skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils

Abstract

Soils impact global carbon cycling and their resident microbes are critical to their biogeochemical processing and ecosystem outputs. Based on studies in marine systems, viruses infecting soil microbes likely modulate host activities via mortality, horizontal gene transfer, and metabolic control. However, their roles remain largely unexplored due to technical challenges with separating, isolating, and extracting DNA from viruses in soils. Some of these challenges have been overcome by using whole genome amplification methods and while these have allowed insights into the identities of soil viruses and their genomes, their inherit biases have prevented meaningful ecological interpretations. Here we experimentally optimized steps for generating quantitatively-amplified viral metagenomes to better capture both ssDNA and dsDNA viruses across three distinct soil habitats along a permafrost thaw gradient. First, we assessed differing DNA extraction methods (PowerSoil, Wizard mini columns, and cetyl trimethylammonium bromide) for quantity and quality of viral DNA. This established PowerSoil as best for yield and quality of DNA from our samples, though ~1/3 of the viral populations captured by each extraction kit were unique, suggesting appreciable differential biases among DNA extraction kits. Second, we evaluated the impact of purifying viral particles after resuspension (by cesium chloride gradients; CsCl) and of viralmore » lysis method (heat vs bead-beating) on the resultant viromes. DNA yields after CsCl particle-purification were largely non-detectable, while unpurified samples yielded 1–2-fold more DNA after lysis by heat than by bead-beating. Virome quality was assessed by the number and size of metagenome-assembled viral contigs, which showed no increase after CsCl-purification, but did from heat lysis relative to bead-beating. We also evaluated sample preparation protocols for ssDNA virus recovery. In both CsCl-purified and non-purified samples, ssDNA viruses were successfully recovered by using the Accel-NGS 1S Plus Library Kit. While ssDNA viruses were identified in all three soil types, none were identified in the samples that used bead-beating, suggesting this lysis method may impact recovery. Further, 13 ssDNA vOTUs were identified compared to 582 dsDNA vOTUs, and the ssDNA vOTUs only accounted for~4% of the assembled reads, implying dsDNA viruses were dominant in these samples. This optimized approach was combined with the previously published viral resuspension protocol into a sample-to-virome protocol for soils now available atprotocols.io, where community feedback creates ‘living’ protocols. This collective approach will be particularly valuable given the high physicochemical variability of soils, which will may require considerable soil type-specific optimization. This optimized protocol provides a starting place for developing quantitatively-amplified viromic datasets and will help enable viral ecogenomic studies on organic-rich soils.« less

Authors:
 [1];  [2];  [3];  [3];  [3];  [4];  [2];  [3];  [3]
  1. The Ohio State Univ., Columbus, OH (United States); Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
  2. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  3. The Ohio State Univ., Columbus, OH (United States)
  4. The Ohio State Univ., Columbus, OH (United States); Colorado State Univ., Fort Collins, CO (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23); USDOE National Nuclear Security Administration (NNSA)
OSTI Identifier:
1559173
Alternate Identifier(s):
OSTI ID: 1569170
Report Number(s):
LLNL-JRNL-789611
Journal ID: ISSN 2167-8359; ark:/13030/qt0vb5k8qg
Grant/Contract Number:  
AC02-05CH11231; AC52-07NA27344
Resource Type:
Accepted Manuscript
Journal Name:
PeerJ
Additional Journal Information:
Journal Volume: 7; Journal ID: ISSN 2167-8359
Publisher:
PeerJ Inc.
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Soil viruses; Viromes; DNA extraction; Organics; Microbiology; ssDNA viruses; dsDNA viruses; Viromics; Environmental sciences

