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Geochemistry and microbiology

Organic geochemistry

Shipboard organic geochemical studies of cores from Site U1351 included monitoring hydrocarbon gases, carbonate carbon, total organic carbon (TOC), total sulfur (TS), and total nitrogen (TN) and characterizing organic matter by pyrolysis assay. The procedures used in these studies are summarized in "Geochemistry and microbiology" in the "Methods" chapter. All depths in this section are reported in CSF-A.

Volatile gases

All cores recovered at Site U1351 were monitored for gaseous hydrocarbons using the headspace (HS) gas technique, and, where possible, core gas voids were analyzed using the vacuum syringe (VAC) technique (Tables T15, T16; Figs. F46, F47).

Sediment gas content is below detection levels in the uppermost three cores from Hole U1351A. Methane is first detectable at 19.7 m in Hole U1351A and at 18.2 m in Hole U1351B. The dissolved methane gradient (equivalent to 0.17 mM/m) from 18 to 40 m projects to 17.4 m as the division between diagenetic zones, characterized by sulfate reduction above and methane generation below.

Headspace methane content generally increases to a maximum of 22,660 ppmv at 117 m and then decreases downhole. Headspace methane content represents residual gas in cores, with some gas having been lost during core retrieval and sampling. Ethane is present in all cores in which gas was detected, but propane is present only in cores below 750 m (Fig. F46). One section (317-U1351B-106X-3; 931 m) contains a trace of ethene, but no propene was detected in any cores (Table T15). The composition of the gas, as expressed by the C1/C2 ratio (Fig. F46), shows the expected gradual increase in relative ethane content with increasing depth and temperature. However, C1/C2 ratios are unusually low for sediments with such shallow depths of burial and are difficult to reconcile with prevailing sediment temperatures at the present time. The relatively high content of ethane at this site could reflect greater subsurface loss of methane (by intense anaerobic methane oxidation at the sulfate–methane transition), perhaps enhanced by the numerous episodes of shelf emergence during periods of lower sea level. However, the presence of ethane in headspace samples at levels of 10–20 ppm immediately beneath the sulfate reduction zone is unusual in sediments recovered during ODP or IODP expeditions, indicating that the sediments have a history of higher temperatures. A series of unconformities in the uppermost 250 m of sediment suggests some removal of sediment (see "Lithostratigraphy"), which, combined with a history of exposure to warmer seafloor temperatures, could account for the apparently anomalous ethane contents.

The C1/C2 results of the six core void gases (Fig. F46) are generally parallel with headspace gas data but are offset to higher values because more C1 was retained during core retrieval and sampling. Core void gases also contain detectable proportions of wet gas components, including propane, butanes, pentanes, and hexanes, in addition to a trace of ethene (but no propene) in two samples (Table T16). In the two deepest cores sampled for core void gas analysis, including the core with the highest hydrocarbon abundance (Section 317-U1351B-93X-6 [810.6 m]) (Table T16), a marked depletion of n-C4 and n-C5 relative to branched i-C4 and i-C5 (Fig. F47) could be interpreted as a partial removal of normal alkanes by biodegradation but more likely reflects the presence of labile hydrocarbon precursors such as isoprene or terpene moieties.

Carbon and elemental analyses

Inorganic carbon (IC), total carbon (TC), total organic carbon by difference (TOCDIFF), TN, and TS were analyzed in 132 sediment samples from 0 to 1014 m (Table T17; Fig. F48). Table T17 also shows TOCSRA, which is derived directly from the source rock analyzer (SRA), whereas TOCDIFF is derived from the difference between TC (measured on the elemental analyzer) and IC (measured by coulometry).

Carbonate content fluctuates between 0.6 and 62.4 wt%, with high carbonate samples concentrated in the uppermost 72 m and scattered high carbonate samples at 144, 172, and 251 m (Table T17). TOCDIFF fluctuates between 0.1 and 1.3 wt% but is mostly <0.5 wt% and averages 0.27 wt%. TOCDIFF is systematically lower than the organic carbon determination given by the SRA (TOCSRA). TOCSRA ranges from 0.3 to 1.5 wt% and averages 0.87 wt% (see "Total organic carbon measurement").

