http://lod.bco-dmo.org/id/dataset/765327
eng; USA
utf8
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
2019-04-18
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Coastal water biogeochemistry collected aboard the R/V Endeavor along the North Atlantic coast from 2017-08-20 to 2017-08-28
2019-04-24
publication
2019-04-24
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2019-09-13
publication
https://doi.org/10.1575/1912/bco-dmo.765327.1
Colleen Hansel
Woods Hole Oceanographic Institution
principalInvestigator
Carl Lamborg
University of California-Santa Cruz
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: Hansel, C., Lamborg, C. (2019) Coastal water biogeochemistry collected aboard the R/V Endeavor along the North Atlantic coast from 2017-08-20 to 2017-08-28. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2019-04-24 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.765327.1 [access date]
Coastal water biogeochemistry along the North Atlantic coast Dataset Description: <p>Sample Collection<br />
Samples were collected from four water column sites along the Northeast Coast of the United States in August 2017 aboard the R/V Endeavor. Samples were collected using a 12-bottle trace metal clean CTD (Conductivity, Temperature and Depth) rosette, and were kept clean by using acid washed tubing to collect water directly into acid-washed 1 L PTFE bottles. Sample depths were chosen based on the water column profile obtained from a separate 24-bottle CTD rosette system equipped with Seabird software, which also provided the temperature, dissolved oxygen, salinity, PAR, beam transmission and fluorescence profiles reported here.</p> Methods and Sampling: <p>Chlorophyll<br />
In the dark, 250 mL of seawater was filtered onto 25 mm GF/F filters.&nbsp; Samples were stored in the dark at -20C until analyzed according to protocols adapted from Strickland and Parsons (1972).&nbsp; Briefly, samples were extracted in 90% acetone in the dark (4C, 9 hr) and measured using an 10AU fluorometer (Turner).&nbsp; Sample signals were calibrated using a chlorophyll-a standard (Sigma C6144) and were corrected for pheopigments by accounting for the fluorescence of extracts before and after acidification to 0.003 M HCl.</p>
<p>Nitrogen Species<br />
Concentrations of nitrate + nitrite were measured by chemiluminescence after reduction in a hot acidic vanadyl sulfate solution on a NOx analyzer (Braman and Hendrix, 1989). Concentrations of nitrite were quantified by using the Griess–Ilosvay method followed by measuring absorption 540 nm (Grasshoff et al., 1999), and nitrate was quantified by difference. Concentrations of ammonium were measured by fluorescence using the OPA method (Holmes et al., 1999).</p>
<p>Microbial Abundance<br />
Seawater samples were preserved for flow cytometry with 0.5% glutaraldehyde (final concentration), flash frozen in liquid nitrogen and stored at -80°C until analysis. Bacteria and group-specific phytoplankton counts were conducted on a Guava EasyCyte HT flow cytometer (Millipore). Instrument-specific beads were used to calibrate the cytometer. Samples were analyzed at a low flow rate (0.24 µL s-1) for 3 min.&nbsp; To enumerate bacteria, samples were diluted (1:100) with filtered seawater (0.01 µm).&nbsp; Samples and filtered seawater blanks were stained with SYBR Green I (Invitrogen) according to the manufacturer’s instructions and incubated in a 96-well plate in the dark at room temperature for 1 hr.&nbsp; Bacterial cells were counted based on diagnostic forward scatter vs. green fluorescence signals.&nbsp; Major phytoplankton groups were distinguished based on plots of forward scatter vs. orange (phycoerythrin-containing Synechococcus sp.), and forward scatter vs. red (eukaryotes).&nbsp; Size classes of eukaryotic phytoplankton were further distinguished based on forward scatter (pico-, nano- and large eukaryotes).&nbsp;</p>
<p>Dissolved organic carbon<br />
Filtered water samples for total dissolved organic carbon were pipetted into acid-washed combusted glass vials, acidified to pH = 2 with 12 M hydrochloric acid, and stored at 4 °C until analysis on a Shimadzu TOC-5050A total organic carbon analyzer. The coefficient of variability between replicate injections was less than 1%.</p>
<p>Reactive oxygen species<br />
