http://lod.bco-dmo.org/id/dataset/668648
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
2016-12-06
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Polysaccharide hydrolysis rates for Marmara Sea, Guaymas Basin, and Eastern Mediterranean Sea sediments collected from R/V El Puma and R/V Meteor cruises
2016-12-09
publication
2016-12-09
revision
BCO-DMO Linked Data URI
2016-12-09
creation
http://lod.bco-dmo.org/id/dataset/668648
Adrienne Hoarfrost
University of North Carolina at Chapel Hill
principalInvestigator
Carol Arnosti
University of North Carolina at Chapel Hill
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: Hoarfrost, A., Arnosti, C. (2016) Polysaccharide hydrolysis rates for Marmara Sea, Guaymas Basin, and Eastern Mediterranean Sea sediments collected from R/V El Puma and R/V Meteor cruises. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 09 December 2016) Version Date 2016-12-09 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/668648 [access date]
Polysaccharide hydrolysis rates for Marmara Sea, Guaymas Basin, and Eastern Mediterranean Sea sediments Dataset Description: <p>Polysaccharide hydrolysis rates for Marmara Sea, Guaymas Basin, and Eastern Mediterranean Sea sediments. The polysaccharide hydrolysis rates for Marmara Sea sediment were generated during methods development experiments.</p>
<p>This dataset contains the final hydrolysis rates. Raw data are also available for download&nbsp;<a href="http://dmoserv3.whoi.edu/data/C-DEBI/Hoarfrost/GPC-activitydata-SedS.zip" target="_blank">in a 20.5 MB .zip file</a>.<br />
The .zip file contains&nbsp;GPC chromatographic output for incubations with sediment from Guaymas Basin and the Eastern Mediterranean, used for hydrolysis rate calculations (CoreComparison folder). The "MarmaraMethods" folder contains GPC output for methods development experiments conducted using mud from the Marmara Sea. The "stds" folders contain GPC output for a set of standards of known molecular weight, which are necessary for rate calculations (each folder is a different run – depending on when a sample is run on the GPC, the standards run most recently are used as reference for rate calculations).&nbsp;Each file is raw chromatographic output is in fluorescence units (mV) over time for a 75-minute run.&nbsp;</p>
<p>The associated processing an analysis scripts are available through GitHub:&nbsp;<a href="https://github.com/ahoarfrost/SedS" target="_blank">https://github.com/ahoarfrost/SedS</a></p> Methods and Sampling: <p>In the Marmara Sea, surficial sediments were collected by multicorer, and deeper sediments from 570-585 cm and 520-530 cm were collected by gravity corer. Eastern Mediterranean sediments were collected by gravity corer. Guaymas Basin sediments were collected by push core.</p>
<p>Sediment incubations with fluorescently labeled organic substrates were set up with three live incubations, a kill control, and one live blank. Incubations were subsampled over time, and each subsample was centrifuged and syringe filtered through a 0.2 um GF filter. Porewater containing partially hydrolyzed fluorescent substrate products were processed using gel permeation chromatography with fluorescence detection. Standards of fluorescent substrates of known molecular weight were also run for the purpose of rate calculations.</p>
<p>GPC chromatographic analysis was conducted on a Shimadzu liquid chromatography system and a Hitachi fluorescence detector.</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
Adrienne Hoarfrost
University of North Carolina at Chapel Hill
3202 Venable Hall, CB3300
Chapel Hill
NC
27599
USA
adrienne.l.hoarfrost@unc.edu
pointOfContact
Carol Arnosti
University of North Carolina at Chapel Hill
919-962-5754
Dept. of Marine Sciences 3117A Venable/Murray Hall
Chapel Hill
NC
27599-3300
USA
arnosti@email.unc.edu
pointOfContact
asNeeded
Dataset Version: 09 December 2016
Unknown
description
sample
kcrate_1_nM_hr
kcrate_2_nM_hr
kcrate_3_nM_hr
kcrate_live_nM_hr
mean_kcrate_nM_hr
sd_kcrate_nM_hr
location
core
seddepth_cm
core_depth
treatment
substrate
timepoint
elapsedtime
Shimadzu liquid chromatography system
theme
None, User defined
No BCO-DMO term
sample identification
treatment
featureType
BCO-DMO Standard Parameters
Gel Permeation Chromatograph
Gravity Corer
Multi Corer
Push Corer
instrument
BCO-DMO Standard Instruments
Guaymas_2014
M84-1
service
Deployment Activity
Guaymas to Mazatlan
Southern Black Sea, Sea of Marmara, and the Eastern Mediterranean
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
