Dataset: Gulf of Mexico deckboard ammonium uptake

Name: Ammonium uptake from short-term 6-hour deckboard incubations on R/V Nancy Foster cruises NF1704 and NF1802 in the Gulf of Mexico in May of 2017 and 2018
Published: 2021-01-12
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.836133.1

Spatial Extent: N:28.354 E:-87.209 S:25.50607 W:-89.396

Temporal Extent: 2017-05-11 - 2018-05-16

Project:

Collaborative Research: Mesoscale variability in nitrogen sources and food-web dynamics supporting larval southern bluefin tuna in the eastern Indian Ocean (BLOOFINZ-IO)

Effects of Nitrogen Sources and Plankton Food-Web Dynamics on Habitat Quality for the Larvae of Atlantic Bluefin Tuna in the Gulf of Mexico (GoMex Tuna Foodweb B)

Program:

Second International Indian Ocean Expedition (IIOE-2)

Principal Investigator:

Michael R. Stukel (Florida State University, FSU)

Co-Principal Investigator:

Thomas Kelly (Florida State University, FSU)

BCO-DMO Data Manager:

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

Version:

Version Date:

2021-01-12

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Ammonium uptake from short-term 6-hour deckboard incubations on R/V Nancy Foster cruises NF1704 and NF1802 in the Gulf of Mexico in May of 2017 and 2018

Abstract:

Ammonium uptake from short-term 6-hour deckboard incubations on R/V Nancy Foster cruises NF1704 and NF1802 in the Gulf of Mexico in May of 2017 and 2018.

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2021-01-12	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.836133.1	2021-04-06

Description

In addition to the funding sources listed in the "Funding Source" section, this dataset was partially funded by:

National Oceanic and Atmospheric Administration's RESTORE Program Grant (Project Title: Effects of nitrogen sources and plankton food-web dynamics on habitat quality for the larvae of Atlantic bluefin tuna in the Gulf of Mexico) under federal funding opportunity NOAA-NOS-NCCOS-2017-2004875, including NOAA JIMAR Cooperative Agreement, award #NA16NMF4320058, NOAA CIMAS Cooperative Agreement, award #NA15OAR4320064, and NOAA CIMEAS Cooperative Agreement, award #NA15OAR4320071.

Methods & Sampling

We conducted short term (6-h) NH4+ uptake experiments in deckboard incubators. Each incubator was uniformly shaded using clear or blue-tinted acrylic sheets to achieve three light levels as determined by simultaneously using a 2-π LI-COR photosynthetically active radiation (PAR) sensor to measure downwelling irradiance and a 4-π water-proof LI-COR PAR sensor to measure ambient irradiance within the incubator. These calibrations were done on the ship to account for light reflection or ship shading. Incubation light levels for the NF17 cruise were determined to be 145% (clear, surface), 79% (mixed layer), and 21% (lower mixed layer) of surface irradiance. For the NF1802 cruise, the clear incubator was replaced with one screened to 1.7% surface irradiance to mimic deep chlorophyll maximum light. All incubators were cooled with mixed-layer seawater. Samples were drawn from depths near these light levels (as determined from noon CTD casts with CTD-mounted PAR sensor).

To determine patterns of ammonium uptake with depth, three 2.7-L samples from each of the three incubator light levels (e.g. 5 m, 15 m, 45 m for surface, 79% and 21% light levels, respectively) were collected near dusk and placed in the incubators until dawn (ship schedule and CTD water budget did not allow dawn sampling for these experiments). At dawn triplicate samples from each depth were spiked with 15NH4+ (final concentration of 9.9 or 4.7 nmol L-1 on NF17 and NF18, respectively) and incubated for 6-h (dawn to roughly local noon). At the end of the incubation bottles were immediately vacuum filtered onto pre-combusted 25-mm GF/F filters in the dark. Filters were rinsed with filtered seawater, wrapped in foil and stored at 80°C. On land, samples were fumigated with HCl vapor to remove inorganic carbon, dried, and placed inside a tin cup for C/N and isotopic analysis at the UC Davis stable isotope facility. NH4+ uptake rates in each incubation bottle (and associated uncertainties) were determined using equations in Stukel (2020).

