Microbial and volatile profiling of soils suppressive to Fusarium culmorum of wheat

Abstract

In disease-suppressive soils, microbiota protect plants from root infections. Bacterial members of this microbiota have been shown to produce specific molecules that mediate this phenotype. To date, however, studies have focused on individual suppressive soils and the degree of natural variability of soil suppressiveness remains unclear. Here, we screened a large collection of field soils for suppressiveness to Fusarium culmorum using wheat ( Triticum aestivum ) as a model host plant. A high variation of disease suppressiveness was observed, with 14% showing a clear suppressive phenotype. The microbiological basis of suppressiveness to F. culmorum was confirmed by gamma sterilization and soil transplantation. Amplicon sequencing revealed diverse bacterial taxonomic compositions and no specific taxa were found exclusively enriched in all suppressive soils. Nonetheless, co-occurrence network analysis revealed that two suppressive soils shared an overrepresented bacterial guild dominated by various Acidobacteria. In addition, our study revealed that volatile emission may contribute to suppression, but not for all suppressive soils. Our study raises new questions regarding the possible mechanistic variability of disease-suppressive phenotypes across physico-chemically different soils. Accordingly, we anticipate that larger-scale soil profiling, along with functional studies, will enable a deeper understanding of disease-suppressive microbiomes.

Application of ecological and evolutionary theory to microbiome community dynamics across systems

“…Such advances require the development of theoretical and conceptual frameworks such as those discussed in §3 to drive hypothesis generation and predictions that can be tested through the careful design of empirical studies. The field of microbiome research therefore transcends disciplines, as exemplified by the diversity of methodological and analytical approaches described in the contributions to the special feature, including mathematical modelling [9,[16][17][18], DNA and RNA sequencing [7,10,14,18], flow cytometry [14], infection tests in model and non-model pathosystems [7,18], physico-chemical and volatile analysis [7], and measures of hormone activity to assess host physiological responses to its environment [10]. A major theme pervading this special feature is the link between mathematical model simulations and empirical studies [9,11,16,17].…”

“…They combined in vitro transcriptome experiments comprising single and poly-species bacterial cultures growing on oak tissue, with more complex infection tests combining bacterial inoculations with the addition of beetle larvae in a novel oak log infection model, to demonstrate the cumulative impact of these interactions on the pathology of AOD. Ossowicki et al [7] used soil transplantation experiments to demonstrate the microbiological basis of disease suppression in wheat (Triticum aestivum) to the soil pathogen Fusarium culmorum, providing fascinating insights into the mechanistic diversity of disease suppression in soils.…”

“…Among the functions of the microbiome is the effect that microbial communities can have on pathogen colonization and disease. Ossowicki et al [7] exemplify this idea in their exploration of disease suppression in wheat (Triticum aestivum) by soil-associated microbiota. They find that suppression of the pathogen Fusarium culmorum is only conferred by 14% of soils, but that this protection cannot simply be ascribed to presence/absence of particular microbiota or function.…”

“…Niche availability and niche discordance are key factors that govern the capacity for a lineage with a certain phenotype to persist in an environment. Two relevant empirical studies in this special feature also address the functional interactions between plant hosts, microbiota and the environment in the context of plant disease [7,18].…”

“…The deterministic assembly of teleost fish microbiomes and possibilities for microbiome manipulation for sustainable aquaculture are also discussed [21]. Empirical studies applied the theory of emergent virulence to demonstrate the emergent properties of complex host-microbiota interactions in the context of plant disease [18], the impact of host physiology on the microbiome [10] and the role of soil microbiota in disease suppressive phenotypes of plants and soil transplantation to confer pathogen resistance [7].…”