TN and TS vary considerably with depth (Fig. F49). TN is significantly higher in the uppermost 165 m (0.4–0.8 wt%, but with wide scatter), whereas TN values cluster tightly between 0.25 and 0.35 wt% at greater depths. The higher nitrogen content in Hole U1351A and at the top of Hole U1351B corresponds to a zone where TS varies widely from near zero to 0.6 wt%. Below 200 m, sulfur content is never less than 0.2 wt% (average = ~0.45 wt%) and in some samples is >0.8 wt% (Fig. F49D). TOCDIFF/TN and TOCDIFF/TS ratios are less variable, with TOCDIFF/TN ratios clustering at ~1 ± 0.5 and TOCDIFF/TS generally clustering between 0.5 and 1, except in the upper section (above 200 m), where values vary widely. TOCDIFF/TN and TOCDIFF/TS values seem somewhat low, but this may be partially due to using TOCDIFF to calculate the ratios.

Organic matter pyrolysis

Samples from Holes U1351A and U1351B were characterized by SRA pyrolysis (Table T18; Figs. F50, F51). S1, S2, and S3 vary most in the uppermost 200 m, mirroring elemental analysis data, which also show more variable and higher weight percent N values in this zone (Fig. F49C). Organic matter is dominantly of terrestrial or degraded marine origin, based on predominantly low hydrogen indexes (most samples = <70 mg/g; all samples = <150 mg/g). Again, higher quality organic matter is indicated in the top part of Hole U1351B and in Hole U1351A, with all of the highest hydrogen indexes being in samples shallower than 100 m (Fig. F51A). Oxygen indexes are also more scattered in the uppermost 200 m, suggesting that greater oxygen-containing functional groups may be attached to the kerogen, which is consistent with the low amount of diagenetic alteration of organic matter expected in this zone.

A modified van Krevelen diagram of hydrogen index versus oxygen index (Fig. F52) shows that the sediments dominantly contain Type IV organic matter (no oil-generative potential; dominated by inertinitic macerals), typical of relatively poorly preserved terrestrial organic matter. These results are consistent with data from smear slides, which indicate that little marine organic matter is present and that the visible kerogen comprises plant cells and poorly preserved pollen (see "Lithostratigraphy" and "Biostratigraphy").

Tmax averages 415° ± 15°C. No consistent trend with depth is visible (Fig. F51C). Some samples have a greater proportion of volatile hydrocarbons (S1) relative to S2, resulting in higher production indexes. This is likely due to better preservation of lipids in these particular sediments rather than to the generation of free hydrocarbons, which would not be measurable at the low thermal maturities estimated for this sedimentary succession (maximum temperature near total depth [~1000 m] is probably only 45°–55°C, based on a typical geothermal gradient of 35°–45°C/km for this region) (Sykes and Funnel, 2002; Reyes, 2007).

Total organic carbon measurement

Sediments at Site U1351 were measured for TOC using two completely independent methods:

  1. TOCSRA is derived directly from the SRA as the sum of pyrolysis carbon (0.83 × [S1 + S2]/10) and residual carbon (S4/10). The S4 parameter is the oxidizable (at 580°C) residual carbon remaining after pyrolysis. This technique has the advantage of being derived directly during an analytical run on one instrument.

  2. TOCDIFF is derived from the difference between TC (measured on the elemental analyzer) and IC (measured by coulometry). This technique has the advantage of being derived partly from the traditional elemental analysis approach but the disadvantage of relying on two separate instruments, because carbon associated with carbonate content must be subtracted from TC.

The cross-plot of TC from the elemental analyzer and TC from the SRA and coulometer demonstrates that there is a good correlation (R2 = 0.95) and that the SRA gives consistently higher values than the elemental analyzer (Fig. F53). The difference is mostly ~40% ± 10%. The calibration method using a 3.1 wt% TOC standard for the SRA may have led to an overestimation of TOC in these organically lean sediments, but it is also possible that the elemental analyzer understated TOC. Inaccuracies in carbonate content or wt% TC measurements are responsible for the apparent negative TOCDIFF values (Table T17).