Water samples were collected directly from a trace metal clean rosette into acid-washed, opaque bottles and stored in a shipboard flow-through seawater incubator. A subset of each water sample was filtered (0.2 um), amended with 50 µM diethylene-triaminepentaacetic acid (DTPA, Sigma), and aged overnight in the shipboard seawater flow through incubator (termed AFSW). Additionally, particle associated superoxide signals were determined by filtering (0.2 um) a subset of each water sample and measuring the chemiluminescent signal within 25-30 minutes after filtering (termed FFSW). Superoxide signals were measured by pumping unfiltered water (UFSW), FFSW, or AFSW from dark bottles using a high accuracy peristaltic pump directly into a flow-through FeLume Mini system (Waterville Analytical, Waterville ME) within the ship laboratory. Superoxide detection was based on the reaction between superoxide and a chemiluminescent probe, a methyl cypridina luciferin analog (MCLA, Santa Cruz Biotechnology) (Rose et al., 2008) as before (Roe et al., 2016). The travel time of the water samples in the opaque FeLume tubing was approximately 20 sec. Data was collected for several minutes (~2-4 min) once a steady-state signal was achieved. At least 12 hours following filtering, the superoxide signals within the AFSW for each depth was measured to establish the baseline. At the end of each run, 800 U L-1 superoxide dismutase (SOD, Sigma) was added to seawater samples. The total dark superoxide signal produced in the seawater was defined as the difference between the UFSW signal (subtracted by the SOD baseline) and AFSW signal (subtracted by the SOD baseline) (similar to (Roe et al., 2016)). The particle associated signal was defined as the UFSW signal (subtracted by the SOD baseline) and FFSW signal (subtracted by the SOD baseline) (similar to (Roe et al., 2016)). While the SOD baseline has an autoxidation artifact, this artifact is canceled by taking the difference between two signals. The chemiluminescent signals were converted to superoxide concentration by conducted calibrations in the same aged-filtered seawater used for the baseline at each depth. Calibrations were conducted using potassium dioxide (Sigma) as detailed previously (Zhang et al., 2016).&nbsp;</p>
<p>Designations are:&nbsp;<br />
Total superoxide = [(UFSW) - (UFSW-SOD)] - [(AFSW)- (AFSW-SOD)]<br />
Particle superoxide = [(UFSW) - (UFSW-SOD)] - [(FFSW)- (FFSW-SOD)]</p>
<p>Hydrogen peroxide concentrations. Hydrogen peroxide concentration was quantified based on the oxidation of colorless AmplifluTM Red (AR, Sigma) to pink-colored resorufin by hydrogen peroxide. For hydrogen peroxide concentration analysis, pre-mixed AR and horse radish peroxidase (HRP) stock solution was added at a final concentration of 50 µmol L-1 AR and 1 kU L-1 HRP to filtered (0.2 um) and unfiltered seawater samples in a clear 96-well microplate (Zhang et al., 2016). Light absorbance was measured at 570 nm (Abs570, maximum absorbance of resorufin) and 700 nm (Abs700, to account for background absorbance) on a SpectraMax® M3 multi-mode microplate reader. The difference between Abs570 and Abs700 (i.e., Abs570-700) was used for calculating hydrogen peroxide concentrations in seawater samples based on a calibration. The calibration factor was determined by standard addition of hydrogen peroxide into 0.2-µm filtered seawater from each station and depth as described previously (Zhang et al., 2016). To account for autoxidation of AR, 200 kU L-1 catalase (Sigma) was added to the blanks prior to the addition of AR and HRP. The hydrogen peroxide concentrations in seawater samples were determined by applying the calibration factor to the blank-corrected Abs570-700values. Net and gross hydrogen peroxide concentrations were defined as the levels measured in unfiltered and filtered seawater samples, respectively.&nbsp;</p>
<p>Manganese<br />
Seawater samples (1 L) were filtered through 0.2 µm membrane filters (Millipore) within one hour of collection using acid-washed Savillex vacuum-filtration rigs. The filtrate was poured into new 15 mL falcon tubes and the filter was immediately amended with a leuco-based dye for Mn oxide concentration in a separate 15 mL falcon tube.</p>
<p>The leucoberbelin blue (LBB) assay for Mn oxides (denoted MnOx hereafter) was previously adapted from Altman (1972) to examine coastal water column sites (Oldham et al., 2015; 2017a, 2017b, 2017c). In this assay, the filter is amended with 3 mL of 20 µM LBB dye solution (LBB, Sigma-Aldrich). The dye color forms upon oxidation of the LBB molecule by Mn oxides and can be measured spectrophotometrically. The LBB stock solution was prepared by dissolving the powder in Milli-Q water to a concentration of 4 % and adding 40 µL of 10 M sodium hydroxide (NaOH) per 10 mL of stock solution. Working solutions are subsequently prepared by diluting the stock solution into 1 % acetic acid, to 0.4 % LBB. A calibration curve was generated using KMnO4, for which equivalent absorbance for Mn(IV) is calculated based on 2.5 more Mn(IV) being required relative to Mn(VII) to oxidize the LBB. In our set-up, a 100 cm pathlength cell (Liquid Waveguide Capillary Cell) was coupled to a Flame UV-Vis (Ocean Optics), set up with SpectraSuite software. Using a 100 cm pathlength cell allows for a detection limit of 0.2 nM but also requires our re-filtration of samples (0.2 µm luer-lok syringe filter, Millipore) prior to injection into the cell to avoid particulate interference and clogging of the capillary cell. Samples reacted with the LBB dye overnight in the dark prior to analysis, then absorbance at 623 nm was recorded.