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| Dataset Title: | [TORCH-II] - Coastal water biogeochemistry collected aboard the R/V Endeavor along the North Atlantic coast from 2017-08-20 to 2017-08-28 (Collaborative Research: Defining the Role of Biologically Produced Reactive Oxygen Species in Dark Mercury Cycling) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_765327) |
| Information: | Summary
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| ISO 19115
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Attributes {
s {
sheet {
String bcodmo_name "unknown";
String description "Name of the sheet from the original data file";
String long_name "Sheet";
String units "unitless";
}
Station {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 1, 6;
String bcodmo_name "sta";
String description "station identifier";
String long_name "Station";
String units "unitless";
}
latitude {
String _CoordinateAxisType "Lat";
Float64 _FillValue NaN;
Float64 actual_range 37.77692, 41.18026;
String axis "Y";
String bcodmo_name "latitude";
Float64 colorBarMaximum 90.0;
Float64 colorBarMinimum -90.0;
String description "station latitude with north positive";
String ioos_category "Location";
String long_name "Latitude";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LATX/";
String standard_name "latitude";
String units "degrees_north";
}
longitude {
String _CoordinateAxisType "Lon";
Float64 _FillValue NaN;
Float64 actual_range -74.56461, -67.92692;
String axis "X";
String bcodmo_name "longitude";
Float64 colorBarMaximum 180.0;
Float64 colorBarMinimum -180.0;
String description "station longitude with east positive";
String ioos_category "Location";
String long_name "Longitude";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LONX/";
String source_name "long";
String standard_name "longitude";
String units "degrees_east";
}
Year {
Int16 _FillValue 32767;
Int16 actual_range 2017, 2017;
String bcodmo_name "year";
String description "year of collection in yyyy format";
String long_name "Year";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/YEARXXXX/";
String units "unitless";
}
Month {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 8, 8;
String bcodmo_name "month";
String description "month of collection in mm format";
String long_name "Month";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/MNTHXXXX/";
String units "unitless";
}
Day {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 20, 28;
String bcodmo_name "day";
String description "day of collection in dd format";
String long_name "Day";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/DAYXXXXX/";
String units "unitless";
}
time2 {
String bcodmo_name "time";
String description "time of collection in HH:MM format";
String long_name "Time";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/AHMSAA01/";
String units "unitless";
}
time {
String _CoordinateAxisType "Time";
Float64 actual_range 1.503259598e+9, 1.5039448e+9;
String axis "T";
String bcodmo_name "ISO_DateTime_UTC";
String description "date and time following ISO format";
String ioos_category "Time";
String long_name "ISO Datetime UTC";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/DTUT8601/";
String source_name "ISO_datetime_UTC";
String standard_name "time";
String time_origin "01-JAN-1970 00:00:00";
String time_precision "1970-01-01T00:00:00Z";
String units "seconds since 1970-01-01T00:00:00Z";
}
depth {
String _CoordinateAxisType "Height";
String _CoordinateZisPositive "down";
Float64 _FillValue NaN;
Float64 actual_range 2.016, 2031.208;
String axis "Z";
String bcodmo_name "depth";
Float64 colorBarMaximum 8000.0;
Float64 colorBarMinimum -8000.0;
String colorBarPalette "TopographyDepth";
String description "water depth";
String ioos_category "Location";
String long_name "Depth";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/DEPH/";
String positive "down";
String standard_name "depth";
String units "m";
}
Temp {
Float32 _FillValue NaN;
Float32 actual_range 3.4031, 25.7564;
String bcodmo_name "temperature";
String description "Water temperature from CTD";
