Pan-genome analysis identifies intersecting roles for Pseudomonas specialized metabolites in potato pathogen inhibition
- John Innes Centre, United Kingdom
- VCS Potatoes, United Kingdom
Abstract
Agricultural soil harbors a diverse microbiome that can form beneficial relationships with plants, including the inhibition of plant pathogens. Pseudomonas spp. are one of the most abundant bacterial genera in the soil and rhizosphere and play important roles in promoting plant health. However, the genetic determinants of this beneficial activity are only partially understood. Here, we genetically and phenotypically characterize the Pseudomonas fluorescens population in a commercial potato field, where we identify strong correlations between specialized metabolite biosynthesis and antagonism of the potato pathogens Streptomyces scabies and Phytophthora infestans. Genetic and chemical analyses identified hydrogen cyanide and cyclic lipopeptides as key specialized metabolites associated with S. scabies inhibition, which was supported by in planta biocontrol experiments. We show that a single potato field contains a hugely diverse and dynamic population of Pseudomonas bacteria, whose capacity to produce specialized metabolites is shaped both by plant colonization and defined environmental inputs.
Data availability
Genome assemblies are available at the European Nucleotide Archive (http://www.ebi.ac.uk/ena/) with the project accession PRJEB34261.Mass spectrometry data are available as a MassIVE dataset at ftp://massive.ucsd.edu/MSV000084283/ and the GNPS analysis is available here:https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=51ac5fe596424cf88cfc17898985cac2All other data generated in this study are included in the manuscript and supporting files.
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Pan-genome analysis identifies intersecting roles for Pseudomonas specialized metabolites in potato pathogen inhibitionEuropean Nucleotide Archive, PRJEB34261.
Article and author information
Author details
Alexander DH Kingdon
Sergey A Nepogodiev
Funding
Biotechnology and Biological Sciences Research Council (BB/J004596/1)
- Andrew W Truman
Biotechnology and Biological Sciences Research Council (BBS/E/J/000PR9790)
- Andrew W Truman
Biotechnology and Biological Sciences Research Council (BB/J004553/1)
- Jacob G Malone
Biotechnology and Biological Sciences Research Council (BBS/E/J/000PR9797)
- Jacob G Malone
Biotechnology and Biological Sciences Research Council (BB/M011216/1)
- Alba Pacheco-Moreno
- Jonathan J Ford
NPRONET (POC021)
- Graham Tomalin
- Jacob G Malone
- Andrew W Truman
Royal Society (URF\R\180007)
- Andrew W Truman
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- María Mercedes Zambrano, CorpoGen, Colombia
Version history
- Preprint posted: September 26, 2019 (view preprint)
- Received: July 2, 2021
- Accepted: November 16, 2021
- Accepted Manuscript published: November 18, 2021 (version 1)
- Version of Record published: December 31, 2021 (version 2)
Copyright
© 2021, Pacheco-Moreno et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Pan-genome analysis identifies intersecting roles for Pseudomonas specialized metabolites in potato pathogen inhibition
eLife 10:e71900.
https://doi.org/10.7554/eLife.71900
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