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Geochemistry and microbiology


A total of 38 interstitial water samples were taken from Holes U1316A, U1316B, and U1316C (19, 12, and 7 samples, respectively). One interstitial water sample per core was collected from Hole U1316A. Two samples per core were collected from Hole U1316B. In Hole U1316C, one interstitial water sample per core was collected from Cores 307-U1316C-4R through 9R and also 11R.

Interstitial water and gas

Variations in interstitial water composition at this site are driven principally by microbially mediated reactions, diffusion of chemical species resulting from diagenesis at depths greater than those sampled, and sediment accumulation and burial (Table T5).

Strontium, lithium, and boron have similar profiles (Fig. F22A–F22C). The concentrations of all three are relatively constant between the seafloor and 20 mbsf. Concentrations then smoothly increase in a concave-upward fashion to a maximum at 120 mbsf. These three elements covary linearly between the seafloor and 105 mbsf, implying that in this interval all three behave nearly conservatively (Fig. F23). Although the decrease in the slope of the profiles with depth may in part reflect decreasing diffusivity with depth, we attribute the shape of the profiles to the high sedimentation rates that characterize Unit 1 sediments at this site. Higher concentrations of these elements at depth are most likely the result of carbonate diagenesis for Sr and silicate diagenesis for Li and B.

In contrast, the concentration profiles of alkalinity, dissolved inorganic carbon (DIC), sulfate, Fe, Mn, ammonium, dissolved methane, and dissolved ethane are affected by microbial activity (Fig. F22D–F22L). Alkalinity and DIC have similar downhole profiles. Both are slightly elevated relative to seawater in the uppermost core at 1.4 mbsf and rise to a local maximum at ~4.5 mbsf. There is a local minimum at ~20 mbsf followed by a broad maximum centered near 100 mbsf. The maximum at 100 mbsf is most likely due to anaerobic methane oxidation. Below this depth, values of both DIC and alkalinity decrease toward the bottom of the hole.

Dissolved methane concentrations (based on analyses of the safety gas samples) (see “Geochemistry and microbiology” in the “Methods” chapter) are below detection (~0.2 µM) to a depth of 49.8 mbsf (Fig. F22J; Table T6). There is a small maximum centered near 80 mbsf and concentrations increase below 100 mbsf, with concentrations reaching 2 µM by 129.8 mbsf. The gradient between 100 mbsf and the bottom of the hole is due to production (methanogenesis) and diffusion from within the deeper Miocene sediments and anaerobic methane oxidation centered at ~100 mbsf. Adsorbed methane (based on the difference of samples treated with NaOH and the safety gas samples) is above the detection limit throughout the hole and generally increases with depth (Fig. F22K).

Dissolved ethane remains below the detection limit until 79 mbsf (Fig. F22L). Like methane, it generally increases at greater depths and the gradient implies anaerobic consumption. At the methane–sulfate transition (~80 mbsf), the ethane/methane ratio is higher than at greater depths, which suggests that methane is preferentially consumed through anaerobic microbial processes.

The seawater concentration of dissolved sulfate is 28.9 mM, and at 1.4 mbsf it is already depleted to 25.2 mM (Fig. F22F). Sulfate reaches a local minimum of 18.3 mM between ~10 and 20 mbsf, indicative of sulfate reduction in the 0–10 mbsf interval. It then decreases nearly linearly until ~110 mbsf. Between 110 and 137.8 mbsf, measured concentrations are between 5 and 7 mM. Minimum sulfate concentrations of 4–6 mM are reached at depths below 95 mbsf and overlap the methane-bearing interstitial waters.

Similar to sulfate, dissolved ammonium reaches a local maximum between 10 and 20 mbsf, consistent with sulfate reduction and the oxidation of nitrogen-containing organic matter (Fig. F22I). Between 40 mbsf and the bottom of the hole, the slight concave-downward profile implies additional metabolism of nitrogen-containing organic matter.

