Towards quantitative viromics for both double-stranded and single-stranded DNA viruses

Simon Roux, Natalie E. Solonenko, Vinh T. Dang, Bonnie T. Poulos, Sarah M. Schwenck, Dawn B. Goldsmith, Maureen L. Coleman, Mya Breitbart, Matthew Sullivan

Research output: Contribution to journalArticle

53 Citations (Scopus)

Abstract

Background. Viruses strongly influence microbial population dynamics and ecosystem functions. However, our ability to quantitatively evaluate those viral impacts is limited to the few cultivated viruses and double-stranded DNA (dsDNA) viral genomes captured in quantitative viral metagenomes (viromes). This leaves the ecology of non- dsDNA viruses nearly unknown, including single-stranded DNA (ssDNA) viruses that have been frequently observed in viromes, but not quantified due to amplification biases in sequencing library preparations (Multiple Displacement Amplification, Linker Amplification or Tagmentation). Methods. Here we designed mock viral communities including both ssDNA and dsDNA viruses to evaluate the capability of a sequencing library preparation approach including an Adaptase step prior to Linker Amplification for quantitative amplification of both dsDNA and ssDNA templates. We then surveyed aquatic samples to provide first estimates of the abundance of ssDNA viruses. Results. Mock community experiments confirmed the biased nature of existing library preparation methods for ssDNA templates (either largely enriched or selected against) and showed that the protocol using Adaptase plus Linker Amplification yielded viromes that were -1.8-fold quantitative for ssDNA and dsDNA viruses. Application of this protocol to community virus DNA from three freshwater and three marine samples revealed that ssDNA viruses as a whole represent only a minor fraction (<5%) of DNA virus communities, though individual ssDNA genomes, both eukaryote- infecting Circular Rep-Encoding Single-Stranded DNA (CRESS-DNA) viruses and bacteriophages from the Microviridae family, can be among the most abundant viral genomes in a sample. Discussion. Together these findings provide empirical data for a new virome library preparation protocol, and a first estimate of ssDNA virus abundance in aquatic systems.

Original languageEnglish (US)
Article numbere2777
JournalPeerJ
Volume2016
Issue number12
DOIs
StatePublished - 2016
Externally publishedYes

Fingerprint

dsDNA viruses
Single-Stranded DNA
Viruses
DNA Viruses
single-stranded DNA
ssDNA viruses
Amplification
DNA libraries
Viral Genome
DNA
Microviridae
genome
Libraries
Genes
Metagenome
viruses
sampling
Population Dynamics
bacteriophages
Ecology

Keywords

  • Environmental virology
  • ssDNA viruses.
  • Viral metagenomics.

ASJC Scopus subject areas

  • Neuroscience(all)
  • Medicine(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Roux, S., Solonenko, N. E., Dang, V. T., Poulos, B. T., Schwenck, S. M., Goldsmith, D. B., ... Sullivan, M. (2016). Towards quantitative viromics for both double-stranded and single-stranded DNA viruses. PeerJ, 2016(12), [e2777]. https://doi.org/10.7717/peerj.2777

Towards quantitative viromics for both double-stranded and single-stranded DNA viruses. / Roux, Simon; Solonenko, Natalie E.; Dang, Vinh T.; Poulos, Bonnie T.; Schwenck, Sarah M.; Goldsmith, Dawn B.; Coleman, Maureen L.; Breitbart, Mya; Sullivan, Matthew.

In: PeerJ, Vol. 2016, No. 12, e2777, 2016.

Research output: Contribution to journalArticle

Roux, S, Solonenko, NE, Dang, VT, Poulos, BT, Schwenck, SM, Goldsmith, DB, Coleman, ML, Breitbart, M & Sullivan, M 2016, 'Towards quantitative viromics for both double-stranded and single-stranded DNA viruses', PeerJ, vol. 2016, no. 12, e2777. https://doi.org/10.7717/peerj.2777
Roux S, Solonenko NE, Dang VT, Poulos BT, Schwenck SM, Goldsmith DB et al. Towards quantitative viromics for both double-stranded and single-stranded DNA viruses. PeerJ. 2016;2016(12). e2777. https://doi.org/10.7717/peerj.2777
Roux, Simon ; Solonenko, Natalie E. ; Dang, Vinh T. ; Poulos, Bonnie T. ; Schwenck, Sarah M. ; Goldsmith, Dawn B. ; Coleman, Maureen L. ; Breitbart, Mya ; Sullivan, Matthew. / Towards quantitative viromics for both double-stranded and single-stranded DNA viruses. In: PeerJ. 2016 ; Vol. 2016, No. 12.
@article{65e24bae962f4cbeacd6af1cfccbbfc3,
title = "Towards quantitative viromics for both double-stranded and single-stranded DNA viruses",
abstract = "Background. Viruses strongly influence microbial population dynamics and ecosystem functions. However, our ability to quantitatively evaluate those viral impacts is limited to the few cultivated viruses and double-stranded DNA (dsDNA) viral genomes captured in quantitative viral metagenomes (viromes). This leaves the ecology of non- dsDNA viruses nearly unknown, including single-stranded DNA (ssDNA) viruses that have been frequently observed in viromes, but not quantified due to amplification biases in sequencing library preparations (Multiple Displacement Amplification, Linker Amplification or Tagmentation). Methods. Here we designed mock viral communities including both ssDNA and dsDNA viruses to evaluate the capability of a sequencing library preparation approach including an Adaptase step prior to Linker Amplification for quantitative amplification of both dsDNA and ssDNA templates. We then surveyed aquatic samples to provide first estimates of the abundance of ssDNA viruses. Results. Mock community experiments confirmed the biased nature of existing library preparation methods for ssDNA templates (either largely enriched or selected against) and showed that the protocol using Adaptase plus Linker Amplification yielded viromes that were -1.8-fold quantitative for ssDNA and dsDNA viruses. Application of this protocol to community virus DNA from three freshwater and three marine samples revealed that ssDNA viruses as a whole represent only a minor fraction (<5{\%}) of DNA virus communities, though individual ssDNA genomes, both eukaryote- infecting Circular Rep-Encoding Single-Stranded DNA (CRESS-DNA) viruses and bacteriophages from the Microviridae family, can be among the most abundant viral genomes in a sample. Discussion. Together these findings provide empirical data for a new virome library preparation protocol, and a first estimate of ssDNA virus abundance in aquatic systems.",
keywords = "Environmental virology, ssDNA viruses., Viral metagenomics.",
author = "Simon Roux and Solonenko, {Natalie E.} and Dang, {Vinh T.} and Poulos, {Bonnie T.} and Schwenck, {Sarah M.} and Goldsmith, {Dawn B.} and Coleman, {Maureen L.} and Mya Breitbart and Matthew Sullivan",
year = "2016",
doi = "10.7717/peerj.2777",
language = "English (US)",
volume = "2016",
journal = "PeerJ",
issn = "2167-8359",
publisher = "PeerJ",
number = "12",

