Mechanisms of basidiomycete yeast function in complex leaf microbial communities

01/12/2018 to 30/11/2021

To facilitate co-habitation of resource-limited niches such as plant leaves by a broad range of organisms, microbes have evolved mechanisms to collaborate or compete with others. The sum of microbes associated with a host is termed the “microbiota”. Microbial communities build integral networks, which are constantly disturbed by biotic and abiotic factors. This requires continuous responsiveness and re-calibration of microbe-microbe interactions. A key to disentangle dynamic network stability might be ‘microbial hubs’, which are microbes that hold a central position in a microbial network and therefore are disproportionally important in shaping microbial communities. Hubs with a high degree of keystoneness, which has been defined as the degree of disproportionate deleterious effects on a community upon microbe removal, are therefore called keystone species. Recent findings suggest particular importance of antagonistic microbes and their negative interactions to stabilize microbial communities over time.
In wild Arabidopsis thaliana populations, we have recently identified an oomycete of the genus Albugo as the main hub. This hub organism, however, is strongly impacted by two basidiomycete yeasts, antagonizing each other. While an isolate of the genus Dioszegia promotes host colonization and reproduction of Albugo laibachii, an Ustilaginomycte of the genus Moesziomyces represses its pathogenicity. Moreover, we found that Moesziomyces has an antagonistic effect on several bacterial members of the A. thaliana leaf microbiome. We therefore hypothesize that Moesziomyces in particular and fungal yeasts of the class Ustilaginomycetes in general are crucial for microbial community structure and are therefore keystone species. To test this hypothesis, we have started a comprehensive yeast collection from A. thaliana leaves. For Moesziomyces, we have established as well a high quality annotated genome sequence and an efficient transformation system which allows functional genetic approaches to verify and identify the genetic bases of interactions.
To dissect interactions of these Ustilaginomycte yeasts within the host microbiota, we will perform microbial profiling of natural A. thaliana populations over time to reconstruct directed networks. These networks, together combined with genome sequencing of isolated Moesziomyces species and transcriptome profiling during different stages of interaction will enable the identification of gene candidates, which are functionally relevant for microbe-microbe interactions and keystone formation. Reverse genetics will be applied to generate fungal mutants for identified candidates, which will allow to test gene functions in a synthetic community context and thereby provide mechanistic insight into the molecular basis of microbial networks.
Our study is therefore a combinatorial approach to elucidate ecology and molecular mechanisms determining the role of basidiomycete yeasts as keystone species in the leaf microbial community.