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R. Tada, R.W. Murray, C.A. Alvarez Zarikian, W.T. Anderson Jr., M.-A. Bassetti, B.J. Brace, S.C. Clemens, M.H. da Costa Gurgel, G.R. Dickens, A.G. Dunlea, S.J. Gallagher, L. Giosan, A.C.G. Henderson, A.E. Holbourn, K. Ikehara, T. Irino, T. Itaki, A. Karasuda, C.W. Kinsley, Y. Kubota, G.S. Lee, K.E. Lee, J. Lofi, C.I.C.D. Lopes, L.C. Peterson, M. Saavedra-Pellitero, T. Sagawa, R.K. Singh, S. Sugisaki, S. Toucanne, S. Wan, C. Xuan, H. Zheng, and M. Ziegler2

Introduction, background, and operations

This chapter documents the procedures and methods employed in the various shipboard laboratories of the drillship R/V JOIDES Resolution during Integrated Ocean Drilling Program (IODP) Expedition 346. This information applies only to shipboard work described in the Expedition Reports section of the Expedition 346 Proceedings of the Integrated Ocean Drilling Program volume. Methods used by investigators for shore-based analyses of Expedition 346 data will be described in separate individual publications. This introductory section provides an overview of operations, curatorial conventions, depth scale terminology, and general core handling and analyses.

Authorship of the site chapters

All shipboard scientists contributed to this volume. However, certain sections were written primarily by discipline-based groups of scientists as listed below (authors are listed in alphabetical order; no seniority is implied):

  • Background and objectives: R.W. Murray, R. Tada
  • Operations: C.A. Alvarez Zarikian, M. Storms
  • Lithostratigraphy: M.-A. Bassetti, A.C.G. Henderson, K. Ikehara, A. Karasuda, L.C. Peterson, T. Sagawa, S. Toucanne, S. Wan, H. Zheng, M. Ziegler
  • Biostratigraphy: C.A. Alvarez Zarikian, B.J. Brace, S.J. Gallagher, A.E. Holbourn, T. Itaki, Y. Kubota, C.I.C.D. Lopes, M. Saavedra-Pellitero, R.K. Singh
  • Geochemistry: W.T. Anderson Jr., M.H. da Costa Gurgel, J. Dickens, A.G. Dunlea, C.W. Kinsley, K.E. Lee
  • Physical properties: L. Giosan, G.S. Lee
  • Paleomagnetism: S. Sugisaki, C. Xuan
  • Downhole measurements: J. Lofi
  • Stratigraphic correlation and sedimentation rates: S.C. Clemens, T. Irino

Site locations

GPS coordinates from precruise site surveys were used to position the vessel at all Expedition 346 sites. A Syquest Bathy 2010 CHIRP subbottom profiler was used to monitor seafloor depth on the approach to each site to reconfirm the depth profiles from precruise surveys. Once the vessel was positioned at a site, the thrusters were lowered and a positioning beacon was dropped to the seafloor. The dynamic positioning control of the vessel used navigational input from the GPS system and triangulation to the seafloor beacon, weighted by the estimated positional accuracy. The final position for each hole of a given site was the mean position calculated from the GPS data collected over a significant portion of the time the hole was occupied. An inspection of the seafloor using the underwater camera system was conducted at IODP Sites U1428 and U1429 to ensure that they were free of obstructions (submarine cables, fishing lines, etc.) before the start of coring operations.

Coring and drilling operations

The full and half advanced piston corer (APC) systems and the extended core barrel (XCB) system were used during Expedition 346. Multiple holes were drilled at all sites to build a composite depth scale and a stratigraphic splice for continuous sampling after the cruise (see “Sample depth calculations” and “Stratigraphic correlation and sedimentation rates”).

The APC cuts soft-sediment cores with minimal coring disturbance relative to other IODP coring systems. After the APC core barrel is lowered through the drill pipe and lands near the bit, the drill pipe is pressured up until one or two shear pins that hold the inner barrel attached to the outer barrel fail. The inner barrel then advances rapidly (“fires”) into the formation and cuts the core. The driller can detect a successful cut, or “full stroke,” from the pressure gauge on the rig floor.

