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The shipboard geochemistry program for Expedition 346 emerged with five concepts in mind. First, the primary objectives of the cruise revolve around paleoceanography, particularly the construction of detailed sedimentary records (see “Introduction, background, and objectives” and “Stratigraphic correlation and sedimentation rates”). As such, the probability of obtaining a continuous sedimentary splice at each drill site, without missing intervals, was maximized as possible.

Second, previous drilling in this region during Legs 127/128 (Tamaki, Pisciotto, Allan, et al., 1990; Ingle, Suyehiro, von Breymann, et al., 1990) demonstrated that sedimentary sequences throughout the region contain abundant authigenic minerals. This includes carbonates and silicates, which stem in part from dissolution of microfossils (Matsumoto, 1992; Nobes et al., 1992), as well as sulfides, which can react with oxygen during transport and storage. Sufficiently resolved interstitial water profiles are desirable to understand the location of authigenic mineral formation because mineral diagenesis impacts the sedimentary record and paleoceanographic objectives.

Third, melting of continental ice sheets decreased global ocean water salinity significantly over the last 20,000 years. For bottom water at a given location, the salinity decrease can be quantified by modeling interstitial water chloride or δ18O profiles (e.g., McDuff, 1985; Schrag et al., 1996; Adkins et al., 2002). The magnitude of salinity change appears to have differed from one deepwater location to another, presumably because of variations in oceanography. Interstitial water profiles amenable for such work have not yet been generated in the northwest Pacific marginal seas.

Fourth, previous work, both on piston cores and on sediment recovered from drilling during Legs 127/128, has emphasized that deep-sea sediment across the Marginal sea spans a particularly wide range of chemical environments derived from microbially mediated organic carbon degradation (Masuzawa and Kitano, 1983; Murray et al., 1992). For example, some locations (Site 794) have a relatively modest maximum alkalinity (<12 mM) and little to no gas in interstitial water at depth; other locations (ODP Site 798) have very high alkalinity (>75 mM) and abundant methane within 100 m of the seafloor (Tamaki, Pisciotto, Allan, et al., 1990; Ingle, Suyehiro, von Breymann, et al., 1990). It is increasingly important to document and understand the deep biosphere across a broad range of sites, given overarching IODP goals.

Fifth, sampling with Rhizons (see “Rhizons”) is evolving to become a complementary approach for collecting interstitial water during drilling expeditions, especially from horizons within the upper 100 m of the sediment column. Such sampling seems especially useful during paleoceanography expeditions, where core flow can be fast and sediment preservation is at a premium. However, Rhizons have been used mostly without basic tests and without clear protocol.

To summarize, the Geochemistry group desired to generate high-quality data sets on a paleoceanography cruise that could enhance rather than hinder primary objectives.

Sample collection

General plan

In line with the paleoceanographic objectives of the expedition and general goals of IODP, we constructed a geochemistry sample plan before drilling began. The strategy accounts for three geochemists on each 12 h shift and a nominal water target of 30–40 mL for squeezed samples. The water budget reflects the desired quantity for a range of analyses, including routine shipboard measurements, several shore-based requests, and extra archive water for potential future work (Table T9). We document the original plan below, which includes our “predrilling” rationale, and discuss modifications and impacts of this plan in various site chapters.

Sampling plan for routine sampling over the upper sedimentary sequence (usually equivalent to APC recovery)
  • Gather a water sample from within the core liner above the uppermost sediment recovered (typically Core 1H in Hole A). This “mudline” sample can be used for comparison with bottom water and interstitial water (Gieskes, 1975).

  • Collect two whole-round samples per APC core in Hole A for interstitial water squeezing (IW-Sq). These IW-Sq samples would be collected at the base of Sections 1 and 4, such that they are evenly spaced down Hole A, and one whole-round sample (Section 1) would likely occur “off-splice.” Whole-round samples from APC cores would begin at a 5 cm length and increase to a maximum of 10 cm downhole because porosity and water content would generally decrease with depth below the seafloor.

  • Obtain two headspace (HS) gas samples per APC core in Hole A. These would be collected at the top of Sections 2 and 5, so as to pair with IW-Sq samples.

  • Collect two sediment samples per APC core in Hole A to be analyzed for carbonate and organic carbon contents. These would be splits of interstitial water squeeze cakes, so as to minimize discrete sampling of sediment core.