&nbsp; If sample absorbance was too high, samples were diluted 10-20 times in Milli-Q water.</p>
<p>For soluble Mn speciation analysis, an established spectrophotometric porphyrin addition method was employed (Madison et al., 2011; Oldham et al., 2017a), which uses the ligand T(4-CP)P (or α, β, γ, δ-tetrakis(4-carboxyphenyl)porphine, to 2.33 x 10-7 M final sample cocentration). In this method, cadmium chloride (CdCl2; to 2.4 x 10-7 M) is added to form a complex with the porphyrin, in the presence of an imidazole tetraborate buffer (pH = 8.2). The sample is added to the mixture (diluted 10-fold with Milli-Q water to avoid chloride interference) and any Mn(II) in the sample undergoes a metal substitution reaction with the Cd over the course of a 1 hour reaction in a 90°C water bath. The solution is cooled, then analyzed using the 100-cm UV-Vis spectrophotometric set-up described above. Total dissolved Mn is analyzed in the same way, but after the addition of 1.4 µM hydroxylamine hydrochloride to the sample (reacted overnight in a refrigerator). The difference between the total dissolved Mn and the Mn(II) gives the Mn(III)-L in the sample. We note that during the heated reaction with no reducing agent, it is likely that some Mn(III)-L complexes undergo a ligand substitution reaction with the added porphyrin, and thus our method likely underestimates Mn(III)-L, particularly for weaker complexes. For all samples, assays were run in triplicate for both Mn(II) and Mn total, and peak height for all assays was determined using a baseline subtraction performed using ECD-Soft peak correction software.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1355720 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1355720
completed
Colleen Hansel
Woods Hole Oceanographic Institution
508-289-3738
266 Woods Hole Road, MS52
Woods Hole
MA
02543
US
chansel@whoi.edu
pointOfContact
Carl Lamborg
University of California-Santa Cruz
831-459-2908
A442 Earth & Marine Sciences 1156 High Street
Santa Cruz
CA
95064
USA
clamborg@ucsc.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Station
lat
long
Year
Month
Day
Time
ISO_datetime_UTC
Depth
Temp
Florescence
Chlorophyll
Chloro_sd
PAR
Beam_Transmission
Salinity
O2
NO2
NH4
NO3
Nanoeuks
Nanoeuks_sd
Picoeuks
Picoeuks_sd
Synechococcus
Synechococcus_sd
Bacteria
Bacteria_sd
DOC
DOC_sd
Tot_O2
Tot_O2_sd
Part_O2
Part_O2_sd
Net_H2O2
Net_H2O2_sd
Gross_H2O2
Gross_H2O2_sd
Total_dHg
Total_dHg_sd
Hg_0
Hg_0_sd
dMn_II
dMn_II_sd
dMn_T
dMn_T_sd
dMn_III_L
dMn_III_L_sd
MnOx
sheet
NOx analyzer
CTD Seabird
Guava EasyCyte HT flow cytometer (Millipore)
10AU fluorometer (Turner)
Shimadzu TOC-5050A total organic carbon analyzer
theme
None, User defined
station number
latitude
longitude
year
month of year
day of month
time of day
ISO_DateTime_UTC
depth
water temperature at measurement depth
fluorescence
chlorophyll a
PAR
transmission
salinity
dissolved Oxygen
Nitrite
Ammonium
Nitrate
abundance
dissolved organic Carbon
No BCO-DMO term
Hydrogen Peroxide
trace metal concentration
Manganese
featureType
BCO-DMO Standard Parameters
Chemiluminescence NOx Analyzer
CTD Sea-Bird
Flow Cytometer
Fluorometer
Total Organic Carbon Analyzer
instrument
BCO-DMO Standard Instruments
EN604
service
Deployment Activity
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: Defining the Role of Biologically Produced Reactive Oxygen Species in Dark Mercury Cycling
https://osprey.bco-dmo.org/project/756930
Collaborative Research: Defining the Role of Biologically Produced Reactive Oxygen Species in Dark Mercury Cycling
<p>NSF Abstract:</p>
