Impact of the fungal pathogen Fusarium oxysporum on the taxonomic and functional diversity of the common bean root microbiome

BackgroundPlants rely on their root microbiome as the first line of defense against soil-borne fungal pathogens. The abundance and activities of beneficial root microbial taxa at the time prior to and during fungal infection are key to their protective success. If and how invading fungal root pathogens can disrupt microbiome assembly and gene expression is still largely unknown. Here, we investigated the impact of the fungal pathogen Fusarium oxysporum (fox) on the assembly of rhizosphere and endosphere microbiomes of a fox-susceptible and fox-resistant common bean cultivar.ResultsIntegration of 16S-amplicon, shotgun metagenome as well as metatranscriptome sequencing with community ecology analysis showed that fox infections significantly changed the composition and gene expression of the root microbiome in a cultivar-dependent manner. More specifically, fox infection led to increased microbial diversity, network complexity, and a higher proportion of the genera Flavobacterium, Bacillus, and Dyadobacter in the rhizosphere of the fox-resistant cultivar compared to the fox-susceptible cultivar. In the endosphere, root infection also led to changes in community assembly, with a higher abundance of the genera Sinorhizobium and Ensifer in the fox-resistant cultivar. Metagenome and metatranscriptome analyses further revealed the enrichment of terpene biosynthesis genes with a potential role in pathogen suppression in the fox-resistant cultivar upon fungal pathogen invasion.ConclusionCollectively, these results revealed a cultivar-dependent enrichment of specific bacterial genera and the activation of putative disease-suppressive functions in the rhizosphere and endosphere microbiome of common bean under siege.

Automated summary

This study found that Fusarium oxysporum infection had different effects on the composition and gene expression of the root microbiome in fox-susceptible and fox-resistant common bean cultivars. The infection increased microbial diversity, network complexity, and the abundance of certain bacterial genera in the rhizosphere and endosphere of the fox-resistant cultivar. Metagenome and metatranscriptome analysis also revealed the enrichment of terpene biosynthesis genes with potential disease-suppressive functions in the fox-resistant cultivar upon fungal pathogen invasion.