  • Obtain one whole-round interval, nominally one per core for the uppermost four cores and every alternate APC core in Hole A after that, for shore-based microbiology research. These would be 5 cm in length and, where appropriate, adjacent to whole-round IW-Sq samples.

  • Obtain two syringe samples (~2.5 cm3) on selected APC cores in Hole A for microbiological cell counts. These samples would be associated with the microbiology whole rounds or IW-Sq samples.

No routine geochemistry sampling was planned for Holes B or C.

Sampling plan for routine sampling over the lower sedimentary sequence (usually equivalent to XCB recovery)
  • During XCB coring, the sediment often becomes “biscuited,” and upward of half the material over a given depth interval is not appropriate for water sampling. To maintain a minimum pore water budget (Table T9), whole-round samples from XCB cores typically need to be thicker. On the other hand, at deep sediment depths, concentration changes in dissolved constituents often occur over longer depth intervals. This means that, for many purposes, interstitial water samples can be spaced farther apart. Thus, for XCB operations, we aimed to collect one 10 cm long whole-round sample per core for interstitial water squeezing in Hole A and over extended depths in Holes B or C should they surpass the total depth of Hole A. The samples would be taken consistently at the base of Section 1 such that, over depths spanned by more than one hole, the probability of collecting the sample off-splice was maximized.

  • Obtain one HS gas sample per core at the top of Section 2, so as to pair with interstitial water samples taken for squeezing. This HS sample would be taken with a cork borer or from chips.

  • Collect one sediment sample per core, a split of the squeeze cake, to analyze for carbonate and organic carbon contents.

The combined routine sampling plans would provide reasonably detailed interstitial water and gas profiles down the cored sedimentary section at all sites, as well as sufficient samples for requested shore-based microbiology work. It should also allow maximum stratigraphic correlation between three holes because no whole-round samples would be taken from Hole B or Hole C, except from XCB cores at deep depths, where decimeter-scale stratigraphic correlation between holes using various techniques (e.g., GRA, magnetic susceptibility, and NGR) often becomes very difficult (e.g., Wilkens et al., 2013).

This sampling strategy, however, will not generate tight depth constraints on chemical reaction horizons, such as the sulfate–methane transition (SMT). The plan also precludes shipboard investigations of probable interest; for example, variability in sediment chemistry over short depth increments (e.g., dark and light intervals) and the composition of unusual sedimentary features (e.g., nodules). Without additional “nonroutine” sampling, several basic studies would have to await initiation of shore-based investigations.

Sampling plan for nonroutine sampling
  1. Collect one Rhizon water sample per section from the upper 50 m of one hole at selected sites to enable construction of δ18O and Cl profiles that relate to changes in bottom water salinity since the Last Glacial Maximum.

  2. Gather Rhizon water samples from several probable off-splice intervals of Hole A at several sites (e.g., upper 70 cm of Section 1 and all of Section 7). The purpose of this sampling would be to conduct tests of Rhizon sampling and to aid stratigraphic correlation through comparison of interstitial water chemistry profiles between Holes A and C.

  3. Obtain higher resolution Rhizon water samples from depth intervals of Hole C where interstitial water analyses of Hole A show major changes in chemical gradients. This would allow definition of precise depths of certain microbial reaction zones. As part of this strategy, it is important to process the samples from Hole A as fast as possible, so as to guide the placement of the high-resolution Rhizon suite of samples.

  4. Collect multiple squeeze and Rhizon samples across numerous intervals in holes specifically dedicated for geochemistry.

In all cases above, Rhizon sampling would commence after core sections pass through the STMSL and during the time (nominally 3–4 h) when cores equilibrate for NGR logging (see “Stratigraphic correlation and sedimentation rates”).

Rhizon sampling occurred in the Downhole Logging Laboratory located immediately adjacent to the lore loggers, thus minimizing impact on core flow. Basic physical properties logs (specifically GRA and magnetic susceptibility) would thus be obtained before Rhizon sampling, in the case that water removal over short distances (several centimeters) might impact overall stratigraphic correlation. Overall, core flow was not negatively impacted by the Rhizon sampling.

The following amendments allow for construction of detailed geochemical profiles across reaction zones but with a very low probability of preventing a continuous sedimentary splice. The amendments also provide a means to generate basic knowledge regarding sediment chemistry on ship before most sediment sampling and analysis occurs on shore.

