Microbial metagenomes and metatranscriptomes during a coastal phytoplankton bloom

Nowinski, Brent; Smith, Christa B.; Thomas, Courtney M.; Esson, Kaitlin; Marin, Roman; Preston, Christina M.; Birch, James M.; Scholin, Christopher A.; Huntemann, Marcel; Clum, Alicia; Foster, Brian; Foster, Bryce; Roux, Simon; Palaniappan, Krishnaveni; Varghese, Neha; Mukherjee, Supratim; Reddy, T. B.  K.; Daum, Chris; Copeland, Alex; Chen, I. -Min A.; Ivanova, Natalia N.; Kyrpides, Nikos C.; Glavina del Rio, Tijana; Whitman, William B.; Kiene, Ronald P.; Eloe-Fadrosh, Emiley A.; Moran, Mary Ann

doi:10.1038/s41597-019-0132-4

Title: Microbial metagenomes and metatranscriptomes during a coastal phytoplankton bloom

Abstract

Metagenomic and metatranscriptomic time-series data covering a 52-day period in the fall of 2016 provide an inventory of bacterial and archaeal community genes, transcripts, and taxonomy during an intense dinoflagellate bloom in Monterey Bay, CA, USA. The dataset comprises 84 metagenomes (0.8 terabases), 82 metatranscriptomes (1.1 terabases), and 88 16S rRNA amplicon libraries from samples collected on 41 dates. The dataset also includes 88 18S rRNA amplicon libraries, characterizing the taxonomy of the eukaryotic community during the bloom. Accompanying the sequence data are chemical and biological measurements associated with each sample. These datasets will facilitate studies of the structure and function of marine bacterial communities during episodic phytoplankton blooms.

Authors:

^[1]; Smith, Christa B. ^[1]; Thomas, Courtney M. ^[1]; Esson, Kaitlin ^[2]; Marin, Roman ^[3]; Preston, Christina M. ^[3]; Birch, James M. ^[3]; Scholin, Christopher A. ^[3];

^[4]; Clum, Alicia ^[4]; Foster, Brian ^[4]; Foster, Bryce ^[4];

^[4]; Palaniappan, Krishnaveni ^[4]; Varghese, Neha ^[4];

^[4]; Reddy, T. B. K. ^[4]; Daum, Chris ^[4]; Copeland, Alex ^[4]; Chen, I. -Min A. ^[4] more »

Univ. of Georgia, Athens, GA (United States)
Univ. of South Alabama, Mobile, AL (United States); Dauphin Island Sea Lab, Dauphin Island, AL (United States)
Monterey Bay Aquarium Research Inst., Moss Landing, CA (United States)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

Publication Date:: Mon Jul 22 00:00:00 EDT 2019

Research Org.:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Org.:: USDOE Office of Science (SC); National Science Foundation (NSF)

OSTI Identifier:: 1559811

Grant/Contract Number:: AC02-05CH11231; OCE-1342694; OCE-1342699; OCE-1342734

Resource Type:: Accepted Manuscript

Journal Name:: Scientific Data

Additional Journal Information:: Journal Volume: 6; Journal Issue: 1; Journal ID: ISSN 2052-4463

Publisher:: Nature Publishing Group

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES

Citation Formats


                    Nowinski, Brent, Smith, Christa B., Thomas, Courtney M., Esson, Kaitlin, Marin, Roman, Preston, Christina M., Birch, James M., Scholin, Christopher A., Huntemann, Marcel, Clum, Alicia, Foster, Brian, Foster, Bryce, Roux, Simon, Palaniappan, Krishnaveni, Varghese, Neha, Mukherjee, Supratim, Reddy, T. B.  K., Daum, Chris, Copeland, Alex, Chen, I. -Min A., Ivanova, Natalia N., Kyrpides, Nikos C., Glavina del Rio, Tijana, Whitman, William B., Kiene, Ronald P., Eloe-Fadrosh, Emiley A., and Moran, Mary Ann. Microbial metagenomes and metatranscriptomes during a coastal phytoplankton bloom.  United States: N. p., 2019. 
Web.  doi:10.1038/s41597-019-0132-4.

