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J.M. Jaeger, S.P.S. Gulick, L.J. LeVay, H. Asahi, H. Bahlburg, C.L. Belanger, G.B.B. Berbel, L.B. Childress, E.A. Cowan, L. Drab, M. Forwick, A. Fukumura, S. Ge, S.M. Gupta, A. Kioka, S. Konno, C.E. März, K.M. Matsuzaki, E.L. McClymont, A.C. Mix, C.M. Moy, J. Müller, A. Nakamura, T. Ojima, K.D. Ridgway, F. Rodrigues Ribeiro, O.E. Romero, A.L. Slagle, J.S. Stoner, G. St-Onge, I. Suto, M.H. Walczak, and L.L. Worthington2


This chapter documents the procedures and methods employed in the various shipboard laboratories of the R/V JOIDES Resolution during Integrated Ocean Drilling Program (IODP) Expedition 341. This information applies only to shipboard work described in the Expedition Reports section of the Expedition 341 Proceedings of the Integrated Ocean Drilling Program volume. Methods used by investigators for shore-based analyses of Expedition 341 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 site chapters

All shipboard scientists contributed to this volume. However, certain sections were written by discipline-based groups of scientists as listed below (listed alphabetically):

  • Background and objectives: S. Gulick, J. Jaeger
  • Operations: S. Gulick, J. Jaeger, L. LeVay, S. Midgley
  • Lithostratigraphy: H. Bahlburg, L. Childress, E. Cowan, M. Forwick, C. Moy, J. Müller, K. Ridgway, F. Rodrigues Ribeiro
  • Biostratigraphy: H. Asahi, C. Belanger, A. Fukumura, S. Gupta, S. Konno, L. LeVay, K. Matsuzaki, O. Romero, I. Suto
  • Stratigraphic correlation: A. Mix, G. St-Onge
  • Geochemistry: G. Berbel, C. März, E. McClymont, A. Nakamura
  • Physical properties: A. Kioka, T. Ojima, M. Walczak, L. Worthington
  • Paleomagnetism: S. Ge, J. Stoner
  • Downhole logging: L. Drab, A. Slagle
  • Core-log-seismic integration: L. Drab, S. Gulick, C. Moy, K. Ridgway, A. Slagle, L. Worthington

Site locations

GPS coordinates from precruise site surveys were used to position the vessel at all Expedition 341 sites. A Syquest Bathy 2010 compressed high-intensity radar pulse (CHIRP) subbottom profiler was used to monitor the 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. A survey of the seafloor was conducted at Site U1420 using the underwater camera system to ensure that it was free of obstructions.

Coring and drilling operations

The advanced piston corer (APC), extended core barrel (XCB), and rotary core barrel (RCB) systems were used during Expedition 341. At Sites U1417–U1419 and U1421, multiple holes were drilled to build a composite depth scale and a stratigraphic splice for continuous subsampling after the expedition (see “Sample depth calculations” and “Stratigraphic correlation”).

The APC system 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 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 system, 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) 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 341, 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-length APC cores were attempted.

The standard APC system contains a 9.5 m long core barrel. Expedition 341 was the first IODP expedition to make use of the half APC system, which uses a 4.7 m long core barrel. In most instances, the half APC system was deployed after the standard APC system reached refusal but was also employed in second or later holes at a site when coring particular depth intervals where previous full APC cores failed to achieve a full stroke. During use of the half APC system, the same criteria were applied in terms of refusal as for the full-length APC system. Use of the half APC system allowed for significantly greater APC sampling depths to be attained than would have otherwise been possible.

Nonmagnetic core barrels were used during all full-length APC system deployments, and steel core barrels were used for the half APC system. Orientation using the FlexIT tool (see “Paleomagnetism”) was completed on standard APC cores taken in various holes at each site, depending on operational conditions. Formation temperature measurements were made when operationally feasible to obtain temperature gradients and heat flow estimates using the advanced piston corer temperature tool (APCT-3) (see “Physical properties”).

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 semiindurated 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. 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 = 11 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 so we could collect downhole logs without dropping the bit when APC/XCB coring.

The RCB system was deployed when APC or XCB coring rates diminished below an acceptable level if the formation was expected to be too indurated for APC/XCB coring (e.g., Site U1420), or if the bit was destroyed by an increasingly hard formation. The RCB is a conventional rotary drilling system that requires a dedicated RCB BHA and a dedicated RCB drilling bit (outer diameter = 9⅞ inches). A typical BHA for RCB coring includes an RCB drill bit, a mechanical bit release, a modified head sub, an outer core barrel, a modified top sub, and a series of drill collars followed by a tapered drill collar and 5½ inch drill pipe.

Drilling disturbance

Cores may be significantly disturbed as a result of the drilling process and may contain extraneous material as a result of the coring and core handling process. In formations with loose sand or gravel 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, 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. Holes are also drilled into the liner for rhizon sampling of pore waters. Drilling disturbances are described in “Lithostratigraphy” in each site chapter and are graphically indicated on the graphic core summary reports (see “Core descriptions”).

