http://lod.bco-dmo.org/id/dataset/815380
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2020-06-15
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
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
2020-07-22
publication
2020-07-22
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2020-07-23
publication
https://doi.org/10.26008/1912/bco-dmo.815380.1
Emily Estes
Texas A&M University
principalInvestigator
Colleen Hansel
Woods Hole Oceanographic Institution
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Estes, E., Hansel, C. (2020) 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. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2020-07-22 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.815380.1 [access date]
Dataset Description: <p>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&nbsp;(R/V Roger Revelle), and ODP leg 201 between 2002 and 2014.&nbsp;&nbsp;</p>
<p>These data were published in Estes et al. (2019).<br />
<br />
These data are available in two forms (see Data Processing Description section on this page for more information).</p> Methods and Sampling: 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.
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.
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0939564 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0939564
completed
Emily Estes
Texas A&M University
413-768-9433
estes@iodp.tamu.edu
pointOfContact
Colleen Hansel
Woods Hole Oceanographic Institution
508-289-3738
266 Woods Hole Road, MS52
Woods Hole
MA
02543
US
chansel@whoi.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
location
date
expedition
site
latitude
longitude
water_depth
core_type
core_depth
eV
absorption
sample_comment
theme
None, User defined
site
date
Cruise identfier
latitude
longitude
depth
sample type
meters below seafloor
Electronvolts
absorbance
comments
featureType
BCO-DMO Standard Parameters
Spectrometer
instrument
BCO-DMO Standard Instruments
KN223
KNOX02RR
JRES-201
service
Deployment Activity
North and West Atlantic Ocean
South Pacific Gyre
Eastern Equatorial Pacific and Peru Margin
place
Locations
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Center for Dark Energy Biosphere Investigations
http://www.darkenergybiosphere.org
Center for Dark Energy Biosphere Investigations
The mission of the Center for Dark Energy Biosphere Investigations (C-DEBI) is to explore life beneath the seafloor and make transformative discoveries that advance science, benefit society, and inspire people of all ages and origins.
C-DEBI provides a framework for a large, multi-disciplinary group of scientists to pursue fundamental questions about life deep in the sub-surface environment of Earth. The fundamental science questions of C-DEBI involve exploration and discovery, uncovering the processes that constrain the sub-surface biosphere below the oceans, and implications to the Earth system. What type of life exists in this deep biosphere, how much, and how is it distributed and dispersed? What are the physical-chemical conditions that promote or limit life? What are the important oxidation-reduction processes and are they unique or important to humankind? How does this biosphere influence global energy and material cycles, particularly the carbon cycle? Finally, can we discern how such life evolved in geological settings beneath the ocean floor, and how this might relate to ideas about the origin of life on our planet?
C-DEBI's scientific goals are pursued with a combination of approaches:
(1) coordinate, integrate, support, and extend the research associated with four major programs—Juan de Fuca Ridge flank (JdF), South Pacific Gyre (SPG), North Pond (NP), and Dorado Outcrop (DO)—and other field sites;
(2) make substantial investments of resources to support field, laboratory, analytical, and modeling studies of the deep subseafloor ecosystems;
(3) facilitate and encourage synthesis and thematic understanding of submarine microbiological processes, through funding of scientific and technical activities, coordination and hosting of meetings and workshops, and support of (mostly junior) researchers and graduate students; and
(4) entrain, educate, inspire, and mentor an interdisciplinary community of researchers and educators, with an emphasis on undergraduate and graduate students and early-career scientists.
Note: Katrina Edwards was a former PI of C-DEBI; James Cowen is a former co-PI.
Data Management:
C-DEBI is committed to ensuring all the data generated are publically available and deposited in a data repository for long-term storage as stated in their Data Management Plan (PDF) and in compliance with the NSF Ocean Sciences Sample and Data Policy. The data types and products resulting from C-DEBI-supported research include a wide variety of geophysical, geological, geochemical, and biological information, in addition to education and outreach materials, technical documents, and samples. All data and information generated by C-DEBI-supported research projects are required to be made publically available either following publication of research results or within two (2) years of data generation.
To ensure preservation and dissemination of the diverse data-types generated, C-DEBI researchers are working with BCO-DMO Data Managers make data publicly available online. The partnership with BCO-DMO helps ensure that the C-DEBI data are discoverable and available for reuse. Some C-DEBI data is better served by specialized repositories (NCBI's GenBank for sequence data, for example) and, in those cases, BCO-DMO provides dataset documentation (metadata) that includes links to those external repositories.
C-DEBI
largerWorkCitation
program
Center for Dark Energy Biosphere Investigations
http://www.darkenergybiosphere.org
Center for Dark Energy Biosphere Investigations
The mission of the Center for Dark Energy Biosphere Investigations (C-DEBI) is to explore life beneath the seafloor and make transformative discoveries that advance science, benefit society, and inspire people of all ages and origins.
C-DEBI provides a framework for a large, multi-disciplinary group of scientists to pursue fundamental questions about life deep in the sub-surface environment of Earth. The fundamental science questions of C-DEBI involve exploration and discovery, uncovering the processes that constrain the sub-surface biosphere below the oceans, and implications to the Earth system. What type of life exists in this deep biosphere, how much, and how is it distributed and dispersed? What are the physical-chemical conditions that promote or limit life? What are the important oxidation-reduction processes and are they unique or important to humankind? How does this biosphere influence global energy and material cycles, particularly the carbon cycle? Finally, can we discern how such life evolved in geological settings beneath the ocean floor, and how this might relate to ideas about the origin of life on our planet?
C-DEBI's scientific goals are pursued with a combination of approaches:
(1) coordinate, integrate, support, and extend the research associated with four major programs—Juan de Fuca Ridge flank (JdF), South Pacific Gyre (SPG), North Pond (NP), and Dorado Outcrop (DO)—and other field sites;
(2) make substantial investments of resources to support field, laboratory, analytical, and modeling studies of the deep subseafloor ecosystems;
(3) facilitate and encourage synthesis and thematic understanding of submarine microbiological processes, through funding of scientific and technical activities, coordination and hosting of meetings and workshops, and support of (mostly junior) researchers and graduate students; and
(4) entrain, educate, inspire, and mentor an interdisciplinary community of researchers and educators, with an emphasis on undergraduate and graduate students and early-career scientists.
Note: Katrina Edwards was a former PI of C-DEBI; James Cowen is a former co-PI.
Data Management:
C-DEBI is committed to ensuring all the data generated are publically available and deposited in a data repository for long-term storage as stated in their Data Management Plan (PDF) and in compliance with the NSF Ocean Sciences Sample and Data Policy. The data types and products resulting from C-DEBI-supported research include a wide variety of geophysical, geological, geochemical, and biological information, in addition to education and outreach materials, technical documents, and samples. All data and information generated by C-DEBI-supported research projects are required to be made publically available either following publication of research results or within two (2) years of data generation.
To ensure preservation and dissemination of the diverse data-types generated, C-DEBI researchers are working with BCO-DMO Data Managers make data publicly available online. The partnership with BCO-DMO helps ensure that the C-DEBI data are discoverable and available for reuse. Some C-DEBI data is better served by specialized repositories (NCBI's GenBank for sequence data, for example) and, in those cases, BCO-DMO provides dataset documentation (metadata) that includes links to those external repositories.
