http://lod.bco-dmo.org/id/dataset/914901
eng; USA
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dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2023-11-14
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
CTD-associated variables, bottle salinity measurements, oxygen titrations, nutrient analyses, biogeochemical/biological variables, and DIC chemistry variables from R/V Thomas G. Thompson cruise TN376 from January to March 2020
2024-04-17
publication
2024-04-17
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2024-04-17
publication
https://doi.org/10.26008/1912/bco-dmo.914901.1
William M. Balch
Bigelow Laboratory for Ocean Sciences
principalInvestigator
Nicholas R. Bates
Bermuda Institute of Ocean Sciences
principalInvestigator
Dennis J. McGillicuddy
Woods Hole Oceanographic Institution
principalInvestigator
Peter L. Morton
Florida State University - National High Magnetic Field Lab
principalInvestigator
Colin Brownlee
The Marine Biological Association of the United Kingdom
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Balch, W. M., Bates, N., McGillicuddy, D. J., Morton, P. L., Brownlee, C. (2024) CTD-associated variables, bottle salinity measurements, oxygen titrations, nutrient analyses, biogeochemical/biological variables, and DIC chemistry variables from R/V Thomas G. Thompson cruise TN376 from January to March 2020. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-04-17 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.914901.1 [access date]
TN376 Bottle Data Dataset Description: Methods and Sampling: <p>R/V Thomas G. Thompson (cruise ID TN376) departed Cape Town, South Africa (SA) on 22 January 2020. The ship transited to the Southern Ocean and returned to Mauritius on 3 March 2020.</p>
<p>Due to the ship breakdown early into the cruise and the need to divert to Durban, SA, for engine repairs, we divided the cruise into five legs, as defined by our revised cruise plan, then pre- and post-diversion engine repairs in Durban, SA. A detailed summary of each of the legs and associated measurements can be found on the BCO-DMO cruise page for TN376: <a href="https://www.bco-dmo.org/deployment/904210" target="_blank">https://www.bco-dmo.org/deployment/904210</a>. (For overall completeness of the sampling timeline, all science activities are included here (not necessarily just those for which this dataset encompasses). This dataset includes the CTD bottle data. Those activities not related to this dataset, but conducted on the cruise are: Video Plankton Recorder (VPR), carboy experiments, barite precipitation experiments, and real-time filter/freeze/transfer preparations for examination of phytoplankton during the cruise.)</p>
<p><strong>Sampling methods:</strong><br />
At sea collections: Water samples were collected using CTD casts from 71 stations encompassing Agulhas, Agulhas Retroflection, Southern Subtropical, and Subantarctic waters in the Indian Sector of the Southern Ocean.</p>
<p><strong>Discrete samples were taken from 10L Niskin bottles for measurements of:</strong></p>
<p><strong>1. Chlorophyll </strong>- Water samples were filtered onto a 25-millimeter (mm) Millipore HA filter (mixed cellulose ester, 0.45-micrometer (µm) pore size). The filters were transferred to test tubes filled with chilled 90% acetone for extraction and vortexed until the filter dissolved. Tubes were stored in the dark in a freezer for 24 hours before analysis. Tubes were then re-vortexed and gently centrifuged (~1300 grams (g)) for 5 minutes before being decanted into a glass cuvette for the fluorometer. We used a Turner Designs 10AU to read Fb of the sample and then add 50 microliters (µl) of 10% HCL and read Fa. The fluorometer was calibrated pre-cruise with a pure chlorophyll extract (Turner Designs part# 10-850) to determine Tau τ=(Fb/Fa pure chl a) and chlorophyll a was then be calculated from: (Fb – Fa) * (τ/ τ-1) * (Vfiltered/Vextracted). Generally, all surface measurements were made in triplicate.</p>
<p>The fluorometers (Turner 10-AUs) were calibrated using the calibration method defined by Turner Designs using standards purchased from Turner Designs. Additionally, for long cruises such as this cruise, a calibration was performed on the ship. References: Trees, et al.</p>
<p><strong>2. Particulate organic carbon (POC) plus particulate organic nitrogen (PON)</strong> - Water samples are filtered onto 25mm GF/F filters which have been pre-combusted (450°, 5 hours). Filters were rinsed with filtered seawater (FSW) and then stored in individual petri-plates and dried (60°) for storage. Prior to analysis, the plates were opened and placed overnight in a sealed container like a desiccator with saturated HCL fumes to remove any PIC. These samples were run by the Bigelow Laboratory Analytical Facility. The filters were packed into pre-combusted nickel sleeves and analyzed on a Perkin Elmer 2400 Series II CHNS/O for C, N, and H. The analyzer was calibrated using tin capsules as blanks and acetanilide to calibrate instrument response to carbon and nitrogen. NIST-certified check standards consisting of either low organic content soil or sediment are analyzed to determine accuracy of carbon detection. NIST-certified organic check standards such as corn flour or rice flour were analyzed to determine the accuracy of nitrogen detection. If values varied by more than 4% from stated values, instrument was examined, any problems were addressed and instrument was recalibrated and checked standards rerun until error was within acceptable limits. Duplicate samples were run during each sample run to ensure results were reproducible. If duplicates could not be run on actual samples, as in the case of filter samples, duplicate check standards were analyzed. Duplicate samples typically varied less than 2%. One instrument blank was analyzed for every 12 samples run. One acetanilide standard was analyzed for every 15 samples run. If blank or acetanilide values differed significantly from previous values, a new series of standards and blanks were analyzed to recalibrate the instrument. The actual minimum detection limit (3 times the standard error) determined from the standard error of the instrument blanks is 2 micrograms for carbon and 4 micrograms for nitrogen. References: JGOFS (1994).</p>
<p><strong>3. PIC (Particulate Inorganic Carbon):</strong> - Water samples were filtered through a 25mm, 0.4 µm pore size polycarbonate filter. The dry filter was rinsed with potassium tetraborate (6.11 g/l K₂B₄O₇ · 4H₂O) buffer while still in the filter tower to remove as much seawater salt and also to maintain a high pH (~8.1) during sample storage and to preserve the CaCO₃ on the filter. Filters were placed into trace metal clean polypropylene centrifuge tubes and dried at approximately 60°. For analysis, the filters were sent to (a) the Sawyer Environmental Chemistry Laboratory at the University of Maine or (b) the Department of Earth Sciences at Boston University. Filters were digested in a 5% nitric acid solution for 12 hours to dissolve all CaCO₃ and the solution was analyzed by ICP-AES (Inductively Couple Plasma - Atomic Emission Spectrometry) for Ca concentration. We ran filter and dissolution blanks as well as QC standards run with each batch of samples. We also used the concentration of dissolved Na in the digestate to correct for any Ca present in sea salts left on the filter. PIC concentrations were calculated using the volumes of water filtered and the volume of the digestions, and assuming all Particulate Inorganic Carbon was in the form of CaCO₃.</p>
<p><strong>4. Biogenic Silicas</strong> - To determine reactive silicate, 200 milliliters (mL) of seawater sample is filtered onto a 25 mm, 0.4um pore size polycarbonate filter. Filters were folded and placed in a super clear polypropylene centrifuge tube and dried in a drying oven at 60°C for 24 hours then tightly capped and stored until analysis. On shore, 0.2N NaOH was added and the sample was placed in a 95°C water bath. The digestions were then cooled and neutralized with 1N HCl. After centrifuging, the supernatant was transferred to a new tube and diluted with MilliQ water. Molybdate reagent was added and then a reducing agent was added to reduce silicomolybdate to silicomolybdous acid. The transmission at 810 nanometers (nm) is read on a Hitachi U-3010 spectrophotometer (SN 0947-010). Reactive silicate is calculated using a silicate standard solution standard curve prepared at least every 5 days or whenever new reagents were prepared. Readings were corrected using a reagent blank run at the same time as the standard curve and three tube blanks interspersed in each batch. References: Brzezinski &amp; Nelson (1989); JGOFS (1994); Strickland &amp; Parsons (1977).</p>
