In-depth evaluation of root infection systems using the vascular fungus Verticillium longisporum as soil-borne model pathogen

BACKGROUND: While leaves are far more accessible for analysing plant defences, roots are hidden in the soil, leading to difficulties in studying soil-borne interactions. Inoculation strategies for infecting model plants with model root pathogens are described in the literature, but it remains demanding to obtain a methodological overview. To address this challenge, this study uses the model root pathogen Verticillium longisporum on Arabidopsis thaliana host plants and provides recommendations for selecting appropriate infection systems to investigate how plants cope with root pathogens. RESULTS: A novel root infection system is introduced, while two existing ones are precisely described and optimized. Step-by-step protocols are presented and accompanied by pathogenicity tests, transcriptional analyses of indole-glucosinolate marker genes and independent confirmations using reporter constructs. Advantages and disadvantages of each infection system are assessed. Overall, the results validate the importance of indole-glucosinolates as secondary metabolites that limit the Verticillium propagation in its host plant. CONCLUSION: Detailed assistances on studying host defence strategies and responses against V. longisporum is provided. Furthermore, other soil-borne microorganisms (e.g., V. dahliae) or model plants, such as economically important oilseed rape and tomato, can be introduced in the infection systems described. Hence, these proven manuals can support finding a root infection system for your specific research questions to further decipher root-microbe interactions. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13007-021-00758-x.