Comparative metagenomics of two distinct biological soil crusts in the Tengger Desert, China

Biological soil crusts (biocrusts) are widely distributed in arid and semi-arid environments worldwide. The microbiome metabolic pathways of biocrusts contribute to important biogeochemical processes that improve the physicochemical properties of the surface soil. However, the differences in microbial processes among different types of biocrusts have been poorly studied by metagenomic analyses. In this study, we compared two types of biocrusts (bacterial-dominated biocrusts and moss-dominated biocrusts) using shotgun metagenomic sequencing. Our results showed that Actinobacteria was the most abundant phylum in the microbiomes of bacterial and moss biocrusts, even though the two biocrusts differed in the composition of the following other abundant phyla Proteobacteria, Acidobacteria, Cyanobacteria, Planctomycetes and Bacteroidetes. The profile of the C- and N- related metabolic pathways of the metagenome differed between the bacterial and moss biocrusts. The results showed that the genes encoding carbon monoxide dehydrogenase were more abundant than the gene encoding the ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) involved in the Calvin cycle, which is actually the main metabolic pathway for carbon fixation in both biocrusts. Low diversity in N-2 fixation pathways appears to be a distinguishing feature of biocrust microbiomes, while nitrogen reduction dominated the metabolic networks of the two biocrusts. The microbiome of bacterial biocrusts rich in assimilatory nitrate reduction genes, while the microbiome of moss biocrusts was rich in dissimilatory nitrate reduction genes. Amongst the (bio-)chemical parameters it is total organic carbon(TOC) that differentiates between the bacterial and moss biocrusts. Our study suggests that the biocrust types have significant effects on the TOC content and taxonomic, gene and metabolic diversity.