Lichens host diverse endolichenic fungi (ELF) within a chemically and structurally complex thallus environment shaped by extreme-environment adaptation and enriched with bioactive secondary metabolites, yet the extent to which these internal chemical ...
Lichens host diverse endolichenic fungi (ELF) within a chemically and structurally complex thallus environment shaped by extreme-environment adaptation and enriched with bioactive secondary metabolites, yet the extent to which these internal chemical traits govern ELF assembly remains poorly understood. In this study, I assessed how ELF communities are structured by host identity and geographic context, and further tested whether host-derived secondary metabolites impose additional internal filtering effects nested within these broader factors. I collected 22 lichen thalli representing three host genera (Cladonia, Parmotrema, and Ramalina) from four regions in South Korea and characterized ELF communities using a metabarcoding on the Illumina MiSeq platform. In parallel, I profiled lichen secondary metabolites by HPLC and detected 17 major compounds, including usnic acid, stictic acid, and other lineage-specific metabolite groups. Sequence processing yielded 392,843 high-quality reads clustered into 166 OTUs. Alpha diversity metrics (richness, diversity, and evenness) did not differ significantly among host genera or locations and were unrelated to metabolite richness, indicating that ELF diversity is not structured at the level of within-sample diversity. In contrast, beta diversity analyses revealed significant shifts in community composition across hosts and locations, consistent with deterministic assembly driven by host identity and regional context. ELF communities were dominated by Ascomycota, particularly Dothideomycetes and Eurotiomycetes, and included functionally diverse taxa such as extremotolerant black yeasts and putatively saprotrophic lineages. HPLC-based metabolite profiles were strongly host-specific, and multivariate analyses showed that distinct metabolite groups were aligned with gradients of ELF community turnover and associated with subsets of OTUs. Variation partitioning further revealed that location, host, and metabolites explained complementary fractions of community variation, with the metabolite effect largely nested within the host component. Together, these results support the view that lichen secondary metabolites function as internal chemical filters that act in concert with host identity and regional species pools to structure ELF communities within lichen thalli.