String long_name "Temperature";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/TEMPP901/";
String units "degrees Celsius (C)";
}
Florescence {
Float32 _FillValue NaN;
Float32 actual_range 0.0462, 3.4339;
String bcodmo_name "fluorescence";
String description "water flourescence from CTD";
String long_name "Florescence";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/CPHLPM01/";
String units "miligrams per meter cubed (mg/m3)";
}
Chlorophyll {
Float64 _FillValue NaN;
Float64 actual_range 0.0, 3.175071375;
String bcodmo_name "chlorophyll a";
Float64 colorBarMaximum 30.0;
Float64 colorBarMinimum 0.03;
String colorBarScale "Log";
String description "Chlorophyll a concentration";
String long_name "Concentration Of Chlorophyll In Sea Water";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/CPHLHPP1/";
String units "micrograms per liter (ug/L)";
}
Chloro_sd {
Float64 _FillValue NaN;
Float64 actual_range 3.8459253727671276e-16, 0.06770068202943032;
String bcodmo_name "chlorophyll a";
Float64 colorBarMaximum 50.0;
Float64 colorBarMinimum 0.0;
String description "Chlorophyll a concentration standard deviation";
String long_name "Chloro Sd";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/CPHLHPP1/";
String units "micrograms per liter (ug/L)";
}
PAR {
Float32 _FillValue NaN;
Float32 actual_range -1.12e-4, 2012.6;
String bcodmo_name "PAR";
Float64 colorBarMaximum 70.0;
Float64 colorBarMinimum 0.0;
String description "Photosynthetically active radiation (CTD)";
String long_name "Downwelling Photosynthetic Photon Radiance In Sea Water";
String units "microeinteins per meter squared second (microE/m2s)";
}
Beam_Transmission {
Float32 _FillValue NaN;
Float32 actual_range 71.9022, 86.8471;
String bcodmo_name "transmission";
String description "Beam transmission (CTD)";
String long_name "Beam Transmission";
String units "percent";
}
Salinity {
Float32 _FillValue NaN;
Float32 actual_range 31.3729, 36.0649;
String bcodmo_name "sal";
Float64 colorBarMaximum 37.0;
Float64 colorBarMinimum 32.0;
String description "Water salinity (CTD)";
String long_name "Sea Water Practical Salinity";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/PSALST01/";
String units "PSU";
}
O2 {
Float32 _FillValue NaN;
Float32 actual_range 2.9535, 6.5497;
String bcodmo_name "dissolved Oxygen";
String description "Water oxygen concentration";
String long_name "O2";
String units "mililiters per liter (mL/L)";
}
NO2 {
Float64 _FillValue NaN;
Float64 actual_range 0.0, 0.5662127;
String bcodmo_name "NO2";
Float64 colorBarMaximum 1.0;
Float64 colorBarMinimum 0.0;
String description "Water nitrite concentration";
String long_name "Mole Concentration Of Nitrite In Sea Water";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/NTRIAAZX/";
String units "micromole (uM)";
}
NH4 {
Float64 _FillValue NaN;
Float64 actual_range 0.0, 2.6446;
String bcodmo_name "Ammonium";
Float64 colorBarMaximum 5.0;
Float64 colorBarMinimum 0.0;
String description "Water ammonium concentration";
String long_name "Mole Concentration Of Ammonium In Sea Water";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/AMONAAZX/";
String units "micromole (uM)";
}
NO3 {
Float64 _FillValue NaN;
Float64 actual_range 0.0, 6.746595499;
String bcodmo_name "NO3";
Float64 colorBarMaximum 50.0;
Float64 colorBarMinimum 0.0;
String description "Water nitrate concentration";
String long_name "Mole Concentration Of Nitrate In Sea Water";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/NTRAIGGS/";
String units "micromole (uM)";
}
Nanoeuks {
String bcodmo_name "abundance";
String description "Nanoeukaryote abundance";
String long_name "Nanoeuks";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P03/current/B070/";
String units "cells per mililiter (cells/mL)";
}
Nanoeuks_sd {
String bcodmo_name "abundance";
String description "Nanoeukaryote abundance standard deviation";
String long_name "Nanoeuks Sd";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P03/current/B070/";
String units "cells per mililiter (cells/mL)";
}
Picoeuks {
String bcodmo_name "abundance";