Citation Formats

Trubl, Gareth, Roux, Simon, Solonenko, Natalie, Li, Yueh-Fen, Bolduc, Benjamin, Rodríguez-Ramos, Josué, Eloe-Fadrosh, Emiley A., Rich, Virginia I., and Sullivan, Matthew B. Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils. United States: N. p., 2019. Web. doi:10.7717/peerj.7265.
Trubl, Gareth, Roux, Simon, Solonenko, Natalie, Li, Yueh-Fen, Bolduc, Benjamin, Rodríguez-Ramos, Josué, Eloe-Fadrosh, Emiley A., Rich, Virginia I., & Sullivan, Matthew B. Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils. United States. doi:10.7717/peerj.7265.
Trubl, Gareth, Roux, Simon, Solonenko, Natalie, Li, Yueh-Fen, Bolduc, Benjamin, Rodríguez-Ramos, Josué, Eloe-Fadrosh, Emiley A., Rich, Virginia I., and Sullivan, Matthew B. Thu . "Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils". United States. doi:10.7717/peerj.7265. https://www.osti.gov/servlets/purl/1559173.
@article{osti_1559173,
title = {Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils},
author = {Trubl, Gareth and Roux, Simon and Solonenko, Natalie and Li, Yueh-Fen and Bolduc, Benjamin and Rodríguez-Ramos, Josué and Eloe-Fadrosh, Emiley A. and Rich, Virginia I. and Sullivan, Matthew B.},
abstractNote = {Soils impact global carbon cycling and their resident microbes are critical to their biogeochemical processing and ecosystem outputs. Based on studies in marine systems, viruses infecting soil microbes likely modulate host activities via mortality, horizontal gene transfer, and metabolic control. However, their roles remain largely unexplored due to technical challenges with separating, isolating, and extracting DNA from viruses in soils. Some of these challenges have been overcome by using whole genome amplification methods and while these have allowed insights into the identities of soil viruses and their genomes, their inherit biases have prevented meaningful ecological interpretations. Here we experimentally optimized steps for generating quantitatively-amplified viral metagenomes to better capture both ssDNA and dsDNA viruses across three distinct soil habitats along a permafrost thaw gradient. First, we assessed differing DNA extraction methods (PowerSoil, Wizard mini columns, and cetyl trimethylammonium bromide) for quantity and quality of viral DNA. This established PowerSoil as best for yield and quality of DNA from our samples, though ~1/3 of the viral populations captured by each extraction kit were unique, suggesting appreciable differential biases among DNA extraction kits. Second, we evaluated the impact of purifying viral particles after resuspension (by cesium chloride gradients; CsCl) and of viral lysis method (heat vs bead-beating) on the resultant viromes. DNA yields after CsCl particle-purification were largely non-detectable, while unpurified samples yielded 1–2-fold more DNA after lysis by heat than by bead-beating. Virome quality was assessed by the number and size of metagenome-assembled viral contigs, which showed no increase after CsCl-purification, but did from heat lysis relative to bead-beating. We also evaluated sample preparation protocols for ssDNA virus recovery. In both CsCl-purified and non-purified samples, ssDNA viruses were successfully recovered by using the Accel-NGS 1S Plus Library Kit. While ssDNA viruses were identified in all three soil types, none were identified in the samples that used bead-beating, suggesting this lysis method may impact recovery. Further, 13 ssDNA vOTUs were identified compared to 582 dsDNA vOTUs, and the ssDNA vOTUs only accounted for~4% of the assembled reads, implying dsDNA viruses were dominant in these samples. This optimized approach was combined with the previously published viral resuspension protocol into a sample-to-virome protocol for soils now available atprotocols.io, where community feedback creates ‘living’ protocols. This collective approach will be particularly valuable given the high physicochemical variability of soils, which will may require considerable soil type-specific optimization. This optimized protocol provides a starting place for developing quantitatively-amplified viromic datasets and will help enable viral ecogenomic studies on organic-rich soils.},
doi = {10.7717/peerj.7265},
journal = {PeerJ},
number = ,
volume = 7,
place = {United States},
year = {2019},
month = {7}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Save / Share:

Works referenced in this record:

Assessment of viral community functional potential from viral metagenomes may be hampered by contamination with cellular sequences
journal, December 2013

  • Roux, Simon; Krupovic, Mart; Debroas, Didier
  • Open Biology, Vol. 3, Issue 12
  • DOI: 10.1098/rsob.130160

Rising to the challenge: accelerated pace of discovery transforms marine virology
journal, February 2015

  • Brum, Jennifer R.; Sullivan, Matthew B.
  • Nature Reviews Microbiology, Vol. 13, Issue 3
  • DOI: 10.1038/nrmicro3404

Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity
journal, January 2017

  • Roux, Simon; Emerson, Joanne B.; Eloe-Fadrosh, Emiley A.
  • PeerJ, Vol. 5
  • DOI: 10.7717/peerj.3817

Microbial network, phylogenetic diversity and community membership in the active layer across a permafrost thaw gradient
journal, July 2017

  • Mondav, Rhiannon; McCalley, Carmody K.; Hodgkins, Suzanne B.
  • Environmental Microbiology, Vol. 19, Issue 8
  • DOI: 10.1111/1462-2920.13809

Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient
journal, January 2016

  • Trubl, Gareth; Solonenko, Natalie; Chittick, Lauren
  • PeerJ, Vol. 4
  • DOI: 10.7717/peerj.1999

Comparative assessment of methods for metagenomic DNA isolation from soils of different crop growing fields
journal, October 2016


Murphy's law—if anything can go wrong, it will: Problems in phage electron microscopy
journal, April 2012

  • Ackermann, Hans-W.; Tiekotter, Kenneth L.
  • Bacteriophage, Vol. 2, Issue 2
  • DOI: 10.4161/bact.20693

Chemical Composition of Soil Organic Matter in a Subarctic Peatland: Influence of Shifting Vegetation Communities
journal, January 2017

