Download URLhttps://www.bco-dmo.org/dataset/815380/data/download
Media Type text/tab-separated-values
Created June 15, 2020
Modified July 23, 2020
State Final no updates expected

Acquisition Description

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 °C into a sterile microcentrifuge tube. Then, 0.2–0.5 ml of 0.2 μm filtered 18 MΩ water was added
and the sample shaken. Sediment slurry (1–10 μl) was pipetted onto silicon wafers and air-dried. The beamline was operated with a 500 l mm–1 spherical grating monochromator and entrance and exit slits set to 40 μm, 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 ~10−9 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°, 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 2–3 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.

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_bulkNEXAFSspectra_data.xlsx” to csv file “Estes_bulkNEXAFSspectra_data.csv” which is available to download in the “Data Files” section of this page.  The following changes were made after discussion with the original submitter.
* 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
* added sample_comment column to capture the difference between the two columns with header information “South Pacific;Knox02-RR;11-Jan-07;9;38° 03.7′ S;133° 05.5′ W;4924;piston;5.125” in the original file (columns CE and CF in original data).
* data sorted by {location}{expedition}{date}{latitude}{longitude}{water_depth}{core_type}{core_depth}{sample_comment}{eV}
* absorption values rounded to 5 decimal places


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)
core_depth [meters below seafloor]

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).

sample_comment [comment]

Comment about sample

free text comments, may only have meaning to submitting PI

Dataset Maintainers

Emily R. EstesTexas A&M University (TAMU)
Colleen M. HanselTexas A&M University (TAMU)
Amber YorkWoods Hole Oceanographic Institution (WHOI)
Amber YorkWoods 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