Dissolved Mn has a maximum at the shallowest depth sampled and drops sharply at 6.9 mbsf (Fig. F22H). From there its concentration decreases until 60 mbsf, where it remains constant at the analytical detection limit. Dissolved Fe is scattered but has higher values in the upper section of the core from 0 to ~50 mbsf (Fig. F22H).

Concentrations of Ca2+ are similar to that of seawater at the top of the pore water profile and increase slightly downcore to a value of 12.2 mM (Fig. F24). This gradual trend is overprinted by short-lived excursions to slightly higher values at ~30, 45, and 120 mbsf. Magnesium concentrations show a gradual decrease downcore, from ~51 mM at the top of the profile to ~35 mM in the deepest sample. At ~30 mbsf, values increase to 51 mM. This excursion matches the excursion evident at the same depth in the calcium pore water profile.


Carbonate is present at significant levels throughout Hole U1316A. In the upper 50 mbsf, it scatters around an average of 17 wt% (Fig. F25; Table T7). It then increases to 60 wt% over a short interval between ~50 and 55 mbsf. Between ~65 and 119 mbsf, it is again relatively constant with an average of 28 wt%. At greater depths there is a monotonic increase to 64 wt%.


Whole-round core and catwalk sampling

Syringe samples were taken from Hole U1316A (Fig. F26), and whole-round cores (WRCs) plus additional syringe samples were taken from Holes U1316B and U1316C for shore-based work. For Hole U1316B, a 2 m section from each core was selected on the catwalk. After removal of the interstitial water sample together with a variety of smaller syringe samples, the remainder was taken directly from the catwalk to cold storage at 10°C, where WRC sections were cut and properly packed. For Hole U1316C, one or two 1.5 m sections from each core were selected and run through the multisensor core logger (MSCL). After the interstitial water and headspace gas samples were taken from the core-end, the remainder of the core was taken to cold storage, where the core section was cut and packed (see “Geochemistry and microbiology” in the “Methods” chapter). Appropriately packed samples were stored at either +4°C or –80°C. The distribution and packing/storing requirements of all samples and their sample codes are given in Figures F27 and F28. A total of 287 WRC/​syringe samples were obtained.

Total prokaryote enumeration

Samples of 1 cm3 plugs for total prokaryote enumeration were taken during core processing on the catwalk from Holes U1316A (19 samples between the near surface and 129.70 mbsf) and U1316C (7 samples between 74.20 and 137.80 mbsf). All the samples in Hole U1316C were stored for later, shore-based processing.

Prokaryotes were present in all samples studied to the depth of 129.70 mbsf (Fig. F29). The detection limit was estimated at 2 × 105 cells/cm3, based on calculations on a single membrane filter. For each sample, duplicate filters were used to provide a measure of variability. Where a zero count occurred, the prokaryote population was estimated by combining the data from both membranes and treating it as one subsample. This provides the only possible estimate of the population size in such samples but does not allow any measure of variability.

The overall depth profile of cell numbers per cubic centimeter initially follows a trend observed at other Ocean Drilling Program sites (Parkes et al., 2000), although there are some substantial deviations (Fig. F29). At approximately the base of lithostratigraphic Unit 1 (40.15 mbsf) (see “Lithostratigraphy”) cell numbers decrease rapidly from the largest population observed in this hole, 3.58 × 107 cells/cm3 (Sample 307-U1316A-5H-3, 135–140 cm), to 3.18 × 105 cells/cm3, the smallest population observed in this hole at 78.65 mbsf (Sample 10X-2, 135–140 cm). This is a 112-fold reduction in number over 38.5 m and approaches the detection limit. From 78.65 mbsf, cell numbers start to increase again and are back within prediction limits by 84.65 mbsf (Sample 307-U1316A-12X-1, 135–140 cm). For the remainder of this hole, they closely follow the predicted profile.

