Dataset: Cruise optical properties: Absorbance

Name: Absorbance spectra from niskin bottle samples collected with depth profiles during R/V Hugh R. Sharp cruise HRS1608 Mid-Atlantic Bight in 2016
Published: 2024-09-25
Keywords: oceans

Cite This Dataset

Spatial Extent: N:37.98133 E:-74.10417 S:34.34967 W:-75.8035

Mid-Atlantic Bight

Temporal Extent: 2016-07-18 - 2016-07-22

Project:

Collaborative Research: Phlorotannins - An Important Source of Marine Chromophoric Dissolved Organic Matter? (Sargassum DOM)

Principal Investigator:

Michael Gonsior (University of Maryland Center for Environmental Science, UMCES)

Co-Principal Investigator:

Neil V. Blough (University of Maryland - College Park, UMD)

Rossana Del Vecchio (University of Maryland - College Park, UMD)

Scientist:

Leanne Powers (University of Maryland Center for Environmental Science, UMCES)

BCO-DMO Data Manager:

Amber D. York (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2024-09-25

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Absorbance spectra from niskin bottle samples collected with depth profiles during R/V Hugh R. Sharp cruise HRS1608 Mid-Atlantic Bight in 2016

Abstract:

Absorbance spectra from niskin bottle samples collected with depth profiles during R/V Hugh R. Sharp cruise HRS1608 Mid-Atlantic Bight in 2016.

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Methods & Sampling

Samples were transferred from Niskin bottles to clean 10L low-density polyethylene cubitainers using silicon tubing. Containers were rinsed three times with sample before final collection.

Sampling and analytical procedures:

Subsamples for fluorescence and absorbance were 0.2 µm filtered using Whatman GD/X cellulose acetate syringe filters. Filters were rinsed with ~20mL sample before collecting samples in combusted 40mL amber glass vials. See "Related Datasets" section for the fluorescence data. Samples stored at 4°C until analysis (within 1 week of collection). For fluorescence and absorbance measurements, samples were transferred to 1 cm quartz fluorescence cuvette and analyzed using a Horiba Aqualog spectrofluorometer. Absorbance was recorded from excitation wavelengths 240 to 600 at 3 nm intervals. Fluorescence emission was recorded from ~243 to 297 nm at fixed ~3.3 nm intervals to created excitation-emission matrix (EEM) spectra. Integration time = 2s. Ultrapure water used as the fluorescence blank and was subtracted from all EEM spectra.

Data Processing Description

Absorbance .dat files (see "Supplemental Files" section): the only data used from these files for this dataset are the first column (Wavelength in nm) and the second to last column (column J, Abs, OD, which is the blank corrected absorbance, OD refers to optical density and is unitless).

Blank corrected absorbance spectra (A(λ)) were converted to Naperian absorption coefficient spectra (a(λ)) using the equation a(λ) = 2.303xa(λ)/L where L = 0.01 m. Spectral slopes were determined from 275-295 nm (S(275-295)) and from 350 – 400 nm (S(350-400)) as the slope of the log-normalized absorbance spectrum from 275-295 nm and 350-400 nm, respectively. Slope ratio (SR) is the ratio of S(275-295) to S(350-400) as defined previously (Helms et al. 2008). E2:E3 ratio is the ratio of absorbance at 250 nm to that 365 nm (De Haan and De Boer 1987).

BCO-DMO Processing

Preprocessing for version 1:
* Sheet "absorbance" of submitted file "Cruise_fluor_abs.xlsx" was imported into the BCO-DMO data system for this dataset. Values "NA" were imported as missing data values. The other sheet in the file "absorbance" was added to BCO-DMO as a related dataset.
** Missing data values are displayed differently based on the file format you download. They are blank in csv files, "NaN" in MatLab files, etc.

* Metadata for this dataset was extracted from file "DATASET_Cruise_optical_properties.rtf"

* Column (E2_to_E3,S275_to_295, S350_to_400, S_R) with values "BD" for below detection limit within the column had an additional _flag column added to indicate why data were blank in the numeric column.

* Column names adjusted to conform to BCO-DMO naming conventions designed to support broad re-use by a variety of research tools and scripting languages. [Only numbers, letters, and underscores. Can not start with a number]

* DateTime with timezone column added (ISO 8601 format).

