Arabidopsis sculpt distinct root-associated microbiomes through the synthesis of secondary metabolites and defense signaling molecules

Abstract

Background Plant mutants with alterations in specific biosynthetic or signaling pathways exhibit distinct biochemical or physiological traits and are, thus, suitable models for studying links between the plant and its associated microbiota. Here, we examined microbial community structures of a range of Arabidopsis thaliana mutants disrupted in metabolic pathways for the production of glucosinolates, flavonoids, or a number of defense signaling molecules. Arabidopsis mutants and their background wild types (controls) were grown in natural soil and maintained in a greenhouse for 4 weeks before collection of roots for microbiome analysis. We characterized bacterial and fungal communities using 16S rRNA and fungal ITS amplicon sequencing, respectively. Results Our results showed that the Arabidopsis mutants had distinct microbial profiles compared to control plants. The relative abundances of the bacterial classes Actinobacteria, Thermoleophilia and Verrucomicrobiae, and the fungal classes Eurotiomycetes and Sordariomycetes were the most affected when comparing mutants and their wild types. At the genus level, the bacterial taxa Azospirillum, Fluviicola, and Flavobacterium were significantly enriched in most glucosinolate, flavonoid and signaling mutants while the fungal taxa Sporobolomyces and Emericellopsis were enriched in several glucosinolate and defense signaling mutants. Conclusion By using different Arabidopsis mutants and their background controls, we showed that plant secondary metabolism and defense signaling molecules affect bacterial and fungal community structures. We conclude that disruption of pathways for secondary metabolite production or disruption of defense signaling pathways affected the innate mechanisms that modulate plant root-associated microbiome assembly.