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                    Nowinski, Brent, Smith, Christa B., Thomas, Courtney M., Esson, Kaitlin, Marin, Roman, Preston, Christina M., Birch, James M., Scholin, Christopher A., Huntemann, Marcel, Clum, Alicia, Foster, Brian, Foster, Bryce, Roux, Simon, Palaniappan, Krishnaveni, Varghese, Neha, Mukherjee, Supratim, Reddy, T. B.  K., Daum, Chris, Copeland, Alex, Chen, I. -Min A., Ivanova, Natalia N., Kyrpides, Nikos C., Glavina del Rio, Tijana, Whitman, William B., Kiene, Ronald P., Eloe-Fadrosh, Emiley A., & Moran, Mary Ann. Microbial metagenomes and metatranscriptomes during a coastal phytoplankton bloom.  United States.  https://doi.org/10.1038/s41597-019-0132-4

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                    Nowinski, Brent, Smith, Christa B., Thomas, Courtney M., Esson, Kaitlin, Marin, Roman, Preston, Christina M., Birch, James M., Scholin, Christopher A., Huntemann, Marcel, Clum, Alicia, Foster, Brian, Foster, Bryce, Roux, Simon, Palaniappan, Krishnaveni, Varghese, Neha, Mukherjee, Supratim, Reddy, T. B.  K., Daum, Chris, Copeland, Alex, Chen, I. -Min A., Ivanova, Natalia N., Kyrpides, Nikos C., Glavina del Rio, Tijana, Whitman, William B., Kiene, Ronald P., Eloe-Fadrosh, Emiley A., and Moran, Mary Ann. Mon .  
"Microbial metagenomes and metatranscriptomes during a coastal phytoplankton bloom".  United States.  https://doi.org/10.1038/s41597-019-0132-4.  https://www.osti.gov/servlets/purl/1559811.

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@article{osti_1559811,

  title        = {Microbial metagenomes and metatranscriptomes during a coastal phytoplankton bloom},

  author       = {Nowinski, Brent and Smith, Christa B. and Thomas, Courtney M. and Esson, Kaitlin and Marin, Roman and Preston, Christina M. and Birch, James M. and Scholin, Christopher A. and Huntemann, Marcel and Clum, Alicia and Foster, Brian and Foster, Bryce and Roux, Simon and Palaniappan, Krishnaveni and Varghese, Neha and Mukherjee, Supratim and Reddy, T. B.  K. and Daum, Chris and Copeland, Alex and Chen, I. -Min A. and Ivanova, Natalia N. and Kyrpides, Nikos C. and Glavina del Rio, Tijana and Whitman, William B. and Kiene, Ronald P. and Eloe-Fadrosh, Emiley A. and Moran, Mary Ann},

  abstractNote = {Metagenomic and metatranscriptomic time-series data covering a 52-day period in the fall of 2016 provide an inventory of bacterial and archaeal community genes, transcripts, and taxonomy during an intense dinoflagellate bloom in Monterey Bay, CA, USA. The dataset comprises 84 metagenomes (0.8 terabases), 82 metatranscriptomes (1.1 terabases), and 88 16S rRNA amplicon libraries from samples collected on 41 dates. The dataset also includes 88 18S rRNA amplicon libraries, characterizing the taxonomy of the eukaryotic community during the bloom. Accompanying the sequence data are chemical and biological measurements associated with each sample. These datasets will facilitate studies of the structure and function of marine bacterial communities during episodic phytoplankton blooms.},

  doi          = {10.1038/s41597-019-0132-4},

  journal      = {Scientific Data},

  number       = 1,

  volume       = 6,

  place        = {United States},

  year         = {Mon Jul 22 00:00:00 EDT 2019},

  month        = {Mon Jul 22 00:00:00 EDT 2019}

}

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Influences of upwelling and downwelling winds on red tide bloom dynamics in Monterey Bay, California
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Continental Shelf Research, Vol. 29, Issue 5-6
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MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices
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Methods, Vol. 102
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Sizing up metatranscriptomics
journal, August 2012

Moran, Mary Ann; Satinsky, Brandon; Gifford, Scott M.
The ISME Journal, Vol. 7, Issue 2
DOI: 10.1038/ismej.2012.94

Microspatial gene expression patterns in the Amazon River Plume
journal, July 2014

Satinsky, B. M.; Crump, B. C.; Smith, C. B.
Proceedings of the National Academy of Sciences, Vol. 111, Issue 30
DOI: 10.1073/pnas.1402782111

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

Microdiversity and temporal dynamics of marine bacterial dimethylsulfoniopropionate genes
journal, March 2019

Nowinski, Brent; Motard‐Côté, Jessie; Landa, Marine
Environmental Microbiology, Vol. 21, Issue 5
DOI: 10.1111/1462-2920.14560

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Works referencing / citing this record:

Unprecedented DMSP Concentrations in a Massive Dinoflagellate Bloom in Monterey Bay, CA
journal, November 2019

Kiene, Ronald P.; Nowinski, Brent; Esson, Kaitlin
Geophysical Research Letters, Vol. 46, Issue 21
DOI: 10.1029/2019gl085496

