Dataset: Field Physiochemical Parameters and Nitrogen Specific Uptake Rates

Name: Field physiochemical parameters including nutrient concentrations and nitrogen specific uptake rates from samples collected between 2017 and 2019 from the Arctic Ocean, California Coastal Current, and a Chesapeake Bay estuary
Published: 2023-05-17
Keywords: nitrogen, uptakes, chlorophyll, nutrients, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.896181.1

Spatial Extent: N:72.55 E:-76.687 S:28.29 W:-115.91

Temporal Extent: 2017-05-03 - 2019-07-16

Project:

Collaborative Research: Creatine Cycling in Marine Bacterial and Phytoplankton Assemblages (Creatine Cycling)

Principal Investigator:

Deborah A. Bronk (Virginia Institute of Marine Science, VIMS)

Co-Principal Investigator:

Boris Wawrik (University of Oklahoma, OU)

Zhibo Yang (University of Oklahoma, OU)

Scientist:

Brianna Stanley (Virginia Institute of Marine Science, VIMS)

Contact:

Deborah A. Bronk

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2023-05-17

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Field physiochemical parameters including nutrient concentrations and nitrogen specific uptake rates from samples collected between 2017 and 2019 from the Arctic Ocean, California Coastal Current, and a Chesapeake Bay estuary

Abstract:

Nitrogen is an important macronutrient for biological growth and while research has been traditionally focused on the dissolved inorganic nitrogen pool, dissolved organic nitrogen (DON) is an important, but historically less understood source of nitrogen. This work focused on creatine, a DON metabolite recognized in human nutrition that has not been heavily studied in aquatic systems. Our research investigates the extent and rate at which aquatic organisms may uptake (use) creatine and compares those rates to other nitrogen compounds including ammonium, nitrate, urea, and amino acids. Samples were collected between 2017 and 2019 and cover three North American regions. These include the polar Arctic Ocean, the California Coastal Current (Baja), and a Chesapeake Bay estuary (York River). Included in this dataset are ambient physiochemical parameters for these systems, along with measured specific uptake rates.

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2023-05-17	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.896181.1	2023-06-05

Methods & Sampling

Site water for incubation experiments and for the analysis of ambient nutrients was collected slightly differently for each of the sampling regions. In the Arctic, site water for incubation experiments was collected on the R/V Ukpik and R/V Sikuliaq (cruise ID number SK201712S) during the summer of 2017 using a submersible pump and CTD rosette, respectively. In Baja, sampling occurred twice on the R/V Robert Gordon Sproul during both May and October 2017 (cruise ID numbers SP1714 and SP1727), and site water was collected using a CTD rosette (Turk-Kubo et al. 2021). In Virginia, surface sites in the York River were sampled by directly filling an acid-washed PETG carboy over the side. Filtrations for sample filtrate and filters also varied. These York Rivers samples were obtained during day trips aboard a variety of small powerboats (<21 feet), every other month from June 2018 to July 2019. Powerboats are housed out of the Virginia Institute of Marine Science.

In the Arctic, filtrations were conducted in parallel, which separately passed site water through a larger Nucleopore Membrane filter (3.0 micrometer (μm) nominal pore size) and a smaller Whatman GF-75 filter (nominal pore size 0.3 μm). This same combination of filters was used in Baja in October 2017. In May 2017, Baja sampling used the same filters, but filtered sequentially, meaning that site water was first passed through the Nucleopore filter before passing through the GF-75. The York River site samples were only filtered using the GF-75. Filtrate for all regions was collected from the GF-75 filtration and kept for later nutrient analyses and filters were used for chlorophyll a analysis.

Pigments (chlorophyll a and phaeopigments) were measured after extraction with 90% acetone overnight (Parsons et al. 1984; Arar and Collins 1997). Concentrations of ammonium were analyzed using the Koroleff (1983) method and amino acids were measured as dissolved primary amines (DPA; Parsons et al. 1984). Concentrations of nitrate, nitrite, phosphate, and silica were measured using a Lachat 8500 Quickchem autoanalyzer. Urea was analyzed using the monoxime method (Price and Harrison 1987). Concentrations of total dissolved nitrogen and dissolved organic carbon were assessed using a Shimadzu TOC-V TNM (Hansell 1993). Dissolved organic nitrogen is calculated as the difference between total dissolved nitrogen and inorganic nitrogen.

