Search Menu
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information
Search Scholarly Publications

Title: Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing

Abstract

ABSTRACT Rapidly thawing permafrost harbors ∼30 to 50% of global soil carbon, and the fate of this carbon remains unknown. Microorganisms will play a central role in its fate, and their viruses could modulate that impact via induced mortality and metabolic controls. Because of the challenges of recovering viruses from soils, little is known about soil viruses or their role(s) in microbial biogeochemical cycling. Here, we describe 53 viral populations (viral operational taxonomic units [vOTUs]) recovered from seven quantitatively derived (i.e., not multiple-displacement-amplified) viral-particle metagenomes (viromes) along a permafrost thaw gradient at the Stordalen Mire field site in northern Sweden. Only 15% of these vOTUs had genetic similarity to publicly available viruses in the RefSeq database, and ∼30% of the genes could be annotated, supporting the concept of soils as reservoirs of substantial undescribed viral genetic diversity. The vOTUs exhibited distinct ecology, with different distributions along the thaw gradient habitats, and a shift from soil-virus-like assemblages in the dry palsas to aquatic-virus-like assemblages in the inundated fen. Seventeen vOTUs were linked to microbial hosts ( in silico ), implicating viruses in infecting abundant microbial lineages from Acidobacteria , Verrucomicrobia , and Deltaproteobacteria , including those encoding key biogeochemical functions suchmore » as organic matter degradation. Thirty auxiliary metabolic genes (AMGs) were identified and suggested virus-mediated modulation of central carbon metabolism, soil organic matter degradation, polysaccharide binding, and regulation of sporulation. Together, these findings suggest that these soil viruses have distinct ecology, impact host-mediated biogeochemistry, and likely impact ecosystem function in the rapidly changing Arctic. IMPORTANCE This work is part of a 10-year project to examine thawing permafrost peatlands and is the first virome-particle-based approach to characterize viruses in these systems. This method yielded >2-fold-more viral populations (vOTUs) per gigabase of metagenome than vOTUs derived from bulk-soil metagenomes from the same site (J. B. Emerson, S. Roux, J. R. Brum, B. Bolduc, et al., Nat Microbiol 3:870–880, 2018, https://doi.org/10.1038/s41564-018-0190-y). We compared the ecology of the recovered vOTUs along a permafrost thaw gradient and found (i) habitat specificity, (ii) a shift in viral community identity from soil-like to aquatic-like viruses, (iii) infection of dominant microbial hosts, and (iv) carriage of host metabolic genes. These vOTUs can impact ecosystem carbon processing via top-down (inferred from lysing dominant microbial hosts) and bottom-up (inferred from carriage of auxiliary metabolic genes) controls. This work serves as a foundation which future studies can build upon to increase our understanding of the soil virosphere and how viruses affect soil ecosystem services.« less

