the selective pressure exerted on the Pseudomonas population by changes to the environment, in the context of fungal pathogen suppression at the field scale.