Moss, lichen, and microbiomes: taxonomic and functional diversity of alpine cryptogam holobionts

Cryptogams, including mosses and lichens, are common features of alpine ecosystems and host taxonomically and functionally diverse microbial communities. This thesis characterises the breadth of microbial diversity and function associated with three alpine cryptogams: Racomitrium lanuginosum, Sphagnum capillifolium, and Cladonia arbuscula. Using amplicon metabarcoding, this thesis demonstrates that cryptogam-associated microbial communities are predominantly structured by host identity, with spatial environmental heterogeneity exerting a greater influence than seasonal variation. In addition to host-specific microbiomes, a small core microbiome was shared across all cryptogam hosts, contributing disproportionately to relative abundance. We further applied deep metagenomic sequencing to provide one of the most comprehensive assessments of cryptogam holobionts to date, providing a holistic characterisation of holobiont taxonomic and functional diversity, recovering almost 2000 high-quality bacterial metagenome-assembled genomes (MAGs). In doing so, we identified an average MAG sequence depth of ~20x as a practical threshold for recovery of high-quality bacterial MAGs. Finally, we investigated the presence of alpine cryptogam-associated diazotrophs as potentially crucial sources of ‘new’ nitrogen within alpine ecosystems. The presence of Nostoc, Methyloferula, and Holophaga were detected within S. capillifolium, and Rhodopila within R. lanuginosum. High-quality MAGs of these putative nitrogen fixing bacteria contained complete nif operons, including nifHDK and nifENB. No evidence of nitrogen fixation was found within the microbiome of C. arbuscula. Together, this thesis demonstrates, from a gene-to-ecosystem perspective, that cryptogams within alpine ecosystems host taxonomically and functionally diverse microbial communities across all microbial groups. By combining community- and genome-level approaches, this thesis provides a holistic view of cryptogam holobionts, emphasises the need for high-resolution sequencing to capture their full taxonomic and functional diversity, and establishes cryptogams as important yet underexplored hotspots of microbial diversity and ecosystem functions in alpine ecosystems.