Download URLhttps://www.bco-dmo.org/dataset/660792/data/download
Media Type text/tab-separated-values
Created October 5, 2016
Modified October 11, 2016
State Final no updates expected
Brief Description

Stable carbon isotopic composition of organic matter from seafloor basalts incubated with labeled bicarbonate

Acquisition Description

Acquisition methods are described in the following publication:
Orcutt, B.N., Sylvan, J.B., Rogers, D.R., Delaney, J., Lee, R.W., & Girguis, P.R. 2015. Carbon fixation by basalt-hosted microbial communities. Front. Microbiol. doi:10.3389/fmicb.2015.00904

In summary (excerpted from above):
Basalt samples used in this study were collected from three different crustal formation areas. One glassy, seafloor-exposed basalt came from the ASHES vent field in the Axial Seamount volcano caldera on the Juan de Fuca Ridge off the western coast of North America. The sample was collected in 2009 with the Alvin submersible during dive AD-4527 on RV Atlantis cruise AT15-51 (Sample JdF2009). The basalt piece had a thick (up to 1 cm depth) glassy rim overlying moderately to sparsely vesicular cryptocrystalline groundmass. A film of iron oxide discoloration was evident in the contact between the glass and groundmass. Two altered, seafloor-exposed basalts were collected from the Loihi Seamount off the coast of the big island of Hawai’i in October 2009 by ROV Jason-II during R/V Kilo Moana cruise KM0923: one from “Marker 2” in Pele’s Pit on the summit of the Loihi Seamount, and one from the Ula Nui vent field at the base of the Loihi Seamount. Sample Ula Nui, collected on dive J2-477, was glassy, highly vesicular, and friable, contained ∼3 mm olivine phenocrysts, and displayed visible iron oxide staining. Sample Marker 2, collected on dive J2-481 from an area away from diffuse venting, was pillow basalt with an altered rind Finally, two seafloor-exposed rocks were collected from outcrops surrounding North Pond in April 2012 by ROV Jason-II on dives J2-626 and J2-627 during the MSM20-5 cruise on the R/V Maria S. Merian. The J2-626-R1 rock was a breccia of mm- to cm-sized clasts of aphanitic basalt in a greenish-gray matrix, while the J2-627-R3 rock was a highly serpentinized harzburgite (25–30% orthopyroxene surrounded by completely serpentinized olivine and with chrysotile-filled veins.

Upon retrieval of the samples, all seafloor-exposed rocks and surrounding water from the plastic sampling containers were immediately transferred to glass jars and placed at 4 degrees C until processing. Basalts were then transferred to ethanol- and flame-sterilized steel processing trays and subsampled with ethanol- and flame-sterilized chisels and tweezers. The experiments utilized the glassy rims of the basalts, which were removed, broken into smaller pieces (<1 cm diameter) and transferred to sterile glass serum vials (30–100 ml volume, depending on experiment) containing 0.2-mm-mesh filter-sterilized oxic bottom seawater. All samples were maintained at 4 degrees C.

Basalt fragments (5–20 cm3) were transferred to sterile and baked glass serum vials (to remove organics, vials had been heated to 500 degrees C for 2 h), which were filled to overflowing with sterile oxic seawater then sealed with autoclaved butyl rubber septa and aluminum crimp seals. Multiple replicate bottles were prepared for each sample to enable as many time series as possible with the limited sample volume, including a no-tracer-addition control.

