Quantitative Viral Community DNA Analysis Reveals the Dominance of Single-Stranded DNA Viruses in Offshore Upper Bathyal Sediment from Tohoku, Japan

Abstract

Previous studies on marine environmental virology have primarily focused on double-stranded DNA (dsDNA) viruses; however, it has recently been suggested that single-stranded DNA (ssDNA) viruses are more abundant in marine ecosystems. In this study, we performed a quantitative viral community DNA analysis to estimate the relative abundance and composition of both ssDNA and dsDNA viruses in offshore upper bathyal sediment from Tohoku, Japan (water depth = 500 m). The estimated dsDNA viral abundance ranged from 3 × 106 to 5 × 106 genome copies per cm3 sediment, showing values similar to the range of fluorescence-based direct virus counts. In contrast, the estimated ssDNA viral abundance ranged from 1 × 108 to 3 × 109 genome copies per cm3 sediment, thus providing an estimation that the ssDNA viral populations represent 96.3–99.8% of the benthic total DNA viral assemblages. In the ssDNA viral metagenome, most of the identified viral sequences were associated with ssDNA viral families such as Circoviridae and Microviridae. The principle components analysis of the ssDNA viral sequence components from the sedimentary ssDNA viral metagenomic libraries found that the different depth viral communities at the study site all exhibited similar profiles compared with deep-sea sediment ones at other reference sites. Our results suggested that deep-sea benthic ssDNA viruses have been significantly underestimated by conventional direct virus counts and that their contributions to deep-sea benthic microbial mortality and geochemical cycles should be further addressed by such a new quantitative approach.

Argonaute bypasses cellular obstacles without hindrance during target search

“…la and lb) (Hegge et al, 2019) suggests a role of host defense against mobile genetic elements and ssDNA viruses. In environments where ssDNA viruses can be abundant, such as in sea water, fresh water, sediment, terrestrial, extreme, metazoan-associated and marine microbial mats 37-39 , pAgos targeting ssDNA would be markedly beneficial for the host. Upon entry in the infected cell, ssDNA binding and recombination proteins may associate with the invading nucleic acid, and DNA polymerase will start to generate the second strand.…”

Contrasting distributions of bacteriophages and eukaryotic viruses from contaminated coastal sediments

“…Circoviridae have been described as the most abundant viruses of deep-sea sediments (Yoshida et al, 2013). The analysis was also performed using multiple displacement amplification similar to our study.…”

“…Approximately 100 ml of surface sediments (0-2 cm) were used for viral community analysis. Viral purification was conducted according to the protocol described by Casas and Rohwer (Casas and Rohwer, 2007) with minor modifications from Yoshida et al (Yoshida et al, 2013). In brief, 130-190 g frozen sediments were re-suspended in 300 ml of modified SM buffer (50 mM Tris 100 mM NaCl 8 mM MgSO 4 pH 8) containing 3% NaCl (w/v) shaken at 180 rpm for 1 h and incubated for 1 h at 4 C. The slurry was clarified by centrifugation at 6000 ×g for 15 min.…”

“…They focused on DNA viruses and found both eukaryotic and prokaryotic viruses (bacteriophages). The dominant viruses in two different studies were single‐stranded DNA (ssDNA) viruses including the families Microviridae and Circoviridae (Yoshida et al, , ). Dell'Anno et al .…”

“…They focused on DNA viruses and found both eukaryotic and prokaryotic viruses (bacteriophages). The dominant viruses in two different studies were single-stranded DNA (ssDNA) viruses including the families Microviridae and Circoviridae (Yoshida et al, 2013(Yoshida et al, , 2018. Dell'Anno et al found high abundances of double-stranded DNA (dsDNA) viruses such as Inoviridae, Siphoviridae and Myoviridae in deep-sea sediments and showed a strong regulatory function of phages on bacterial communities, which was accompanied by a high decomposition rate of viruses that fuel the biogeochemical cycle (Dell'Anno et al, 2015).…”