The depth limit of the APC, often referred to as APC refusal, is indicated in two ways: (1) the piston consistently fails to achieve a complete stroke (as determined from the pump pressure reading) because the formation is too hard and limited core recovery is achieved or (2) excessive force (>60,000 lb; ~267 kN as an example) is required to pull the core barrel out of the formation. When a full stroke could not be achieved, one or more additional attempts were typically made, and each time the bit was advanced by the length of recovered core. Note that this resulted in a nominal recovery of ~100% based on the assumption that the barrel penetrated the formation by the length of core recovered. During Expedition 346, there were a number of partial strokes that still returned nearly full core liners. In these cases, the partial strokes were not viewed as refusal and additional full APC cores were attempted. When a full or partial stroke was achieved but excessive force could not retrieve the barrel, the core barrel was sometimes “drilled over,” meaning after the inner core barrel was successfully shot into the formation, the drill bit was advanced to total depth to free the APC barrel.

The standard (full) APC system contains a 9.5 m long core barrel. In addition to this standard 9.5 m APC system, Expedition 346 used the newly engineered half APC coring system extensively. The half APC system uses a 4.7 m long core barrel. In most instances, the half APC was deployed after the full APC reached refusal. During use of the half APC, the same criteria were applied in terms of refusal as for the full APC system. Use of this new technology allowed for significantly greater continuous APC sampling depths to be attained than would have otherwise been possible without this system. For example, the half APC enabled us to recover the deepest piston core in Deep Sea Drilling Project (DSDP)/Ocean Drilling Program (ODP)/IODP history (Core 346-U1427A-81H from 486.5 to 490.4 m core depth below seafloor, Method A [CSF-A]). This achievement was also the deepest continuously recovered piston cored sequence, initiated at the seafloor and penetrating 490.4 m solely by piston coring (see “Operations” in the “Site U1427” chapter [Tada et al., 2015c]).

Nonmagnetic core barrels were used during all full and half APC deployments. Orientation using the FlexIT tool (see “Paleomagnetism”) was used on standard 9.5 m APC cores, taken most commonly in the earliest deep hole of each site. Formation temperature measurements were made to obtain temperature gradients and heat flow estimates using the third-generation advanced piston corer temperature tool (APCT-3) (see “Downhole measurements”).

The XCB system was used to advance the hole when half APC refusal occurred before the target depth was reached. The XCB is a rotary system with a small cutting shoe that extends below the large rotary APC/XCB bit. The smaller bit can cut a semi-indurated core with less torque and fluid circulation than the main bit, optimizing recovery. The XCB cutting shoe (bit) extends ~30.5 cm ahead of the main bit in soft sediment but retracts into the main bit when hard formations are encountered. The XCB core barrels are 9.5 m long.

The bottom-hole assembly (BHA) is the lowermost part of the drill string. A typical APC/XCB BHA consists of a drill bit (outer diameter = 117/16 inch), a bit sub, a seal bore drill collar, a landing saver sub, a modified top sub, a modified head sub, a nonmagnetic drill collar (for APC/XCB), a number of 8 inch (~20.32 cm) drill collars, a tapered drill collar, six joints (two stands) of 5½ inch (~13.97 cm) drill pipe, and one crossover sub. A lockable flapper valve was used to enable collection of downhole logs without dropping the bit when APC/XCB coring.

The rotary core barrel (RCB) system was not deployed during Expedition 346.

Drilling disturbance

Cores may be significantly disturbed as a result of the drilling process and contain extraneous material as a result of the coring and core handling process. In formations with loose layers, material from intervals higher in the borehole may be washed down by drilling circulation, accumulate at the bottom of the hole, and be sampled with the next core. The uppermost 10–50 cm of each core must therefore be examined critically during description for potential “cave-in.” Common coring-induced deformation includes the concave-downward appearance of originally horizontal bedding. Piston action may result in fluidization (flow-in) at the bottom of APC cores. Retrieval from depth to the surface may result in elastic rebound. Gas that is in solution at depth may become free and drive core segments within the liner apart. When gas content is high, as was the case at many of the sites drilled during Expedition 346, pressure must be relieved for safety reasons before the cores are cut into segments. This is accomplished by drilling holes into the liner, which forces some sediment as well as gas out of the liner. After gas was released, segmented sediments were slid back together with a mechanical pusher to close voids. This procedure may affect physical properties. Drilling disturbances are described in the “Lithostratigraphy” sections in each site chapter and are graphically indicated on the core summary graphic reports.