Preliminary interpretation of organic matter

TOC values are low for typical coastal sediments, regardless of the TOC method considered, likely because of the poor preservation of terrestrially derived organic matter in both carbonate- and siliciclastic-rich sediments that were exposed to extensive bioturbation and sediment reworking. The dilution of organic matter by high sedimentation rates may also be a factor in the low TOC. There is no correlation between carbonate content and TOCSRA (Fig. F54). Samples with high TOCSRA (>1 wt%) have carbonate contents between <1 and >40 wt%, whereas organically lean samples can be either rich or poor in carbonate, which is suggestive of a primary preservation control on organic matter rather than depositional facies. Low TOC contents and the SRA data indicate that Site U1351 sediments contain predominantly terrestrial organic matter and suggest that marine productivity was low. In this respect, this Canterbury Basin shelf site contrasts strongly with New Jersey shelf sites (e.g., ODP Site 902 [Shipboard Scientific Party, 1994] and ODP Sites 1071 and 1072 [Austin, Christie-Blick, Malone, et al., 1998]), which contain high amounts of marine algal–derived organic matter.

Inorganic geochemistry

Forty-nine interstitial water samples (Tables T19, T20) from Site U1351 were collected and analyzed. Eleven samples were taken from Hole U1351A, which was cored to 28 m and dedicated largely to chemistry and microbiological sampling. The intended sampling frequency for Hole U1351B was approximately one sample per core to ~270 m and one sample every other core below that, but actual sample spacing was highly dependent on irregular core recovery. Results from Holes U1351A and U1351B are plotted together in Figures F55, F56, F57, F58, and F59.

Salinity, chloride, and pH

The salinities of interstitial water samples primarily range from 3.1 to 3.4 (Fig. F55D), with the two shallowest samples (at 1.1 and 3.8 m) having somewhat higher salinities (3.8 and 3.5, respectively). Chloride increases steadily downhole in the uppermost 80 m from a near-surface value of 545 mM to a maximum of 612 mM at 52 m (Fig. F55A). Below this depth, chloride fluctuates, decreasing to near-seawater values at 240 m and below and irregularly increasing to 570–572 mM in the less frequently sampled intervals below 400 m. Below 920 m, chloride rises slightly.

pH values measured on pore water samples generally vary between 7.3 and 7.5, a somewhat lower range than that observed in typical or deeper water ODP/IODP core samples (Fig. F56C).

Alkalinity, sulfate, ammonium, phosphate, and dissolved silica

The measured alkalinity of interstitial water samples increases immediately beneath the seafloor, reaching a maximum of 10.1 mM at 16.3 m (Fig. F57A). Alkalinity then decreases steadily throughout the rest of the cored section, reaching 1.2–1.3 mM in the interval from 350 m to total depth in Hole U1351B. The alkalinity increase is mirrored by a decrease in sulfate from 28 mM at 1.1 m to 0.31 mM at 16.3 m (Fig. F57B), defining a sulfate reduction zone. Sulfate remains at or near zero throughout the rest of Hole U1351B, with departures from zero probably representing seawater contamination in the cores.

Ammonium initially increases downhole from near zero at the sediment/water interface to relatively low concentrations (2–3 mM) and then remains relatively constant (Fig. F58C). Phosphate initially increases (from 1.9 to 8.6 µM) in the sulfate reduction zone and then rapidly drops off to essentially zero. Silica initially increases from approximate seawater values to a peak of ~750 µM at 60 m and then decreases to values mostly between 200 and 400 µM throughout the rest of Hole U1351B (Fig. F58B).

