Intra-genomic variation in G + C content and its implications for DNA stable isotope probing: DNA-SIP and intra-genomic variation in G + C content

Youngblut, Nicholas D.; Buckley, Daniel H.

doi:10.1111/1758-2229.12201

Title: Intra-genomic variation in G + C content and its implications for DNA stable isotope probing: DNA-SIP and intra-genomic variation in G + C content

Authors:

Youngblut, Nicholas D. ^[1]; Buckley, Daniel H. ^[1]

Department of Crop and Soil Sciences, Cornell University, 306 Tower Road Ithaca NY 14853 USA

Publication Date:: Tue Oct 07 00:00:00 EDT 2014

Sponsoring Org.:: USDOE

OSTI Identifier:: 1401585

Grant/Contract Number:: SC0004486; SC0010558

Resource Type:: Publisher's Accepted Manuscript

Journal Name:: Environmental Microbiology Reports

Additional Journal Information:: Journal Name: Environmental Microbiology Reports Journal Volume: 6 Journal Issue: 6; Journal ID: ISSN 1758-2229

Publisher:: Wiley-Blackwell

Country of Publication:: United States

Language:: English

Citation Formats


                    Youngblut, Nicholas D., and Buckley, Daniel H. Intra-genomic variation in G + C content and its implications for DNA stable isotope probing: DNA-SIP and intra-genomic variation in G + C content.  United States: N. p., 2014. 
Web.  doi:10.1111/1758-2229.12201.

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                    Youngblut, Nicholas D., & Buckley, Daniel H. Intra-genomic variation in G + C content and its implications for DNA stable isotope probing: DNA-SIP and intra-genomic variation in G + C content.  United States.  https://doi.org/10.1111/1758-2229.12201

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                    Youngblut, Nicholas D., and Buckley, Daniel H. Tue .  
"Intra-genomic variation in G + C content and its implications for DNA stable isotope probing: DNA-SIP and intra-genomic variation in G + C content".  United States.  https://doi.org/10.1111/1758-2229.12201.

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@article{osti_1401585,

  title        = {Intra-genomic variation in G + C content and its implications for DNA stable isotope probing: DNA-SIP and intra-genomic variation in G + C content},

  author       = {Youngblut, Nicholas D. and Buckley, Daniel H.},

  abstractNote = {},

  doi          = {10.1111/1758-2229.12201},

  journal      = {Environmental Microbiology Reports},

  number       = 6,

  volume       = 6,

  place        = {United States},

  year         = {Tue Oct 07 00:00:00 EDT 2014},

  month        = {Tue Oct 07 00:00:00 EDT 2014}

}

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https://doi.org/10.1111/1758-2229.12201

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Title: Intra-genomic variation in G + C content and its implications for DNA stable isotope probing: DNA-SIP and intra-genomic variation in G + C content

Citation Formats

Quantifying intrachromosomal GC heterogeneity in prokaryotic genomes journal, May 2004

A Statistical Analysis of Deoxyribonucleic acid Distribution in Density Gradient Centrifugation journal, October 1959

Improvement of RNA-SIP by pyrosequencing to identify putative 4-n-nonylphenol degraders in activated sludge journal, March 2012

The mechanism of upstream activation in the rrnB operon of Mycobacterium smegmatis is different from the Escherichia coli paradigm journal, February 2005

The Bioperl Toolkit: Perl Modules for the Life Sciences journal, October 2002

Host-compound foraging by intestinal microbiota revealed by single-cell stable isotope probing journal, March 2013

Selective Silencing of Foreign DNA with Low GC Content by the H-NS Protein in Salmonella journal, July 2006

Stable-isotope probing as a tool in microbial ecology journal, February 2000

ggplot2 book, January 2009

Stable isotope probing — linking microbial identity to function journal, May 2005

RNAmmer: consistent and rapid annotation of ribosomal RNA genes journal, April 2007

Discovery of a bacterium, with distinctive dioxygenase, that is responsible for in situ biodegradation in contaminated sediment journal, November 2003

Technical considerations for the use of15N-DNA stable-isotope probing for functional microbial activity in soils journal, January 2005

Stable Isotope Probing with 15N Achieved by Disentangling the Effects of Genome G+C Content and Isotope Enrichment on DNA Density journal, March 2007

When metagenomics meets stable-isotope probing: progress and perspectives journal, April 2010

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Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance journal, October 2012

Stable isotope probing of rRNA and DNA reveals a dynamic methylotroph community and trophic interactions with fungi and protozoa in oxic rice field soil: SIP of methylotrophs in rice field soil journal, December 2003

Stable-isotope probing of DNA: insights into the function of uncultivated microorganisms from isotopically labeled metagenomes journal, February 2006

Identification of Bacterial Micropredators Distinctively Active in a Soil Microbial Food Web journal, August 2006

