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Shipboard geochemistry for Expedition 342 included routine sets of analyses for

  • Hydrocarbon gases;

  • Interstitial water composition;

  • Sedimentary geochemistry including inorganic carbon, sedimentary organic carbon, total carbon and nitrogen, and C/N ratios; and

  • Pyrolysis characterization of sedimentary organic matter.

These analyses were conducted to satisfy routine shipboard safety and pollution prevention requirements, to characterize interstitial water and sediment geochemistry for shipboard interpretation, to guide shore-based sampling, and to provide samples for shore-based research. The procedures and instruments used during Expedition 342 are generally similar to those used during recent IODP expeditions; many of these are described by Pimmel and Claypool (2001). Comments on routine sampling and deviations from standard practice are noted below and in the individual site chapters.

Hydrocarbon gases

Sediment gas composition was typically determined at each interstitial water sampling point once every core. The routine headspace procedure involved the placement of a 5 cm3 sediment sample in a 21 cm3 glass serum vial that was sealed with a septum and metal crimp cap and heated at 70°C for 30 min for standard IODP hydrocarbon safety monitoring. After heating, a 5 cm3 volume of headspace gas was removed with a glass syringe for analysis by gas chromatography. A second gas sampling procedure using a vacuum container was used when gas pockets or expansion voids appeared in the core while still in the core liner. A device with a heavy-duty needle was used to penetrate the core liner, and an attached syringe was employed to collect the gas.

Headspace gas samples were analyzed with an Agilent/HP 6890 Series II gas chromatograph equipped with a 2.4 m × 2.0 mm stainless steel column packed with 80/100 mesh HayeSep R and a flame ionization detector (FID). The instrument quickly measures concentrations of methane (C1), ethane (C2), ethene (C2=), propane (C3), and propene (C3=). Gases were introduced by injection from a 5 mL syringe directly connected to the gas chromatograph system through a 1 cm3 sample loop. Helium was used as the carrier gas, and the gas chromatograph oven temperature was programmed to start at 80°C and hold that temperature for 8.25 min before ramping at 40°C/min to 150°C, with a final holding time of 5 min. The FID temperature was 250°C.

In instances where samples were collected in vacuum containers, gases were analyzed with an Agilent/HP 6890A Series II gas chromatograph equipped with a FID and a thermal conductivity detector (TCD) to measure concentrations of C1–C6 hydrocarbons, N2, O2, and CO2. Gases were introduced by injection from a 5 mL syringe directly connected to the gas chromatograph system through a 1 cm3 sample loop.

TCD separation used three columns:

  1. A 6 ft × 2.0 mm inner diameter (ID) stainless steel column (Poropak T; 50/80 mesh),

  2. A 3 ft × 2.00 mm ID stainless steel molecular sieve column (13X; 60/80 mesh), and

  3. A 2.4 m × 3.2 mm ID stainless steel column packed with 80/100 mesh HayeSep R (Restek).

FID separation was performed on a DB1 capillary column (60 m × 0.32 mm) with 1.5 µm phase thickness. FID separation used helium as the carrier gas, and the gas chromatograph oven temperature was programmed to hold for 2 min at 50°C, ramp at 8°C/min to 70°C, and then ramp at 25°C/min to 200°C, with a final holding time of 5 min. The FID temperature was 250°C.

Data were collected and evaluated with an Agilent ChemStation data-handling program. Chromatographic response was calibrated to different gas standards with variable quantities of low–molecular weight hydrocarbons. Gas components are reported as parts per million by volume (ppmv) of the injected sample. Methane in the uppermost headspace samples is also expressed as millimoles per liter per volume (mM), assuming a porosity of 0.45 µm, a sample volume of 5 cm3, and a vial volume of 21.5 cm3:

C1 (mM) = ppmv C1 × [(21.5 – 5)/(22,400 × 5 × 0.45)]
= ppmv C1 × 0.0003.