Time series samples were injected with a small volume of 0.2-um filter-sterilized 13C-bicarbonate-labeled solution (in sterile filtered seawater) to achieve the following starting concentrations: JdF2009 incubations received a final concentration of 0.75 mM 13C-labeled bicarbonate against a background of seawater bicarbonate (∼2 mM, or, 27% 13C label); the Ula Nui and Marker 2 rock incubations received a final concentration of 2.7 mM 13C-labeled bicarbonate in background bottom seawater (57% 13C label); and the seafloor-exposed North Pond basalt incubations contained a final concentration of 4.5 mM 13C-labeled bicarbonate in surface seawater (69% 13C label). Vials were incubated in the dark at 4 degrees C until sampling. At each time point, the vials were opened and rock fragments were transferred to sterile plastic centrifuge tubes and frozen for shore-based DNA and organic carbon extraction and analysis. For the JdF2009, Marker 2, and Ula Nui samples, time series were stopped after 1 h, 1 day, and 1 week of incubation. The North Pond samples were incubated for 2-weeks, 2-months, and 4-months intervals. Final concentrations of dissolved inorganic carbon were not measured, as rates of carbon consumption were presumed to be significantly slow compared to the bulk pool size.

The carbon content and stable carbon isotopic composition of biofilms on the incubated basalts were determined by IRMS analysis of subsamples of the basalts that had been stored frozen. Samples were analyzed using a Costech elemental analyzer in line with a Micromass Isoprime continuous flow stable isotope mass spectrometer. Results are presented in the standard δ notation, where isotopic ratios (R) are expressed in per mil (‰) differences relative to the conventional standard, the PeeDee Belemnite limestone. Although the instrument precision was established as 0.3‰, rates of change were conservatively assumed to be robust if there was more than a 2‰ difference between samples; values less than 2‰ difference are reported as below the detection limit (BDL).

Processing Description

BCO-DMO Processing:
– Added the following columns from information Orcutt et al. (2015) paper: cruise, dive, date, water_depth, depth_mbsf, lat, lon;
– replaced “b.d.l.” with “BDL” (below detection limit), “n.a.” with “na”, “n.d.” and blanks with “nd” (no data);
– replaced spaces with underscores in sample names.


ROV Jason [ROV Jason]
The Remotely Operated Vehicle (ROV) Jason is operated by the Deep Submergence Laboratory (DSL) at Woods Hole Oceanographic Institution (WHOI). WHOI engineers and scientists designed and built the ROV Jason to give scientists access to the seafloor that didn't require them leaving the deck of the ship. Jason is a two-body ROV system. A 10-kilometer (6-mile) fiber-optic cable delivers electrical power and commands from the ship through Medea and down to Jason, which then returns data and live video imagery. Medea serves as a shock absorber, buffering Jason from the movements of the ship, while providing lighting and a bird’s eye view of the ROV during seafloor operations. During each dive (deployment of the ROV), Jason pilots and scientists work from a control room on the ship to monitor Jason’s instruments and video while maneuvering the vehicle and optionally performing a variety of sampling activities. Jason is equipped with sonar imagers, water samplers, video and still cameras, and lighting gear. Jason’s manipulator arms collect samples of rock, sediment, or marine life and place them in the vehicle’s basket or on "elevator" platforms that float heavier loads to the surface. More information is available from the operator site at URL.
Micromass Isoprime continuous flow stable isotope mass spectrometer [Isotope-ratio Mass Spectrometer]
Instance Description (Micromass Isoprime continuous flow stable isotope mass spectrometer)

Dried samples of basalt (20–70 mg) were placed into tin foil capsules for isotopic analysis of 13C/12C ratios. Samples were analyzed using a Costech elemental analyzer in line with a Micromass Isoprime continuous flow stable isotope mass spectrometer.

The Isotope-ratio Mass Spectrometer is a particular type of mass spectrometer used to measure the relative abundance of isotopes in a given sample (e.g. VG Prism II Isotope Ratio Mass-Spectrometer).
Costech elemental analyzer [Elemental Analyzer]
Instance Description (Costech elemental analyzer)

Dried samples of basalt (20–70 mg) were placed into tin foil capsules for isotopic analysis of 13C/12C ratios. Samples were analyzed using a Costech elemental analyzer in line with a Micromass Isoprime continuous flow stable isotope mass spectrometer.