String description "Picoeukayrote abundance";
String long_name "Picoeuks";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P03/current/B070/";
String units "cells per mililiter (cells/mL)";
}
Picoeuks_sd {
String bcodmo_name "abundance";
String description "Picoeukayrote abundance standard deviation";
String long_name "Picoeuks Sd";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P03/current/B070/";
String units "cells per mililiter (cells/mL)";
}
Synechococcus {
Float64 _FillValue NaN;
Float64 actual_range 216.89821638477133, 359209.4188332472;
String bcodmo_name "abundance";
String description "Synechococcus abundance";
String long_name "Synechococcus";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P03/current/B070/";
String units "cells per mililiter (cells/mL)";
}
Synechococcus_sd {
String bcodmo_name "abundance";
String description "Synechococcus abundance standard deviation";
String long_name "Synechococcus Sd";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P03/current/B070/";
String units "cells per mililiter (cells/mL)";
}
Bacteria {
Float64 _FillValue NaN;
Float64 actual_range 41416.94360106493, 4188788.3068036768;
String bcodmo_name "abundance";
String description "Bacteria concentration";
String long_name "Bacteria";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P03/current/B070/";
String units "cells per mililiter (cells/mL)";
}
Bacteria_sd {
Float64 _FillValue NaN;
Float64 actual_range 11174.976795122218, 141799.111136533;
String bcodmo_name "abundance";
Float64 colorBarMaximum 50.0;
Float64 colorBarMinimum 0.0;
String description "Bacteria concentration standard deviation";
String long_name "Bacteria Sd";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P03/current/B070/";
String units "cells per mililiter (cells/mL)";
}
DOC {
Float64 _FillValue NaN;
Float64 actual_range 0.5609000000000001, 1.4446666666666665;
String bcodmo_name "DOC";
String description "Dissolved organic carbon";
String long_name "DOC";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/CORGZZZX/";
String units "miligrams per liter (mg/L)";
}
DOC_sd {
Float64 _FillValue NaN;
Float64 actual_range 0.018193405398660236, 0.17077330978034413;
String bcodmo_name "DOC";
Float64 colorBarMaximum 50.0;
Float64 colorBarMinimum 0.0;
String description "Dissolved organic carbon standard deviation";
String long_name "DOC Sd";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/CORGZZZX/";
String units "miligrams per liter (mg/L)";
}
Tot_O2 {
Float64 _FillValue NaN;
Float64 actual_range 10.60227148330597, 2362.1644493177378;
String bcodmo_name "unknown";
String description "Total superoxide";
String long_name "Tot O2";
String units "picomole (pM)";
}
Tot_O2_sd {
Float64 _FillValue NaN;
Float64 actual_range 0.0, 415.79304171248594;
String bcodmo_name "unknown";
Float64 colorBarMaximum 50.0;
Float64 colorBarMinimum 0.0;
String description "Total superoxide standard deviation";
String long_name "Tot O2 Sd";
String units "picomole (pM)";
}
Part_O2 {
Float64 _FillValue NaN;
Float64 actual_range 0.8597278761411509, 2462.811999999999;
String bcodmo_name "unknown";
String description "Particle associated superoxide";
String long_name "Part O2";
String units "picomole (pM)";
}
Part_O2_sd {
Float64 _FillValue NaN;
Float64 actual_range 0.0, 415.7930417124871;
String bcodmo_name "unknown";
Float64 colorBarMaximum 50.0;
Float64 colorBarMinimum 0.0;
String description "Particle associated superoxide standard deviation";
String long_name "Part O2 Sd";
String units "picomole (pM)";
}
Net_H2O2 {
Float64 _FillValue NaN;
Float64 actual_range 4.379275135171688, 257.0328945421757;
String bcodmo_name "Hydrogen Peroxide";
String description "Net hydrogen peroxide";
String long_name "Net H2 O2";
String units "nanomole (nM)";
}
Net_H2O2_sd {
Float64 _FillValue NaN;
Float64 actual_range 1.625384364522924, 204.67434195024987;
String bcodmo_name "Hydrogen Peroxide";
Float64 colorBarMaximum 50.0;
Float64 colorBarMinimum 0.0;
String description "Net hydrogen peroxide standard deviation";
String long_name "Net H2 O2 Sd";