Core handling and curatorial procedures

Cores recovered during Expedition 341 were extracted from the core barrel in plastic liners. These 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 (typically one per core if recovery allowed) 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 (IW) and physical properties 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. Rarely, APC cores were plugged and the liner could not be easily extracted; see the drillers core tech summary sheet for a list of cores for which this was required. In this situation, the liner was hydraulically extruded on the rig floor into half-round liner sections and curated the same as normally extracted liners.

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 “341-U1417A-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) of Hole A of Site U1417 during Expedition 341. The “U” preceding the hole number indicates that the hole was drilled by the United States Implementing Organization (USIO) platform, the JOIDES Resolution. Other core types are designated by “R” for cores taken with the RCB system and “X” for cores taken by the XCB system. Half APC cores also were 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) when necessary for stratigraphic correlation after being cut on the catwalk. The STMSL measures density and magnetic susceptibility at a low resolution and is used to aid in real-time stratigraphic correlation. 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).

Typically, core sections were allowed to reach equilibrium with laboratory temperature (after ~4 h) prior to running through the whole-round core logging systems (see “Physical properties” for exceptions). However, when the sediment had higher concentrations of gas, sections were immediately run through the STMSL and the WRMSL prior to gas expansion of the cores. When liner sections were fractured from coring disturbance and patched on the catwalk, the resulting section diameter was too wide to fit through the magnetic susceptibility loop on the WRMSL and was measured on the STMSL instead (see the Laboratory Information Management System [LIMS] database for sections where this was required). Each section from a given core was split lengthwise from bottom to top into working and archive halves. Investigators should note that older material, especially lonestones, might have been transported upward on the split face of each section during splitting. The working half of each section was run on the Section Half Measurement Gantry, which includes the P-wave caliper (PWC) 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 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, archive halves were described macroscopically and microscopically by means of smear slides. Finally, 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 Gulf Coast Repository at Texas A&M University (USA).

Sample depth calculations

The primary depth scale types are based on the measurement of the drill string length deployed beneath the rig floor (drillers depth below rig floor [DRF] and drillers 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.

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 or by tagging the seafloor with the camera system in place.

Standard depths of cores on the CSF-A scale are determined based on the assumptions that (1) the top depth of a recovered core corresponds to the top depth of its cored interval (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 subsamples and associated measurements (CSF-A scale) are calculated by adding the offset of the subsample or measurement from the top of its section, as well as 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) 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 on the CSF-A scale).

Core composite depth scales (CCSF) are constructed for sites, whenever feasible, to mitigate the CSF-A core overlap problem as well as the coring gap problem and to create as continuous a stratigraphic record as possible. Using shipboard core logger–based physical properties 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 on 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. This process produces the CCSF-D depth scale, which is strictly correct only along the splice. Because of core expansion, the CCSF-A/D depths of stratigraphic intervals are typically 10%–15% deeper than their CSF-A depths. CCSF-A depth scale construction also reveals that coring gaps on the order of 1–1.5 m typically occur between two subsequent cores, despite the apparent >100% recovery. Based on discussions between Expedition 341 participants, we suggest that these gaps may be produced by either rebound during piston coring or vertical rise of the floor of the borehole between coring runs in response to overburden reduction. Lastly, in order to compare intervals along the splice with drilling data, logging data, and seismic data, a final depth scale, CCSF-B, is created by correcting the CCSF-D depth scale back to the true drilled interval. For detailed depth scale definitions, see “Stratigraphic correlation.”

When coring multiple holes to establish composite depths and continuous spliced records, drilling depths were corrected for tides. At each site, tides were predicted at 30 min intervals throughout the time of coring, using the Oregon State University Tidal Prediction Software (copyright Oregon State University 2012, G. Egbert and L. Erofeeva, and used by permission). Tidal variations during Expedition 341 were up to 4 m over a diurnal–semidiurnal cycle, so proper tide corrections were needed to obtain complete composite sections and splices (see “Stratigraphic correlation”). The first APC core at each site established the reference depth of the mudline below sea level at the time of coring. For each core taken after the first mudline core, drilling advances were based on recovery plus a correction for the deviation of the sea level (as predicted from the tide model) relative to the reference sea level for the first core at the site. Tidal deviations at the time of each coring operation define the drilldown between cores. During each coring operation, the drill string is advanced either less than the previous core’s recovery (for a falling tide) or greater the previous recovery (for a rising tide).

1 Jaeger, J.M., Gulick, S.P.S., LeVay, L.J., Asahi, H., Bahlburg, H., Belanger, C.L., Berbel, G.B.B., Childress, L.B., Cowan, E.A., Drab, L., Forwick, M., Fukumura, A., Ge, S., Gupta, S.M., Kioka, A., Konno, S., März, C.E., Matsuzaki, K.M., McClymont, E.L., Mix, A.C., Moy, C.M., Müller, J., Nakamura, A., Ojima, T., Ridgway, K.D., Rodrigues Ribeiro, F., Romero, O.E., Slagle, A.L.,Stoner, J.S., St-Onge, G., Suto, I., Walczak, M.H., and Worthington, L.L., 2014. Methods. In Jaeger, J.M., Gulick, S.P.S., LeVay, L.J., and the Expedition 341 Scientists, Proc. IODP, 341: College Station, TX (Integrated Ocean Drilling Program). doi:10.2204/iodp.proc.341.102.2014

2Expedition 341 Scientists’ addresses.

Publication: 22 November 2014
MS 341-102