Mauchline, T. | Search bioRxiv

bioRxiv2025

Development of a bioassay guided genome mining approach for antifungal natural product discovery from pseudomonads

Zymoseptoria tritici causes Septoria Leaf Blotch disease of wheat and has evolved to overcome most chemical and genetic control methods. As such, new tools are required for future disease control. We identified Pseudomonas isolates that antagonise Z. tritici through the production of secreted secondary metabolites, using a novel in vitro Z. tritici antagonism assay. In addition to high-throughput qualitative assessment of Pseudomonas antagonism of Z. tritici, a quantitative assessment identified variation in the sensitivity of Z. tritici isolates to antagonism by a subset of Pseudomonas isolates. Genome assemblies of 3 strongly antagonistic Pseudomonas isolates were found to contain a predicted Biosynthetic Gene Cluster (BGC) with high sequence similarity to a reference BGC encoding the biosynthesis of the known antifungal compound 2,4-diacetylphloroglucinol (2,4-DAPG). Mutagenesis of the core biosynthetic gene phlD resulted in a loss of 2,4-DAPG production in Pseudomonas isolate Roth82, and a loss of Z. tritici inhibition in the antagonism assay. These results demonstrate that the described in vitro antagonism assay can be used to identify, quantify and mechanistically characterise bacterial antagonism of Z. tritici through the production of secondary metabolites. This is the first study to find significant differences in the response of genetically diverse isolates of Z. tritici isolates to bacterial antagonists, suggesting sensitivity to bacterial antagonism exists as a quantitative trait within natural Z. tritici populations. Our approach can be used to identify and characterise putatively novel BGCs that encode natural products with antifungal activity against Z. tritici.

microbiology↗

bioRxiv2025

Uncovering functional deterioration in the rhizosphere microbiome associated with wheat dwarfing

BackgroundOne of the biggest developments of wheat domestication was the development of semi-dwarf cultivars that respond well to fertilisers and produce higher yields without lodging. Consequently, this change has also impacted the wheat microbiome, often resulting in reduced selection of taxa and a loss of network complexity in the rhizospheres of semi-dwarf cultivars. Given the importance of rhizosphere microbiomes for plant health and performance, it is imperative that we understand if and how these changes have affected their function. Here, we use shotgun metagenomics to classify the functional potential of prokaryote communities from the rhizospheres of tall and semi-dwarf cultivars to compare the impact of wheat dwarfing on rhizosphere microbiome functions. ResultsWe found distinct taxonomic and functional differences between tall and semi-dwarf wheat rhizosphere communities and identified that semi-dwarf wheat microbiomes were less distinct from bulk soil communities. Of the 113 functional genes that were differentially abundant between tall and semi-dwarf cultivars, 95 % were depleted in semi-dwarf cultivars and 65 % of differentially abundant reads best mapped to genes involved in staurosporine biosynthesis (antibiotic product), plant cell wall degradation (microbial mediation of plant root architecture, overwintering energy source for microbes) and sphingolipid metabolism (signal bioactive molecules). ConclusionsOverall, our findings indicate that green revolution breeding has developed wheat cultivars with a reduced rhizosphere effect. The consequences of this are likely detrimental to the development of microbiome-assisted agriculture which will require a strong rhizosphere selective environment for the establishment of a beneficial plant root microbiome. We believe our results are of striking importance and highlight that implementation of microbiome facilitated agriculture as part of a sustainable crop production strategy will require an overhaul of wheat breeding programmes to consider plant-microbe interactions, especially in the root environment.

microbiology↗