<p><strong>5. Dissolved Inorganic Carbon and Total Alkalinity Measurements - </strong>The analytical method followed standardized protocols (Bates et al., 1996; Bates et al., 2001; Dickson et al., 2007; Knap et al., 1993). Samples for DIC and TA were collected in 250ml borosilicate glass bottles according to standard JGOFS methods. Milli‐Q cleaned bottles were rinsed out 3 times, bottom filled using silicone tubing, allowed to overflow at least 1X the bottle volume, ensuring no bubbles were in the sample and that it was sealed with a small headspace to allow for water expansion. Water samples were collected from all depths the CTD‐rosette sampled on full casts and from eight depths on the ‘trip‐on‐fly’ casts. Two samples were collected from each Niskin bottle on the full casts. The first sample was poisoned with 100μl saturated mercuric chloride solution for analysis ashore. The second sample was not spiked and stored in the dark for no longer than 12 hours (to minimize any biological activity altering the sample) before being run aboard the ship, DIC first then TA. In addition to sampling from the rosette, samples were also collected and analyzed on board from the underway system. Both the underway and carboy samples were unpreserved, stored in the dark, and analyzed on board the ship. Samples were processed at sea using a highly precise (0.02%; 0.4 millimoles per kilogram (mmoles kg-1)) VINDTA system (Bates, 2007; Bates et al., 1996; Bates &amp; Peters, 2007). TA was measured on the VINDTA 3S by titration with a strong acid (HCl). The titration curve shows 2 inflection points, characterizing the protonation of carbonate and bicarbonate respectively, where consumption of acid at the second point is equal to the titration alkalinity. DIC was measured on the AIRICA by the extraction of total dissolved inorganic carbon content from the sample by phosphoric acid addition. The liberated CO2 flowed with a N2 carrier gas into a Li‐Cor non‐dispersive IR gas analyzer where the CO2 levels were measured. For both instruments, within bottle replicates were run consecutively on start up to check the precision, continuing once the instrument precision was ±2μmol kg‐1 or better. These were followed by a combination of Certified Reference Materials (CRMs) produced by the Marine Physical Laboratory at UCSD and low nutrient surface water from the Bermuda Atlantic Time Series (BATS) site, which were run every 20‐24 samples on the VINDTA and every 6 samples on the AIRICA, to determine the accuracy and precision of the measurements and to correct for any discrepancies. The TA system CRM values did not vary more than 2mmol within each batch of HCl acid. The AIRICA was more susceptible to drift and was affected by the lab temperature which is why CRMs were run much more often on the AIRICA, the system did not drift much and the lab temperature did not vary markedly. Both of the DIC and TA methods had a precision and accuracy of ~1 mmol kg-1 (precision estimates were determined from between-bottle and within-bottle replicates, and accuracy assessed using CRMs). The values for DIC and TA were used to calculate other parameters of the carbonate system using the software CO2sys (Lewis and Wallace, 1998). The calculated parameters were: pH, fCO2, pCO2, [HCO3‐], [CO3=], [CO2], alkalinity from borate; hydroxide ion; phosphate and silicate, Revelle Factor, plus the saturation states of calcite and aragonite.</p>
<p><strong>6. Nutrient analyses (phosphate, silicate, nitrate+nitrite, nitrite, and ammonia)</strong> - Analyses were performed at sea on a Seal Analytical continuous-flow AutoAnalyzer 3 (AA3). The methods used were described by Gordon et al [Gordon1992] Hager et al. [1972], and Atlas et al. [1971]. Details of modification of analytical methods used in this cruise are also compatible with the methods described in the nutrient section of the GO-SHIP repeat hydrography manual (Hydes et al., 2010).</p>
<p><strong>7. Coccolithophore enumeration</strong> - Polarized microscopy was used to determine the concentration of coccolithophores and detached coccoliths in samples collected during cruise TN376. A volume of 200mL was filtered onto 0.4μm-pore size, 25mm diameter polycarbonate filter then processed according to Balch &amp; Utgoff (2009).</p>
<p><strong>8. Enumeration of major algal classes</strong> - A shipboard Yokogawa Fluid Imaging Technologies FlowCam imaging cytometer was used to enumerate the major microalgal classes and estimate the particle size distribution function. The instrument was keyed on particle backscattering and fluorescence properties. Samples were first filtered through 100um Nitex mesh to make sure the 100um diameter flow chamber did not clog. The instrument was run with a 10X objective in order to reliably count particles bigger than 4-5um diameter. Samples were processed according to Poulton and Martin (2010). Concentrations (per mL), percent contribution with respect to total particles, and biomass are presented. Carbon biomass was determined based on the method described by Menden-Deuer &amp; Lessard (2000).</p>
<p><strong>9. Primary Production and Calcification Carbon Fixation Rates</strong> - Samples were also taken for measuring photosynthesis and calcification rates from 21 morning, full-CTD stations over the course of the trip (here called Productivity Stations). For these measurements, Niskin bottles were tripped at specific light depths throughout the euphotic zone (0.56%, 3.86%, 7.10%, 23.4%, 42.2%, and 73.6%). During casts where there was sufficient light to measure PAR throughout the euphotic zone, these depths were calculated assuming a constant diffuse attenuation coefficient. For samples taken during the nighttime, estimation of those light depths was performed based on the assumption that the fluorescence maximum was located at the 1% light depth (Poulton et al., 2017). Water samples for incubation were transferred from Niskin bottles to incubation bottles, typically inside the ship's enclosed hanger, under subdued light conditions. Water samples were pre-filtered through 120µm nitex mesh to remove large grazers. Incubations were performed in 70 mL polystyrene tissue culture bottles that were previously acid-cleaned, rinsed with ethanol, reverse-osmosis water, then rinsed 5x with each sea water sample prior to filling. Photosynthesis and calcification were measured using the microdiffusion technique (Paasche &amp; Brubak, 1994) with modifications by Balch et al. (2000) (see also Fabry (2010)). 14C bicarbonate (~30 uCi) was added for each water sample. Incubations were performed in triplicate (with an additional 2% buffered formalin sample (final concentration) used as a killed control) in simulated in situ conditions on-deck, corrected for both light quantity (extinction using bags made of neutral-density shade cloth) and quality (spectral narrowing) using blue acetate bag inserts. Bottle transfers between the incubators and radioisotope van were always done in darkened bags to avoid light shock to the phytoplankton. Deck incubators consisted of blue plastic tubs open to sky light, chilled using surface seawater from the ship's flowing sea water system. Calibration of those light levels in the bag were previously made using a Biospherical OSR2100 scalar PAR sensor inserted into each bag relative to a scalar PAR sensor outside the bag. All filtrations were performed using 0.4 mm pore-size polycarbonate filters. Following sample filtration, polycarbonate filters were rinsed three times with filtered seawater, then carefully given a "rim rinse" to make sure that all 14C-HCO3 in interstitial seawater in the filters was rinsed out. Filters and sample "boats" were placed in scintillation vials with 7mL of Ecolume scintillation cocktail. Samples were counted using a high-sensitivity Beckman Tricarb liquid scintillation counter with channel windows set for 14C counting. Counts were performed for sufficient time to reach 1% precision or 25 minutes for samples with lower counts. Blank 14C counts were always run for scintillation cocktail as well as the phenethylamine CO2 absorbent. Standard equations were used for calculating primary production and calcification from the 14C counts with a 5% isotope discrimination factor assumed for the physiological fixation of 14C-HCO3 as opposed to 12C-HCO3. Specific intrinsic growth rates of organic matter were calculated by dividing daily photosynthetic carbon estimates by the concentration of POC. Carbon-specific intrinsic growth rates for PIC were calculated by dividing the calcification rate by the concentration of PIC.</p>
<p><strong>10. Photophysiological variables</strong> - PAM fluorimetry is a widely used method for rapid assessment of the physiological state of the photosynthetic machinery in plants. The approach is based on measurement of chlorophyll fluorescence of photosystem II (PSII) as an indicator of the efficiency with which light absorbed by the photosynthetic machinery and converted into useful work in the form of electron transport in the chloroplast thylakoid membrane. The electron transport chains are ultimately responsible for providing the chemical energy for photosynthetic carbon fixation. Experimental measurements were made with a PAM fluorimeter (Water PAM, Walz, Germany) with 3 mL cuvette samples that were dark-adapted for &gt;30 minutes prior to analysis. The following key photosynthetic parameters were calculated from values of Fo, Fm, F'm and F':</p>
<p>- Maximum photosynthetic efficiency/capacity of dark-adapted cells: Fv/Fm = (Fm-Fo)/Fm<br />
- Effective photochemical quantum yield of PSII (photosynthetic efficiency in light conditions): Y(II) = (Fm'-F')/Fm'<br />
- Electron transfer rate (ETR) at a given irradiance value = proportion of photons at a given light intensity that are converted into useful energy. ETR = Y(II) x PAR<br />
- Non-photochemical quenching: NPQ = Fm/Fm'-1<br />
&gt; - Rapid light curves were also carried out to acquire ETR values at different irradiance values, providing information on initial slope (alpha), ETRmax at saturating irradiance and photoinhibition.</p>