String units "nanomole (nM)";
}
Gross_H2O2 {
Float64 _FillValue NaN;
Float64 actual_range 9.384161003939033, 236.07968842897944;
String bcodmo_name "Hydrogen Peroxide";
String description "Gross hydrogen peroxide";
String long_name "Gross H2 O2";
String units "nanomole (nM)";
}
Gross_H2O2_sd {
Float64 _FillValue NaN;
Float64 actual_range 0.002632328618744691, 88.36608183688755;
String bcodmo_name "Hydrogen Peroxide";
Float64 colorBarMaximum 50.0;
Float64 colorBarMinimum 0.0;
String description "Gross hydrogen peroxide standard deviation";
String long_name "Gross H2 O2 Sd";
String units "nanomole (nM)";
}
Total_dHg {
Float64 _FillValue NaN;
Float64 actual_range 0.41351546121593363, 2.467451519129822;
String bcodmo_name "trace_metal_conc";
String description "Total dissolved Hg";
String long_name "Total D Hg";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P03/current/C035/";
String units "picomole (pM)";
}
Total_dHg_sd {
Float64 _FillValue NaN;
Float64 actual_range 0.001644542107712444, 1.188640589545043;
String bcodmo_name "trace_metal_conc";
Float64 colorBarMaximum 50.0;
Float64 colorBarMinimum 0.0;
String description "Total dissolved Hg standard deviation";
String long_name "Total D Hg Sd";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P03/current/C035/";
String units "picomole (pM)";
}
Hg_0 {
Float64 _FillValue NaN;
Float64 actual_range 0.05494494055154578, 0.30003286883856095;
String bcodmo_name "trace_metal_conc";
String description "Elemental Hg";
String long_name "HG 0";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P03/current/C035/";
String units "picomole (pM)";
}
Hg_0_sd {
Float64 _FillValue NaN;
Float64 actual_range 2.9741736172874837e-4, 0.07440280528199449;
String bcodmo_name "trace_metal_conc";
Float64 colorBarMaximum 50.0;
Float64 colorBarMinimum 0.0;
String description "Elemental Hg standard deviation";
String long_name "HG 0 SD";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P03/current/C035/";
String units "picomole (pM)";
}
dMn_II {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 40.9;
String bcodmo_name "Mn";
String description "Dissolved Mn(II)";
String long_name "D Mn II";
String units "nanomole (nM)";
}
dMn_II_sd {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 7.55;
String bcodmo_name "Mn";
Float64 colorBarMaximum 50.0;
Float64 colorBarMinimum 0.0;
String description "Dissolved Mn(II) standard deviation";
String long_name "D Mn II Sd";
String units "nanomole (nM)";
}
dMn_T {
Float32 _FillValue NaN;
Float32 actual_range 6.19, 152.7;
String bcodmo_name "Mn";
String description "Total dissolved Mn";
String long_name "D MN T";
String units "nanomole (nM)";
}
dMn_T_sd {
Float32 _FillValue NaN;
Float32 actual_range 0.08, 18.73;
String bcodmo_name "Mn";
Float64 colorBarMaximum 50.0;
Float64 colorBarMinimum 0.0;
String description "Total dissolved Mn standard deviation";
String long_name "D MN T SD";
String units "nanomole (nM)";
}
dMn_III_L {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 147.49;
String bcodmo_name "Mn";
String description "Dissolved Mn(III)-L";
String long_name "D Mn III L";
String units "nanomole (nM)";
}
dMn_III_L_sd {
Float32 _FillValue NaN;
Float32 actual_range 0.16, 13.31;
String bcodmo_name "Mn";
Float64 colorBarMaximum 50.0;
Float64 colorBarMinimum 0.0;
String description "Dissolved Mn(III)-L standard deviation";
String long_name "D Mn III L Sd";
String units "nanomole (nM)";
}
MnOx {
Float32 _FillValue NaN;
Float32 actual_range 0.02, 3.85;
String bcodmo_name "Mn";
String description "Mn oxides";
String long_name "Mn Ox";
String units "nanomole";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson,.odvTxt";
String acquisition_description
"Chlorophyll
In the dark, 250 mL of seawater was filtered onto 25 mm GF/F filters.\\u00a0
Samples were stored in the dark at -20C until analyzed according to protocols
adapted from Strickland and Parsons (1972).\\u00a0 Briefly, samples were
extracted in 90% acetone in the dark (4C, 9 hr) and measured using an 10AU
fluorometer (Turner).\\u00a0 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.
