Dataset: GT10 - CDOM
Deployment: KN199-04

Absorption coefficients of Colored Dissolved Organic matter (CDOM)

Principal Investigator:

Charles McClain (National Aeronautics and Space Administration, NASA)

Co-Principal Investigator:

Joaquin Chaves (National Aeronautics and Space Administration, NASA)

BCO-DMO Data Manager:

Danie Kinkade (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

U.S. GEOTRACES North Atlantic Transect (GA03) (U.S. GEOTRACES NAT)

Current State:

Preliminary and in progress

Version:

2013-01-31

Deployment Synonyms:

GA03, GT10, USGT-NAT-2010, KN199-4, GNAT, U.S. GEOTRACES NAZT Leg 1, knorr199-4/5, Section Cruise (GA03), 316N20101015

Version Date:

2013-01-31

Data URL:

https://www.bco-dmo.org/dataset-deployment/455743/data

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Description

Optical absorption coefficient of chromophoric dissolved organic matter (aCDOM) on samples collected during Geotraces 2010 (kn199-04).

Note: These data are considered preliminary. As per PI: "CDOM data will be, unfortunately, sent as "preliminary" since our efforts to develop a satisfactory salinity correction did not yield convincing results. We will have to reanalyze the data from the stored samples. The relative magnitudes of the samples are probably OK, which is probably good, if anybody wants to use the data as a conservative tracer, but absolute magnitudes are suspect. Lots of negative values might be a good hint."

The following metadata was extracted from the original file header:

/begin_header
/investigators=Charles_McClain Joaquin_Chaves
/affiliations=NASA
/contact=joaquin.chaves@nasa.gov
/experiment=GEOTRACES
/cruise=kn199-4
/station=NA
/data_file_name=kn199-4_CDOM_reportBCDMO.csv
/documents=CDOM_protocols.pdf
/calibration_files=NA
/data_type=bottle
/data_status=preliminary
/start_date=20101016
/end_date=20101103
/start_time=15:10:00[GMT]
/end_time=00:19:00[GMT]
/north_latitude=38.3307[DEG]
/south_latitude=17.3497[DEG]
/east_longitude=-9.66[DEG]
/west_longitude=-24.4998[DEG]
/water_depth=-999
/measurement_depth=-999
/secchi_depth=-999
/wind_speed=-999
/cloud_percent=-999
/wave_height=-999
!
!The field "replicates" indicates how many replicate samples were
!averaged to produce the reported value
!
/missing=-999
/delimiter=comma

Methods & Sampling

Dataset acquisition description

Methods for the Collection and Measurement of the Spectral Absorption Coefficient (a_gλ) of Chromophoric Dissolved Organic Matter (CDOM):
Seawater samples for the measurement of chromophoric dissolved organic matter (CDOM) absorption (a_g) are filtered under a gentle vacuum (<5 in Hg) through precombusted (6 hours at 450°C) Whatman GF/F glass fiber filters and collected directly into pre-cleaned and pre-combusted sample glass bottles. Samples for determination of CDOM spectral absorption coefficients are stored under refrigeration at 4°C. In the laboratory, CDOM samples are warmed to room temperature and filtered through 0.2 μm Whatman Nuclepore polycarbonate filters or Gelman Supor (polyethersulfone) filters prior to analysis (Mitchell et al. 2000). Filtration samples through GF/F filters is necessary for coastal ocean waters due to the high particle load that quickly clog Nuclepore and Supor filters. Absorption spectra of CDOM are measured using a multiple pathlength, liquid core waveguide (MPLCW) system (World Precision Instruments, Inc., Sarasota, FL) with UV oxidized Milli-Q water as a reference (Miller et al., 2002). CDOM absorbance spectra are measured between 370 and 725 nm at 1 nm intervals normalized to the reference spectrum.

Data Processing Description

Dataset Processing Description

Data Processing:
CDOM absorbance spectra are measured on a multiple pathlength, liquid core waveguide between 370 and 725 nm at 1 nm intervals normalized to the reference spectrum. For seawater samples, an absorbance correction to account for the different refractive indices of Milli-Q water and seawater is applied. The correction is based on previously measured solutions of known salinity devoid of CDOM. The corresponding spectral absorbance correction for a given salinity is subtracted from the observed spectrum of a sample of the same salinity.