Authors:
ORCiD logo; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1475081
Alternate Identifier(s):
OSTI ID: 1506353
Grant/Contract Number:  
SC0004632; SC0010580; SC0016440; AC02-05CH11231
Resource Type:
Published Article
Journal Name:
mSystems
Additional Journal Information:
Journal Name: mSystems Journal Volume: 3 Journal Issue: 5; Journal ID: ISSN 2379-5077
Publisher:
American Society for Microbiology
Country of Publication:
United States
Language:
English
Subject:
54 ENVIRONMENTAL SCIENCES; 59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Trubl, Gareth, Jang, Ho Bin, Roux, Simon, Emerson, Joanne B., Solonenko, Natalie, Vik, Dean R., Solden, Lindsey, Ellenbogen, Jared, Runyon, Alexander T., Bolduc, Benjamin, Woodcroft, Ben J., Saleska, Scott R., Tyson, Gene W., Wrighton, Kelly C., Sullivan, Matthew B., Rich, Virginia I., and Bordenstein, ed., Seth. Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing. United States: N. p., 2018. Web. doi:10.1128/mSystems.00076-18.
Copy to clipboard
Trubl, Gareth, Jang, Ho Bin, Roux, Simon, Emerson, Joanne B., Solonenko, Natalie, Vik, Dean R., Solden, Lindsey, Ellenbogen, Jared, Runyon, Alexander T., Bolduc, Benjamin, Woodcroft, Ben J., Saleska, Scott R., Tyson, Gene W., Wrighton, Kelly C., Sullivan, Matthew B., Rich, Virginia I., & Bordenstein, ed., Seth. Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing. United States. https://doi.org/10.1128/mSystems.00076-18
Copy to clipboard
Trubl, Gareth, Jang, Ho Bin, Roux, Simon, Emerson, Joanne B., Solonenko, Natalie, Vik, Dean R., Solden, Lindsey, Ellenbogen, Jared, Runyon, Alexander T., Bolduc, Benjamin, Woodcroft, Ben J., Saleska, Scott R., Tyson, Gene W., Wrighton, Kelly C., Sullivan, Matthew B., Rich, Virginia I., and Bordenstein, ed., Seth. Tue . "Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing". United States. https://doi.org/10.1128/mSystems.00076-18.
Copy to clipboard
@article{osti_1475081,
title = {Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing},
author = {Trubl, Gareth and Jang, Ho Bin and Roux, Simon and Emerson, Joanne B. and Solonenko, Natalie and Vik, Dean R. and Solden, Lindsey and Ellenbogen, Jared and Runyon, Alexander T. and Bolduc, Benjamin and Woodcroft, Ben J. and Saleska, Scott R. and Tyson, Gene W. and Wrighton, Kelly C. and Sullivan, Matthew B. and Rich, Virginia I. and Bordenstein, ed., Seth},
abstractNote = {ABSTRACT Rapidly thawing permafrost harbors ∼30 to 50% of global soil carbon, and the fate of this carbon remains unknown. Microorganisms will play a central role in its fate, and their viruses could modulate that impact via induced mortality and metabolic controls. Because of the challenges of recovering viruses from soils, little is known about soil viruses or their role(s) in microbial biogeochemical cycling. Here, we describe 53 viral populations (viral operational taxonomic units [vOTUs]) recovered from seven quantitatively derived (i.e., not multiple-displacement-amplified) viral-particle metagenomes (viromes) along a permafrost thaw gradient at the Stordalen Mire field site in northern Sweden. Only 15% of these vOTUs had genetic similarity to publicly available viruses in the RefSeq database, and ∼30% of the genes could be annotated, supporting the concept of soils as reservoirs of substantial undescribed viral genetic diversity. The vOTUs exhibited distinct ecology, with different distributions along the thaw gradient habitats, and a shift from soil-virus-like assemblages in the dry palsas to aquatic-virus-like assemblages in the inundated fen. Seventeen vOTUs were linked to microbial hosts ( in silico ), implicating viruses in infecting abundant microbial lineages from Acidobacteria , Verrucomicrobia , and Deltaproteobacteria , including those encoding key biogeochemical functions such as organic matter degradation. Thirty auxiliary metabolic genes (AMGs) were identified and suggested virus-mediated modulation of central carbon metabolism, soil organic matter degradation, polysaccharide binding, and regulation of sporulation. Together, these findings suggest that these soil viruses have distinct ecology, impact host-mediated biogeochemistry, and likely impact ecosystem function in the rapidly changing Arctic. IMPORTANCE This work is part of a 10-year project to examine thawing permafrost peatlands and is the first virome-particle-based approach to characterize viruses in these systems. This method yielded >2-fold-more viral populations (vOTUs) per gigabase of metagenome than vOTUs derived from bulk-soil metagenomes from the same site (J. B. Emerson, S. Roux, J. R. Brum, B. Bolduc, et al., Nat Microbiol 3:870–880, 2018, https://doi.org/10.1038/s41564-018-0190-y). We compared the ecology of the recovered vOTUs along a permafrost thaw gradient and found (i) habitat specificity, (ii) a shift in viral community identity from soil-like to aquatic-like viruses, (iii) infection of dominant microbial hosts, and (iv) carriage of host metabolic genes. These vOTUs can impact ecosystem carbon processing via top-down (inferred from lysing dominant microbial hosts) and bottom-up (inferred from carriage of auxiliary metabolic genes) controls. This work serves as a foundation which future studies can build upon to increase our understanding of the soil virosphere and how viruses affect soil ecosystem services.},
doi = {10.1128/mSystems.00076-18},
journal = {mSystems},
number = 5,
volume = 3,
place = {United States},
year = {Tue Oct 02 00:00:00 EDT 2018},
month = {Tue Oct 02 00:00:00 EDT 2018}
}
Copy to clipboard
Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1128/mSystems.00076-18
Copyright Statement
Other availability
Search WorldCat Search WorldCat to find libraries that may hold this journal
Citation Metrics:
Cited by: 115 works
Citation information provided by
Web of Science
Save / Share:
Export Metadata
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.