Nitrogen Species
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\\u2013Ilosvay 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).
Microbial Abundance
Seawater samples were preserved for flow cytometry with 0.5% glutaraldehyde
(final concentration), flash frozen in liquid nitrogen and stored at
-80\\u00b0C 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 \\u00b5L s-1) for 3 min.\\u00a0 To enumerate bacteria,
samples were diluted (1:100) with filtered seawater (0.01 \\u00b5m).\\u00a0
Samples and filtered seawater blanks were stained with SYBR Green I
(Invitrogen) according to the manufacturer\\u2019s instructions and incubated
in a 96-well plate in the dark at room temperature for 1 hr.\\u00a0 Bacterial
cells were counted based on diagnostic forward scatter vs. green fluorescence
signals.\\u00a0 Major phytoplankton groups were distinguished based on plots of
forward scatter vs. orange (phycoerythrin-containing Synechococcus sp.), and
forward scatter vs. red (eukaryotes).\\u00a0 Size classes of eukaryotic
phytoplankton were further distinguished based on forward scatter (pico-,
nano- and large eukaryotes).\\u00a0
Dissolved organic carbon
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 \\u00b0C until analysis on a Shimadzu TOC-5050A total
organic carbon analyzer. The coefficient of variability between replicate
injections was less than 1%.
Reactive oxygen species
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 \\u00b5M 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).\\u00a0
Designations are:\\u00a0
Total superoxide = [(UFSW) - (UFSW-SOD)] - [(AFSW)- (AFSW-SOD)]
Particle superoxide = [(UFSW) - (UFSW-SOD)] - [(FFSW)- (FFSW-SOD)]
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 \\u00b5mol 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\\u00ae 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-\\u00b5m 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.\\u00a0
Manganese
Seawater samples (1 L) were filtered through 0.2 \\u00b5m 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.
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 \\u00b5M 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
\\u00b5L 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 \\u00b5m 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.\\u00a0 If
sample absorbance was too high, samples were diluted 10-20 times in Milli-Q
water.
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 \\u03b1, \\u03b2, \\u03b3,
\\u03b4-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\\u00b0C 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
\\u00b5M 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.";
String awards_0_award_nid "756929";
String awards_0_award_number "OCE-1355720";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1355720";
String awards_0_funder_name "NSF Division of Ocean Sciences";
String awards_0_funding_acronym "NSF OCE";
String awards_0_funding_source_nid "355";
String awards_0_program_manager "Henrietta N Edmonds";
String awards_0_program_manager_nid "51517";
String cdm_data_type "Other";
String comment
"Coastal water biogeochemistry along the North Atlantic coast
PI: Colleen Hansel
Version: 2019-04-24";
String Conventions "COARDS, CF-1.6, ACDD-1.3";
String creator_email "info@bco-dmo.org";
String creator_name "BCO-DMO";
String creator_type "institution";
String creator_url "https://www.bco-dmo.org/";
String data_source "extract_data_as_tsv version 2.3 19 Dec 2019";
String date_created "2019-04-18T19:47:26Z";
String date_modified "2019-09-13T13:00:25Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.765327.1";
Float64 Easternmost_Easting -67.92692;
Float64 geospatial_lat_max 41.18026;
Float64 geospatial_lat_min 37.77692;
String geospatial_lat_units "degrees_north";
Float64 geospatial_lon_max -67.92692;
Float64 geospatial_lon_min -74.56461;
String geospatial_lon_units "degrees_east";
Float64 geospatial_vertical_max 2031.208;
Float64 geospatial_vertical_min 2.016;
String geospatial_vertical_positive "down";
String geospatial_vertical_units "m";
