Accessing BCO-DMO data
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| Dataset Title: | [Sulfate reduction energetics] - Sulfate reduction energetics at Main Endeavor grotto chimney from samples collected on RV Atlantis (AT18-08) during Jason II dives in the Juan de Fuca Ridge from July to August 2011 (Characterizing the distribution and rates of microbial sulfate reduction at Middle Valley hydrothermal vents) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_661659) |
| Information: | Summary
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| FGDC
| ISO 19115
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Attributes {
s {
experiment_num {
String bcodmo_name "exp_id";
String description "PI issued experiment ID number";
String long_name "Experiment Num";
String units "unitless";
}
latitude {
String _CoordinateAxisType "Lat";
Float64 _FillValue NaN;
Float64 actual_range 47.95, 47.95;
String axis "Y";
String bcodmo_name "latitude";
Float64 colorBarMaximum 90.0;
Float64 colorBarMinimum -90.0;
String description "Latitude";
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 -129.1, -129.1;
String axis "X";
String bcodmo_name "longitude";
Float64 colorBarMaximum 180.0;
Float64 colorBarMinimum -180.0;
String description "Longitude";
String ioos_category "Location";
String long_name "Longitude";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LONX/";
String standard_name "longitude";
String units "degrees_east";
}
sulfide {
Float32 _FillValue NaN;
Float32 actual_range 1.0e-9, 0.001;
String bcodmo_name "sulfide";
String description "Independently varied concentration of sulfide";
String long_name "Sulfide";
String units "molar (M)";
}
sulfate {
Float32 _FillValue NaN;
Float32 actual_range 1.0e-5, 14.0;
String bcodmo_name "SO4";
String description "Independently varied concentration of sulfate";
String long_name "Sulfate";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/SPHTMAXX/";
String units "millimoles (mM)";
}
DOC {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 50.0;
String bcodmo_name "DOC";
String description "Independently varied dissolved oxygen concentration";
String long_name "DOC";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/CORGZZZX/";
String units "micromoles (uM)";
}
citrate {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 1.0e-5;
String bcodmo_name "unknown";
String description "Citrate concentration which made up DOC";
String long_name "Citrate";
String units "molar (M)";
}
formate {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 1.0e-5;
String bcodmo_name "unknown";
String description "Formate concentration which made up DOC";
String long_name "Formate";
String units "molar (M)";
}
pyruvate {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 1.0e-5;
String bcodmo_name "unknown";
String description "Pyruvate concentration which made up DOC";
String long_name "Pyruvate";
String units "molar (M)";
}
acetate {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 1.0e-5;
String bcodmo_name "unknown";
String description "Acetate concentration which made up DOC";
String long_name "Acetate";
String units "molar (M)";
}
lactate {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 1.0e-5;
String bcodmo_name "unknown";
String description "Lactate concentration which made up DOC";
String long_name "Lactate";
String units "molar (M)";
}
bicarbonate {
Float32 _FillValue NaN;
Float32 actual_range 0.0023, 0.0023;
String bcodmo_name "bicarbonate";
String description "Concentration of bicarbonate which made up artificial seawater mix";
String long_name "Bicarbonate";
String units "millimoles (mM)";
}
K {
Float32 _FillValue NaN;
Float32 actual_range 0.025, 0.025;
String bcodmo_name "K";
String description "Concentration of K which made up artificial seawater mix";
String long_name "K";
String units "molar (M)";
}
Ca {
Float32 _FillValue NaN;
Float32 actual_range 0.033, 0.033;
String bcodmo_name "Ca";
String description "Concentration of Ca which made up artificial seawater mix";
String long_name "Ca";
String units "molar (M)";
}
Na {
Float64 _FillValue NaN;
Float64 actual_range 0.4006, 0.45895;
String bcodmo_name "Na";
String description "Concentration of Na which made up artificial seawater mix";
String units "molar (M)";
