http://lod.bco-dmo.org/id/dataset/806920
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
2020-03-25
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Table 1: Experimental conditions and fluid carbonate chemistry for RPI-3 run where only aragonite precipitated
2020-03-25
publication
2020-03-25
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2020-04-09
publication
https://doi.org/10.26008/1912/bco-dmo.806920.1
Rinat Gabitov
Mississippi State University
principalInvestigator
Chiara Borrelli
University of Rochester
principalInvestigator
Karyn Rogers
Rensselaer Polytechnic Institute
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: Gabitov, R., Borrelli, C., Rogers, K. (2020) Table 1: Experimental conditions and fluid carbonate chemistry for RPI-3 run where only aragonite precipitated. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2020-03-25 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.806920.1 [access date]
Table 1: Carbonate chemistry Dataset Description: <p>Table 1: Experimental conditions and fluid carbonate chemistry for RPI-3 run where only aragonite precipitated</p> Methods and Sampling: <p><strong>Crystallization experiment</strong><br />
In order to simulate the high-pressure conditions at the seafloor, three laboratory experiments involving aragonite precipitation were conducted.&nbsp; Two experiments were conducted using a high-pressure apparatus (Figure 1). The control experiment was performed at atmospheric pressure and 8°C in a container immersed in a constant temperature bath. The experimental fluid (growth medium) was prepared by mixing artificial seawater (ASW) and small aliquots of Na2CO3. The addition of Na2CO3 allowed the saturation state of the fluid with respect to aragonite to be increased, in order to promote nucleation and crystallization on carbonate minerals. Artificial seawater was prepared by dissolving 32 g of Instant Ocean salt (Instant Ocean Spectrum Brands) mix in 1 kg of distilled water and filtering it through a 0.2 µm Nalgene filter. A small amount of 0.1M Na2CO3 was then introduced into the continuously stirred artificial seawater using a syringe pump set at a rate of ~1 ml/min, to reach a final volume ratio of Na2CO3 to artificial seawater of ~1:13. During the addition of Na2CO3, the solution was in contact with the atmosphere. This procedure homogenized the fluid and also precluded aragonite nucleation prior to the beginning of the experiment. The absence of crystal nucleation was confirmed visually by monitoring the solution pH, which remained stable for the 1-2 hours needed for the experiment setup. The observation that aragonite crystallization did not start prior to the beginning of the experiment is consistent with previously published data, which show that 6 hours elapsed before onset of crystallization in the solution similar to the one we used (7.4 mmol of Na2CO3 :1 liter of seawater) (Pytkowicz, 1965).</p>
<p>Petrographic glass slides frosted with silicon carbide (SiC) abrasive paper were used to promote aragonite crystallization along scratches. For each experiment, one slide was placed into the high-pressure vessel prior to the transfer of the experimental fluid. The experimental fluid was then placed into the vessel after it was precooled to 8°C. After that, the air space above the solution (&lt;200 cm3) was purged with nitrogen three times before the pressure was increased to a desired value (110 or 345 bars). The experimental fluid was sampled daily using a valve on the pressure vessel (Figure 1) and pH was measured to estimate time of nucleation and crystallization of CaCO3. For pH measurements, electrode calibration and measurements were conducted at temperatures similar to those of the experiment. NBS buffer solutions with pH of 4, 7, and 10 were used for electrode calibration. The pH initially decreased due to carbonate precipitation and reached near-constant values less than 170 hrs from the beginning of the experiments, suggesting that most of the CaCO3 precipitated in the first few days of each experiment. At the end of each run, the experimental products were extracted from the pressure vessel. Crystals (&lt;10 µm in size) were rinsed with distilled water and dried, whereas the experimental fluid was filtered and refrigerated for subsequent elemental analyses. The alkalinity of the final fluid was measured the day after the end of each experiment. Experimental parameters are presented in Table -1.</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
Rinat Gabitov
Mississippi State University
108 Hilbun Hall PO Box 5448
Mississippi
39762
USA
rinat.gabitov@gmail.com
