Abstract
Single stranded DNA viruses have been previously shown to populate the oceans on a global scale, and are endemic in microbialites of both marine and freshwater systems. We undertook for the first time direct viral metagenomic shotgun sequencing to explore the diversity of viruses in the modern stromatolites of Shark Bay Australia. The data indicate that Shark Bay marine stromatolites have similar diversity of ssDNA viruses to that of Highbourne Cay, Bahamas. ssDNA viruses in cluster uniquely in Shark Bay and Highbourne Cay, potentially due to enrichment by phi29-mediated amplification bias. Further, pyrosequencing data was assembled from the Shark Bay systems into two putative viral genomes that are related to Genomoviridae family of ssDNA viruses. In addition, the cellular fraction was shown to be enriched for antiviral defense genes including CRISPR-Cas, BREX (bacteriophage exclusion), and DISARM (defense island system associated with restriction-modification), a potentially novel finding for these systems. This is the first evidence for viruses in the Shark Bay stromatolites, and these viruses may play key roles in modulating microbial diversity as well as potentially impacting ecosystem function through infection and the recycling of key nutrients.
Highlights
Viruses represent the largest genetic repository and most abundant host-associated replicating entities on the planet (Breitbart and Rohwer, 2005; Suttle, 2005, 2007)
DNA sequences for viral and cellular fractions from Shark Bay stromatolites were determined for viral homology and taxonomy using MetaVir2, and MG-RAST for functional annotation
MetaVir2 predicted viral sequences based on Basic local alignment search tool (BLAST) to refseq (2017-01-11) found that regardless of the e-value (10−3, 10−5, 10−7 with Genomerelative Abundance and Average Size (GAAS) normalization) that >5% have a significant viral hit to known viruses within the database, whereas the cellular fraction had >10% for significant viral hits (Table 1)
Summary
Viruses represent the largest genetic repository and most abundant host-associated replicating entities on the planet (Breitbart and Rohwer, 2005; Suttle, 2005, 2007). Environmental viral metagenomics (i.e., viromics) has revealed that >90% of genes are hypothetical or uncharacterized (Angly et al, 2006), and it is likely that new genes will be found amongst viruses. A recent metagenomic study that exhaustively analyzed 3,042 geographically diverse samples revealed extensive global viral diversity, including recovering ∼125,000 partial DNA viral genomes, and yet more than 75% of the viral genes were hypothetical or uncharacterized (PaezEspino et al, 2016). This indicated that more than two-thirds of all viral protein coding genes have currently no known function. Viruses play a key role in carbon cycling representing >20% of all microbial biomass lysed daily in marine ecosystems
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