The spectral absorption coefficients, a_g(λ) (m-1) are obtained by

a_g(λ) = 2.303A(λ) /L,
where A(λ) is the absorbance at wavelength λ and L is the pathlength in meters. Absorption data are also corrected for baseline offsets by subtracting the average absorption value between 690-700nm.

BCO-DMO Processing Notes:
- One data file sent by Chaves in excel spreadsheet format on 2013.01.31
- Update (v1) sent on 2013.02.01 included station numbers
- Update (v2) sent on 2013.02.01 corrected column/row alignment

Edits made:
- Parameter header names were renamed to BCO-DMO convention
- Blank data fields and data reported as -999 were edited to 'nd'
- Edited time to remove colons and drop unused seconds
- Edited precision of lat/lon to four decimals.
- Edited precision of absorption coefficients to three decimals.
- Transposed rows and columns in file to view values vertically rather than horizontally. Created column for 'wavelength' to accommodate original parameter names and column for absorption coefficient 'absp_coef' to hold values. Removed header information from the file. Where necessary, the information was incorporated into BCO-DMO metadata fields and retained entirely as 'additional information'.

Note: Correspondence with the PI on 2013.01.12, necessitated editing the header note indicating NASA's pump. Therefore, this comment was retained in the header has been edited to the following text:

#samples from station 1 with 0 depth were collected with WHOI's GEOTRACES pump
#sample numbers for stations > 1 with depth = 0 were collected with NASA's
#surface peristaltic pump

Note: Further correspondence with the PI on 2013.03.06, edited sample 5880 (station 3 cast 6) to 5280.

Additional GEOTRACES Processing: After the data were submitted to the International Data Management Office, BODC, the office noticed that important identifying information was missing in many datasets. With the agreement of BODC and the US GEOTRACES lead PIs, BCO-DMO added standard US GEOTRACES information, such as the US GEOTRACES event number, to each submitted dataset lacking this information. To accomplish this, BCO-DMO compiled a 'master' dataset composed of the following parameters: station_GEOTRC, cast_GEOTRC (bottle and pump data only), event_GEOTRC, sample_GEOTRC, sample_bottle_GEOTRC (bottle data only), bottle_GEOTRC (bottle data only), depth_GEOTRC_CTD (bottle data only), depth_GEOTRC_CTD_rounded (bottle data only), BTL_ISO_DateTime_UTC (bottle data only), and GeoFish_id (GeoFish data only). This added information will facilitate subsequent analysis and inter comparison of the datasets.

Bottle parameters in the master file were taken from the GT-C_Bottle_GT10, GT-C_Bottle_GT11, ODF_Bottle_GT10, and ODF_Bottle_GT11 datasets. Non-bottle parameters, including those from GeoFish tows, Aerosol sampling, and McLane Pumps, were taken from the Event_Log_GT10 and Event_Log_GT11 datasets. McLane pump cast numbers missing in event logs were taken from the Particulate Th-234 dataset submitted by Ken Buesseler.

A standardized BCO-DMO method (called “join”) was then used to merge the missing parameters to each US GEOTRACES dataset, most often by matching on sample_GEOTRC or on some unique combination of other parameters.

If the master parameters were included in the original data file and the values did not differ from the master file, the original data columns were retained and the name of the parameters were changed from the PI-submitted names to the standardized master names. If there were differences between the PI-supplied parameter values and those in the master file, both columns were retained. If the original data submission included all of the master parameters, no additional columns were added, but parameter names were modified to match the naming conventions of the master file.

See the dataset parameters documentation for a description of which parameters were supplied by the PI and which were added via the join method.

More information about this dataset deployment

Funding

Award Number	Funding Source
NNX09AN94G	National Aeronautics & Space Administration

Instruments

Pump surface

Supplied Description:

NASA's surface peristaltic pump was used to collect surface samples from station 1. WHOI's GEOTRACES pump was used to collect surface samples from all other stations.

Instrument Type

Generic Name: Pump surface

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/31/

Generic Description:

A source of uncontaminated near-surface seawater pumped onto the deck of the research vessel that can be sampled and analyzed. This pumped seawater supply is from an over-the-side pumping system, and is therefore different from the vessel underway seawater system.