  • Normand, Anna E.; Smith, Adam N.; Clark, Mark W.
  • Soil Science Society of America Journal, Vol. 81, Issue 1
  • DOI: 10.2136/sssaj2016.05.0148

Host-linked soil viral ecology along a permafrost thaw gradient
journal, July 2018


Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics
journal, January 2016


Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components
journal, March 1997

  • Porebski, Sue; Bailey, L. Grant; Baum, Bernard R.
  • Plant Molecular Biology Reporter, Vol. 15, Issue 1
  • DOI: 10.1007/BF02772108

Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing
journal, October 2018


Forensic implications of PCR inhibition—A review
journal, May 2012


High Initial Sputter Rate Found for Vaccinia Virions Using Isotopic Labeling, NanoSIMS, and AFM
journal, January 2018


An efficient and cost-effective method for DNA extraction from athalassohaline soil using a newly formulated cell extraction buffer
journal, February 2016


Fake virus particles generated by fluorescence microscopy
journal, January 2013


Viruses as new agents of organomineralization in the geological record
journal, July 2014

  • Pacton, Muriel; Wacey, David; Corinaldesi, Cinzia
  • Nature Communications, Vol. 5, Issue 1
  • DOI: 10.1038/ncomms5298

Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data
journal, July 2017

  • Paez-Espino, David; Pavlopoulos, Georgios A.; Ivanova, Natalia N.
  • Nature Protocols, Vol. 12, Issue 8
  • DOI: 10.1038/nprot.2017.063

Trimmomatic: a flexible trimmer for Illumina sequence data
journal, April 2014


Patterns and ecological drivers of ocean viral communities
journal, May 2015


Diversity of environmental single-stranded DNA phages revealed by PCR amplification of the partial major capsid protein
journal, April 2014

  • Hopkins, Max; Kailasan, Shweta; Cohen, Allison
  • The ISME Journal, Vol. 8, Issue 10
  • DOI: 10.1038/ismej.2014.43

Detection of genetically modified soybean DNA in refined vegetable oils
journal, February 2010

  • Costa, Joana; Mafra, Isabel; Amaral, Joana S.
  • European Food Research and Technology, Vol. 230, Issue 6
  • DOI: 10.1007/s00217-010-1238-2

Marine DNA Viral Macro- and Microdiversity from Pole to Pole
journal, May 2019


Amplification of Uncultured Single-Stranded DNA Viruses from Rice Paddy Soil
journal, August 2008

  • Kim, K. -H.; Chang, H. -W.; Nam, Y. -D.
  • Applied and Environmental Microbiology, Vol. 74, Issue 19
  • DOI: 10.1128/AEM.01275-08

The ‘Neglected’ Soil Virome – Potential Role and Impact
journal, August 2018


Changes in peat chemistry associated with permafrost thaw increase greenhouse gas production
journal, April 2014

  • Hodgkins, S. B.; Tfaily, M. M.; McCalley, C. K.
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 16
  • DOI: 10.1073/pnas.1314641111

The Effect of Preprocessing by Sequence-Independent, Single-Primer Amplification (SISPA) on Metagenomic Detection of Viruses
journal, September 2013

  • Karlsson, Oskar Erik; Belák, Sándor; Granberg, Fredrik
  • Biosecurity and Bioterrorism: Biodefense Strategy, Practice, and Science, Vol. 11, Issue S1
  • DOI: 10.1089/bsp.2013.0008

Dynamics of autochthonous soil viral communities parallels dynamics of host communities under nutrient stimulation
journal, July 2015

  • Srinivasiah, Sharath; Lovett, Jacqueline; Ghosh, Dhritiman
  • FEMS Microbiology Ecology, Vol. 91, Issue 7
  • DOI: 10.1093/femsec/fiv063

Diversity and Ecology of Viruses in Hyperarid Desert Soils
journal, November 2015

  • Zablocki, Olivier; Adriaenssens, Evelien M.; Cowan, Don
  • Applied and Environmental Microbiology, Vol. 82, Issue 3
  • DOI: 10.1128/AEM.02651-15

VIROME: a standard operating procedure for analysis of viral metagenome sequences
journal, July 2012

  • Wommack, K. Eric; Bhavsar, Jaysheel; Polson, Shawn W.
  • Standards in Genomic Sciences, Vol. 6, Issue 3
  • DOI: 10.4056/sigs.2945050

Metagenomic Approaches to Assess Bacteriophages in Various Environmental Niches
journal, May 2017

  • Hayes, Stephen; Mahony, Jennifer; Nauta, Arjen
  • Viruses, Vol. 9, Issue 6
  • DOI: 10.3390/v9060127

Towards quantitative viromics for both double-stranded and single-stranded DNA viruses
journal, January 2016


Exploring Viral Diversity in a Unique South African Soil Habitat
journal, January 2018


Viral tagging reveals discrete populations in Synechococcus viral genome sequence space
journal, July 2014

