Enterobacteriaceae populations in the arugula microbiome

Arugula (Eruca vesicaria var. sativa (Mill.) Thell.) is a traditional medicinal plant and popular leafy green today. In comparison to other leafy greens, less outbreaks of related to human pathogens are reported. To understand the structure, function and specificity of the arugula microbiota, we have employed an approach linking metagenomics, amplicon sequencing and isolate characterization. Arugula is colonized by a highly specific microbiota. The rhizosphere provides habitat for diverse phyla, e.g. Actinobacteria, Bacteriodetes and Proteobacteria, while the phyllosphere representing the edible part is dominated by Gammaproteobacteria. This phylum was further studied regarding its function, and it was shown to be well-equipped with various antibiotic resistances. Unexpectedly, the prevalence of specific resistance mechanisms targeting therapeutic antibiotics was only exceeded by efflux pumps. High frequencies for fluoroquinolone, chloramphenicol, phenicol, macrolide, and aminocoumarin resistances were detected. In a strain collection, we showed that prevalent enterobacteria, as core microbiome members of arugula, have a substantial implication in the overall resistome. The present study provides novel insights into the natural occurrence of antibiotic resistances in Eruca sativa and brings them into relation with ecosystem functioning.