<p>Mercury (Hg) is a toxic trace element that bioaccumulates into marine food webs, imposing a health threat to humans through the consumption of seafood. However, controls on the cycling of Hg in the ocean are poorly understood. Most research to date has focused on sun-lit and/or Hg-laden environments, where light-induced chemical and mercury resistance reactions, respectively, have been identified as dominant pathways for Hg cycling. The paradigm that dark Hg reactions are irrelevant is fading and it is now apparent that dark redox reactions, both reduction and oxidation, are important in the cycling of Hg. In this study, researchers at the Woods Hole Oceanographic Institution and Colorado School of Mines will obtain a better understanding of the biogeochemical reactions responsible for dark redox transformations of mercury (Hg) in marine systems. The researchers will explore the relationship between microbial activity, reactive oxygen species, and Hg speciation in a series of laboratory- and field-based investigations to obtain a mechanistic understanding of dark Hg cycling. By identifying new controls on the redox cycling of Hg in the ocean, this research will help inform global and ecosystem models used to predict Hg bioavailability.</p>
<p>Broader Impacts: The proponents plan to educate high school teachers from Boston Green Academy in South Boston on mercury biogeochemistry and have one teacher participate in the summer research cruises, as well as develop science curricula to engage the underrepresented students at the school in science. One postdoc and one graduate student from Woods Hole Oceanographic Institution and one graduate student from the Colorado School of Mines would be supported and trained as part of this project. It is anticipated that undergraduate students would have the opportunity to participate in the study as summer interns.</p>
ROS in Hg Cycling
largerWorkCitation
project
eng; USA
oceans
-74.56461
-67.92692
37.77692
41.18026
2017-08-20
2017-08-28
Coastal North Atlantic
0
BCO-DMO catalogue of parameters from Coastal water biogeochemistry collected aboard the R/V Endeavor along the North Atlantic coast from 2017-08-20 to 2017-08-28
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/765596.rdf
Name: Station
Units: unitless
Description: <p>station identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/765597.rdf
Name: lat
Units: decimal degrees
Description: <p>station latitude with north positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/765598.rdf
Name: long
Units: decimal degrees
Description: <p>station longitude with east positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/765599.rdf
Name: Year
Units: unitless
Description: <p>year of collection in yyyy format</p>
http://lod.bco-dmo.org/id/dataset-parameter/765600.rdf
Name: Month
Units: unitless
Description: <p>month of collection in mm format</p>
http://lod.bco-dmo.org/id/dataset-parameter/765601.rdf
Name: Day
Units: unitless
Description: <p>day of collection in dd format</p>
http://lod.bco-dmo.org/id/dataset-parameter/765602.rdf
Name: Time
Units: unitless
Description: <p>time of collection in HH:MM format</p>
http://lod.bco-dmo.org/id/dataset-parameter/765603.rdf
Name: ISO_datetime_UTC
Units: yyyy-MM-dd'T'HH:mm:ss'Z'
Description: <p>date and time following ISO format</p>
http://lod.bco-dmo.org/id/dataset-parameter/765604.rdf
Name: Depth
Units: meters (m)
Description: <p>water depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/765605.rdf
Name: Temp
Units: degrees Celsius (C)
Description: <p>Water temperature from CTD</p>
http://lod.bco-dmo.org/id/dataset-parameter/765606.rdf
Name: Florescence
Units: miligrams per meter cubed (mg/m3)
Description: <p>water flourescence from CTD</p>
http://lod.bco-dmo.org/id/dataset-parameter/765607.rdf
Name: Chlorophyll
Units: micrograms per liter (ug/L)
Description: <p>Chlorophyll a concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/765608.rdf
Name: Chloro_sd
Units: micrograms per liter (ug/L)
Description: <p>Chlorophyll a concentration standard deviation</p>
http://lod.bco-dmo.org/id/dataset-parameter/765609.rdf
Name: PAR
Units: microeinteins per meter squared second (microE/m2s)
Description: <p>Photosynthetically active radiation (CTD)</p>
http://lod.bco-dmo.org/id/dataset-parameter/765610.rdf
Name: Beam_Transmission
Units: percent
Description: <p>Beam transmission (CTD)</p>
http://lod.bco-dmo.org/id/dataset-parameter/765611.rdf
Name: Salinity
Units: PSU
Description: <p>Water salinity (CTD)</p>
http://lod.bco-dmo.org/id/dataset-parameter/765612.rdf
Name: O2
Units: mililiters per liter (mL/L)
Description: <p>Water oxygen concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/765613.rdf
Name: NO2
Units: micromole (uM)
Description: <p>Water nitrite concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/765614.rdf
Name: NH4
Units: micromole (uM)
Description: <p>Water ammonium concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/765615.rdf
Name: NO3
Units: micromole (uM)