  • Collect Vacutainer (VAC) samples of selected gas voids at sites and across depth intervals where they occur.

  • Collect supplementary sediment samples from the working half of Hole A, assuming sufficient time for sediment processing and analyses exists. These would be analyzed for carbonate and organic carbon contents. Generally, these would be splits of samples taken for physical property measurements (see “Physical properties”) or discrete samples of interesting sedimentary horizons (e.g., dark and light layers; Tada et al., 1992).

  • Collect selected sediment samples from the working half of Hole A for examination by SEM. For example, SEM analyses of sulfide phases on the ship and later on shore may provide insight into the effects of sulfide oxidation upon surrounding sediment over time.

Gas hydrate recovery was a possibility at several drill sites, given that it was recovered at ODP Site 796 (Shipboard Scientific Party, 1990), in drill sites of the Ulleung Basin (e.g., Kim et al., 2013), and in piston cores along the western slope of Japan (e.g., Snyder et al., 2007). Along with the above plan, we submitted details on how these ephemeral solids would be handled. However, specimens of gas hydrate were not recovered during Expedition 346.

As can be seen by progressing through the “Geochemistry” sections in each site chapter, the sampling plans outlined above were modified extensively for several reasons. For example, the ability to generate a composite sediment record in almost “real time” with two holes (see “Stratigraphic correlation and sedimentation rates”) meant that a Hole C was not needed at most sites. The quick realization that Rhizons gave excellent interstitial water samples also opened exciting avenues for research.

Gas sampling

Volatile hydrocarbons and other gases in sediment were collected by two techniques: HS and VAC. Most gas samples were collected by the HS procedure, as required by IODP safety protocols, even though measured values are not easily interpreted at high gas concentrations (Paull et al., 2000).

For the HS procedure, 3–5 cm3 of sediment was collected from the top of core sections on the catwalk using a graduated syringe or cork borer. Samples were extruded into a 21.5 cm3 glass serum vial containing 5 mL of saturated NaCl solution. The vial was then sealed with a septum and metal crimp cap and lightly swirled. Measuring sediment volume and placing into a saturated NaCl solution remain nonroutine during IODP expeditions but allow for systematic semiquantification of interstitial gas volume at low gas concentrations (D’Hondt, Jørgensen, Miller, et al., 2003). Vials were then heated at 70°C for 30 min. After heating, a 5 cm3 volume of gas from the headspace in the vial was sampled with a glass syringe for analysis by gas chromatography.

At sites with high gas concentrations at in situ pressure, gas voids develop during core recovery because of supersaturation at atmospheric pressure. Some of these voids were sampled using the Vacutainer approach (even though traditional vacuum containers were not used). A device with a heavy-duty needle and valve was pushed through the core liner. A closed syringe was attached and then filled with gas through the valve. A 5 cm3 volume of the gas sample was directly analyzed by gas chromatography.

Interstitial water sampling

Interstitial water was extracted from sediment cores by two different techniques: squeezing of whole-round intervals and removal using Rhizon samplers. The first technique has been used routinely during scientific ocean drilling expeditions for nearly four decades (Manheim and Sayles, 1974; Sayles and Manheim, 1975; Gieskes, 1975), and resultant waters are commonly referred to as interstitial water samples. The second technique was first used for scientific drilling during IODP Expedition 302 in 2004 (Dickens et al., 2007) and has steadily become more common (e.g., Expedition 320/321 Scientists, 2010b; Schrum et al., 2012). Each technique appears to have advantages and disadvantages, but a series of unanswered questions surrounds the use of Rhizons. For these reasons, we have distinguished interstitial water samples as coming through a squeezer (IW-Sq) or a Rhizon (IW-Rh) and have dedicated part of our geochemistry program to tests involving Rhizon sampling. All whole-round and Rhizon samples were taken at room temperature (and pressure), although we are aware of potential temperature effects on interstitial water chemistry (Sayles and Manheim, 1975; Gieskes, 1975).

