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

Frontiers in Microbiology
Mitsuhiro YoshidaKen Takai

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 × 106to 5 × 106genome copies per cm3sediment, showing values similar to the range of fluorescence-based direct virus counts. In contrast, the estimated ssDNA viral abundance ranged from 1 × 108to 3 × 109genome copies per cm3sediment, 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 asCircoviridaeandMicroviridae. 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 profi...Continue Reading

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Citations

Oct 20, 2018·Science·Lucas B HarringtonJennifer A Doudna
May 10, 2019·RNA Biology·Tao Ju Cui, Chirlmin Joo
Sep 29, 2019·Nature Communications·Tao Ju CuiChirlmin Joo
Nov 22, 2019·Frontiers in Microbiology·Sonia Dávila-RamosRamón Alberto Batista-García
Feb 25, 2021·The Journal of Microbiology·Kira Moon, Jang-Cheon Cho

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Datasets Mentioned

BETA
DRA005987

Methods Mentioned

BETA
MDA
PCR
Assay
PCA
transmission electron microscopy

Software Mentioned

FASTX
PEAR
BLASTx
CLC Genomics Workbench
Cutadapt
QIIME
- Toolkit
MEGAN
MEGAN ( MEtaGenome Analyzer
BLAST

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