Calcium, magnesium, and strontium

Calcium and magnesium both initially decrease in the sulfate reduction zone (Fig. F56), probably in relation to the buildup of dissolved bicarbonate and the precipitation of authigenic carbonate. Below the sulfate reduction zone (0–16 m), calcium increases slightly and magnesium decreases or is relatively constant to ~200 m. Below this depth, magnesium decreases again to ~20 mM and remains constant throughout the remainder of Hole U1351B. In contrast, calcium rapidly increases from 16 mM at 200 m to >30 mM below 220 m (Fig. F56D). The Mg/Ca ratio decreases correspondingly. Thereafter, calcium remains relatively constant, decreasing in the middle of the section with poor recovery, before increasing again to >45 mM in the deepest sample (989.75 m). Strontium increases throughout the sulfate reduction zone, stays constant to ~200 m, and then increases steadily to ~800 m, where it reaches a peak of 2.1 mM (Fig. F56A). The Sr/Ca ratio decreases sharply at ~200 m and also declines significantly below ~800 m.

Sodium, potassium, barium, boron, silicon, and lithium

Sodium increases to ~12% above seawater values in the uppermost 50 m and then fluctuates before decreasing below seawater values at ~200 m (Fig. F59B). At ~250 m and below, sodium levels out at values ~8% lower than seawater.

Potassium decreases markedly (from 11 to 2 mM) in the uppermost 250 m and then varies between 2 and 4 mM in the lower 750 m (Fig. F59C).

Barium peaks at 23 µM at 6.8 m before decreasing rapidly to ~3 µM at 16 m (Fig. F59D). Thereafter, the profile is relatively constant to 620 m before decreasing to 1 µM at 760 m. In the deepest section of Hole U1351B, barium increases again from 1 to 6.1 µM.

Boron increases rapidly in the sulfate reduction zone and then increases gradually downhole to ~200 m (Fig. F59E). From 200 to 230 m, boron rapidly increases in concentration again. Below 230 m, boron fluctuates mainly between 3 and 5 mM.

Silicon has a maximum value of 756 µM at 10 m and gradually decreases to ~400 µM below ~200 m (Fig. F58D).

Lithium is low from the surface to 150 m and then increases slowly to 200 m, below which it rapidly increases between 200 and 330 m (Fig. F59A). Below this abrupt increase, lithium remains relatively constant before gradually increasing between 750 m and the bottom of the hole. Some of the inductively coupled plasma–atomic emission spectroscopy data for the sample at 555 m may be spurious (boron, strontium, silicon, and lithium).

Preliminary interpretation of diagenesis

Figure F60 is a combined depth plot of methane, alkalinity, sulfate, calcium, magnesium, phosphate, silica, and barium in the uppermost 100 m of Holes U1351A and U1351B. This plot emphasizes the almost exact synchronicity of some of the microbially mediated biogeochemical changes at Site U1351. The increase in alkalinity represents dissolved bicarbonate generated during sulfate reduction. The alkalinity increase, when corrected for the amount of carbonate precipitation represented by the decrease in calcium and magnesium, just balances the millimolar amount of sulfate removed (Table T21). This approximate 1:1 proportion of bicarbonate added and sulfate removed is consistent with sulfate reduction being driven primarily by the anaerobic oxidation of methane. Methane only appears below 17 m (Fig. F60). The relatively low maximum concentrations of ammonium (3 mM) and phosphate (9 µM) at Site U1351 are also consistent with methane oxidation. Oxidation of marine organic matter during sulfate reduction could potentially produce up to 8 mM of ammonium and 500 µM of phosphate during the reduction of 28 mM of sulfate. Methane oxidation generates no ammonium or phosphate and is thus consistent with the observed low concentrations of these ions.

The increase in dissolved silica throughout the sulfate reduction zone also reflects the decomposition of organic matter, although an increase in silica can also be influenced by the dissolution of diatoms. Changes in calcium and magnesium with depth to 17 m (Fig. F61) probably reflect the precipitation and dissolution of carbonates and/or cation exchange with clay minerals. Both cations decrease rapidly during sulfate reduction, probably because of the formation of isotopically light (from methane oxidation) carbonate. However, little dolomite was observed by XRD analysis of these sediments, so an additional reason for the magnesium trend is possible. Moreover, the increase in ammonium could potentially expel cations from exchangeable positions in clay minerals (Gieskes, 1983). Ammonium ions are known to compete with cations for exchange sites at mineral surfaces (von Breymann et al., 1990). Changes in the concentration of ammonium might lead to other changes in the adsorbed ion fractions.

