ERDDAP > info > bcodmo_dataset_816576

Grid DAP Data	Sub- set	Table DAP Data	Make A Graph	W M S	Source Data Files	Acces- sible	Title	Sum- mary	FGDC, ISO, Metadata	Back- ground Info	RSS	E mail	Institution	Dataset ID
		data	graph		files	public	[TP sediments with pretreatment] - Total phosphorus concentrations in NMR sediment pretreatment extracts from samples collected during R/V JOIDES Resolution cruise JRES- 336 (IODP336, North Pond) to the western flank of the mid-Atlantic Ridge in November of 2011 (Potential phosphorus uptake mechanisms of the deep sedimentary biosphere)		I   M	background			BCO-DMO	bcodmo_dataset_816576

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	Location:\u00a0North Atlantic, western flank of the mid-Atlantic Ridge\u00a022.75589 N 46.08125 W Methodology: Prior to the extraction, we freeze-dried, ground and sieved sediment samples to less than 125 \u03bcm (Ruttenberg 1992). For a given sample, we weighed four sample replicates (2 g) and placed each in 250 mL HDPE bottles. Sodium dithionite (F.W. 147.12 g/mol; 7.4 g) was added to each sample split, followed by 200 mL of citrate-bicarbonate solution (pH 7.6). This step produces effervescence, so the solution should be added slowly to the sample. We shook samples for 8 h and then centrifuged them at 3,700 rpm for 15 min. We filtered the supernatants with a 0.4 \u03bcm polycarbonate filter. We took 20 mL aliquots from the filtrate for each sample split for MRP and total P analyses, and kept them refrigerated until analysis within 24 h. We added 200 mL of ultrapure water to the solid residue for each sample split as a wash step after the above reductive step, shook samples for 2 h, and then centrifuged them at 3,700 rpm for 15 min. We filtered the supernatants with 0.4 \u03bcm polycarbonate filters and set aside 20 mL of filtrate from each sample split for MRP and total P analyses. We then extracted the solid sample residues in 200 mL of sodium acetate buffer (pH 4.0) for 6 h. At the end of this extraction step, we centrifuged the bottles at 3,700 rpm for 15 min, filtered the supernatants with 0.4 \u03bcm polycarbonate filters and took a 20 mL aliquot of filtrate from each sample split for MRP and total P analyses. We added 200 mL of ultrapure water to the solid residue for each sample split as a wash step, shook samples for 2 h, and then centrifuged them at 3,700 rpm for 15 min.\u00a0 We filtered the supernatants with 0.4 \u03bcm polycarbonate filters and set aside 20 mL of filtrate from each sample split for MRP and total P analyses. We repeated the water rinse step, and collected aliquots for MRP and total P analyses as in the previous steps. The concentrations of\u00a0 TP were determined as described below. Solid sediment sample residues following the pretreatment described above were transferred to two 50 mL centrifuge tubes (2 sample replicates combined per tube). We added 20 mL of 0.25 M NaOH + 0.05 M Na2EDTA solution to each tube, vortexed until all sediment was resuspended and then shook samples for 6 h at room temperature (Cade-Menun et al. 2005). We used a solid to solution ratio of 1:5 for this step to minimize the amount of freeze-dried material that will need to be dissolved for the 31P NMR experiments. Large amounts of salts from the NaOH-EDTA concentrated in NMR samples lead to higher viscosity and increase line broadening on NMR spectra (Cade-Menun and Liu 2014). We chose an extraction time of 6 h to improve total P recovery while limiting the degradation of natural P compounds in the sample. At the end of the extraction, samples were centrifuged at 3,700 rpm for 15 min and supernatants decanted into 50 mL centrifuge tubes. We collected a 500 \u03bcL aliquot from each sample, which we diluted with 4.5 mL of ultrapure water. These were refrigerated until analysis for total P content on the ICP-OES. The sample residues and supernatants were frozen on a slant to maximize the exposed surface area during the lyophilization step; this was done immediately after the removal of the 500 \u03bcL aliquot. Once completely frozen, the uncapped tubes containing supernatants and residues were freeze-dried over the course of 48 h. Each tube was covered with parafilm with small holes from a tack to minimize contamination. Freeze-dried supernatants from identical sample splits were combined and dissolved in 500 \u03bcL each of ultrapure water, D2O, NaOH- EDTA and 10 M NaOH prior to 31P NMR analysis.\u00a0 The D2O is required as signal lock in the spectrometer (Cade-Menun and Liu 2014). Sample pH was maintained at a pH > 12 to optimize peak separation (Cade-Menun 2005; Cade- Menun and Liu 2014). Sample pH was assessed with a glass electrode, and verified with pH paper to account for the alkaline error caused by the high salt content of our samples (Covington 1985). Freeze-dried sample residues were ashed in crucibles at 550oC for 2 h and then extracted in 25 mL of 0.5 M sulfuric acid for 16 h (Olsen and Sommers 1982; Cade-Menun and Lavkulich 1997). We centrifuged samples at 3,700 rpm for 15 min, filtered supernatants with 0.4 \u03bcm polycarbonate filters, and measured P content on an ICP-OES.\u00a0 Total P concentrations in sediment extracts were measured using inductively coupled plasma optical emission spectroscopy (ICP-OES). Standards were prepared with the same solutions as those used for the extraction procedure in order to minimize matrix effects on P measurements. Sediment extracts and standards (0 \u03bcM, 3.2 \u03bcM, 32 \u03bcM and 320 \u03bcM) were diluted to lower salt content to prevent salt buildup on the nebulizer (1:20 dilution for step 1, 1:10 for steps 2 \u2013 4). Concentration data from both wavelengths (213 nm and 214 nm) were averaged to obtain extract concentrations for each sample. The detection limit for P on this instrument for both wavelengths is 0.4 \u03bcM. The MRP concentrations were measured on a QuikChem 8000 automated ion analyzer. Standards were prepared with the same solutions used for the extraction step to minimize matrix effects on P measurements. Sediment extracts and standards (0 \u2013 30 \u03bcM PO4) were diluted ten-fold to prevent matrix interference with color development. The detection limit for P on this instrument is 0.2 \u03bcM. We derived MUP concentrations by subtracting MRP from total P concentrations.
attribute	NC_GLOBAL	awards_0_award_nid	String	554980
attribute	NC_GLOBAL	awards_0_award_number	String	OCE-0939564
attribute	NC_GLOBAL	awards_0_data_url	String	http://www.nsf.gov/awardsearch/showAward?AWD_ID=0939564
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	David L. Garrison
attribute	NC_GLOBAL	awards_0_program_manager_nid	String	50534
attribute	NC_GLOBAL	cdm_data_type	String	Other
attribute	NC_GLOBAL	comment	String	Iodp336-tp-sed-pre PI: Adina Paytan Data Version 1: 2020-06-23
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	dataset_current_state	String	Final and no updates
attribute	NC_GLOBAL	date_created	String	2020-06-23T18:47:07Z
attribute	NC_GLOBAL	date_modified	String	2020-06-30T18:11:16Z
attribute	NC_GLOBAL	defaultDataQuery	String	&time<now
attribute	NC_GLOBAL	doi	String	10.26008/1912/bco-dmo.816576.1
attribute	NC_GLOBAL	infoUrl	String	https://www.bco-dmo.org/dataset/816576
attribute	NC_GLOBAL	institution	String	BCO-DMO
attribute	NC_GLOBAL	instruments_0_acronym	String	ICP-OES
attribute	NC_GLOBAL	instruments_0_dataset_instrument_nid	String	816583
attribute	NC_GLOBAL	instruments_0_description	String	Also referred to as an Inductively coupled plasma atomic emission spectroscope (ICP-AES). These instruments pass nebulised samples into an inductively-coupled gas plasma (8-10000 K) where they are atomised and excited. The de-excitation optical emissions at characteristic wavelengths are spectroscopically analysed. It is often used in the detection of trace metals.
attribute	NC_GLOBAL	instruments_0_instrument_name	String	Inductively Coupled Plasma Optical Emission Spectrometer
attribute	NC_GLOBAL	instruments_0_instrument_nid	String	639924
attribute	NC_GLOBAL	instruments_0_supplied_name	String	ICP-OES
attribute	NC_GLOBAL	keywords	String	analyte, Analyte_Name, bco, bco-dmo, biological, calib, chemical, conc, Conc_Calib, corr, data, dataset, date, dilution, dmo, erddap, extract, int, Int_Corr, management, name, oceanography, office, preliminary, rsd, RSD_Corr_Int, sample, Sample_ID, step, time
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/816576/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/816576
attribute	NC_GLOBAL	param_mapping	String	{'816576': {}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/816576/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	Adina Paytan
attribute	NC_GLOBAL	people_0_person_nid	String	50821
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	University of California-Santa Cruz
attribute	NC_GLOBAL	people_1_affiliation_acronym	String	UC Santa Cruz
attribute	NC_GLOBAL	people_1_person_name	String	Dr Delphine Defforey
attribute	NC_GLOBAL	people_1_person_nid	String	664058
attribute	NC_GLOBAL	people_1_role	String	Co-Principal Investigator
attribute	NC_GLOBAL	people_1_role_type	String	originator
attribute	NC_GLOBAL	people_2_affiliation	String	Woods Hole Oceanographic Institution
attribute	NC_GLOBAL	people_2_affiliation_acronym	String	WHOI BCO-DMO
attribute	NC_GLOBAL	people_2_person_name	String	Amber D. York
attribute	NC_GLOBAL	people_2_person_nid	String	643627
attribute	NC_GLOBAL	people_2_role	String	BCO-DMO Data Manager
attribute	NC_GLOBAL	people_2_role_type	String	related
attribute	NC_GLOBAL	project	String	Deep sea sediments
attribute	NC_GLOBAL	projects_0_acronym	String	Deep sea sediments
attribute	NC_GLOBAL	projects_0_description	String	The goal of this project is to explore potential microbial P uptake mechanisms in marine sediments beneath the North Atlantic Gyre and their effects on the relative distribution of organic P compounds as a function of burial depth and changing redox conditions. We use a combination of metagenomic analyses and solution 31P nuclear magnetic resonance spectroscopy (31P NMR) to investigate (1) the presence of microbial functional genes pertaining to P uptake and metabolism and (2) the possible P substrates for the deep biosphere in these oligotrophic sediments. NSF C-DEBI Award #156246 to Dr. Adina Paytan NSF C-DEBI Award #157598 to Dr. Delphine Defforey
attribute	NC_GLOBAL	projects_0_end_date	String	2015-04
attribute	NC_GLOBAL	projects_0_geolocation	String	Mid-Atlantic Ridge flank
attribute	NC_GLOBAL	projects_0_name	String	Potential phosphorus uptake mechanisms of the deep sedimentary biosphere
attribute	NC_GLOBAL	projects_0_project_nid	String	664073
attribute	NC_GLOBAL	projects_0_start_date	String	2015-03
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	Total phosphorus concentrations in nuclear magnetic resonance (NMR) sediment pretreatment extracts from samples collected during R/V JOIDES Resolution cruise JRES-336 (IODP336, North Pond) to the western flank of the mid-Atlantic Ridge in November of 2011. Samples were analyzed in 2016.