Investigating microbial activities driving organic matter transformations in the deep subsurface
https://osprey.bco-dmo.org/project/662055
Investigating microbial activities driving organic matter transformations in the deep subsurface
<p>Project description from <a href="http://www.darkenergybiosphere.org/?s=&type=award" target="_blank">C-DEBI</a>:<br />
Heterotrophic organisms are central to subsurface microbial communities and play an important role in carbon cycling. Most approaches to measuring enzymatic activities rely on the addition of a fluorescently labeled substrate to a sediment incubation. However, quantifying rates of extracellular enzymatic hydrolysis of organic matter is often problematic due to the tendency for a fluorescently labeled organic substrate to sorb to the sediment matrix. This results in lower fluorescence intensities and distorted, inaccurate hydrolysis rate calculations. In this project, a desorption treatment was developed to counteract the adverse effects of sorption on enzymatic activity measurements. Upon subsampling a sediment incubation amended with a fluorescently labeled substrate, the subsample is treated with a concentrated solution of unlabeled substrate, along with 0.2% sodium dodecyl sulfate (SDS), in order to competitively desorb the adsorbed, fluorescent substrate target. This treatment improves measured fluorescence intensities by a median of 62.5%, and is particularly effective at desorbing high molecular weight substrate products, resulting in debiased hydrolysis rates that are 14.75 nM/hr lower on average. Competitive desorption treatment was demonstrated to be effective for multiple substrates and in a broad range of sediments from diverse geological and geochemical contexts. Future applications of this method will result in more quantitative and comparable hydrolysis rates in subsurface sediments, will enable enzymatic activity measurements in problematic sediments that were previously infeasible, and will facilitate physiological characterization of microbial communities and model organisms in order to better understand heterotrophic carbon cycling in the subsurface environment.</p>
<p>This project was funded by a <a href="http://www.darkenergybiosphere.org/research-activities/research-support/fellowships/" target="_blank">C-DEBI Graduate Fellowship</a>.</p>
SedS
largerWorkCitation
project
eng; USA
oceans
Guaymas to Mazatlan; Southern Black Sea, Sea of Marmara, and the Eastern Mediterranean
2016-12-09
Eastern Mediterranean, Guaymas Basin, Marmara Sea
0
BCO-DMO catalogue of parameters from Polysaccharide hydrolysis rates for Marmara Sea, Guaymas Basin, and Eastern Mediterranean Sea sediments collected from R/V El Puma and R/V Meteor cruises
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/671018.rdf
Name: description
Units: unitless
Description: <p>Maximum potential hydrolysis rates of six polysaccharides measured in sediment incubations</p>
http://lod.bco-dmo.org/id/dataset-parameter/671019.rdf
Name: sample
Units: unitless
Description: <p>Sample identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/671020.rdf
Name: kcrate_1_nM_hr
Units: nM/hr
Description: <p>kill-corrected hydrolysis rate of experimental replicate 1, in nM/hr</p>
http://lod.bco-dmo.org/id/dataset-parameter/671021.rdf
Name: kcrate_2_nM_hr
Units: nM/hr
Description: <p>kill-corrected hydrolysis rate of experimental replicate 2, in nM/hr</p>
http://lod.bco-dmo.org/id/dataset-parameter/671022.rdf
Name: kcrate_3_nM_hr
Units: nM/hr
Description: <p>kill-corrected hydrolysis rate of experimental replicate 3, in nM/hr</p>
http://lod.bco-dmo.org/id/dataset-parameter/671023.rdf
Name: kcrate_live_nM_hr
Units: nM/hr
Description: <p>mean hydrolysis rate before kill correction</p>
http://lod.bco-dmo.org/id/dataset-parameter/671024.rdf
Name: mean_kcrate_nM_hr
Units: nM/hr
Description: <p>mean kill-corrected hydrolysis rate of all replicates</p>
http://lod.bco-dmo.org/id/dataset-parameter/671025.rdf
Name: sd_kcrate_nM_hr
Units: nM/hr
Description: <p>Standard deviation</p>
http://lod.bco-dmo.org/id/dataset-parameter/671026.rdf
Name: location
Units: unitless
Description: <p>Location source of the sediment sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/671027.rdf
Name: core
Units: unitless
Description: <p>Identifier for the sediment core</p>
http://lod.bco-dmo.org/id/dataset-parameter/671028.rdf
Name: seddepth_cm
Units: centimeter (cm)
Description: <p>Sediment depth within the core</p>
http://lod.bco-dmo.org/id/dataset-parameter/671029.rdf
Name: core_depth
Units: centimeter (cm)