Works referenced in this record:

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

Pattern Recognition Receptors and the Innate Immune Response to Viral Infection
journal, June 2011

  • Thompson, Mikayla R.; Kaminski, John J.; Kurt-Jones, Evelyn A.
  • Viruses, Vol. 3, Issue 6
  • DOI: 10.3390/v3060920

Sulfur Oxidation Genes in Diverse Deep-Sea Viruses
journal, May 2014

Brine Assemblages of Ultrasmall Microbial Cells within the Ice Cover of Lake Vida, Antarctica
journal, April 2014

  • Kuhn, Emanuele; Ichimura, Andrew S.; Peng, Vivian
  • Applied and Environmental Microbiology, Vol. 80, Issue 12
  • DOI: 10.1128/AEM.00276-14

TM-align: a protein structure alignment algorithm based on the TM-score
journal, April 2005

Estimates of viral abundance in soils are strongly influenced by extraction and enumeration methods
journal, February 2013

  • Williamson, Kurt E.; Corzo, Krysten A.; Drissi, Camelia L.
  • Biology and Fertility of Soils, Vol. 49, Issue 7
  • DOI: 10.1007/s00374-013-0780-z

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

Depth-stratified functional and taxonomic niche specialization in the ‘core’ and ‘flexible’ Pacific Ocean Virome
journal, August 2014

  • Hurwitz, Bonnie L.; Brum, Jennifer R.; Sullivan, Matthew B.
  • The ISME Journal, Vol. 9, Issue 2
  • DOI: 10.1038/ismej.2014.143

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

High Resolution Mapping of Peatland Hydroperiod at a High-Latitude Swedish Mire
journal, June 2012

  • Torbick, Nathan; Persson, Andreas; Olefeldt, David
  • Remote Sensing, Vol. 4, Issue 7
  • DOI: 10.3390/rs4071974

Gene and translation initiation site prediction in metagenomic sequences
journal, July 2012

The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families
journal, March 2007

Reticulate Representation of Evolutionary and Functional Relationships between Phage Genomes
journal, February 2008

  • Lima-Mendez, G.; Van Helden, J.; Toussaint, A.
  • Molecular Biology and Evolution, Vol. 25, Issue 4
  • DOI: 10.1093/molbev/msn023

Effect of soil moisture on the release of organic carbon from wheat roots
journal, January 1977

Improved Attribution of Climate Forcing to Emissions
journal, October 2009

Cellulolytic bacteria from soils in harsh environments
journal, February 2012

  • Soares, Fábio Lino; Melo, Itamar Soares; Dias, Armando Cavalcante Franco
  • World Journal of Microbiology and Biotechnology, Vol. 28, Issue 5
  • DOI: 10.1007/s11274-012-1025-2

KEGG: Kyoto Encyclopedia of Genes and Genomes
journal, January 2000

  • Kanehisa, Minoru; Goto, Susumu
  • Nucleic Acids Research, Vol. 28, Issue 1, p. 27-30
  • DOI: 10.1093/nar/28.1.27

NCBI Viral Genomes Resource
journal, November 2014

  • Brister, J. Rodney; Ako-adjei, Danso; Bao, Yiming
  • Nucleic Acids Research, Vol. 43, Issue D1
  • DOI: 10.1093/nar/gku1207

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

Adding stable carbon isotopes improves model representation of the role of microbial communities in peatland methane cycling
journal, May 2017

  • Deng, Jia; McCalley, Carmody K.; Frolking, Steve
  • Journal of Advances in Modeling Earth Systems, Vol. 9, Issue 2
  • DOI: 10.1002/2016MS000817

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible
journal, April 2014

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

Genome Sequence of "Pedosphaera parvula" Ellin514, an Aerobic Verrucomicrobial Isolate from Pasture Soil
journal, April 2011

  • Kant, R.; van Passel, M. W. J.; Sangwan, P.
  • Journal of Bacteriology, Vol. 193, Issue 11
  • DOI: 10.1128/JB.00299-11

