Acquisition methods are described in the following publication: Orcutt, B.N. et al. 2005

Core sectioning, porewater collection and analysis

At each sampling site, sediment sub-samples were collected for porewater analyses and at selected depths for microbial rate assays (AOM, anaerobic oxidation of methane oxidation; methanogenesis (MOG) from bicarbonate and acetate). Sediment was expelled from core liner using a hydraulic extruder under anoxic conditions. The depth intervals for extrusion varied. At each depth interval, a sub-sample was collected into a cut-off syringe for dissolved methane concentration quantification. Another 5 mL sub-sample was collected into pre-weighed and pre-combusted glass vial for determination of porosity (determined by the change in weight after drying at 80 degrees celsius to a constant weight). The remaining material was used for porewater extraction. Sample fixation and analyses for dissolved constituents followed the methods of Joye et al. (2010). 

Microbial Activity Measurements 

To determine AOM and MOG rates, 8 to 12 sub-samples (5 cm3) were collected from a core by manual insertion of a glass tube. For AOM, 100 uL of dissolved 14CH4 tracer (about 2,000,000 DPM as gas) was injected into each core. Samples were incubated for 36 to 48 hours at in situ temperature.  Following incubation, samples were transferred to 20 mL glass vials containing 2 mL of 2M NaOH (which served to arrest biological activity and fix 14CO2 as 14C-HCO3-).  Each vial was sealed with a teflon-lined screw cap, vortexed to mix the sample and base, and immediately frozen. Time zero samples were fixed immediately after radiotracer injection. The specific activity of the tracer substrate (14CH4) was determined by injecting 50 uL directly into scintillation cocktail (Scintiverse BD) followed by liquid scintillation counting. The accumulation of 14C product (14CO2) was determined by acid digestion following the method of Joye et al. (2010).  The AOM rate was calculated using equation 1:

AOM Rate = [CH4] x alphaCH4 /t x (a-14CO2/a-14CH4)            (Eq. 1)

Here, the AOM Rate is expressed as nmol CH4 oxidized per cm3 sediment per day (nmol cm-3 d-1), [CH4] is the methane concentration (uM), alphaCH4 is the isotope fractionation factor for AOM (1.06; (ALPERIN and REEBURGH, 1988)), t is the incubation time (d), a-14CO2 is the activity of the product pool, and a-14CH4 is the activity of the substrate pool. If methane concentration was not available, the turnover time of the 14CH4 tracer is presented.

Rates of bicarbonate-based-methanogenesis and acetoclastic methanogenesis were determined by incubating samples in gas-tight, closed-tube vessels without headspace, to prevent the loss of gaseous 14CH4 product during sample manipulation. These sample tubes were sealed using custom-designed plungers (black Hungate stoppers with the lip removed containing a plastic “tail” that was run through the stopper) were inserted at the base of the tube; the sediment was then pushed via the plunger to the top of the tube until a small amount protruded through the tube opening. A butyl rubber septa was then eased into the tube opening to displace sediment in contact with the atmosphere and close the tube, which was then sealed with a open-top screw cap.  The rubber materials used in these assays were boiled in 1N NaOH for 1 hour, followed by several rinses in boiling milliQ, to leach potentially toxic substances.    

A volume of radiotracer solution (100 uL of 14C-HCO3- tracer (~1 x 107 dpm in slightly alkaline milliQ water) or 1,2-14C-CH3COO- tracer (~5 x 107 dpm in slightly alkaline milliQ water)) was injected into each sample. Samples were incubated as described above and then 2 ml of 2N NaOH was injected through the top stopper into each sample to terminate biological activity (time zero samples were fixed prior to tracer injection).  Samples were mixed to evenly distribute NaOH through the sample.  Production of 14CH4 was quantified by stripping methane from the tubes with an air carrier, converting the 14CH4 to 14CO2 in a combustion furnace, and subsequent trapping of the 14CO2 in NaOH as carbonate (CRAGG et al., 1990; CRILL and MARTENS, 1986).  Activity of 14CO2 was measured subsequently by liquid scintillation counting. 

The rates of Bi-MOG and Ac-MOG rates were calculated using equations 2 and 3, respectively:

Bi-MOG Rate = [HCO3-] x alphaHCO3/t x  (a-14CH4/a-H14CO3-)     (Eq. 2)

Ac-MOG Rate = [CH3COO-] x alphaCH3COO-/t  x  (a-14CH4/a-14CH314COO-)     (Eq. 3)

Both rates are expressed as nmol HCO3- or CH3COO-, respectively, reduced cm-3 d-1, alphaHCO3 and alphaCH3COO- are the isotope fractionation factors for MOG (assumed to be 1.06). [HCO3-] and [CH3COO-] are the pore water bicarbonate (mM) and acetate (uM) concentrations, respectively, t is incubation time (d), a-14CH4 is the activity of the product pool, and a-H14CO3 and a-14CH314COO are the activities of the substrate pools. If samples for substrate concentration determination were not available, the substrate turnover constant instead of the rate is presented.

For water column methane oxidation rate assays, triplicate 20 mL of live water (in addition to one 20 mL sample which was killed with ethanol (750 uL of pure EtOH) before tracer addition) were transferred from the CTD into serum vials. Samples were amended with 2 x 10^6 DPM of 3H-labeled-methane tracer and incubated for 24 to 72 hours (linearity of activity was tested and confirmed). After incubation, samples were fixed with ethanol, as above, and a sub-sample to determine total sample activity (3H-methane + 3H-water) was collected. Next, the sample was purged with nitrogen to remove the 3H-methane tracer and a sub-sample was amended with scintillation fluid and counted on a shipboard scintillation counter to determine the activity of tracer in the product of 3H-methane oxidation, 3H-water. The methane oxidation rate was calculated as:

MOX Rate = [methane concentration in nM] x alphaCH4/t  x  (a-3H-H2O/a-3H-CH4-)     (Eq. 3)