Red clover root-associated microbiota is shaped by geographic location and choice of farming system

Aims: This study evaluated the red clover (Trifolium pratense) root-associated microbiota to clarify the presence of pathogenic and beneficial microorganisms in 89 Swedish field sites.Methods and results: 16S rRNA and ITS amplicon sequencing analysis were performed on DNA extracted from the red clover root samples collected to determine the composition of the prokaryotic and eukaryotic root-associated microbe communities. Alpha and beta diversities were calculated and relative abundance of various microbial taxa and their co-occurrence were analyzed. Rhizobium was the most prevalent bacterial genus, followed by Sphingomonas, Mucilaginibacter, Flavobacterium, and the unclassified Chloroflexi group KD4-96. The Leptodontidium, Cladosporium, Clonostachys, and Tetracladium fungal genera known for endophytic, saprotrophic, and mycoparasitic lifestyles were also frequently observed in all samples. Sixty-two potential pathogenic fungi were identified with a bias toward grass pathogens and a higher abundance in samples from conventional farms.Conclusions: We showed that the microbial community was mainly shaped by geographic location and management procedures. Co-occurrence networks revealed that the Rhizobiumleguminosarum bv. trifolii was negatively associated with all fungal pathogenic taxa recognized in this study.

Automated summary

This study evaluated the red clover root-associated microbiota in 89 Swedish field sites to determine the presence of pathogenic and beneficial microorganisms. Analysis of DNA extracted from the root samples using 16S rRNA and ITS amplicon sequencing identified the composition of prokaryotic and eukaryotic root-associated microbial communities. The microbial community was mostly influenced by geographic location and management procedures, with Rhizobium being the most prevalent bacterial genus and Leptodontidium, Cladosporium, Clonostachys, and Tetracladium frequently observed fungal genera.