pointOfContact
Chiara Borrelli
University of Rochester
202 Hutchison Hall University of Rochester
Rochester
New York
USA
cborrelli@UR.Rochester.edu
pointOfContact
Karyn Rogers
Rensselaer Polytechnic Institute
518-276-2372
100 8th St
Troy
NY
12180
USA
rogerk5@rpi.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
fluid
temp
press
S
TA
pH_meas
pH_calc
CO3
Ca
OM_ar
high-pressure apparatus
theme
None, User defined
treatment
water temperature at measurement depth
water pressure
salinity
total alkalinity (TA)
pH
Carbonate concentration [CO3]2-
Calcium
Aragonite Saturation State
featureType
BCO-DMO Standard Parameters
Benchtop pH Meter
Elemental Analyzer
no_bcodmo_term
instrument
BCO-DMO Standard Instruments
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
Biologically induced methane oxidation and precipitation of carbonate minerals: An experimental study
https://www.darkenergybiosphere.org/award/biologically-induced-methane-oxidation-and-precipitation-of-carbonate-minerals-an-experimental-study/
Biologically induced methane oxidation and precipitation of carbonate minerals: An experimental study
<p>Biologically-mediated CaCO3 precipitation widely occurs in aquatic systems and is often directly linked to the metabolic activity of microorganisms, which could significantly affect the local environment. An example is oxidation of methane and reduction of sulfate mediated by a consortium of Bacteria and Archaea. In order to investigate geochemistry of CaCO3precipitated abiotically and under microbial activity experimental work was initiated. The abiotic experiments were performed at different temperatures and pressures (nitrogen and nitrogen-methane mixture). Further geochemical analyses will allow evaluating of the effect of total pressure and methane partial pressure on the geochemistry of CaCO3. Sulfate reducing bacterial (<em>Desulfovibrio salexigens</em>) was successfully cultured and precipitation experiments on microbially mediated CaCO3 are in progress. This work is relevant to C-DEBI Research Theme I (Activity in the Deep Subseafloor Biosphere: function & rates of global biogeochemical processes) because carbonate growth rate is linked to microbial activity and the rate of methane oxidation.</p>
Deep Sea Geochem CaCO3
largerWorkCitation
project
eng; USA
oceans
2014-01-01
2014-12-31
0
BCO-DMO catalogue of parameters from Table 1: Experimental conditions and fluid carbonate chemistry for RPI-3 run where only aragonite precipitated
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/806932.rdf
Name: fluid
Units: unitless
Description: <p>exprimental fluid (growth medium): ASW= artificial seawater; initial= artificial seawater doped with aliquot 0.1M Na2CO3 in the proportion of ~1:13 to ASW; final= fluid at end of experiment</p>
http://lod.bco-dmo.org/id/dataset-parameter/806933.rdf
Name: temp
Units: degrees Celsius
Description: <p>temperature</p>
http://lod.bco-dmo.org/id/dataset-parameter/806934.rdf
Name: press
Units: bars
Description: <p>pressure</p>
http://lod.bco-dmo.org/id/dataset-parameter/806935.rdf
Name: S
Units: salinity units
Description: <p>salinity</p>
http://lod.bco-dmo.org/id/dataset-parameter/806936.rdf
Name: TA
Units: micromole per kg of water
Description: <p>total alkalinity</p>
http://lod.bco-dmo.org/id/dataset-parameter/806937.rdf
Name: pH_meas
Units: pH units
Description: <p>pH measured</p>
http://lod.bco-dmo.org/id/dataset-parameter/806938.rdf
Name: pH_calc
Units: pH units
Description: <p>pH calculated</p>
http://lod.bco-dmo.org/id/dataset-parameter/806939.rdf
Name: CO3
Units: micromole per kg of water
Description: <p>carbonate ion</p>
http://lod.bco-dmo.org/id/dataset-parameter/806940.rdf
Name: Ca
Units: milligram per kg of water
Description: <p>calcium ion</p>
http://lod.bco-dmo.org/id/dataset-parameter/806941.rdf
Name: OM_ar
Units: unitless
Description: <p>saturation state of the fluid with respect to aragonite</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
291
https://darchive.mblwhoilibrary.org/bitstream/1912/25620/1/dataset-806920_carbonate-chemistry__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.806920.1
download
onLine
dataset
<p><strong>Crystallization experiment</strong><br />