<p><strong>11. PAM microscopy</strong> - Analysis of single-cell chlorophyll fluorescence was applied using similar PAM protocols to the above PAM fluorimeter measurements. The PAM microscope (PSI, Cz) allows images of Fo, Fm, F'm and F' by using LED arrays to provide measuring pulses, saturating pulses, and actinic light. Under rough weather conditions, it was only possible to obtain Fv/Fm values due to focus drift associated with vertical movements of the ship. The microscope allowed the acquisition of bright field and polarized light images to identify individual phytoplankton cells and calcifying coccolithophores. Cells were allowed to settle in darkness for &gt;1 hour before gentle transfer to the microscope imaging chamber, which comprised a glass-bottomed dish and X20 or X40 Zeiss water immersion objectives. The dish was mounted on a temperature-controlled perfusion cell, which allowed cells to be maintained at the precise collection temperature. All manipulations were carried out in darkness. Bright field images were obtained using far red light, which does not activate the PSII reaction centers.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1735664 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1735664
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1735783 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1735783
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1735846 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1735846
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1736375 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1736375
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1735436 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1735436
completed
William M. Balch
Bigelow Laboratory for Ocean Sciences
207-315-2567
60 Bigelow Drive
East Boothbay
ME
04544
USA
bbalch@bigelow.org
pointOfContact
Nicholas R. Bates
Bermuda Institute of Ocean Sciences
1-441-297-1880
17 Biological Lane GE 01
St. Georges
Bermuda
nick.bates@bios.edu
pointOfContact
Dennis J. McGillicuddy
Woods Hole Oceanographic Institution
508-289-2683
266 Woods Hole Road Bigelow 209B, Mail Stop 11
Woods Hole
MA
02543
USA
dmcgillicuddy@whoi.edu
pointOfContact
Peter L. Morton
Florida State University - National High Magnetic Field Lab
757-375-2904
Eller O&M 609
College Station
TX
77843
USA
pete.morton@tamu.edu
pointOfContact
Colin Brownlee
The Marine Biological Association of the United Kingdom
The Laboratory, Citadel Hill
Plymouth
Devon
PL1 2PB
UK
cbr@mba.ac.uk
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Station
Bottle
Cruise
Type
Longitude
Latitude
Depth
ISO_DateTime_UTC
Event
Month
Day
Year
Sigma_E900
Sigma_E911
Sbeox0
Sbeox1
Oxsol
Oxsol2
Sbox0
Sbox1
Potemp090C
Potemp190C
Salinity1_PSU
Salinity2_PSU
Density00
Density11
SvCM
SvCM1
Depth_m
Temperature
Temperature_2
C0
C1
Sbeox0V
Sbeox1V
Fluorescence
CStarTr0
AltM
PAR
V4
Scan
POC_ug_per_L
PON_ug_per_L
POC_umol_per_L
PON_umol_per_L
PIC_umol_per_L
PIC_ug_per_L
PIC_mol_per_cubic_m
Single_Lith_count_per_mL
Double_Lith_count_per_mL
Triple_Lith_count_per_mL
Quadruple_Lith_count_per_mL
Tot_Lith_count_per_mL
Cell_Agg_count_per_mL
Lith_Area_square_um_per_mL
Cell_Agg_Area_square_um_per_mL
BSi_umol_per_L
Avg_Corr_Chl_a_ug_per_L
Avg_Corr_Phaeo_ug_per_L
Avg_Corr_Chl_a_Phaeo_ug_per_L
PSD_Slope_logABD_grthan_point_75
Std_Err_of_PSD_Slope_logABD_grthan_point_75
Y_int_of_PSD_Slope_logABD_grthan_point_75
R2of_PSD_Slope_logABD_grthan_point_75
F_statistic_of_PSD_Slope_logABD_grthan_point_75
Total_cells_per_mL
Small_0_4um_cells_per_mL
Round_4_12um_cells_per_mL
Ovoid_4_12um_cells_per_mL
Dinoflagellates_cells_per_mL
Ciliates_cells_per_mL
Diatoms_cells_per_mL
Silicoflagellates_cells_per_mL
Other_Cells_cells_per_mL
Small_0_4um_pcnt
Round_4_12um_pcnt
Ovoid_4_12um_pcnt
Dinoflagellates_pcnt
Ciliates_pcnt
Diatoms_pcnt
Silicoflagellates_pcnt
Other_Cells_pcnt
Total_C_Biomass_Menden_Deuer_ug_per_L
Small_0_4um_C_Biomass_Menden_Deuer_ug_per_L
Round_4_12um_C_Biomass_Menden_Deuer_ug_per_L
Ovoid_4_12um_C_Biomass_Menden_Deuer_ug_per_L
Dinoflagellates_C_Biomass_Menden_Deuer_ug_per_L
Ciliates_C_Biomass_Menden_Deuer_ug_per_L
Diatoms_C_Biomass_Menden_Deuer_ug_per_L
Silicoflagellates_C_Biomass_Menden_Deuer_ug_per_L
Other_Cells_C_Biomass_Menden_Deuer_ug_per_L
Psy_Avg_C_to_P
Psy_Avg_P
Psy_Avg_C
Psy_P_SD
Psy_C_SD
Psy_Avg_Pmb_ug_C_per_ug_chl_d
Psy_Avg_Cmb_ug_C_per_ug_chl_d
NO3_umol_per_L
PO4_umol_per_L
SIL_umol_per_L
NO2_umol_per_L
NH4_umol_per_L
Bottle_O2_mL_per_L
Bottle_Salts
DIC_umol_per_kg
TA_umol_per_kg
Avg_F
Avg_Fm_Light
Avg_Y_II
Avg_ETR
Avg_qP
Avg_qN
Avg_qL
Avg_NPQ
Avg_Y_NO
Avg_Y_NPQ
Avg_Fo
Avg_Fm_Dark
Avg_Fv_Fm
Coccolithophore_single_cell_Avg_Fv_Fm
Dinoflagellate_single_cell_Avg_Fv_Fm
Diatom_single_cell_Avg_Fv_Fm
Water PAM
FluorCam Imaging Pulse Amplitude Modulation system
A3 microscope (Zeiss UK)
TC-344C Dual channel temperature controller
Yokogowa FlowCAM imaging cytometer
theme
None, User defined
station
bottle
Cruise identfier
sample type
longitude
latitude
depth_w
ISO_DateTime_UTC
event
month of year
day of month
year
density
dissolved Oxygen
O2 saturation
potential temperature
salinity
sound velocity
depth
water temperature at measurement depth
conductivity
fluorescence
transmission
altitude
PAR
scan
particulate organic Carbon (POC)
particulate organic nitrogen
particulate inorganic Carbon
count
area
biogenic silica concentration
chlorophyll a
total phaeopigment
Chl_a_plus_Phaeo
No BCO-DMO term
correlation coefficient
F statistic
cell_concentration
relative abundance
biomass_C
ratio
photosynthetic rate
calcification
primary production
Nitrate
reactive phosphorus (PO4)
Silicate, Si(OH)4, silicic acid
Ammonium
bottle salinity
dissolved inorganic Carbon
total alkalinity (TA)
quantum yield
Electron Transport Rate (ETR)
Fv to Fm ratio
featureType
BCO-DMO Standard Parameters
Fluorometer
Fluorometer
Microscope - Optical
thermostat
Yokogawa Fluid Imaging Technologies FlowCam VS particle imaging system
instrument
BCO-DMO Standard Instruments
TN376
service
Deployment Activity
South Indian Ocean
place
Locations
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Collaborative Research: Biogeochemical and Physical Conditioning of Sub-Antarctic Mode Water in the Southern Ocean
https://osprey.bco-dmo.org/project/738118
Collaborative Research: Biogeochemical and Physical Conditioning of Sub-Antarctic Mode Water in the Southern Ocean
<p><em>NSF Award Abstract:</em><br />
Cold surface water in the southern Indian Ocean sinks to about 500 meters and travels in the dark for thousands of miles before it resurfaces some 40 years later near the equator in the other ocean basins. This major water mass is named the Sub-Antarctic Mode Water (SAMW). Nutrients it contains when it warms and rises into the sunlit subtropical and tropical waters are estimated to fuel up to 75% of the microscopic plant growth there. Before it sinks, the chemical properties of the SAMW are modified by the growth and distinct physiology of two common phytoplankton; diatoms with shells made of silica, and coccolithophores with carbonate shells. Local physical dynamics influence where and how fast these two phytoplankton classes grow. Consequently, differing nutrient and trace chemical fingerprints are established at the point of SAMW formation. This project is an exceptionally detailed field and modeling effort that will document and quantify the remarkable, interconnected processes that chemically connect two important oceanic ecosystems half a world apart. The scientists leading the project will study the complexity of the biological and chemical conditioning of the SAMW and thus provide critical data about the large-scale oceanic controls of the biological carbon pump that removes atmospheric carbon dioxide to the deep ocean over millennial timescales. Scientific impact from this project will stem from significant peer-reviewed publications and improved predictive models. Societal benefits will develop from training of a range of scholars, including high school, undergraduate, and graduate students, as well as technical and post-doctoral participants. A high school teacher and science communication specialist will go to sea with the project and share experiences from the ship with students on shore via social media and scheduled web interactions.</p>
<p>To examine how SAMW formation and subduction controls the productivity of global waters well to the north, two January expeditions to the SE Indian Ocean will identify, track, and study the unique mesoscale eddies that serve as discrete water parcels supporting rich populations of either coccolithophores or diatoms plus their associated microbial communities. The eddies will be tracked with Lagrangian Argo drifters and observations will be made of exactly how SAMW is chemically conditioned (i.e. Si, N, P, Fe, and carbonate chemistry) over time scales of months. Using data obtained on the feedback between ecological processes and nutrient, trace metal, and carbonate chemistry in these eddies and on related transect cruises, the project will have three main goals: (1) determine the rates at which SAMW coccolithophores and diatoms condition the carbonate chemistry plus nutrient and trace metal concentrations, as well as assess taxonomic and physiological diversity in the study area with traditional methods plus next-generation sequence DNA/RNA profiling, (2) explore growth limitations by iron, silicate and/or nitrate in controlling algal assemblages and genetic diversity, and (3) combine these findings with the Ekman- and eddy-driven subduction of SAMW to examine biogeochemical impact on a basin scale, using both observations and global numerical models. A meridional survey from 30 to 60 degrees south latitude will be used to characterize the larger-scale variability of carbonate chemistry, nutrient distributions, productivity, genetics and biomass of various plankton groups as SAMW is subducted and proceeds northward.</p>
Conditioning_SAMW
largerWorkCitation
project
eng; USA
oceans
South Indian Ocean
24.0011
37.6305
-41.5013
-35.3848
2020-01-27
2020-02-25
0
