Dataset: Bottle TN368

Name: Bottle sample data from CTD casts from the third cruise of SPIROPA project, R/V Thomas G. Thompson cruise TN368, to the New England Shelfbreak in July of 2019
Published: 2022-06-08
Keywords: nutrients, Productivity, chlorophyll, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.849340.2

Spatial Extent: N:41.391 E:-70.0012 S:39.1242 W:-71.337

Temporal Extent: 2019-07-08 - 2019-07-16

Project:

Collaborative Research: Shelfbreak Frontal Dynamics: Mechanisms of Upwelling, Net Community Production, and Ecological Implications (SPIROPA)

Principal Investigator:

Dennis J. McGillicuddy (Woods Hole Oceanographic Institution, WHOI)

Co-Principal Investigator:

Christian Petitpas (Massachusetts Division of Marine Fisheries)

Walker O. Smith (Virginia Institute of Marine Science, VIMS)

Heidi M. Sosik (Woods Hole Oceanographic Institution, WHOI)

Rachel Stanley (Wellesley College)

Jefferson Turner (University of Massachusetts Dartmouth, UMass Dartmouth)

Weifeng Gordon Zhang (Woods Hole Oceanographic Institution, WHOI)

Contact:

Dennis J. McGillicuddy (Woods Hole Oceanographic Institution, WHOI)

Data Manager:

Olga Kosnyrev (Woods Hole Oceanographic Institution, WHOI)

BCO-DMO Data Manager:

Karen Soenen (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

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

Version:

Version Date:

2022-06-08

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Bottle sample data from CTD casts from the third cruise of SPIROPA project, R/V Thomas G. Thompson cruise TN368, to the New England Shelfbreak in July of 2019

Abstract:

Bottle sample data from CTD casts from the third cruise of SPIROPA project, R/V Thomas G. Thompson cruise TN368, to the New England Shelfbreak in July of 2019.

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2022-06-08	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.849340.2	2022-08-11
2021-04-19	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.849340.1	2021-04-21

Description

Cast numbers in version 1 are: [39,62,70:71,81:82, 86, 89,100,118]

Cast numbers in version 2 are: [1:4,6:18,20,24,26,28,30:89,91:140]. Version 2 of the dataset also has extra parameter Triple Oxygen Isotope (TOI).

Methods & Sampling

Location: New England Shelfbreak 40 S 71W depth : 0-2000m.

Standard station CTD profiles measurements (down casts, see related dataset ID: 807119) with water sampling (up casts). This dataset (dataset ID 849340) includes the bottle sample data which is from the up casts.

Twenty-four 10 L Niskin bottles fitted with Teflon-coated external closures were used for water column sampling. At each station, samples were typically collected at 12 discrete depths for assessment of nutrient concentrations. These samples were syringe-filtered and stored at -20°C until analysis at the WHOI Nutrient Analytical Facility. Nitrate and silicate were measured using standard AutoAnalyzer techniques. To measure ammonium concentrations, site water was cartridge-filtered (0.1 µm, Pall Co.) directly from Niskin bottles using a peristaltic pump. Filtrate was collected in FalconTM tubes that were pre-treated with orthophthaldialdehyde (OPA) and measured on-board via the OPA method (Holmes et al., 1999) with a detection limit of 10 nM.

To measure particulate organic carbon and nitrogen, water was collected from the Niskin bottles and filtered through combusted 0.7 µm glass fiber filters (Whatman GF/F), rinsed with a weak acid (0.01 N HCl in seawater) to remove carbonates, then dried in combusted glass vials at 60 °C. Diatom biomass was assessed by sampling for biogenic silica. Samples were filtered through 0.6 µm polycarbonate filters, dried at 60°C in plastic Petri dishes, and dissolved in strong acid.

For incubation-based primary productivity, water samples were taken from Niskin bottles at known isolumes, then placed in sterile 285 mL Qorpak bottles, then ~20 µCi NaH14CO3 was added. An on-deck incubator holding the bottles had surface seawater flowing through it, with irradiance attenuated by neutral density filters to the light levels at the isolumes sampled. Blue filters were used for isolumes below 30% Eo. After 24 h, samples were filtered through GFF filters and placed in 7 mL scintillation vials. Size fractionations were conducted at all stations using 20 µm Poretics filters on subsamples from each bottle. 100 µL 1N HCl was added to volatilize absorbed inorganic 14C. Ecolume (5 mL) was then added to each vial, and all vials were counted after 24 h on a liquid scintillation counter. Total activity was measured by counting 100 μL of non-acidified sample in β-phenethanylamine.

