An analysis of Pseudomonas genomic diversity in take-all infected wheat fields reveals the lasting impact of wheat cultivars on the soil microbiota.
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 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.
Department of AgroEcology, Rothamsted Research, Harpenden, UK.
T H
TH
Mauchline
The Wellcome Trust Centre for Human Genetics.
D
D
Chedom-Fotso
Molecular Microbiology Department, John Innes Centre, Norwich, UK.
G
G
Chandra
School of Biological Sciences, University of East Anglia, Norwich, UK.|School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK.
T
T
Samuels
School of Biological Sciences, University of East Anglia, Norwich, UK.
N
N
Greenaway
School of Biological Sciences, University of East Anglia, Norwich, UK.
A
A
Backhaus
Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, UK.
V
V
McMillan
Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, UK.
G
G
Canning
Department of Computational and Systems Biology, Rothamsted Research, Harpenden, UK.
S J
SJ
Powers
Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, UK.
K E
KE
Hammond-Kosack
Department of AgroEcology, Rothamsted Research, Harpenden, UK.
P R
PR
Hirsch
Department of AgroEcology, Rothamsted Research, Harpenden, UK.
I M
IM
Clark
Department of AgroEcology, Rothamsted Research, Harpenden, UK.|Oxford Long-term Ecology and Resource Stewardship Lab, University of Oxford, Oxford, UK.
Z
Z
Mehrabi
Department of AgroEcology, Rothamsted Research, Harpenden, UK.|Department of Computational and Systems Biology, Rothamsted Research, Harpenden, UK.
J
J
Roworth
Department of AgroEcology, Rothamsted Research, Harpenden, UK.
J
J
Burnell
Molecular Microbiology Department, John Innes Centre, Norwich, UK.|School of Biological Sciences, University of East Anglia, Norwich, UK.
J G
JG
Malone
D001483:Base Sequence; D018556:Crops, Agricultural / Q000382:microbiology; D004269:DNA, Bacterial / Q000235:genetics; D014644:Genetic Variation / Q000235:genetics*; D023281:Genomics; D005838:Genotype; D064307:Microbiota / Q000235:genetics*; D010935:Plant Diseases / Q000382:microbiology; D018517:Plant Roots / Q000382:microbiology*; D011551:Pseudomonas fluorescens / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D058441:Rhizosphere; D017422:Sequence Analysis, DNA; D012988:Soil Microbiology; D014908:Triticum / Q000145:classification / Q000382:microbiology*
D004269:DNA, Bacterial