Core handling

Cores recovered during Expedition 346 were extracted from the core barrel in plastic liners. Except for when a series of cores were recovered for optically stimulated luminescence (OSL) dating (IODP Sites U1424 and U1425), core liners were carried from the rig floor to the core processing area on the catwalk outside the Core Laboratory and cut into ~1.5 m long sections. The exact section length was noted and later entered into the database as “created length” using the Sample Master application. This number was used to calculate recovery. Headspace samples were taken from selected section ends (at least one per core) using a syringe for immediate hydrocarbon analysis as part of the shipboard safety and pollution prevention program. Similarly, microbiology samples were taken immediately after the core was sectioned. Whole-round samples for interstitial water were cut on the catwalk. Core catcher samples were taken for biostratigraphic analysis. When catwalk sampling was complete, liner caps (blue = top; colorless = bottom; yellow = bottom; whole-round cut) were glued with acetone onto liner sections, and the sections were placed in core racks in the laboratory for analysis.

Sampling for optical dating of sediment using OSL was conducted in Holes U1424C and U1425C and involved special core handling procedures. Dedicated holes for OSL studies were planned intentionally to be cored during the night to minimize the core’s exposure to light. Cores were cut into 1.5 m whole-round sections directly on the drill floor. Then, in sequence as the core was pulled out of the core barrel, the whole rounds were placed into 1.5 m long precut opaque aluminum-lined pouches, labeled, sealed, and stored in the refrigerated core storage.

Curatorial procedures

The numbering of sites, holes, cores, and samples followed standard IODP procedure. A full curatorial sample identifier consists of the following information: expedition, site, hole, core number, core type, section number, and offset in centimeters measured from the top of a given section. For example, a sample identification of “346-U1425A-1H-2, 10–12 cm,” represents a sample taken from the interval between 10 and 12 cm below the top of Section 2 of Core 1 (“H” designates that this core was taken with the APC system and “X” designates XCB cores) of Hole A of Site U1425 during Expedition 346. The “U” preceding the hole number indicates that the hole was drilled by the United States Implementing Organization (USIO) platform, the JOIDES Resolution. Half APC cores were also given the “H” designation, and the usage of the half APC system was noted in the core tech summary sheet by the drillers.

Shipboard core analysis

Whole-round core sections were immediately run through the Special Task Multisensor Logger (STMSL) after being cut on the catwalk. The STMSL measures density and magnetic susceptibility at a 5 cm resolution and is used to aid in real-time stratigraphic correlation. The whole-round core sections were run through the Whole-Round Multisensor Logger (WRMSL; measuring P-wave velocity, density, and magnetic susceptibility) and the Natural Gamma Radiation Logger (NGRL) (see “Physical properties”). For most of Expedition 346, we ran all cores through the whole-round core loggers only once, prior to thermal equilibrium. We studied the effect of temperature on the gamma ray attenuation (GRA) and magnetic susceptibility measurements and found it to be negligible.

Core sections were allowed to reach equilibrium with laboratory temperature (after ~4 h) prior to being split. Each section from a given core was split lengthwise from bottom to top into working (“W”) and archive (“A”) halves. Investigators should note that older material might have been transported upward on the split face of each section during splitting. As part of the measurements plan for each site, the working half of each section was run on the physical properties gantry, which includes the P-wave caliper and vane shear, prior to being sampled for shipboard analysis (biostratigraphy, physical properties, geochemistry, and bulk X-ray diffraction [XRD] mineralogy). The archive half of each section for each core was scanned on the Section Half Imaging Logger (SHIL) and measured for color reflectance and magnetic susceptibility on the Section Half Multisensor Logger (SHMSL). At the same time, the archive halves were described macroscopically as well as microscopically by means of smear slides. Finally, the archive halves were run through the cryogenic magnetometer. Both halves of the core were then put into labeled plastic tubes that were sealed and transferred to cold storage space aboard the ship.

At the end of the expedition, all archive and working halves were transported from the ship to permanent cold storage at the IODP core repository at Kochi University, in Kochi, Japan.

