http://lod.bco-dmo.org/id/dataset/685944
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
2017-03-27
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
3H-leucine and thymidine incorporation of North Atlantic subseafloor sediments from cruise KN223 on R/V Knorr in the North and West Atlantic Ocean in November 2014
2017-03-27
publication
2017-03-27
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-12-27
publication
https://doi.org/10.26008/1912/bco-dmo.685944.1
Eric S. Boyd
Montana State University
principalInvestigator
Maximiliano J. Amenabar
Montana State University
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: Boyd, E. S., Amenabar, M. J. (2021) 3H-leucine and thymidine incorporation of North Atlantic subseafloor sediments from cruise KN223 on R/V Knorr in the North and West Atlantic Ocean in November 2014. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2017-03-27 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.685944.1 [access date]
3H-leucine and thymidine incorporation of North Atlantic subseafloor sediments from cruise KN223 Dataset Description: <p>3H-leucine and thymidine incorporation of North Atlantic&nbsp;subseafloor sediments collected on cruise KN223 on R/V Knorr in November 2014.</p> Methods and Sampling: <p>All samples used in this work were collected as part of the North Atlantic long-coring expedition in Oct.-Dec. 2014 (R/V Knorr, Cruise KN223); this project focuses on sediments from 4 sites (2, 3, 11, 12) exhibiting variations in the depth to which oxygen penetrates. The sediment subsamples were collected from long piston cores or shorter gravity cores. While oxygen penetrates through the full long core depth at sites 11 and 12, oxygen was consumed in the sediment column at site 3 and especially at site 2. All samples were collected anaerobically in order to perform on-board culture enrichments via the most probable number (MPN) method. Sediments were placed in sterile serum vials, capped with butyl rubber stoppers and flushed with N2 for 2 min and maintained at 4 degrees C for immediate shipboard MPN inoculation work (see <a href="https://www.bco-dmo.org/dataset/686389" target="_blank">MPN dataset</a>). Parallel samples were similarly collected from these and additional core sections and maintained at 4 degrees C for later determination of microbial production rates (this dataset).</p>
<p>We assessed microbial production on selected core sections at sites 11 and 12 using proxies for DNA synthesis (incorporation of methyl-3H thymidine) and protein synthesis (incorporation of 4,5-3H leucine). Core material was retained at 4 degrees C under an N2 atmosphere prior to slurry preparation. Aerobic slurry was prepared 1:1 by volume with 0.2 um-filtered deep seawater and incubations began immediately thereafter. Incubations (n=4 live treatments, n=4 TCA-killed controls) of 0.5 ml slurry each were conducted in sterile microfuge tubes for each label addition. Seawater-only blanks incubated and processed along with samples exhibited near background levels of activity. 50 ul of working 3H-Thy or 3H-Leu stock was added at time zero. This equates to 3.75 uCi Leu or 4.4375 uCi Thy per sample at concentrations of appx. 114 nmol label compound per liter slurry final. Incubations were carried out at 4 degrees C in the dark.</p>
<p>Incubations were terminated at 18-24 hr; a time-course experiment confirmed linearity of incorporation out to at least 24 hr. Live incubations were terminated with TCA and an extraction protocol modified from Dixon &amp; Turley (2001, Microb. Ecol. 42:549) was used to isolate the protein + DNA fraction, which was analyzed by liquid scintillation counting for 3H-Leu incorporation; the DNA fraction alone was isolated and similarly analyzed for 3H-Thy incorporation. Rates are reported as pmol leucine or thymidine incorporated per ml of sediment per day (based on mean treatment minus mean control). Errors were calculated by propagating the standard deviations of treatments and controls.</p>
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
Eric S. Boyd
Montana State University
(406) 994-7046
Department of Microbiology and Immunology, 109 Lewis Hall PO Box 173520
Bozeman
MT
59717
USA
eboyd@montana.edu
