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Title Sum-
Institution Dataset ID
     data   graph     files  public Carbon near edge X-ray absorption fine structure (NEXAFS) spectra from pelagic sediment from
the North Atlantic gyre, South Pacific gyre, and Peru Basin from cruises KN223 (R/V Knorr),
KNOX02RR (R/V Roger Revelle), and ODP leg 201 between 2002 and 2014
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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,.esriCsv,.geoJson
attribute NC_GLOBAL acquisition_description String See Estes el al. (2019) for complete methods.

Sediment slurries were generated by subsampling ~0.1 g of wet sediment from
samples stored at 4 \u00b0C into a sterile microcentrifuge tube. Then,
0.2\u20130.5 ml of 0.2 \u03bcm filtered 18 M\u03a9 water was added
and the sample shaken. Sediment slurry (1\u201310 \u03bcl) 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 bulk data
PI: Emily Estes
Data Version 1: 2020-07-22
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 2020-06-15T21:58:56Z
attribute NC_GLOBAL date_modified String 2020-07-23T15:27:52Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.26008/1912/bco-dmo.815380.1
attribute NC_GLOBAL Easternmost_Easting double -50.62
attribute NC_GLOBAL geospatial_lat_max double 45.96333
attribute NC_GLOBAL geospatial_lat_min double 12.01667
attribute NC_GLOBAL geospatial_lat_units String degrees_north
attribute NC_GLOBAL geospatial_lon_max double -50.62
attribute NC_GLOBAL geospatial_lon_min double -165.64333
attribute NC_GLOBAL geospatial_lon_units String degrees_east
attribute NC_GLOBAL geospatial_vertical_max double 5699.0
attribute NC_GLOBAL geospatial_vertical_min double 3705.0
attribute NC_GLOBAL geospatial_vertical_positive String down
attribute NC_GLOBAL geospatial_vertical_units String m
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/815380 (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 815390
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 absorption, bco, bco-dmo, biological, chemical, comment, core, core_depth, core_type, data, dataset, date, depth, dmo, erddap, expedition, latitude, longitude, management, oceanography, office, preliminary, sample, sample_comment, site, time, type, v, water, water_depth
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/815380/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/815380 (external link)
attribute NC_GLOBAL Northernmost_Northing double 45.96333
attribute NC_GLOBAL param_mapping String {'815380': {'latitude': 'master - latitude', 'water_depth': 'master - depth', 'longitude': 'master - longitude'}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/815380/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 Southernmost_Northing double 12.01667
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 from pelagic sediment from the North Atlantic gyre, South Pacific gyre, and Peru Basin from cruises KN223 (R/V Knorr), KNOX02RR (R/V Roger Revelle), and ODP leg 201 between 2002 and 2014.
attribute NC_GLOBAL title String Carbon near edge X-ray absorption fine structure (NEXAFS) spectra from pelagic sediment from the North Atlantic gyre, South Pacific gyre, and Peru Basin from cruises KN223 (R/V Knorr), KNOX02RR (R/V Roger Revelle), and ODP leg 201 between 2002 and 2014
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL Westernmost_Easting double -165.64333
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.5
variable location   String  
attribute location bcodmo_name String site
attribute location description String Sample origin
attribute location long_name String Location
attribute location units String unitless
variable expedition   String  
attribute expedition bcodmo_name String cruise_id
attribute expedition description String Cruise name
attribute expedition long_name String Expedition
attribute expedition units String unitless
variable date   String  
attribute date bcodmo_name String date
attribute date description String date sample collection 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/ (external link)
attribute date source_name String date
attribute date time_precision String 1970-01-01
attribute date units String unitless
variable latitude   double  
attribute latitude _CoordinateAxisType String Lat
attribute latitude _FillValue double NaN
attribute latitude actual_range double 12.01667, 45.96333
attribute latitude axis String Y
attribute latitude bcodmo_name String latitude
attribute latitude colorBarMaximum double 90.0
attribute latitude colorBarMinimum double -90.0
attribute latitude description String Latitude
attribute latitude ioos_category String Location
attribute latitude long_name String Latitude
attribute latitude nerc_identifier String https://vocab.nerc.ac.uk/collection/P09/current/LATX/ (external link)
attribute latitude standard_name String latitude
attribute latitude units String degrees_north
variable longitude   double  
attribute longitude _CoordinateAxisType String Lon
attribute longitude _FillValue double NaN
attribute longitude actual_range double -165.64333, -50.62
attribute longitude axis String X
attribute longitude bcodmo_name String longitude
attribute longitude colorBarMaximum double 180.0
attribute longitude colorBarMinimum double -180.0
attribute longitude description String Longitude
attribute longitude ioos_category String Location
attribute longitude long_name String Longitude
attribute longitude nerc_identifier String https://vocab.nerc.ac.uk/collection/P09/current/LONX/ (external link)
attribute longitude standard_name String longitude
attribute longitude units String degrees_east
variable depth   double  
attribute depth _CoordinateAxisType String Height
attribute depth _CoordinateZisPositive String down
attribute depth _FillValue double NaN
attribute depth actual_range double 3705.0, 5699.0
attribute depth axis String Z
attribute depth bcodmo_name String depth
attribute depth description String Water depth
attribute depth ioos_category String Location
attribute depth long_name String Water Depth
attribute depth nerc_identifier String https://vocab.nerc.ac.uk/collection/P09/current/DEPH/ (external link)
attribute depth positive String down
attribute depth standard_name String depth
attribute depth units String m
variable core_type   String  
attribute core_type bcodmo_name String sample_type
attribute core_type description String Coring device used
attribute core_type long_name String Core Type
attribute core_type units String unitless
variable core_depth   float  
attribute core_depth _FillValue float NaN
attribute core_depth actual_range float 0.0125, 112.65
attribute core_depth bcodmo_name String meters below seafloor
attribute core_depth description String Sample depth (meters below seafloor)
attribute core_depth long_name String Core Depth
attribute core_depth units String meters (m)
variable site   String  
attribute site bcodmo_name String site
attribute site description String Site number
attribute site long_name String Site
attribute site units String unitless
variable sample_comment   String  
attribute sample_comment bcodmo_name String comment
attribute sample_comment description String Comment about sample
attribute sample_comment long_name String Sample Comment
variable absorption   float  
attribute absorption _FillValue float NaN
attribute absorption actual_range float -1.28061, 13.96284
attribute absorption bcodmo_name String absorbance
attribute absorption description String absorption. arbitrary units (normalized)
attribute absorption long_name String Absorption
attribute absorption units String unitless
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 electron volts (incident energy)
attribute eV long_name String E V
attribute eV units String electron volts (eV)

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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