Importance of DNA quality in comparative soil microbial community structure analyses journal, June 2008

Functional Convergence in Reduced Genomes of Bacterial Symbionts Spanning 200 My of Evolution journal, January 2010

DNA isolation from soil samples for cloning in different hosts journal, June 2004

Measurement of in Situ Activities of Nonphotosynthetic Microorganisms in Aquatic and Terrestrial Habitats journal, October 1985

The Genome Sequences of Cellulomonas fimi and “Cellvibrio gilvus” Reveal the Cellulolytic Strategies of Two Facultative Anaerobes, Transfer of “Cellvibrio gilvus” to the Genus Cellulomonas, and Proposal of Cellulomonas gilvus sp. nov journal, January 2013

Identification of cellulolytic bacteria in soil by stable isotope probing journal, March 2007

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Grinder: a versatile amplicon and shotgun sequence simulator journal, March 2012

Characterization of Growing Microorganisms in Soil by Stable Isotope Probing with H218O journal, February 2007

DNA-, rRNA- and mRNA-based stable isotope probing of aerobic methanotrophs in lake sediment: Stable isotope probing of methanotrophs journal, January 2011

Stable-isotope probing of nucleic acids: a window to the function of uncultured microorganisms journal, June 2003

GenBank journal, December 2007

Methodological Considerations for the Use of Stable Isotope Probing in Microbial Ecology journal, October 2006

Quantifying intrachromosomal GC heterogeneity in prokaryotic genomes
journal, May 2004

A Statistical Analysis of Deoxyribonucleic acid Distribution in Density Gradient Centrifugation
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Improvement of RNA-SIP by pyrosequencing to identify putative 4-n-nonylphenol degraders in activated sludge
journal, March 2012

The mechanism of upstream activation in the rrnB operon of Mycobacterium smegmatis is different from the Escherichia coli paradigm
journal, February 2005

The Bioperl Toolkit: Perl Modules for the Life Sciences
journal, October 2002

Host-compound foraging by intestinal microbiota revealed by single-cell stable isotope probing
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Selective Silencing of Foreign DNA with Low GC Content by the H-NS Protein in Salmonella
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Stable-isotope probing as a tool in microbial ecology
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book, January 2009

Stable isotope probing — linking microbial identity to function
journal, May 2005

RNAmmer: consistent and rapid annotation of ribosomal RNA genes
journal, April 2007

Discovery of a bacterium, with distinctive dioxygenase, that is responsible for in situ biodegradation in contaminated sediment
journal, November 2003

Technical considerations for the use of15N-DNA stable-isotope probing for functional microbial activity in soils
journal, January 2005

Stable Isotope Probing with 15N Achieved by Disentangling the Effects of Genome G+C Content and Isotope Enrichment on DNA Density
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When metagenomics meets stable-isotope probing: progress and perspectives
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Who eats what, where and when? Isotope-labelling experiments are coming of age
journal, May 2007

Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance
journal, October 2012

Stable isotope probing of rRNA and DNA reveals a dynamic methylotroph community and trophic interactions with fungi and protozoa in oxic rice field soil: SIP of methylotrophs in rice field soil
journal, December 2003

Stable-isotope probing of DNA: insights into the function of uncultivated microorganisms from isotopically labeled metagenomes
journal, February 2006

Identification of Bacterial Micropredators Distinctively Active in a Soil Microbial Food Web
journal, August 2006

Importance of DNA quality in comparative soil microbial community structure analyses
journal, June 2008

Functional Convergence in Reduced Genomes of Bacterial Symbionts Spanning 200 My of Evolution
journal, January 2010

DNA isolation from soil samples for cloning in different hosts
journal, June 2004

Measurement of in Situ Activities of Nonphotosynthetic Microorganisms in Aquatic and Terrestrial Habitats
journal, October 1985

The Genome Sequences of Cellulomonas fimi and “Cellvibrio gilvus” Reveal the Cellulolytic Strategies of Two Facultative Anaerobes, Transfer of “Cellvibrio gilvus” to the Genus Cellulomonas, and Proposal of Cellulomonas gilvus sp. nov
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Identification of cellulolytic bacteria in soil by stable isotope probing
journal, March 2007

The Relative Homogeneity of Microbial dna
journal, July 1959

Grinder: a versatile amplicon and shotgun sequence simulator
journal, March 2012

Characterization of Growing Microorganisms in Soil by Stable Isotope Probing with H218O
journal, February 2007

DNA-, rRNA- and mRNA-based stable isotope probing of aerobic methanotrophs in lake sediment: Stable isotope probing of methanotrophs
journal, January 2011

Stable-isotope probing of nucleic acids: a window to the function of uncultured microorganisms
journal, June 2003

GenBank
journal, December 2007

Methodological Considerations for the Use of Stable Isotope Probing in Microbial Ecology
journal, October 2006