Dataset: Cruise optical properties: Fluorescence

Name: Fluorescence spectra from niskin bottle samples collected with depth profiles during R/V Hugh R. Sharp cruise HRS1608 Mid-Atlantic Bight in 2016
Published: 2024-10-03
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:

2024-10-03

Restricted:

Validated:

Yes

Current State:

Final no updates expected

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

Abstract:

Fluorescence 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.

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. Samples stored at 4°C until analysis (within 1 week of collection). See "Related Datasets" section for the absorbance data. 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

Fluorescence .dat files: columns are excitation wavelength (nm) and rows are emission wavelength (nm). The value in each cell is the blank corrected and normalized (by fluorescence of a quinine sulfate standard, described in detail below) fluorescence for each exciation/emission pair.

Blank corrected EEM spectra were corrected for any inner filter effects using the Aqualog software. All spectra were normalized to the fluorescence of a 1 ppb quinine sulfate (QS) standard in 0.1 N HClO₄ (STARNA) at excitation 347.5 nm, corrected for sample integration time. A 0.1 N HClO₄ solution (STARNA) was used as the QS blank. Therefore all EEM spectra are reported in QS units (QSU). Rayleigh scattering signals were removed from EEM spectra using the Matlab ® (version 2015a) routine outlined previously (Zepp et al. 2004 doi: 10.1016/j.marchem.2004.02.006).

The following additional parameters were also calculated:

Apeak: intensity and location of maximum in the "A" region (ex/em <260 nm/400 – 460 nm) in (intensity x ex. location x em. location) (Coble et al. 1996)

Cpeak: intensity and location of maximum in the "C" region (ex/em 320 – 360 nm/420 – 460 nm) in (intensity x ex. location x em. location) (Coble et al. 1996)

Fluorescence Index, FI Ratio of fluorescence emission at 470 nm / 520 nm at 370 nm excitation Indicative of DOM source (McKnight et al. 2001)

normalized HIX (nHIX) Integrated emission from 435-480 / (300-345 + 435-480) nm at 254 nm excitation Indicative of DOM source and processing (Ohno 2002a)

Biological Index (BIX) Ratio of the fluorescence intensity at 380 nm to 430 nm at 310 nm excitation Indication of recent microbial activity (Huguet et al. 2009)

BCO-DMO Processing

Preprocessing for version 1:

* Sheet "fluorescence" of submitted file "Cruise_fluor_abs.xlsx" was imported into the BCO-DMO data system for this dataset. Values "NA" and "NaN" 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 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).

* Three out of bounds latitudes (originally provided as decimal decimal minutes "345 56.14") were removed (all were at time 2016-07-21T15:56Z).

* 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-fluor 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
938774_v1_cruise-opt-prop-fluor.csv (Comma Separated Values (.csv), 5.12 KB) MD5:e210305b3fd0f02c3c4573f56c39234b Primary data file for dataset ID 938774, version 1

Supplemental Files

File

Raw fluorescence Aqualog (.dat files)
filename: SharpCruise_optics_fluor.zip

(ZIP Archive (ZIP), 2.22 MB)
MD5:d344f1f276f4f902e60db0460411e401

Raw fluorescence data exported from Aqualog (.dat files). Columns are excitation wavelength (nm) and rows are emission wavelength (nm). The value in each cell is the blank corrected and normalized (by fluorescence of a quinine sulfate standard, described in detail below) fluorescence for each exciation/emission pair.

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 fluorescence file (.dat). These files are included in SharpCruise_optics_fluor.zip (See supplemental files).	unitless	file_name
Apeak	Apeak fluorescence intensity. Intensity and location of maximum in the "A" region (ex/em <260 nm/400 - 460 nm) in (intensity x ex. location x em. location) (Coble et al. 1996)	QSU	no_bcodmo_term
Apeak_ex_wave	Apeak excitation wavelength	nm	no_bcodmo_term
Apeak_em_wave	Apeak emission wavelength	nm	no_bcodmo_term
Cpeak	Cpeak fluorescence intensity. Intensity and location of maximum in the "C" region (ex/em 320 - 360 nm/420 - 460 nm) in (intensity x ex. location x em. location) (Coble et al. 1996)	QSU	no_bcodmo_term
Cpeak_ex_wave	Cpeak excitation wavelength	nm	no_bcodmo_term
Cpeak_em_wave	Cpeak emission wavelength	nm	no_bcodmo_term
FI	fluorescence index. FI Ratio of fluorescence emission at 470 nm / 520 nm at 370 nm excitation Indicative of DOM source (McKnight et al. 2001)	unitless	no_bcodmo_term
BIX	biological index (BIX). Ratio of the fluorescence intensity at 380 nm to 430 nm at 310 nm excitation Indication of recent microbial activity (Huguet et al. 2009)	unitless	no_bcodmo_term
nHIX	normalized humification index. Normalized HIX (nHIX) Integrated emission from 435-480 / (300-345 + 435-480) nm at 254 nm excitation Indicative of DOM source and processing (Ohno 2002a)	unitless	no_bcodmo_term

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Dataset: Cruise optical properties: Fluorescence