Created June 15, 2020
Modified July 16, 2020
State Data not available yet

Processing Description

Spectral processing was completed by subtracting a line fit to the pre-edge region (281–283 eV), followed by an area normalization between 282 and 310 eV with the high-energy intensity kept constant (atomic normalization). The entire pre-edge region appeared linear; fitting and background subtraction was conducted over a smaller energy range due to the presence of oxygen harmonic peaks. All the data normalization was conducted in Igor Pro (WaveMetrics).

BCO-DMO Data Manager Processing Notes:
* exported data in xlsx file “Estes_NEXAFSstds_data.xlsx” to csv file
* original data had 10 header rows with sample, and cruise information e.g. cruise_id, date, latitude, sample_depth, etc.  The data were unpivoted so these values became new columns in the dataset.
* added a conventional header with dataset name, PI name, version date
* modified parameter names to conform with BCO-DMO naming conventions
* blank values in this dataset are displayed as “nd” for “no data.”  nd is the default missing data identifier in the BCO-DMO system.
* latitude and longitude in degrees decimal minutes converted to decimal degrees then rounded to 5 decimal places.
* date format converted to ISO 8601 format yyyy-mm-dd


Instance Description

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.

A spectrometer is an optical instrument used to measure properties of light over a specific portion of the electromagnetic spectrum.


location [site]
Sample origin
Sampling site identification.
date [date]
date sample collection in ISO 8601 format yyyy-mm-dd

date; generally reported in GMT as YYYYMMDD (year; month; day); also as MMDD (month; day); EqPac dates are local Hawaii time. ISO_Date format is YYYY-MM-DD (http://www.iso.org/iso/home/standards/iso8601.htm)

expedition [cruise_id]
Cruise name
cruise designation; name
site [site]
Site number
Sampling site identification.
latitude [latitude]

latitude, in decimal degrees, North is positive, negative denotes South; Reported in some datasets as degrees, minutes

longitude [longitude]

longitude, in decimal degrees, East is positive, negative denotes West; Reported in some datsets as degrees, minutes

water_depth [depth]
Water depth

Observation/sample depth below the sea surface. Units often reported as: meters, feet.

When used in a JGOFS/GLOBEC dataset the depth is a best estimate; usually but not always calculated from pressure; calculated either from CTD pressure using Fofonoff and Millard (1982; UNESCO Tech Paper #44) algorithm adjusted for 1980 equation of state for seawater (EOS80) or simply equivalent to nominal depth as recorded during sampling if CTD pressure was unavailable.

core_type [sample_type]
Coring device used
text description of type of sample collected (rock, bio, fluid, etc)
Sample depth (meters below seafloor)

Meters below seafloor (mbsf); convention used for depths below the seabed in geology, oceanography, petrology and ocean drilling; often used in reporting measurements made from sediment cores.

eV [eV]

electron volts (incident energy)

The amount of energy gained or lost by the charge of a single electron moving across an electric potential difference of one volt. One electronvolt equal to 1.602*10−19 joules.

absorption [absorbance]
absorption. arbitrary units (normalized)

The fraction of radiant flux absorbed (at a specific wavelength).

Dataset Maintainers

Emily R. EstesTexas A&M University (TAMU)
Colleen M. HanselWoods Hole Oceanographic Institution (WHOI)
Amber YorkWoods Hole Oceanographic Institution (WHOI BCO-DMO)

BCO-DMO Project Info

Project Title Elucidating the extent and composition of mineral-hosted carbon in the deep biosphere
Acronym Org C Sed I
Created October 16, 2019
Modified October 16, 2019
Project Description

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.

Data Project Maintainers
Colleen M. HanselWoods Hole Oceanographic Institution (WHOI)Principal Investigator
Gariela FarfanWoods Hole Oceanographic Institution (WHOI)Co-Principal Investigator
Emily R. EstesWoods Hole Oceanographic Institution (WHOI)Co-Principal Investigator

BCO-DMO Project Info

Project Title Geochemical controls on organic carbon quantity and quality in the deep subsurface
Acronym Org C Sed II
Created October 15, 2019
Modified October 16, 2019
Project Description

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.

Data Project Maintainers
Emily R. EstesWoods Hole Oceanographic Institution (WHOI)Principal Investigator