Description: <p>Water nitrate concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/765616.rdf
Name: Nanoeuks
Units: cells per mililiter (cells/mL)
Description: <p>Nanoeukaryote abundance</p>
http://lod.bco-dmo.org/id/dataset-parameter/765617.rdf
Name: Nanoeuks_sd
Units: cells per mililiter (cells/mL)
Description: <p>Nanoeukaryote abundance standard deviation</p>
http://lod.bco-dmo.org/id/dataset-parameter/765618.rdf
Name: Picoeuks
Units: cells per mililiter (cells/mL)
Description: <p>Picoeukayrote abundance</p>
http://lod.bco-dmo.org/id/dataset-parameter/765619.rdf
Name: Picoeuks_sd
Units: cells per mililiter (cells/mL)
Description: <p>Picoeukayrote abundance standard deviation</p>
http://lod.bco-dmo.org/id/dataset-parameter/765620.rdf
Name: Synechococcus
Units: cells per mililiter (cells/mL)
Description: <p>Synechococcus abundance</p>
http://lod.bco-dmo.org/id/dataset-parameter/765621.rdf
Name: Synechococcus_sd
Units: cells per mililiter (cells/mL)
Description: <p>Synechococcus abundance standard deviation</p>
http://lod.bco-dmo.org/id/dataset-parameter/765622.rdf
Name: Bacteria
Units: cells per mililiter (cells/mL)
Description: <p>Bacteria concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/765623.rdf
Name: Bacteria_sd
Units: cells per mililiter (cells/mL)
Description: <p>Bacteria concentration standard deviation</p>
http://lod.bco-dmo.org/id/dataset-parameter/765624.rdf
Name: DOC
Units: miligrams per liter (mg/L)
Description: <p>Dissolved organic carbon</p>
http://lod.bco-dmo.org/id/dataset-parameter/765625.rdf
Name: DOC_sd
Units: miligrams per liter (mg/L)
Description: <p>Dissolved organic carbon standard deviation</p>
http://lod.bco-dmo.org/id/dataset-parameter/765626.rdf
Name: Tot_O2
Units: picomole (pM)
Description: <p>Total superoxide</p>
http://lod.bco-dmo.org/id/dataset-parameter/765627.rdf
Name: Tot_O2_sd
Units: picomole (pM)
Description: <p>Total superoxide standard deviation</p>
http://lod.bco-dmo.org/id/dataset-parameter/765628.rdf
Name: Part_O2
Units: picomole (pM)
Description: <p>Particle associated superoxide</p>
http://lod.bco-dmo.org/id/dataset-parameter/765629.rdf
Name: Part_O2_sd
Units: picomole (pM)
Description: <p>Particle associated superoxide standard deviation</p>
http://lod.bco-dmo.org/id/dataset-parameter/765630.rdf
Name: Net_H2O2
Units: nanomole (nM)
Description: <p>Net hydrogen peroxide</p>
http://lod.bco-dmo.org/id/dataset-parameter/765631.rdf
Name: Net_H2O2_sd
Units: nanomole (nM)
Description: <p>Net hydrogen peroxide standard deviation</p>
http://lod.bco-dmo.org/id/dataset-parameter/765632.rdf
Name: Gross_H2O2
Units: nanomole (nM)
Description: <p>Gross hydrogen peroxide</p>
http://lod.bco-dmo.org/id/dataset-parameter/765633.rdf
Name: Gross_H2O2_sd
Units: nanomole (nM)
Description: <p>Gross hydrogen peroxide standard deviation</p>
http://lod.bco-dmo.org/id/dataset-parameter/765634.rdf
Name: Total_dHg
Units: picomole (pM)
Description: <p>Total dissolved Hg</p>
http://lod.bco-dmo.org/id/dataset-parameter/765635.rdf
Name: Total_dHg_sd
Units: picomole (pM)
Description: <p>Total dissolved Hg standard deviation</p>
http://lod.bco-dmo.org/id/dataset-parameter/765636.rdf
Name: Hg_0
Units: picomole (pM)
Description: <p>Elemental Hg</p>
http://lod.bco-dmo.org/id/dataset-parameter/765637.rdf
Name: Hg_0_sd
Units: picomole (pM)
Description: <p>Elemental Hg standard deviation</p>
http://lod.bco-dmo.org/id/dataset-parameter/765638.rdf
Name: dMn_II
Units: nanomole (nM)
Description: <p>Dissolved Mn(II)</p>
http://lod.bco-dmo.org/id/dataset-parameter/765639.rdf
Name: dMn_II_sd
Units: nanomole (nM)
Description: <p>Dissolved Mn(II) standard deviation</p>
http://lod.bco-dmo.org/id/dataset-parameter/765640.rdf
Name: dMn_T
Units: nanomole (nM)
Description: <p>Total dissolved Mn</p>
http://lod.bco-dmo.org/id/dataset-parameter/765641.rdf
Name: dMn_T_sd
Units: nanomole (nM)
Description: <p>Total dissolved Mn standard deviation</p>
http://lod.bco-dmo.org/id/dataset-parameter/765642.rdf
Name: dMn_III_L
Units: nanomole (nM)
Description: <p>Dissolved Mn(III)-L</p>
http://lod.bco-dmo.org/id/dataset-parameter/765643.rdf
Name: dMn_III_L_sd
Units: nanomole (nM)
Description: <p>Dissolved Mn(III)-L standard deviation</p>
http://lod.bco-dmo.org/id/dataset-parameter/765644.rdf
Name: MnOx
Units: nanomole
Description: <p>Mn oxides</p>
http://lod.bco-dmo.org/id/dataset-parameter/765645.rdf
Name: sheet
Units: unitless
Description: <p>Name of the sheet from the original data file</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
519311
https://darchive.mblwhoilibrary.org/bitstream/1912/24549/1/dataset-765327_torch-ii__v1.tsv
download
https://doi.org/10.1575/1912/bco-dmo.765327.1
