Unveiling Cross-Kingdom Interactions in Natural Arabidopsis thaliana Leaf Microbial Communities

Abstract

Microbial colonizers of natural plant populations play a pivotal role in shaping microbial community composition, influencing host physiology, and either promoting or suppressing disease development. Investigating the microbiome of Arabidopsis thaliana populations in the Tübingen region provided valuable insights into community structure and its interaction with the obligate biotrophic pathogen Albugo laibachii. Identified as a hub species through correlation network analysis, A. laibachii emerged as a key player in the phyllosphere, actively shaping the surrounding microbial community. In the same study, basidiomycete yeasts were found to be more stable than bacteria and occurred both in the presence and absence of the oomycete pathogen. While many yeasts co-occur with Albugo, some — particularly Moesziomyces bullatus and Cystofilobasidium — were predominantly found in its absence. These yeasts were shown to significantly reduce pathogen infection, with glycoside hydrolase 25 (GH25) identified as the key effector enzyme in the case of M. bullatus. In the present study, we sought to elucidate the mechanism behind the inhibitory effect of Cystofilobasidium and uncovered an intriguing cross-kingdom synergy with a Pseudomonas extremaustralis strain frequently co-isolated with Cystofilobasidium from natural A. thaliana populations. Initial analyses confirmed that neither GH25 nor its orthologs are present in the Cystofilobasidium genome, suggesting a previously uncharacterized mechanism. Confrontation assays showed that the antimicrobial activity of our P. extremaustralis isolate is enhanced in the presence of Cystofilobasidium yeasts against various A. thaliana-associated bacteria. Notably, co-cultures of Cystofilobasidium and Pseudomonas exhibited increased biofilm formation in the presence of these previously inhibited bacterial strains. Transcriptomic analysis of the yeast revealed a distinct response to P. extremaustralis, and subsequent qPCR validation identified two candidate genes: the ABC transporter g5886 and the glycoside hydrolase g4647. Together, these findings support a model in which the inhibition of A. laibachii observed in initial infection assays results from a natural synergistic interaction between Cystofilobasidium and P. extremaustralis. This interaction likely enhances biofilm formation, thereby reducing pathogen adhesion, and promotes selective microbial inhibition that indirectly limits pathogen colonization.