BCO-DMO ERDDAP
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Row Type Variable Name Attribute Name Data Type Value
attribute NC_GLOBAL access_formats String .htmlTable,.csv,.json,.mat,.nc,.tsv
attribute NC_GLOBAL acquisition_description String Culturing\n \nThe marine diatom Thalassiosira weiss\\ufb02ogii Grunow (strain CCMP 1010) was\ncultured in sterile filtered natural North Sea water (Schleswig-Holstein,\nGermany) or Baltic Sea water (Schleswig-Holstein, Germany). The medium was\nenriched with f/4 concentrations of macro- and micronutrients (nitrate,\nphosphate, silicic acid, trace metal mixture, vitamin mixture (Guillard and\nRyther, 1962). All experiments were performed in sterile 2.1 L Schott Duran\nglass bottles. These bottles were made of borosilicate glass (filters UV\nradiation <310 nm) except for the quartz glass bottles (pure silica without UV\nradiation filter) used in the UV experiment. The cultures were either\nincubated in climate chambers with 400 \\u2013700 nm radiation or 10 cm below\nwater level at low tide in Kiel Fjord in May 2011. Water temperature and light\nirradiance data were obtained from the weather station maintained by the\nGEOMAR institute in Kiel, Germany. Growth conditions for the various\ntreatments, i.e. salinity, pH, temperature, and irradiance are given in Table\n1. pH values (reported on free scale) were measured \\u00a0with separate glass\nand reference electrodes (Metrohm) and calculated with equation 3 from DOE\n2007 chapter 6b (Dickson et al., 2007) as described in (Bach et al., 2012).\nCultures were inoculated with densities of 20 cells ml-1. \\u00a0Cell densities\nand equivalent spherical diameters were determined with a Coulter Counter\n(Beckman Coulter) at the beginning and the end of the experiment,\nrespectively. When incubations ended, cells were filtered on 47 mm diameter, 5\num mesh size Nucleopore Track-Etch Membrane filters (Whatman) and frozen at\n-18 deg C immediately after filtration.\n \nSediment sampling\n \nSediment samples were retrieved from a 14.97 m core, station M772-003-2,\ncollected November 26, 2008 by the Meteor cruise M77 at 271 m water depth\nwithin the main upwelling area off Peru (15 deg 06.21\\u00b4S, 75 deg\n41.28\\u00b4W). The Peruvian ocean margin is characterized by a high particle\nflux and a well-defined oxygen minimum zone. At the time of sampling, the O2\nconcentration at the seafloor was measured to 1.1 uM, the salinity to 34.9 psu\nand the temperature to 12.2 \\u00a0deg C.\n \nPrior to analysis, sediment samples were pre-treated with an acid-alkali-acid\ncleaning with HCl and NaOH (Grootes et al., 2004).) \\u00a0 \\u00a0 \\u00a0\n\\u00a0\n \nAnalyses\n \nBoth diatom and sediment samples were freeze dried prior to isotopic analysis.\nTo prepare aliquots for derivatization of amino acids, we used 3-4 mg of\ndiatoms and 100-150 mg of sediments. The samples were transferred to Pyrex\nculture tubes (13 x 100 mm), flushed with N2 gas, sealed, and hydrolysed in 1\nml 6N HCl at 110 \\u00a0deg C for 20 h. After hydrolysis, lipophilic compounds\nwere removed by vortexing with 2 ml n-hexane/DCM (6:5, v/v) for 30 sec. The\naqueous phase was subsequently transferred through disposable glass pipettes\nlined with glass wool into 4 ml dram vials. Samples were evaporated to dryness\nunder a stream of N2 gas for 30 min at 110 deg C before being stored at 18 deg\nC until required for analysis. The derivatisation procedure was modified from\nCorr et al. (2007) as described by Larsen et al. (2013). In short, the dried\nsamples were methylated with acidified methanol and subsequently acetylated\nwith a mixture of acetic anhydride, triethylamine, and acetone, forming\nN-acetyl methyl ester derivatives. As a precautionary measure to reduce the\noxidation of amino acids, we flushed and sealed reaction vials with N2 gas\nprior to methylation and acetylation. Another modification from Corr et al.