pointOfContact
Maximiliano J. Amenabar
Montana State University
(406) 595-1968
Department of Microbiology and Immunology, 109 Lewis Hall PO Box 173520
Bozeman
MT
59717
United States
maximiliano.amenabar@msu.montana.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
site
lat
lon
depth_w
sed_thickness
basement_age
date_coring
cruise_id
platform
core
core_section
depth_mbsf
leucine_incorp
leu_sd
thymidine_incorp
thy_sd
gravity core
liquid scintillation counting
long piston core
theme
None, User defined
site
latitude
longitude
depth_w
sed_thickness
No BCO-DMO term
date
Cruise identfier
ship
core id
sample identification
meters below seafloor
leucine incorporation rate
standard deviation of leucine incorporation rate
thymidine incorporation rate
standard deviation of thymidine incorporation rate
featureType
BCO-DMO Standard Parameters
Gravity Corer
Liquid Scintillation Counter
Piston Corer
instrument
BCO-DMO Standard Instruments
KN223
service
Deployment Activity
North and West Atlantic Ocean
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
Defining the interplay between oxygen, organic carbon, and metabolism in subseafloor sediment communities
http://www.darkenergybiosphere.org/award/defining-the-interplay-between-oxygen-organic-carbon-and-metabolism-in-subseafloor-sediment-communities/
Defining the interplay between oxygen, organic carbon, and metabolism in subseafloor sediment communities
<p>Abstract from C-DEBI:</p>
<p>Deep marine sediments harbor an abundance of microbial cells that, if active, are likely to exert a strong influence on element biogeochemical cycling. Despite decades of study, our understanding of the fraction of cells that are active in situ and the metabolic processes that sustain them remain under-explored. We propose an integrated set of analyses aimed at unraveling the links between geochemical heterogeneity, cellular viability and synthesis, and metabolism along a vertical depth profile in four sediment cores collected during the North Atlantic long coring expedition. These sediment columns exhibit varying levels of organic carbon and differences in the degree of oxygen penetration along the depth profile which we hypothesize exert strong influence on the extent and nature of microbial life. Most probable number assays containing nine different selective enrichment conditions were initiated using subsamples from these cores in Nov. 2014. Separate subsamples were preserved for use in measuring rates of secondary production. Multivariate modeling tools will be applied to integrate these measurements with co-registered geochemical measurements, cell counts, and molecular data provided by collaborators. This work will provide new insight into the dynamic interplay between O2 and organic carbon and microbial activity, viability, and productivity in deep marine sediments.</p>
<p>NOTE: This project follows the C-DEBI program <a href="http://www.darkenergybiosphere.org/internal/docs/C-DEBIDataManagementPlan_2015.pdf" target="_blank">Data Management Plan (PDF)</a>.</p>
Subseafloor metabolisms
largerWorkCitation
project
eng; USA
oceans
North and West Atlantic Ocean
-58.3283
-56.5173
22.7835
29.6767
2014-11-19
2014-11-21
SW North Atlantic sediments (13-42° N, 48-71° W)
0
BCO-DMO catalogue of parameters from 3H-leucine and thymidine incorporation of North Atlantic subseafloor sediments from cruise KN223 on R/V Knorr in the North and West Atlantic Ocean in November 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/686349.rdf
Name: site
Units: unitless
Description: <p>Site name</p>
http://lod.bco-dmo.org/id/dataset-parameter/686350.rdf
Name: lat
Units: decimal degrees
Description: <p>Site latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/686351.rdf
Name: lon
Units: decimal degrees
Description: <p>Site longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/686352.rdf
Name: depth_w
Units: meters (m)
Description: <p>Water depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/686353.rdf
Name: sed_thickness
Units: meters (m)
Description: <p>Sediment thickness</p>
http://lod.bco-dmo.org/id/dataset-parameter/686354.rdf
Name: basement_age
Units: millions of years ago (Ma)
Description: <p>Basement age</p>
http://lod.bco-dmo.org/id/dataset-parameter/686355.rdf