Data Processing Description

In situ ammonium uptake rates were estimated using either equation ρkan,is (Eq. 6) or ρreg,is (Eq. 14) from Stukel (2020). ρkan,is was used if there was not evidence for high recycling within the incubation bottle (Φ<0.6). ρreg,is was used if there was evidence for high recycling within the incubation bottle (Φ>0.6). See Fig. 4 of Stukel (2020).

BCO-DMO Data Manager Processing Notes:
* Data in original excel file "Deckboard Ammonium Uptake.xlsx" exported as csv with the formatting that was set in Excel.
* Cells with value #NUM! in excel were imported as blank cells (meaning no data).
* Converted Date format to ISO 8601 format yyyy-mm-dd
* modified parameter names to conform with BCO-DMO naming conventions: only A-Za-z0-9 and underscore allowed. Can not start with a number. (spaces, +, and - changed to underscores).
* Removed percent character "%" from the values in the Light_Level column so it could be typed as numeric. The units (percent) are described in the parameter description section.

Data Files

File
deckboard_ammonium_uptake.csv (Comma Separated Values (.csv), 18.06 KB) MD5:7a85bbe863e3ab7b9cdbe4d6c7acf16e Primary data file for dataset ID 836133

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1851347
National Oceanic and Atmospheric Administration	NA16NMF4320058

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
NF1704	BLOOFINZ-GoM	2017-05-07	R/V Nancy Foster	Estrella Malca (Chief Scientist)	data info
NF1802	BLOOFINZ-GoM	2018-04-27	R/V Nancy Foster	John Lamkin (Chief Scientist)	data info

Instruments

CTD - profiler

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: CTD - profiler

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/130/

Generic Description:

The Conductivity, Temperature, Depth (CTD) unit is an integrated instrument package designed to measure the conductivity, temperature, and pressure (depth) of the water column. The instrument is lowered via cable through the water column. It permits scientists to observe the physical properties in real-time via a conducting cable, which is typically connected to a CTD to a deck unit and computer on a ship. The CTD is often configured with additional optional sensors including fluorometers, transmissometers and/or radiometers. It is often combined with a Rosette of water sampling bottles (e.g. Niskin, GO-FLO) for collecting discrete water samples during the cast.

This term applies to profiling CTDs. For fixed CTDs, see https://www.bco-dmo.org/instrument/869934.

Elemental Analyzer

Supplied Name: PDZ Europa ANCA-GSL elemental analyzer

Supplied Description:

PDZ Europa ANCA-GSL elemental analyzer interfaced to a PDZ Europa 20-20 isotope ratio mass spectrometer (Sercon Ltd., Cheshire, UK). C/N and isotopic analysis at the UC Davis stable isotope facility.

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.

Isotope-ratio Mass Spectrometer

Supplied Name: PDZ Europa 20-20 isotope ratio mass spectrometer (Sercon Ltd., Cheshire, UK)

Supplied Description:

PDZ Europa ANCA-GSL elemental analyzer interfaced to a PDZ Europa 20-20 isotope ratio mass spectrometer (Sercon Ltd., Cheshire, UK). C/N and isotopic analysis at the UC Davis stable isotope facility.

Instrument Type

Generic Name: Isotope-ratio Mass Spectrometer

Acronym: IR Mass Spec; IRMS

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/

Generic Description:

The Isotope-ratio Mass Spectrometer is a particular type of mass spectrometer used to measure the relative abundance of isotopes in a given sample (e.g. VG Prism II Isotope Ratio Mass-Spectrometer).

Photosynthetically Available Radiation Sensor

Supplied Name:

Supplied Description:

2-π LI-COR photosynthetically active radiation (PAR) sensor to measure downwelling irradiance.

4-π water-proof LI-COR PAR sensor to measure ambient irradiance.

