The microbiome in lichen and moss biocrust differentially contribute to carbon and nitrogen cycles in arid ecosystems

Abstract Biological soil crusts (biocrusts) are the main cover in arid and semi-arid regions worldwide. Microbes are an essential component in biocrusts and mediate many critical biochemical processes. However, little is known about the taxonomic composition and the functions of microbiomes in lichen and moss biocrusts. The shotgun metagenomic sequencing was used to compare two biocrust types (lichen-dominated and moss-dominated) in this study to reveal the microbial genes and metabolic pathways involved in carbon and nitrogen cycling. The results showed that the most abundant phylum in the two types of biocrust microbiomes was Actinobacteria, but their composition differed for the other abundant phyla (Proteobacteria, Cyanobacteria, Bacteroidetes, and Acidobacteria). The relative abundance of carbohydrate-active enzymes and enzymes associated with carbon and nitrogen metabolism significantly differed in both biocrust types. There is a clear dominance of respiration pathways over carbon fixation pathways in the microbial communities of both biocrust types. The genes encoding carbon monoxide dehydrogenase were more abundant than those encoding ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCo) involved in the C fixation. N 2 fixation had low metabolic pathways diversity in biocrust microbiomes, while nitrogen reduction dominated. The assimilatory nitrate reduction genes showed higher relative abundance in lichen biocrusts, while the dissimilatory nitrate reduction genes showed higher relative abundance in moss biocrusts. Dissolved organic carbon and soil organic carbon were considered as critical environmental factors affecting biocrust type. Our study suggests that biocrust type has significant effects on microbial biodiversity and biogeochemical cycling, providing new insights into biocrust microbiome responses to climate change at the gene level.