Name: date_coring
Units: unitless
Description: <p>Date of coring in yyyy-mm-dd format</p>
http://lod.bco-dmo.org/id/dataset-parameter/686356.rdf
Name: cruise_id
Units: unitless
Description: <p>Cruise identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/686357.rdf
Name: platform
Units: unitless
Description: <p>Platform (e.g. vessel) name</p>
http://lod.bco-dmo.org/id/dataset-parameter/686358.rdf
Name: core
Units: unitless
Description: <p>Core identifier. LC = long core; GC = gravity core.</p>
http://lod.bco-dmo.org/id/dataset-parameter/686359.rdf
Name: core_section
Units: unitless
Description: <p>Core section</p>
http://lod.bco-dmo.org/id/dataset-parameter/686360.rdf
Name: depth_mbsf
Units: meters below sea floor (mbsf)
Description: <p>Sample depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/686361.rdf
Name: leucine_incorp
Units: picomoles Leucine per milliliter sediment per day (pmol Leu/ml sed/d)
Description: <p>Leucine incorporation; mean rate of incorporation of leucine based on mean live treatment (n=4) minus mean killed control (n=4).</p>
http://lod.bco-dmo.org/id/dataset-parameter/686362.rdf
Name: leu_sd
Units: picomoles Leucine per milliliter sediment per day (pmol Leu/ml sed/d)
Description: <p>Standard deviation of rate of leucine incorporation based on propagation of sd of treatments and sd of controls.</p>
http://lod.bco-dmo.org/id/dataset-parameter/686363.rdf
Name: thymidine_incorp
Units: picomoles Thymidine per milliliter sediment per day (pmol Thy/ml sed/d)
Description: <p>Thymidine incorporation; mean rate of incorporation of thymidine based on mean live treatment (n=4) minus mean killed control (n=4).</p>
http://lod.bco-dmo.org/id/dataset-parameter/686364.rdf
Name: thy_sd
Units: picomoles Thymidine per milliliter sediment per day (pmol Thy/ml sed/d)
Description: <p>Standard deviation of rate of thymidine incorporation based on propagation of sd of treatments and sd of controls.</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
1105
https://darchive.mblwhoilibrary.org/bitstream/1912/27861/1/dataset-685944_sediment-microbial-production__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.685944.1
download
onLine
dataset
<p>All samples used in this work were collected as part of the North Atlantic long-coring expedition in Oct.-Dec. 2014 (R/V Knorr, Cruise KN223); this project focuses on sediments from 4 sites (2, 3, 11, 12) exhibiting variations in the depth to which oxygen penetrates. The sediment subsamples were collected from long piston cores or shorter gravity cores. While oxygen penetrates through the full long core depth at sites 11 and 12, oxygen was consumed in the sediment column at site 3 and especially at site 2. All samples were collected anaerobically in order to perform on-board culture enrichments via the most probable number (MPN) method. Sediments were placed in sterile serum vials, capped with butyl rubber stoppers and flushed with N2 for 2 min and maintained at 4 degrees C for immediate shipboard MPN inoculation work (see <a href="https://www.bco-dmo.org/dataset/686389" target="_blank">MPN dataset</a>). Parallel samples were similarly collected from these and additional core sections and maintained at 4 degrees C for later determination of microbial production rates (this dataset).</p>
<p>We assessed microbial production on selected core sections at sites 11 and 12 using proxies for DNA synthesis (incorporation of methyl-3H thymidine) and protein synthesis (incorporation of 4,5-3H leucine). Core material was retained at 4 degrees C under an N2 atmosphere prior to slurry preparation. Aerobic slurry was prepared 1:1 by volume with 0.2 um-filtered deep seawater and incubations began immediately thereafter. Incubations (n=4 live treatments, n=4 TCA-killed controls) of 0.5 ml slurry each were conducted in sterile microfuge tubes for each label addition. Seawater-only blanks incubated and processed along with samples exhibited near background levels of activity. 50 ul of working 3H-Thy or 3H-Leu stock was added at time zero. This equates to 3.75 uCi Leu or 4.4375 uCi Thy per sample at concentrations of appx. 114 nmol label compound per liter slurry final. Incubations were carried out at 4 degrees C in the dark.</p>