Data Processing Description

CTD Sea-Bird Software:

Data acquisition: SBE Seasave, version 7.26.7.107

Data processing: SBE Data Processing, version 7.26.7.114

BCO-DMO data manager processing notes version 1:
* Data form file tn368_bottle_data_Feb_2021_diatom_hotspot.txt imported into the BCO-DMO data system.
* Data imported with missing data identifier NaN will be displayed differently based on the file type downloaded by the user. It will be blank values in .csv files, NaN in matlab files, etc.
* Constructed ISO_DateTime_UTC from year, month, day and time columns which were NMEA UTC times. I checked the cast start times in the corresponding CTD dataset https://www.bco-dmo.org/dataset/807119 to make sure it was correct to pad 0s for time (e.g. 13 is 00:13 not 13:00).
* Made longitude negative since West is negative in decimal degrees.

BCO-DMO data manager processing notes version 2 (replaces version 1):
* Data imported into the BCO-DMO dataset system from file tn368_bottle_data_Dec_2021.txt
* Constructed ISO_DateTime_UTC from year, month, day and time columns which were NMEA UTC times.

Data Files

File
tn368_bottle_v2.csv (Comma Separated Values (.csv), 738.68 KB) MD5:b0744c541649c9fffd05f765777622e9 Primary data file for dataset ID 849340

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1657803

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
TN368		2019-07-05	R/V Thomas G. Thompson	Dennis J. McGillicuddy (Chief Scientist)	data info

Instruments

CTD Sea-Bird SBE 911plus

Supplied Name:

Supplied Description:

Dataset-specific Description SeaBird 911+ Rosette 24-position, 10-liter bottle Rosette with dual T/C sensors At each station, CTD casts measured temperature, salinity and PAR. Water samples collected at depths of 500, 300, 250, 200, 150, 120, 100, 80, 60, 40, 30, 20, 10 m, and the surface were filtered, processed or preserved for further analysis.

Instrument Type

Generic Name: CTD Sea-Bird SBE 911plus

Acronym: CTD SBE 911plus

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0058/

Generic Description:

The Sea-Bird SBE 911 plus is a type of CTD instrument package for continuous measurement of conductivity, temperature and pressure. The SBE 911 plus includes the SBE 9plus Underwater Unit and the SBE 11plus Deck Unit (for real-time readout using conductive wire) for deployment from a vessel. The combination of the SBE 9 plus and SBE 11 plus is called a SBE 911 plus. The SBE 9 plus uses Sea-Bird's standard modular temperature and conductivity sensors (SBE 3 plus and SBE 4). The SBE 9 plus CTD can be configured with up to eight auxiliary sensors to measure other parameters including dissolved oxygen, pH, turbidity, fluorescence, light (PAR), light transmission, etc.). more information from Sea-Bird Electronics

LI-COR Biospherical PAR Sensor

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: LI-COR Biospherical PAR Sensor

Acronym: LI-COR Biospherical PAR

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0074/

Generic Description:

The LI-COR Biospherical PAR Sensor is used to measure Photosynthetically Available Radiation (PAR) in the water column. This instrument designation is used when specific make and model are not known.

Photosynthetically Available Radiation Sensor

Supplied Name: LI-COR Biospherical SPAR

Supplied Description:

The LI-COR Biospherical SPAR Sensor is used to measure Surface Photosynthetically Available Radiation (SPAR).

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.

Pressure Sensor

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Pressure Sensor

Generic Description:

A pressure sensor is a device used to measure absolute, differential, or gauge pressures. It is used only when detailed instrument documentation is not available.