BCO-DMO catalogue of parameters from CTD-associated variables, bottle salinity measurements, oxygen titrations, nutrient analyses, biogeochemical/biological variables, and DIC chemistry variables from R/V Thomas G. Thompson cruise TN376 from January to March 2020
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/914995.rdf
Name: Station
Units: unitless
Description: <p>station number (between 1 and 103)</p>
http://lod.bco-dmo.org/id/dataset-parameter/914996.rdf
Name: Bottle
Units: unitless
Description: <p>number of the Niskin bottle tripped on CTD cast</p>
http://lod.bco-dmo.org/id/dataset-parameter/914997.rdf
Name: Cruise
Units: unitless
Description: <p>cruise ID number (TN376)</p>
http://lod.bco-dmo.org/id/dataset-parameter/914998.rdf
Name: Type
Units: unitless
Description: <p>All "B" (bottle) (added to make data set Ocean Data View-compatible)</p>
http://lod.bco-dmo.org/id/dataset-parameter/914999.rdf
Name: Longitude
Units: decimal degrees
Description: <p>longitude of sample location; negative values = West</p>
http://lod.bco-dmo.org/id/dataset-parameter/915000.rdf
Name: Latitude
Units: decimal degrees
Description: <p>latitude of sample location; negative values = South</p>
http://lod.bco-dmo.org/id/dataset-parameter/915001.rdf
Name: Depth
Units: meters (m)
Description: <p>water depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/915002.rdf
Name: ISO_DateTime_UTC
Units: unitless
Description: <p>Date and time (UTC) in ISO 8601 format</p>
http://lod.bco-dmo.org/id/dataset-parameter/915003.rdf
Name: Event
Units: unitless
Description: <p>unique event number for start time of each event given as year (4 digits), month (2 digits), day (2 digits), and then a period followed by GMT time (4 digits)</p>
http://lod.bco-dmo.org/id/dataset-parameter/915004.rdf
Name: Month
Units: unitless
Description: <p>month of year</p>
http://lod.bco-dmo.org/id/dataset-parameter/915005.rdf
Name: Day
Units: unitless
Description: <p>day of month</p>
http://lod.bco-dmo.org/id/dataset-parameter/915006.rdf
Name: Year
Units: unitless
Description: <p>year</p>
http://lod.bco-dmo.org/id/dataset-parameter/915007.rdf
Name: Sigma_E900
Units: kilograms per cubic meter (kg m-3)
Description: <p>density anomaly of seawater calculated from salinity derived from conductivity probe 0</p>
http://lod.bco-dmo.org/id/dataset-parameter/915008.rdf
Name: Sigma_E911
Units: kilograms per cubic meter (kg m-3)
Description: <p>density anomaly of seawater calculated from salinity derived from conductivity probe 1</p>
http://lod.bco-dmo.org/id/dataset-parameter/915009.rdf
Name: Sbeox0
Units: milliliters per liter (mL L-1)
Description: <p>Oxygen concentration derived from primary Sea Bird oxygen probe #0 on CTD</p>
http://lod.bco-dmo.org/id/dataset-parameter/915010.rdf
Name: Sbeox1
Units: milliliters per liter (mL L-1)
Description: <p>Oxygen concentration derived from secondary Sea Bird oxygen probe #1 on CTD</p>
http://lod.bco-dmo.org/id/dataset-parameter/915011.rdf
Name: Oxsol
Units: milliliters per liter (mL L-1)
Description: <p>Estimated 100%-saturated concentration of oxygen based on primary temperature and primary salinity probes</p>
http://lod.bco-dmo.org/id/dataset-parameter/915012.rdf
Name: Oxsol2
Units: milliliters per liter (mL L-1)
Description: <p>Estimated 100%-saturated concentration of oxygen based on secondary temperature and secondary salinity probes</p>
http://lod.bco-dmo.org/id/dataset-parameter/915013.rdf
Name: Sbox0
Units: micromoles per kilogram (umol kg-1)
Description: <p>primary oxygen probe</p>
http://lod.bco-dmo.org/id/dataset-parameter/915014.rdf
Name: Sbox1
Units: micromoles per kilogram (umol kg-1)
Description: <p>secondary oxygen probe</p>
http://lod.bco-dmo.org/id/dataset-parameter/915015.rdf
Name: Potemp090C
Units: degrees Celsius (ITS-90)
Description: <p>Potential temperature (primary temperature probe)</p>
http://lod.bco-dmo.org/id/dataset-parameter/915016.rdf
Name: Potemp190C
Units: degrees Celsius (ITS-90)
Description: <p>Potential temperature (secondary temperature probe)</p>
http://lod.bco-dmo.org/id/dataset-parameter/915017.rdf
Name: Salinity1_PSU
Units: PSU
Description: <p>salinity of water sample as estimated by primary conductivity probe</p>
http://lod.bco-dmo.org/id/dataset-parameter/915018.rdf
Name: Salinity2_PSU
Units: PSU
Description: <p>salinity of water sample as estimated by secondary conductivity probe</p>
http://lod.bco-dmo.org/id/dataset-parameter/915019.rdf
Name: Density00
Units: kilograms per cubic meter (kg m-3)
Description: <p>density of seawater calculated from salinity derived from primary conductivity probe and primary thermo probe</p>
http://lod.bco-dmo.org/id/dataset-parameter/915020.rdf
Name: Density11
Units: kilograms per cubic meter (kg m-3)
Description: <p>density anomaly of seawater calculated from salinity derived from secondary conductivity probe 1 and secondary thermo probe 1</p>
http://lod.bco-dmo.org/id/dataset-parameter/915021.rdf
Name: SvCM
Units: meters per second (m/s)
Description: <p>Sound Velocity [Chen-Millero 1977] based on temperature & salinity primary probes</p>
http://lod.bco-dmo.org/id/dataset-parameter/915022.rdf
Name: SvCM1
Units: meters per second (m/s)
Description: <p>Sound Velocity [Chen-Millero 1977] based on temperature & salinity secondary probes</p>
http://lod.bco-dmo.org/id/dataset-parameter/915023.rdf
Name: Depth_m
Units: meters (m)
Description: <p>depth of water sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/915024.rdf
Name: Temperature
Units: degrees Celsius
Description: <p>CTD temperature (ITS-90) primary probe</p>
http://lod.bco-dmo.org/id/dataset-parameter/915025.rdf
Name: Temperature_2
Units: degrees Celsius
Description: <p>CTD temperature (ITS-90) secondary probe</p>
http://lod.bco-dmo.org/id/dataset-parameter/915026.rdf
Name: C0
Units: Siemens per meter (S/m)
Description: <p>Conductivity based on primary conductivity probe</p>
http://lod.bco-dmo.org/id/dataset-parameter/915027.rdf
Name: C1
Units: Siemens per meter (S/m)
Description: <p>Conductivity based on secondary conductivity probe</p>
http://lod.bco-dmo.org/id/dataset-parameter/915028.rdf
Name: Sbeox0V
Units: Volts
Description: <p>SeaBird oxygen probe 0</p>
http://lod.bco-dmo.org/id/dataset-parameter/915029.rdf
Name: Sbeox1V
Units: Volts
Description: <p>SeaBird oxygen probe 1</p>
http://lod.bco-dmo.org/id/dataset-parameter/915030.rdf
Name: Fluorescence
Units: Volts DC
Description: <p>Chlorophyll Fluorescence, WET Labs ECO-AFL/FL sensor 0</p>
http://lod.bco-dmo.org/id/dataset-parameter/915031.rdf
Name: CStarTr0
Units: percent (%)
Description: <p>Beam transmission WetLabs Cstar</p>
http://lod.bco-dmo.org/id/dataset-parameter/915032.rdf
Name: AltM
Units: meters (m)
Description: <p>Altitude of CTD from sea floor</p>
http://lod.bco-dmo.org/id/dataset-parameter/915033.rdf
Name: PAR
Units: microEinsteins per square centimeter per second (uE/(cm^2 sec))
Description: <p>Photosynthetically Available Radiation measured at depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/915034.rdf
Name: V4
Units: Volts
Description: <p>Voltage of fluorescence sensor</p>
http://lod.bco-dmo.org/id/dataset-parameter/915035.rdf
Name: Scan
Units: unitless
Description: <p>number of the CTD scan in which measurements were made</p>
http://lod.bco-dmo.org/id/dataset-parameter/915036.rdf
Name: POC_ug_per_L
Units: micrograms per liter (ug/L)
Description: <p>concentration of particulate organic carbon</p>
http://lod.bco-dmo.org/id/dataset-parameter/915037.rdf
Name: PON_ug_per_L
Units: micrograms per liter (ug/L)
Description: <p>concentration of particulate organic nitrogen</p>
http://lod.bco-dmo.org/id/dataset-parameter/915038.rdf
Name: POC_umol_per_L
Units: micromoles per liter (umol/L)
Description: <p>concentration of particulate organic carbon</p>
http://lod.bco-dmo.org/id/dataset-parameter/915039.rdf
Name: PON_umol_per_L
Units: micromoles per liter (umol/L)
Description: <p>concentration of particulate organic nitrogen</p>
http://lod.bco-dmo.org/id/dataset-parameter/915040.rdf
Name: PIC_umol_per_L
Units: micromoles per liter (umol/L)
Description: <p>concentration of particulate inorganic carbon</p>
http://lod.bco-dmo.org/id/dataset-parameter/915041.rdf
Name: PIC_ug_per_L
Units: micrograms per liter (ug/L)
Description: <p>concentration of particulate inorganic carbon</p>
http://lod.bco-dmo.org/id/dataset-parameter/915042.rdf
Name: PIC_mol_per_cubic_m
Units: moles per cubic meter (mol/m^3)
Description: <p>concentration of particulate inorganic carbon</p>
http://lod.bco-dmo.org/id/dataset-parameter/915043.rdf
Name: Single_Lith_count_per_mL
Units: number per milliliter (mL)
Description: <p>concentration of birefringent particles-singlets</p>
http://lod.bco-dmo.org/id/dataset-parameter/915044.rdf
Name: Double_Lith_count_per_mL
Units: number per milliliter (mL)
Description: <p>concentration of birefringent particles-doublets</p>
http://lod.bco-dmo.org/id/dataset-parameter/915045.rdf
Name: Triple_Lith_count_per_mL
Units: number per milliliter (mL)
Description: <p>concentration of birefringent particles-triplets</p>
http://lod.bco-dmo.org/id/dataset-parameter/915046.rdf
Name: Quadruple_Lith_count_per_mL
Units: number per milliliter (mL)
Description: <p>concentration of birefringent particles-quadruplets</p>
http://lod.bco-dmo.org/id/dataset-parameter/915047.rdf
Name: Tot_Lith_count_per_mL
Units: number per milliliter (mL)
Description: <p>concentration of birefringent particles-all</p>
http://lod.bco-dmo.org/id/dataset-parameter/915048.rdf
Name: Cell_Agg_count_per_mL
Units: number per milliliter (mL)
Description: <p>concentration of birefringent plated cells, coccospheres and aggregates</p>
http://lod.bco-dmo.org/id/dataset-parameter/915049.rdf
