ERDDAP > info > bcodmo_dataset_815362

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	[Carbon NEXAFS standards] - Carbon near edge X-ray absorption fine structure (NEXAFS) spectra of standard compounds (Geochemical controls on organic carbon quantity and quality in the deep subsurface)		I   M	background			BCO-DMO	bcodmo_dataset_815362

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	See Estes el al. (2019) for complete methods. 1\u201310 \u03bcL of standard compounds was pipetted onto silicon wafers and air-dried. The beamline was operated with a 500 l mm\u20131 spherical grating monochromator and entrance and exit slits set to 40 \u03bcm, which yielded an absolute energy resolution of less than 0.3 eV. The samples were attached to an aluminium sample stick in a single load and analysed under ultrahigh vacuum conditions (pressure ~10\u22129 mbar). The measurements were made in the total electron yield (TEY) mode on a spot size of less than 1 mm2 using a grazing incidence angle of 45\u00b0, where previous trials determined that the incidence angle did not yield a difference in results. The TEY mode was selected instead of fluorescence as we observed dampening of the fluorescence signal, probably due to matrix- induced absorption. Spectra were collected around the C 1s edge, from 260 to 340 eV, with a dwell time of 0.2 s. To avoid beam damage and variation of the background due to charging, scans were taken at different positions on the sample. The spectra analysed were the average of 2\u20133 scans taken at different positions on the sample. The dark current was measured prior to the collection of each spectrum and subtracted from the raw data. Spectra were then normalized to no load current measured by a mesh upstream of the chamber with freshly evaporated gold. Instruments: Bulk carbon NEXAFS spectroscopy was conducted on beamlines 8-2 and 10-1 at the Stanford Synchrotron Radiation Lightsource. The absolute energy calibration of the carbon spectra was achieved by shifting the energy such that the first dip in the incoming intensity due to carbon contamination on the beamline optics (carbon dip) occurred at 284.7 eV.
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	Carbon NEXAFS standards PI: Emily Estes Data Version 1: 2020-06-15
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	2020-06-15T21:07:20Z
attribute	NC_GLOBAL	date_modified	String	2020-07-23T15:20:37Z
attribute	NC_GLOBAL	defaultDataQuery	String	&time<now
attribute	NC_GLOBAL	doi	String	10.26008/1912/bco-dmo.815362.1
attribute	NC_GLOBAL	infoUrl	String	https://www.bco-dmo.org/dataset/815362
attribute	NC_GLOBAL	institution	String	BCO-DMO
attribute	NC_GLOBAL	instruments_0_acronym	String	Spectrometer
attribute	NC_GLOBAL	instruments_0_dataset_instrument_description	String	Bulk carbon synchrotron-based near edge x-ray fine structure (NEXAFS) spectroscopy was conducted on beamlines 8-2 and 10-1 at the Stanford Synchrotron Radiation Lightsource.
attribute	NC_GLOBAL	instruments_0_dataset_instrument_nid	String	815379
attribute	NC_GLOBAL	instruments_0_description	String	A spectrometer is an optical instrument used to measure properties of light over a specific portion of the electromagnetic spectrum.
attribute	NC_GLOBAL	instruments_0_instrument_external_identifier	String	https://vocab.nerc.ac.uk/collection/L22/current/TOOL0460/
attribute	NC_GLOBAL	instruments_0_instrument_name	String	Spectrometer
attribute	NC_GLOBAL	instruments_0_instrument_nid	String	667
attribute	NC_GLOBAL	keywords	String	acid, agarose, alginate, bco, bco-dmo, biological, bsa, chemical, data, dataset, dmo, erddap, hmwdom, humic, humic_acid, leucine, lipo, management, oceanography, office, phenylalanin, phospholipid, preliminary, v
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/815362/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/815362
attribute	NC_GLOBAL	param_mapping	String	{'815362': {}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/815362/parameters
attribute	NC_GLOBAL	people_0_affiliation	String	Texas A&M University
attribute	NC_GLOBAL	people_0_affiliation_acronym	String	TAMU
attribute	NC_GLOBAL	people_0_person_name	String	Emily Estes
attribute	NC_GLOBAL	people_0_person_nid	String	779219
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
attribute	NC_GLOBAL	people_1_person_name	String	Colleen Hansel
attribute	NC_GLOBAL	people_1_person_nid	String	756932
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	Org C Sed II,Org C Sed I
attribute	NC_GLOBAL	projects_0_acronym	String	Org C Sed II