Whole rounds

Whole-round samples for squeezing (IW-Sq) were taken on the catwalk after a core was cut into 1.5 m (nominal) sections. The samples were taken to the Geochemistry Laboratory, where they were pushed out of the liner onto a tray, trimmed to remove potential contaminating sediment and water, and placed into a Manheim Ti squeezer (modified from Manheim and Sayles, 1974). When there was a backlog, such as occurs when several whole rounds are taken over a short duration, some whole rounds were stored in a refrigerator. For all squeezed samples, times from collection through squeezing did not exceed more than 2 h.

During extraction of interstitial water, gauge pressures as high as 24,000 lb force were applied to squeezers using a Carver laboratory hydraulic press. Emerging interstitial water passed through a prewashed (18.2 MΩ water) Whatman Number 1 filter fitted above a titanium screen within the squeezer and a 0.45 µm polysulfone disposable filter (Whatman Puradisc PES) outside the squeezer before entering a precleaned (10% HCl) 60 mL syringe. For the last three IODP drilling sites (U1428, U1429, and U1430), we also placed a 0.20 µm polysulfone disposable filter (Whatman Puradisc PES) between the 0.45 µm filter and the syringe in an effort to remove very small particles.

After squeezing, the compressed cylinder of sediment (squeeze cake) was removed and the squeezing apparatus was cleaned. Portions of the squeeze cake were used for shipboard sediment analyses (below), whereas the rest (>75%) was saved for future shore-based examination. Cleaning the squeezers involved initial scrubbing with water, thorough rinsing with 18.2 MΩ water, and air-drying of all components (including using compressed air) and oven-drying of the screens.


Rhizons are thin tubes of hydrophylic porous polymer. When inserted into a sediment core through a hole in the liner and attached to a collection tube and an evacuated syringe, they permit collection of small volumes (typically <12 mL) of interstitial water through suction filtering. Such interstitial water samples are collected without removal of whole rounds, thus preserving the sedimentary record. They also enable water sampling at very high depth resolution (<5 cm). For Expedition 346, the chosen samplers were Rhizon CCS 5 cm female Luers (flat tip and 2.5 mm outer diameter) from Rhizosphere Research Products (Netherlands).

A basic procedure for collecting Rhizon samples on drilled cores has been developed over the last few years. After a core section is cut on the catwalk and brought to the Core Laboratory, it is placed on the STMSL, which quickly generates a record of GRA and magnetic susceptibility along the section. This step is important because GRA and magnetic susceptibility records often form the backbone for stratigraphic correlation between holes, because GRA measurements closely correspond to wet bulk density, and because Rhizon sampling could potentially decrease wet bulk density over several centimeters. The latter effect occurs because water removal introduces air along the inside of the core liner (Dickens et al., 2007). The core is then turned so the plane separating the archive and working halves of the core is vertical. Small holes (~3 mm diameter) are drilled through the core liner along this vertical plane, and Rhizon samplers with accompanying tubes, valves, and 10 mL syringes are inserted. The time required to extract 10 mL of interstitial water is dependent on the porosity and permeability of the sediment as well as the strength of suction generated by the syringe. New syringes extracted interstitial water much more quickly than syringes that had been used and acid-washed. Interstitial water is extracted over 0.1–3 h (unless modified for a specific reason) as a core section equilibrates for NGR logging. The water sample is then taken to the Geochemistry Laboratory for analyses.

Despite this general procedure, numerous issues concerning Rhizon sampling of drilled cores remain. Do Rhizons need pretreatment before insertion? How much do they impact sediment properties, such as wet bulk density and construction of spliced sediment records? Do they render significantly different chemistry than squeezed samples? We conducted a series of tests during Expedition 346 to evaluate some of these questions. Results are reported in the site chapters of this volume.

Solid-phase sampling

Small volumes of sediment were taken from squeeze cakes or the discrete intervals of interesting sedimentary horizons from the working halves of cores. These samples were freeze-dried and subsequently powdered by hand with an agate mortar and pestle for chemical analyses. The samples generally contain 1–5 wt% salt, which precipitated from pore space during the freeze-drying process.

Microbiology sampling


A set of sterilized 2.5 cm3 syringes with the tapered tips removed was provided to the Geochemistry Laboratory before departure. These syringes were used to collect samples for cell counting.

After a core was sectioned on the catwalk and a whole-round IW-Sq was sliced off with an ethanol-sterilized spatula, a syringe was plunged into the center of the exposed core to collect a cylinder of sediment. While holding the plunger, about 2.0 cm3 of sediment was ejected from the syringe into a tube containing 10% filtered formalin solution. The tubes were labeled and stored in a refrigerator at 4°C within 20 min after arrival on the catwalk.