Interstitial water analyses

Interstitial water analyses were carried out on cores from Sites U1402–U1407. Interstitial water was extracted from 5 to 10 cm long whole-round sections that were cut and capped immediately after core retrieval on deck. Whole-round sections for interstitial water analyses were taken from the bottom of Section 6 in Hole A or, alternatively, from the bottom of Section 1 in Hole A. This strategy was used to avoid removing whole rounds from the middle of cores, thereby preserving material integral to the splicing process (see “Stratigraphic correlation”). Occasionally, samples from more than one hole were analyzed and integrated in a single depth profile (splice) using the appropriate composite depth scale as the depth reference, if possible. Before squeezing, samples were removed from the core liner and the outer surfaces were carefully scraped with spatulas to minimize potential contamination by the coring process.

Whole rounds were placed into a titanium and steel squeezing device modified after the stainless steel squeezer of Manheim and Sayles (1974) and squeezed at ambient temperature with a hydraulic press at pressures of up to 170 MPa (~25,000 psi). The interstitial water squeezed out of the sediment was extruded into a prewashed (in 10% HCl) 60 mL plastic syringe attached to the bottom of the squeezer assembly. The solution was subsequently split into five parts:

  1. One part (10 mL) was filtered through a 0.45 µm polysulfone disposable filter (Whatman) into a vial for shipboard routine analyses of salinity, pH and alkalinity, chlorinity, dissolved inorganic carbon (DIC), anions and cations (Cl, SO42–, Na+, K+, Ca2+, and Mg2+), nutrients (PO43–, NH4+, and NO2 + NO3), and minor elements (Li, B, Mn, Fe, Sr, Ba, Si, and P).

  2. One part (5 mL) was added to 225 µL mercuric chloride and 10 µL of concentrated sulfuric acid and refrigerated in headspace-free vials for shore-based ammonium δ15N measurements.

  3. One part (2 mL) was added to 100 µL of mercuric chloride for shore-based liquid DIC measurement.

  4. A water split was placed into a 5 mL cryovial and spiked with 10 µL HNO3 for inductively coupled plasma–atomic emission spectroscopy (ICP-AES) analysis.

  5. The remaining interstitial fluids were sealed in glass ampules and archived.

Following interstitial water removal, squeeze cakes were removed from the squeezing device, placed in sterile bags, and stored at –20°C for postcruise molecular biomarker analyses.

Interstitial water was also sampled at higher resolution (every 50 cm) from Hole U1404C to test for the presence of gas hydrates with Rhizon samplers. Originally developed as soil moisture samplers for root zones, rhizon samplers consist of thin tubes of hydrophilic porous polymer that extract water from sediment under vacuum. Rhizon samplers have recently been applied to sampling of sediment interstitial water, including during IODP Expeditions 302 (Dickens et al., 2007) and 320/321. Rhizon CSS-F 5 cm core solution samplers (Rhizosphere Research Products) were soaked in distilled water for ~1 h before use. Rhizon samplers were wiped clean of excess water and carefully inserted through holes drilled through the core liner at a 55° angle so that the 5 cm porous tube was in contact with presumably undisturbed sediment away from the core liner on either side. Samples were taken after the core was run through the STMSL. Acid-washed 10 mL syringes were attached to each Rhizon sampler, pulled to generate vacuum, and held open by hand. The first ~1 mL of water was discarded, with the rest collected and split for shore-based and shipboard analyses. Collection of 10–12 mL typically took 30 min.

Salinity, pH, and alkalinity analyses

Interstitial water analyses followed the procedures outlined by Gieskes et al. (1991), Murray et al. (2000), and user manuals for new shipboard instrumentation with modifications, as indicated. Interstitial water was analyzed for salinity with a Fischer Model S66366 salinity refractometer previously calibrated using the International Association of Physical Sciences of the Ocean (IAPSO) seawater standard. Alkalinity and pH were measured by Gran titration with a Brinkman pH electrode Metrohm autotitrator. The IAPSO seawater standard was used for standardization of alkalinity.

