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Fungal communities associated with the phyllosphere can influence plant health, stress responses, and disease dynamics in managed crop systems. However, limited information is available on fungal microbiome structure across phyllosphere compartments of Eucalyptus cinerea cultivated for cut foliage production. In this study, fungal communities (including epiphytic and endophytic fungi) associated with leaf, stem, and bark tissues of intensively managed E. cinerea grown in Ireland were characterised using ITS amplicon sequencing. Samples were collected from five trees, with tissues pooled by compartment to generate 15 biological samples. Following quality control and denoising, 405 fungal amplicon sequence variants (ASVs) were retained for analysis. Observed richness, Shannon and Simpson indices, and Faith’s phylogenetic diversity differed among compartments, with bark exhibiting higher values than leaf and stem tissues (p < 0.05). PERMANOVA analysis indicated that both compartment (R2 = 0.239, p = 0.002) and tree identity (R2 = 0.451, p = 0.002) significantly influenced fungal community composition. Bark communities were dominated by Diaporthe (52.9%), Peniophora (12.8%), and Talaromyces (10.4%), whereas leaf and stem communities were characterised primarily by Vishniacozyma and Sporobolomyces. Differential abundance analysis identified 26 and 23 differentially abundant ASVs between bark and leaf, and bark and stem tissues, respectively, whereas no significant differences were detected between leaf and stem communities. Weighted UniFrac analyses further revealed separation of bark-associated communities from photosynthetic tissues. These findings demonstrate compartment-associated variation in fungal community structure within the phyllosphere of managed E. cinerea and highlight the importance of considering both host-level and tissue-level effects in plant microbiome studies. This study provides a baseline assessment of fungal assemblages associated with commercially managed Eucalyptus under Irish growing conditions and supports future investigations into the functional significance of these microbial communities for plant health and resilience.
Byrne et al. (Tue,) studied this question.