Whole rounds

There was interest in collecting sediment for shore-based microbiological DNA/RNA analyses. Soon after selected cores arrived on the catwalk, a 5 cm long whole-round interval of sediment was cut from the core using an ethanol-sterilized spatula. Typically, such whole-rounds were located directly above an IW-Sq sample, which meant near the bottom of Section 1 and included the interval that was sampled for microbial cell counting (above). The whole round was capped on both ends, placed in an opaque gray Ziploc bag, flushed with nitrogen, and heat sealed. This bag was placed in a clear plastic bag and heat sealed again. Samples were processed and stored in a –80°C freezer within 15 min after arrival on the catwalk.

General commentary

Before examining our analytical methods and ultimately traveling along our geochemical odyssey (see the “Geochemistry” section in each site chapter), we thought it appropriate to insert an interlude briefly commenting on four topics.

First, volatile gas concentrations determined on HS samples are imperfect measurements. The gases evolve as they pass from the pore space of a sediment plug into a headspace within a closed container. At low gas concentrations, the volume of sediment and headspace within the vial are important, as is the solubility of gas, which depends on temperature and salinity. Of course, gas solubility is also important at high gas concentrations, but in this case, much of the gas can escape sediment before the HS sample is even collected (Paull et al., 2000). Volatile gases measured by the HS technique during most drilling expeditions are presented as parts per million by volume (ppmv), although millimolar is a far more useful unit. We have maintained the use of ppmv but have measured the volume of sediment such that shore-based work might convert to mM with physical property measurements.

Second, the chemistry of seawater, and by extension interstitial water in the marine environment, can be expressed using several different units (e.g., Millero et al., 2008). Within the laboratory on board the JOIDES Resolution, the customary unit for reporting concentrations of dissolved species is molarity (M), or mole per liter of solution (seawater) (Gieskes et al., 1991; Murray et al., 2000). This differs from the unit expressed in much of the literature, including classic papers on interstitial water chemistry (e.g., Sayles and Manheim, 1975), which is mole per kilogram of solution (seawater). However, such reporting of mole per liter is common practice and convention in the water column chemistry community. Conversion between the two units is straightforward (Table T10). The reason why this subject arose during Expedition 346 is that deep waters of the marginal sea are slightly but noticeably fresher than most of the ocean. Below ~300 m water depth, these waters are typically referred to as Japan Sea Proper Water and have a salinity of ~34.05 (Sudo, 1986). This becomes important to understanding the interstitial water chemistry.

Third, most dissolved constituents have more than one species of significance. For example, in seawater, B can occur as B(OH)4 or B(OH)3 (Millero et al., 2008). We have avoided assigning charge to many dissolved constituents throughout this volume, in part to emphasize that the measured value typically reflects the sum of multiple species.

Fourth, the depth of most samples needs consideration. This reflects the vicissitudes of drilling, including the presence of core gaps and overlaps and differential stretching of sediment. When comparing samples between holes at a given site, it is typically appropriate to convert reported depths beneath the seafloor to a composite depth scale (see “Stratigraphic correlation and sedimentation rates”). However, when using concentration gradients to estimate fluxes, a justified depth below seafloor is more correct.

Gas analyses

Two gas chromatographs were used for gas analyses. One was specially calibrated for determining methane concentrations, and the other was calibrated for determining higher hydrocarbon concentrations. Both gas chromatographs are Agilent 6890 models equipped with a 2.4 m × 3.2 mm stainless steel column packed with 80/100 mesh HayeSep R and a flame ionization detector. The instruments quickly measure concentrations of methane (C1), ethane (C2), ethene (C2=), propane (C3), and propene (C3=).

The gas syringe was directly connected to the gas chromatograph through a 1 cm3 sample loop, and 5.0 mL gas was injected. Helium was used as the carrier gas, and the gas chromatograph was programmed to start with an oven temperature of 80°C held for 8.25 min before ramping at 40°C/min to 150°C, with a final holding time of 5 min. Data were collected and evaluated with an Agilent Chemstation data-handling program. Chromatographic response was calibrated against known standards provided by Scott Specialty Gases.