download
onLine
dataset
<p>Chlorophyll<br />
In the dark, 250 mL of seawater was filtered onto 25 mm GF/F filters.&nbsp; Samples were stored in the dark at -20C until analyzed according to protocols adapted from Strickland and Parsons (1972).&nbsp; Briefly, samples were extracted in 90% acetone in the dark (4C, 9 hr) and measured using an 10AU fluorometer (Turner).&nbsp; Sample signals were calibrated using a chlorophyll-a standard (Sigma C6144) and were corrected for pheopigments by accounting for the fluorescence of extracts before and after acidification to 0.003 M HCl.</p>
<p>Nitrogen Species<br />
Concentrations of nitrate + nitrite were measured by chemiluminescence after reduction in a hot acidic vanadyl sulfate solution on a NOx analyzer (Braman and Hendrix, 1989). Concentrations of nitrite were quantified by using the Griess–Ilosvay method followed by measuring absorption 540 nm (Grasshoff et al., 1999), and nitrate was quantified by difference. Concentrations of ammonium were measured by fluorescence using the OPA method (Holmes et al., 1999).</p>
<p>Microbial Abundance<br />
Seawater samples were preserved for flow cytometry with 0.5% glutaraldehyde (final concentration), flash frozen in liquid nitrogen and stored at -80°C until analysis. Bacteria and group-specific phytoplankton counts were conducted on a Guava EasyCyte HT flow cytometer (Millipore). Instrument-specific beads were used to calibrate the cytometer. Samples were analyzed at a low flow rate (0.24 µL s-1) for 3 min.&nbsp; To enumerate bacteria, samples were diluted (1:100) with filtered seawater (0.01 µm).&nbsp; Samples and filtered seawater blanks were stained with SYBR Green I (Invitrogen) according to the manufacturer’s instructions and incubated in a 96-well plate in the dark at room temperature for 1 hr.&nbsp; Bacterial cells were counted based on diagnostic forward scatter vs. green fluorescence signals.&nbsp; Major phytoplankton groups were distinguished based on plots of forward scatter vs. orange (phycoerythrin-containing Synechococcus sp.), and forward scatter vs. red (eukaryotes).&nbsp; Size classes of eukaryotic phytoplankton were further distinguished based on forward scatter (pico-, nano- and large eukaryotes).&nbsp;</p>
<p>Dissolved organic carbon<br />
Filtered water samples for total dissolved organic carbon were pipetted into acid-washed combusted glass vials, acidified to pH = 2 with 12 M hydrochloric acid, and stored at 4 °C until analysis on a Shimadzu TOC-5050A total organic carbon analyzer. The coefficient of variability between replicate injections was less than 1%.</p>
<p>Reactive oxygen species<br />
Water samples were collected directly from a trace metal clean rosette into acid-washed, opaque bottles and stored in a shipboard flow-through seawater incubator. A subset of each water sample was filtered (0.2 um), amended with 50 µM diethylene-triaminepentaacetic acid (DTPA, Sigma), and aged overnight in the shipboard seawater flow through incubator (termed AFSW). Additionally, particle associated superoxide signals were determined by filtering (0.2 um) a subset of each water sample and measuring the chemiluminescent signal within 25-30 minutes after filtering (termed FFSW). Superoxide signals were measured by pumping unfiltered water (UFSW), FFSW, or AFSW from dark bottles using a high accuracy peristaltic pump directly into a flow-through FeLume Mini system (Waterville Analytical, Waterville ME) within the ship laboratory. Superoxide detection was based on the reaction between superoxide and a chemiluminescent probe, a methyl cypridina luciferin analog (MCLA, Santa Cruz Biotechnology) (Rose et al., 2008) as before (Roe et al., 2016). The travel time of the water samples in the opaque FeLume tubing was approximately 20 sec. Data was collected for several minutes (~2-4 min) once a steady-state signal was achieved. At least 12 hours following filtering, the superoxide signals within the AFSW for each depth was measured to establish the baseline. At the end of each run, 800 U L-1 superoxide dismutase (SOD, Sigma) was added to seawater samples. The total dark superoxide signal produced in the seawater was defined as the difference between the UFSW signal (subtracted by the SOD baseline) and AFSW signal (subtracted by the SOD baseline) (similar to (Roe et al., 2016)). The particle associated signal was defined as the UFSW signal (subtracted by the SOD baseline) and FFSW signal (subtracted by the SOD baseline) (similar to (Roe et al., 2016)). While the SOD baseline has an autoxidation artifact, this artifact is canceled by taking the difference between two signals. The chemiluminescent signals were converted to superoxide concentration by conducted calibrations in the same aged-filtered seawater used for the baseline at each depth. Calibrations were conducted using potassium dioxide (Sigma) as detailed previously (Zhang et al., 2016).&nbsp;</p>
