Viruses in the Oceanic Basement

Abstract

Microbial life has been detected well into the igneous crust of the seafloor (i.e., the oceanic basement), but there have been no reports confirming the presence of viruses in this habitat. To detect and characterize an ocean basement virome, geothermally heated fluid samples (ca. 60 to 65°C) were collected from 117 to 292 m deep into the ocean basement using seafloor observatories installed in two boreholes (Integrated Ocean Drilling Program [IODP] U1362A and U1362B) drilled in the eastern sediment-covered flank of the Juan de Fuca Ridge. Concentrations of virus-like particles in the fluid samples were on the order of 0.2 × 105 to 2 × 105 ml−1 (n = 8), higher than prokaryote-like cells in the same samples by a factor of 9 on average (range, 1.5 to 27). Electron microscopy revealed diverse viral morphotypes similar to those of viruses known to infect bacteria and thermophilic archaea. An analysis of virus-like sequences in basement microbial metagenomes suggests that those from archaeon-infecting viruses were the most common (63 to 80%). Complete genomes of a putative archaeon-infecting virus and a prophage within an archaeal scaffold were identified among the assembled sequences, and sequence analysis suggests that they represent lineages divergent from known thermophilic viruses. Of the clustered regularly interspaced short palindromic repeat (CRISPR)-containing scaffolds in the metagenomes for which a taxonomy could be inferred (163 out of 737), 51 to 55% appeared to be archaeal and 45 to 49% appeared to be bacterial. These results imply that the warmed, highly altered fluids in deeply buried ocean basement harbor a distinct assemblage of novel viruses, including many that infect archaea, and that these viruses are active participants in the ecology of the basement microbiome.

Novel Caudovirales associated with Marine Group I Thaumarchaeota assembled from metagenomes

“…Nitrosopumilus) but also to viral‐related genes, including predicted major capsid proteins (MCP), portal proteins, tail tape measure proteins and the large subunit of viral terminases. Both the terminase and the MCP proteins gave hits with low identity (32–35%) to a complete, unclassified archaeal virus (KY229235) recovered from a metagenomic assembly of a sample ~550 m below the seafloor (Nigro et al, ). Like in the case of KY229235, our contig had identical repeated sequences (>30 nucleotides) at the 5′ and 3′ terminal regions suggesting a complete viral genome.…”

The Geographic Structure of Viruses in the Cuatro Ciénegas Basin, a Unique Oasis in Northern Mexico, Reveals a Highly Diverse Population on a Small Geographic Scale

“…V iruses infect all known forms of life and are the most abundant and diverse biological entities of all Earth's ecosystems, including extreme environments such as the oceanic basement (1). Viruses play an integral role in the life cycle of their hosts, affecting not only their population demography but also their genetic diversity, thus strongly influencing the function, ecology, and evolution of complete communities and ecosystems (2).…”

“…Metagenomic studies of the oceans (5)(6)(7)(8)(9)(10)(11)(12)(13)(14) and other environments (15)(16)(17)(18)(19) have shown that viruses indeed are diverse and abundant in most habitats. Viruses have been found even below the basaltic basement (1), where most of them were related to Archaea and were hard to classify. This reflects a constant technical caveat in all viromic studies, since databases are incomplete and a large number of reads remains uncharacterized and are referred to as "dark matter," correlating with the "dark biodiversity" of their hosts (20).…”

“…The phylogenetic analyses confirmed the uniqueness of CCB; they revealed the biogeographic isolation signature in the 7 major viral families associated with different hosts that were used as examples. Different protein sequences, previously reported as markers for viral phylogeny analysis, were considered (1). The viral reads of these families were assem- (Table S3).…”

Contesting the evidence for gene expression in lower oceanic crust

“…Despite being included in the database (Figure 1B), sequences annotated to MAGs and SAGs from inhabitants of crustal subsurface habitats such as ammonia oxidixing Thaumarchaeota, Bathyarchaeota, sulfide oxidizing Epsilonproteobacteria, and iron oxidizing Zetaproteobacteria 4,5,12 are notably missing in the gene expression dataset of Li et al 1 (Figure 1B). While all subsurface gene expression data are prone to contamination due to the low biomass as an unavoidable challenge, it is nevertheless expected in the case of truly active subsurface microbial communities that at least some sequences derived the typical inhabitants of these extreme environments should be represented with reliable levels of sequencing coverage.…”