Identification of the microbial consortia and mechanisms of soil suppressiveness to Fusarium culmorum

Soil and plant microbiomes harbour diverse beneficial and commensal microorganisms that are important for plant growth and for protection against soil-borne disease1. Among the soil-borne diseases, root-infecting fungi form a major threat to the cultivation of agricultural and horticultural crops worldwide2. In some soils, however, root infection does not occur or only little. This is referred to as soil disease-suppressiveness and strongly associated with the composition and activity of the soil and rhizosphere microbiome. Recently, Carrión et al. (2019) integrated multiple next-generation sequencing approaches to identify root endophytic bacterial consortia and functional gene clusters associated with disease suppression, a systems approach that provided a new paradigm to study the diversity and functions of microbiomes for different phenotypes3. My PhD project focuses on the identification of microorganisms and mechanisms involved in soils that are suppressive to Fusarium culmorum of wheat. F. culmorum is one of the most widespread fungal plant pathogens of both cereal and non-cereal crops. However, little is known so far regarding soil suppressiveness to F. culmorum and biocontrol of this soil-borne plant pathogen. In a large screening of soils from different regions in the Netherlands and Germany for suppressiveness to root rot of wheat caused by F. culmorum, a high and consistent level of suppressiveness was found in four soils5. Subsequent analyses affirmed that the suppressiveness is (micro)biological in nature, as it is eliminated by selective heat treatments and is transferable, via rhizosphere transplantations, to susceptible plants grown in non-suppressive (conducive) soils. Comparative taxonomic and functional analysis of root-associated bacterial communities were performed to reveal the putative microorganisms and mechanisms associated with the disease-suppressive phenotype. The result of the taxonomic analysis showed only limited commonalities between the four suppressive soils5, while the functional analysis indicated that several important gene clusters and specific gene functions were more highly abundant in the suppressive soils6. The functional amplicon sequencing analysis based on dom2BGC, a pipeline developed in the course of this previous study, provided central information of biosynthetic gene clusters, associated with various known compounds, and natural products related to the disease-suppressive phenotype of different soils. Notable compounds involved siderophores, lipopeptides, and known antifungal compounds, which may simultaneously or sequentially inhibit the growth of the invading pathogen and suppress root infection6. In addition, volatiles emitted by different soils may affect growth and disease suppression. Indeed, results showed that several soils emit pathogen-suppressing volatiles5. In vitro and in situ studies indicate that the production and efficacy of pathogen-suppressing volatiles are related to the composition of soil bacterial communities7-8. All these research approaches and results laid a strong foundation for my PhD project. The production of siderophores is widespread among microorganisms to acquire iron from the soil environment. Siderophores have also been found to play a role in soil disease suppressiveness against Fusarium wilt9-11, take-all disease in wheat12 and damping-off of sugar beet3. Also, bacterially produced lipopeptides are of importance; while many are made by plant pathogens as pathogenicity factors, others have been implicated in soil disease-suppressiveness and antagonistic interactions with fungi or breaking down bacterial biofilms13. The use of ‘omics methods allows us to macroscopically determine the associations between specific genera or functions and phenotypes. However, more experimental approaches are needed to further elucidate the complex plant-microbe and microbe-microbe interactions under the influence of adjustable factors14. These adjustable factors include the presence/absence and abundance of microbes, the order in which various microbes are introduced, genetic alterations of strains or the host, and growth conditions. The construction of synthetic communities (SynComs) can help to effectively explore this combinatorial space, by assessing how phenotypes vary when the taxonomic and functional composition of the communities is modified15-16. In this project, such communities will be designed by combining and applying selected strains to plants to study various aspects of plant-microbe interactions, to uncover fundamental principles and underlying mechanisms of how rhizosphere microbial communities confer a specific disease-suppressive phenotype. As starting materials for this project, we already have available a) agricultural soils that protect wheat plants from F. culmorum infections through a microbial component; b) ≥200 isolates from these soils and glycerol stocks with isolated communities, which can be used for isolation of more bacteria; and c) metagenomic and amplicon sequencing data of these native communities applied to wheat plants, in presence/absence of the pathogen and with several dilutions of community complexity. Based on this, we have an excellent agriculturally relevant ‘model’ system to zoom into the mechanisms of soil suppressiveness and to reveal the role of specific microorganisms and genes. Furthermore, this project will reveal how soil suppressiveness affects the expression of specific pathogenicity factors of F. culmorum and whether/how root exudates of wheat plants under attack by the fungal root pathogen contribute to the expression of microbial genes mediating disease suppression.