Name: Lith_Area_square_um_per_mL
Units: square micrometers per milliliter (um^2 per mL)
Description: <p>total area subtended by by detached coccoliths</p>
http://lod.bco-dmo.org/id/dataset-parameter/915050.rdf
Name: Cell_Agg_Area_square_um_per_mL
Units: square micrometers per milliliter (um^2 per mL)
Description: <p>total area subtended by by plated coccolithophores, coccospheres and aggregates</p>
http://lod.bco-dmo.org/id/dataset-parameter/915051.rdf
Name: BSi_umol_per_L
Units: micromoles per liter (umol/L)
Description: <p>concentration of biogenic silica</p>
http://lod.bco-dmo.org/id/dataset-parameter/915052.rdf
Name: Avg_Corr_Chl_a_ug_per_L
Units: micrograms per liter (ug/L)
Description: <p>concentration of chlorophyll a</p>
http://lod.bco-dmo.org/id/dataset-parameter/915053.rdf
Name: Avg_Corr_Phaeo_ug_per_L
Units: micrograms per liter (ug/L)
Description: <p>concentration of phaeopigments</p>
http://lod.bco-dmo.org/id/dataset-parameter/915054.rdf
Name: Avg_Corr_Chl_a_Phaeo_ug_per_L
Units: micrograms per liter (ug/L)
Description: <p>concentration of chlorophyll a plus phaeopigments</p>
http://lod.bco-dmo.org/id/dataset-parameter/915055.rdf
Name: PSD_Slope_logABD_grthan_point_75
Units: unitless
Description: <p>PDF Slope logABD>0.75 (only particles >5um); Particle size Distribution Function slope of the plot of log cell abundance (particles per mL) versus Area Based Diameter (micrometers) calculated for particles of >5 micrometers diameter using a Yokogowa FlowCAM. Area Based Diameter (ABD) is defined as the diameter measured by the number of grey scale pixels of the binary image converted to a circle with the same number of pixels</p>
http://lod.bco-dmo.org/id/dataset-parameter/915056.rdf
Name: Std_Err_of_PSD_Slope_logABD_grthan_point_75
Units: unitless
Description: <p>Std Err of PDF Slope logABD>0.75 (for particles >5um); Standard error of the above particle size distribution slope for only particles of 5 micrometers diameter or larger using a Yokogowa FlowCAM</p>
http://lod.bco-dmo.org/id/dataset-parameter/915057.rdf
Name: Y_int_of_PSD_Slope_logABD_grthan_point_75
Units: unitless
Description: <p>Y-int of PDF Slope logABD>0.75 (only particles >5um); the Y intercept of above PDF for only particles of ~5um diameter or larger using a Yokogowa FlowCAM</p>
http://lod.bco-dmo.org/id/dataset-parameter/915058.rdf
Name: R2of_PSD_Slope_logABD_grthan_point_75
Units: unitless
Description: <p>R-squared value of PDF Slope logABD>0.75(only particles >5um); squared correlation coefficient of above PDF for only particles of >5um diameter or larger using a Yokogowa FlowCAM</p>
http://lod.bco-dmo.org/id/dataset-parameter/915059.rdf
Name: F_statistic_of_PSD_Slope_logABD_grthan_point_75
Units: unitless
Description: <p>F-statistic of PDF Slope logABD>0.75 (only particles >5um); the F statistic of of above PDF for only particles of >5um diameter or larger using a Yokogowa FlowCAM</p>
http://lod.bco-dmo.org/id/dataset-parameter/915060.rdf
Name: Total_cells_per_mL
Units: cells per milliliter (cells/mL)
Description: <p>Concentration of total particles measured by Yokogowa measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/915061.rdf
Name: Small_0_4um_cells_per_mL
Units: cells per milliliter (cells/mL)
Description: <p>Concentration of small particles with diameters of 0 to 4 micrometers measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/915062.rdf
Name: Round_4_12um_cells_per_mL
Units: cells per milliliter (cells/mL)
Description: <p>Concentration of round particles with diameters of 4 to 12 micrometers measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/915063.rdf
Name: Ovoid_4_12um_cells_per_mL
Units: cells per milliliter (cells/mL)
Description: <p>Concentration of ovoid particles with diameters of 4 to 12 micrometers measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/915064.rdf
Name: Dinoflagellates_cells_per_mL
Units: cells per milliliter (cells/mL)
Description: <p>Concentration of dinoflagellates measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/915065.rdf
Name: Ciliates_cells_per_mL
Units: cells per milliliter (cells/mL)
Description: <p>Concentration of ciliates measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/915066.rdf
Name: Diatoms_cells_per_mL
Units: cells per milliliter (cells/mL)
Description: <p>Concentration of diatoms measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/915067.rdf
Name: Silicoflagellates_cells_per_mL
Units: cells per milliliter (cells/mL)
Description: <p>Concentration of silicoflagellates measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/915068.rdf
Name: Other_Cells_cells_per_mL
Units: cells per milliliter (cells/mL)
Description: <p>Concentration of other unidentified cells as measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/915069.rdf
Name: Small_0_4um_pcnt
Units: unitless
Description: <p>Percent of total particles contributed by small (0-4 um) particles as measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/915070.rdf
Name: Round_4_12um_pcnt
Units: unitless
Description: <p>Percent of total particles contributed by round (4-12 um) particles as measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/915071.rdf
Name: Ovoid_4_12um_pcnt
Units: unitless
Description: <p>Percent of total particles contributed by ovoid (4-12 um) particles as measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/915072.rdf
Name: Dinoflagellates_pcnt
Units: unitless
Description: <p>Percent of total particles contributed by dinoflagellates as measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/915073.rdf
Name: Ciliates_pcnt
Units: unitless
Description: <p>Percent of total particles contributed by ciliates as measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/915074.rdf
Name: Diatoms_pcnt
Units: unitless
Description: <p>Percent of total particles contributed by diatoms as measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/915075.rdf
Name: Silicoflagellates_pcnt
Units: unitless
Description: <p>Percent of total particles contributed by silicoflagellates as measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/915076.rdf
Name: Other_Cells_pcnt
Units: unitless
Description: <p>Percent of total particles contributed by unidentified other cells as measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/915077.rdf
Name: Total_C_Biomass_Menden_Deuer_ug_per_L
Units: micrograms per liter (ug/L)
Description: <p>Total carbon biomass (based on Menden-Deuer and Lessard 2000) for total particles measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/915078.rdf
Name: Small_0_4um_C_Biomass_Menden_Deuer_ug_per_L
Units: micrograms per liter (ug/L)
Description: <p>Carbon biomass of small 0-4um cells (based on Menden-Deuer and Lessard 2000) for total particles measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/915079.rdf
Name: Round_4_12um_C_Biomass_Menden_Deuer_ug_per_L
Units: micrograms per liter (ug/L)
Description: <p>Carbon biomass of round 4-12um cells (based on Menden-Deuer and Lessard 2000) for total particles measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/915080.rdf
Name: Ovoid_4_12um_C_Biomass_Menden_Deuer_ug_per_L
Units: micrograms per liter (ug/L)
Description: <p>Carbon biomass of ovoid 4-12um cells (based on Menden-Deuer and Lessard 2000) for total particles measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/915081.rdf
Name: Dinoflagellates_C_Biomass_Menden_Deuer_ug_per_L
Units: micrograms per liter (ug/L)
Description: <p>Carbon biomass of dinoflagellates (based on Menden-Deuer and Lessard 2000) for total particles measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/915082.rdf
Name: Ciliates_C_Biomass_Menden_Deuer_ug_per_L
Units: micrograms per liter (ug/L)
Description: <p>Carbon biomass of ciliates (based on Menden-Deuer and Lessard 2000) for total particles measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/915083.rdf
Name: Diatoms_C_Biomass_Menden_Deuer_ug_per_L
Units: micrograms per liter (ug/L)
Description: <p>Carbon biomass of diatoms (based on Menden-Deuer and Lessard 2000) for total particles measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/915084.rdf
Name: Silicoflagellates_C_Biomass_Menden_Deuer_ug_per_L
Units: micrograms per liter (ug/L)
Description: <p>Carbon biomass of silicoflagellates (based on Menden-Deuer and Lessard 2000) for total particles measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/915085.rdf
Name: Other_Cells_C_Biomass_Menden_Deuer_ug_per_L
Units: micrograms per liter (ug/L)
Description: <p>Carbon biomass of unidentified other cells (based on Menden-Deuer and Lessard 2000) for total particles measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/915086.rdf
Name: Psy_Avg_C_to_P
Units: unitless
Description: <p>Ratio of calcification to photosynthesis</p>
http://lod.bco-dmo.org/id/dataset-parameter/915087.rdf
Name: Psy_Avg_P
Units: micromoles C per liter per day (umol C/L/d)
Description: <p>Average photosynthesis rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/915088.rdf
Name: Psy_Avg_C
Units: micromoles C per liter per day (umol C/L/d)
Description: <p>Average calcification rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/915089.rdf
Name: Psy_P_SD
Units: micromoles C per liter per day (umol C/L/d)
Description: <p>standard deviation of photosynthesis rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/915090.rdf
Name: Psy_C_SD
Units: micromoles C per liter per day (umol C/L/d)
Description: <p>standard deviation of calcification rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/915091.rdf
Name: Psy_Avg_Pmb_ug_C_per_ug_chl_d
Units: micrograms C per microgram chlorophyll per day (ugC/ugchl/d)