Metagenomic Analysis of a Southern Maritime Antarctic Soil
journal, January 2012

  • Pearce, David A.; Newsham, Kevin K.; Thorne, Michael A. S.
  • Frontiers in Microbiology, Vol. 3
  • DOI: 10.3389/fmicb.2012.00403

Marine viruses — major players in the global ecosystem
journal, October 2007

The genomic content and context of auxiliary metabolic genes in marine cyanomyoviruses
journal, December 2016

Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation
journal, October 2006

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

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

Exploring the viral world through metagenomics
journal, October 2011

Dark Matter of the Biosphere: the Amazing World of Bacteriophage Diversity
journal, May 2015

Linking habitat modification to catastrophic shifts and vegetation patterns in bogs
journal, June 2007

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

Are we missing half of the viruses in the ocean?
journal, November 2012

  • Steward, Grieg F.; Culley, Alexander I.; Mueller, Jaclyn A.
  • The ISME Journal, Vol. 7, Issue 3
  • DOI: 10.1038/ismej.2012.121

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

Viruses from extreme thermal environments
journal, October 2001

  • Rice, G.; Stedman, K.; Snyder, J.
  • Proceedings of the National Academy of Sciences, Vol. 98, Issue 23
  • DOI: 10.1073/pnas.231170198

The soil microbiome — from metagenomics to metaphenomics
journal, June 2018

The I-TASSER Suite: protein structure and function prediction
journal, December 2014

  • Yang, Jianyi; Yan, Renxiang; Roy, Ambrish
  • Nature Methods, Vol. 12, Issue 1
  • DOI: 10.1038/nmeth.3213

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

Vegetation, climatic changes and net carbon sequestration in a North-Scandinavian subarctic mire over 30 years
journal, October 2005

Greenhouse gas balance over thaw-freeze cycles in discontinuous zone permafrost: C Balance of Permafrost Peat
journal, February 2017

  • Wilson, R. M.; Fitzhugh, L.; Whiting, G. J.
  • Journal of Geophysical Research: Biogeosciences, Vol. 122, Issue 2
  • DOI: 10.1002/2016JG003600

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

Seascapes as a new vernacular for pelagic ocean monitoring, management and conservation
journal, July 2016

  • Kavanaugh, Maria T.; Oliver, Matthew J.; Chavez, Francisco P.
  • ICES Journal of Marine Science: Journal du Conseil, Vol. 73, Issue 7
  • DOI: 10.1093/icesjms/fsw086

Viral dynamics and patterns of lysogeny in saline Antarctic lakes
journal, August 2006

  • Laybourn-Parry, Johanna; Marshall, William A.; Madan, Nanette J.
  • Polar Biology, Vol. 30, Issue 3
  • DOI: 10.1007/s00300-006-0191-9

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

Environmental drivers of viral community composition in Antarctic soils identified by viromics
journal, July 2017

Viruses in the sea
journal, September 2005

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

Peat: home to novel syntrophic species that feed acetate- and hydrogen-scavenging methanogens
journal, January 2016

  • Schmidt, Oliver; Hink, Linda; Horn, Marcus A.
  • The ISME Journal, Vol. 10, Issue 8
  • DOI: 10.1038/ismej.2015.256

Annual carbon gas budget for a subarctic peatland, Northern Sweden
journal, January 2010

  • Bäckstrand, K.; Crill, P. M.; Jackowicz-Korczyñski, M.
  • Biogeosciences, Vol. 7, Issue 1
  • DOI: 10.5194/bg-7-95-2010

Phages across the biosphere: contrasts of viruses in soil and aquatic environments
journal, June 2008

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

vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria
journal, January 2017

MUSCLE: multiple sequence alignment with high accuracy and high throughput
journal, March 2004

  • Edgar, R. C.
  • Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797
  • DOI: 10.1093/nar/gkh340

Using Metagenomics to Characterize an Expanding Virosphere
journal, March 2018

A global atlas of the dominant bacteria found in soil
journal, January 2018

  • Delgado-Baquerizo, Manuel; Oliverio, Angela M.; Brewer, Tess E.
  • Science, Vol. 359, Issue 6373
  • DOI: 10.1126/science.aap9516

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix
journal, April 2009

  • Price, M. N.; Dehal, P. S.; Arkin, A. P.
  • Molecular Biology and Evolution, Vol. 26, Issue 7
  • DOI: 10.1093/molbev/msp077

