Accessing BCO-DMO data
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BCO-DMO ERDDAP
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| Dataset Title: | Redox data from RV/Atlantic Explorer AE1812 in the northwest Atlantic, May 2018
|
| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_762772) |
| Information: | Summary
| License
| ISO 19115
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Attributes {
s {
Station {
Byte _FillValue 127;
Byte actual_range 1, 14;
String bcodmo_name "station";
String description "Numeric identifier for the station where the data was collected.";
String long_name "Station";
String units "unitless";
}
CTD_Cast {
Byte _FillValue 127;
Byte actual_range 2, 40;
String bcodmo_name "cast";
String description "Numeric identifier for the CTD cast where the data was collected.";
String long_name "CTD Cast";
String units "unitless";
}
Sample_type {
String bcodmo_name "sample_type";
String description "Sample type: Comm.=Whole community; CommD.=Whole communinty in dark incubation; Tricho.=Trichodesmium colonies; Sed.=Sinking particles";
String long_name "Sample Type";
String units "unitless";
}
depth {
String _CoordinateAxisType "Height";
String _CoordinateZisPositive "down";
Float64 _FillValue NaN;
Float64 actual_range 4.0, 172.0;
String axis "Z";
String bcodmo_name "depth";
Float64 colorBarMaximum 8000.0;
Float64 colorBarMinimum -8000.0;
String colorBarPalette "TopographyDepth";
String description "Depth at which the samples were collected.";
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";
}
P33_PO4_incorp_PIII_rate {
String bcodmo_name "unknown";
String description "33P-phosphate incorporation into P(III) compounds (blank corrected).";
String long_name "P33 PO4 Incorp PIII Rate";
String units "counts per minutes per liter per hour (cpm/(L h))";
}
P33_PO4_uptake {
String bcodmo_name "P33_PO4_uptake";
String description "33P-phosphate uptake (blank corrected)";
String long_name "P33 PO4 Uptake";
String units "counts per minutes per liter per hour (cpm/(L h))";
}
P33_PO4_incorp_PIII_pcent {
Float32 _FillValue NaN;
Float32 actual_range 0.23, 74.6;
String bcodmo_name "unknown";
String description "Percentage of 33P-phosphate incorporation into P(III) compounds";
String long_name "Mass Concentration Of Phosphate In Sea Water";
String units "percentage (%)";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
String acquisition_description
"All data were collected from a modified procedure as described in Van Mooy et
al (2015).
Sampling - Sampling was conducted aboard the R/V Atlantic Explorer during a
cruise in May 2018.\\u00a0 Water samples for whole community analyses were
collected from Niskin bottles deployed on a rosette with a CTD.\\u00a0
Subsamples (1-4 L) for incubations were dispensed from the Niskin bottle into
acid-washed polyethylene bottles and promptly taken to a laboratory van for
incubation setup and processing. At two stations Trichodesmium colonies were
also acquired for uptake and reduction experiments. Briefly, colonies were
collected near the surface with a handheld 130 \\u00b5m net. 6 to 20 colonies
were washed twice with freshly filtered (0.2 \\u00b5m pore size polycarbonate
membrane) surface seawater before being transferred into 50 mL of filtered
seawater for incubation as described below. At three stations sinking
particles were collected using 1.25 m diameter free-floating net traps for
24-hour deployments (Peterson et al. 2005). Once recovered, the particle
slurry was further split into 12 equal fractions using an electric splitter
(Lamborg et al. 2008). One split was used for total phosphate uptake and
reduction measurements as described below where particle slurries were
incubated in the dark in 50 to 125 mL of seawater. [C.H. Lamborg, K.O.
Bruesseler, J. Valdes, C.H. Bertrand, R. Bidigare, S. Manganini, etc, The flux
of bio- and lithogenic material associated with sinking particles in the
mesopelagic \\u201ctwilight zone\\u201d of the northwest and North Central
Pacific Ocean. Deep-Sea Res II 55, 1540 (2008). M.L. Peterson, S.G. Wakeham,
C. Lee, M.A. Askea, J.C. Miquel, Novel techniques for collection of sinking
particles in the ocean and determining their settling rates. Limnol Oceanogr
Methods 3, 520 (2005).]
