Characteristics of Wetting-Induced Bacteriophage Blooms in Biological Soil Crust
- Authors:
-
[2];
[3];
[4];
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- Univ. of California, Irvine, CA (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 National Nuclear Security Administration (NNSA); USDOE Office of Science (SC)
- OSTI Identifier:
- 1591855
- Alternate Identifier(s):
- OSTI ID: 1603877
- Report Number(s):
- LLNL-JRNL-789612
Journal ID: ISSN 2150-7511; ark:/13030/qt1zv0c2jv
- Grant/Contract Number:
- AC02-05CH11231; AC52-07NA27344
- Resource Type:
- Accepted Manuscript
- Journal Name:
- mBio (Online)
- Additional Journal Information:
- Journal Name: mBio (Online); Journal Volume: 10; Journal Issue: 6; Journal ID: ISSN 2150-7511
- Publisher:
- American Society for Microbiology
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; firmicutes; bacteriophages; biocrust; soil microbiology; virus-host interactions; wetting
Citation Formats
Van Goethem, Marc W., Swenson, Tami L., Trubl, Gareth, Roux, Simon, Northen, Trent R., and Martiny, Jennifer B. H. Characteristics of Wetting-Induced Bacteriophage Blooms in Biological Soil Crust. United States: N. p., 2019.
Web. doi:10.1128/mBio.02287-19.
Van Goethem, Marc W., Swenson, Tami L., Trubl, Gareth, Roux, Simon, Northen, Trent R., & Martiny, Jennifer B. H. Characteristics of Wetting-Induced Bacteriophage Blooms in Biological Soil Crust. United States. https://doi.org/10.1128/mBio.02287-19
Van Goethem, Marc W., Swenson, Tami L., Trubl, Gareth, Roux, Simon, Northen, Trent R., and Martiny, Jennifer B. H. Tue .
"Characteristics of Wetting-Induced Bacteriophage Blooms in Biological Soil Crust". United States. https://doi.org/10.1128/mBio.02287-19. https://www.osti.gov/servlets/purl/1591855.
@article{osti_1591855,
title = {Characteristics of Wetting-Induced Bacteriophage Blooms in Biological Soil Crust},
author = {Van Goethem, Marc W. and Swenson, Tami L. and Trubl, Gareth and Roux, Simon and Northen, Trent R. and Martiny, Jennifer B. H.},
abstractNote = {},
doi = {10.1128/mBio.02287-19},
journal = {mBio (Online)},
number = 6,
volume = 10,
place = {United States},
year = {2019},
month = {12}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
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:
The potential roles of biological soil crusts in dryland hydrologic cycles
journal, January 2006
- Belnap, Jayne
- Hydrological Processes, Vol. 20, Issue 15
STAMP: statistical analysis of taxonomic and functional profiles
journal, July 2014
- Parks, Donovan H.; Tyson, Gene W.; Hugenholtz, Philip
- Bioinformatics, Vol. 30, Issue 21
Xerotolerant bacteria: surviving through a dry spell
journal, March 2017
- Lebre, Pedro H.; De Maayer, Pieter; Cowan, Don A.
- Nature Reviews Microbiology, Vol. 15, Issue 5
Microbial colonization and controls in dryland systems
journal, July 2012
- Pointing, Stephen B.; Belnap, Jayne
- Nature Reviews Microbiology, Vol. 10, Issue 8
TM-align: a protein structure alignment algorithm based on the TM-score
journal, April 2005
- Zhang, Y.
- Nucleic Acids Research, Vol. 33, Issue 7
Quality control and preprocessing of metagenomic datasets
journal, January 2011
- Schmieder, R.; Edwards, R.
- Bioinformatics, Vol. 27, Issue 6
Biological Feedbacks in Global Desertification
journal, March 1990
- Schlesinger, W. H.; Reynolds, J. F.; Cunningham, G. L.
- Science, Vol. 247, Issue 4946
Host-linked soil viral ecology along a permafrost thaw gradient
journal, July 2018
- Emerson, Joanne B.; Roux, Simon; Brum, Jennifer R.
- Nature Microbiology, Vol. 3, Issue 8
Trade-Offs between Competition and Defense Specialists among Unicellular Planktonic Organisms: the "Killing the Winner" Hypothesis Revisited
journal, March 2010
- Winter, C.; Bouvier, T.; Weinbauer, M. G.
- Microbiology and Molecular Biology Reviews, Vol. 74, Issue 1
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
journal, August 2017
- Bowers, Robert M.; Kyrpides, Nikos C.; Stepanauskas, Ramunas
- Nature Biotechnology, Vol. 35, Issue 8
Ecological Dynamics of the Toxic Bloom-Forming Cyanobacterium Microcystis aeruginosa and Its Cyanophages in Freshwater
journal, March 2008
- Yoshida, M.; Yoshida, T.; Kashima, A.