Description: <p>chlorophyll-normalized primary production rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/915092.rdf
Name: Psy_Avg_Cmb_ug_C_per_ug_chl_d
Units: micrograms C per microgram chlorophyll per day (ugC/ugchl/d)
Description: <p>chlorophyll-normalized calcification rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/915093.rdf
Name: NO3_umol_per_L
Units: micromoles per liter (umoles/L)
Description: <p>concentration of nitrate</p>
http://lod.bco-dmo.org/id/dataset-parameter/915094.rdf
Name: PO4_umol_per_L
Units: micromoles per liter (umoles/L)
Description: <p>concentration of phosphate</p>
http://lod.bco-dmo.org/id/dataset-parameter/915095.rdf
Name: SIL_umol_per_L
Units: micromoles per liter (umoles/L)
Description: <p>concentration of silicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/915096.rdf
Name: NO2_umol_per_L
Units: micromoles per liter (umoles/L)
Description: <p>concentration of nitrite</p>
http://lod.bco-dmo.org/id/dataset-parameter/915097.rdf
Name: NH4_umol_per_L
Units: micromoles per liter (umoles/L)
Description: <p>concentration of ammonium</p>
http://lod.bco-dmo.org/id/dataset-parameter/915098.rdf
Name: Bottle_O2_mL_per_L
Units: millilieters per liter ( mL/L)
Description: <p>Oxygen concentration from shipboard titration</p>
http://lod.bco-dmo.org/id/dataset-parameter/915099.rdf
Name: Bottle_Salts
Units: PSU (Practical Salinity Units)
Description: <p>salinometer-derived salinity</p>
http://lod.bco-dmo.org/id/dataset-parameter/915100.rdf
Name: DIC_umol_per_kg
Units: micromoles per kilogram (umol kg-1)
Description: <p>dissolved inorganic carbon concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/915101.rdf
Name: TA_umol_per_kg
Units: micromoles per kilogram (umol kg-1)
Description: <p>Total akalinity</p>
http://lod.bco-dmo.org/id/dataset-parameter/915102.rdf
Name: Avg_F
Units: Arbitrary fluorescence units
Description: <p>Average Fluorescence</p>
http://lod.bco-dmo.org/id/dataset-parameter/915103.rdf
Name: Avg_Fm_Light
Units: Arbitrary fluorescence units
Description: <p>Maximum Fluorescence, Fm’, measured in the light</p>
http://lod.bco-dmo.org/id/dataset-parameter/915104.rdf
Name: Avg_Y_II
Units: unitless
Description: <p>Effective photochemical quantum yield of PSII (photosynthetic efficiency in light conditions = proportion of photons at a given light intensity that are converted into useful energy)</p>
http://lod.bco-dmo.org/id/dataset-parameter/915105.rdf
Name: Avg_ETR
Units: micromoles electrons per square meter per second (umol electrons m-2 s-1) (Y-II x PAR(umol photos m-2s-1) x 0.42 )
Description: <p>Electron transfer rate (ETR) at a given irradiance</p>
http://lod.bco-dmo.org/id/dataset-parameter/915106.rdf
Name: Avg_qP
Units: arbitrary units
Description: <p>Average photochemical quenching</p>
http://lod.bco-dmo.org/id/dataset-parameter/915107.rdf
Name: Avg_qN
Units: arbitrary units
Description: <p>average qN</p>
http://lod.bco-dmo.org/id/dataset-parameter/915108.rdf
Name: Avg_qL
Units: arbitrary units
Description: <p>Average qL</p>
http://lod.bco-dmo.org/id/dataset-parameter/915109.rdf
Name: Avg_NPQ
Units: unitless
Description: <p>Non-photochemical quenching</p>
http://lod.bco-dmo.org/id/dataset-parameter/915110.rdf
Name: Avg_Y_NO
Units: unitless
Description: <p>Average Y_NO</p>
http://lod.bco-dmo.org/id/dataset-parameter/915111.rdf
Name: Avg_Y_NPQ
Units: unitless
Description: <p>Average Y_NPQ</p>
http://lod.bco-dmo.org/id/dataset-parameter/915112.rdf
Name: Avg_Fo
Units: Arbitrary fluorescence units
Description: <p>average dark fluorescence of all cells</p>
http://lod.bco-dmo.org/id/dataset-parameter/915113.rdf
Name: Avg_Fm_Dark
Units: Arbitrary fluorescence units
Description: <p>Maximum Fluorescence, Fm, immediately after dark adaptation (i.e. at the beginning of the measurements).</p>
http://lod.bco-dmo.org/id/dataset-parameter/915114.rdf
Name: Avg_Fv_Fm
Units: unitless
Description: <p>average Fv/Fm</p>
http://lod.bco-dmo.org/id/dataset-parameter/915115.rdf
Name: Coccolithophore_single_cell_Avg_Fv_Fm
Units: unitless
Description: <p>Coccolithophore single cell Avg Fv_Fm</p>
http://lod.bco-dmo.org/id/dataset-parameter/915116.rdf
Name: Dinoflagellate_single_cell_Avg_Fv_Fm
Units: unitless
Description: <p>Dinoflagellate single cell Avg Fv_Fm</p>
http://lod.bco-dmo.org/id/dataset-parameter/915117.rdf
Name: Diatom_single_cell_Avg_Fv_Fm
Units: unitless
Description: <p>Diatom single cell Avg Fv_Fm</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
968159
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/4c05069e-3608-47ef-815e-a1de4b20fce3/content
download
https://doi.org/10.26008/1912/bco-dmo.914901.1
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dataset
<p>R/V Thomas G. Thompson (cruise ID TN376) departed Cape Town, South Africa (SA) on 22 January 2020. The ship transited to the Southern Ocean and returned to Mauritius on 3 March 2020.</p>
<p>Due to the ship breakdown early into the cruise and the need to divert to Durban, SA, for engine repairs, we divided the cruise into five legs, as defined by our revised cruise plan, then pre- and post-diversion engine repairs in Durban, SA. A detailed summary of each of the legs and associated measurements can be found on the BCO-DMO cruise page for TN376: <a href="https://www.bco-dmo.org/deployment/904210" target="_blank">https://www.bco-dmo.org/deployment/904210</a>. (For overall completeness of the sampling timeline, all science activities are included here (not necessarily just those for which this dataset encompasses). This dataset includes the CTD bottle data. Those activities not related to this dataset, but conducted on the cruise are: Video Plankton Recorder (VPR), carboy experiments, barite precipitation experiments, and real-time filter/freeze/transfer preparations for examination of phytoplankton during the cruise.)</p>
<p><strong>Sampling methods:</strong><br />
At sea collections: Water samples were collected using CTD casts from 71 stations encompassing Agulhas, Agulhas Retroflection, Southern Subtropical, and Subantarctic waters in the Indian Sector of the Southern Ocean.</p>
<p><strong>Discrete samples were taken from 10L Niskin bottles for measurements of:</strong></p>
<p><strong>1. Chlorophyll </strong>- Water samples were filtered onto a 25-millimeter (mm) Millipore HA filter (mixed cellulose ester, 0.45-micrometer (µm) pore size). The filters were transferred to test tubes filled with chilled 90% acetone for extraction and vortexed until the filter dissolved. Tubes were stored in the dark in a freezer for 24 hours before analysis. Tubes were then re-vortexed and gently centrifuged (~1300 grams (g)) for 5 minutes before being decanted into a glass cuvette for the fluorometer. We used a Turner Designs 10AU to read Fb of the sample and then add 50 microliters (µl) of 10% HCL and read Fa. The fluorometer was calibrated pre-cruise with a pure chlorophyll extract (Turner Designs part# 10-850) to determine Tau τ=(Fb/Fa pure chl a) and chlorophyll a was then be calculated from: (Fb – Fa) * (τ/ τ-1) * (Vfiltered/Vextracted). Generally, all surface measurements were made in triplicate.</p>
<p>The fluorometers (Turner 10-AUs) were calibrated using the calibration method defined by Turner Designs using standards purchased from Turner Designs. Additionally, for long cruises such as this cruise, a calibration was performed on the ship. References: Trees, et al.</p>
<p><strong>2. Particulate organic carbon (POC) plus particulate organic nitrogen (PON)</strong> - Water samples are filtered onto 25mm GF/F filters which have been pre-combusted (450°, 5 hours). Filters were rinsed with filtered seawater (FSW) and then stored in individual petri-plates and dried (60°) for storage. Prior to analysis, the plates were opened and placed overnight in a sealed container like a desiccator with saturated HCL fumes to remove any PIC. These samples were run by the Bigelow Laboratory Analytical Facility. The filters were packed into pre-combusted nickel sleeves and analyzed on a Perkin Elmer 2400 Series II CHNS/O for C, N, and H. The analyzer was calibrated using tin capsules as blanks and acetanilide to calibrate instrument response to carbon and nitrogen. NIST-certified check standards consisting of either low organic content soil or sediment are analyzed to determine accuracy of carbon detection. NIST-certified organic check standards such as corn flour or rice flour were analyzed to determine the accuracy of nitrogen detection. If values varied by more than 4% from stated values, instrument was examined, any problems were addressed and instrument was recalibrated and checked standards rerun until error was within acceptable limits. Duplicate samples were run during each sample run to ensure results were reproducible. If duplicates could not be run on actual samples, as in the case of filter samples, duplicate check standards were analyzed. Duplicate samples typically varied less than 2%. One instrument blank was analyzed for every 12 samples run. One acetanilide standard was analyzed for every 15 samples run. If blank or acetanilide values differed significantly from previous values, a new series of standards and blanks were analyzed to recalibrate the instrument. The actual minimum detection limit (3 times the standard error) determined from the standard error of the instrument blanks is 2 micrograms for carbon and 4 micrograms for nitrogen. References: JGOFS (1994).</p>
