Arabidopsis thaliana growth and microbial community composition - Greenhouse and gnotobiotic system comparison. Arabidopsis thaliana growth and microbial community composition - Greenhouse and gnotobiotic system comparison

In recent years the plant microbiome has become a subject of high importance within the field of plant science. Thereby several studies were trying to evaluate the link between plant growth, stress resistance and the plant associated microbiome. Although more natural conditions, such as field or greenhouse experiments, give the advantage to investigate physiologically more relevant processes, the immense complexity and number of factors affecting both the plant and its microbiome means a burden to disentangle all the factors in detail. Especially when working with immunocompromised plant mutants, natural systems can suffer from side-effects. For that reason, in this paper we attempted to recreate our previously published experiment from natural soil (Berens et al. 2019) in a more controlled environment of a Magenta boxes gnotobiotic system (Bai et al. 2015) and focus on the method comparison. Our aim was to evaluate the possibility to study host and compositional effects seen in natural conditions in greater detail using a simplified setup. Using a gnotobiotic system we were able to recreate the interaction between the A. thaliana genotype and salt stress and determine its effect on bacterial community present in the system. Congruently, we observed taxonomically similar community shifts, as in our previous research (Berens et al. 2019). Additionally, we were also able to recapitulate the PBS3-dependent leaf-age effect, indicating that even complex multi-factor interactions can be studied in simplified set-up of gnotobiotic system. In summary, the experiments described in this paper, give a better overview of the effects caused by host mutations in phytohormone pathways on bacterial community establishment as well as a critical comparison of the Magenta box gnotobiotic system advantages and disadvantages which may help in designing future experiments.