Metaviromics of Namib Desert Salt Pans: A Novel Lineage of Haloarchaeal Salterproviruses and a Rich Source of ssDNA Viruses

Abstract

Viral communities of two different salt pans located in the Namib Desert, Hosabes and Eisfeld, were investigated using a combination of multiple displacement amplification of metaviromic DNA and deep sequencing, and provided comprehensive sequence data on both ssDNA and dsDNA viral community structures. Read and contig annotations through online pipelines showed that the salt pans harbored largely unknown viral communities. Through network analysis, we were able to assign a large portion of the unknown reads to a diverse group of ssDNA viruses. Contigs belonging to the subfamily Gokushovirinae were common in both environmental datasets. Analysis of haloarchaeal virus contigs revealed the presence of three contigs distantly related with His1, indicating a possible new lineage of salterproviruses in the Hosabes playa. Based on viral richness and read mapping analyses, the salt pan metaviromes were novel and most closely related to each other while showing a low degree of overlap with other environmental viromes.

Keywords: Gokushovirinae; Microviridae; Namib Desert playa; environmental viromics; haloarchaeal viruses; hypersaline; metaviromics; ssDNA viruses.

Figure 1

Eisfeld playa (Swakopmund Saline) microbial mat as collected in this sample and mixed with water from the spring (Picture courtesy of E. Rybicki).

Figure 2

Network representation of the contigs of the Gobabeb Saline (A) and Swakopmund Saline (B) metaviromes. Connections between the contigs (circles) are based on read pairs mapping to different contigs. The circle size is proportional with contig length and the darker the color (light to dark blue for GS, light to dark green for SS), the higher the coverage of the reads mapping to a specific contig. Contig networks containing at least one contig with coverage higher than 1000× were investigated and are numbered. Only the contigs connected to at least one other are shown.

Figure 3

Maximum likelihood amino acid phylogenetic tree of the predicted capsid proteins (VP1) of presumed members of the Microviridae family. Sequences from this study are indicated by squares, known isolates by triangles and capsid proteins extracted from assembled genomes from previous metagenomic studies by circles [66]. The arches represent the presumed taxonomic distribution of the genomes. The tree with the highest log likelihood (−104,932.0787) is shown. Initial tree(s) for the heuristic search were obtained by applying the Neighbor-Joining method to a matrix of pairwise distances estimated using a Jones-Taylor-Thornton model. The analysis involved 133 amino acid sequences. There were a total of 1145 positions in the final dataset. Bootstrap percentages (on 100) are indicated at the branches.

Figure 4

Pairwise genomic comparison of the salterprovirus His1 with metaviromic contigs from the Gobabeb Saline metavirome. The predicted coding sequences are depicted by arrows. The putative polymerase B gene is colored blue, the major capsid protein (mcp) red and the minor structural proteins in blue-green. Grey areas between the genomes are pairwise tBLASTx similarities (areas of amino acid sequence identity).

Figure 5

Maximum Likelihood phylogenetic tree of the predicted major capsid proteins (mcp) of the GS metavirome contigs, the salterprovirus His1, the proposed gammapleiolipovirus His2 and representative isolates of the family Fuselloviridae, Sulfolobus spindle-shaped virus 1 (SSV1) and Acidianus spindle-shaped virus 1 (ASV1). The tree with the highest log likelihood (−1555) is depicted here, showing only the topology. Bootstrap values (calculated on 100) are shown for each branch. The final alignment contained 142 amino acid positions.

Figure 6

Cluster analysis of a Bray Curtis dissimilarity matrix based on the presence/absence of viral species in the investigated metaviromes as found by the MetaVir pipeline. Metaviromes were colored according to their biome. The Gobabeb Saline and Swakopmund Saline metaviromes are indicated with a red box.