<p><strong>3. PIC (Particulate Inorganic Carbon):</strong> - Water samples were filtered through a 25mm, 0.4 µm pore size polycarbonate filter. The dry filter was rinsed with potassium tetraborate (6.11 g/l K₂B₄O₇ · 4H₂O) buffer while still in the filter tower to remove as much seawater salt and also to maintain a high pH (~8.1) during sample storage and to preserve the CaCO₃ on the filter. Filters were placed into trace metal clean polypropylene centrifuge tubes and dried at approximately 60°. For analysis, the filters were sent to (a) the Sawyer Environmental Chemistry Laboratory at the University of Maine or (b) the Department of Earth Sciences at Boston University. Filters were digested in a 5% nitric acid solution for 12 hours to dissolve all CaCO₃ and the solution was analyzed by ICP-AES (Inductively Couple Plasma - Atomic Emission Spectrometry) for Ca concentration. We ran filter and dissolution blanks as well as QC standards run with each batch of samples. We also used the concentration of dissolved Na in the digestate to correct for any Ca present in sea salts left on the filter. PIC concentrations were calculated using the volumes of water filtered and the volume of the digestions, and assuming all Particulate Inorganic Carbon was in the form of CaCO₃.</p>
<p><strong>4. Biogenic Silicas</strong> - To determine reactive silicate, 200 milliliters (mL) of seawater sample is filtered onto a 25 mm, 0.4um pore size polycarbonate filter. Filters were folded and placed in a super clear polypropylene centrifuge tube and dried in a drying oven at 60°C for 24 hours then tightly capped and stored until analysis. On shore, 0.2N NaOH was added and the sample was placed in a 95°C water bath. The digestions were then cooled and neutralized with 1N HCl. After centrifuging, the supernatant was transferred to a new tube and diluted with MilliQ water. Molybdate reagent was added and then a reducing agent was added to reduce silicomolybdate to silicomolybdous acid. The transmission at 810 nanometers (nm) is read on a Hitachi U-3010 spectrophotometer (SN 0947-010). Reactive silicate is calculated using a silicate standard solution standard curve prepared at least every 5 days or whenever new reagents were prepared. Readings were corrected using a reagent blank run at the same time as the standard curve and three tube blanks interspersed in each batch. References: Brzezinski &amp; Nelson (1989); JGOFS (1994); Strickland &amp; Parsons (1977).</p>
<p><strong>5. Dissolved Inorganic Carbon and Total Alkalinity Measurements - </strong>The analytical method followed standardized protocols (Bates et al., 1996; Bates et al., 2001; Dickson et al., 2007; Knap et al., 1993). Samples for DIC and TA were collected in 250ml borosilicate glass bottles according to standard JGOFS methods. Milli‐Q cleaned bottles were rinsed out 3 times, bottom filled using silicone tubing, allowed to overflow at least 1X the bottle volume, ensuring no bubbles were in the sample and that it was sealed with a small headspace to allow for water expansion. Water samples were collected from all depths the CTD‐rosette sampled on full casts and from eight depths on the ‘trip‐on‐fly’ casts. Two samples were collected from each Niskin bottle on the full casts. The first sample was poisoned with 100μl saturated mercuric chloride solution for analysis ashore. The second sample was not spiked and stored in the dark for no longer than 12 hours (to minimize any biological activity altering the sample) before being run aboard the ship, DIC first then TA. In addition to sampling from the rosette, samples were also collected and analyzed on board from the underway system. Both the underway and carboy samples were unpreserved, stored in the dark, and analyzed on board the ship. Samples were processed at sea using a highly precise (0.02%; 0.4 millimoles per kilogram (mmoles kg-1)) VINDTA system (Bates, 2007; Bates et al., 1996; Bates &amp; Peters, 2007). TA was measured on the VINDTA 3S by titration with a strong acid (HCl). The titration curve shows 2 inflection points, characterizing the protonation of carbonate and bicarbonate respectively, where consumption of acid at the second point is equal to the titration alkalinity. DIC was measured on the AIRICA by the extraction of total dissolved inorganic carbon content from the sample by phosphoric acid addition. The liberated CO2 flowed with a N2 carrier gas into a Li‐Cor non‐dispersive IR gas analyzer where the CO2 levels were measured. For both instruments, within bottle replicates were run consecutively on start up to check the precision, continuing once the instrument precision was ±2μmol kg‐1 or better. These were followed by a combination of Certified Reference Materials (CRMs) produced by the Marine Physical Laboratory at UCSD and low nutrient surface water from the Bermuda Atlantic Time Series (BATS) site, which were run every 20‐24 samples on the VINDTA and every 6 samples on the AIRICA, to determine the accuracy and precision of the measurements and to correct for any discrepancies. The TA system CRM values did not vary more than 2mmol within each batch of HCl acid. The AIRICA was more susceptible to drift and was affected by the lab temperature which is why CRMs were run much more often on the AIRICA, the system did not drift much and the lab temperature did not vary markedly. Both of the DIC and TA methods had a precision and accuracy of ~1 mmol kg-1 (precision estimates were determined from between-bottle and within-bottle replicates, and accuracy assessed using CRMs). The values for DIC and TA were used to calculate other parameters of the carbonate system using the software CO2sys (Lewis and Wallace, 1998). The calculated parameters were: pH, fCO2, pCO2, [HCO3‐], [CO3=], [CO2], alkalinity from borate; hydroxide ion; phosphate and silicate, Revelle Factor, plus the saturation states of calcite and aragonite.</p>
<p><strong>6. Nutrient analyses (phosphate, silicate, nitrate+nitrite, nitrite, and ammonia)</strong> - Analyses were performed at sea on a Seal Analytical continuous-flow AutoAnalyzer 3 (AA3). The methods used were described by Gordon et al [Gordon1992] Hager et al. [1972], and Atlas et al. [1971]. Details of modification of analytical methods used in this cruise are also compatible with the methods described in the nutrient section of the GO-SHIP repeat hydrography manual (Hydes et al., 2010).</p>
<p><strong>7. Coccolithophore enumeration</strong> - Polarized microscopy was used to determine the concentration of coccolithophores and detached coccoliths in samples collected during cruise TN376. A volume of 200mL was filtered onto 0.4μm-pore size, 25mm diameter polycarbonate filter then processed according to Balch &amp; Utgoff (2009).</p>
<p><strong>8. Enumeration of major algal classes</strong> - A shipboard Yokogawa Fluid Imaging Technologies FlowCam imaging cytometer was used to enumerate the major microalgal classes and estimate the particle size distribution function. The instrument was keyed on particle backscattering and fluorescence properties. Samples were first filtered through 100um Nitex mesh to make sure the 100um diameter flow chamber did not clog. The instrument was run with a 10X objective in order to reliably count particles bigger than 4-5um diameter. Samples were processed according to Poulton and Martin (2010). Concentrations (per mL), percent contribution with respect to total particles, and biomass are presented. Carbon biomass was determined based on the method described by Menden-Deuer &amp; Lessard (2000).</p>
<p><strong>9. Primary Production and Calcification Carbon Fixation Rates</strong> - Samples were also taken for measuring photosynthesis and calcification rates from 21 morning, full-CTD stations over the course of the trip (here called Productivity Stations). For these measurements, Niskin bottles were tripped at specific light depths throughout the euphotic zone (0.56%, 3.86%, 7.10%, 23.4%, 42.2%, and 73.6%). During casts where there was sufficient light to measure PAR throughout the euphotic zone, these depths were calculated assuming a constant diffuse attenuation coefficient. For samples taken during the nighttime, estimation of those light depths was performed based on the assumption that the fluorescence maximum was located at the 1% light depth (Poulton et al., 2017). Water samples for incubation were transferred from Niskin bottles to incubation bottles, typically inside the ship's enclosed hanger, under subdued light conditions. Water samples were pre-filtered through 120µm nitex mesh to remove large grazers. Incubations were performed in 70 mL polystyrene tissue culture bottles that were previously acid-cleaned, rinsed with ethanol, reverse-osmosis water, then rinsed 5x with each sea water sample prior to filling. Photosynthesis and calcification were measured using the microdiffusion technique (Paasche &amp; Brubak, 1994) with modifications by Balch et al. (2000) (see also Fabry (2010)). 14C bicarbonate (~30 uCi) was added for each water sample. Incubations were performed in triplicate (with an additional 2% buffered formalin sample (final concentration) used as a killed control) in simulated in situ conditions on-deck, corrected for both light quantity (extinction using bags made of neutral-density shade cloth) and quality (spectral narrowing) using blue acetate bag inserts. Bottle transfers between the incubators and radioisotope van were always done in darkened bags to avoid light shock to the phytoplankton. Deck incubators consisted of blue plastic tubs open to sky light, chilled using surface seawater from the ship's flowing sea water system. Calibration of those light levels in the bag were previously made using a Biospherical OSR2100 scalar PAR sensor inserted into each bag relative to a scalar PAR sensor outside the bag. All filtrations were performed using 0.4 mm pore-size polycarbonate filters. Following sample filtration, polycarbonate filters were rinsed three times with filtered seawater, then carefully given a "rim rinse" to make sure that all 14C-HCO3 in interstitial seawater in the filters was rinsed out. Filters and sample "boats" were placed in scintillation vials with 7mL of Ecolume scintillation cocktail. Samples were counted using a high-sensitivity Beckman Tricarb liquid scintillation counter with channel windows set for 14C counting. Counts were performed for sufficient time to reach 1% precision or 25 minutes for samples with lower counts. Blank 14C counts were always run for scintillation cocktail as well as the phenethylamine CO2 absorbent. Standard equations were used for calculating primary production and calcification from the 14C counts with a 5% isotope discrimination factor assumed for the physiological fixation of 14C-HCO3 as opposed to 12C-HCO3. Specific intrinsic growth rates of organic matter were calculated by dividing daily photosynthetic carbon estimates by the concentration of POC. Carbon-specific intrinsic growth rates for PIC were calculated by dividing the calcification rate by the concentration of PIC.</p>