Nitrogen uptakes were measured after incubation for a set time (1 to 24 hours) in either 0.5 or 1-liter PETG bottles. Stable isotope tracer methods were used according to those described in Baer et al (2017). Uptake rates for inorganic and organic nitrogen were measured by incubating water with 15N- ammonium, nitrate, creatine, urea, and/or an amino acid mixture under in situ light and temperature conditions in a flow-through system on deck or in a cold room set to ambient site water temperatures. Rate incubation experiments were terminated with the same filtration methods as collection of site water ambients with the exception that a Sterlitech silver filter was used in lieu of the Nucleopore Membrane filter. The exact combination of nitrogen substrates varied between sites and regions. All nitrogen uptake samples were analyzed on a Sercon Integra 2 isotope ratio mass spectrometer.

Known Issues/Problems:
Note that for the October sampling in the Baja region, chlorophyll a concentrations for the nutrient size fractions are unavailable. Instead, chlorophyll a concentrations for the >0.7 μm size fraction are available thanks to the Arrigo and Zehr dataset (listed under "Related Datasets").

Data Processing Description

Data Processing:
It is important to note that potential specific uptake rates are reported based on sampled size fraction (i.e. >3.0 or >0.3 μm). When applicable, the rates of different size fractions were combined for the final reported specific uptake rate (i.e >3.0 and 0.3 - 3.0 μm fractions added to report a >0.3 μm rate). Rates of ammonium-specific uptake were corrected for isotope dilution when possible. These rates were corrected according to Gilbert et al. (1982).

BCO-DMO Processing:
- removed "NA" and "ND" (missing data values are blank/empty in the final .csv data file);
- converted the Date column to YYYY-mm-dd format;
- converted the Time column to HH:MM format;
- created the ISO_DateTime_UTC column, which presents date and time in UTC in ISO 8601 format;
- renamed fields to comply with BCO-DMO naming conventions in which the only allowed characters are letters (A-Z, a-z), numbers (0-9), and underscores.

Data Files

File
creatine_nutrients_n_rates.csv (Octet Stream, 26.24 KB) MD5:8ceb2a679904acfff535b19228a77d46 Primary data file for dataset ID 896181

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1635369

Deployments

Deployment	Start Date	Platform	Investigator
SKQ201712S	2017-08-06	R/V Sikuliaq	Laurie Juranek (Chief Scientist)	data info
SP1714	2017-05-03	R/V Robert Gordon Sproul	Matthew M. Mills (Chief Scientist)	data info
SP1727	2017-10-04	R/V Robert Gordon Sproul	Matthew M. Mills (Chief Scientist)	data info
Ukpik_July-August_2017	2017-07-25	R/V Ukpik	Rachel E. Sipler (Chief Scientist)	data info

Instruments

Mass Spectrometer

Supplied Name: Sercon Integra2 Mass Spectrometer

Supplied Description:

Used to measure isotope ratios and particulate masses

Instrument Type

Generic Name: Mass Spectrometer

Acronym: Mass Spec

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

Generic Description:

General term for instruments used to measure the mass-to-charge ratio of ions; generally used to find the composition of a sample by generating a mass spectrum representing the masses of sample components.

Niskin bottle

Supplied Name: 8-liter Niskin bottles

Supplied Description:

Used for site water sampling on R/V Sikuliaq and R/V Robert Gordon Sproul cruises

Instrument Type

Generic Name: Niskin bottle

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/

Generic Description:

A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc.

Nutrient Autoanalyzer

Supplied Name: Lachat QuickChem 8500 autoanalyzer

Supplied Description:

Used to measure nitrate, nitrite, phosphate, and silicate concentrations

Instrument Type

Generic Name: Nutrient Autoanalyzer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB04/

Generic Description:

Nutrient Autoanalyzer is a generic term used when specific type, make and model were not specified. In general, a Nutrient Autoanalyzer is an automated flow-thru system for doing nutrient analysis (nitrate, ammonium, orthophosphate, and silicate) on seawater samples.

Pump

Supplied Name: Johnson Pump model # 16004

Supplied Description:

Used to collect site water samples on R/V Ukpik cruise

Instrument Type

Generic Name: Pump

Generic Description:

A pump is a device that moves fluids (liquids or gases), or sometimes slurries, by mechanical action. Pumps can be classified into three major groups according to the method they use to move the fluid: direct lift, displacement, and gravity pumps

Shimadzu TOC-V Analyzer

Supplied Name: Shimadzu 5000A TOC-V/TNM

Supplied Description:

Used to measure dissolved organic carbon and total dissolved nitrogen concentrations

Instrument Type

Generic Name: Shimadzu TOC-V Analyzer

Acronym: Shimadzu TOC-V

Community Identifier: http://onto.nerc.ac.uk/CAST/124

Generic Description:

A Shimadzu TOC-V Analyzer measures DOC by high temperature combustion method.