Description: <p>Core + sediment depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/671030.rdf
Name: treatment
Units: unitless
Description: <p>Experimental treatment of sediment incubation</p>
http://lod.bco-dmo.org/id/dataset-parameter/671031.rdf
Name: substrate
Units: unitless
Description: <p>Polysaccharide substrate for which hydrolysis rates were measured</p>
http://lod.bco-dmo.org/id/dataset-parameter/671032.rdf
Name: timepoint
Units: unitless
Description: <p>Timepoint label of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/671033.rdf
Name: elapsedtime
Units: hours (hr)
Description: <p>Time since incubation start time</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
15187
https://datadocs.bco-dmo.org/file/B11vABQiD7rMr0/Hydrolysis_Rates.csv
Hydrolysis_Rates.csv
Primary data file for dataset ID 668648
download
https://osprey.bco-dmo.org/dataset/668648/data/download
download
onLine
dataset
<p>In the Marmara Sea, surficial sediments were collected by multicorer, and deeper sediments from 570-585 cm and 520-530 cm were collected by gravity corer. Eastern Mediterranean sediments were collected by gravity corer. Guaymas Basin sediments were collected by push core.</p>
<p>Sediment incubations with fluorescently labeled organic substrates were set up with three live incubations, a kill control, and one live blank. Incubations were subsampled over time, and each subsample was centrifuged and syringe filtered through a 0.2 um GF filter. Porewater containing partially hydrolyzed fluorescent substrate products were processed using gel permeation chromatography with fluorescence detection. Standards of fluorescent substrates of known molecular weight were also run for the purpose of rate calculations.</p>
<p>GPC chromatographic analysis was conducted on a Shimadzu liquid chromatography system and a Hitachi fluorescence detector.</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
Shimadzu liquid chromatography system
Shimadzu liquid chromatography system
PI Supplied Instrument Name: Shimadzu liquid chromatography system PI Supplied Instrument Description:GPC chromatographic analysis was conducted on a Shimadzu liquid chromatography system and a Hitachi fluorescence detector. Instrument Name: Gel Permeation Chromatograph Instrument Short Name:GPC Instrument Description: Instruments that separate components in aqueous or organic solution based on molecular size generally for molecular weight determination. Gel permeation chromatography (GPC) is a type of size exclusion chromatography (SEC), that separates analytes on the basis of size.
PI Supplied Instrument Name: PI Supplied Instrument Description:Eastern Mediterranean sediments were collected by gravity corer. In the Marmara Sea, deeper sediments (from 570-585 cm and 520-530 cm) were collected by gravity corer. 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/
PI Supplied Instrument Name: PI Supplied Instrument Description:In the Marmara Sea, surficial sediments were collected by multicorer. Instrument Name: Multi Corer Instrument Short Name:Multi Corer Instrument Description: The Multi Corer is a benthic coring device used to collect multiple, simultaneous, undisturbed sediment/water samples from the seafloor. Multiple coring tubes with varying sampling capacity depending on tube dimensions are mounted in a frame designed to sample the deep ocean seafloor. For more information, see Barnett et al. (1984) in Oceanologica Acta, 7, pp. 399-408. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/51/
PI Supplied Instrument Name: PI Supplied Instrument Description:Guaymas Basin sediments were collected by push core. Instrument Name: Push Corer Instrument Short Name: Instrument Description: Capable of being performed in numerous environments, push coring is just as it sounds. Push coring is simply pushing the core barrel (often an aluminum or polycarbonate tube) into the sediment by hand. A push core is useful in that it causes very little disturbance to the more delicate upper layers of a sub-aqueous sediment.
Description obtained from: http://web.whoi.edu/coastal-group/about/how-we-work/field-methods/coring/
Cruise: Guaymas_2014
Guaymas_2014
R/V El Puma
vessel
Guaymas_2014
Andreas Teske
University of North Carolina at Chapel Hill
Cruise: M84-1
M84-1
Community Standard Description
International Council for the Exploration of the Sea
R/V Meteor
vessel
M84-1
Dr Matthias Zabel
Marum Centre for Marine Environmental Sciences at University Bremen
http://dmoserv3.whoi.edu/data_docs/C-DEBI/cruise_reports/awi_doi-10.2312_2Fcr_m84_1.pdf
Report describing M84-1
R/V El Puma
vessel