Dataset: 16S rRNA gene and particulate monooxygenase diversity

Name: 16S rRNA gene and particulate monooxygenase diversity from R/V Atlantis AT15-68, AT18-10, AT15-44, AT15-59 off Costa Rica and USA, Pacific Ocean, 2009-2011 (Authigenic Carbonate Ecosystems project)
Published: 2014-01-31
Keywords: oceans

Cite This Dataset

Project:

Structure, Function and Evolution of Authigenic, Methane-Derived Carbonate Ecosystems (Authigenic Carbonate Ecosystems)

Program:

Integrated Marine Biogeochemistry and Ecosystem Research -US (IMBER-US)

U.S. GLOBal ocean ECosystems dynamics (U.S. GLOBEC)

United States Surface Ocean Lower Atmosphere Study (U.S. SOLAS)

Principal Investigator:

Victoria J. Orphan (California Institute of Technology, Caltech)

BCO-DMO Data Manager:

Nancy Copley (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

2014-01-31

Version Date:

2014-01-31

Validated:

Yes

Current State:

Final no updates expected

16S rRNA gene and particulate monooxygenase diversity from R/V Atlantis AT15-68, AT18-10, AT15-44, AT15-59 off Costa Rica and USA, Pacific Ocean, 2009-2011 (Authigenic Carbonate Ecosystems project)

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Description

PCR amplicon data pertaining to this project has been submitted to Genbank at the National Center for Biotechnology Information (NCBI)- www.ncbi.nlm.nih.gov referenced by the following accession numbers:

Three Datasets:

1) Archaeal and Bacterial 16S rRNA gene sequences from carbonate rocks and sediment near the methane seeps of Hydrate Ridge, OR. In preparation, released by NCBI March 2014. NCBI accession numbers KF616507-KF616827.

http://www.ncbi.nlm.nih.gov/nuccore/?term=KF616507%3AKF616827+[ACCN]

2) Particulate methane monooxygenase gene and 16S rRNA gene sequences of methanotrophs – water column Costa Rica Margin. Tavormina et al. 2013, Environmental Microbiology Reports (2013) 5(3), 414–423 doi:10.1111/1758-2229.12025. NCBI accession numbers JX569083-JX569145.

http://www.ncbi.nlm.nih.gov/nuccore/?term=JX569083%3AJX569145+[ACCN]

3) Particulate methane monooxygenase and 16S rRNA genes sequences of bacteria from overlying water, sediment and carbonates near methane seeps Santa Monica Basin and Eel River Basin, CA. Tavormina et al. 2008, Appl. Environ. Microbiol. 2008, 74(13):3985. DOI: 10.1128/AEM.00069-08. NCBI accession numbers EU444837-EU444876.

http://www.ncbi.nlm.nih.gov/nuccore/?term=EU444837%3AEU444876+[ACCN]

Methods & Sampling

Sample locations: Hydrate Ridge, Oregon Coast, USA; Eel River Basin and Santa Monica Basin, California Coast, USA; Costa Rica Margins.

Data Processing Description

Sequenced using Sanger method by Laragen, http://www.laragen.com/.

Edited in software programs Sequencher, Mothur and ARB.

Relevant References:

Patricia L. Tavormina, William Ussler III, Joshua A. Steele, Stephanie A. Connon, Martin G. Klotz and Victoria J. Orphan. Abundance and distribution of diverse membrane-bound monooxygenase (Cu-MMO) genes within the Costa Rica oxygen minimum zone. Environmental Microbiology Reports. 2013, 5(3), 414-423. doi:10.1111/1758-2229.12025.

Patricia L. Tavormina, William Ussler III and Victoria J.Orphan. Planktonic and Sediment-Associated Aerobic Methanotrophs in Two Seep Systems along the North American Margin. Appl. Environ. Microbiol. 2008, 74(13):3985. doi:10.1128/AEM.00069-08.

Data Files

File
accession_numbers.csv (Comma Separated Values (.csv), 74.77 KB) MD5:2e591f03581300955fdfda9c254dddf9 Primary data file for dataset ID 489401

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-0826254
NSF Division of Ocean Sciences	OCE-0825436
NSF Division of Ocean Sciences	OCE-0825791

Deployments

Deployment	Start Date	Platform	Investigator
AT15-44	2009-02-21	R/V Atlantis	Lisa A. Levin (Chief Scientist)	data info
AT15-59	2010-01-06	R/V Atlantis	Lisa A. Levin (Chief Scientist) Victoria J. Orphan (Co-Chief Scientist) Anthony E Rathburn (Co-Chief Scientist) Gregory Rouse (Co-Chief Scientist)	data info
AT15-68	2010-07-31	R/V Atlantis	Lisa A. Levin (Chief Scientist)	data info
AT18-10	2011-08-31	R/V Atlantis	Lisa A. Levin (Chief Scientist)	data info

Instruments

Automated DNA Sequencer

Supplied Name: Automated Sequencer

Supplied Description:

Instrument Type

Generic Name: Automated DNA Sequencer

Acronym: Automated Sequencer

Generic Description:

General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
organism	source organism of genetic sequence	unitless	no_bcodmo_term
gene	gene types	unitless	no_bcodmo_term
sample_descrip	type of material from which sequences were obtained	unitless	sample_descrip
location	location of source material	unitless	no_bcodmo_term
accession_number	NCBI accession number	unitless	accession_number

Status message

Database

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Dataset: 16S rRNA gene and particulate monooxygenase diversity