Spectrophotometer

Supplied Name: Shimadzu RF-600 Spectrofluorophotometer

Supplied Description:

Used to measure concentrations of dissolved primary amines

Instrument Type

Generic Name: Spectrophotometer

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

Generic Description:

An instrument used to measure the relative absorption of electromagnetic radiation of different wavelengths in the near infra-red, visible and ultraviolet wavebands by samples.

Turner Designs Fluorometer 10-AU

Supplied Name: Turner Design Model 10-AU fluorometer

Supplied Description:

Used to measure cholrophyll a and phaeopigement concentrations

Instrument Type

Generic Name: Turner Designs Fluorometer 10-AU

Acronym: Turner Fluorometer 10-AU

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0393/

Generic Description:

The Turner Designs 10-AU Field Fluorometer is used to measure Chlorophyll fluorescence. The 10AU Fluorometer can be set up for continuous-flow monitoring or discrete sample analyses. A variety of compounds can be measured using application-specific optical filters available from the manufacturer. (read more from Turner Designs, turnerdesigns.com, Sunnyvale, CA, USA)

UV Spectrophotometer-Shimadzu

Supplied Name: Shimadzu UV-1800 spectrophotometer

Supplied Description:

Used to measure urea and ammonium concentrations

Instrument Type

Generic Name: UV Spectrophotometer-Shimadzu

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

Generic Description:

The Shimadzu UV Spectrophotometer is manufactured by Shimadzu Scientific Instruments (ssi.shimadzu.com). Shimadzu manufacturers several models of spectrophotometer; refer to dataset for make/model information.