\n(2007) was that icebaths were substituted with solid aluminum blocks at room\ntemperature. We used known d13C values of pure amino acids prepared and\nanalyzed under the same conditions as the samples to calculate correction\nfactors specific to each amino acid to account for carbon addition and\nfractionation during derivatization. The derivatised AAs were dissolved in 250\nul ethyl acetate and stored at 18 deg C until required for analysis.\n \nAmino acid d13C values were obtained from Leibniz-Laboratory for Radiometric\nDating and Stable Isotope Research in Kiel. We injected the AA derivatives\ninto a PTV injector held at 250 deg C for 4 min. before GC separation on an\nAgilent 6890N GC. Diatom samples were separated on an Rtx-200 column (60m x\n0.32mm x 0.25um, Fig. S1) and sediment samples on a Thermo Trace GOLD TG-200MS\nGC column (60m x 0.32mm x 0.25um). For both GC columns, the oven temperature\nof the GC was started at 50 deg C and heated at 15 deg C min-1 to 140 deg C,\nfollowed by 3 deg C min-1 to 152 deg C and held for 4 min, then 10 deg C min-1\nto 245 deg C and held for 10 min, and finally 5 deg C min-1 to 290 deg C and\nheld for 5 min. The GC was interfaced with a MAT 253 isotope ratio mass\nspectrometer (IRMS) via a GC-III combustion (C) interface (Thermo-Finnigan\nCorporation). We obtained consistently good chromatography for alanine (Ala),\nvaline (Val), leucine (Leu), isoleucine (Ile), asparagine/aspartate (Asx),\nthreonine (Thr), methionine (Met), glutamine/glutamate (Glx), phenylalanine\n(Phe), tyrosine (Tyr), lysine (Lys), and arginine (Arg) with the exception\nthat Asx and Thr partially coeluted with the Rtx-200 column. Serine (Ser) and\nproline (Pro) coeluted on both columns. The average reproducibility for the\nnorleucine internal standard was \\u00b1 0.4\\u2030 (n = 3 for each sample), and\nthe reproducibility of amino acid standards ranged from \\u00b1 0.1\\u2030 for\nPhe to \\u00b1 0.6\\u2030 for Thr (n = 3).\n \nAmino acid composition of the diatom samples was determined with the\nderivative samples used for d13CAA analysis. The amino acids were separated on\nan Rxi-35SIL MS column (30m x 0.32mm x 0.25um) with an Agilent 6890 N GC with\na flame ionization detector. With this column we obtained good chromatography\nfor Ala, Asx, Glx, Gly, Ser, Tyr, Arg, Ile, Leu, Lys, Met, Phe, Thr, and Val.\nFor quantification, we used internal references consisting of pure amino acids\n(Alfa Aesar, Karlsruhe, Germany). The composition of the amino acids are shown\nin Table 3 according to the following biosynthetic families: \\u00a0Pyruvate\n(Ala, Leu, Val), Oxaloacetate (Asx, Ile, Lys, Met, Thr), \\u03b1-ketoglutarate\n(Arg, Glx), 3-phosphoglycerate (Gly, Ser), and Shikimate (Phe, Tyr).\n \nBulk 13C, %C, 15N and %N values of the diatom samples were determined at the\nUC Davis Stable Isotope Facility using a PDZ Europa ANCA-GSL elemental\nanalyzer interfaced to a PDZ Europa 20-20 isotope ratio mass spectrometer\n(Sercon Ltd., Cheshire, UK). The dry weight of the samples ranged between 1.5\nand 2.5 mg. During analysis, samples were interspersed with several replicates\nof at least three different laboratory standards. These laboratory standards,\nwhich were selected to be compositionally similar to the samples being\nanalyzed, had previously calibrated against NIST Standard Reference Materials\n(IAEA-N1, IAEA-N2, IAEA-N3, USGS-40, and USGS-41). A sample\\u2019s preliminary\nisotope ratio was measured relative to reference gases analyzed with each\nsample. These preliminary values were finalized by correcting the values for\nthe entire batch based on the known values of the included laboratory\nstandards. The long term standard deviation is 0.2\\u2030 for 13C and 0.3\\u2030\nfor 15N.