attribute	NC_GLOBAL	title	String	[TP sediments with pretreatment] - Total phosphorus concentrations in NMR sediment pretreatment extracts from samples collected during R/V JOIDES Resolution cruise JRES-336 (IODP336, North Pond) to the western flank of the mid-Atlantic Ridge in November of 2011 (Potential phosphorus uptake mechanisms of the deep sedimentary biosphere)
attribute	NC_GLOBAL	version	String	1
attribute	NC_GLOBAL	xml_source	String	osprey2erddap.update_xml() v1.5
variable	Extract		String
attribute	Extract	bcodmo_name	String	sample_descrip
attribute	Extract	description	String	Extract solution
attribute	Extract	long_name	String	Extract
attribute	Extract	units	String	unitless
variable	Step		String
attribute	Step	bcodmo_name	String	sample_descrip
attribute	Step	description	String	Step in the sequential extraction scheme (1-4)
attribute	Step	long_name	String	Step
attribute	Step	units	String	unitless
variable	Dilution		String
attribute	Dilution	bcodmo_name	String	sample_descrip
attribute	Dilution	description	String	Sample dilution
attribute	Dilution	long_name	String	Dilution
attribute	Dilution	units	String	unitless
variable	Sample_ID		String
attribute	Sample_ID	bcodmo_name	String	sample
attribute	Sample_ID	description	String	Sample ID, unique sample identifier
attribute	Sample_ID	long_name	String	Sample ID
attribute	Sample_ID	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P02/current/ACYC/
attribute	Sample_ID	units	String	unitless
variable	Date		String
attribute	Date	bcodmo_name	String	date
attribute	Date	description	String	Date the samples were analyzed in ISO 8601 format yyyy-mm-dd
attribute	Date	long_name	String	Date
attribute	Date	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/
attribute	Date	source_name	String	Date
attribute	Date	time_precision	String	1970-01-01
attribute	Date	units	String	nd
variable	Analyte_Name		String
attribute	Analyte_Name	bcodmo_name	String	sample_descrip
attribute	Analyte_Name	description	String	Element analyzed
attribute	Analyte_Name	long_name	String	Analyte Name
attribute	Analyte_Name	units	String	unitless
variable	Int_Corr		double
attribute	Int_Corr	_FillValue	double	NaN
attribute	Int_Corr	actual_range	double	-8736.84, 3.163645165E7
attribute	Int_Corr	bcodmo_name	String	unknown
attribute	Int_Corr	description	String	Intensity (corrected)
attribute	Int_Corr	long_name	String	Int Corr
attribute	Int_Corr	units	String	unitless
variable	RSD_Corr_Int		float
attribute	RSD_Corr_Int	_FillValue	float	NaN
attribute	RSD_Corr_Int	actual_range	float	0.14, 1383.25
attribute	RSD_Corr_Int	bcodmo_name	String	unknown
attribute	RSD_Corr_Int	description	String	Relative standard deviation (RSD) of corrected intensity
attribute	RSD_Corr_Int	long_name	String	RSD Corr Int
attribute	RSD_Corr_Int	units	String	unitless
variable	Conc_Calib		float
attribute	Conc_Calib	_FillValue	float	NaN
attribute	Conc_Calib	actual_range	float	-0.2, 122.54
attribute	Conc_Calib	bcodmo_name	String	P
attribute	Conc_Calib	description	String	Calibrated concentration of total phosphorous
attribute	Conc_Calib	long_name	String	Conc Calib
attribute	Conc_Calib	units	String	parts per million (ppm)

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.