Phosphate uptake rates \\u2013 50 mL samples of seawater were added to acid-
washed polycarbonate incubation bottles. Each incubation bottle was spiked
with approximately 2 \\u00b5Ci of 33P-phosphoric acid.\\u00a0 The final
concentration of 33P-phosphate in the incubations was less than 10 pmol L-1,
which was likely two orders of magnitude smaller than ambient phosphate
concentrations. The bottles were capped and mixed by gently inverting.\\u00a0
To account for any abiotic adsorption of the radioactive tracer, additional 50
mL subsamples were spiked with 10% paraformaldehyde prior to the addition of
the 33P-phosphoric acid. These \\u201ckilled controls\\u201d were used for blank
subtractions in uptake and reduction rate calculations. All bottles were
placed in a flow-through on-deck incubator that was maintained at surface
seawater temperatures by continually flushing it with the surface seawater
from the ship\\u2019s pumping system.\\u00a0 Temperature in the incubators was
occasionally monitored with a waterproof temperature logger (Onset).\\u00a0 The
incubators used blue transparent film to achieve a light intensity to mimic
30% PAR. About half of the surface water samples were placed in a dark
incubator to determine the affect light had on the incubations. For depth
profiles, the incubators used a combination of neutral density screening and
blue transparent film to achieve a light intensity to mimic PAR throughout the
water column while samples with less than 1% PAR were placed in a dark
incubator. After an appropriate amount of time, the incubations were
terminated and 5 mL of sample was vacuum filtered (approximately 200 mbar)
onto 25 mm diameter 0.2 \\u00b5m pore size polycarbonate membranes (Millipore).
The membranes were quickly rinsed three times with freshly filtered (0.2
\\u00b5m pore size polycarbonate membrane) surface seawater.\\u00a0 The
membranes were then immediately placed in a liquid scintillation vial
containing 10 mL of UltimaGold liquid (Perkin Elmer) scintillation cocktail,
which was then shaken vigorously.\\u00a0 The 33P-radioacitivity in the vials
was determined using a liquid scintillation counter (Perkin Elmer).
Phosphate reduction to intracellular P(III) compounds \\u2013 The remaining 45
mL of sample was vacuum filtered as described above. Next, the membranes were
immersed in 1.0 mL of ultra-high purity (UHP) deionized water (18 M\\u03a9*cm)
in a cryovial (Fisher).\\u00a0 The vials were immediately capped and flash
frozen for storage and transport back to the on-shore laboratory. For further
analysis, the samples were subject to three freeze/thaw cycles where the
cryovial was immersed in liquid nitrogen for approximately 10 min, before they
were immersed in boiling-hot water for 10 min, and then vigorously
shaken.\\u00a0 Next, 100 \\u00b5L aliquots of the samples were injected onto an
IC system (Dionex) which pumped an eluent gradient of 23 mmol L-1 to 90 mmol
L-1 sodium hydroxide through an IonPac AS18 (Dionex) column at a rate of 1.0
mL min-1.\\u00a0 An ion suppressor using UHP water as a regenerant removed
sodium hydroxide from the eluent. Three fractions were collected in 60 second
intervals at retention times where pure standards of (1) hypophosphorus acid
(2) methyl-phosphonate, 2-hydroxethyl-phosphonate, and (3) phosphorus acid
elute and the 33P-radioactivity determined as described above. The 33P-
radioactivity of the three fractions was summed, corrected for dilution, and
then divided by the 33P-radioactivity from the parallel 33P-phosphate uptake
subsamples to determine the fraction (%) of 33P uptake that was incorporated
into P (III) compounds.\\u00a0 All uptake samples were processed at sea in May
2018 and all reduction samples were processed onshore in July 2018.