<p><strong>10. Photophysiological variables</strong> - PAM fluorimetry is a widely used method for rapid assessment of the physiological state of the photosynthetic machinery in plants. The approach is based on measurement of chlorophyll fluorescence of photosystem II (PSII) as an indicator of the efficiency with which light absorbed by the photosynthetic machinery and converted into useful work in the form of electron transport in the chloroplast thylakoid membrane. The electron transport chains are ultimately responsible for providing the chemical energy for photosynthetic carbon fixation. Experimental measurements were made with a PAM fluorimeter (Water PAM, Walz, Germany) with 3 mL cuvette samples that were dark-adapted for &gt;30 minutes prior to analysis. The following key photosynthetic parameters were calculated from values of Fo, Fm, F'm and F':</p>
<p>- Maximum photosynthetic efficiency/capacity of dark-adapted cells: Fv/Fm = (Fm-Fo)/Fm<br />
- Effective photochemical quantum yield of PSII (photosynthetic efficiency in light conditions): Y(II) = (Fm'-F')/Fm'<br />
- Electron transfer rate (ETR) at a given irradiance value = proportion of photons at a given light intensity that are converted into useful energy. ETR = Y(II) x PAR<br />
- Non-photochemical quenching: NPQ = Fm/Fm'-1<br />
&gt; - Rapid light curves were also carried out to acquire ETR values at different irradiance values, providing information on initial slope (alpha), ETRmax at saturating irradiance and photoinhibition.</p>
<p><strong>11. PAM microscopy</strong> - Analysis of single-cell chlorophyll fluorescence was applied using similar PAM protocols to the above PAM fluorimeter measurements. The PAM microscope (PSI, Cz) allows images of Fo, Fm, F'm and F' by using LED arrays to provide measuring pulses, saturating pulses, and actinic light. Under rough weather conditions, it was only possible to obtain Fv/Fm values due to focus drift associated with vertical movements of the ship. The microscope allowed the acquisition of bright field and polarized light images to identify individual phytoplankton cells and calcifying coccolithophores. Cells were allowed to settle in darkness for &gt;1 hour before gentle transfer to the microscope imaging chamber, which comprised a glass-bottomed dish and X20 or X40 Zeiss water immersion objectives. The dish was mounted on a temperature-controlled perfusion cell, which allowed cells to be maintained at the precise collection temperature. All manipulations were carried out in darkness. Bright field images were obtained using far red light, which does not activate the PSII reaction centers.</p>
Specified by the Principal Investigator(s)
<p>PAM fluorometry data were processed with with Walz (Germany) WinControl-3 software. (<a href="https://www.walz.com/products/chl_p700/water-pam/downloads.html" target="_blank">https://www.walz.com/products/chl_p700/water-pam/downloads.html</a>). Imaging PAM data were processed with Photon Systems Instruments Fluorcam 7 software (<a href="https://psi.cz/imaging-sensors/fluorescence-imaging/" target="_blank">https://psi.cz/imaging-sensors/fluorescence-imaging/</a>).</p>
Specified by the Principal Investigator(s)
- Imported original file "TN376 MergedMasterBottleFile_06072022_CTD_DatawBalchBatesBrownleeFinal for BCO-DMO V4 corrected.xlsx" into the BCO-DMO system.
- Flagged "-999" as a missing data value (missing data are empty/blank in the final CSV file).
- Re-named fields to comply with BCO-DMO naming conventions.
- Changed the year from 2021 to 2020 for Station 51.
- Converted the date/time field to ISO 8601 format.
- Saved the final file as "914901_v1_tn376_bottle_data.csv".
Specified by BCO-DMO Data Managers
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Water PAM
Water PAM
PI Supplied Instrument Name: Water PAM PI Supplied Instrument Description:The Water PAM (Walz, Germany) is a portable cuvette system for analyzing the photosynthetic activity of a wide variety of phytoplankton samples. Instrument Name: Fluorometer Instrument Short Name:Fluorometer Instrument Description: A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/113/
FluorCam Imaging Pulse Amplitude Modulation system
FluorCam Imaging Pulse Amplitude Modulation system
PI Supplied Instrument Name: FluorCam Imaging Pulse Amplitude Modulation system PI Supplied Instrument Description:The FluorCam Imaging Pulse Amplitude Modulation system (Photon Systems Instruments Cz) is a Fluorescence Kinetic Microscope (FKM) that extends the complete capacity of kinetic chlorophyll or multicolor fluorescence imaging to the realm of individual cells and subcellular structures. Instrument Name: Fluorometer Instrument Short Name:Fluorometer Instrument Description: A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/113/
A3 microscope (Zeiss UK)
A3 microscope (Zeiss UK)
PI Supplied Instrument Name: A3 microscope (Zeiss UK) Instrument Name: Microscope - Optical Instrument Short Name: Instrument Description: Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of visible light. Includes conventional and inverted instruments. Also called a "light microscope". Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB05/
TC-344C Dual channel temperature controller
TC-344C Dual channel temperature controller
PI Supplied Instrument Name: TC-344C Dual channel temperature controller PI Supplied Instrument Description:The TC-324C and TC-344C temperature controllers (Warner Instruments, USA) provide power to a variety of heating devices including Warner heated platforms such as the microscope stage used here. Each channel supplies up to 22 watts into a load of 10 ohms. Heat setpoint was controlled automatically in Auto mode via thermistor feedback. A loop-speed selector provided three feedback speeds to optimize the thermal stability of the device being heated. Heat setpoint also could be manually controlled in Manual mode. Instrument Name: thermostat Instrument Short Name: Instrument Description: A device designed to regulate temperature by controlling the starting and stopping of a heating/cooling system.
Yokogowa FlowCAM imaging cytometer
Yokogowa FlowCAM imaging cytometer
PI Supplied Instrument Name: Yokogowa FlowCAM imaging cytometer Instrument Name: Yokogawa Fluid Imaging Technologies FlowCam VS particle imaging system Instrument Short Name:FlowCAM Instrument Description: Imaging cytometers are automated instruments that quantify properties of single cells, one cell at a time. They combine some aspects of flow cytometry with particle imaging capabilities in an automated device to classify small particles, including phytoplankton and protozoa. They can measure a variety of properties: cell size, cell granularity, cell aspect ratio, equivalent spherical diameter (ESD) and area-based diameter (ABD) [to estimate bio-volume, which is used to estimate cell carbon biomass]. Particle images are digitally recorded and sorted into different classes according to training libraries using a support vector machine (supervised learning methods). The instruments particle-size is calibrated using different sizes of latex beads.
The FlowCam VS series are automated imaging-in-flow instruments that generate high-resolution digital images for measuring size and shape of microscopic particles. The sample introduced in the system is attracted by a peristaltic or a syringe pump into a flow cell (or flow chamber) with known dimensions, located in front of a microscope objective which is connected to a camera video. The benchtop model is ideally suited to a typical laboratory environment with applications in oceanographic research, municipal water, biopharmaceutical formulations, chemicals, oil and gas, biofuels, and many other markets. FlowCam VS is available in four models, from the imaging-only VS-I (i.e. without excitation wavelength or fluorescence emission wavelengths) to the top-of-the-line VS-IV with two channels of fluorescence measurement and scatter triggering capabilities. The instrument can measure particles between 2µm and 2mm; can analyse in vivo or fixed samples; has a flow rate between 0.005 ml/minute and 250 ml/minute (dependant upon magnification, flow cell depth, camera frame rate, efficiency desired, etc.). It can produce either 8-bit Grayscale (Monochrome Camera) or 24-bit Colour (Colour Camera) images, depending on the model.
Cruise: TN376
TN376
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel
TN376
William M. Balch
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel