ERDDAP > info > bcodmo_dataset_715903

Grid DAP Data	Sub- set	Table DAP Data	Make A Graph	W M S	Source Data Files	Acces- sible	Title	Sum- mary	ISO, Metadata	Back- ground Info	RSS	E mail	Institution	Dataset ID
		data			files	public	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.		I   M	background			BCO-DMO	bcodmo_dataset_715903

The Dataset's Variables and Attributes

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 The marine diatom Thalassiosira weiss\ufb02ogii Grunow (strain CCMP 1010) was cultured in sterile filtered natural North Sea water (Schleswig-Holstein, Germany) or Baltic Sea water (Schleswig-Holstein, Germany). The medium was enriched with f/4 concentrations of macro- and micronutrients (nitrate, phosphate, silicic acid, trace metal mixture, vitamin mixture (Guillard and Ryther, 1962). All experiments were performed in sterile 2.1 L Schott Duran glass bottles. These bottles were made of borosilicate glass (filters UV radiation <310 nm) except for the quartz glass bottles (pure silica without UV radiation filter) used in the UV experiment. The cultures were either incubated in climate chambers with 400 \u2013700 nm radiation or 10 cm below water level at low tide in Kiel Fjord in May 2011. Water temperature and light irradiance data were obtained from the weather station maintained by the GEOMAR institute in Kiel, Germany. Growth conditions for the various treatments, i.e. salinity, pH, temperature, and irradiance are given in Table 1. pH values (reported on free scale) were measured \u00a0with separate glass and reference electrodes (Metrohm) and calculated with equation 3 from DOE 2007 chapter 6b (Dickson et al., 2007) as described in (Bach et al., 2012). Cultures were inoculated with densities of 20 cells ml-1. \u00a0Cell densities and equivalent spherical diameters were determined with a Coulter Counter (Beckman Coulter) at the beginning and the end of the experiment, respectively. When incubations ended, cells were filtered on 47 mm diameter, 5 um mesh size Nucleopore Track-Etch Membrane filters (Whatman) and frozen at -18 deg C immediately after filtration. Sediment sampling Sediment samples were retrieved from a 14.97 m core, station M772-003-2, collected November 26, 2008 by the Meteor cruise M77 at 271 m water depth within the main upwelling area off Peru (15 deg 06.21\u00b4S, 75 deg 41.28\u00b4W). The Peruvian ocean margin is characterized by a high particle flux and a well-defined oxygen minimum zone. At the time of sampling, the O2 concentration at the seafloor was measured to 1.1 uM, the salinity to 34.9 psu and the temperature to 12.2 \u00a0deg C. Prior to analysis, sediment samples were pre-treated with an acid-alkali-acid cleaning with HCl and NaOH (Grootes et al., 2004).) \u00a0 \u00a0 \u00a0 \u00a0 Analyses Both diatom and sediment samples were freeze dried prior to isotopic analysis. To prepare aliquots for derivatization of amino acids, we used 3-4 mg of diatoms and 100-150 mg of sediments. The samples were transferred to Pyrex culture tubes (13 x 100 mm), flushed with N2 gas, sealed, and hydrolysed in 1 ml 6N HCl at 110 \u00a0deg C for 20 h. After hydrolysis, lipophilic compounds were removed by vortexing with 2 ml n-hexane/DCM (6:5, v/v) for 30 sec. The aqueous phase was subsequently transferred through disposable glass pipettes lined with glass wool into 4 ml dram vials. Samples were evaporated to dryness under a stream of N2 gas for 30 min at 110 deg C before being stored at 18 deg C until required for analysis. The derivatisation procedure was modified from Corr et al. (2007) as described by Larsen et al. (2013). In short, the dried samples were methylated with acidified methanol and subsequently acetylated with a mixture of acetic anhydride, triethylamine, and acetone, forming N-acetyl methyl ester derivatives. As a precautionary measure to reduce the oxidation of amino acids, we flushed and sealed reaction vials with N2 gas prior to methylation and acetylation. Another modification from Corr et al. (2007) was that icebaths were substituted with solid aluminum blocks at room temperature. We used known d13C values of pure amino acids prepared and analyzed under the same conditions as the samples to calculate correction factors specific to each amino acid to account for carbon addition and fractionation during derivatization. The derivatised AAs were dissolved in 250 ul ethyl acetate and stored at 18 deg C until required for analysis. Amino acid d13C values were obtained from