Radioactive decay was accounted for in the final counts per minute (cpm)
values.";
String awards_0_award_nid "704767";
String awards_0_award_number "OCE-1558490";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1558490";
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 "David L. Garrison";
String awards_0_program_manager_nid "50534";
String awards_1_award_nid "704773";
String awards_1_award_number "OCE-1558506";
String awards_1_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1558506";
String awards_1_funder_name "NSF Division of Ocean Sciences";
String awards_1_funding_acronym "NSF OCE";
String awards_1_funding_source_nid "355";
String awards_1_program_manager "David L. Garrison";
String awards_1_program_manager_nid "50534";
String awards_2_award_nid "746564";
String awards_2_award_number "OCE-1536346";
String awards_2_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1536346";
String awards_2_funder_name "NSF Division of Ocean Sciences";
String awards_2_funding_acronym "NSF OCE";
String awards_2_funding_source_nid "355";
String awards_2_program_manager "Henrietta N Edmonds";
String awards_2_program_manager_nid "51517";
String cdm_data_type "Other";
String comment
"Redox data
from RV/Atlantic Explorer AE1812, May 2018
PI: T. Rynearson (URI)
version date: 2019-03-20
NOTE: Sample_type: Comm.=Whole community, CommD.=Whole communinty in dark incubation, Tricho.=Trichodesmium colonies, Sed.=Sinking particles
33P-phosphate rates and uptake values are blank corrected";
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 "2019-03-20T19:03:37Z";
String date_modified "2019-03-21T21:08:53Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.762772.1";
Float64 geospatial_vertical_max 172.0;
Float64 geospatial_vertical_min 4.0;
String geospatial_vertical_positive "down";
String geospatial_vertical_units "m";
String history
"2024-04-24T05:24:25Z (local files)
2024-04-24T05:24:25Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_762772.html";
String infoUrl "https://www.bco-dmo.org/dataset/762772";
String institution "BCO-DMO";
String instruments_0_acronym "Niskin bottle";
String instruments_0_dataset_instrument_nid "762785";
String instruments_0_description "A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24 or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc.";
String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/";
String instruments_0_instrument_name "Niskin bottle";
String instruments_0_instrument_nid "413";
String instruments_1_acronym "CTD";
String instruments_1_dataset_instrument_nid "762784";
String instruments_1_description "The Conductivity, Temperature, Depth (CTD) unit is an integrated instrument package designed to measure the conductivity, temperature, and pressure (depth) of the water column. The instrument is lowered via cable through the water column and permits scientists observe the physical properties in real time via a conducting cable connecting the CTD to a deck unit and computer on the ship. The CTD is often configured with additional optional sensors including fluorometers, transmissometers and/or radiometers. It is often combined with a Rosette of water sampling bottles (e.g. Niskin, GO-FLO) for collecting discrete water samples during the cast. This instrument designation is used when specific make and model are not known.";
String instruments_1_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/130/";
String instruments_1_instrument_name "CTD profiler";
String instruments_1_instrument_nid "417";
String instruments_2_acronym "Sed Trap - Part Int";
String instruments_2_dataset_instrument_description "\"Based on the design of a closing plankton net capable of collecting large amounts (~1 g) of very fresh sinking particulate material in short time periods (24-36 h) to facilitate microbial decomposition experiment.\" (Peterson et al, 2005)";
String instruments_2_dataset_instrument_nid "762790";
String instruments_2_description "A Particle Interceptor Trap is a prototype sediment trap designed in the mid 1990s to segregate 'swimmers' from sinking particulate material sampled from the water column. The prototype trap used 'segregation plates' to deflect and segregate 'swimmers' while a series of funnels collected sinking particles in a chamber (see Dennis A. Hansell and Jan A. Newton. September 1994. Design and Evaluation of a \"Swimmer\"-Segregating Particle Interceptor Trap, Limnology and Oceanography, Vol. 39, No. 6, pp. 1487-1495).";
String instruments_2_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/33/";
String instruments_2_instrument_name "Sediment Trap - Particle Interceptor";
String instruments_2_instrument_nid "550";
String instruments_2_supplied_name "free-floating NetTrap";
String instruments_3_acronym "LSC";
String instruments_3_dataset_instrument_nid "762793";
String instruments_3_description "Liquid scintillation counting is an analytical technique which is defined by the incorporation of the radiolabeled analyte into uniform distribution with a liquid chemical medium capable of converting the kinetic energy of nuclear emissions into light energy. Although the liquid scintillation counter is a sophisticated laboratory counting system used the quantify the activity of particulate emitting (ß and a) radioactive samples, it can also detect the auger electrons emitted from 51Cr and 125I samples.";