Ion chromatography

Sulfate, chloride, magnesium, calcium, sodium, and potassium concentrations in interstitial water were determined with a Dionex ICS-3000 ion chromatograph on 1:200 diluted aliquots in 18 MΩ water. The IAPSO seawater standard was used for standardization of measurements made on the ion chromatograph.

Spectrophotometric analyses

Phosphate, ammonium, and total nitrate and nitrite concentrations in interstitial water were determined by an Agilent Cary 100 UV-Vis spectrophotometer unit, an automated system that controls sample analysis and reagent aspiration, dispensing, heating, and mixing. In the phosphate method, orthophosphate reacts with Mo(VI) and Sb(III) in an acidic solution to form an antimony phosphomolybdate complex. Ascorbic acid reduces this complex to form a blue color, measured at 885 nm. Potassium phosphate monobasic (KH2PO4) was used to produce a calibration curve and as an internal standard. In the ammonium method, phenol undergoes diazotization and the subsequent diazo compound is oxidized by sodium hypochlorite to yield a blue color, measured spectrophotometrically at 640 nm. Ammonium chloride (NH4Cl) was used to produce a calibration curve and as an internal standard. In the nitrate/nitrite method, the sample passes through an open, tubular, copperized cadmium coil that reduces nitrate to nitrite. Both the reduced nitrate and any preexisting nitrite are diazotized with sulfanilamide and coupled with N-(1-naphthyl)ethylenediamine dihydrochloride to form a colored azo dye, measured spectrophotometrically at 540 nm.

Major and trace element analyses by ICP-AES

Concentrations of selected elements (Li, B, Mn, Fe, Sr, Ba, and Si) in interstitial water were determined by ICP-AES with a Teledyne Prodigy high-dispersion ICP-AES. The method for shipboard ICP-AES analysis of samples is described in detail in Murray et al. (2000).

Each batch of ~20 samples run on the ICP-AES contained six artificial standards of known increasing concentrations for all elements of interest, as well as two additional standards to monitor instrumental drift. Samples were analyzed in batches to take advantage of achieved calibration, and each sample was analyzed three times from the same dilute solution (i.e., in triplicate) within a given sample run. Samples and standards were diluted 1:10 using 2% HNO3 prior to analyses.

Following each run of the instrument, the measured raw-intensity values are transferred to a data file. Instrument drift was negligible during analyses of interstitial water, and therefore no correction was applied. A calibration line for each element was calculated using the results for the known standard solutions. Element concentrations in the samples were subsequently calculated from the relevant calibration line. Replicate analyses of one of the artificial standards were used to estimate precision and accuracy for minor elements, which typically was between 2% and 5%.

Depletion of shipboard supplies of the laboratory strontium standard at Site U1407 prompted a mission to collect seawater for preparation as a replacement standard. Four batches of 150 mL of seawater were filtered with 0.2 µm filters to remove colloidal particles, transferred to precleaned 200 mL beakers and heated to concentrate solutions by evaporation until ~2% of the original volumes remained.  When complete and cooled, batches were combined to make one uniform solution, which was then acidified to 2% nitric acid, the same as the original standard used aboard Expedition 342. We were ultimately unable to confirm the calibration range; therefore, strontium values for Sites U1407–U1411 are not reported.

Bulk sediment geochemistry

We routinely took one 5 cm3 sample of sediment for bulk geochemistry from the working section half of each core. Sample intervals were occasionally adjusted depending on the prevailing lithology, and not all samples were analyzed for every element in order to best approach the scientific questions in the available time and with the available resources. Whenever possible, samples were taken adjacent to moisture and density samples to maximize integration of analytical data (e.g., calcium carbonate content), to calibrate higher resolution core logging data, and to calculate mass accumulation rates. Samples were freeze-dried for 24 h and ground in a mortar for subsequent analyses. Geochemical analyses included percent carbonate and elemental analyses of carbon and nitrogen.

