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An analysis of P seudomonas genomic diversity in take‐all infected wheat fields reveals the lasting impact of wheat cultivars on the soil microbiota
Author(s) -
Mauchline T. H.,
ChedomFotso D.,
Chandra G.,
Samuels T.,
Greenaway N.,
Backhaus A.,
McMillan V.,
Canning G.,
Powers S. J.,
HammondKosack K. E.,
Hirsch P. R.,
Clark I. M.,
Mehrabi Z.,
Roworth J.,
Burnell J.,
Malone J. G.
Publication year - 2015
Publication title -
environmental microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.954
H-Index - 188
eISSN - 1462-2920
pISSN - 1462-2912
DOI - 10.1111/1462-2920.13038
Subject(s) - biology , pseudomonas fluorescens , rhizosphere , context (archaeology) , cultivar , crop , population , microbiology and biotechnology , pseudomonas , microbiome , agronomy , genetics , bacteria , paleontology , demography , sociology
Summary Manipulation 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.