attribute NC_GLOBAL awards_0_award_nid String 704683
attribute NC_GLOBAL awards_0_award_number String OCE-1131816
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1131816 (external link)
attribute NC_GLOBAL awards_0_funder_name String NSF Division of Ocean Sciences
attribute NC_GLOBAL awards_0_funding_acronym String NSF OCE
attribute NC_GLOBAL awards_0_funding_source_nid String 355
attribute NC_GLOBAL awards_0_program_manager String Candace O. Major
attribute NC_GLOBAL awards_0_program_manager_nid String 51690
attribute NC_GLOBAL cdm_data_type String Other
attribute NC_GLOBAL comment String Growth Data \n  M. McCarthy, PI \n  Version 14 September 2017
attribute NC_GLOBAL Conventions String COARDS, CF-1.6, ACDD-1.3
attribute NC_GLOBAL creator_email String info at bco-dmo.org
attribute NC_GLOBAL creator_name String BCO-DMO
attribute NC_GLOBAL creator_type String institution
attribute NC_GLOBAL creator_url String https://www.bco-dmo.org/ (external link)
attribute NC_GLOBAL data_source String extract_data_as_tsv version 2.3  19 Dec 2019
attribute NC_GLOBAL date_created String 2017-09-29T20:36:56Z
attribute NC_GLOBAL date_modified String 2019-03-19T17:33:22Z
attribute NC_GLOBAL defaultDataQuery String &amp;time&lt;now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.715903.1
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/715903 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_acronym String IR Mass Spec
attribute NC_GLOBAL instruments_0_dataset_instrument_description String Used with PDZ Europa ANCA-GSL elemental analyzer
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 715934
attribute NC_GLOBAL instruments_0_description String The Isotope-ratio Mass Spectrometer is a particular type of mass spectrometer used to measure the relative abundance of isotopes in a given sample (e.g. VG Prism II Isotope Ratio Mass-Spectrometer).
attribute NC_GLOBAL instruments_0_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/LAB16/ (external link)
attribute NC_GLOBAL instruments_0_instrument_name String Isotope-ratio Mass Spectrometer
attribute NC_GLOBAL instruments_0_instrument_nid String 469
attribute NC_GLOBAL instruments_0_supplied_name String PDZ Europa 20-20 isotope ratio mass spectrometer
attribute NC_GLOBAL instruments_1_acronym String IR Mass Spec
attribute NC_GLOBAL instruments_1_dataset_instrument_description String Used with Thermo Trace GOLD GC
attribute NC_GLOBAL instruments_1_dataset_instrument_nid String 715935
attribute NC_GLOBAL instruments_1_description String The Isotope-ratio Mass Spectrometer is a particular type of mass spectrometer used to measure the relative abundance of isotopes in a given sample (e.g. VG Prism II Isotope Ratio Mass-Spectrometer).
attribute NC_GLOBAL instruments_1_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/LAB16/ (external link)
attribute NC_GLOBAL instruments_1_instrument_name String Isotope-ratio Mass Spectrometer
attribute NC_GLOBAL instruments_1_instrument_nid String 469
attribute NC_GLOBAL instruments_1_supplied_name String MAT 253 isotope ratio mass spectrometer (IRMS)
attribute NC_GLOBAL instruments_2_acronym String Water Temp Sensor
attribute NC_GLOBAL instruments_2_dataset_instrument_description String Used to measure temperature
attribute NC_GLOBAL instruments_2_dataset_instrument_nid String 715911
attribute NC_GLOBAL instruments_2_description String General term for an instrument that measures the temperature of the water with which it is in contact (thermometer).
attribute NC_GLOBAL instruments_2_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/134/ (external link)
attribute NC_GLOBAL instruments_2_instrument_name String Water Temperature Sensor
attribute NC_GLOBAL instruments_2_instrument_nid String 647
attribute NC_GLOBAL instruments_2_supplied_name String Water Temperature Sensor
attribute NC_GLOBAL instruments_3_acronym String Gas Chromatograph
attribute NC_GLOBAL instruments_3_dataset_instrument_description String Used with MAT 253 isotope ratio mass spectrometer (IRMS) via a GC-III combustion (C) interface (Thermo-Finnigan Corporation)
attribute NC_GLOBAL instruments_3_dataset_instrument_nid String 715933
attribute NC_GLOBAL instruments_3_description String Instrument separating gases, volatile substances, or substances dissolved in a volatile solvent by transporting an inert gas through a column packed with a sorbent to a detector for assay. (from SeaDataNet, BODC)
attribute NC_GLOBAL instruments_3_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/LAB02/ (external link)
attribute NC_GLOBAL instruments_3_instrument_name String Gas Chromatograph
attribute NC_GLOBAL instruments_3_instrument_nid String 661
attribute NC_GLOBAL instruments_3_supplied_name String Thermo Trace GOLD GC
attribute NC_GLOBAL instruments_4_acronym String pH Sensor
attribute NC_GLOBAL instruments_4_dataset_instrument_description String Used to measure pH
attribute NC_GLOBAL instruments_4_dataset_instrument_nid String 715910
attribute NC_GLOBAL instruments_4_description String General term for an instrument that measures the pH or how acidic or basic a solution is.