The downhole decrease in potassium appears to be unrelated to sulfate reduction because the decrease extends considerably farther from the surface to ~150 m (Fig. F59C). Glauconite becomes abundant between 125 and 350 m (see "Lithostratigraphy"), and this may well explain the decrease in potassium in the interstitial waters. A similar but less well defined decrease in sodium (Fig. F59B) extends to ~250 m, and this could also be partly related to glauconite.

Beneath the zone of sulfate reduction, calcium increases, whereas magnesium is relatively constant to ~200 m (Fig. F61). Below 200 m, calcium increases from 16 to 40 mM, whereas magnesium drops from 30 to 20 mM and chloride also decreases. This may represent the dissolution of biogenic calcite with some reprecipitation of diagenetic carbonate. Similar deflections are evident in the depth profiles of lithium, strontium, and boron, although the profiles of other minor and major elements do not show deflections at 200 m. The lack of a consistent swing in all analytes may suggest that the increases in calcium, lithium, and boron are not due to an influx of basinal brine. The abrupt changes between 200 and 230 m could be due to a major change in lithology or an unconformity that promotes these changes in diagenetic processes.

The increase in calcium, lithium, and barium in the interstitial waters deeper in Hole U1351B (>850 m) may also be related to similar diagenetic processes caused by a lithostratigraphic break (Figs. F56, F59). Chloride, salinity, and silica also increase slightly in this depth interval (Figs. F55, F58), whereas strontium decreases (Fig. F56A). Below 800 m, the dominant lithology changes from muddy sand to sandy mud, with occasional mud intervals (see "Lithostratigraphy"). However, XRD data show little mineralogical variation across this zone, although there is a slight increase in mica content in smear slides below 800 m. Specifically, there is no evidence at present for the dissolution of barite or lithium-rich micas that might explain this significant shift in interstitial water composition. The increase in lithium below 850 m also does not correspond to the more subtle increases in silica and silicon, which occur deeper (Fig. F58B, F58D). Therefore, lithium enrichment is probably not from the transformation of biogenic opal; rather, it may reflect ion-exchange or desorption reactions in which lithium that is adsorbed onto marine sediments becomes incorporated into authigenic clays.

In Holes U1351A and U1351B, boron enrichment is pronounced, having values as high as 11 times that of seawater, with two remarkable increases in the sulfate reduction zone and at ~200–230 m. Boron is usually enriched in marine sediments because it has a great affinity for clay minerals (Hingston, 1964). The deeper boron increase is possibly related to the diagenetic opal-A/opal-CT transition. A smaller fraction of boron may also be associated with bacterial degradation of organic matter.


Microbiological shipboard investigations included testing samples for contamination and performing total cell counts.

Sample collection

At this site, 194 samples were collected for microbiological investigations. These were divided in the cold room into three groups for (1) determining the abundance, identity, and distribution of microbial groups (84 samples); (2) determining intact polar lipid concentrations, types, and stable carbon isotope compositions (26 samples); and (3) conducting contamination tests (84 samples). The sampling strategy is described in "Geochemistry and microbiology" in the "Methods" chapter (see Fig. F10 in the "Methods" chapter).

Contamination tracer tests

In order to reveal the extent to which seawater or individual prokaryotic cells penetrated a sediment sample during drilling operations, a particulate tracer (submicron microspheres) and a water-soluble chemical tracer (PFT) were used. Water-soluble and particulate tracer tests have been successfully employed during other ODP/IODP expeditions (e.g., ODP Legs 185 and 201 and IODP Expedition 301) because the tracers are chemically inert and can be detected with high sensitivity (Smith et al., 2000; House et al., 2003; Expedition 301 Scientists, 2005). After core retrieval and the cutting of the 9.5 m core into six 1.5 m sections, 3 cm3 samples for PFT measurement were immediately taken from the section ends adjacent to the whole-round samples selected for microbiological analysis (see "Geochemistry and microbiology" in the "Methods" chapter and Fig. F10 in the "Methods" chapter). Samples for PFT analysis were not taken from the actual whole-round samples because we assumed that flushing the samples with nitrogen in the glove box would remove a large quantity of PFT.