The major decrease starting between 40.19 mbsf (Sample 307-U1316A-5H-3, 135–140 cm) and 49.65 mbsf (Sample 6H-3, 135–140 cm) seems clearly linked to the lithologic change between Subunit 1B and Subunit 2B at 44.4 mbsf, where the sediment changes from laminated silty clays to silty clay and fine to medium sand (see “Lithostratigraphy”). However, the striking increase in prokaryote numbers from ~78.65 mbsf (Sample 307-U1316A-10X-2, 135–140 cm) seems to be related to pore water geochemical changes (Fig. F22) (see “Geochemistry”). At 78.8 mbsf there is the first significant appearance of methane and this continues to increase, albeit to low concentrations (maximum = 6000 ppm at 118.69 mbsf), over the remainder of the hole. Methane represents a significant carbon source for some prokaryotes and is probably the reason for the increase in cell numbers. Interestingly, below 80 mbsf there is a small but persistent concave-downward departure from the linear decrease in the sulfate concentration profile that is observed between 20 and 80 mbsf. The changes in these two geochemical profiles suggest prokaryotic anaerobic oxidation of methane may be occurring below 80 mbsf.

Numbers of dividing cells (an index of growth activity) are typically between 5% and 10% of the total count. As expected, dividing cells, as a percentage of the total count, are high near the surface (Fig. F29). They then decrease rapidly to ~5.3% at 11.65 mbsf (Sample 307-U1316A-2H-3, 135–140 cm) before increasing again to 13.1% at 21.15 mbsf (Sample 3H-3, 135–140 cm). Thereafter they decrease rapidly to 0% by 56.15 mbsf (Sample 307-U1316A-7H-1, 135–140 cm), where they remain until 84.65 mbsf (Sample 12X-1, 135–140 cm). This nearly 30 m thick zone is characterized by a rapidly decreasing prokaryotic population and absence of any evidence of cell division and represents a dead zone in the sediment column. The reasons for this are not immediately apparent. Below 84.65 mbsf, significant numbers of cells in division were observed, rising from 0% at 84.65 mbsf to ~22% at 94.35 mbsf (Sample 307-U1316A-15X-1, 0–5 cm) and correlating with an increasing prokaryote population. These data need to be interpreted with caution as the absolute numbers of dividing and divided cells are very low and thus data variability is high. Nevertheless, the change from zero to high although variable levels of cell division is striking.

Contamination tests

Perfluorocarbon tracer

PFT was injected continuously into the drilling fluid during coring of Holes U1316B and U1316C (1 mL/L seawater drill fluid). Because PFT is dissolved in the drilling fluid rather than suspended as particles, these results are estimates of the potential for microbial contamination and provide an upper limit of actual microbial contamination. All air samples taken from the catwalk and the laboratory air tested negative for PFT, indicating that no background PFT signal was provided by the analytical procedures. All drill fluid samples investigated were positive for PFT, and some of the outer core scrapings were also positive (Table T8), whereas the maximum concentration of PFT in the outer core sections (Sample 307-U1316C-9R-4, 125–130 cm) was about a factor of 5 times lower than in the drill fluid. In contrast to the outer core samples, PFT signal was not detected in any inner core samples (both APC and RCB) at Site U1316, indicating that seawater penetration into the core was minimal or absent.

Particulate tracer

Fluorescent microspheres were deployed in all cores from which microbiology (MBIO) samples were taken in Holes U1316B and U1316C. Subcores of 5 cm3 were taken from the bottom cut end of each MBIO section adjacent to the interstitial water WRC. Microspheres were detected in one sample from Hole U1316B and two samples from Hole U1316C (Table T8). Although it is not possible to accurately quantify the level of contamination, these numbers must be compared with the original microsphere suspension of 7,000,000 microspheres per microliter. The number of microspheres detected in Sample 307-U1316B-6H-3, 48.35–48.4 cm (42/cm3) is still only equivalent to the estimated minimum of 6 pL/cm3, or 6 ppb.