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.
Highlights
Plant pathogenic microorganisms are responsible for major crop losses worldwide and represent a substantial threat to food security
To effectively determine the relationship between the soil Pseudomonas population and disease suppression, it is important to accurately survey genotypic and phenotypic variability at the level of individual isolates, and to determine how this variation is linked to agriculturally relevant environmental changes (Mauchline and Malone, 2017). 91 To investigate the genetic bases for S. scabies inhibition by P. fluorescens and to assess whether the scab-suppressive effects of irrigation derive from increased populations of biocontrol genotypes in the soil or on the plant, we focused on the Pseudomonas population from a potato field susceptible to potato scab
There is limited understanding of the genetic factors that are critical for such activity, and little is known about the diversity of the P. fluorescens species group within a given agricultural field or how this population is shaped by environmental changes
Summary
Plant pathogenic microorganisms are responsible for major crop losses worldwide and represent a substantial threat to food security. The Gram-positive bacterium Streptomyces scabies, which is the causal organism of potato scab, is ubiquitous and presents a threat in almost all soils (Bignell et al, 2010; Lerat et al, 2009). Managed irrigation is a reasonably effective control measure for potato scab. Scab outbreaks still regularly occur in irrigated soil, and with increasing pressures on water use it is clear that alternative approaches to the control of scab are needed. An attractive potential alternative involves the exploitation of soil microorganisms that suppress or kill plant pathogens, known as biocontrol agents (Köhl et al, 2019; Weller, 2007). LuxCDABE cassette into the neutral att::Tn7 site of the Ps682 chromosome using the Tn7-based expression system A. fischeri luxCDABE cassette into the neutral att::Tn7 site of the Ps682 Δvisc chromosome using the Tn7-based expression system
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