Dataset: Geochemistry
Deployment: JRES-204

Elemental composition for 16S rRNA gene amplicon and metagenomic sequences

Principal Investigator:

Jennifer B. Glass (Georgia Institute of Technology, GA Tech)

Scientist:

James McManus (University of Akron, UAkron)

BCO-DMO Data Manager:

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

Project:

Functional gene diversity and expression in methane-hydrate bearing deep subsurface sediments (Methane-Hydrate Sediment Omics)

Current State:

Final no updates expected

Version:

2015-12-02

Version Date:

2015-12-02

Data URL:

https://osprey.bco-dmo.org/dataset-deployment/626744/data

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Description

This dataset was generated under a C-DEBI research grant.

Related References:

Tréhu, A.M, Bohrmann, G., Rack, F.R., Torres, M.E., et al., 2003. Proc. ODP, Init. Repts., 204: College Station, TX (Ocean Drilling Program).doi:10.2973/odp.proc.ir.204.2003

Shipboard Scientific Party, 2003. Site 1244. In Tréhu, A.M, Bohrmann, G., Rack, F.R., Torres, M.E., et al., Proc. ODP, Init. Repts., 204: College Station, TX (Ocean Drilling Program), 1–132. doi:10.2973/odp.proc.ir.204.103.2003

Tréhu, A.M., Bohrmann, G., Torres, M.E., and Colwell, F.S. (Eds.), 2006. Proc. ODP, Sci. Results, 204: College Station, TX (Ocean Drilling Program).doi:10.2973/odp.proc.sr.204.2006

Methods & Sampling

Dataset acquisition description

Analyses performed on “Mobio” IODP samples previously frozen at -80C. Reactive Fe and Mn were extracted using the citrate-dithionite method and measured on an ICP OES (Agilent Technologies 700 series axial). Analysis for TC, TN, and TS were determined using PE 2400 CN(S) analyzer. Analysis for TIC was determined by CM5014 CO2 coulometer with a CM5130 Acidification module.

Data Processing Description

Dataset Processing Description

BCO-DMO Processing:
- Added cruise_id, lat and lon columns

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-0939564	NSF Division of Ocean Sciences

Instruments

CO2 Coulometer

Supplied Name:

Supplied Description:

CM5014 CO2 coulometer with a CM5130 Acidification module.

Instrument Type

Generic Name: CO2 Coulometer

Acronym: CO2 coulometer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB12

Generic Description:

A CO2 coulometer semi-automatically controls the sample handling and extraction of CO2 from seawater samples. Samples are acidified and the CO2 gas is bubbled into a titration cell where CO2 is converted to hydroxyethylcarbonic acid which is then automatically titrated with a coulometrically-generated base to a colorimetric endpoint.

Elemental Analyzer

Supplied Name:

Supplied Description:

PE 2400 CN(S) analyzer

Instrument Type

Generic Name: Elemental Analyzer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB01/

Generic Description:

Instruments that quantify carbon, nitrogen and sometimes other elements by combusting the sample at very high temperature and assaying the resulting gaseous oxides. Usually used for samples including organic material.

Spectrometer

Supplied Name:

Supplied Description:

ICP OES (Agilent Technologies 700 series axial)

Instrument Type

Generic Name: Spectrometer

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0460/

Generic Description:

A spectrometer is an optical instrument used to measure properties of light over a specific portion of the electromagnetic spectrum.

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
cruise_id	cruise identification	unitless	cruise_id
site	site identification	unitless	site
lat	latitude; north is positive	decimal degrees	lat
lon	longitude; east is positive	decimal degrees	lon
core	core identification	unitless	sample
type	type of sample: H = hole?	unitless	sample_type
section	core section identification	unitless	sample
depth	depth below seafloor	meters	depth
comments	molecular biology samples frozen at -80C	unitless	comment
TC_pcent	total carbon	percent	no_bcodmo_term
TN_pcent	total nitrogen	percent	no_bcodmo_term
TS_pcent	total sulfur	percent	no_bcodmo_term
TIC_pcent	total inorganic carbon	percent	no_bcodmo_term
TOC_pcent	total organic carbon	percent	TOC
C_N	carbon:nitrogen ratio	unitless	C_to_N
CaCO3_pcent	calcium carbonate	percent	CaCO3
Fe_pcent	percent reactive iron	percent	Fe
Fe_err	reactive iron standard deviation of duplicate extractions and analyses	percent	std_dev
Fe_RSD_pcent	iron % relative standard deviation: ratio of standard deviation to mean multiplied by 100 to express as percentage	percent	std_dev
Mn_pcent	percent reactive manganese	percent	Mn
Mn_err	standard deviation of duplicate extractions and analyses for reactive manganese	percent	std_dev
Mn_RSD_pcent	manganese % relative standard deviation: ratio of standard deviation to mean multiplied by 100 to express as percentage	percent	std_dev

Database

Contribute Data

Dataset: Geochemistry
Deployment: JRES-204

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: GeochemistryDeployment: JRES-204

Dataset acquisition description

Dataset Processing Description

Dataset: Geochemistry
Deployment: JRES-204