String instruments_3_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB21/";
String instruments_3_instrument_name "Liquid Scintillation Counter";
String instruments_3_instrument_nid "624";
String instruments_3_supplied_name "liquid scintillation counter (Perkin Elmer)";
String instruments_4_acronym "Ion Chromatograph";
String instruments_4_dataset_instrument_nid "762794";
String instruments_4_description "Ion chromatography is a form of liquid chromatography that measures concentrations of ionic species by separating them based on their interaction with a resin. Ionic species separate differently depending on species type and size. Ion chromatographs are able to measure concentrations of major anions, such as fluoride, chloride, nitrate, nitrite, and sulfate, as well as major cations such as lithium, sodium, ammonium, potassium, calcium, and magnesium in the parts-per-billion (ppb) range. (from http://serc.carleton.edu/microbelife/research_methods/biogeochemical/ic.html)";
String instruments_4_instrument_name "Ion Chromatograph";
String instruments_4_instrument_nid "662";
String instruments_4_supplied_name "IC system (Dionex)";
String instruments_5_dataset_instrument_nid "762792";
String instruments_5_description "A device mounted on a ship that holds water samples under conditions of controlled temperature or controlled temperature and illumination.";
String instruments_5_instrument_name "Shipboard Incubator";
String instruments_5_instrument_nid "629001";
String keywords "bco, bco-dmo, biological, cast, chemical, chemistry, concentration, conductivity, ctd, CTD_Cast, data, dataset, depth, dmo, earth, Earth Science > Oceans > Ocean Chemistry > Phosphate, erddap, incorp, management, mass, mass_concentration_of_phosphate_in_sea_water, ocean, oceanography, oceans, office, p33, P33_PO4_incorp_PIII_pcent, P33_PO4_incorp_PIII_rate, P33_PO4_uptake, phosphate, piii, po4, preliminary, rate, sample, Sample_type, science, sea, seawater, sonde, station, temperature, type, uptake, water";
String keywords_vocabulary "GCMD Science Keywords";
String license "https://www.bco-dmo.org/dataset/762772/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/762772";
String param_mapping "{'762772': {'Depth': 'master - depth'}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/762772/parameters";
String people_0_affiliation "Woods Hole Oceanographic Institution";
String people_0_affiliation_acronym "WHOI";
String people_0_person_name "Benjamin A.S. Van Mooy";
String people_0_person_nid "50975";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "University of Rhode Island";
String people_1_affiliation_acronym "URI-GSO";
String people_1_person_name "Tatiana Rynearson";
String people_1_person_nid "511706";
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 "Nancy Copley";
String people_2_person_nid "50396";
String people_2_role "BCO-DMO Data Manager";
String people_2_role_type "related";
String project "North Atlantic Diatoms,Phosphorus Redox Cycling";
String projects_0_acronym "North Atlantic Diatoms";
String projects_0_description
"NSF abstract:
About half of photosynthesis on earth is generated by marine phytoplankton, single celled organisms that drift with tides and currents. Within the phytoplankton, the diatoms conduct nearly half of this photosynthesis, exerting profound control over global carbon cycling. Despite their importance, there are surprisingly fundamental gaps in understanding how diatoms function in their natural environment, in part because methods to assess in situ physiology are lacking. This project focuses on the application of a powerful new approach, called Quantitative Metabolic Fingerprinting (QMF), to address this knowledge gap and examine species-specific physiology in the field. The project will provide transformative insights into how ocean geochemistry controls the distribution of diatoms, the metabolic responses of individual diatom species, and how metabolic potential is partitioned between diatom species, thus providing new insights into the structure and function of marine systems. The overarching goal is to examine how diatom species respond to changes in biogeochemistry across marine provinces, from the coast to the open ocean, by following shifts in diatom physiology using QMF. This research is critical to understand future changes in oceanic phytoplankton in response to climate and environmental change. Furthermore, activities on this project will include supporting a graduate student and postdoctoral fellow and delivering the Artistic Oceanographer Program (AOP) to diverse middle school age children and teachers in the NYC metropolitan area and to middle-school girls in the Girl Scouts of RI, reaching an anticipated 60 children and 30 teachers annually. The programs will foster multidisciplinary hands-on learning and will directly impact STEM education at a critical point in the pipeline by targeting diverse middle-school aged groups in both NY and RI.