In order to simulate the high-pressure conditions at the seafloor, three laboratory experiments involving aragonite precipitation were conducted.&nbsp; Two experiments were conducted using a high-pressure apparatus (Figure 1). The control experiment was performed at atmospheric pressure and 8°C in a container immersed in a constant temperature bath. The experimental fluid (growth medium) was prepared by mixing artificial seawater (ASW) and small aliquots of Na2CO3. The addition of Na2CO3 allowed the saturation state of the fluid with respect to aragonite to be increased, in order to promote nucleation and crystallization on carbonate minerals. Artificial seawater was prepared by dissolving 32 g of Instant Ocean salt (Instant Ocean Spectrum Brands) mix in 1 kg of distilled water and filtering it through a 0.2 µm Nalgene filter. A small amount of 0.1M Na2CO3 was then introduced into the continuously stirred artificial seawater using a syringe pump set at a rate of ~1 ml/min, to reach a final volume ratio of Na2CO3 to artificial seawater of ~1:13. During the addition of Na2CO3, the solution was in contact with the atmosphere. This procedure homogenized the fluid and also precluded aragonite nucleation prior to the beginning of the experiment. The absence of crystal nucleation was confirmed visually by monitoring the solution pH, which remained stable for the 1-2 hours needed for the experiment setup. The observation that aragonite crystallization did not start prior to the beginning of the experiment is consistent with previously published data, which show that 6 hours elapsed before onset of crystallization in the solution similar to the one we used (7.4 mmol of Na2CO3 :1 liter of seawater) (Pytkowicz, 1965).</p>
<p>Petrographic glass slides frosted with silicon carbide (SiC) abrasive paper were used to promote aragonite crystallization along scratches. For each experiment, one slide was placed into the high-pressure vessel prior to the transfer of the experimental fluid. The experimental fluid was then placed into the vessel after it was precooled to 8°C. After that, the air space above the solution (&lt;200 cm3) was purged with nitrogen three times before the pressure was increased to a desired value (110 or 345 bars). The experimental fluid was sampled daily using a valve on the pressure vessel (Figure 1) and pH was measured to estimate time of nucleation and crystallization of CaCO3. For pH measurements, electrode calibration and measurements were conducted at temperatures similar to those of the experiment. NBS buffer solutions with pH of 4, 7, and 10 were used for electrode calibration. The pH initially decreased due to carbonate precipitation and reached near-constant values less than 170 hrs from the beginning of the experiments, suggesting that most of the CaCO3 precipitated in the first few days of each experiment. At the end of each run, the experimental products were extracted from the pressure vessel. Crystals (&lt;10 µm in size) were rinsed with distilled water and dried, whereas the experimental fluid was filtered and refrigerated for subsequent elemental analyses. The alkalinity of the final fluid was measured the day after the end of each experiment. Experimental parameters are presented in Table -1.</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Data Manager Processing Notes:</strong><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 />
- reformatted table so each column is unique</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:Used to measure pH. Instrument Name: Benchtop pH Meter Instrument Short Name:Benchtop pH Meter Instrument Description: An instrument consisting of an electronic voltmeter and pH-responsive electrode that gives a direct conversion of voltage differences to differences of pH at the measurement temperature. (McGraw-Hill Dictionary of Scientific and Technical Terms)
This instrument does not map to the NERC instrument vocabulary term for 'pH Sensor' which measures values in the water column. Benchtop models are typically employed for stationary lab applications.
PI Supplied Instrument Name: PI Supplied Instrument Description:Used to measure concentrations of ions. Instrument Name: Elemental Analyzer Instrument Short Name: Instrument Description: Instruments that quantify carbon, nitrogen and sometimes other elements by combusting the sample at very high temperature and assaying the resulting gaseous oxides. Usually used for samples including organic material. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB01/
high-pressure apparatus
high-pressure apparatus
PI Supplied Instrument Name: high-pressure apparatus PI Supplied Instrument Description:Custom designed pressure chamber used to simulate the high-pressure conditions at the seafloor for this set of experiments.(designed at Rensselaer Polytech Institute, Department of Earth and Environmental Sciences) Instrument Name: no_bcodmo_term Instrument Short Name: Instrument Description: No relevant match in BCO-DMO instrument vocabulary. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/999/