For intervals sampled for microbiology, squeeze cakes from the interstitial water samples were freeze-dried for onshore elemental analyses (C/N) and intact polar lipids.

Inorganic carbon and carbonate

Inorganic carbon content of sediment samples was determined using a Coulometrics 5011 CO2 coulometer. One carbonate determination was performed typically every 1.5 m section of core and at higher resolution (up to every 10 cm) across selected lithologic transitions or in zones of pronounced changes.

Freeze-dried and ground sediment (~10–15 mg) was reacted with 2N HCl. The liberated CO2 was backtitrated to a colorimetric end point. Sediment carbonate content (in weight percent) was calculated from inorganic carbon (IC) content by assuming all carbonate occurs as calcium carbonate:

wt% CaCO3 = wt% IC × 8.33.

Reproducibility was determined by replicate measurements of selected samples and standards (100 wt% CaCO3) treated as samples (every 10 samples). Typical standard deviations are 0.3–0.4 wt% on sample and standard replicates.

Elemental analyses

Total carbon (TC) and total nitrogen (TN) contents of sediment samples were determined with a ThermoElectron FlashEA elemental analyzer 1112 equipped with a ThermoElectron packed column (CHNS/NCS) and a TCD. An aliquot of ~8–20 mg of freeze-dried, ground sediment was weighed into tin cups, and the sample was combusted in a stream of oxygen at 950°C. The reaction gases were passed through a reduction column to reduce CO3 to CO2, nitrogen oxides to nitrogen, SO3 to SO2, and H2O to H2. The gases were then separated by the CHNS/NCS multiseparation column (Thermo 26008215) before detection by the TCD. H2 values are not useful because they represent hydrogen from both organic matter and (clay) minerals. Sulfur values were not reported after Site U1403 because the vanadium pentoxide catalyst was contaminated.

All measurements were calibrated to two reference materials: the National Institute of Standards and Technology (NIST) 1646a Estuarine Sediment reference material (TN = 16.27 wt%; TC = 41.84 wt%) or La Luna Shale (TC = 11.32 wt%). Reference material was run after every 10 samples. Analyses were only continued if standard data varied by <1% from these values for N and C. During Expedition 342, the mean total organic carbon (TOC) value measured for NIST1646a Estuarine Sediment reference material was 0.87 ± 0.01 wt% (1σ; N = 10).

Typical precision was assessed using 10 replicate analyses of a rock standard from Weatherford Laboratories (99986; PWDR5) with a minimal TOC content of 3.11 wt% and an IC content of 0.43 ± 0.02 wt% based on coulometry (total carbon = 3.54 wt%). These replicate analyses show standard deviations of 0.032 and 0.046 for N and C, respectively. The coefficients of variation are 0.055 and 0.013 wt% for N and C, respectively.

TOCDIFF content was calculated as the difference between TC (measured on the elemental analyzer) and IC (measured by the coulometry):


These values are probably overestimates because they are determined as a small difference between two numbers comparable in magnitude.

Total organic carbon measurement

During Expedition 342, TOC values determined against the two reference materials gave different values by a factor of ~3 (2.913 derived from cross-calibration and duplicate sample runs under each standard calibration), even for cases where their calibration ranges overlap. For example, low-carbonate samples determined under the La Luna Shale calibration yielded a TC value of 0.5 wt% but ~1.5 wt% under the Estuarine Sediment calibration.  This discrepancy seriously compromises confidence in the shipboard total carbon results. The sources of this discrepancy should be resolved for future shipboard measurements. In order to recover an estimate of TC from the data we had in hand, Scientist Zhonghui Liu developed a mixed-model correction scheme using data from the two calibrations. This method is based on the supposition that the Estuarine Sediment standard applies best for samples with low TC, whereas La Luna Shale applies best for samples with high TC. Using the calibration maximum points we applied onboard (2.2 wt% for Estuarine Sediment and 15.36 wt% for La Luna Shale, normalized to a typical 15 mg sediment sample to be analyzed), mathematically, correction factors can be derived for both calibrations. Under the Estuarine Sediment calibration, if TC < 2.2 wt%, no correction is applied, and if TC > 2.2 wt%,