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

Comparative activity and functional ecology of permafrost soils and lithic niches in a hyper-arid polar desert: Ecology of Dry Valley permafrost and cryptoendoliths
journal, June 2016

  • Goordial, Jacqueline; Davila, Alfonso; Greer, Charles W.
  • Environmental Microbiology, Vol. 19, Issue 2
  • DOI: 10.1111/1462-2920.13353

The Ecology of Acidobacteria: Moving beyond Genes and Genomes
journal, May 2016

  • Kielak, Anna M.; Barreto, Cristine C.; Kowalchuk, George A.
  • Frontiers in Microbiology, Vol. 7
  • DOI: 10.3389/fmicb.2016.00744

Hydrogenation of organic matter as a terminal electron sink sustains high CO2:CH4 production ratios during anaerobic decomposition
journal, October 2017

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

The population biology of bacterial viruses: Why be temperate
journal, August 1984

Biological species in the viral world
journal, May 2018

  • Bobay, Louis-Marie; Ochman, Howard
  • Proceedings of the National Academy of Sciences, Vol. 115, Issue 23
  • DOI: 10.1073/pnas.1717593115

Soil organic carbon pools in the northern circumpolar permafrost region: SOIL ORGANIC CARBON POOLS
journal, June 2009

  • Tarnocai, C.; Canadell, J. G.; Schuur, E. A. G.
  • Global Biogeochemical Cycles, Vol. 23, Issue 2
  • DOI: 10.1029/2008GB003327

Seasonal time bombs: dominant temperate viruses affect Southern Ocean microbial dynamics
journal, August 2015

  • Brum, Jennifer R.; Hurwitz, Bonnie L.; Schofield, Oscar
  • The ISME Journal, Vol. 10, Issue 2
  • DOI: 10.1038/ismej.2015.125

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

A myovirus encoding both photosystem I and II proteins enhances cyclic electron flow in infected Prochlorococcus cells
journal, August 2017

  • Fridman, Svetlana; Flores-Uribe, José; Larom, Shirley
  • Nature Microbiology, Vol. 2, Issue 10
  • DOI: 10.1038/s41564-017-0002-9

What Determines the Current Presence or Absence of Permafrost in the Torneträsk Region, a Sub-arctic Landscape in Northern Sweden?
journal, June 2006

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 Genomics of Cluster O Mycobacteriophages
journal, March 2015

Climate change and the permafrost carbon feedback
journal, April 2015

  • Schuur, E. A. G.; McGuire, A. D.; Schädel, C.
  • Nature, Vol. 520, Issue 7546
  • DOI: 10.1038/nature14338

Genes for the establishment and maintenance of lysogeny by the temperate coliphage 186.
journal, August 1993

InterProScan: protein domains identifier
journal, July 2005

  • Quevillon, E.; Silventoinen, V.; Pillai, S.
  • Nucleic Acids Research, Vol. 33, Issue Web Server
  • DOI: 10.1093/nar/gki442

Regional Variation in Lytic and Lysogenic Viral Infection in the Southern Ocean and Its Contribution to Biogeochemical Cycling
journal, July 2012

  • Evans, Claire; Brussaard, Corina P. D.
  • Applied and Environmental Microbiology, Vol. 78, Issue 18
  • DOI: 10.1128/AEM.01388-12

Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer
journal, November 2016

  • Gregory, Ann C.; Solonenko, Sergei A.; Ignacio-Espinoza, J. Cesar
  • BMC Genomics, Vol. 17, Issue 1
  • DOI: 10.1186/s12864-016-3286-x

Peripheral Blood Mononuclear Cell Gene Expression Remains Broadly Altered Years after Successful Interferon-Based Hepatitis C Virus Treatment
journal, January 2015

  • Waldron, Paul Ravi; Holodniy, Mark
  • Journal of Immunology Research, Vol. 2015
  • DOI: 10.1155/2015/958231

Distinct Anaerobic Bacterial Consumers of Cellobiose-Derived Carbon in Boreal Fens with Different CO 2 /CH 4 Production Ratios
journal, December 2016

  • Juottonen, Heli; Eiler, Alexander; Biasi, Christina
  • Applied and Environmental Microbiology, Vol. 83, Issue 4
  • DOI: 10.1128/AEM.02533-16

High-Level Diversity of Tailed Phages, Eukaryote-Associated Viruses, and Virophage-Like Elements in the Metaviromes of Antarctic Soils
journal, August 2014