}
Cl {
Float32 _FillValue NaN;
Float32 actual_range 0.489, 0.489;
String bcodmo_name "unknown";
String description "Concentration of Cl which made up artificial seawater mix";
String long_name "CL";
String units "molar (M)";
}
pH {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 4, 6;
String bcodmo_name "pH";
Float64 colorBarMaximum 9.0;
Float64 colorBarMinimum 7.0;
String description "pH of media added to incubations; Incubations were carried out at either pH 4 or 6; 4: simulates the pH of end-member Grotto vent fluid and the average calculated pH of mixed fluids in highly reduced zones within flange (Tivey 2004). 6: represents the calculated pH in fluid mixing zones (Tivey 2004).";
String long_name "Sea Water Ph Reported On Total Scale";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/PHXXZZXX/";
String units "pH";
}
temperature {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 4, 90;
String bcodmo_name "temperature";
String description "Temperatures at which samples were incubated anaerobically for 1 3 or 7 days. 4 C: ambient seawater; 50 C: thermophilic; 90 C: hyperthermophilic.";
String long_name "Temperature";
String units "celsius (C)";
}
sulfateRed_formate {
Float32 _FillValue NaN;
Float32 actual_range -23.04, -2.76;
String bcodmo_name "unknown";
String description "(DeltaGr KJ/mol e-) of formate calculated at pH 6 and 50 deg C for heterotrophic sulfate reduction via organic acids";
String long_name "Sulfate Red Formate";
String units "DeltaGr KJ/mol e-";
}
sulfateRed_acetate {
Float32 _FillValue NaN;
Float32 actual_range -14.05, -4.89;
String bcodmo_name "unknown";
String description "(DeltaGr KJ/mol e-) of acetate calculated at pH 6 and 50 deg C for heterotrophic sulfate reduction via organic acids";
String long_name "Sulfate Red Acetate";
String units "DeltaGr KJ/mol e-";
}
sulfateRed_pyruvate {
Float32 _FillValue NaN;
Float32 actual_range -22.18, -13.14;
String bcodmo_name "unknown";
String description "(DeltaGr KJ/mol e-) of pyruvate calculated at pH 6 and 50 deg C for heterotrophic sulfate reduction via organic acids";
String long_name "Sulfate Red Pyruvate";
String units "DeltaGr KJ/mol e-";
}
sulfateRed_lactate {
Float32 _FillValue NaN;
Float32 actual_range -20.24, -11.23;
String bcodmo_name "unknown";
String description "(DeltaGr KJ/mol e-) of lactate calculated at pH 6 and 50 deg C for heterotrophic sulfate reduction via organic acids";
String long_name "Sulfate Red Lactate";
String units "DeltaGr KJ/mol e-";
}
sulfateRed_citrate {
Float32 _FillValue NaN;
Float32 actual_range -20.49, -11.67;
String bcodmo_name "unknown";
String description "(DeltaGr KJ/mol e-) of citrate calculated at pH 6 and 50 deg C for heterotrophic sulfate reduction via organic acids";
String long_name "Sulfate Red Citrate";
String units "DeltaGr KJ/mol e-";
}
c_limiting_totalEnergy {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 1.49;
String bcodmo_name "unknown";
String description "Carbon limiting total energy available in bottle for sulfate reduction";
String long_name "C Limiting Total Energy";
String units "joules (J)";
}
S_limiting_totalEnergy {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 167.06;
String bcodmo_name "unknown";
String description "Sulfate limiting total energy available in bottle for sulfate reduction";
String long_name "S limiting totalEnergy";
String units "joules (J)";
}
total_energy {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 1.49;
String bcodmo_name "unknown";
String description "Total energy available for sulfate reduction";
String long_name "Total Energy";
String units "joules (J)";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson";
String acquisition_description
"Tables and Figures referenced in the acquisition description are found in the
paper Frank et al., 2015
For each independent treatment, aliquots of 7.5 mL flange slurry (approx. 29 g
wet weight and 20 g dry weight) were transferred into Balch tubes in an
anaerobic chamber, and supplemented with 15 mL of sterile artificial seawater
media designed to mimic the geochemical conditions within a hydrothermal
flange (400 mM NaCl, 25 mM KCl, 30 mM CaCl2, 2.3 mM NaHCO3, 14 mM NaSO42-, 1
mM H2S, and 50 uM dissolved organic carbon - consisting of equimolar