wt% corrected TC = 2.2 + (x – 2.2) × (15.36 – 2.2)/(15.36 × 2.913 – 2.2),

where x is the measured value and 2.913 is the difference factor between the two standards. Under the La Luna Shale calibration, if TC < 2.2 wt%,

wt% corrected TC = x × 2.913.

If TC > 2.2 wt%,

wt% corrected TC = 2.2 + (x – 2.2/2.913) × (15.36 – 2.2)/(15.36 – 2.2/2.913).

We therefore report TC measurements with the understanding that they should be considered provisional and are likely subject to substantial nonrandom errors that we cannot, at present, estimate. Postexpedition research on these cores should not rely on the TC values reported here, and should seek to make more reliable TC determinations. 

The “acidification method” of TOC analysis was also applied to determine if the analytical precision of TOC in high-CaCO3–low-TOC sediment could be improved. A pilot study from Hole U1404A of 10 freeze-dried samples (~30 mg) in precombusted silver capsules were treated with small aliquots (10 µL) of 2 N HCl at room temperature to remove CaCO3; samples were treated with repeated aliquots until no further reaction was visible and then dried. The 10 selected samples have variable carbonate contents (1.9–56.9 wt%) and thus variable original IC contents (2.9–10.35 wt%) (Fig. F9).

TOC concentration was determined using a Thermo Electron Flash EA 1112 element analyzer for TC. Decarbonated TOC varied from showing increases relative to TOC by difference (two cases with increases of 29% and 75%) to the remainder showing moderate to strong decreases, with reductions of up to 85% compared to original TOC. Removing carbonate should lead to an increase in TOC in the residue weight, not a decrease, so bulk removal of carbonate using the technique described above alters and removes a portion of organic matter. This means that the technique commonly used to measure TOC (bulk offline removal of carbonates by acid digestion followed by TC measurement) results in under-reporting of organic carbon and nitrogen content in the samples in the process.

Organic matter characterization

The type and quantity of organic matter in some sediments was evaluated by pyrolysis assay using the source rock analyzer (SRA) (Weatherford Laboratories). Between 60 and 180 mg of freeze-dried, ground sediment was weighed into SRA crucibles. Volatile hydrocarbon content (HC) was released when the sample was heated at 340°C for 3 min as the S1 peak (mg HC/g rock). Hydrocarbons were released during the pyrolysis of kerogen as the temperature was increased from 340°C to 640°C at 25°C/min as the S2 peak (mg HC/g rock). The nominal temperature of the maximum rate of hydrocarbon yield during the S2 analysis is Tmax. CO2 (as mg C/g rock) released during pyrolysis between 340°C and 390°C is the S3 peak. CO2 (as mg C/g rock) produced by oxidizing the pyrolysis residue at 580°C is the S4 peak, but this is not directly reported. TOCSRA was calculated from S1, S2, and S4, assuming that S1 and S2 are 83% carbon:

wt% TOCSRA = (0.83 × [S1 + S2] + S4)/10.

The carbon-normalized hydrogen index (HI) (mg HC/g C) and the oxygen index (OI) (mg CO2/g C) were calculated from pyrolysis values:

HI = (100 × S2)/TOC and

OI = (100 × S3)/TOC.

All measurements were preceded by a blank and then calibrated to a rock standard from Weatherford Laboratories (99986; PWDR5). The same standard was used for quality control every 10 samples. Analysis was only continued if quality control data fell within the permitted range for this standard, as defined by Weatherford Laboratories. Typical precision was assessed using eight replicate analyses of the rock standard. Coefficients of variation for this data set fell between 0.005 (Tmax) and 0.1 (OI).