* Lat lon columns converted to decimal degrees.

Dataset Version 1:

* Submitter used the revised data described above and resubmitted the data table as "938783_v1_cruise-opt-prop-abs REVISED.csv" which corrected three out of bounds latitudes (originally provided as decimal decimal minutes "345 56.14") with the correct value in decimal degree format 35.93567 (should have been 35 56.14 in "Cruise_fluor_abs.xlsx" ).

* raw .dat files were bundled into a .zip file and attached as a supplemental file to this dataset.

Data Files

File
938783_v1_cruise-opt-prop-abs.csv (Comma Separated Values (.csv), 3.58 KB) MD5:894211a78c5a66498fbc7ecde9ced034 Primary data file for dataset ID 938783, version 1

Supplemental Files

File

Raw absorbance Aqualog (.dat files)
filename: SharpCruise_optics_abs.zip

(ZIP Archive (ZIP), 318.91 KB)
MD5:b3abbdb1e33bb0c181565ccf5e869e95

Raw absorbance data exported from Aqualog (.dat files). Columns are excitation wavelength (nm) and rows are emission wavelength (nm).  The only data used from these .dat files for this dataset was the first column (Wavelength in nm) and the second to last column (column J, Abs, OD, which is the blank corrected absorbance, OD refers to optical density and is unitless).

Column information for .dat files (colname, units, description): 

Wavelength,nm,
I1,uA,Abs Detector Raw
I1 dark,uA,Dark Offset for Abs Detector
R1,uA,Ref Detector Raw
R1dark,uA,Dark Offset for Ref Detector
XCorrect,,Linear interp
I1c,uA,Dark subtracted Abs Detector
R1c,uA,Corrected Ref Detector
I1c/R1c,uA/uA,Corrected Intensity 
Abs,OD,"""-LOG(T)"""
Percent T,T*100,% Transmittance

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1536888
NSF Division of Ocean Sciences	OCE-1536927

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
HRS1608		2016-07-18	R/V Hugh R. Sharp	Michael Gonsior (Chief Scientist)	data info

Instruments

Spectrometer

Supplied Name: Horiba Aqualog spectrofluorometer

Supplied Description:

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

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

Supplied Name	Supplied description	Supplied Units	Standard Name
date	Sampling date Format: %y%m%d	unitless	date
Time	Time of cast (in UTC time zone) Format: %H:%M	unitless	time
ISO_DateTime_UTC	DateTime of cast with time zone (in ISO 8601 format) Format: %Y-%m-%dT%H:%MZ	unitless	ISO_DateTime_UTC
Lat	Latitude	decimal degrees	lat
Long	Longitude	decimal degrees	lon
Salinity	Salinity. Practical Salinity Scale 1978 (PSS-78)	unitless	sal
depth_sample	sampling depth	meters (m)	depth
depth_sample_comment	sampling depth description (e.g. "Chl max")	unitless	sample_descrip
file_name	associated absorbance file (.dat). These files are included in SharpCruise_optics_abs.zip (See supplemental files).	unitless	file_name
E2_to_E3	E2:E3. Ratio of A(250)/A(364)	unitless	no_bcodmo_term
E2_to_E3_flag	Flag column for the E2_to_E3 column. "BD" indicates the E2_to_E3 value is missing due to being below the detection limit.	unitless	no_bcodmo_term
S275_to_295	S(275-295). spectral slope from 275-295 nm	1/nm	no_bcodmo_term
S275_to_295_flag	Flag column for the S275_to_295 column. "BD" indicates the S275_to_295 value is missing due to being below the detection limit.	unitless	no_bcodmo_term
S350_to_400	S(350-400). spectral slope from 350-400 nm	1/nm	no_bcodmo_term
S350_to_400_flag	Flag column for the S350_to_400 column. "BD" indicates the S350_to_400 value is missing due to being below the detection limit.	unitless	no_bcodmo_term
S_R	ratio of S(275-295)/S(350-400)	unitless	no_bcodmo_term
S_R_flag	Flag column for the S_R column. Indicates BD if the S_R value is missing due to being below the detection limit.	unitless	no_bcodmo_term

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Dataset: Cruise optical properties: Absorbance