Taxonomic and functional diversity of alpine cryptogam holobionts
Cryptogams, including mosses and lichens, are widespread components of alpine ecosystems and provide habitats for diverse microbial communities. However, the taxonomic and functional diversity of these associated microorganisms remains comparatively underexplored, particularly across different cryptogam hosts and environmental conditions. This study investigates the diversity, composition, and functional potential of microbial communities associated with three alpine cryptogams: Racomitrium lanuginosum, Sphagnum capillifolium, and Cladonia arbuscula.  First, amplicon metabarcoding was used to characterise bacterial, archaeal, fungal, and micro-eukaryotic communities associated with each host across multiple seasons and environmental locations. These community-level approaches were used to examine variation in microbial diversity and composition among host species, across seasons, and between spatially distinct environments, as well as to identify taxa consistently associated with the different cryptogam hosts.  Second, deep shotgun metagenomic sequencing was used to provide a genome-resolved characterisation of cryptogam holobionts. Metagenomic datasets were assembled and analysed to investigate the taxonomic and functional composition of microbial communities, with metagenome-assembled genomes (MAGs) recovered and assessed for genome quality, taxonomy, and functional potential. Genome-resolved analyses were further used to examine the relationship between sequencing depth and MAG recovery and to investigate the genomic characteristics of individual microbial lineages within cryptogam microbiomes.  Finally, the study investigates the potential for biological nitrogen fixation within alpine cryptogam-associated microbial communities. Nitrogenase-associated sequences were screened using targeted nifH amplicon sequencing and metagenomic approaches, with candidate diazotrophic taxa and nitrogen fixation genes subsequently investigated at genome level. High-quality MAGs were used to examine the presence and organisation of nitrogen fixation genes and to assess the genomic potential for nitrogen fixation within cryptogam-associated bacteria.
Cryptogams, including mosses and lichens, are widespread components of alpine ecosystems and provide habitats for diverse microbial communities. However, the taxonomic and functional diversity of these associated microorganisms remains comparatively underexplored, particularly across different cryptogam hosts and environmental conditions. This study investigates the diversity, composition, and functional potential of microbial communities associated with three alpine cryptogams: Racomitrium lanuginosum, Sphagnum capillifolium, and Cladonia arbuscula.  First, amplicon metabarcoding was used to characterise bacterial, archaeal, fungal, and micro-eukaryotic communities associated with each host across multiple seasons and environmental locations. These community-level approaches were used to examine variation in microbial diversity and composition among host species, across seasons, and between spatially distinct environments, as well as to identify taxa consistently associated with the different cryptogam hosts.  Second, deep shotgun metagenomic sequencing was used to provide a genome-resolved characterisation of cryptogam holobionts. Metagenomic datasets were assembled and analysed to investigate the taxonomic and functional composition of microbial communities, with metagenome-assembled genomes (MAGs) recovered and assessed for genome quality, taxonomy, and functional potential. Genome-resolved analyses were further used to examine the relationship between sequencing depth and MAG recovery and to investigate the genomic characteristics of individual microbial lineages within cryptogam microbiomes.  Finally, the study investigates the potential for biological nitrogen fixation within alpine cryptogam-associated microbial communities. Nitrogenase-associated sequences were screened using targeted nifH amplicon sequencing and metagenomic approaches, with candidate diazotrophic taxa and nitrogen fixation genes subsequently investigated at genome level. High-quality MAGs were used to examine the presence and organisation of nitrogen fixation genes and to assess the genomic potential for nitrogen fixation within cryptogam-associated bacteria.