Sample depth calculations

The primary depth scale types are based on the measurement of the drill string length deployed beneath the rig floor (drilling depth below rig floor [DRF] and drilling depth below seafloor [DSF]), the length of each core recovered (core depth below seafloor [CSF] and core composite depth below seafloor [CCSF]), and the length of the logging wireline deployed (wireline log depth below rig floor [WRF], wireline log depth below seafloor [WSF], and wireline log matched depth below seafloor [WMSF]). All units are in meters. Depths of samples and measurements are calculated at the applicable depth scale either by fixed protocol (e.g., CSF) or by combinations of protocols with user-defined correlations (e.g., CCSF). The definition of these depth scale types, and the distinction in nomenclature, should keep the user aware that a nominal depth value at two different depth scale types usually does not refer to exactly the same stratigraphic interval in a hole (see “Stratigraphic correlation and sedimentation rates” for detailed information).

Depths of cored intervals are measured from the drill floor based on the length of drill pipe deployed beneath the rig floor (DRF scale). The depth of the cored interval is referenced to the seafloor (DSF scale) by subtracting the seafloor depth at the time of the first hole from the DRF depth of the interval. In most cases, the seafloor depth is the length of pipe deployed minus the length of the mudline core recovered. However, some of the seafloor depths were determined by offset from a previous known measurement of depth, or by tagging the seafloor with the camera system in place.

Standard depths of cores in meters below the seafloor (CSF-A scale) are determined based on the assumption that (1) the top depth of a recovered core corresponds to the top depth of its cored interval (at DSF scale) and (2) the recovered material is a contiguous section even if core segments are separated by voids when recovered. Voids in the core are closed by pushing core segments together, if possible, during core handling. This convention is also applied if a core has incomplete recovery, in which case the true position of the core within the cored interval is unknown and should be considered a sample depth uncertainty, up to the length of the core barrel used, when analyzing data associated with the core material. Standard depths of samples and associated measurements (CSF-A scale) are calculated by adding the offset of the sample or measurement from the top of its section, and the lengths of all higher sections in the core, to the top depth of the cored interval.

A soft to semisoft sediment core from less than a few hundred meters below seafloor expands upon recovery (typically a few percent to as much as 15%), so the length of the recovered core exceeds that of the cored interval. Therefore, a stratigraphic interval may not have the same nominal depth at the DSF and CSF scales in the same hole. When core recovery (the ratio of recovered core to cored interval times 100%) is >100%, the CSF depth of a sample taken from the bottom of a core will be deeper than that of a sample from the top of the subsequent core (i.e., the data associated with the two core intervals overlap at the CSF-A scale).

Core composite depth scales (CCSF) are constructed for all sites drilled during Expedition 346 to mitigate the CSF-A core overlap or coring gap problems and to create as continuous a stratigraphic record as possible. Using shipboard core logger–based physical property data, verified with core photos, core depths in adjacent holes at a site are vertically shifted to correlate between cores recovered in adjacent holes. This process produces the CCSF-A depth scale. The correlation process results in affine tables, indicating the vertical shift of cores at the CCSF scale relative to the CSF-A scale. Once the CCSF scale is constructed, a splice can be defined that best represents the stratigraphy of a site by utilizing and splicing the best portions of individual sections and cores from each hole at a site. This process produces the CCSF-D depth scale, which is strictly correct only along the splice. Because of core expansion, the CCSF-A/CCSF-D depths of stratigraphic intervals are typically 10%–15% deeper than their CSF-A depths. CCSF-A construction also reveals that coring gaps on the order of 1–1.5 m may occur between two subsequent cores, despite the apparent >100% recovery.

1 Tada, R., Murray, R.W., Alvarez Zarikian, C.A., Anderson, W.T., Jr., Bassetti, M.-A., Brace, B.J., Clemens, S.C., da Costa Gurgel, M.H., Dickens, G.R., Dunlea, A.G., Gallagher, S.J., Giosan, L., Henderson, A.C.G., Holbourn, A.E., Ikehara, K., Irino, T., Itaki, T., Karasuda, A., Kinsley, C.W., Kubota, Y., Lee, G.S., Lee, K.E., Lofi, J., Lopes, C.I.C.D., Peterson, L.C., Saavedra-Pellitero, M., Sagawa, T., Singh, R.K., Sugisaki, S., Toucanne, S., Wan, S., Xuan, C., Zheng, H., and Ziegler, M., 2015. Methods. In Tada, R., Murray, R.W., Alvarez Zarikian, C.A., and the Expedition 346 Scientists, Proc. IODP, 346: College Station, TX (Integrated Ocean Drilling Program). doi:10.2204/iodp.proc.346.102.2015

2Expedition 346 Scientists’ addresses.

Publication: 28 March 2015
MS 346-102