C-DEBI
largerWorkCitation
program
Geochemical controls on organic carbon quantity and quality in the deep subsurface
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/
Geochemical controls on organic carbon quantity and quality in the deep subsurface
<p>Abstract from the C-DEBI project page:</p>
<p>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.</p>
Org C Sed II
largerWorkCitation
project
Elucidating the extent and composition of mineral-hosted carbon in the deep biosphere
https://www.darkenergybiosphere.org/award/elucidating-the-extent-and-composition-of-mineral-hosted-carbon-in-the-deep-biosphere/
Elucidating the extent and composition of mineral-hosted carbon in the deep biosphere
<p>Abstract from the C-DEBI project page:</p>
<p>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.</p>
Org C Sed I
largerWorkCitation
project
eng; USA
oceans
North and West Atlantic Ocean; South Pacific Gyre; Eastern Equatorial Pacific and Peru Margin
-165.6433
-50.62
-38.0617
33.4833
2002-01-01
2014-01-01
North Atlantic gyre, South Pacific gyre
0
BCO-DMO catalogue of parameters from 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
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/818845.rdf
Name: location
Units: unitless
Description: <p>Sample origin</p>
http://lod.bco-dmo.org/id/dataset-parameter/818846.rdf
Name: date
Units: unitless
Description: <p>date sample collection in ISO 8601 format yyyy-mm-dd</p>
http://lod.bco-dmo.org/id/dataset-parameter/818847.rdf
Name: expedition
Units: unitless
Description: <p>Cruise name</p>
http://lod.bco-dmo.org/id/dataset-parameter/818848.rdf
Name: site
Units: unitless
Description: <p>Site number</p>
http://lod.bco-dmo.org/id/dataset-parameter/818849.rdf
Name: latitude
Units: decimal degrees
Description: <p>Latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/818850.rdf
Name: longitude
Units: decimal degrees
Description: <p>Longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/818851.rdf
Name: water_depth
Units: meters (m)
Description: <p>Water depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/818852.rdf
Name: core_type
Units: unitless
Description: <p>Coring device used</p>
http://lod.bco-dmo.org/id/dataset-parameter/818853.rdf
Name: core_depth
Units: meters (m)
Description: <p>Sample depth (meters below seafloor)</p>
http://lod.bco-dmo.org/id/dataset-parameter/818854.rdf
Name: eV
Units: electron volts (eV)
Description: <p>electron volts (incident energy)</p>
http://lod.bco-dmo.org/id/dataset-parameter/818855.rdf
Name: absorption
Units: unitless
Description: <p>absorption. arbitrary units (normalized)</p>
http://lod.bco-dmo.org/id/dataset-parameter/819273.rdf
Name: sample_comment
Units: unknown
Description: <p>Comment about sample</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
957896
https://darchive.mblwhoilibrary.org/bitstream/1912/25983/1/Estes_bulkNEXAFSspectra_data.csv
download
7978292
https://darchive.mblwhoilibrary.org/bitstream/1912/25983/2/dataset-815380_carbon-nexafs-bulk-data__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.815380.1
download
onLine
dataset
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.
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.
Specified by the Principal Investigator(s)
<p>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).<br />
<br />
BCO-DMO Data Manager Processing Notes:<br />
* 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.&nbsp; The following changes were made after discussion with the original submitter.<br />
* original data had 10 header rows with sample, and cruise information e.g. cruise_id, date, latitude, sample_depth, etc.&nbsp; The data were unpivoted so these values became new columns in the dataset.<br />
* added a conventional header with dataset name, PI name, version date<br />
* modified parameter names to conform with BCO-DMO naming conventions<br />
* blank values in this dataset are displayed as "nd" for "no data."&nbsp; nd is the default missing data identifier in the BCO-DMO system.<br />
* latitude and longitude in degrees decimal minutes converted to decimal degrees then rounded to 5 decimal places.<br />
* date format converted to ISO 8601 format yyyy-mm-dd<br />
* 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).<br />
* data sorted by&nbsp;{location}{expedition}{date}{latitude}{longitude}{water_depth}{core_type}{core_depth}{sample_comment}{eV}<br />
* absorption values rounded to 5 decimal places</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
PI Supplied Instrument Name: PI Supplied Instrument 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. Instrument Name: Spectrometer Instrument Short Name:Spectrometer Instrument Description: A spectrometer is an optical instrument used to measure properties of light over a specific portion of the electromagnetic spectrum. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0460/
Cruise: KN223
KN223
R/V Knorr
Community Standard Description
International Council for the Exploration of the Sea
R/V Knorr
vessel
KN223
Richard W Murray
Boston University
Cruise: KNOX02RR
KNOX02RR
R/V Roger Revelle
Community Standard Description
International Council for the Exploration of the Sea
R/V Roger Revelle
vessel
KNOX02RR
Steven L. D'Hondt
University of Rhode Island
Cruise: JRES-201
JRES-201
R/V JOIDES Resolution
Community Standard Description
International Council for the Exploration of the Sea
R/V JOIDES Resolution
vessel
JRES-201
Steven L. D'Hondt
University of Rhode Island
http://dmoserv3.whoi.edu/data_docs/C-DEBI/cruise_reports/201PREL-1.pdf
Report describing JRES-201
R/V Knorr
Community Standard Description
International Council for the Exploration of the Sea
R/V Knorr
vessel
R/V Roger Revelle
Community Standard Description
International Council for the Exploration of the Sea
R/V Roger Revelle
vessel
R/V JOIDES Resolution
Community Standard Description
International Council for the Exploration of the Sea
R/V JOIDES Resolution
vessel