attribute NC_GLOBAL instruments_4_instrument_name String pH Sensor
attribute NC_GLOBAL instruments_4_instrument_nid String 674
attribute NC_GLOBAL instruments_4_supplied_name String pH sensor
attribute NC_GLOBAL instruments_5_acronym String Light Meter
attribute NC_GLOBAL instruments_5_dataset_instrument_description String Used to measure irradiance
attribute NC_GLOBAL instruments_5_dataset_instrument_nid String 715909
attribute NC_GLOBAL instruments_5_description String Light meters are instruments that measure light intensity. Common units of measure for light intensity are umol/m2/s or uE/m2/s (micromoles per meter squared per second or microEinsteins per meter squared per second). (example: LI-COR 250A)
attribute NC_GLOBAL instruments_5_instrument_name String Light Meter
attribute NC_GLOBAL instruments_5_instrument_nid String 703
attribute NC_GLOBAL instruments_5_supplied_name String Light meter
attribute NC_GLOBAL instruments_6_acronym String Salinity Sensor
attribute NC_GLOBAL instruments_6_dataset_instrument_description String Used to measure salinity
attribute NC_GLOBAL instruments_6_dataset_instrument_nid String 715912
attribute NC_GLOBAL instruments_6_description String Category of instrument that simultaneously measures electrical conductivity and temperature in the water column to provide temperature and salinity data.
attribute NC_GLOBAL instruments_6_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/350/ (external link)
attribute NC_GLOBAL instruments_6_instrument_name String Salinity Sensor
attribute NC_GLOBAL instruments_6_instrument_nid String 710
attribute NC_GLOBAL instruments_6_supplied_name String Salinity sensor
attribute NC_GLOBAL instruments_7_dataset_instrument_description String Interfaced to a PDZ Europa 20-20 isotope ratio mass spectrometer (Sercon Ltd., Cheshire, UK)
attribute NC_GLOBAL instruments_7_dataset_instrument_nid String 715932
attribute NC_GLOBAL instruments_7_description String Instruments that quantify carbon, nitrogen and sometimes other elements by combusting the sample at very high temperature and assaying the resulting gaseous oxides. Usually used for samples including organic material.
attribute NC_GLOBAL instruments_7_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/LAB01/ (external link)
attribute NC_GLOBAL instruments_7_instrument_name String Elemental Analyzer
attribute NC_GLOBAL instruments_7_instrument_nid String 546339
attribute NC_GLOBAL instruments_7_supplied_name String PDZ Europa ANCA-GSL elemental analyzer
attribute NC_GLOBAL keywords String atomic, bco, bco-dmo, biological, bulk, Bulk_stable_isotope_d13C, Bulk_stable_isotope_d15N, cell, Cell_density, Cell_size, chemical, composition, d13, d15, data, dataset, density, dmo, elemental, elemental_composition_C, elemental_composition_C_N_atomic, elemental_composition_N, erddap, growth, Growth_rate, isotope, management, oceanography, office, preliminary, rate, size, stable, treatment, Treatment_ID
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/715903/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/715903 (external link)
attribute NC_GLOBAL param_mapping String {'715903': {}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/715903/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String University of California-Santa Cruz
attribute NC_GLOBAL people_0_affiliation_acronym String UC Santa Cruz
attribute NC_GLOBAL people_0_person_name String Matthew D. McCarthy
attribute NC_GLOBAL people_0_person_nid String 557245
attribute NC_GLOBAL people_0_role String Principal Investigator
attribute NC_GLOBAL people_0_role_type String originator
attribute NC_GLOBAL people_1_affiliation String Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_1_affiliation_acronym String WHOI BCO-DMO
attribute NC_GLOBAL people_1_person_name String Hannah Ake
attribute NC_GLOBAL people_1_person_nid String 650173
attribute NC_GLOBAL people_1_role String BCO-DMO Data Manager
attribute NC_GLOBAL people_1_role_type String related
attribute NC_GLOBAL project String Amino Acid Sediment 15N
attribute NC_GLOBAL projects_0_acronym String Amino Acid Sediment 15N
attribute NC_GLOBAL projects_0_description String The bioavailability of nutrients plays a crucial role in oceanic biological productivity, the carbon cycle, and climate change. The global ocean inventory of nitrogen (N) is determined by the balance of N-fixation (sources) and denitrification (sinks). In this three-year project, a researcher from the University of California, Santa Cruz, will focus on developing compound-specific N isotope (d15N) analysis of amino acids as a new tool for understanding N source and transformation of organic matter in paleo-reservoirs. The offsets in the isotopic ratios of individual amino acid groups may yield information about trophic transfer, heterotrophic microbial reworking, and autotrophic versus heterotrophic sources. By measuring and comparing the bulk and amino acid d15N in size-fractioned samples from plankton tows, sediments traps, and multi-cores in oxic and suboxic depositional environments, the researcher will: (1) Provide a proxy of the d15N of average exported photoautotrophic organic matter; and (2) Provide a new level of detail into sedimentary organic N degradation and preservation.\nBroader impacts:\nThis project will improve understanding of the fundamental underpinnings and behaviors of d15N amino acid patterns and how they behave in contrasting sedimentary environments, while also developing a potential paleoceanographic proxy. Funding will support a graduate student and undergraduate research at the institution. The researcher will also conduct community outreach in the form of a workshop/tutorial on the proxy development.