Spectrophotometer with Liquid Core Waveguide- WPI

Supplied Name: spectrophotometer with liquid core waveguide- World Precision Instruments

Supplied Description:

Instrument Type

Generic Name: Spectrophotometer with Liquid Core Waveguide- WPI

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB20/

Generic Description:

The World Precision Instruments (WPI) Multiple Pathlength Liquid Core Waveguide (MPLCW) system is an instrument package combining a Liquid Waveguide Capillary Cell (LWCC) and a WPI spectrophotometer via fiber optics. The waveguide is a fiber optic cell that combines an increased optical pathlength (50–500cm) with small sample volume (125–1250µL). Ultra-sensitive absorbance measurements can be performed in the ultraviolet (UV), visible (VIS) and near-infrared (NIR) to detect low sample concentrations in a laboratory or process control environment. (www.whpiinc.com)

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
station_GEOTRC	GEOTRACES station number; ranges from 1 through 12 for KN199-04 and 1 through 24 for KN204-01. Stations 7 and 9 were skipped on KN204-01. PI-supplied values were identical to those in the intermediate US GEOTRACES master file. Originally submitted as 'station'; this parameter name has been changed to conform to BCO-DMO's GEOTRACES naming conventions.	dimensionless	station
time_gmt	Time of sampling, reported in GMT. in the format hhmm	unitless	time_gmt
yrday	Year day recorded in GMT time, where Jan 1 is day 1. in the format ddd	unitless	yrday
date_gmt	Date, recorded in GMT time. in the format yyyymmdd	unitless	date_gmt
lon	Longitude component of geographic position where samples were collected.	decimal degrees	lon
lat	Latitude component of geographic position where samples were collected.	decimal degrees	lat
depth	Originator's sample depth.	meters	depth
replicates	A number indicating how many replicate samples were averaged to produce the reported value.	dimensionless	replicate
wavelength	Wavelength (between 400-700nm) at which measurements were performed at a 1nm data interval.	nanometers	wavelength
absp_coef	Coefficient of absorption at the given wavelength as defined by: ag([lambda]) = 2.303A([lambda])/L, where A([lambda]) is the absorbance at wavelength [lambda] and L is the pathlength in meters.	1/meters	absorption_coefficient
cast_GEOTRC	Cast identifier numbered consecutively within a station. Values were added from the intermediate US GEOTRACES master file (see Processing Description).	dimensionless	cast
event_GEOTRC	Unique identifying number for US GEOTRACES sampling events; ranges from 2001 to 2225 for KN199-04 events and from 3001 to 3282 for KN204-01 events. Values were added from the intermediate US GEOTRACES master file (see Processing Description).	dimensionless	event
sample_GEOTRC	Unique identifying number for US GEOTRACES samples; ranges from 5033 to 6078 for KN199-04 and from 6112 to 8148 for KN204-01. PI-supplied values were identical to those in the intermediate US GEOTRACES master file Originally submitted as 'sample'; this parameter name has been changed to conform to BCO-DMO's GEOTRACES naming conventions. Sample numbers from station 1 with 0 depth were collected with WHOI's GEOTRACES pump and samples for stations > 1 from depth = 0.	dimensionless	sample
sample_bottle_GEOTRC	Unique identification numbers given to samples taken from bottles; ranges from 1 to 24; often used synonymously with bottle number. Values were added from the intermediate US GEOTRACES master file (see Processing Description).	dimensionless	sample
bottle_GEOTRC	Alphanumeric characters identifying bottle type (e.g. NIS representing Niskin and GF representing GOFLO) and position on a CTD rosette. Values were added from the intermediate US GEOTRACES master file (see Processing Description).	dimensionless	bottle
depth_GEOTRC_CTD	Observation/sample depth in meters; calculated from CTD pressure. Values were added from the intermediate US GEOTRACES master file (see Processing Description).	meters	depth
BTL_ISO_DateTime_UTC	Date and time (UTC) variable recorded at the bottle sampling time in ISO compliant format. Values were added from the intermediate US GEOTRACES master file (see Processing Description). This standard is based on ISO 8601:2004(E) and takes on the following form: 2009-08-30T14:05:00[.xx]Z (UTC time)	yyyy-MM-dd'T'HH:mm:ss.SS'Z'	ISO_DateTime_UTC
cruise_id	Official cruise identifier e.g. KN199-04 = R/V Knorr cruise number 199-04.	dimensionless	cruise_id

Database

Contribute Data

Dataset: GT10 - CDOM
Deployment: KN199-04

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: GT10 - CDOMDeployment: KN199-04

Dataset acquisition description

Dataset Processing Description

Dataset: GT10 - CDOM
Deployment: KN199-04