- Applied and Environmental Microbiology, Vol. 74, Issue 10
Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing
journal, October 2018
- Trubl, Gareth; Jang, Ho Bin; Roux, Simon
- mSystems, Vol. 3, Issue 5
Viruses manipulate the marine environment
journal, May 2009
- Rohwer, Forest; Thurber, Rebecca Vega
- Nature, Vol. 459, Issue 7244
The bacteria and bacteriophages from a Mesquite Flats site of the Death Valley desert
journal, April 2013
- Prestel, Eric; Regeard, Christophe; Salamitou, Sylvie
- Antonie van Leeuwenhoek, Vol. 103, Issue 6
NCBI Viral Genomes Resource
journal, November 2014
- Brister, J. Rodney; Ako-adjei, Danso; Bao, Yiming
- Nucleic Acids Research, Vol. 43, Issue D1
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
Metagenomic analysis of the viral community in Namib Desert hypoliths: Metaviromics of Namib hypoliths
journal, July 2014
- Adriaenssens, Evelien M.; Van Zyl, Lonnie; De Maayer, Pieter
- Environmental Microbiology, Vol. 17, Issue 2
MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
journal, January 2015
- Li, Dinghua; Liu, Chi-Man; Luo, Ruibang
- Bioinformatics, Vol. 31, Issue 10
Rainfall-induced carbon dioxide pulses result from sequential resuscitation of phylogenetically clustered microbial groups
journal, June 2012
- Placella, S. A.; Brodie, E. L.; Firestone, M. K.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 27
Marine viruses — major players in the global ecosystem
journal, October 2007
- Suttle, Curtis A.
- Nature Reviews Microbiology, Vol. 5, Issue 10
Large Blooms of Bacillales ( Firmicutes ) Underlie the Response to Wetting of Cyanobacterial Biocrusts at Various Stages of Maturity
journal, March 2018
- Karaoz, Ulas; Couradeau, Estelle; da Rocha, Ulisses Nunes
- mBio, Vol. 9, Issue 2
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
Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation
journal, October 2006
- Letunic, I.; Bork, P.
- Bioinformatics, Vol. 23, Issue 1
Inferring Correlation Networks from Genomic Survey Data
journal, September 2012
- Friedman, Jonathan; Alm, Eric J.
- PLoS Computational Biology, Vol. 8, Issue 9
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
Prodigal: prokaryotic gene recognition and translation initiation site identification
journal, March 2010
- Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F.
- BMC Bioinformatics, Vol. 11, Issue 1
VirSorter: mining viral signal from microbial genomic data
journal, January 2015
- Roux, Simon; Enault, Francois; Hurwitz, Bonnie L.
- PeerJ, Vol. 3
Transfer of photosynthesis genes to and from Prochlorococcus viruses
journal, July 2004
- Lindell, D.; Sullivan, M. B.; Johnson, Z. I.
- Proceedings of the National Academy of Sciences, Vol. 101, Issue 30
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
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
journal, May 2015
- Parks, Donovan H.; Imelfort, Michael; Skennerton, Connor T.
- Genome Research, Vol. 25, Issue 7
Temperature Drives the Continental-Scale Distribution of Key Microbes in Topsoil Communities
journal, June 2013
- Garcia-Pichel, Ferran; Loza, Virginia; Marusenko, Yevgeniy
- Science, Vol. 340, Issue 6140
I-TASSER server for protein 3D structure prediction
journal, January 2008
- Zhang, Yang
- BMC Bioinformatics, Vol. 9, Issue 1
Fast and sensitive protein alignment using DIAMOND
journal, November 2014
- Buchfink, Benjamin; Xie, Chao; Huson, Daniel H.
- Nature Methods, Vol. 12, Issue 1
An in vivo membrane fusion assay implicates SpoIIIE in the final stages of engulfment during Bacillus subtilis sporulation
journal, December 1999
- Sharp, M. D.; Pogliano, K.
- Proceedings of the National Academy of Sciences, Vol. 96, Issue 25
Genome Diversity of Spore-Forming Firmicutes
journal, December 2013
- Galperin, Michael Y.
- Microbiology Spectrum, Vol. 1, Issue 2
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
journal, January 2013
- Katoh, K.; Standley, D. M.
- Molecular Biology and Evolution, Vol. 30, Issue 4
MEGAN analysis of metagenomic data
journal, February 2007
- Huson, D. H.; Auch, A. F.; Qi, J.