<p>Incubations were terminated at 18-24 hr; a time-course experiment confirmed linearity of incorporation out to at least 24 hr. Live incubations were terminated with TCA and an extraction protocol modified from Dixon &amp; Turley (2001, Microb. Ecol. 42:549) was used to isolate the protein + DNA fraction, which was analyzed by liquid scintillation counting for 3H-Leu incorporation; the DNA fraction alone was isolated and similarly analyzed for 3H-Thy incorporation. Rates are reported as pmol leucine or thymidine incorporated per ml of sediment per day (based on mean treatment minus mean control). Errors were calculated by propagating the standard deviations of treatments and controls.</p>
Specified by the Principal Investigator(s)
<p>These data represent short-term rates of label incorporation at the stated levels of addition. No corrections for potential isotope dilution were attempted, given the overall low metabolic rates of the system. Rates are reported as determined; therefore, where mean controls exceeded mean treatments, negative rates are reported.</p>
<p>BCO-DMO Processing:<br />
- modified parameter names to conform with BCO-DMO naming conventions;<br />
- re-formatted date to yyyy-mm-dd;<br />
- replaced "R/V Knorr" with "RV_Knorr" in data.</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
gravity core
gravity core
PI Supplied Instrument Name: gravity core PI Supplied Instrument Description:The sediment subsamples were collected from long piston cores or shorter gravity cores. Instrument Name: Gravity Corer Instrument Short Name:Gravity Corer Instrument Description: The gravity corer allows researchers to sample sediment layers at the bottom of lakes or oceans. The coring device is deployed from the ship and gravity carries it to the seafloor. (http://www.whoi.edu/instruments/viewInstrument.do?id=1079). Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/51/
liquid scintillation counting
liquid scintillation counting
PI Supplied Instrument Name: liquid scintillation counting PI Supplied Instrument Description:Live incubations were terminated with TCA and an extraction protocol modified from Dixon & Turley (2001, Microb. Ecol. 42:549) was used to isolate the protein + DNA fraction, which was analyzed by liquid scintillation counting for 3H-Leu incorporation. Instrument Name: Liquid Scintillation Counter Instrument Short Name:LSC Instrument Description: Liquid scintillation counting is an analytical technique which is defined by the incorporation of the radiolabeled analyte into uniform distribution with a liquid chemical medium capable of converting the kinetic energy of nuclear emissions into light energy. Although the liquid scintillation counter is a sophisticated laboratory counting system used to quantify the activity of particulate emitting (ß and a) radioactive samples, it can also detect the auger electrons emitted from 51Cr and 125I samples.
Liquid scintillation counters are instruments assaying alpha and beta radiation by quantitative detection of visible light produced by the passage of rays or particles through a suitable scintillant incorporated into the sample. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB21/
long piston core
long piston core
PI Supplied Instrument Name: long piston core PI Supplied Instrument Description:The sediment subsamples were collected from long piston cores or shorter gravity cores. Instrument Name: Piston Corer Instrument Short Name:Piston Corer Instrument Description: The piston corer is a type of bottom sediment sampling device. A long, heavy tube is plunged into the seafloor to extract samples of mud sediment. A piston corer uses a "free fall" of the coring rig to achieve a greater initial force on impact than gravity coring. A sliding piston inside the core barrel reduces inside wall friction with the sediment and helps to evacuate displaced water from the top of the corer. A piston corer is capable of extracting core samples up to 90 feet in length. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/51/
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
R/V Knorr
Community Standard Description
International Council for the Exploration of the Sea
R/V Knorr
vessel