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.


incubation_sample [sample]
Name of sample set

unique sample identification or number; any combination of alpha numeric characters; precise definition is file dependent

cruise [cruise_id]
Cruise identifier
cruise designation; name
dive [dive_id]
Dive identifier (A = HOV Alvin; J = ROV Jason)
Unique dive id or number for ROV, AUV or HOV type system dive or deployment
date [date]
Date of sample collection in yyyy-mm-dd format

date; generally reported in GMT as YYYYMMDD (year; month; day); also as MMDD (month; day); EqPac dates are local Hawaii time. ISO_Date format is YYYY-MM-DD (http://www.iso.org/iso/home/standards/iso8601.htm)

water_depth [depth_w]
Depth of water

water depth, in meters

depth_mbsf [meters below seafloor]
Depth of sample

Meters below seafloor (mbsf); convention used for depths below the seabed in geology, oceanography, petrology and ocean drilling; often used in reporting measurements made from sediment cores.

lat [latitude]

latitude, in decimal degrees, North is positive, negative denotes South; Reported in some datasets as degrees, minutes

lon [longitude]

longitude, in decimal degrees, East is positive, negative denotes West; Reported in some datsets as degrees, minutes

incubation_time [incubation time]
Time of incubation

Duration of sample incubation; used in laboratory experiments. Refer to dataset for units of measure.

org_C_wt [C_org]
Weight percent of organic carbon in a sample
organic carbon; CAUTION; usage is in sediment related files
del13C [delta13C]
Stable carbon isotopic composition of basalt organic matter after incubation
Carbon 13 to Carbon 12 ratio of TCO2; CAUTION file dependent definition changes slightly between EqPac and Southern basin studies
ratio_13C_to_12C [unknown]
Absolute ratio of carbon-13 to carbon-12 of basalt organic matter after incubation
association with a community-wide standard parameter is not yet defined
d13C_to_12C [unknown]
Change in ratio of carbon-13 to carbon-12 ration over incubation
association with a community-wide standard parameter is not yet defined
d13C_per_rock [unknown]
Change in nanograms (ng) of carbon-13 in organic matter per gram (g) of rock during experiment
association with a community-wide standard parameter is not yet defined
d13C_per_rock_per_day [unknown]
Change in nanomoles (nm) of carbon in organic matter per gram (g) rock per day
association with a community-wide standard parameter is not yet defined

Dataset Maintainers

Beth N. OrcuttBigelow Laboratory for Ocean Sciences
Shannon RauchBigelow Laboratory for Ocean Sciences

BCO-DMO Project Info

Project Title Primary productivity in young, oxic oceanic crust: rates of activity and autotrophic groups in subsurface and seafloor-exposed basalts from North Pond, Mid-Atlantic Ridge
Acronym Basalt carbon fixation
Created September 30, 2016
Modified October 5, 2016
Project Description

Project description obtained from C-DEBI:
We conducted stable carbon isotope incubations with four subsurface rocks and two seafloor-exposed rocks collected from the North Pond major program site during IODP Expedition 336 in 2011 and the MSM20-5 cruise in 2012, respectively. In combination with similar experiments done with basalts from the Loihi Seamount and the Juan de Fuca Ridge, our experiments document the potential for carbon fixation by basalt biofilm communities, providing the first empirical assessment of potential rates for this process. When scaled to the global production of oceanic crust, our results suggest carbon fixation rates that match earlier predictions based on thermodynamic calculations. Functional gene analyses indicate that the Calvin cycle is likely the dominant biochemical mechanism for carbon fixation in basalt-hosted biofilms. These results provide empirical evidence for autotrophy in oceanic crust, suggesting that basalt-hosted autotrophy could be a significant contributor of organic matter in this vast, dark environment.

Related Publications:
Orcutt, B.N., Sylvan, J.B., Rogers, D.R., Delaney, J., Lee, R.W. Girguis, P.R. 2015. Carbon fixation by basalt-hosted microbial communities. Frontiers in Microbiology, 6: 904.C-DEBI Contribution 277. doi:10.3389/fmicb.2015.00904

Note: This project was funded by a C-DEBI Research Grant. 

Data Project Maintainers
Beth N. OrcuttBigelow Laboratory for Ocean SciencesPrincipal Investigator