Interstitial water analyses


The general standard used for interstitial water analyses was International Association for the Physical Sciences of the Oceans (IAPSO) standard seawater. This was Batch P154 obtained from OSIL Environmental Instruments and Systems. However, IAPSO is not fully appropriate for certain interstitial water analyses (e.g., samples with very high concentrations of Ba or Fe).


Salinity was analyzed with a Fisher Model S66366 portable salinity refractometer named Erik. A few drops of sample were applied to the daylight plate assembly with an eye dropper, and the measurement was read through the eye piece. Typical measurement precision is ±1‰, and blanks were analyzed routinely to check for contamination.

Alkalinity and pH

We began with the strict goal of pH and alkalinity being generally measured immediately after squeezing or Rhizon extraction. The pH was measured with a combination glass electrode (Brinkman pH electrode), and alkalinity was determined by Gran titration with an autotitrator (Metrohm 794 Titrino). Three milliliters of interstitial water was titrated with 0.1 M HCl at 25°C. The electrode was calibrated using a series of buffers with a pH of 4, 7, and 10. Standard ratios were calculated by running a series of standard solutions of different concentrations of Na2CO3 (5, 20, 40, 50, and 100 mM) and IAPSO seawater. The standard correction factor was specified before each analysis depending on the alkalinity.

IAPSO seawater was analyzed every ~12 h or after a period of nonuse to check accuracy. Concentrations were typically within 5% of the expected value for IAPSO (2.325 mM), and correction factors were adjusted if the measured value was outside of the accepted range (2.21–2.44 mM). Alkalinity is reported in millimolar units throughout this report, rather than milliequivalents per liter (meq/L), following previous discussion (Gieskes et al., 1991).

As will become obvious later in the site chapters of this volume, alkalinity was measured on some samples 24 h after collection. This is not ideal because alkalinity of interstitial water samples generally decreases over time (Gieskes, 1975). However, the change in alkalinity is not as great as perceived.


Chloride concentrations were measured by titration with 0.1 M silver nitrate (AgNO3) using a Metrohm 785 DMP Titrino autotitration system. Interstitial water aliquots of 0.5 mL were diluted with 30 mL of dilute nitric acid to keep precipitated flocculent well separated, which increased the probability of contact between Cland Ag+ during titration. IAPSO seawater standard was analyzed to check precision and accuracy (expected chlorinity = 559 mM). The instrument was recalibrated if it was not within 0.5% of the expected concentration (556.2–561.8 mM). A recalibration was not required during Expedition 346 because the standard checks always fell within range.

Ion chromatography

In June 2013, a new Metrohm 850 professional ion chromatograph with an 858 professional sample processor was added to the Geochemistry Laboratory. In principle, this instrument can measure concentrations of major anions (Cl, SO42–, and Br) and major cations (Ca2+, Na+, Mg2+, and K+). Only anion measurements from ion chromatography are reported for Expedition 346 drilling sites because instrument problems precluded meaningful analyses of cation concentrations (although these were quantified using inductively coupled plasma–atomic emission spectroscopy [ICP-AES], see below).

Interstitial water was diluted 1:100 with 18.2 MΩ deionized water in preparation for ion chromatography analysis. The IAPSO seawater standard was diluted by various amounts (1:80 to 1:500) to create a six-point calibration curve. The r2 for the calibration curve was always >0.99, and relative standard deviation varied from 0.8% to 3.4%.

Accuracy was checked by running 1:100 dilution of IAPSO standard seawater every ~10 samples, and a new calibration curve was run if measured concentrations deviated from the expected values (28.9 mM for SO42– and 0.865 mM for Br). Precision was 3% for SO42– and Br.

After instrument repairs during the expedition, SO42– concentrations approached ~2 mM in samples deeper than the SMT boundary, whereas prior to the repairs they had approached zero. Procedural blanks were analyzed and repeatedly yielded zero SO42–, indicating that there was no instrument contamination. The reason for the 2 mM results generated at depths where SO42– should be completely absent is currently unknown.

Inductively coupled plasma–atomic emission spectroscopy

Suites of major (Ca, Mg, K, and Na) and minor (B, Ba, Fe, Li, Mn, Si, and Sr) elements were analyzed by ICP-AES with a Teledyne Prodigy high-dispersion ICP spectrometer.