  • Deng, Li; Ignacio-Espinoza, J. Cesar; Gregory, Ann C.
  • Nature, Vol. 513, Issue 7517
  • DOI: 10.1038/nature13459

Computational approaches to predict bacteriophage–host relationships
journal, December 2015

  • Edwards, Robert A.; McNair, Katelyn; Faust, Karoline
  • FEMS Microbiology Reviews, Vol. 40, Issue 2
  • DOI: 10.1093/femsre/fuv048

VirSorter: mining viral signal from microbial genomic data
journal, January 2015

  • Roux, Simon; Enault, Francois; Hurwitz, Bonnie L.
  • PeerJ, Vol. 3
  • DOI: 10.7717/peerj.985

Embracing the unknown: disentangling the complexities of the soil microbiome
journal, August 2017


Minimum Information about an Uncultivated Virus Genome (MIUViG)
journal, December 2018

  • Roux, Simon; Adriaenssens, Evelien M.; Dutilh, Bas E.
  • Nature Biotechnology, Vol. 37, Issue 1
  • DOI: 10.1038/nbt.4306

Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands
journal, January 2019

  • Warwick-Dugdale, Joanna; Solonenko, Natalie; Moore, Karen
  • PeerJ, Vol. 7
  • DOI: 10.7717/peerj.6800

Metabolic reprogramming by viruses in the sunlit and dark ocean
journal, January 2013


Genome-centric view of carbon processing in thawing permafrost
journal, July 2018


Evaluation of Real-Time PCR Amplification Efficiencies to Detect PCR Inhibitors
journal, July 2006


Prevalence of Lysogeny among Soil Bacteria and Presence of 16S rRNA and trzN Genes in Viral-Community DNA
journal, November 2007

  • Ghosh, D.; Roy, K.; Williamson, K. E.
  • Applied and Environmental Microbiology, Vol. 74, Issue 2
  • DOI: 10.1128/AEM.01435-07

Development of a method to recovery and amplification DNA by real-time PCR from commercial vegetable oils
journal, September 2014


Using MUMmer to Identify Similar Regions in Large Sequence Sets
journal, January 2003

  • Delcher, Arthur L.; Salzberg, Steven L.; Phillippy, Adam M.
  • Current Protocols in Bioinformatics, Vol. 00, Issue 1
  • DOI: 10.1002/0471250953.bi1003s00

Uncovering Earth’s virome
journal, August 2016

  • Paez-Espino, David; Eloe-Fadrosh, Emiley A.; Pavlopoulos, Georgios A.
  • Nature, Vol. 536, Issue 7617
  • DOI: 10.1038/nature19094

Viral ecology comes of age: Crystal ball
journal, February 2017

  • Sullivan, Matthew B.; Weitz, Joshua S.; Wilhelm, Steven
  • Environmental Microbiology Reports, Vol. 9, Issue 1
  • DOI: 10.1111/1758-2229.12504

The Distribution, Evolution, and Roles of Gene Transfer Agents in Prokaryotic Genetic Exchange
journal, September 2017


Sequencing platform and library preparation choices impact viral metagenomes
journal, January 2013

  • Solonenko, Sergei A.; Ignacio-Espinoza, J.; Alberti, Adriana
  • BMC Genomics, Vol. 14, Issue 1
  • DOI: 10.1186/1471-2164-14-320

Viral metagenomics
journal, May 2005

  • Edwards, Robert A.; Rohwer, Forest
  • Nature Reviews Microbiology, Vol. 3, Issue 6
  • DOI: 10.1038/nrmicro1163

Distinct Circular Single-Stranded DNA Viruses Exist in Different Soil Types
journal, April 2015

  • Reavy, Brian; Swanson, Maud M.; Cock, Peter J. A.
  • Applied and Environmental Microbiology, Vol. 81, Issue 12
  • DOI: 10.1128/AEM.03878-14

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
journal, May 2012

  • Bankevich, Anton; Nurk, Sergey; Antipov, Dmitry
  • Journal of Computational Biology, Vol. 19, Issue 5
  • DOI: 10.1089/cmb.2012.0021

The choice of the DNA extraction method may influence the outcome of the soil microbial community structure analysis
journal, February 2017

  • Zielińska, Sylwia; Radkowski, Piotr; Blendowska, Aleksandra
  • MicrobiologyOpen, Vol. 6, Issue 4
  • DOI: 10.1002/mbo3.453

Thawing sub-arctic permafrost: Effects on vegetation and methane emissions
journal, January 2004


Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology
journal, February 2008

  • Binga, Erik K.; Lasken, Roger S.; Neufeld, Josh D.
  • The ISME Journal, Vol. 2, Issue 3
  • DOI: 10.1038/ismej.2008.10

The contentious nature of soil organic matter
journal, November 2015


Multiple displacement amplification compromises quantitative analysis of metagenomes
journal, November 2010