In laboratory studies with cultured isolates, there are profound differences among diatom species' responses to nutrient limitation. Thus, it is likely that different species contribute differently to nutrient uptake, carbon flux and burial. However, marine ecosystem models often rely on physiological attributes drawn from just one species and apply those attributes globally (e.g. coastal species used to model open ocean dynamics) or choose a single average value to represent all species across the world's oceans. In part, this is due to a relatively poor understanding of diatom physiological ecology and a limited tool set for assessing in situ diatom physiological ecology. This research project will address this specific challenge by explicitly tracking metabolic pathways, measuring their regulation and determining their taxonomic distribution in a suite of environmentally significant diatoms using a state of the art, species-specific approach. A research expedition is set in the North Atlantic, a system that plays a major role in carbon cycling. Starting with a New England coastal shelf site, samples will be collected from the coast where diatoms thrive, to the open ocean and a site of a long term ocean time series station (the Bermuda Atlantic Time Series) where diatom growth is muted by nutrient limitation. This research takes advantage of new ocean observatories initiative (OOI) and time series information. Through the research expedition and downstream laboratory experiments, the molecular pathways of nutrient metabolism and related gene expression in a suite of environmentally significant diatoms will be identified. Data will be combined to predict major limiting factors and potentially important substrates for diatoms across marine provinces. Importantly, this integrated approach takes advantage of new advances in molecular and bioinformatics tools to examine in situ physiological ecology at the species-specific level, a key knowledge gap in the field.";
String projects_0_end_date "2019-08";
String projects_0_geolocation "North Atlantic";
String projects_0_name "Collaborative Research: Defining the biogeochemical drivers of diatom physiological ecology in the North Atlantic";
String projects_0_project_nid "704768";
String projects_0_start_date "2016-09";
String projects_1_acronym "Phosphorus Redox Cycling";
String projects_1_description
"NSF Award Abstract:
Redox Cycling of Phosphorus in the Western North Atlantic Ocean
Benjamin Van Mooy
ID: 1536346
Understanding controls on the growth of plankton in the upper ocean, which plays an essential role in the sequestration of carbon dioxide, is an important endeavor for chemical oceanography. Phosphorus is an essential element for marine plankton, and has been a research focus of chemical oceanography for nearly a century. Yet, phosphorus redox cycling rates are almost completely unknown throughout the ocean, and the specific molecular identities of the phosphonates, a form of phosphate, in seawater have defied elucidation. This project will explore and refine entirely new pathways for the biological cycling of phosphorus. This project will support teaching and learning by funding the PhD research of a graduate student, and through the continuation of conducting K-12 classroom laboratory modules and hosting 6-8th grade science fair participants in the investigator's lab.
Phosphorus has never been viewed by oceanographers as an element that actively undergoes chemical redox reactions in the water column, and it was believed to occur only in the +5 valence state, in compounds such as phosphate. However, over the last 17 years, numerous lines of geochemical and genomic information have emerged to show that phosphorus in the +3 valence state (P(+3)), particularly dissolved phosphonate compounds, may play a very important role within open ocean planktonic communities. This is particularly true in oligotrophic gyres such as the Sargasso Sea, where growth of phytoplankton can be limited by the scarcity of phosphate. To better understand these new data, the investigators will design and execute a research program that spans at-sea chemical oceanographic experimentation, state-of-the-art chromatography and mass spectrometry, and novel organic synthesis of 33P-labeled P(+3) compounds. Specifically, they will answer questions about rates of production and consumption of low molecular weight P(+3) compounds, the impact of phosphate availability on the production and consumption of P(+3) compounds, and the groups of phytoplankton that utilize low molecular weight P(+3) compounds. Results of this project have the potential to contribute to the transformation of our understanding of the marine phosphorus cycle.";
String projects_1_end_date "2018-09";
String projects_1_geolocation "western north Atlantic";
String projects_1_name "Redox Cycling of Phosphorus in the Western North Atlantic Ocean";
String projects_1_project_nid "746565";
String projects_1_start_date "2015-10";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
String standard_name_vocabulary "CF Standard Name Table v55";
String summary "This dataset includes redox data from RV/Atlantic Explorer AE1812 in the northwest Atlantic, May 2018.";
String title "Redox data from RV/Atlantic Explorer AE1812 in the northwest Atlantic, May 2018";
String version "1";
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.