The shipboard ICP-AES procedure is based on Murray et al. (2000) and the user manuals for new shipboard instrumentation with modifications as indicated. Samples and standards were diluted using 2% ultrapure HNO3 spiked with 10 ppm Y with dilution ratios of 1:200 for major element analyses (Na, K, Ca, and Mg) and 1:20 for trace element analyses (B, Mn, Fe, Sr, and Ba).

Samples were run in batches of typically 30–50 samples. With every batch run for minor elements (B, Ba, Fe, Li, Mn, Si, and Sr), an eight-point calibration curve was created using synthetic seawater spiked with minor elements to varying degrees and used to convert background-corrected intensities to concentrations. For major elements (Ca, Mg, K, and Na), a seven-point calibration curve was created using different dilution levels of IAPSO seawater. A drift solution was run every five samples. Blanks were run with every batch to check for contamination and allow for blank subtractions. The standard reference material, IAPSO seawater, was prepared three times using a separate pipette tip for each dilution, and all three were run as unknowns. The standard deviation of these triplicate analyses divided by the average value indicated the precision of each run. The IAPSO precision within a single run and between all runs was <2% of the measured value for Ca, K, Mg, Na, B, Li, and Sr. Concentrations of Ba, Fe, Mn, and Si in IAPSO commonly fell below detection limit and could not be used to quantify precision for these elements. The IAPSO values were compared to the known concentrations (for the conservative elements in IAPSO with known concentrations) to check that the results were accurate.

Each run used background-corrected intensities that were drift corrected, and a procedural blank was subtracted if there was significant drift (>5%). For some elements (e.g., Fe, Si, and B), the standards prepared with synthetic seawater showed a lower background level around the spectral peak than IAPSO standard seawater and pore water samples. The matrix difference is likely responsible, and in the future, spiking IAPSO with minor elements would aid in reducing this matrix affect. There was a spectral interference between Ba and Li when Ba concentrations were high. Samples with high Ba created a spectral peak that overlapped with the lower background point on the ICP-AES peak for Li. On sites with high Ba, Li was background corrected only using the right-hand background point (higher wavelength).

The Ba lines on the ICP were problematic at high concentrations because the instrument response was not linear at that range. Although the shape of the Ba profiles and relative intensities are likely accurate, Ba concentrations are too high and a correction is required using samples analyzed on shore after the expedition. In this report, unconstrained Ba concentrations are reported and the inaccuracies are noted in the specific site chapters when necessary.


Dissolved ammonium (NH4+), phosphate (PO43–), silica (H4SiO4), sulfide (HS), and “yellowness” were determined spectrophotometrically using an Agilent Cary 100 ultraviolet-visible (UV-VIS) light spectrophotometer. In general, interstitial water samples can have color either because of microbial reactions below the seafloor or because of addition of reagents in the laboratory. Colored samples were then “sipped” from a vial (~3 mL) into a cell and measured for absorbance at a specific wavelength. The size of the sample cell was 715 µL. Measurements of the first three species listed above are routine during scientific drilling expeditions (Gieskes et al., 1991), but a brief description of the methods is outlined below.

Ammonium concentrations were determined using the method of Solórzano (1969), which relies on the diazotization of phenol and the subsequent oxidation of the diazo compound by Chlorox to yield a blue color that is analyzed at 640 nm. With each run, standards were prepared to make a 13-point calibration curve covering the range of ammonium concentrations encountered in interstitial water samples. When concentrations exceeded the maximum calibration standard, which is common at sites with high levels of organic matter degradation, samples were diluted as necessary and corrected for the dilution after conversion to concentration. A standard was run independent of the calibration curve to check for accuracy, and sample replicates were run to check for precision. Precision was at 2% of the measured value, and results were accurate within precision.

Phosphate concentrations were determined using the method described by Strickland and Parsons (1968) as modified by Presley (1971). In this method, orthophosphate reacts with Mo(VI) and Sb(III) in an acidic solution to form an antimony-phosphomolybdate complex. Ascorbic acid reduces this complex, forming a blue color that is measured at 885 nm. Standards were prepared with each run to create a nine-point calibration curve to convert absorbance to concentration. Samples were diluted as necessary if concentrations exceeded the calibration range and were corrected after conversion to concentration. Precision and accuracy checks were quantified the same way as in the ammonium procedure. Precision was <0.5% of the measured value, and independent standard checks were accurate within precision.