  • Yilmaz, Suzan; Allgaier, Martin; Hugenholtz, Philip
  • Nature Methods, Vol. 7, Issue 12
  • DOI: 10.1038/nmeth1210-943

VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data
journal, July 2017


Decadal vegetation changes in a northern peatland, greenhouse gas fluxes and net radiative forcing
journal, December 2006


MARVEL, a Tool for Prediction of Bacteriophage Sequences in Metagenomic Bins
journal, August 2018


Fast gapped-read alignment with Bowtie 2
journal, March 2012

  • Langmead, Ben; Salzberg, Steven L.
  • Nature Methods, Vol. 9, Issue 4
  • DOI: 10.1038/nmeth.1923

Viral Transmission Dynamics at Single-Cell Resolution Reveal Transiently Immune Subpopulations Caused by a Carrier State Association
journal, December 2015


iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure
journal, July 2016

  • Bolduc, Benjamin; Youens-Clark, Ken; Roux, Simon
  • The ISME Journal, Vol. 11, Issue 1
  • DOI: 10.1038/ismej.2016.89

Viruses in Soil Ecosystems: An Unknown Quantity Within an Unexplored Territory
journal, September 2017


Nanopore sequencing and full genome de novo assembly of human cytomegalovirus TB40/E reveals clonal diversity and structural variations
journal, August 2018


Net carbon accumulation of a high-latitude permafrost palsa mire similar to permafrost-free peatlands: CARBON BALANCE OF A SUBARCTIC PEATLAND
journal, February 2012

  • Olefeldt, David; Roulet, Nigel T.; Bergeron, Onil
  • Geophysical Research Letters, Vol. 39, Issue 3
  • DOI: 10.1029/2011GL050355

Methane dynamics regulated by microbial community response to permafrost thaw
journal, October 2014

  • McCalley, Carmody K.; Woodcroft, Ben J.; Hodgkins, Suzanne B.
  • Nature, Vol. 514, Issue 7523
  • DOI: 10.1038/nature13798

Ocean viruses: Rigorously evaluating the metagenomic sample-to-sequence pipeline
journal, December 2012


Extraction and purification of microbial DNA from soil and sediment samples
journal, September 2001


Plankton networks driving carbon export in the oligotrophic ocean
journal, February 2016

  • Guidi, Lionel; Chaffron, Samuel; Bittner, Lucie
  • Nature, Vol. 532, Issue 7600
  • DOI: 10.1038/nature16942

Comparative Viral Metagenomics of Environmental Samples from Korea
journal, January 2013


Accessing the Soil Metagenome for Studies of Microbial Diversity
journal, December 2010

  • Delmont, Tom O.; Robe, Patrick; Cecillon, Sébastien
  • Applied and Environmental Microbiology, Vol. 77, Issue 4
  • DOI: 10.1128/AEM.01526-10

Evaluation of commercial kits for the extraction and purification of viral nucleic acids from environmental and fecal samples
journal, July 2013


Laboratory procedures to generate viral metagenomes
journal, March 2009

  • Thurber, Rebecca V.; Haynes, Matthew; Breitbart, Mya
  • Nature Protocols, Vol. 4, Issue 4
  • DOI: 10.1038/nprot.2009.10

Optimizing de novo genome assembly from PCR-amplified metagenomes
journal, January 2019


Discovery of a novel methanogen prevalent in thawing permafrost
journal, February 2014

  • Mondav, Rhiannon; Woodcroft, Ben J.; Kim, Eun-Hae
  • Nature Communications, Vol. 5, Issue 1
  • DOI: 10.1038/ncomms4212

Environmental Monitoring and Research in the Abisko Area—An Overview
journal, July 2012


Quantifying aquatic viral community change associated with stormwater runoff in a wet retention pond using metagenomic time series data
journal, January 2018

  • Green, Jc; Rahman, F.; Saxton, Ma
  • Aquatic Microbial Ecology, Vol. 81, Issue 1
  • DOI: 10.3354/ame01856

Diversity of DNA and RNA Viruses in Indoor Air As Assessed via Metagenomic Sequencing
journal, January 2018

  • Rosario, Karyna; Fierer, Noah; Miller, Shelly
  • Environmental Science & Technology, Vol. 52, Issue 3
  • DOI: 10.1021/acs.est.7b04203

Metagenomic and Small-Subunit rRNA Analyses Reveal the Genetic Diversity of Bacteria, Archaea, Fungi, and Viruses in Soil
journal, September 2007

  • Fierer, N.; Breitbart, M.; Nulton, J.
  • Applied and Environmental Microbiology, Vol. 73, Issue 21
  • DOI: 10.1128/AEM.00358-07

Interrogating marine virus-host interactions and elemental transfer with BONCAT and nanoSIMS-based methods: BONCAT and nanoSIMS measurements of viruses
journal, December 2017

  • Pasulka, Alexis L.; Thamatrakoln, Kimberlee; Kopf, Sebastian H.
  • Environmental Microbiology, Vol. 20, Issue 2
  • DOI: 10.1111/1462-2920.13996

    Works referencing / citing this record:

    Using MUMmer to Identify Similar Regions in Large Sequence Sets
    journal, January 2003

    • Delcher, Arthur L.; Salzberg, Steven L.; Phillippy, Adam M.
    • Current Protocols in Bioinformatics, Vol. 00, Issue 1
    • DOI: 10.1002/0471250953.bi1003s00

    The choice of the DNA extraction method may influence the outcome of the soil microbial community structure analysis
    journal, February 2017

    • Zielińska, Sylwia; Radkowski, Piotr; Blendowska, Aleksandra
    • MicrobiologyOpen, Vol. 6, Issue 4
    • DOI: 10.1002/mbo3.453

    Detection of genetically modified soybean DNA in refined vegetable oils
    journal, February 2010

    • Costa, Joana; Mafra, Isabel; Amaral, Joana S.
    • European Food Research and Technology, Vol. 230, Issue 6
    • DOI: 10.1007/s00217-010-1238-2

    An efficient and cost-effective method for DNA extraction from athalassohaline soil using a newly formulated cell extraction buffer
    journal, February 2016


    Comparative assessment of methods for metagenomic DNA isolation from soils of different crop growing fields
    journal, October 2016


    Environmental Monitoring and Research in the Abisko Area—An Overview
    journal, July 2012


    Marine DNA Viral Macro- and Microdiversity from Pole to Pole
    journal, May 2019


    Development of a method to recovery and amplification DNA by real-time PCR from commercial vegetable oils
    journal, September 2014


    Forensic implications of PCR inhibition—A review
    journal, May 2012


    Evaluation of commercial kits for the extraction and purification of viral nucleic acids from environmental and fecal samples
    journal, July 2013


    Fake virus particles generated by fluorescence microscopy
    journal, January 2013


    The ‘Neglected’ Soil Virome – Potential Role and Impact
    journal, August 2018


    Ocean viruses: Rigorously evaluating the metagenomic sample-to-sequence pipeline
    journal, December 2012


    High Initial Sputter Rate Found for Vaccinia Virions Using Isotopic Labeling, NanoSIMS, and AFM
    journal, January 2018


    Diversity of DNA and RNA Viruses in Indoor Air As Assessed via Metagenomic Sequencing
    journal, January 2018

    • Rosario, Karyna; Fierer, Noah; Miller, Shelly
    • Environmental Science & Technology, Vol. 52, Issue 3
    • DOI: 10.1021/acs.est.7b04203

    Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology
    journal, February 2008

    • Binga, Erik K.; Lasken, Roger S.; Neufeld, Josh D.
    • The ISME Journal, Vol. 2, Issue 3
    • DOI: 10.1038/ismej.2008.10

    Diversity of environmental single-stranded DNA phages revealed by PCR amplification of the partial major capsid protein
    journal, April 2014

    • Hopkins, Max; Kailasan, Shweta; Cohen, Allison
    • The ISME Journal, Vol. 8, Issue 10
    • DOI: 10.1038/ismej.2014.43

    iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure
    journal, July 2016

    • Bolduc, Benjamin; Youens-Clark, Ken; Roux, Simon
    • The ISME Journal, Vol. 11, Issue 1
    • DOI: 10.1038/ismej.2016.89

    Viral tagging reveals discrete populations in Synechococcus viral genome sequence space
    journal, July 2014

    • Deng, Li; Ignacio-Espinoza, J. Cesar; Gregory, Ann C.
    • Nature, Vol. 513, Issue 7517
    • DOI: 10.1038/nature13459

    Methane dynamics regulated by microbial community response to permafrost thaw
    journal, October 2014

    • McCalley, Carmody K.; Woodcroft, Ben J.; Hodgkins, Suzanne B.
    • Nature, Vol. 514, Issue 7523
    • DOI: 10.1038/nature13798

    The contentious nature of soil organic matter
    journal, November 2015


    Plankton networks driving carbon export in the oligotrophic ocean
    journal, February 2016

    • Guidi, Lionel; Chaffron, Samuel; Bittner, Lucie
    • Nature, Vol. 532, Issue 7600
    • DOI: 10.1038/nature16942

    Uncovering Earth’s virome
    journal, August 2016

    • Paez-Espino, David; Eloe-Fadrosh, Emiley A.; Pavlopoulos, Georgios A.
    • Nature, Vol. 536, Issue 7617
    • DOI: 10.1038/nature19094

    Minimum Information about an Uncultivated Virus Genome (MIUViG)
    journal, December 2018

    • Roux, Simon; Adriaenssens, Evelien M.; Dutilh, Bas E.
    • Nature Biotechnology, Vol. 37, Issue 1
    • DOI: 10.1038/nbt.4306

    Discovery of a novel methanogen prevalent in thawing permafrost
    journal, February 2014

    • Mondav, Rhiannon; Woodcroft, Ben J.; Kim, Eun-Hae
    • Nature Communications, Vol. 5, Issue 1
    • DOI: 10.1038/ncomms4212

    Viruses as new agents of organomineralization in the geological record
    journal, July 2014

    • Pacton, Muriel; Wacey, David; Corinaldesi, Cinzia
    • Nature Communications, Vol. 5, Issue 1
    • DOI: 10.1038/ncomms5298

    Fast gapped-read alignment with Bowtie 2
    journal, March 2012

    • Langmead, Ben; Salzberg, Steven L.
    • Nature Methods, Vol. 9, Issue 4
    • DOI: 10.1038/nmeth.1923

    Multiple displacement amplification compromises quantitative analysis of metagenomes
    journal, November 2010

    • Yilmaz, Suzan; Allgaier, Martin; Hugenholtz, Philip
    • Nature Methods, Vol. 7, Issue 12
    • DOI: 10.1038/nmeth1210-943

    Laboratory procedures to generate viral metagenomes
    journal, March 2009

    • Thurber, Rebecca V.; Haynes, Matthew; Breitbart, Mya
    • Nature Protocols, Vol. 4, Issue 4
    • DOI: 10.1038/nprot.2009.10

    Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data
    journal, July 2017

    • Paez-Espino, David; Pavlopoulos, Georgios A.; Ivanova, Natalia N.
    • Nature Protocols, Vol. 12, Issue 8
    • DOI: 10.1038/nprot.2017.063

    Embracing the unknown: disentangling the complexities of the soil microbiome
    journal, August 2017


    Viral metagenomics
    journal, May 2005

    • Edwards, Robert A.; Rohwer, Forest
    • Nature Reviews Microbiology, Vol. 3, Issue 6
    • DOI: 10.1038/nrmicro1163

    Rising to the challenge: accelerated pace of discovery transforms marine virology
    journal, February 2015

    • Brum, Jennifer R.; Sullivan, Matthew B.
    • Nature Reviews Microbiology, Vol. 13, Issue 3
    • DOI: 10.1038/nrmicro3404

    Host-linked soil viral ecology along a permafrost thaw gradient
    journal, July 2018


    Genome-centric view of carbon processing in thawing permafrost
    journal, July 2018


    Exploring Viral Diversity in a Unique South African Soil Habitat
    journal, January 2018


    Changes in peat chemistry associated with permafrost thaw increase greenhouse gas production
    journal, April 2014

    • Hodgkins, S. B.; Tfaily, M. M.; McCalley, C. K.
    • Proceedings of the National Academy of Sciences, Vol. 111, Issue 16
    • DOI: 10.1073/pnas.1314641111

    The Effect of Preprocessing by Sequence-Independent, Single-Primer Amplification (SISPA) on Metagenomic Detection of Viruses
    journal, September 2013

    • Karlsson, Oskar Erik; Belák, Sándor; Granberg, Fredrik
    • Biosecurity and Bioterrorism: Biodefense Strategy, Practice, and Science, Vol. 11, Issue S1
    • DOI: 10.1089/bsp.2013.0008

    SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
    journal, May 2012

    • Bankevich, Anton; Nurk, Sergey; Antipov, Dmitry
    • Journal of Computational Biology, Vol. 19, Issue 5
    • DOI: 10.1089/cmb.2012.0021

    Trimmomatic: a flexible trimmer for Illumina sequence data
    journal, April 2014


    Dynamics of autochthonous soil viral communities parallels dynamics of host communities under nutrient stimulation
    journal, July 2015

    • Srinivasiah, Sharath; Lovett, Jacqueline; Ghosh, Dhritiman
    • FEMS Microbiology Ecology, Vol. 91, Issue 7
    • DOI: 10.1093/femsec/fiv063

    Computational approaches to predict bacteriophage–host relationships
    journal, December 2015

    • Edwards, Robert A.; McNair, Katelyn; Faust, Karoline
    • FEMS Microbiology Reviews, Vol. 40, Issue 2
    • DOI: 10.1093/femsre/fuv048

    Assessment of viral community functional potential from viral metagenomes may be hampered by contamination with cellular sequences
    journal, December 2013

    • Roux, Simon; Krupovic, Mart; Debroas, Didier
    • Open Biology, Vol. 3, Issue 12
    • DOI: 10.1098/rsob.130160

    Microbial network, phylogenetic diversity and community membership in the active layer across a permafrost thaw gradient
    journal, July 2017

    • Mondav, Rhiannon; McCalley, Carmody K.; Hodgkins, Suzanne B.
    • Environmental Microbiology, Vol. 19, Issue 8
    • DOI: 10.1111/1462-2920.13809