<p>Designations are:&nbsp;<br />
Total superoxide = [(UFSW) - (UFSW-SOD)] - [(AFSW)- (AFSW-SOD)]<br />
Particle superoxide = [(UFSW) - (UFSW-SOD)] - [(FFSW)- (FFSW-SOD)]</p>
<p>Hydrogen peroxide concentrations. Hydrogen peroxide concentration was quantified based on the oxidation of colorless AmplifluTM Red (AR, Sigma) to pink-colored resorufin by hydrogen peroxide. For hydrogen peroxide concentration analysis, pre-mixed AR and horse radish peroxidase (HRP) stock solution was added at a final concentration of 50 µmol L-1 AR and 1 kU L-1 HRP to filtered (0.2 um) and unfiltered seawater samples in a clear 96-well microplate (Zhang et al., 2016). Light absorbance was measured at 570 nm (Abs570, maximum absorbance of resorufin) and 700 nm (Abs700, to account for background absorbance) on a SpectraMax® M3 multi-mode microplate reader. The difference between Abs570 and Abs700 (i.e., Abs570-700) was used for calculating hydrogen peroxide concentrations in seawater samples based on a calibration. The calibration factor was determined by standard addition of hydrogen peroxide into 0.2-µm filtered seawater from each station and depth as described previously (Zhang et al., 2016). To account for autoxidation of AR, 200 kU L-1 catalase (Sigma) was added to the blanks prior to the addition of AR and HRP. The hydrogen peroxide concentrations in seawater samples were determined by applying the calibration factor to the blank-corrected Abs570-700values. Net and gross hydrogen peroxide concentrations were defined as the levels measured in unfiltered and filtered seawater samples, respectively.&nbsp;</p>
<p>Manganese<br />
Seawater samples (1 L) were filtered through 0.2 µm membrane filters (Millipore) within one hour of collection using acid-washed Savillex vacuum-filtration rigs. The filtrate was poured into new 15 mL falcon tubes and the filter was immediately amended with a leuco-based dye for Mn oxide concentration in a separate 15 mL falcon tube.</p>
<p>The leucoberbelin blue (LBB) assay for Mn oxides (denoted MnOx hereafter) was previously adapted from Altman (1972) to examine coastal water column sites (Oldham et al., 2015; 2017a, 2017b, 2017c). In this assay, the filter is amended with 3 mL of 20 µM LBB dye solution (LBB, Sigma-Aldrich). The dye color forms upon oxidation of the LBB molecule by Mn oxides and can be measured spectrophotometrically. The LBB stock solution was prepared by dissolving the powder in Milli-Q water to a concentration of 4 % and adding 40 µL of 10 M sodium hydroxide (NaOH) per 10 mL of stock solution. Working solutions are subsequently prepared by diluting the stock solution into 1 % acetic acid, to 0.4 % LBB. A calibration curve was generated using KMnO4, for which equivalent absorbance for Mn(IV) is calculated based on 2.5 more Mn(IV) being required relative to Mn(VII) to oxidize the LBB. In our set-up, a 100 cm pathlength cell (Liquid Waveguide Capillary Cell) was coupled to a Flame UV-Vis (Ocean Optics), set up with SpectraSuite software. Using a 100 cm pathlength cell allows for a detection limit of 0.2 nM but also requires our re-filtration of samples (0.2 µm luer-lok syringe filter, Millipore) prior to injection into the cell to avoid particulate interference and clogging of the capillary cell. Samples reacted with the LBB dye overnight in the dark prior to analysis, then absorbance at 623 nm was recorded.&nbsp; If sample absorbance was too high, samples were diluted 10-20 times in Milli-Q water.</p>
<p>For soluble Mn speciation analysis, an established spectrophotometric porphyrin addition method was employed (Madison et al., 2011; Oldham et al., 2017a), which uses the ligand T(4-CP)P (or α, β, γ, δ-tetrakis(4-carboxyphenyl)porphine, to 2.33 x 10-7 M final sample cocentration). In this method, cadmium chloride (CdCl2; to 2.4 x 10-7 M) is added to form a complex with the porphyrin, in the presence of an imidazole tetraborate buffer (pH = 8.2). The sample is added to the mixture (diluted 10-fold with Milli-Q water to avoid chloride interference) and any Mn(II) in the sample undergoes a metal substitution reaction with the Cd over the course of a 1 hour reaction in a 90°C water bath. The solution is cooled, then analyzed using the 100-cm UV-Vis spectrophotometric set-up described above. Total dissolved Mn is analyzed in the same way, but after the addition of 1.4 µM hydroxylamine hydrochloride to the sample (reacted overnight in a refrigerator). The difference between the total dissolved Mn and the Mn(II) gives the Mn(III)-L in the sample. We note that during the heated reaction with no reducing agent, it is likely that some Mn(III)-L complexes undergo a ligand substitution reaction with the added porphyrin, and thus our method likely underestimates Mn(III)-L, particularly for weaker complexes. For all samples, assays were run in triplicate for both Mn(II) and Mn total, and peak height for all assays was determined using a baseline subtraction performed using ECD-Soft peak correction software.</p>
