Metagenomic analysis of the viral community in Namib Desert hypoliths

Abstract

Hypolithic microbial communities are specialized desert communities inhabiting the underside of translucent rocks where they are sheltered from harsh environmental conditions. Here, we present the first study of the viral fraction of these communities isolated from the hyperarid Namib Desert (coastal South Western Africa). Using next-generation sequencing of the isolated viral fraction, the diversity and taxonomic composition of hypolith communities was mapped and a functional assessment of the sequences determined. Phylotypic analysis showed that bacteriophages belonging to the order Caudovirales with the family Siphoviridae were most prevalent. A major fraction of phage types was linked by database homologies to Bacillus or Geobacillus sp. as a host. Phylogenetic analyses of terL and phoH marker genes indicated that many of the sequences were novel and distinct from known isolates and environments, an observation supported by the class distribution of identified ribonucleotide reductases. The composition of the viral hypolith fraction was not completely consistent with Namib hypolith phylotypic surveys, in which the cyanobacterial genus Chroococcidiopsis was found to be dominant. This could be attributed to lacking sequence information about hypolith viruses/bacteria in public databases or the hypothesis that hypolithic communities actively recruit viruses from the surrounding open soil in which Bacillaceae-infecting phages are more commonly found.

High-Level Diversity of Tailed Phages, Eukaryote-Associated Viruses, and Virophage-Like Elements in the Metaviromes of Antarctic Soils

“…On the basis of identified phage species, only members of Firmicutes were found in both soil habitats in this study, but not in the 16S/terminal restriction fragment length polymorphism (TRFLP) bacterial data of Makhalanyane et al (35). This discrepancy between phage and bacterial data was also observed for hypoliths in hot desert soils (22). The other major bacterial phyla marker genes based on protein alignments retrieved from the MetaVir 2.0 analysis server (metagenomic read selection and tree construction methods outlined by Roux et al [26]).…”

“…Processing of both types of samples was performed similar to the methods in reference 22. Both the open-soil sample and pooled hypolithic samples were suspended in 3 liters of deionized water and shaken vigorously.…”

Diversity and Ecology of Viruses in Hyperarid Desert Soils

“…Viral community analyses have been conducted on surface soil samples from three hot hyperarid deserts: the Sahara (29), Namib (31,38), and Mojave (30,36). In each of those studies, difficulties in detecting extracellular VLPs by electron microscopy (EM) or pulse field gel electrophoresis (PFGE) profiling were reported, suggesting a very low viral abundance within these soils.…”

“…Using a similar methodology, 50% of the viral sequences from three Namib Desert surface sand samples had no homologs in public sequence databases, with most positive hits showing homology to Siphoviridae phages linked to Gram-positive bacteria (31). Most recently, a shotgun NGS approach was used to investigate the metavirome of Namib Desert hypoliths (38), cyanobacterium-dominated microbial niche communities on the ventral surfaces of translucent rocks (46). The most abundant sequences belonged to Geobacillus-and Bacillus-infecting phages, while cyanophage markers were unexpectedly found only in low numbers.…”

“…The most abundant sequences belonged to Geobacillus-and Bacillus-infecting phages, while cyanophage markers were unexpectedly found only in low numbers. The distinct phylogenetic clustering of assembled phoH genes (a cyanophage marker [47]) suggested that desert soil cyanophages were related only distantly to their well-studied marine counterparts (38) and that the dominance of marine cyanophage sequences in sequence databases might account for the low cyanophage hit rate of homologous sequences in the Namib Desert hypolithon metavirome. This observation has wider implications for studies of soil metaviromics, where an underestimation of cyanophage abundance and diversity may skew estimates of the functional importance (and population dynamics) of soil cyanobacteria, arguably the most important taxonomic group in desert soil microbial communities (27,28).…”