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Title Sum-
Institution Dataset ID
     data   graph     files  public Carbon near edge X-ray absorption fine structure (NEXAFS) spectra of standard compounds    ?     I   M   background (external link) RSS Subscribe 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.


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 (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 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/ (external link)
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 (external link)
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/ (external link)
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 (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/815362 (external link)
attribute NC_GLOBAL param_mapping String {'815362': {}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/815362/parameters (external link)
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/ (external link)
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/ (external link)
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 near edge X-ray absorption fine structure (NEXAFS) spectra of standard compounds
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.

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