  • Zablocki, Olivier; van Zyl, Lonnie; Adriaenssens, Evelien M.
  • Applied and Environmental Microbiology, Vol. 80, Issue 22
  • DOI: 10.1128/AEM.01525-14

Unraveling the viral tapestry (from inside the capsid out)
journal, June 2010

  • Polson, Shawn W.; Wilhelm, Steven W.; Wommack, K. Eric
  • The ISME Journal, Vol. 5, Issue 2
  • DOI: 10.1038/ismej.2010.81

Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales
journal, September 2016

To kill or not to kill: The balance between lytic and lysogenic viral infection is driven by trophic status
journal, February 2013

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

Niche-dependent genetic diversity in Antarctic metaviromes
journal, December 2014

Identification and characterization of sporulation gene spoVS from Bacillus subtilis.
journal, October 1995

Large uncertainty in permafrost carbon stocks due to hillslope soil deposits: HILLSLOPE, PERMAFROST, SOC
journal, June 2017

  • Shelef, Eitan; Rowland, Joel C.; Wilson, Cathy J.
  • Geophysical Research Letters, Vol. 44, Issue 12
  • DOI: 10.1002/2017GL073823

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

A simple and efficient method for concentration of ocean viruses by chemical flocculation: Virus concentration by flocculation with iron
journal, August 2010

Dietary energy drives the dynamic response of bovine rumen viral communities
journal, November 2017

  • Anderson, Christopher L.; Sullivan, Matthew B.; Fernando, Samodha C.
  • Microbiome, Vol. 5, Issue 1
  • DOI: 10.1186/s40168-017-0374-3

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

Putative archaeal viruses from the mesopelagic ocean
journal, January 2017

The under-recognized dominance of Verrucomicrobia in soil bacterial communities
journal, July 2011

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses
journal, September 2016

  • Roux, Simon; Brum, Jennifer R.; Dutilh, Bas E.
  • Nature, Vol. 537, Issue 7622
  • DOI: 10.1038/nature19366

Ecology of viruses in soils: Past, present and future perspectives
journal, February 2008

Bioreactor virome metagenomics sequencing using DNA spike-ins
journal, January 2018

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

Determinants of Acidobacteria activity inferred from the relative abundances of 16S rRNA transcripts in German grassland and forest soils : Determinants of
journal, June 2013

  • Foesel, Bärbel U.; Nägele, Verena; Naether, Astrid
  • Environmental Microbiology, Vol. 16, Issue 3
  • DOI: 10.1111/1462-2920.12162

Search and clustering orders of magnitude faster than BLAST
journal, August 2010

Monitoring the Multi-Year Carbon Balance of a Subarctic Palsa Mire with Micrometeorological Techniques
journal, July 2012

  • Christensen, Torben R.; Jackowicz-Korczyński, Marcin; Aurela, Mika
  • AMBIO, Vol. 41, Issue S3
  • DOI: 10.1007/s13280-012-0302-5

Comparative metagenomics of microbial traits within oceanic viral communities
journal, February 2011

  • Sharon, Itai; Battchikova, Natalia; Aro, Eva-Mari
  • The ISME Journal, Vol. 5, Issue 7
  • DOI: 10.1038/ismej.2011.2

Long-term CO2 production following permafrost thaw
journal, July 2013

  • Elberling, Bo; Michelsen, Anders; Schädel, Christina
  • Nature Climate Change, Vol. 3, Issue 10
  • DOI: 10.1038/nclimate1955

Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses
journal, July 2014

  • Hurwitz, B. L.; Westveld, A. H.; Brum, J. R.
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 29
  • DOI: 10.1073/pnas.1319778111

Functional metagenomic profiling of nine biomes
journal, March 2008

  • Dinsdale, Elizabeth A.; Edwards, Robert A.; Hall, Dana
  • Nature, Vol. 452, Issue 7187
  • DOI: 10.1038/nature06810

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
journal, April 2012

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

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
journal, November 2012

  • Quast, Christian; Pruesse, Elmar; Yilmaz, Pelin
  • Nucleic Acids Research, Vol. 41, Issue D1
  • DOI: 10.1093/nar/gks1219

Cellulose utilization in forest litter and soil: identification of bacterial and fungal decomposers
journal, March 2012

Streptomyces aureofaciens whiB gene encoding putative transcription factor essential for differentiation
journal, January 1993