Sea-Bird SBE 43 Dissolved Oxygen Sensor

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Sea-Bird SBE 43 Dissolved Oxygen Sensor

Acronym: SBE-43 DO

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0036/

Generic Description:

The Sea-Bird SBE 43 dissolved oxygen sensor is a redesign of the Clark polarographic membrane type of dissolved oxygen sensors. more information from Sea-Bird Electronics

Turbidity Meter

Supplied Name: Turbidity, WET Labs ECO

Supplied Description:

Instrument Type

Generic Name: Turbidity Meter

Generic Description:

A turbidity meter measures the clarity of a water sample. A beam of light is shown through a water sample. The turbidity, or its converse clarity, is read on a numerical scale. Turbidity determined by this technique is referred to as the nephelometric method from the root meaning "cloudiness". This word is used to form the name of the unit of turbidity, the NTU (Nephelometric Turbidity Unit). The meter reading cannot be used to compare the turbidity of different water samples unless the instrument is calibrated. Description from: http://www.gvsu.edu/wri/education/instructor-s-manual-turbidity-10.htm

(One example is the Orion AQ4500 Turbidimeter)

Wet Labs ECO-AFL/FL Fluorometer

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Wet Labs ECO-AFL/FL Fluorometer

Acronym: ECO AFL/FL

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0172/

Generic Description:

The Environmental Characterization Optics (ECO) series of single channel fluorometers delivers both high resolution and wide ranges across the entire line of parameters using 14 bit digital processing. The ECO series excels in biological monitoring and dye trace studies. The potted optics block results in long term stability of the instrument and the optional anti-biofouling technology delivers truly long term field measurements.
more information from Wet Labs

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
cruise	Cruise identifier	unitless	cruise_id
cast	CTD cast number	unitless	cast
station	Station number	unitless	station
station_id	Station ID: 1-A, 2-B, 3-AUV, 4-AL-CTD, 5-P, 6-NS, 7-EW, 8-NS6A, 9-A10z, 10-SLP, 11-SSF, 12-ALF, 13-AC, 14-AL, 15-HS, 16-S, 17-L'; E.g.: st#=14, stId=1 => stName=14A	unitless	station
year	NMEA UTC year (yyyy)	year	year
month	NMEA UTC month (mm)	month number	month
day	NMEA UTC day (dd)	day of month	day
time	NMEA UTC time (HHMM)	hhmm	time
ISO_DateTime_UTC	Cast start time in ISO8601 format yyyy-mm-ddTHH:MMZ (UTC time) Format: %Y-%m-%dT%H:%MZ	unitless	ISO_DateTime_UTC
latitude	NMEA latitude	decimal degrees	lat
longitude	NMEA longitude (west is negative)	decimal degrees	lon
target_depth	target depth	m	depth_n
depth	depth	m	depth
press	pressure	db	press
niskin_used	The number of bottles used for CTD BTL data averaging if more than	unitless	count
sigmat	Sigma-theta density from primary sensors	kg/m^3	sigma_t
sigmat2	Sigma-theta density from secondary sensors	kg/m^3	sigma_t
oxy	Dissolved oxygen concentration	ml/l	O2
oxyM	Dissolved oxygen concentration	Mm/Kg	O2
oxySat	Dissolved oxygen concentration	Mm/Kg	O2
potTemp	Potential temperature from primary sensor	ITS-90, deg C	potemp
potTemp2	Potential temperature from secondary sensor	ITS-90, deg C	potemp
sal	Salinity practical from primary sensors	unitless	sal
sal2	Salinity practical from secondary sensors	unitless	sal
dens	Density from primary sensors	kg/m^3	density
dens2	Density from secondary sensors	kg/m^3	density
svCM	Sound velocity (chen-millero) from primary sensors	m/s	sound_vel
svCM2	Sound velocity (chen-millero) from secondary sensors	m/s	sound_vel
temp	temperature from primary sensor	ITS-90, deg C	temp
temp2	temperature from secondary sensor	ITS-90, deg C	temp
cond	conductivity from primary sensor	S/m	cond
cond2	conductivity from secondary sensor	S/m	cond
oxyV	oxygen raw	V	O2_v
fluor1	Fluorescence, WET Labs ECO-AFL/FL	mg/m^3	fluor
fluor2	Fluorescence, WET labs CDOM	mg/m^3	fluor
upoly0	Upoly 0, SUNA 2km ASY-NTR-00081	micromolar nitrate (mmol nitrate per m^3)	NO3
trans	CStarTr0: Beam Transmission, WET Labs C-Star	%	trans
turb	turbWETntu0: Turbidity, WET Labs ECO	NTU	turbidity
alt	Altitude (from Altimeter)	m	altitude
salDC	Salinity practical from primary sensor (output from Data Conversion)	Practical Salinity Units (PSU)	sal
spar	SPAR/surface irradiance	microEinsteins/m^2/second	SPAR
par	PAR/irradiance	microEinsteins/m^2/second	PAR
cpar	CPAR/Corrected Irradiance	%	irradiance
V0	Fluor1 Voltage	Volt	flvolt
V6	UserPoly Voltage	Volt	fluor
bottle_nuts	CTD bottle number for nutrient analyses	unitless	bottle
NO3	Nitrate concentration	umol L-1	NO3
NH4	Ammonium concentration	umol L-1	NH4
PO4	Phosphate concentration	umol L-1	PO4
Si	Silicate (SiO4) concentration	umol L-1	SiO4
PPVial	Vial number (primary productivity)	unitless	sample_descrip
Volfilt	Filter Volume (primary productivity)	ml	vol_filt
N_mg	Nitrogen	mg	N
C_mg	Carbon	mg	C
PON	particulate organic Nitrogen	umol L-1	PON
POC	particulate organic Carbon	umol L-1	POC
CN_ratio	Carbon/Nitrogen ratio	mol/mol	C_to_N
Exp	Experiment ID. 1-experiment; 0-regular	unitless	exp_id
Proc_io	irradiance/surface irradiance ratio	%	irradiance
Prod	primary productivity	mg m-3 h-1	PP
IntProd	integrated primary productivity per day	mg C m-2 d-1	PP
Bsi	biogenic silica	umol L-1	Si_bio
Csi	Carbon/silacate ratio	umol kg -1	Silicate
bottle_chl	CTD bottle number for Chlorophyll analyses	unitless	bottle
Filt_0	Filt_0 ID=0. 0 = whole seawater. No water filtering.	unitless	sample_descrip
Chl_x_0	Chlorophyll Filt_0	ug L-1	chl_a
Chl_y_0	Chlorophyll Filt_0 (replicates)	ug L-1	chl_a
Phaeo_x_0	total phaeopigment Filt_0	ug L-1	phaeo
Phaeo_y_0	total phaeopigment Filt_0 (replicates)	ug L-1	phaeo
QCflag_x_0	Filt_0 Quality flag: 1-inspected, 2-some question	unitless	q_flag
QCflag_y_0	Filt_0 (replicates) Quality flag: 1-inspected, 2-some question	unitless	q_flag
Filt_10	Filt_10 ID=10. 10 = <10um size fractionated chl	unitless	sample_descrip
Chl_x_10	Chlorophyll Filt_10	ug L-1	chl_a
Chl_y_10	chlorophyll Filt_10 (replicates)	ug L-1	chl_a
Phaeo_x_10	total phaeopigment Filt_10	ug L-1	phaeo
Phaeo_y_10	total phaeopigment Filt_10 (replicates)	ug L-1	phaeo
QCflag_x_10	Filt_10 Quality flag: 1-inspected, 2-some question	unitless	q_flag
QCflag_y_10	Filt_10 (replicates) Quality flag: 1-inspected, 2-some question	unitless	q_flag
bottle_alk	CTD bottle number for Alkalinity analyses	unitless	bottle
CO3	carbonate ion [CO3]2-	umol/kg	carbonate
HCO3	Bicarbonate.	umol/kg	bicarbonate
Ar	Aragonite	umol / kg	no_bcodmo_term
Ca	Calcium	umol / kg	Ca
Alk	Alkalinity	umol / kg	TALK
Dic	dissolved inorganic carbon	umol / kg	DIC
PCO2	Partial Pressure of Carbon Dioxide	uatm	pCO2
PH	pH	total scale	pH
bottle_nh4HR	CTD bottle number for Ammonium High resolution analyses	unitless	bottle
NH4HR	Ammonium High resolution	nmol L-1	NH4
Sd	Ammonium high resolution Standard deviation.	nmol L-1	std_dev
bottle_toi	CTD bottle number for Triple Oxygen Isotope (TOI) analyses	unitless	bottle
D17corr	D17corr	per meg	17O
Littled17corr	Littled17corr	per mil	17O
D18corr	D18corr	per meg	18O
dO2Arhscorr	O2Arcorr	unitless	O2Ar
Samp_toi	Sample TOI	unitless	TOI
Vial_toi	Vial TOI	unitless	TOI
Dep_toi	Depth TOI	m	TOI
Sample_date_toi	Sanple date TOI	unitless	TOI

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Dataset: Bottle TN368