proportions 10 uM of pyruvate, citrate, formate, acetate, lactate) under a
pure nitrogen headspace.\\u00a0
Concentrations of sulfide, sulfate and dissolved organic carbon (DOC) were
varied independently to investigate concentration dependent effects on the
rates of SR. The range of experimental conditions tested was determined from
previously published concentration profiles of aqueous species modeled as
functions of temperature and position within the Grotto vent structure (Tivey,
2004). Concentrations were varied by orders of magnitude within the modeled
ranges to simulate conditions representative of different mixing regimes
between seawater and vent fluid (Table 1). The range of DOC (which we
approximate as a mix of pyruvate, citrate, formate, acetate, lactate \\u2013
most of which have been identified to varying degrees within vent fluid and
are known carbon sources for heterotrophic SR in culture) concentrations
tested were based on the average DOC concentrations measured within diffuse
fluids at the Main Endeavor Field (Lang\\u00a0et al., 2006; Lang\\u00a0et
al.,\\u00a02010). Hydrogen sulfide was present as H2S (pKa\\u00a0in seawater of
6.60) across all the conditions tested (Amend & Shock, 2001). Incubations were
carried out at pH 4 (to simulate the pH of end-member Grotto vent fluid and
the average calculated pH of\\u00a0mixed fluids in highly reduced zones within
the flange; Tivey 2004) as well as pH 6 (representative of the calculated pH
in fluid mixing zones; Tivey 2004). All the results are presented and
discussed in the context of the initial measured media conditions.";
String awards_0_award_nid "554913";
String awards_0_award_number "OCE-1061934";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1061934";
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 "626305";
String awards_1_award_number "OCE-0838107";
String awards_1_data_url "http://www.nsf.gov/awardsearch/showAward?AWD_ID=0838107";
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 "Kandace S Binkley";
String awards_1_program_manager_nid "51512";
String awards_2_award_nid "626308";
String awards_2_award_number "NNX09AB78G";
String awards_2_funder_name "NASA Astrobiology Science & Technology for Exploring Planets";
String awards_2_funding_acronym "NASA-ASTEP";
String awards_2_funding_source_nid "626307";
String awards_3_award_nid "626309";
String awards_3_award_number "NNX07AV51G";
String awards_3_funder_name "NASA Astrobiology Science & Technology for Exploring Planets";
String awards_3_funding_acronym "NASA-ASTEP";
String awards_3_funding_source_nid "626307";
String cdm_data_type "Other";
String comment
"Sulfate Reduction Energetics
P. Girguis & K. Rogers, PIs
Version 13 October 2016";
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 "2016-10-14T17:33:03Z";
String date_modified "2019-06-12T12:59:36Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.661659.1";
Float64 Easternmost_Easting -129.1;
Float64 geospatial_lat_max 47.95;
Float64 geospatial_lat_min 47.95;
String geospatial_lat_units "degrees_north";
Float64 geospatial_lon_max -129.1;
Float64 geospatial_lon_min -129.1;
String geospatial_lon_units "degrees_east";
String history
"2024-11-21T11:48:00Z (local files)
2024-11-21T11:48:00Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_661659.html";
String infoUrl "https://www.bco-dmo.org/dataset/661659";
String institution "BCO-DMO";
String instruments_0_acronym "in-situ incubator";
String instruments_0_dataset_instrument_description "Used aboard ship and in lab";
String instruments_0_dataset_instrument_nid "661747";
String instruments_0_description "A device on shipboard or in the laboratory that holds water samples under controlled conditions of temperature and possibly illumination.";
String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/82/";
String instruments_0_instrument_name "In-situ incubator";
String instruments_0_instrument_nid "494";
String instruments_0_supplied_name "Incubator";
String instruments_1_acronym "pH Sensor";
String instruments_1_dataset_instrument_description "pH sensor";
String instruments_1_dataset_instrument_nid "661672";
String instruments_1_description "General term for an instrument that measures the pH or how acidic or basic a solution is.";
String instruments_1_instrument_name "pH Sensor";
String instruments_1_instrument_nid "674";
String instruments_1_supplied_name "pH sensor";
String instruments_2_acronym "Dissolved Oxygen Sensor";
String instruments_2_dataset_instrument_description "DOC was measured";
String instruments_2_dataset_instrument_nid "661673";
String instruments_2_description "An electronic device that measures the proportion of oxygen (O2) in the gas or liquid being analyzed";
String instruments_2_instrument_name "Dissolved Oxygen Sensor";
String instruments_2_instrument_nid "705";
String instruments_2_supplied_name "DO sensor";
String keywords "acetate, bco, bco-dmo, bicarbonate, biological, c_limiting_totalEnergy, chemical, chemistry, citrate, commerce, data, dataset, department, dmo, doc, earth, Earth Science > Oceans > Ocean Chemistry > pH, energy, erddap, experiment, experiment_num, formate, lactate, latitude, limiting, longitude, management, num, ocean, oceanography, oceans, office, preliminary, pyruvate, red, reported, S_limiting_totalEnergy, scale, science, sea, sea_water_ph_reported_on_total_scale, seawater, sulfate, sulfateRed_acetate, sulfateRed_citrate, sulfateRed_formate, sulfateRed_lactate, sulfateRed_pyruvate, sulfide, temperature, total, total_energy, totalenergy, water";
String keywords_vocabulary "GCMD Science Keywords";
String license "https://www.bco-dmo.org/dataset/661659/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/661659";
Float64 Northernmost_Northing 47.95;
String param_mapping "{'661659': {'lat': 'master - latitude', 'lon': 'master - longitude'}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/661659/parameters";
String people_0_affiliation "Harvard University";
String people_0_person_name "Peter Girguis";
String people_0_person_nid "544586";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "Rensselaer Polytechnic Institute";
String people_1_affiliation_acronym "RPI";
String people_1_person_name "Karyn Rogers";
String people_1_person_nid "661573";
String people_1_role "Co-Principal Investigator";
String people_1_role_type "originator";
String people_2_affiliation "University of Hawaii at Manoa";
String people_2_affiliation_acronym "SOEST";
String people_2_person_name "Kiana Frank";
String people_2_person_nid "626318";
String people_2_role "Contact";
String people_2_role_type "related";
String people_3_affiliation "Woods Hole Oceanographic Institution";
String people_3_affiliation_acronym "WHOI BCO-DMO";
String people_3_person_name "Hannah Ake";
String people_3_person_nid "650173";
String people_3_role "BCO-DMO Data Manager";
String people_3_role_type "related";
String project "North Pond Microbes,Middle Valley Vents";
String projects_0_acronym "North Pond Microbes";
String projects_0_description
"Description from NSF award abstract:
Current estimates suggest that the volume of ocean crust capable of sustaining life is comparable in magnitude to that of the oceans. To date, there is little understanding of the composition or functional capacity of microbial communities in the sub-seafloor, or their influence on the chemistry of the oceans and subsequent consequences for global biogeochemical cycles. This project focuses on understanding the relationship between microbial communities and fluid chemistry in young crustal fluids that are responsible for the transport of energy, nutrients, and organisms in the crust. Specifically, the PIs will couple microbial activity measurements, including autotrophic carbon, nitrogen and sulfur metabolisms as well as mineral oxide reduction, with quantitative assessments of functional gene expression and geochemical transformations in basement fluids. Through a comprehensive suite of in situ and shipboard analyses, this research will yield cross-disciplinary advances in our understanding of the microbial ecology and geochemistry of the sub-seafloor biosphere. The focus of the effort is at North Pond, an isolated sediment pond located on ridge flank oceanic crust 7-8 million years old on the western side of the Mid-Atlantic Ridge. North Pond is currently the target for drilling on IODP expedition 336, during which it will be instrumented with three sub-seafloor basement observatories.
