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

Environmental Microbiology
T H MauchlineJ G Malone

Abstract

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 Pseudomonas spp. were particularly affected by the wheat cultivar grown in year one. Consequently, 318 rhizosphere-associated Pseudomonas 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 Pseudomonas 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 enviro...Continue Reading

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Citations

Dec 23, 2015·Environmental Microbiology·Lynn M NaughtonJ Maxwell Dow
Sep 4, 2018·Frontiers in Plant Science·Chrysi SergakiPatrick Schäfer
Jan 31, 2020·Scientific Reports·Vanessa N KavamuraTim H Mauchline
Dec 6, 2019·Frontiers in Microbiology·Vanessa Nessner KavamuraTim H Mauchline
May 7, 2020·Scientific Reports·E Masters-ClarkT H Mauchline
Mar 9, 2021·Computational and Structural Biotechnology Journal·Vanessa N KavamuraTim H Mauchline
Mar 24, 2021·Trends in Plant Science·Javier Palma-GuerreroKim E Hammond-Kosack

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Methods Mentioned

BETA
environmental stress
amplicon sequencing
PCR
genotyping

Software Mentioned

rpsblast B last + suite
TGAC
qiime
Geneious tree builder
en S
eneious

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