- Genome Research, Vol. 17, Issue 3
Bacteriophages of soil bacilli: A new multivalent phage of Bacillus altitudinis
journal, April 2017
- Shah Mahmud, R.; Garifulina, K. I.; Ulyanova, V. V.
- Molecular Genetics, Microbiology and Virology, Vol. 32, Issue 2
The RAST Server: Rapid Annotations using Subsystems Technology
journal, January 2008
- Aziz, Ramy K.; Bartels, Daniela; Best, Aaron A.
- BMC Genomics, Vol. 9, Issue 1, Article No. 75
Uncovering Earth’s virome
journal, August 2016
- Paez-Espino, David; Eloe-Fadrosh, Emiley A.; Pavlopoulos, Georgios A.
- Nature, Vol. 536, Issue 7617
Prokka: rapid prokaryotic genome annotation
journal, March 2014
- Seemann, T.
- Bioinformatics, Vol. 30, Issue 14
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
Three Prochlorococcus Cyanophage Genomes: Signature Features and Ecological Interpretations
journal, April 2005
- Sullivan, Matthew B.; Coleman, Maureen L.; Weigele, Peter
- PLoS Biology, Vol. 3, Issue 5
Changes to dryland rainfall result in rapid moss mortality and altered soil fertility
journal, July 2012
- Reed, Sasha C.; Coe, Kirsten K.; Sparks, Jed P.
- Nature Climate Change, Vol. 2, Issue 10
Sporulation genes in members of the low G+C Gram-type-positive phylogenetic branch (Firmicutes)
journal, August 2004
- Onyenwoke, RobU.; Brill, JuliaA.; Farahi, Kamyar
- Archives of Microbiology, Vol. 182, Issue 2-3
Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes
journal, March 2015
- Hultman, Jenni; Waldrop, Mark P.; Mackelprang, Rachel
- Nature, Vol. 521, Issue 7551
SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data
journal, October 2012
- Kopylova, Evguenia; Noé, Laurent; Touzet, Hélène
- Bioinformatics, Vol. 28, Issue 24
Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity
journal, April 2018
- Rodriguez-R, Luis M.; Gunturu, Santosh; Tiedje, James M.
- mSystems, Vol. 3, Issue 3
Desert Ecosystems: Environment and Producers
journal, November 1973
- Noy-Meir, I.
- Annual Review of Ecology and Systematics, Vol. 4, Issue 1
Theoretical models for the control of bacterial growth rate, abundance, diversity and carbon demand
journal, January 1997
- Thingstad, Tf; Lignell, R.
- Aquatic Microbial Ecology, Vol. 13
Environmental drivers of viral community composition in Antarctic soils identified by viromics
journal, July 2017
- Adriaenssens, Evelien M.; Kramer, Rolf; Van Goethem, Marc W.
- Microbiome, Vol. 5, Issue 1
Soil microstructure as an under-explored feature of biological soil crust hydrological properties: case study from the NW Negev Desert
journal, April 2014
- Felde, Vincent John Martin Noah Linus; Peth, Stephan; Uteau-Puschmann, Daniel
- Biodiversity and Conservation, Vol. 23, Issue 7
Fast gapped-read alignment with Bowtie 2
journal, March 2012
- Langmead, Ben; Salzberg, Steven L.
- Nature Methods, Vol. 9, Issue 4
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
journal, November 2003
- Shannon, P.
- Genome Research, Vol. 13, Issue 11
Hidden diversity of soil giant viruses
journal, November 2018
- Schulz, Frederik; Alteio, Lauren; Goudeau, Danielle
- Nature Communications, Vol. 9, Issue 1
Unipro UGENE: a unified bioinformatics toolkit
journal, February 2012
- Okonechnikov, Konstantin; Golosova, Olga; Fursov, Mikhail
- Bioinformatics, Vol. 28, Issue 8
Albedo feedbacks to future climate via climate change impacts on dryland biocrusts
journal, March 2017
- Rutherford, William A.; Painter, Thomas H.; Ferrenberg, Scott
- Scientific Reports, Vol. 7, Issue 1
DADA2: High-resolution sample inference from Illumina amplicon data
journal, May 2016
- Callahan, Benjamin J.; McMurdie, Paul J.; Rosen, Michael J.
- Nature Methods, Vol. 13, Issue 7
Viruses in Soil Ecosystems: An Unknown Quantity Within an Unexplored Territory
journal, September 2017
- Williamson, Kurt E.; Fuhrmann, Jeffry J.; Wommack, K. Eric
- Annual Review of Virology, Vol. 4, Issue 1
Assembling metagenomes, one community at a time
journal, July 2017
- van der Walt, Andries Johannes; van Goethem, Marc Warwick; Ramond, Jean-Baptiste
- BMC Genomics, Vol. 18, Issue 1
MetaQUAST: evaluation of metagenome assemblies
journal, November 2015
- Mikheenko, Alla; Saveliev, Vladislav; Gurevich, Alexey
- Bioinformatics, Vol. 32, Issue 7
The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level
journal, June 2018
- Rodriguez-R, Luis M.; Gunturu, Santosh; Harvey, William T.