attribute NC_GLOBAL projects_0_end_date String 2016-09
attribute NC_GLOBAL projects_0_geolocation String California Margin , Santa Barbara Basin , CA current system,  Eastern Tropical Pacific
attribute NC_GLOBAL projects_0_name String The Use of Nitrogen Isotopes of Amino Acids To Understand Marine Sedimentary 15N Records
attribute NC_GLOBAL projects_0_project_nid String 704684
attribute NC_GLOBAL projects_0_start_date String 2011-10
attribute NC_GLOBAL publisher_name String Biological and Chemical Oceanographic Data Management Office (BCO-DMO)
attribute NC_GLOBAL publisher_type String institution
attribute NC_GLOBAL sourceUrl String (local files)
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL summary String Growth rates, bulk isotope values, elemental composition data from the R/V Meteor M77 cruise in the Peruvian ocean margin from November to December 2008.
attribute NC_GLOBAL title String [Growth rates and bulk isotope values] - Growth rates, bulk isotope values, elemental composition data from the R/V Meteor M77 cruise in the Peruvian ocean margin from November to December 2008. (The Use of Nitrogen Isotopes of Amino Acids To Understand Marine Sedimentary 15N Records)
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable Treatment_ID String
attribute Treatment_ID bcodmo_name String sample
attribute Treatment_ID description String Treatment ID
attribute Treatment_ID long_name String Treatment ID
attribute Treatment_ID nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute Treatment_ID units String unitless
variable Growth_rate String
attribute Growth_rate bcodmo_name String growth
attribute Growth_rate description String Growth rate per day
attribute Growth_rate long_name String Growth Rate
attribute Growth_rate units String days
variable Cell_density String
attribute Cell_density bcodmo_name String cell_concentration
attribute Cell_density description String Cell density
attribute Cell_density long_name String Cell Density
attribute Cell_density units String cells per milliliter
variable Cell_size String
attribute Cell_size bcodmo_name String cell_size
attribute Cell_size description String Diameter of cell
attribute Cell_size long_name String Cell Size
attribute Cell_size units String microns
variable Bulk_stable_isotope_d13C String
attribute Bulk_stable_isotope_d13C bcodmo_name String d13C
attribute Bulk_stable_isotope_d13C description String d13C concentration
attribute Bulk_stable_isotope_d13C long_name String Bulk Stable Isotope D13 C
attribute Bulk_stable_isotope_d13C units String per mil
variable Bulk_stable_isotope_d15N String
attribute Bulk_stable_isotope_d15N bcodmo_name String d15N
attribute Bulk_stable_isotope_d15N description String d15N concentration
attribute Bulk_stable_isotope_d15N long_name String Bulk Stable Isotope D15 N
attribute Bulk_stable_isotope_d15N units String per mil
variable elemental_composition_C String
attribute elemental_composition_C bcodmo_name String C
attribute elemental_composition_C description String Elemental composition of cell; percent carbon
attribute elemental_composition_C long_name String Elemental Composition C
attribute elemental_composition_C units String percent
variable elemental_composition_N String
attribute elemental_composition_N bcodmo_name String N
attribute elemental_composition_N description String Elemental composition of cell; percent Nitrogen
attribute elemental_composition_N long_name String Elemental Composition N
attribute elemental_composition_N units String percent
variable elemental_composition_C_N_atomic String
attribute elemental_composition_C_N_atomic bcodmo_name String C_to_N
attribute elemental_composition_C_N_atomic description String Elemental composition of cell; C:N atomic ratio
attribute elemental_composition_C_N_atomic long_name String Elemental Composition C N Atomic
attribute elemental_composition_C_N_atomic units String percent

 
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