    Interrogating marine virus-host interactions and elemental transfer with BONCAT and nanoSIMS-based methods: BONCAT and nanoSIMS measurements of viruses
    journal, December 2017

    • Pasulka, Alexis L.; Thamatrakoln, Kimberlee; Kopf, Sebastian H.
    • Environmental Microbiology, Vol. 20, Issue 2
    • DOI: 10.1111/1462-2920.13996

    Viral ecology comes of age: Crystal ball
    journal, February 2017

    • Sullivan, Matthew B.; Weitz, Joshua S.; Wilhelm, Steven
    • Environmental Microbiology Reports, Vol. 9, Issue 1
    • DOI: 10.1111/1758-2229.12504

    Decadal vegetation changes in a northern peatland, greenhouse gas fluxes and net radiative forcing
    journal, December 2006


    Evaluation of Real-Time PCR Amplification Efficiencies to Detect PCR Inhibitors
    journal, July 2006


    Patterns and ecological drivers of ocean viral communities
    journal, May 2015


    The Distribution, Evolution, and Roles of Gene Transfer Agents in Prokaryotic Genetic Exchange
    journal, September 2017


    Viruses in Soil Ecosystems: An Unknown Quantity Within an Unexplored Territory
    journal, September 2017


    Sequencing platform and library preparation choices impact viral metagenomes
    journal, January 2013

    • Solonenko, Sergei A.; Ignacio-Espinoza, J.; Alberti, Adriana
    • BMC Genomics, Vol. 14, Issue 1
    • DOI: 10.1186/1471-2164-14-320

    Metabolic reprogramming by viruses in the sunlit and dark ocean
    journal, January 2013


    Nanopore sequencing and full genome de novo assembly of human cytomegalovirus TB40/E reveals clonal diversity and structural variations
    journal, August 2018


    VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data
    journal, July 2017


    Viral Transmission Dynamics at Single-Cell Resolution Reveal Transiently Immune Subpopulations Caused by a Carrier State Association
    journal, December 2015


    Chemical Composition of Soil Organic Matter in a Subarctic Peatland: Influence of Shifting Vegetation Communities
    journal, January 2017

    • Normand, Anna E.; Smith, Adam N.; Clark, Mark W.
    • Soil Science Society of America Journal, Vol. 81, Issue 1
    • DOI: 10.2136/sssaj2016.05.0148

    Quantifying aquatic viral community change associated with stormwater runoff in a wet retention pond using metagenomic time series data
    journal, January 2018

    • Green, Jc; Rahman, F.; Saxton, Ma
    • Aquatic Microbial Ecology, Vol. 81, Issue 1
    • DOI: 10.3354/ame01856

    MARVEL, a Tool for Prediction of Bacteriophage Sequences in Metagenomic Bins
    journal, August 2018


    Metagenomic Approaches to Assess Bacteriophages in Various Environmental Niches
    journal, May 2017

    • Hayes, Stephen; Mahony, Jennifer; Nauta, Arjen
    • Viruses, Vol. 9, Issue 6
    • DOI: 10.3390/v9060127

    VIROME: a standard operating procedure for analysis of viral metagenome sequences
    journal, July 2012

    • Wommack, K. Eric; Bhavsar, Jaysheel; Polson, Shawn W.
    • Standards in Genomic Sciences, Vol. 6, Issue 3
    • DOI: 10.4056/sigs.2945050

    Murphy's law—if anything can go wrong, it will: Problems in phage electron microscopy
    journal, April 2012

    • Ackermann, Hans-W.; Tiekotter, Kenneth L.
    • Bacteriophage, Vol. 2, Issue 2
    • DOI: 10.4161/bact.20693

    Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient
    journal, January 2016

    • Trubl, Gareth; Solonenko, Natalie; Chittick, Lauren
    • PeerJ, Vol. 4
    • DOI: 10.7717/peerj.1999

    Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics
    journal, January 2016


    Towards quantitative viromics for both double-stranded and single-stranded DNA viruses
    journal, January 2016


    Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity
    journal, January 2017

    • Roux, Simon; Emerson, Joanne B.; Eloe-Fadrosh, Emiley A.
    • PeerJ, Vol. 5
    • DOI: 10.7717/peerj.3817

    Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands
    journal, January 2019

    • Warwick-Dugdale, Joanna; Solonenko, Natalie; Moore, Karen
    • PeerJ, Vol. 7
    • DOI: 10.7717/peerj.6800

    Optimizing de novo genome assembly from PCR-amplified metagenomes
    journal, January 2019


    VirSorter: mining viral signal from microbial genomic data
    journal, January 2015

    • Roux, Simon; Enault, Francois; Hurwitz, Bonnie L.
    • PeerJ, Vol. 3
    • DOI: 10.7717/peerj.985