Spatial variation shapes lichen-associated bacterial and fungal communities more than host identity or season

Abstract

Lichens are increasingly recognised as complex holobionts whose associated microbial communities contribute to host physiology and ecological resilience. However, the relative influence of host identity, geographic location and seasonal variation on these microbiomes remains poorly resolved. Here, we characterised bacterial (16S rRNA) and fungal (ITS) communities associated with two foliose lichens (Flavopunctelia<i></i> and Parmotrema<i></i>) sampled across three geographically distinct urban locations in Gauteng Province, South Africa, during summer and winter. Amplicon sequencing yielded 2,112 bacterial and 1,730 non-host fungal amplicon sequence variants (ASVs). Microbial alpha- and beta-diversity analyses demonstrated that spatial variation is the dominant driver of microbiome structure for both bacteria and fungi. Bacterial communities showed clear host-associated structuring, including enrichment of Cyanobacteriota in Parmotrema<i></i>, while fungal communities were comparatively conserved across both hosts but exhibited significant seasonal shifts in diversity. Despite this variability, a conserved core microbiome was identified across all samples, including the bacterial genera Sphingomonas<i></i>, Methylobacterium<i></i> and <i>Lichenibacterium</i>, and fungal taxa dominated by stress-tolerant lineages within the class Dothideomycetes. Together, these findings demonstrate that lichen microbiomes are structured by hierarchical ecological filters, with spatial environmental gradients exerting the strongest influence, thereby reflecting their sensitivity to fine-scale environmental variability.