attribute	NC_GLOBAL	projects_0_description	String	Abstract from the C-DEBI project page: Sediment underlying ocean gyres receives minimal input of fresh organic matter yet sustains a small but active heterotrophic microbial community. The concentration and composition of the organic carbon (OC) available to this deep biosphere however is unknown. We analyzed the content and composition of OC in pelagic sediment in order to identify mechanism(s) that dictate the balance between OC preservation and utilization by microorganisms. Sediment cores from the North Atlantic gyre (KN223), South Pacific Gyre (Knox02-RR), and Peru Basin (IODP site 1231) allowed for a global comparison and a test of how sediment lithology and redox state affect OC preservation. OC was present in low concentrations in all samples (0.01—0.61%), at depths up to 112 meters below seafloor and estimated sediment ages of up to 50 million years. Synchrotron-based near edge X-ray absorption fine structure (NEXAFS) spectroscopy was conducted on over 100 samples, one of the first applications of NEXAFS to sedimentary environments. NEXAFS revealed an OC reservoir dominated by amide and carboxylic functionalities in a scaffolding of O-alkyl and aliphatic carbons. Detection of extractable, extracellular proteins supports this composition and suggests that sedimentary OC is protein-derived. This composition was common across all sites and depths, implicating physical rather than chemical mechanisms in OC preservation on long timescales. This study thereby points to physical access rather than energy or metabolic potential as a key constraint on subsurface heterotrophic life.
attribute	NC_GLOBAL	projects_0_end_date	String	2017-07
attribute	NC_GLOBAL	projects_0_geolocation	String	North Atlantic gyre, South Pacific gyre
attribute	NC_GLOBAL	projects_0_name	String	Geochemical controls on organic carbon quantity and quality in the deep subsurface
attribute	NC_GLOBAL	projects_0_project_nid	String	779216
attribute	NC_GLOBAL	projects_0_project_website	String	https://www.darkenergybiosphere.org/award/3d-spatial-mapping-of-the-energetic-return-of-1000-metabolisms-within-the-compositional-variation-of-oceanic-crusts-near-mid-ocean-ridges/
attribute	NC_GLOBAL	projects_0_start_date	String	2016-06
attribute	NC_GLOBAL	projects_1_acronym	String	Org C Sed I
attribute	NC_GLOBAL	projects_1_description	String	Abstract from the C-DEBI project page: Minerals have recently been identified as a primary host for organic carbon (OC) within marine sediments. This strong physical and chemical carbon-mineral association is believed to reduce, and in some cases completely eliminate, the bioavailablilty of this carbon for microbial life. The paucity of information regarding the nature of this carbon-mineral association and the composition of the hosted carbon, however, precludes our ability to predict the ultimate fate of this OC and its involvement in deep subsurface life. Here, we addressed this knowledge gap by using a suite of bulk and spatially-resolved geochemical and mineralogical techniques to characterize OC-mineral associations within the deep subsurface. We characterized sediment samples collected on the 2014 North Atlantic long coring expedition (KN223) in the western subtropical North Atlantic that included three geochemically distinct long cores to a depth of 24-30 m and spanned OC-limited oxic to anoxic sediments. We find measurable and relevant OC concentrations throughout the sediment cores, that decreases linearly over ~25 meters burial depth, from ~0.15 to 0.075 mol OC/kg solid. OC within the sediments is compositionally complex on both a macro- and micro-scale, spanning a gradient of lability even at depth. Proteins are observed throughout the sediment depth profiles, where they appear to constitute a substantial fraction of the TOC. Correspondingly, a low C:N ratio is observed, consistent with proteinaceous carbon within the sediments. In sum, these findings point to a substantial mineral-hosted OC reservoir within the deep subsurface that may fuel the deep biosphere and select for protein-based heterotrophy.
attribute	NC_GLOBAL	projects_1_end_date	String	2016-03
attribute	NC_GLOBAL	projects_1_geolocation	String	North Atlantic gyre, South Pacific gyre
attribute	NC_GLOBAL	projects_1_name	String	Elucidating the extent and composition of mineral-hosted carbon in the deep biosphere
attribute	NC_GLOBAL	projects_1_project_nid	String	779223
attribute	NC_GLOBAL	projects_1_project_website	String	https://www.darkenergybiosphere.org/award/elucidating-the-extent-and-composition-of-mineral-hosted-carbon-in-the-deep-biosphere/
attribute	NC_GLOBAL	projects_1_start_date	String	2015-04
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	Carbon near edge X-ray absorption fine structure (NEXAFS) spectra of standard compounds. These data contain incident energy and absorption values at that energy for a standard compounds.
attribute	NC_GLOBAL	title	String	[Carbon NEXAFS standards] - Carbon near edge X-ray absorption fine structure (NEXAFS) spectra of standard compounds (Geochemical controls on organic carbon quantity and quality in the deep subsurface)
attribute	NC_GLOBAL	version	String	1
attribute	NC_GLOBAL	xml_source	String	osprey2erddap.update_xml() v1.5
variable	eV		double
attribute	eV	_FillValue	double	NaN
attribute	eV	actual_range	double	280.0, 320.0
attribute	eV	bcodmo_name	String	eV
attribute	eV	description	String	incident energy
attribute	eV	long_name	String	E V
attribute	eV	units	String	electron volts (eV)
variable	BSA		double
attribute	BSA	_FillValue	double	NaN
attribute	BSA	actual_range	double	-0.00797300853694, 0.45672515810322
attribute	BSA	bcodmo_name	String	absorbance
attribute	BSA	description	String	absorption values for protein (bovine serum albumin (BSA)). arbitrary units (normalized)
attribute	BSA	long_name	String	BSA
attribute	BSA	units	String	unitless
variable	phenylalanin		double
attribute	phenylalanin	_FillValue	double	NaN
attribute	phenylalanin	actual_range	double	-0.00189616148905, 0.63686872685069
attribute	phenylalanin	bcodmo_name	String	absorbance
attribute	phenylalanin	description	String	absorption values of phenylalanin. arbitrary units (normalized)
attribute	phenylalanin	long_name	String	Phenylalanin
attribute	phenylalanin	units	String	unitless
variable	leucine		double
attribute	leucine	_FillValue	double	NaN
attribute	leucine	actual_range	double	-0.00150841788173, 1.79254321817363
attribute	leucine	bcodmo_name	String	absorbance
attribute	leucine	description	String	absorption values of leucine. arbitrary units (normalized)
attribute	leucine	long_name	String	Leucine
attribute	leucine	units	String	unitless
variable	agarose		double
attribute	agarose	_FillValue	double	NaN
attribute	agarose	actual_range	double	-0.00489097551973, 0.46939224944519
attribute	agarose	bcodmo_name	String	absorbance
attribute	agarose	description	String	absorption values of agarose. arbitrary units (normalized)
attribute	agarose	long_name	String	Agarose
attribute	agarose	units	String	unitless
variable	alginate		double
attribute	alginate	_FillValue	double	NaN
attribute	alginate	actual_range	double	-0.00417239166851, 0.90592744921794
attribute	alginate	bcodmo_name	String	absorbance
attribute	alginate	description	String	absorption values of alginate. arbitrary units (normalized)
attribute	alginate	long_name	String	Alginate
attribute	alginate	units	String	unitless
variable	lipo		double
attribute	lipo	_FillValue	double	NaN
attribute	lipo	actual_range	double	-0.00163233708639, 0.56126001867199
attribute	lipo	bcodmo_name	String	absorbance
attribute	lipo	description	String	absorption values of lipo. arbitrary units (normalized)
attribute	lipo	long_name	String	Lipo
attribute	lipo	units	String	unitless
variable	phospholipid		double
attribute	phospholipid	_FillValue	double	NaN
attribute	phospholipid	actual_range	double	-7.6736447302E-4, 1.78986871519392
attribute	phospholipid	bcodmo_name	String	absorbance
attribute	phospholipid	description	String	absorption values of phospholipid. arbitrary units (normalized)
attribute	phospholipid	long_name	String	Phospholipid
attribute	phospholipid	units	String	unitless
variable	HMWDOM		double
attribute	HMWDOM	_FillValue	double	NaN
attribute	HMWDOM	actual_range	double	-0.00565777265214, 1.76599418481696
attribute	HMWDOM	bcodmo_name	String	absorbance
attribute	HMWDOM	description	String	absorption values of high molecular weight dissolved organic matter (HMWDOM). arbitrary units (normalized)
attribute	HMWDOM	long_name	String	HMWDOM
attribute	HMWDOM	units	String	unitless
variable	humic_acid		double
attribute	humic_acid	_FillValue	double	NaN
attribute	humic_acid	actual_range	double	-0.00271618200714, 1.63426099814073
attribute	humic_acid	bcodmo_name	String	absorbance
attribute	humic_acid	description	String	absorption values of humic acid. arbitrary units (normalized)
attribute	humic_acid	long_name	String	Humic Acid
attribute	humic_acid	units	String	unitless

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.