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

Phage-Host Interaction: an Ecological Perspective
journal, June 2004

The microbial ecology of permafrost
journal, May 2014

  • Jansson, Janet K.; Taş, Neslihan
  • Nature Reviews Microbiology, Vol. 12, Issue 6
  • DOI: 10.1038/nrmicro3262

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

Characterization of Novel Bacteriophages for Biocontrol of Bacterial Blight in Leek Caused by Pseudomonas syringae pv. porri
journal, March 2016

Viruses in extreme environments
journal, September 2006

  • Le Romancer, Marc; Gaillard, Mélusine; Geslin, Claire
  • Reviews in Environmental Science and Bio/Technology, Vol. 6, Issue 1-3
  • DOI: 10.1007/s11157-006-0011-2

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

Insights into the function of the WhiB-like protein of mycobacteriophage TM4 - a transcriptional inhibitor of WhiB2: WhiBTM4 and WhiB2
journal, June 2010

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

Diverse uncultivated ultra-small bacterial cells in groundwater
journal, February 2015

  • Luef, Birgit; Frischkorn, Kyle R.; Wrighton, Kelly C.
  • Nature Communications, Vol. 6, Issue 1
  • DOI: 10.1038/ncomms7372

Linking environmental prokaryotic viruses and their host through CRISPRs
journal, May 2015

  • Sanguino, Laura; Franqueville, Laure; Vogel, Timothy M.
  • FEMS Microbiology Ecology, Vol. 91, Issue 5
  • DOI: 10.1093/femsec/fiv046

Environmental microbiology through the lens of high-throughput DNA sequencing: Synopsis of current platforms and bioinformatics approaches
journal, October 2012

  • Logares, Ramiro; Haverkamp, Thomas H. A.; Kumar, Surendra
  • Journal of Microbiological Methods, Vol. 91, Issue 1
  • DOI: 10.1016/j.mimet.2012.07.017

Marine Viruses: Truth or Dare
journal, January 2012

Pathway of Glucose Catabolism by Strain VeGlc2, an Anaerobe Belonging to the Verrucomicrobiales Lineage of Bacterial Descent
journal, December 1998

The bright side of microbial dark matter: lessons learned from the uncultivated majority
journal, June 2016

Marine Viruses: Key Players in Marine Ecosystems
journal, October 2017

  • Middelboe, Mathias; Brussaard, Corina
  • Viruses, Vol. 9, Issue 10
  • DOI: 10.3390/v9100302

Viral dark matter and virus–host interactions resolved from publicly available microbial genomes
journal, July 2015

Identification of four genes involved in the lysogenic pathway of theSalmonella newington bacterial virus ?34
journal, March 1994

  • Villafane, R.; Black, Jennifer
  • Archives of Virology, Vol. 135, Issue 1-2
  • DOI: 10.1007/BF01309776

Marine viruses and their biogeochemical and ecological effects
journal, June 1999

  • Fuhrman, Jed A.
  • Nature, Vol. 399, Issue 6736
  • DOI: 10.1038/21119

CsCl Density Gradient Centrifugation Studies of Intact Bacterial Cells
journal, March 1967

The Sphagnome Project: enabling ecological and evolutionary insights through a genus-level sequencing project
journal, October 2017

  • Weston, David J.; Turetsky, Merritt R.; Johnson, Matthew G.
  • New Phytologist, Vol. 217, Issue 1
  • DOI: 10.1111/nph.14860

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

Crass: identification and reconstruction of CRISPR from unassembled metagenomic data
journal, March 2013

  • Skennerton, Connor T.; Imelfort, Michael; Tyson, Gene W.
  • Nucleic Acids Research, Vol. 41, Issue 10
  • DOI: 10.1093/nar/gkt183

Network analyses structure genetic diversity in independent genetic worlds
journal, December 2009

  • Halary, S.; Leigh, J. W.; Cheaib, B.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 1
  • DOI: 10.1073/pnas.0908978107

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

Toward an Ecological Classification of soil Bacteria
journal, June 2007

  • Fierer, Noah; Bradford, Mark A.; Jackson, Robert B.
  • Ecology, Vol. 88, Issue 6
  • DOI: 10.1890/05-1839
    Sort by:
    [ × clear filter / sort ]

    Similar Records in DOE PAGES and OSTI.GOV collections: