Accessing BCO-DMO data
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BCO-DMO ERDDAP
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| Dataset Title: | Porewater sulfate from samples collected by pushcore from Guaymas Basin hydrothermal sediments on R/V Atlantis cruise AT37-06 in the Guaymas Basin in December 2016 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_720669) |
| Information: | Summary
| License
| ISO 19115
| Metadata
| Background
| Files
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Attributes {
s {
Sample_ID {
String bcodmo_name "sample";
String description "Sample identification number";
String long_name "Sample ID";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
String units "unitless";
}
Sulfate_Concentration {
Float32 _FillValue NaN;
Float32 actual_range 5.118, 28.68;
String bcodmo_name "SO4";
String description "Sulfate concentration";
String long_name "Sulfate Concentration";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/SPHTMAXX/";
String units "millimoles per liter (mMol/L)";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
String acquisition_description
"Sampling and Analytical Methodology: Freshly collected sediment cores were
sliced on the ship into 3 cm layers; porewater was obtained by gently
centrifuging freshly collected sediment in 50 ml conical Falcon tubes for ca.
5 to 10 minutes until the sediment had settled; one Falcon tube produced ca. 8
to 10 ml of porewater. For porewater sulfate measurements, 1 ml subsamples of
the overlying porewater were drawn into syringes and injected through 0.45
\\u03bcm filters into screw cap Eppendorf vials, each acidified with 50 \\u00b5l
of 6N HCl, and then gently bubbled with nitrogen for 4 min to remove sulfide;
the samples were then stored at 4\\u00baC before shipping and analysis.
Geochemical Analyses:\\u00a0SO4 was analyzed on a Dionex ICS-1000 using a RFIC
IonPac AS22 4 X 250mm column and a RFIC IonPac AG22 Guard column 4 X 50 mm.
The IC was calibrated using a 5 point std curve and a minimum r^2 value of
0.999. The MDL measured at 0.10 ppm SO4. A check standard from a 1000 ppm was
made fom a Dionex 7 anion standard to a concentration of 15 ppm. An external
Standard from HACH 100 ppm SO4 was used to make a 20 ppm QC standard. In
general, QCs were analyzed for 10% of the samples.
Data Processing: The porewater data of Guaymas Basin sand Sonora Margin piston
cores were tabulated in Excel sheets.
Quality Control: Note that Sample_IDs \\\"D7A_10X_CKS\\\" are internal quality
control standards (15.5 mg/L) and\\u00a0Sample_IDs \\\"DI_SPK\\\" are external
quality control standards (20.0 mg/L).";
String awards_0_award_nid "505555";
String awards_0_award_number "OCE-1357238";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward?AWD_ID=1357238";
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 "Michael E. Sieracki";
String awards_0_program_manager_nid "50446";
String cdm_data_type "Other";
String comment
"Porewater Geochemistry: SO4
Cruise AT37-06, Guaymas Basin
PI: Andreas Teske (UNC Chapel Hill)
Version: 07 December 2017
NOTES:
Sample_IDs \"D7A_10X_CKS\" are internal quality control standards (15.5 mg/L)
Sample_IDs \"DI_SPK\" are external quality control standards (20.0 mg/L)";
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 "2017-12-08T20:28:22Z";
String date_modified "2020-01-14T16:41:54Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.720669.1";
String history
"2024-04-19T20:04:58Z (local files)
2024-04-19T20:04:58Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_720669.html";
String infoUrl "https://www.bco-dmo.org/dataset/720669";
String institution "BCO-DMO";
String instruments_0_acronym "Tube Core";
String instruments_0_dataset_instrument_nid "720888";
String instruments_0_description "A plastic tube, about 40 cm (16 inches) long, is pushed into the sediment by Alvin's manipulator arm to collect a sediment core.";
String instruments_0_instrument_name "Alvin tube core";
String instruments_0_instrument_nid "641";
String instruments_1_acronym "Ion Chromatograph";
String instruments_1_dataset_instrument_description "SO4 was analyzed on a Dionex ICS-1000 using a RFIC IonPac AS22 4 X 250mm column and a RFIC IonPac AG22 Guard column 4 X 50 mm.";
String instruments_1_dataset_instrument_nid "720887";
String instruments_1_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_1_instrument_name "Ion Chromatograph";
String instruments_1_instrument_nid "662";
String instruments_1_supplied_name "Dionex ICS-1000";
String keywords "bco, bco-dmo, biological, chemical, concentration, data, dataset, dmo, erddap, management, oceanography, office, preliminary, sample, Sample_ID, sulfate, Sulfate_Concentration";
String license "https://www.bco-dmo.org/dataset/720669/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/720669";
String param_mapping "{'720669': {}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/720669/parameters";
String people_0_affiliation "University of North Carolina at Chapel Hill";
String people_0_affiliation_acronym "UNC-Chapel Hill";
String people_0_person_name "Andreas P. Teske";
String people_0_person_nid "51412";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "Woods Hole Oceanographic Institution";
String people_1_affiliation_acronym "WHOI BCO-DMO";
String people_1_person_name "Shannon Rauch";
String people_1_person_nid "51498";
String people_1_role "BCO-DMO Data Manager";
String people_1_role_type "related";
String project "Guaymas Basin interactions";
String projects_0_acronym "Guaymas Basin interactions";
String projects_0_description
"Description from NSF award abstract:
Hydrothermally active sediments in the Guaymas Basin are dominated by novel microbial communities that catalyze important biogeochemical processes in these seafloor ecosystems. This project will investigate genomic potential, physiological capabilities and biogeochemical roles of key uncultured organisms from Guaymas sediments, especially the high-temperature anaerobic methane oxidizers that occur specifically in hydrothermally active sediments (ANME-1Guaymas). The study will focus on their role in carbon transformations, but also explore their potential involvement in sulfur and nitrogen transformations. First-order research topics include quantifying anaerobic methane oxidation under high temperature,in situ concentrations of phosphorus and methane , and with alternate electron acceptors; sulfate and sulfur-dependent microbial pathways and isotopic signatures under these conditions; and nitrogen transformations in methane-oxidizing microbial communities, hydrothermal mats and sediments.
This integrated biogeochemical and microbiological research will explore the pathways of and environmental controls on the consumption and production of methane, other alkanes, inorganic carbon, organic acids and organic matter that fuel the Guaymas sedimentary microbial ecosystem. The hydrothermal sediments of Guaymas Basin provide a spatially compact, high-activity location for investigating novel modes of methane cycling and carbon assimilation into microbial biomass. In the case of anaerobic methane oxidation, the high temperature and pressure tolerance of Guaymas Basin methane-oxidizing microbial communities, and their potential to uncouple from the dominant electron acceptor sulfate, vastly increase the predicted subsurface habitat space and biogeochemical role for anaerobic microbial methanotrophy in global deep subsurface diagenesis. Further, microbial methane production and oxidation interlocks with syulfur and nitrogen transformations, which will be explored at the organism and process level in hydrothermal sediment microbial communities and mats of Guaymas Basin. In general, first-order research tasks (rate measurements, radiotracer incorporation studies, genomes, in situ microgradients) define the key microbial capabilities, pathways and processes that mediate chemical exchange between the subsurface hydrothermal/seeps and deep ocean waters.
Publications associated with this project are as follows:
Note: this is now a list of all publications that use samples collected from the NSF-funded Guaymas cruises AT15-40 and AT15-56. All these publications were funded from NSF award OCE-0647633, the grant that funded these two cruises. Those publications that were written and published after 2013 continue to use samples collected and analyzed on cruises AT15-40 and AT15-56 under NSF award OCE-0647633, but the effort in analyzing the data and writing the manuscript also relied on funding by OCE-1357238. Since we will not have new samples until late in 2016, current work and publications on OCE-1357238 will continue to rely on samples collected during cruises AT15-40 and AT15-56.
Holler, T. F. Widdel, K. Knittel, R. Amann, M. Y. Kellermann, K.-. Hinrichs, A. Teske, A. Boetius, and G. Wegener. 2011. Thermophilic anaerobic oxidation of methane by marine microbial consortia. The ISME Journal 5:1946-1956. doi:10.1038/ismej.2011.77
Biddle, J.F., Z. Cardman, H. Mendlovitz, D.B. Albert, K.G. Lloyd, A. Boetius, and A. Teske. 2012. Anaerobic oxidation of methane at different temperature regimes in Guaymas Basin hydrothermal sediments. The ISME Journal 6:1018-1031. doi:10.1038/ismej.2011.164
McKay, L.J., B.J. MacGregor, J.F. Biddle, H.P. Mendlovitz, D. Hoer, J.S. Lipp, K.G. Lloyd, and A.P. Teske. 2012. Spatial heterogeneity and underlying geochemistry of phylogenetically diverse orange and white Beggiatoa mats in Guaymas Basin hydrothermal sediments. Deep-Sea Research I, 67:21-31. doi:10.1016/j.dsr.2012.04.011
Bowles, M.W., L.M. Nigro, A.P. Teske, and S.B. Joye.. 2012. Denitrification and environmental factors influencing nitrate removal in Guaymas Basin hydrothermally-altered sediments. Frontiers in Microbiology 3:377. doi:10.3389/fmicb.2012.03377
MacGregor, B.J., J.F. Biddle, J.R. Siebert, E. Staunton, E. Hegg, A.G. Matthysse, and A. Teske. 2013. Why orange Guaymas Basin Beggiatoa spp. are orange: Single-filament genome-enabled identification of an abundant octaheme cytochrome with hydroxylamine oxidase, hydrazine oxidase and nitrite reductase activities. Applied and Environmental Microbiology 79:1183-1190. doi:10.1128/AEM.02538-12
MacGregor, B.J., J.F. Biddle, and A. Teske. 2013. Mobile elements in a single-filament orange Guaymas Basin Beggiatoa (\"Candidatus Maribeggiatoa\") sp. draft genome; evidence for genetic exchange with cyanobacteria. Applied and Environmental Microbiology 79:3974-3985. doi:10.1128/AEM.03821-12
Meyer, S., G. Wegener, K.G. Lloyd, A. Teske, A. Boetius, and A. Ramette. 2013. Microbial habitat connectivity across spatial scales and hydrothermal temperature gradients at Guaymas Basin. Frontiers in Microbiology 4:207. doi:10.3389/fmic.2013.00207
MacGregor, B.J., J.F. Biddle, C. Harbort, A.G. Matthysse, and A. Teske. 2013. Sulfide oxidation, nitrate respiration, carbon acquisition and electron transport pathways suggested by the draft genome of a single orange Guaymas Basin Beggiatoa (Cand. Maribeggiatoa) sp. filament. Marine Genomics 11:53-65. doi:10.1016/j.margen.2013.08.001
Ruff, E., J.F. Biddle, A. Teske, K. Knittel, A. Boetius, and A. Ramette. 2015. Global dispersion and local diversification of the methane seep microbiome. Proc. Natl. Acad. Sci. USA, 112:4015-4020. doi:10.1073/pnas.1421865112
McKay, L., V. Klokman, H. Mendlovitz, D. LaRowe, M. Zabel, D. Hoer, D. Albert, D. de Beer, J. Amend, A. Teske. Thermal and geochemical influences on microbial biogeography in the hydrothermal sediments of Guaymas Basin. Environmental Microbiology, in revision.
Teske, A., D. de Beer, L. McKay, M.K. Tivey, J.F. Biddle, D. Hoer, K.G. Lloyd, M.A. Lever, H.Røy, D.B. Albert, H. Mendlovitz, B. J. MacGregor. 2016. The Guaymas Basin hiking guide to hydrothermal mounds, chimneys and microbial mats: complex seafloor expressions of subsurface hydrothermal circulation. Frontiers in Microbiology 7:75, doi:10.3389/fmicb.2016.00075.
Dowell, F., Z. Cardman, S. Dasarathy, M.Y. Kellermann, L.J. McKay, B.J. MacGregor, S.E. Ruff, J.F. Biddle, K.G. Lloyd, J.S. Lipp, K-U. Hinrichs, D.B. Albert, H. Mendlovitz, and A. Teske. 2016. Microbial communities in methane and short alkane-rich hydrothermal sediments of Guaymas Basin. Frontiers in Microbiology 7:17, doi:10.3389/fmicb.2016.00017.
Conference abstracts (post 2013, only NSF-OCE 1357238):
B.J. MacGregor. 2014. Receiver (REC) domains in the orange Guaymas \"Maribeggiatoa\" (BOGUAY) draft genome: an evolutionary network of sensor networks. The Human and Environmental Microbiome Symposium 2014. Duke Center for the Genomics of Microbial Systems, Durham, NC.
B.J. MacGregot. 2015. Abundant intergenic repeats and a possible alternate RNA polymerase betra subunit in the orange Guaymas \"Maribeggiatoa\" genome. American Society for Microbiology 2015 General Meeting. New Orleans, LA.
Z. Cardman, L.J. McKay, E. Dowell, S. Dasarathy, V. Klokman, J.F. Biddle, K.G. Lloyd, H. Mendlovitz, D. Albert, M. Kellermann, K.-U. Hinrichs, B.J. MacGregir and A.P. Teske. 2014. American Society for Microbiology 2014 General Meeting. Boston, MA.";
String projects_0_end_date "2017-01";
String projects_0_geolocation "Guaymas Basin, Gulf of California, 27.00 N, 111.00W";
String projects_0_name "Microbial Carbon cycling and its interactions with Sulfur and Nitrogen transformations in Guaymas Basin hydrothermal sediments";
String projects_0_project_nid "474317";
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)";
String standard_name_vocabulary "CF Standard Name Table v55";
String summary "Porewater sulfate from samples collected by pushcore from Guaymas Basin hydrothermal sediments on cruise AT37-06 in December 2016.";
String title "Porewater sulfate from samples collected by pushcore from Guaymas Basin hydrothermal sediments on R/V Atlantis cruise AT37-06 in the Guaymas Basin in December 2016";
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.