Silica concentrations were determined by the molybdate method, where dissolved silica reacts with a molybdate reagent in an acid solution to form molybdosilicic acid. The complex then is reduced by ascorbic acid to form molybdenum blue, which is measured at 812 nm. A 10-point calibration curve was analyzed with each run to convert absorbance to concentration. Precision, quantified similarly to ammonium and phosphate, was <0.5%, and independent standards were accurate within precision.

Total dissolved sulfide (ΣH2S = H2S + HS) was determined by the methylene blue method (Cline, 1969). As soon as the interstitial water was extracted by squeezing or Rhizons, 0.6 mL of 5 wt% zinc acetate was added to 3 mL of sample in a glass vial to fix the sulfide in solution. A mixed diamine reagent was added to the vial and reacted with the fixed sulfide to form methylene blue. The absorption of the blue color is measured at a wavelength of 670 nm. Concentrations were diluted as necessary for absorbance to fall within the calibration range and corrected after conversion to concentrations. A seven-point calibration curve was created from standards that were analyzed with each run. During every run for all analyses, samples and standards were analyzed in random order to ensure that downcore trends are not an artifact of varying instrument response.

Interstitial water can become visibly yellow at sites with high amounts of organic carbon degradation because certain dissolved organic compounds impart color (You et al., 1993; D’Hondt, Jørgensen, Miller, et al., 2003). At the beginning of Expedition 346, we decided to systematically quantify this yellowness by measuring the absorbance of samples at 325 nm. This wavelength was chosen because it had been used to examine the color of interstitial water at several previously drilled sites (You et al., 1993; D’Hondt, Jørgensen, Miller, et al., 2003). However, examination of absorbance at multiple wavelengths across a suite of samples showed that the color spectrum is complex, as known from studies of seawater color (Briucaud et al., 1981). Thus, analyses evolved as the expedition progressed so that samples were eventually measured for absorbance at 227, 325, and 375 nm. Initially, 1.0 mL aliquots of interstitial water were placed into vials with 2.0 mL of deionized water. These were measured for absorbance along with a standard in every batch, so the measurement could be compared with those determined elsewhere independent of instrument parameters, especially including the path length of light. However, at sites with interstitial water having low absorbance, samples were eventually analyzed without dilution, as this improves analytical precision. In all cases, the standard used for comparison was the internationally recognized JWBL standard, procured from Kilmarnock, Scotland. Postcruise data processing will use the standard to quantify the magnitude of yellowness in JWBL units for intersite, interlaboratory comparisons, but in this report, yellowness is reported in units of absorbances.

Solid-phase analyses

Sedimentary inorganic and organic carbon

Inorganic carbon (IC) contents were determined using a Coulometrics 5011 carbon dioxide coulometer. Samples of ~10 mg of freeze-dried, ground sediment were reacted with 2 M HCl. The evolved CO2 was back-titrated to a colorimetric end-point. Carbonate content, reported as weight percent, was calculated from the IC content based on the assumption that all inorganic carbon exists as CaCO3:

wt% CaCO3 = wt% IC × 8.33.

Analytical reproducibility was determined by replicate measurements of selected samples and internal standards. Expected errors (1σ), based on previous expeditions, range from 0.3 to 0.4 wt%.

Total carbon (TC) content was determined using a Thermo Electron Flash EA 1112 elemental analyzer equipped with a Thermo Electron packed GC column CHNS/NCS (polytetrafluoroethylene; length = 2 m; diameter = 6 mm × 5 mm) and thermal conductivity detector (TCD). Aliquots of 10 mg of freeze-dried, ground sediment in tin cups were combusted in the reactor oven of the instrument with a pulse of O2. In cases of high carbonate, the sample amount was cut in half. Nitrogen oxides were reduced to N2, and the mixture of gases produced (N2, CO2, H2O, and SO2) was separated by gas chromatography and measured by the TCD. The gas chromatograph oven temperature was held at 65°C. All EA measurements were calibrated by comparison to a pure sulfanilamide standard. Total organic carbon (TOC) was determined as the difference between TC and IC:

wt% TOC = wt% TC – wt% IC.

The C/N ratio was determined and reported as an atomic percent (at%).