The project will leverage this opportunity for targeted and distinct sampling at North Pond on two German-US research cruises to accomplish three main objectives:
1. to determine if different basement fluid horizons across North Pond host distinct microbial communities and chemical milieus and the degree to which they change over a two-year post-drilling period.
2. to quantify the extent of autotrophic metabolism via microbially-mediated transformations in carbon, nitrogen, and sulfur species in basement fluids at North Pond.
3. to determine the extent of suspended particulate mineral oxides in basement fluids at North Pond and to characterize their role as oxidants for fluid-hosted microbial communities.
Specific outcomes include quantitative assessments of microbial activity and gene expression as well as geochemical transformations. The program builds on the integrative research goals for North Pond and will provide important data for guiding the development of that and future deep biosphere research programs. Results will increase understanding of microbial life and chemistry in young oceanic crust as well as provide new insights into controls on the distribution and activity of marine microbial communities throughout the worlds oceans.
There are no data about microbial communities in ubiquitous cold, oceanic crust, the emphasis of the proposed work. This is an interdisciplinary project at the interface of microbial ecology, chemistry, and deep-sea oceanography with direct links to international and national research and educational organizations.";
String projects_0_end_date "2015-05";
String projects_0_geolocation "North Pond, mid-Atlantic Ridge";
String projects_0_name "Collaborative Research: Characterization of Microbial Transformations in Basement Fluids, from Genes to Geochemical Cycling";
String projects_0_project_nid "554914";
String projects_0_start_date "2011-06";
String projects_1_acronym "Middle Valley Vents";
String projects_1_description
"This project characterizes rates of microbially mediated sulfate reduction from three distinct hydrothermal vents in the Middle Valley vent field along the Juan de Fuca Ridge, as well as assessments of bacterial and archaeal diversity, estimates of total biomass and the abundance of functional genes related to sulfate reduction, and in situ geochemistry. Maximum rates of sulfate reduction occurred at 90°C in all three deposits. Pyrosequencing and functional gene abundance data reveal differences in both biomass and community composition among sites, including differences in the abundance of known sulfate reducing bacteria. The abundance of sequences for Thermodesulfovibro-like organisms and higher sulfate reduction rates at elevated temperatures, suggests that Thermodesulfovibro-like organisms may play a role in sulfate reduction in warmer environments. The rates of sulfate reduction observed suggest that - within anaerobic niches of hydrothermal deposits - heterotrophic sulfate reduction may be quite common and might contribute substantially to secondary productivity, underscoring the potential role of this process in both sulfur and carbon cycling at vents.
This project was funded, in part, by a C-DEBI Graduate Student Fellowship.";
String projects_1_geolocation "Middle Valley vent field along the Juan de Fuca Ridge";
String projects_1_name "Characterizing the distribution and rates of microbial sulfate reduction at Middle Valley hydrothermal vents";
String projects_1_project_nid "626603";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
Float64 Southernmost_Northing 47.95;
String standard_name_vocabulary "CF Standard Name Table v55";
String subsetVariables "latitude,longitude,bicarbonate,K,Ca,Cl";
String summary "Sulfate reduction energetics at Main Endeavor grotto chimney from samples collected on RV Atlantis (AT18-08) during Jason II dives in the Juan de Fuca Ridge from July to August 2011";
String title "[Sulfate reduction energetics] - Sulfate reduction energetics at Main Endeavor grotto chimney from samples collected on RV Atlantis (AT18-08) during Jason II dives in the Juan de Fuca Ridge from July to August 2011 (Characterizing the distribution and rates of microbial sulfate reduction at Middle Valley hydrothermal vents)";
String version "1";
Float64 Westernmost_Easting -129.1;
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.