String history
"2024-11-23T08:01:56Z (local files)
2024-11-23T08:01:56Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_765327.html";
String infoUrl "https://www.bco-dmo.org/dataset/765327";
String institution "BCO-DMO";
String instruments_0_acronym "CTD Sea-Bird";
String instruments_0_dataset_instrument_description "Samples were collected using a 12-bottle trace metal clean CTD (Conductivity, Temperature and Depth) rosette";
String instruments_0_dataset_instrument_nid "765588";
String instruments_0_description "Conductivity, Temperature, Depth (CTD) sensor package from SeaBird Electronics, no specific unit identified. This instrument designation is used when specific make and model are not known. See also other SeaBird instruments listed under CTD. More information from Sea-Bird Electronics.";
String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/130/";
String instruments_0_instrument_name "CTD Sea-Bird";
String instruments_0_instrument_nid "447";
String instruments_0_supplied_name "CTD Seabird";
String instruments_1_acronym "Fluorometer";
String instruments_1_dataset_instrument_description "Briefly, samples were extracted in 90% acetone in the dark (4C, 9 hr) and measured using an 10AU fluorometer (Turner).";
String instruments_1_dataset_instrument_nid "765589";
String instruments_1_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.";
String instruments_1_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/113/";
String instruments_1_instrument_name "Fluorometer";
String instruments_1_instrument_nid "484";
String instruments_1_supplied_name "10AU fluorometer (Turner)";
String instruments_2_acronym "TOC analyzer";
String instruments_2_dataset_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.";
String instruments_2_dataset_instrument_nid "765592";
String instruments_2_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";
String instruments_2_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB04/";
String instruments_2_instrument_name "Total Organic Carbon Analyzer";
String instruments_2_instrument_nid "652";
String instruments_2_supplied_name "Shimadzu TOC-5050A total organic carbon analyzer";
String instruments_3_acronym "Flow Cytometer";
String instruments_3_dataset_instrument_description "Bacteria and group-specific phytoplankton counts were conducted on a Guava EasyCyte HT flow cytometer (Millipore).";
String instruments_3_dataset_instrument_nid "765591";
String instruments_3_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)";
String instruments_3_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB37/";
String instruments_3_instrument_name "Flow Cytometer";
String instruments_3_instrument_nid "660";
String instruments_3_supplied_name "Guava EasyCyte HT flow cytometer (Millipore)";
String instruments_4_dataset_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)";
String instruments_4_dataset_instrument_nid "765590";
String instruments_4_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: http://www.teledyne-api.com/products/T200.asp";
String instruments_4_instrument_name "Chemiluminescence NOx Analyzer";
String instruments_4_instrument_nid "542895";
String instruments_4_supplied_name "NOx analyzer";
String keywords "active, ammonia, ammonium, available, bacteria, Bacteria_sd, bco, bco-dmo, beam, Beam_Transmission, biological, chemical, chemistry, chloro, Chloro_sd, chlorophyll, commerce, concentration, concentration_of_chlorophyll_in_sea_water, data, dataset, datetime, day, density, department, depth, dMn_II, dMn_II_sd, dMn_III_L, dMn_III_L_sd, dMn_T, dMn_T_sd, dmo, doc, DOC_sd, downwelling, downwelling_photosynthetic_photon_radiance_in_sea_water, earth, Earth Science > Oceans > Ocean Chemistry > Ammonia, Earth Science > Oceans > Ocean Chemistry > Chlorophyll, Earth Science > Oceans > Ocean Chemistry > Nitrate, Earth Science > Oceans > Ocean Optics > Photosynthetically Active Radiation, Earth Science > Oceans > Ocean Optics > Radiance, Earth Science > Oceans > Salinity/Density > Salinity, erddap, florescence, gross, Gross_H2O2, Gross_H2O2_sd, Hg_0, Hg_0_sd, iii, iso, latitude, longitude, management, MnOx, mole, mole_concentration_of_ammonium_in_sea_water, mole_concentration_of_nitrate_in_sea_water, mole_concentration_of_nitrite_in_sea_water, month, n02, nanoeuks, Nanoeuks_sd, net, Net_H2O2, Net_H2O2_sd, nh4, nitrate, nitrite, NO2, no3, O2, ocean, oceanography, oceans, office, optics, oxygen, PAR, part, Part_O2, Part_O2_sd, photon, photosynthetic, photosynthetically, picoeuks, Picoeuks_sd, practical, preliminary, radiance, radiation, salinity, science, sea, sea_water_practical_salinity, seawater, sheet, station, synechococcus, Synechococcus_sd, Temp, temperature, time, time2, tot, Tot_O2, Tot_O2_sd, total, Total_dHg, Total_dHg_sd, transmission, water, year";
String keywords_vocabulary "GCMD Science Keywords";
String license "https://www.bco-dmo.org/dataset/765327/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/765327";
Float64 Northernmost_Northing 41.18026;
String param_mapping "{'765327': {'lat': 'flag - latitude', 'Depth': 'flag - depth', 'long': 'flag - longitude', 'ISO_datetime_UTC': 'flag - time'}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/765327/parameters";
String people_0_affiliation "Woods Hole Oceanographic Institution";
String people_0_affiliation_acronym "WHOI";
String people_0_person_name "Colleen Hansel";
String people_0_person_nid "756932";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "University of California-Santa Cruz";
String people_1_affiliation_acronym "UC Santa Cruz";
String people_1_person_name "Carl Lamborg";
String people_1_person_nid "50968";
String people_1_role "Co-Principal Investigator";
String people_1_role_type "originator";
String people_2_affiliation "Woods Hole Oceanographic Institution";
String people_2_affiliation_acronym "WHOI BCO-DMO";
String people_2_person_name "Mathew Biddle";
String people_2_person_nid "708682";
String people_2_role "BCO-DMO Data Manager";
String people_2_role_type "related";
String project "ROS in Hg Cycling";
String projects_0_acronym "ROS in Hg Cycling";
String projects_0_description
"NSF Abstract:
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.
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.";
String projects_0_end_date "2019-07";
String projects_0_geolocation "Coastal North Atlantic";
String projects_0_name "Collaborative Research: Defining the Role of Biologically Produced Reactive Oxygen Species in Dark Mercury Cycling";
String projects_0_project_nid "756930";
String projects_0_start_date "2014-02";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
Float64 Southernmost_Northing 37.77692;
String standard_name_vocabulary "CF Standard Name Table v55";
String subsetVariables "Year,Month";
String summary "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.";
String time_coverage_end "2017-08-28T18:26:40Z";
String time_coverage_start "2017-08-20T20:06:38Z";
String title "[TORCH-II] - Coastal water biogeochemistry collected aboard the R/V Endeavor along the North Atlantic coast from 2017-08-20 to 2017-08-28 (Collaborative Research: Defining the Role of Biologically Produced Reactive Oxygen Species in Dark Mercury Cycling)";
String version "1";
Float64 Westernmost_Easting -74.56461;
String xml_source "osprey2erddap.update_xml() v1.3";
}
}
Data Access Protocol (DAP) and its
selection constraints.
The URL specifies what you want: the dataset, a description of the graph or the subset of the data, and the file type for the response.
Tabledap request URLs must be in the form
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/datasetID.fileType{?query}
For example,
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/pmelTaoDySst.htmlTable?longitude,latitude,time,station,wmo_platform_code,T_25&time>=2015-05-23T12:00:00Z&time<=2015-05-31T12:00:00Z
Thus, the query is often a comma-separated list of desired variable names,
followed by a collection of
constraints (e.g., variable<value),
each preceded by '&' (which is interpreted as "AND").
For details, see the tabledap Documentation.