Samples were drawn from depths near these light levels (as determined from noon CTD casts with CTD-mounted PAR sensor).

Instrument Type

Generic Name: Photosynthetically Available Radiation Sensor

Acronym: PAR sensor

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/122/

Generic Description:

A PAR sensor measures photosynthetically available (or active) radiation. The sensor measures photon flux density (photons per second per square meter) within the visible wavelength range (typically 400 to 700 nanometers). PAR gives an indication of the total energy available to plants for photosynthesis. This instrument name is used when specific type, make and model are not known.

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
Cruise	Name of cruise	unitless	cruise_id
Sample	Sample name	unitless	sample
Cycle	Lagrangian Experiment Number	unitless	exp_id
Date	Date of collection and incubation Format: %Y-%m-%d	unitless	date_local
Cast	CTD-Niskin rosette cast number	unitless	cast
Lon	Longitude	decimal degrees	lon
Lat	Latitude	decimal degrees	lat
Depth	Depth	meters (m)	depth
Light_Level	Percent surface irradiance	percent (%)	irradiance
T	Duration of Incubation in decimal hours.	hours	time_elapsed
Sigma_T	Estimated measurement uncertainty (sigma, σ) for duration	hours	time_elapsed
P	PON, Particulate organic nitrogen (final)	micromoles of nitrogen per liter (µmol N L-1)	PON
Sigma_P	Estimated measurement uncertainty (sigma, σ) for PON	micromoles of nitrogen per liter (µmol N L-1)	PON
Ip_T	Ip(T), Isotope ratio of PON (final)	atom percent (%)	no_bcodmo_term
Sigma_Ip_T	Estimated measurement uncertainty (sigma, σ) for Ip(T)	atom percent (%)	no_bcodmo_term
Ip_0	Ip(0), Isotope ratio of PON (initial)	atom percent (%)	no_bcodmo_term
Sigma_Ip_0	Estimated measurement uncertainty (sigma, σ) for Ip(0)	atom percent (%)	no_bcodmo_term
I_spk	Isotope ratio of tracer spike	atom percent (%)	no_bcodmo_term
Sigma_I_spk	Estimated measurement uncertainty (sigma, σ) for I_spk	atom percent (%)	no_bcodmo_term
I_amb	Isotope ratio of ambient ammonium	atom percent (%)	NH4
Sigma_I_amb	Estimated measurement uncertainty (sigma, σ) for I_amb	atom percent (%)	NH4
N_spk	Final concentration of tracer spike. [N]spk	micromoles of nitrogen per liter (µmol N L-1)	no_bcodmo_term
Sigma_N_spk	Estimated measurement uncertainty (sigma, σ) for [N]spk	micromoles of nitrogen per liter (µmol N L-1)	no_bcodmo_term
N_amb	Ambient ammonium concentration	micromoles of nitrogen per liter (µmol N L-1)	NH4
Sigma_N_amb	Estimated measurement uncertainty (sigma, σ) for [N]amb	micromoles of nitrogen per liter (µmol N L-1)	no_bcodmo_term
a	Assumed ratio of regeneration to uptake	dimensionless	no_bcodmo_term
Sigma_a	Estimated measurement uncertainty (sigma, σ) for "a" (Assumed ratio of regeneration to uptake).	dimensionless	no_bcodmo_term
L10KS	Assumed log10(half-saturation constant)	micromoles of nitrogen per liter (µmol N L-1)	no_bcodmo_term
Sigma_L10KS	Estimated measurement uncertainty (sigma, σ) for L10KS	micromoles of nitrogen per liter (µmol N L-1)	no_bcodmo_term
Ammonium_Uptake	Ammonium Uptake	nanomoles of nitorgen per liter per hour (nmol N L-1 h-1)	no_bcodmo_term
Sigma_Ammonium_Uptake	Propagated measurement uncertainty (sigma, σ) for ammonium uptake	nanomoles of nitorgen per liter per hour (nmol N L-1 h-1)	no_bcodmo_term

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Dataset: Gulf of Mexico deckboard ammonium uptake