- Nucleic Acids Research, Vol. 46, Issue W1
Lysogeny and Lytic Viral Production during a Bloom of the Cyanobacterium Synechococcus spp.
journal, February 2002
- Ortmann, A. C.; Lawrence, J. E.; Suttle, C. A.
- Microbial Ecology, Vol. 43, Issue 2
Regional synchrony in full-scale activated sludge bioreactors due to deterministic microbial community assembly
journal, December 2016
- Griffin, James S.; Wells, George F.
- The ISME Journal, Vol. 11, Issue 2
Bacterial Endospores as Phage Genome Carriers and Protective Shells
journal, July 2018
- Gabiatti, Naiana; Yu, Pingfeng; Mathieu, Jacques
- Applied and Environmental Microbiology, Vol. 84, Issue 18
vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria
journal, January 2017
- Bolduc, Benjamin; Jang, Ho Bin; Doulcier, Guilhem
- PeerJ, Vol. 5
MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies
journal, January 2019
- Kang, Dongwan D.; Li, Feng; Kirton, Edward
- PeerJ, Vol. 7
Elucidating the microbial resuscitation cascade in biological soil crusts following a simulated rain event: Microbial resuscitation in biological soil crusts
journal, May 2013
- Angel, Roey; Conrad, Ralf
- Environmental Microbiology
Contribution of cryptogamic covers to the global cycles of carbon and nitrogen
journal, June 2012
- Elbert, Wolfgang; Weber, Bettina; Burrows, Susannah
- Nature Geoscience, Vol. 5, Issue 7
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
Vulnerability of desert biological soil crusts to wind erosion: the influences of crust development, soil texture, and disturbance
journal, June 1998
- Belnap, Jayne; Gillette, Dale A.
- Journal of Arid Environments, Vol. 39, Issue 2
Linking soil biology and chemistry in biological soil crust using isolate exometabolomics
journal, January 2018
- Swenson, Tami L.; Karaoz, Ulas; Swenson, Joel M.
- Nature Communications, Vol. 9, Issue 1
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
Characterization of a Bacillus megaterium strain with metal bioremediation potential and in silico discovery of novel cadmium binding motifs in the regulator, CadC
journal, March 2021
- Kumari, Weerasingha Mudiyanselage Nilmini H.; Thiruchittampalam, Shalini; Weerasinghe, Mahinagoda Siril Samantha
- Applied Microbiology and Biotechnology, Vol. 105, Issue 6
Erratum: Seasonal time bombs: dominant temperate viruses affect Southern Ocean microbial dynamics
journal, January 2017
- Brum, Jennifer R.; Hurwitz, Bonnie L.; Schofield, Oscar
- The ISME Journal, Vol. 11, Issue 2
Systematic discovery of pseudomonad genetic factors involved in sensitivity to tailocins
journal, March 2021
- Carim, Sean; Azadeh, Ashley L.; Kazakov, Alexey E.
- The ISME Journal, Vol. 15, Issue 8
Analysis of immune, microbiota and metabolome maturation in infants in a clinical trial of Lactobacillus paracasei CBA L74-fermented formula
journal, June 2020
- Roggero, Paola; Liotto, Nadia; Pozzi, Chiara
- Nature Communications, Vol. 11, Issue 1
Draft Genome Sequence of Comamonas aquatilis Strain LK (= CSUR P6418 = CECT 9772), Isolated from the Planarian Schmidtea mediterranea
journal, February 2021
- Kangale, Luis Johnson; Levasseur, Anthony; Raoult, Didier
- Microbiology Resource Announcements, Vol. 10, Issue 5
Systems Analysis of Gut Microbiome Influence on Metabolic Disease in HIV-Positive and High-Risk Populations
journal, June 2021
- Armstrong, Abigail J. S.; Quinn, Kevin; Fouquier, Jennifer
- mSystems, Vol. 6, Issue 3
Polinton-like viruses are abundant in aquatic ecosystems
journal, January 2021
- Bellas, Christopher M.; Sommaruga, Ruben
- Microbiome, Vol. 9, Issue 1
Minimum information about an uncultivated virus genome (MIUVIG)
text, January 2019
- Roux, Simon; Adriaenssens, Evelien M.; Dutilh, Bas E.
- ETH Zurich
MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
preprint, January 2014
- Li, Dinghua; Liu, Chi-Man; Luo, Ruibang
- arXiv