Water-soluble tracer

A calibration curve for the PFT analysis could not be achieved despite several attempts. No consistent set of tests on the samples could be performed because relatively high peaks were observed in the same retention time period as the expected PFT peak when a blank run was analyzed. Additionally, peaks located close to the expected retention time of PFT were sometimes present in the chromatograms of the few samples that were analyzed.

Particulate tracer

The number of fluorescent microspheres (2 × 1011/20 mL bag) deployed is equivalent to the number of prokaryotes in ~400 L of seawater (assuming 5 × 108 bacteria/L). Fluorescent beads were successfully deployed in all cores sampled at Site U1351 except Section 317-U1351A-1H-1, whose microsphere bag broke on the catwalk after the core had been retrieved. Beads were detected on the outside of all cores from which samples were taken except Section 317-U1351A-2H-3 (Table T22). Nevertheless, their deployment was not homogeneous along the core liner. Consequently, microsphere concentrations may temporarily exceed the natural seawater concentrations of prokaryotes in some locations but be absent elsewhere. No difference in microsphere deployment was found between APC and XCB coring. There was a difference in microsphere concentrations of about three orders of magnitude between the outside and the inside part of the cores. Beads were absent from the center of most cores. Between 10 and 100 beads/cm3 were detected in only 6 of the 21 whole rounds collected at this site, which indicates potential contamination of samples with a maximum of 100 prokaryotes/cm3 (Section 317-U1351B-25X-1; Table T22). Therefore, the beads are at best a semiquantitative measure of contamination. The presence of multiple microspheres is a strong indication that contamination by microbe-sized particles has occurred, but their absence cannot confirm that a sample is uncontaminated. At this site, microspheres in the outer part of the sediments were not detected in only one sample (Table T22). Consequently, additional samples were taken from the drilling fluid to screen potential contaminants and compare them with the phylotypes found in the potentially contaminated samples.

Total cell counts

For prokaryotic cell enumeration, 1 cm3 plugs were taken from whole-round microbial characterization samples at 21 depths (between 1.4 and 52.1 m in Hole U1351A [12 samples] and between 117.3 and 989.9 m in Hole U1351B [9 samples]). Prokaryotes were present at all 21 depths, with the exception of two samples (Sections 317-U1351A-31X-3 [261.1 m] and 92X-1 [930.9 m]) in which no cells were detected (Fig. F62). The greatest abundance of cells was found in the near-surface sample (Section 317-U1351A-1H-1 [1.4–1.5 m]), which contains 1.08 × 108 cells/cm3; the lowest number of cells (1.34 × 105 cells/cm3) was found at 930.9 m (Section 317-U1351B-106X-2), a decrease in cell density of a factor of 800. Generally, the total number of cells decreases rapidly with depth in the upper layers of sediment (uppermost 4 m). This depth profile follows the same trend observed at other ODP sites (Parkes et al., 2000). However, the absolute numbers of prokaryotes are lower than the average numbers for all previously examined sites, particularly below 4 m (Fig. F62). These results might be related to the detection limit, which is ultimately controlled by counting statistics. In practice, variability in the blanks (arising from the presence of cells resulting from contamination of reagents and during handling) can actually determine the detection limit (in this case the detection limit is 33 cells/filter membrane). If the number of cells counted in the blank is negligible, then the detection limit is estimated to be the number of cells in a sample required for one cell to be detected with a specified probability (Kallmeyer et al., 2008; Morono et al., 2009). For 2 × 10–4 cm3 of sediment applied to the filter and 200 fields of view counted at 63× and 100× magnification, between 6.02 × 105 and 1.5 × 106 cells/cm3, respectively, must be present in the original sample for one cell to be detected with 95% probability. Treating samples with 1% hydrofluoric acid solution reduced much of the autofluorescence of the filters and allowed the counting of larger amounts of sediment. However, a detection limit <6.02 × 105 cells/cm3 could only be achieved by counting a larger number of fields of view, which was not possible on board ship. Therefore, we decided to count some of the samples with values below detection limit on shore (Fig. F62).