Improving the ecological knowledge on phyllosphere yeasts

Abstract

The phyllosphere, encompassing all aboveground plant surfaces such as leaves, fruits, and flowers, represents a highly dynamic habitat that supports diverse microbial communities, including bacteria, yeasts, filamentous fungi, algae, and viruses. Among these, yeasts frequently emerge as hub taxa, yet their ecological roles and interactions with other microbes remain poorly characterized. In Chapter 1, previous literature and overview covering yeast and phyllosphere along with what is known for the bacteria-fungal interaction is reviewed. In Chapter 2, we investigated the spectrum of interactions between yeasts and bacteria; two major epiphytic groups inhabiting the phyllosphere, using a series of pairwise in vitro co-culture assays. Our results revealed a wide range of interaction outcomes, from neutral to antagonistic and facilitative, driven by contact-dependent, distance-dependent, and distance-independent mechanisms. Further experiment using Splitplate assay for distance-independent interactions validated the involvement of yeast-derived volatile organic compounds (VOCs). From that assay, it was also found that the diverse yeasts taxa can produce volatiles that can inhibit bacterial growth. While volatile-mediated interactions are well documented in filamentous fungi, our findings provide novel evidence that yeast volatiles also influence bacterial physiology, underscoring an overlooked dimension of phyllosphere microbial ecology. In Chapter 3, we sought to explore the taxonomic and genomic identity of EMM_F5, a novel yeast isolate obtained from the phyllosphere of Magnolia grandiflora. Phylogenomic and multi-locus phylogenetic analyses placed EMM_F5 within the class Cystobasidiomycetes (Basidiomycota, Pucciniomycotina), in the same clade with Microsporomyces folliicola, a taxon currently proposed for reclassification into the new genus Persimmoniomyces. EMM_F5 forms a basal branch within the family Microsporomycetaceae, which is under revision toward inclusion in Occultifurales. The EMM_F5 genome constitutes the first available genomic resource for this family, offering valuable insights into an understudied and taxonomically complex lineage. However, the limited genomic representation of Cystobasidiomycetes, currently encompassing less than one-fifth of its known diversity restricts comprehensive comparative analyses. This gap emphasizes the need for expanded genomic exploration within the class to elucidate evolutionary trajectories and lifestyle associations such as lichen symbiosis and mycoparasitism. Together, these findings bridge ecological and evolutionary perspectives by revealing how phyllosphere yeasts can modulate bacterial communities through multiple interaction mechanisms, while simultaneously expanding the genomic and taxonomic framework of Cystobasidiomycetes. This study lays the foundation for future studies linking microbial ecology, evolution, and taxonomy. In Chapter 4, the final conclusion of the whole study is briefed with the impacts of the study. Thus, this study bridges ecological and evolutionary perspectives by revealing how phyllosphere yeasts can modulate bacterial communities through multiple interaction mechanisms, while simultaneously expanding the genomic and taxonomic framework of Cystobasidiomycetes.