Microbial and biochemical basis of a Fusarium wilt-suppressive soil

Abstract

Crops lack genetic resistance to most necrotrophic pathogens. To compensate for this disadvantage, plants recruit antagonistic members of the soil microbiome to defend their roots against pathogens and other pests. The best examples of this microbially based defense of roots are observed in disease-suppressive soils in which suppressiveness is induced by continuously growing crops that are susceptible to a pathogen, but the molecular basis of most is poorly understood. Here we report the microbial characterization of a Korean soil with specific suppressiveness to Fusarium wilt of strawberry. In this soil, an attack on strawberry roots by Fusarium oxysporum results in a response by microbial defenders, of which members of the Actinobacteria appear to have a key role. We also identify Streptomyces genes responsible for the ribosomal synthesis of a novel heat-stable antifungal thiopeptide antibiotic inhibitory to F. oxysporum and the antibiotic’s mode of action against fungal cell wall biosynthesis. Both classical- and community-oriented approaches were required to dissect this suppressive soil from the field to the molecular level, and the results highlight the role of natural antibiotics as weapons in the microbial warfare in the rhizosphere that is integral to plant health, vigor and development.

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

“…Although we have described only one simple application of GNPS in this Perspective ( identification of a stenothricin analog), the community has already begun to utilize GNPS to expedite natural product analysis 28,41,43,45,46,50,52 . Furthermore, we expect the user base of GNPS to expand to include other communities that use MS/MS data, including those studying metabolomics, exposomes, the chemistry of the human habitat, drug discovery, microbiomes, immunology, food industry, agricultural industry, stratification of patients in clinical trials, clinical adsorption/metabolism and ocean science to name a few, resulting in different GNPS workflows 42,44,47,51,53 .…”

“…Several published applications of molecular networking and MS/MS based dereplication using GNPS have been reported while the infrastructure has been under development. Specifically, GNPS has enabled the discovery of natural products including colibactin 41–45 , characterization of biosynthetic pathways 46,47 , understanding of the chemistry of ecological interactions 28,48–52 , and development of metabolomics bioinformatics methods 53 . The application of GNPS workflows to such diverse research areas demonstrates its utility.…”

Microbiome Selection Could Spur Next-Generation Plant Breeding Strategies

“…Therefore, the overall fitness of the plant is governed by the self and its microbiota (Vandenkoornhuyse et al, 2015). Several examples where the plant microbiome, particularly of the root and endophytic compartments, has been used to suppress diseases of field and horticultural crops (Mendes et al, 2011; Spence et al, 2014; Cha et al, 2016), improve drought resistance in desert crops (Lau and Lennon, 2012; Marasco et al, 2012) and grapevine (Rolli et al, 2015) and alter above-ground herbivory (Hol et al, 2010; Badri et al, 2013b) have unequivocally proved that the host microbiome indeed impact the fitness of the plants. Next-generation sequencing technologies, advanced bioinformatic analyses coupled with meticulous culture-dependent isolations had been employed in all the above studies to decode the plant microbiome and get to the important bacterial species involved in regulating the phenotypic expression of the plants.…”

Relationships between Root Pathogen Resistance, Abundance and Expression of Pseudomonas Antimicrobial Genes, and Soil Properties in Representative Swiss Agricultural Soils

“…Suppressive soils have been found to host distinct microbial communities that are thought to be responsible for the natural disease control effect (Weller et al, 2002; Haas and Défago, 2005; Mendes et al, 2011, 2013; Klein et al, 2013; Kyselkova et al, 2014; Cha et al, 2016). In particular, bacteria of the Pseudomonas fluorescens group have been isolated from suppressive soils and used as plant or soil inoculants.…”