Metagenomic analysis provides insights into functional capacity in a hyperarid desert soil niche community

Abstract

Environmental stressors such as low water activity and temperature extremes impose severe limitations on the productivity of soils in hyperarid deserts. In such ecosystems, macroscopic communities are often restricted to cryptic niche habitats, such as hypoliths (microbial communities found beneath translucent rocks), which are widely distributed in hyperarid desert environments. While hypolithic communities are considered to play a major role in the productivity of hyperarid habitats, the functional guilds implicated in these processes remain unclear. Here, we describe the Illumina-based metagenomic sequencing (± 30 Gb), assembly and analysis of hypolithic microbial communities from the south-west African Namib Desert. Taxonomic analyses using Small Subunit (SSU) phylogenetic markers showed that bacterial phylotypes (93%) dominated the communities, with relatively small proportions of archaea (0.43%) and fungi (5.6%). BlastX analysis against the refseq-viral database showed the presence of double stranded DNA viruses (7.8% contigs), dominated by Caudovirales (59.2%). Analysis of functional genes and metabolic pathways revealed that cyanobacteria were primarily responsible for photosynthesis with the presence of multiple copies of genes for both photosystems I and II, with a smaller but significant fraction of proteobacterial anoxic photosystem II genes. Hypolithic community members demonstrated an extensive genetic capacity for the degradation of phosphonates and mineralization of organic sulfur. Our data suggest that Proteobacterial guilds may be more significant in desert niches than previously recognized, as they showed widespread genetic capacity for mediating key stages in all biogeochemical cycles. Surprisingly, we were unable to show the presence of genes representative of complete nitrogen cycles. The diversity of nif genes was low, and the metagenome showed no evidence of other key N-cycling genes. Taken together, our analyses suggest an extensive capacity for carbon, phosphate and sulphate cycling but only limited nitrogen biogeochemistry.