Skip to main content
SLU publication database (SLUpub)
Research article - Peer-reviewed, 2023

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

Jambagi, Shridhar; Hoden, Kristian Persson; Ohlund, Linda; Dixelius, Christina


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.


co-occurrence networks; farming systems; geographic locations; Rhizobium; root-associated microbiota; Trifolium pratense

Published in

Journal of Applied Microbiology
2023, Volume: 134, number: 4, article number: lxad067