Download URLhttps://www.bco-dmo.org/dataset/806920/data/download
Media Type text/tab-separated-values
Created March 25, 2020
Modified April 8, 2020
State Final no updates expected
Brief Description

Table 1: Carbonate chemistry

Acquisition Description

Crystallization experiment
In order to simulate the high-pressure conditions at the seafloor, three laboratory experiments involving aragonite precipitation were conducted.  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).

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 (<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 (<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.

Processing Description

BCO-DMO Data Manager Processing Notes:
– 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.
– reformatted table so each column is unique


high-pressure apparatus [unknown]
Instance Description (high-pressure apparatus)

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)

No relevant match in BCO-DMO instrument vocabulary.

Instance Description

Used to measure pH.

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.
Instance Description

Used to measure concentrations of ions.

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.


fluid [treatment]
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

Experimental conditions applied to experimental units.  In comparative experiments, members of the complementary group, the control group, receive either no treatment or a standard treatment.

temp [temperature]
water temperature at measurement depth
press [pressure]
water pressure at measurement; depth reported as pressure; positive number increasing with water depth
S [sal]

salinity, calculated from the CTD 'primary sensors' of conductivity and temperature, Practical Salinity Scale (PSS-78), dimensionless. Depending on the input source, salinity from the primary sensors can have a variety of names i.e. s0, s00, sal0, sal00.

total alkalinity

Total alkalinity per unit mass of the water body.

pH_meas [pH]
pH measured

pH: The measure of the acidity or basicity of an aqueous solution

pH_calc [pH]
pH calculated

pH: The measure of the acidity or basicity of an aqueous solution

CO3 [carbonate]
carbonate ion

Concentration of carbonate ion ([CO3]2-) in seawater. Refer to dataset for units of measure.

Ca [Ca]
calcium ion

Ca (Calcium) concentration. May be reported in parts per million, nanomoles/Liter, or other units. Refer to dataset metadata for units.

OM_ar [OM_ar]
saturation state of the fluid with respect to aragonite

The saturation state of seawater with respect to aragonite (known as OMEGA_ar) is a measure of the thermodynamic potential for aragonite to form or to dissolve, and is defined as the product of the concentrations of dissolved calcium and carbonate ions in seawater, divided by their product at equilibrium.

Dataset Maintainers

Rinat GabitovMississippi State University (MSU)
Karyn L. RogersRensselaer Polytechnic Institute (RPI)
Chiara BorrelliUniversity of Rochester
Nancy CopleyWoods Hole Oceanographic Institution (WHOI BCO-DMO)

BCO-DMO Project Info

Project Title Biologically induced methane oxidation and precipitation of carbonate minerals: An experimental study
Acronym Deep Sea Geochem CaCO3
Created August 9, 2018
Modified September 14, 2018
Project Description

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 (Desulfovibrio salexigens) 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.

Data Project Maintainers
Rinat GabitovMississippi State University (MSU)Principal Investigator
Karyn L. RogersRensselaer Polytechnic Institute (RPI)Co-Principal Investigator
Chiara BorrelliUniversity of RochesterContact