Leibniz-Laboratory for Radiometric Dating and Stable Isotope Research in Kiel. We injected the AA derivatives into a PTV injector held at 250 deg C for 4 min. before GC separation on an Agilent 6890N GC. Diatom samples were separated on an Rtx-200 column (60m x 0.32mm x 0.25um, Fig. S1) and sediment samples on a Thermo Trace GOLD TG-200MS GC column (60m x 0.32mm x 0.25um). For both GC columns, the oven temperature of the GC was started at 50 deg C and heated at 15 deg C min-1 to 140 deg C, followed by 3 deg C min-1 to 152 deg C and held for 4 min, then 10 deg C min-1 to 245 deg C and held for 10 min, and finally 5 deg C min-1 to 290 deg C and held for 5 min. The GC was interfaced with a MAT 253 isotope ratio mass spectrometer (IRMS) via a GC-III combustion (C) interface (Thermo-Finnigan Corporation). We obtained consistently good chromatography for alanine (Ala), valine (Val), leucine (Leu), isoleucine (Ile), asparagine/aspartate (Asx), threonine (Thr), methionine (Met), glutamine/glutamate (Glx), phenylalanine (Phe), tyrosine (Tyr), lysine (Lys), and arginine (Arg) with the exception that Asx and Thr partially coeluted with the Rtx-200 column. Serine (Ser) and proline (Pro) coeluted on both columns. The average reproducibility for the norleucine internal standard was \u00b1 0.4\u2030 (n = 3 for each sample), and the reproducibility of amino acid standards ranged from \u00b1 0.1\u2030 for Phe to \u00b1 0.6\u2030 for Thr (n = 3). Amino acid composition of the diatom samples was determined with the derivative samples used for d13CAA analysis. The amino acids were separated on an Rxi-35SIL MS column (30m x 0.32mm x 0.25um) with an Agilent 6890 N GC with a flame ionization detector. With this column we obtained good chromatography for Ala, Asx, Glx, Gly, Ser, Tyr, Arg, Ile, Leu, Lys, Met, Phe, Thr, and Val. For quantification, we used internal references consisting of pure amino acids (Alfa Aesar, Karlsruhe, Germany). The composition of the amino acids are shown in Table 3 according to the following biosynthetic families: \u00a0Pyruvate (Ala, Leu, Val), Oxaloacetate (Asx, Ile, Lys, Met, Thr), \u03b1-ketoglutarate (Arg, Glx), 3-phosphoglycerate (Gly, Ser), and Shikimate (Phe, Tyr). Bulk 13C, %C, 15N and %N values of the diatom samples were determined at the UC Davis Stable Isotope Facility using a PDZ Europa ANCA-GSL elemental analyzer interfaced to a PDZ Europa 20-20 isotope ratio mass spectrometer (Sercon Ltd., Cheshire, UK). The dry weight of the samples ranged between 1.5 and 2.5 mg. During analysis, samples were interspersed with several replicates of at least three different laboratory standards. These laboratory standards, which were selected to be compositionally similar to the samples being analyzed, had previously calibrated against NIST Standard Reference Materials (IAEA-N1, IAEA-N2, IAEA-N3, USGS-40, and USGS-41). A sample\u2019s preliminary isotope ratio was measured relative to reference gases analyzed with each sample. These preliminary values were finalized by correcting the values for the entire batch based on the known values of the included laboratory standards. The long term standard deviation is 0.2\u2030 for 13C and 0.3\u2030 for 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
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 M. McCarthy, PI 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/
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
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/
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/
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/
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/
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/
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/
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
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/715903
attribute	NC_GLOBAL	param_mapping	String	{'715903': {}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/715903/parameters
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. Broader impacts: This 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, 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	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/
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

The information in the table above is also available in other file formats (.csv, .htmlTable, .itx, .json, .jsonlCSV1, .jsonlCSV, .jsonlKVP, .mat, .nc, .nccsv, .tsv, .xhtml) via a RESTful web service.