}

TY - JOUR

T1 - Towards quantitative viromics for both double-stranded and single-stranded DNA viruses

AU - Roux, Simon

AU - Solonenko, Natalie E.

AU - Dang, Vinh T.

AU - Poulos, Bonnie T.

AU - Schwenck, Sarah M.

AU - Goldsmith, Dawn B.

AU - Coleman, Maureen L.

AU - Breitbart, Mya

AU - Sullivan, Matthew

PY - 2016

Y1 - 2016

N2 - Background. Viruses strongly influence microbial population dynamics and ecosystem functions. However, our ability to quantitatively evaluate those viral impacts is limited to the few cultivated viruses and double-stranded DNA (dsDNA) viral genomes captured in quantitative viral metagenomes (viromes). This leaves the ecology of non- dsDNA viruses nearly unknown, including single-stranded DNA (ssDNA) viruses that have been frequently observed in viromes, but not quantified due to amplification biases in sequencing library preparations (Multiple Displacement Amplification, Linker Amplification or Tagmentation). Methods. Here we designed mock viral communities including both ssDNA and dsDNA viruses to evaluate the capability of a sequencing library preparation approach including an Adaptase step prior to Linker Amplification for quantitative amplification of both dsDNA and ssDNA templates. We then surveyed aquatic samples to provide first estimates of the abundance of ssDNA viruses. Results. Mock community experiments confirmed the biased nature of existing library preparation methods for ssDNA templates (either largely enriched or selected against) and showed that the protocol using Adaptase plus Linker Amplification yielded viromes that were -1.8-fold quantitative for ssDNA and dsDNA viruses. Application of this protocol to community virus DNA from three freshwater and three marine samples revealed that ssDNA viruses as a whole represent only a minor fraction (<5%) of DNA virus communities, though individual ssDNA genomes, both eukaryote- infecting Circular Rep-Encoding Single-Stranded DNA (CRESS-DNA) viruses and bacteriophages from the Microviridae family, can be among the most abundant viral genomes in a sample. Discussion. Together these findings provide empirical data for a new virome library preparation protocol, and a first estimate of ssDNA virus abundance in aquatic systems.

AB - Background. Viruses strongly influence microbial population dynamics and ecosystem functions. However, our ability to quantitatively evaluate those viral impacts is limited to the few cultivated viruses and double-stranded DNA (dsDNA) viral genomes captured in quantitative viral metagenomes (viromes). This leaves the ecology of non- dsDNA viruses nearly unknown, including single-stranded DNA (ssDNA) viruses that have been frequently observed in viromes, but not quantified due to amplification biases in sequencing library preparations (Multiple Displacement Amplification, Linker Amplification or Tagmentation). Methods. Here we designed mock viral communities including both ssDNA and dsDNA viruses to evaluate the capability of a sequencing library preparation approach including an Adaptase step prior to Linker Amplification for quantitative amplification of both dsDNA and ssDNA templates. We then surveyed aquatic samples to provide first estimates of the abundance of ssDNA viruses. Results. Mock community experiments confirmed the biased nature of existing library preparation methods for ssDNA templates (either largely enriched or selected against) and showed that the protocol using Adaptase plus Linker Amplification yielded viromes that were -1.8-fold quantitative for ssDNA and dsDNA viruses. Application of this protocol to community virus DNA from three freshwater and three marine samples revealed that ssDNA viruses as a whole represent only a minor fraction (<5%) of DNA virus communities, though individual ssDNA genomes, both eukaryote- infecting Circular Rep-Encoding Single-Stranded DNA (CRESS-DNA) viruses and bacteriophages from the Microviridae family, can be among the most abundant viral genomes in a sample. Discussion. Together these findings provide empirical data for a new virome library preparation protocol, and a first estimate of ssDNA virus abundance in aquatic systems.

KW - Environmental virology

KW - ssDNA viruses.

KW - Viral metagenomics.

UR - http://www.scopus.com/inward/record.url?scp=85006073389&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85006073389&partnerID=8YFLogxK

U2 - 10.7717/peerj.2777

DO - 10.7717/peerj.2777

M3 - Article

AN - SCOPUS:85006073389

VL - 2016

JO - PeerJ

JF - PeerJ

SN - 2167-8359

IS - 12

M1 - e2777

ER -