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
Ship	Name of research vessel	unitless	ship
Region	General geogrpaphic region for the data collected	unitless	region
Designator	Numerical cruise number or other descriptor	unitless	cruise_id
Site_Name	Name or descriptor of sampled site location	unitless	site
Latitude	Latitude (the North direction is represented by positive numbers)	decimal degrees	lat
Longitude	Longitude (the West direction is represented by negative numbers)	decimal degrees	lon
Date	Date of sample collection in the local time zone Format: %Y-%m-%d	unitless	date
Time	Time of sample collection recorded in the respective local time using a 24 hour clock Format: %H:%M	unitless	time
Time_Zone	Respective local time zone where AKDT is Alaska Daylight Time, EST is Eastern Standard Time, and EDT is Eastern Daylight Time	unitless	time_zone
ISO_DateTime_UTC	Date and time of sample collection in UTC in ISO 8601 format Format: %Y-%m-%dT%H:%MZ	unitless	ISO_DateTime_UTC
Water_Depth	General descriptor (e.g., surface, Chlorophyll maximum, etc.)	unitless	sample_descrip
Sample_Depth	Depth sample collected at in meters	meters (m)	depth
Total_Water_Column_Depth	Depth of the total water column in meters	meters (m)	depth_w
Salinity	Salinity of site water in parts per trillion	parts per trillion	sal
Temperature	Temperature of site water in degrees Celsius	degrees Celsius	temp
Total_Dissolved_N	Total dissolved nitrogen in micromoles nitrogen per liter	micromoles per liter (umol/L)	TDN
Total_Dissolved_Nz_Std	One standard deviation of Total_Dissolved_N	micromoles per liter (umol/L)	TDN
Nitrite	Nitrite in micromoles nitrogen per liter; 0.000 = Below detection; Detection limit: 0.05 umol N L-1	micromoles per liter (umol/L)	NO2
Nitrite_Std	One standard deviation of Nitrite. "SL" means "Sample lost".	micromoles per liter (umol/L)	NO2
Nitrate	Nitrate in micromoles nitrogen per liter; 0.000 = Below detection; Detection limit: 0.05 umol N L-1	micromoles per liter (umol/L)	NO3
Nitrate_Std	One standard deviation of Nitrate	micromoles per liter (umol/L)	NO3
Ammonium	Ammonium in micromoles nitrogen per liter; 0.000 = Below detection; Detection limit: 0.03 umol N L-1	micromoles per liter (umol/L)	NH4
Ammonium_Std	One standard deviation of Ammonium	micromoles per liter (umol/L)	NH4
Dissolved_Organic_N	Dissolved organic nitrogen in micromoles nitrogen per liter	micromoles per liter (umol/L)	DON
Dissolved_Organic_N_Std	One standard deviation of Dissolved_Organic_N. "SL" means "Sample lost".	micromoles per liter (umol/L)	DON
Urea	Urea in micromoles nitrogen per liter; 0.000 = Below detection; Detection limit: 0.1 umol N L-1	micromoles per liter (umol/L)	Urea
Urea_Std	One standard deviation of Urea	micromoles per liter (umol/L)	Urea
Dissolved_Primary_Amines	Dissolved primary amine in micromoles nitrogen per liter; 0.000 = Below detection; Detection limit: 0.025 umol N L-1	micromoles per liter (umol/L)	primary_amines
Dissolved_Primary_Amines_Std	One standard deviation of Dissolved_Primary_Amines	micromoles per liter (umol/L)	primary_amines
Dissolved_Organic_C	Dissolved organic carbon in micromoles carbon per liter	micromoles per liter (umol/L)	DOC
Dissolved_Organic_C_Std	One standard deviation of Dissolved_Organic_C	micromoles per liter (umol/L)	DOC
Phosphate	Phosphate in micromoles phosphorus per liter; 0.000 = Below detection; Detection limit: 0.05 umol N L-1	micromoles per liter (umol/L)	PO43-
Phosphate_Std	One standard deviation of Phosphate	micromoles per liter (umol/L)	PO43-
Silicate	Silicate in micromoles silica per liter; 0.000 = Below detection; Detection limit: 0.11 umol N L-1	micromoles per liter (umol/L)	Silicate
Silicate_Std	One standard deviation of Silicate	micromoles per liter (umol/L)	Silicate
Chl_a_gt_3um	Chlorophyl a in micrograms per liter in the size fraction representing the community greater than 3.0 micrometers (>3.0um); 0.000 = Below detection; Detection limit: 0.025 ug L-1	micrograms per liter (ug/L)	chl_a
Chl_a_gt_3um_Std	One standard deviation of Chl_a_gt_3um	micrograms per liter (ug/L)	chl_a
Chl_a_gt_7tenths_um	Chlorophyl a in micrograms per liter in the size fraction representing the community greater than 0.7 micrometers (>0.7um); 0.000 = Below detection; Detection limit: 0.025 ug L-1	micrograms per liter (ug/L)	chl_a
Chl_a_gt_7tenths_um_Std	One standard deviation of Chl_a_gt_7tenths_um	micrograms per liter (ug/L)	chl_a
Phaeo_gt_3um	Phaeopigment in micrograms per liter in the size fraction representing the community greater than 3.0 micrometers (>3.0um)	micrograms per liter (ug/L)	phaeo
Phaeo_gt_3um_Std	One standard deviation of Phaeo_gt_3um	micrograms per liter (ug/L)	phaeo
Chl_a_gt_3tenths_um	Chlorophyl a in micrograms per liter in the size fraction representing the community greater than 0.3 micrometers (>0.3um); 0.000 = Below detection; Detection limit: 0.025 ug L-1	micrograms per liter (ug/L)	chl_a
Chl_a_gt_3tenths_um_Std	One standard deviation of Chl_a_gt_3tenths_um	micrograms per liter (ug/L)	chl_a
Phaeo_gt_3tenths_um	Phaeopigment in micrograms per liter in the size fraction representing the community greater than 0.3 micrometers (>0.3um)	micrograms per liter (ug/L)	phaeo
Phaeo_gt_3tenths_um_Std	One standard deviation of Phaeo_gt_3tenths_um	micrograms per liter (ug/L)	phaeo
Creatine_V_gt_3um	Specific uptake rate of creatine per hour in the size fraction representing the community greater than 3.0 micrometers (>3.0um)	per hour	creatine
Creatine_V_gt_3um_Std	One standard deviation of Creatine_V_gt_3um	per hour	creatine
Creatine_V_3tenths_to_3um	Specific uptake rate of creatine per hour in the size fraction representing the community between 0.3 and 3.0 micrometers (0.3-3.0um)	per hour	creatine
Creatine_V_3tenths_to_3um_Std	One standard deviation of Creatine_V_3tenths_to_3um	per hour	creatine
Creatine_V_gt_3tenths_um	Specific uptake rate of creatine per hour in the size fraction representing the community greater than 0.3 micrometers (>0.3um)	per hour	creatine
Creatine_V_gt_3tenths_um_Std	One standard deviation of Creatine_V_gt_3tenths_um	per hour	creatine
Isotope_Dilution_Corrected_Ammonium_V_gt_3um	Specific uptake rate per hour for ammonium, corrected for isotope dilution, in the size fraction representing the community greater than 3.0 micrometers (>3.0um)	per hour	NH4
Isotope_Dilution_Corrected_Ammonium_V_gt_3um_Std	One standard deviation of Isotope_Dilution_Corrected_Ammonium_V_gt_3um	per hour	NH4
Isotope_Dilution_Corrected_Ammonium_V_gt_3tenths_um	Specific uptake rate per hour for ammonium, corrected for isotope dilution, in the size fraction representing the community greater than 0.3 micrometers (>0.3um)	per hour	NH4
Isotope_Dilution_Corrected_Ammonium_V_gt_3tenths_um_Std	One standard deviation of Isotope_Dilution_Corrected_Ammonium_V_gt_3tenths_um	per hour	NH4
Ammonium_V_gt_3um	Specific uptake rate of ammonium per hour in the size fraction representing the community greater than 3.0 micrometers (>3.0um)	per hour	NH4
Ammonium_V_gt_3um_Std	One standard deviation of Ammonium_V_gt_3um	per hour	NH4
Ammonium_V_3tenths_to_3um	Specific uptake rate of ammonium per hour in the size fraction representing the community between 0.3 and 3.0 micrometers (0.3-3.0um)	per hour	NH4
Ammonium_V_3tenths_to_3um_Std	One standard deviation of Ammonium_V_3tenths_to_3um	per hour	NH4
Ammonium_V_gt_3tenths_um	Specific uptake rate of ammonium per hour in the size fraction representing the community greater than 0.3 micrometers (>0.3um)	per hour	NH4
Ammonium_V_gt_3tenths_um_Std	One standard deviation of Ammonium_V_gt_3tenths_um	per hour	NH4
Nitrate_V_gt_3um	Specific uptake rate of nitrate per hour in the size fraction representing the community greater than 3.0 micrometers (>3.0um)	per hour	NO3
Nitrate_V_gt_3um_Std	One standard deviation of Nitrate_V_gt_3um	per hour	NO3
Nitrate_V_gt_3tenths_um	Specific uptake rate of nitrate per hour in the size fraction representing the community greater than 0.3 micrometers (>0.3um)	per hour	NO3
Nitrate_V_gt_3tenths_um_Std	One standard deviation of Nitrate_V_gt_3tenths_um	per hour	NO3
Urea_V_gt_3um	Specific uptake rate of urea per hour in the size fraction representing the community greater than 3.0 micrometers (>3.0um)	per hour	Urea
Urea_V_gt_3um_Std	One standard deviation of Urea_V_gt_3um	per hour	Urea
Urea_V_gt_3tenths_um	Specific uptake rate of urea per hour in the size fraction representing the community greater than 0.3 micrometers (>0.3um)	per hour	Urea
Urea_V_gt_3tenths_um_Std	One standard deviation of Urea_V_gt_3tenths_um	per hour	Urea
AA_V_gt_3um	Specific uptake rate of amino acids per hour in the size fraction representing the community greater than 3.0 micrometers (>3.0um)	per hour	no_bcodmo_term
AA_V_gt_3um_Std	One standard deviation of AA_V_gt_3um	per hour	no_bcodmo_term
AA_V_3tenths_to_3um	Specific uptake rate of amino acids per hour in the size fraction representing the community between 0.3 and 3.0 micrometers (0.3-3.0um)	per hour	no_bcodmo_term
AA_V_3tenths_to_3um_Std	One standard deviation of AA_V_3tenths_to_3um	per hour	no_bcodmo_term
AA_V_gt_3tenths_um	Specific uptake rate of amino acids per hour in the size fraction representing the community greater than 0.3 micrometers (>0.3um)	per hour	no_bcodmo_term
AA_V_gt_3tenths_um_Std	One standard deviation of AA_V_gt_3tenths_um	per hour	no_bcodmo_term

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Dataset: Field Physiochemical Parameters and Nitrogen Specific Uptake Rates