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Title: Microbial metagenomes and metatranscriptomes during a coastal phytoplankton bloom

Abstract

Citation Formats

Microspatial gene expression patterns in the Amazon River Plume journal, July 2014

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

Phytoplankton and microbial abundance and bloom dynamics in the upwelling shadow of Monterey Bay, California, from 2006 to 2013 journal, May 2017

Cutadapt removes adapter sequences from high-throughput sequencing reads journal, May 2011

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

The Ecological Role of Water-Column Microbes in the Sea journal, January 1983

Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water journal, March 2010

The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4) journal, February 2016

Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples: Primers for marine microbiome studies journal, October 2015

The global ocean microbiome journal, December 2015

Use of Internal Standards for Quantitative Metatranscriptome and Metagenome Analysis book, January 2013

The Quest to Develop Ecogenomic Sensors: A 25-Year History of the Environmental Sample Processor (ESP) as a Case Study journal, December 2017

Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton journal, June 2015

IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes journal, October 2018

Seasonal fluctuations of temperature, salinity, nitrate, chlorophyll and primary production at station H3/M1 over 1989–1996 in Monterey Bay, California journal, May 2000

Influences of upwelling and downwelling winds on red tide bloom dynamics in Monterey Bay, California journal, March 2009

Microdiversity and temporal dynamics of marine bacterial dimethylsulfoniopropionate genes journal, March 2019

MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices journal, June 2016

BFC: correcting Illumina sequencing errors journal, May 2015

Sizing up metatranscriptomics journal, August 2012

Expression patterns reveal niche diversification in a marine microbial assemblage journal, August 2012

Analysis of immune, microbiota and metabolome maturation in infants in a clinical trial of Lactobacillus paracasei CBA L74-fermented formula journal, June 2020

Influences of upwelling and downwelling winds on red tide bloom dynamics in Monterey Bay, California journal, March 2009

MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices journal, June 2016

Sizing up metatranscriptomics journal, August 2012

Microspatial gene expression patterns in the Amazon River Plume journal, July 2014

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

Microdiversity and temporal dynamics of marine bacterial dimethylsulfoniopropionate genes journal, March 2019

Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton journal, June 2015

Unprecedented DMSP Concentrations in a Massive Dinoflagellate Bloom in Monterey Bay, CA journal, November 2019

Microspatial gene expression patterns in the Amazon River Plume
journal, July 2014

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

Phytoplankton and microbial abundance and bloom dynamics in the upwelling shadow of Monterey Bay, California, from 2006 to 2013
journal, May 2017

Cutadapt removes adapter sequences from high-throughput sequencing reads
journal, May 2011

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

The Ecological Role of Water-Column Microbes in the Sea
journal, January 1983

Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water
journal, March 2010

The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4)
journal, February 2016

Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples: Primers for marine microbiome studies
journal, October 2015

The global ocean microbiome
journal, December 2015

Use of Internal Standards for Quantitative Metatranscriptome and Metagenome Analysis
book, January 2013

The Quest to Develop Ecogenomic Sensors: A 25-Year History of the Environmental Sample Processor (ESP) as a Case Study
journal, December 2017

Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton
journal, June 2015

IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes
journal, October 2018

Seasonal fluctuations of temperature, salinity, nitrate, chlorophyll and primary production at station H3/M1 over 1989–1996 in Monterey Bay, California
journal, May 2000

Influences of upwelling and downwelling winds on red tide bloom dynamics in Monterey Bay, California
journal, March 2009

Microdiversity and temporal dynamics of marine bacterial dimethylsulfoniopropionate genes
journal, March 2019

MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices
journal, June 2016

BFC: correcting Illumina sequencing errors
journal, May 2015

Sizing up metatranscriptomics
journal, August 2012

Expression patterns reveal niche diversification in a marine microbial assemblage
journal, August 2012

Analysis of immune, microbiota and metabolome maturation in infants in a clinical trial of Lactobacillus paracasei CBA L74-fermented formula
journal, June 2020

Influences of upwelling and downwelling winds on red tide bloom dynamics in Monterey Bay, California
journal, March 2009

MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices
journal, June 2016

Sizing up metatranscriptomics
journal, August 2012

Microspatial gene expression patterns in the Amazon River Plume
journal, July 2014

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

Microdiversity and temporal dynamics of marine bacterial dimethylsulfoniopropionate genes
journal, March 2019

Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton
journal, June 2015

Unprecedented DMSP Concentrations in a Massive Dinoflagellate Bloom in Monterey Bay, CA
journal, November 2019