Specified by the Principal Investigator(s)
<p>BCO-DMO Processing Notes:<br />
-&nbsp;added conventional header with dataset name, PI name, version date<br />
- modified parameter names to conform with BCO-DMO naming conventions<br />
- added ISO Date fromate generated from date and time values<br />
- concatenated the two sheets "CTD data" and "Full Data for discrete depths".<br />
- added a column to identify the sheet the data came from</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
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info@bco-dmo.org
http://www.bco-dmo.org
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For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
NOx analyzer
NOx analyzer
PI Supplied Instrument Name: NOx analyzer PI Supplied Instrument Description:Concentrations of nitrate + nitrite were measured by chemiluminescence after reduction in a hot acidic vanadyl sulfate solution on a NOx analyzer (Braman and Hendrix, 1989) Instrument Name: Chemiluminescence NOx Analyzer Instrument Short Name: Instrument Description: The chemiluminescence method for gas analysis of oxides of nitrogen relies on the measurement of light produced by the gas-phase titration of nitric oxide and ozone. A chemiluminescence analyzer can measure the concentration of NO/NO2/NOX.
One example is the Teledyne Model T200: https://www.teledyne-api.com/products/nitrogen-compound-instruments/t200
CTD Seabird
CTD Seabird
PI Supplied Instrument Name: CTD Seabird PI Supplied Instrument Description:Samples were collected using a 12-bottle trace metal clean CTD (Conductivity, Temperature and Depth) rosette Instrument Name: CTD Sea-Bird Instrument Short Name:CTD Sea-Bird Instrument Description: A Conductivity, Temperature, Depth (CTD) sensor package from SeaBird Electronics. This instrument designation is used when specific make and model are not known or when a more specific term is not available in the BCO-DMO vocabulary. Refer to the dataset-specific metadata for more information about the specific CTD used. More information from: http://www.seabird.com/ Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/130/
Guava EasyCyte HT flow cytometer (Millipore)
Guava EasyCyte HT flow cytometer (Millipore)
PI Supplied Instrument Name: Guava EasyCyte HT flow cytometer (Millipore) PI Supplied Instrument Description:Bacteria and group-specific phytoplankton counts were conducted on a Guava EasyCyte HT flow cytometer (Millipore). Instrument Name: Flow Cytometer Instrument Short Name:Flow Cytometer Instrument Description: Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells.
(from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm) Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB37/
10AU fluorometer (Turner)
10AU fluorometer (Turner)
PI Supplied Instrument Name: 10AU fluorometer (Turner) PI Supplied Instrument Description:Briefly, samples were extracted in 90% acetone in the dark (4C, 9 hr) and measured using an 10AU fluorometer (Turner). 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/
Shimadzu TOC-5050A total organic carbon analyzer
Shimadzu TOC-5050A total organic carbon analyzer
PI Supplied Instrument Name: Shimadzu TOC-5050A total organic carbon analyzer PI Supplied Instrument Description:Filtered water samples for total dissolved organic carbon were pipetted into acid-washed combusted glass vials, acidified to pH = 2 with 12 M hydrochloric acid, and stored at 4 °C until analysis on a Shimadzu TOC-5050A total organic carbon analyzer. Instrument Name: Total Organic Carbon Analyzer Instrument Short Name:TOC analyzer Instrument Description: A unit that accurately determines the carbon concentrations of organic compounds typically by detecting and measuring its combustion product (CO2). See description document at: http://bcodata.whoi.edu/LaurentianGreatLakes_Chemistry/bs116.pdf Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB04/
Cruise: EN604
EN604
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel