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Expedition 339 Scientists2

Introduction, background, and operations

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 339. This information applies only to shipboard work described in the Expedition Reports section of the Expedition 339 Proceedings of the Integrated Ocean Drilling Program volume. Methods for shore-based analyses of Expedition 339 samples and data will be described in individual scientific contributions to be published elsewhere. All shipboard scientists contributed to the completion of this volume.

Site locations

GPS coordinates from precruise site surveys were used to position the vessel at all Expedition 339 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 hole position 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 all sites using the underwater camera system to ensure that it was free of obstructions.

Coring and drilling operations

All three standard coring systems, the advanced piston corer (APC), the extended core barrel (XCB), and the rotary core barrel (RCB), were used during Expedition 339. The APC was used in the upper portion of each hole when coring in the top of the hole was the objective. 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 the 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 (Fig. F1). The driller can detect a successful cut, or “full stroke,” from the pressure gauge on the rig floor.

APC refusal is conventionally defined in two ways: (1) the piston fails to achieve a complete stroke (as determined from the pump pressure reading) because the formation is too hard or (2) excessive force (>60,000 lb; ~267 kN) is required to pull the core barrel out of the formation. When a full stroke cannot be achieved, one or two additional attempts are typically made, and each time the bit is advanced by the length of recovered core. Note that this results in a nominal recovery of ~100% based on the assumption that the barrel penetrates the formation by the equivalent of the length of core recovered. When a full or partial stroke is achieved but excessive force cannot retrieve the barrel, the core barrel is sometimes “drilled over,” meaning after the inner core barrel is successfully shot into the formation, the drill bit is advanced to total depth to free the APC barrel.

Nonmagnetic core barrels were used during all conventional APC coring to a pull force of ~40,000 lb. Most APC cores recovered during Expedition 339 were oriented using the FlexIt tool (see “Paleomagnetism”). Formation temperature measurements were made to obtain temperature gradients and heat flow estimates (see “In situ temperature measurements”).

The XCB system was used to advance the hole when APC refusal occurred before the target depth was reached or when the formation became either too stiff for APC coring or hard substrate was encountered. 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 sediments but retracts into the main bit when hard formations are encountered (Fig. F2). The XCB system was used extensively during Expedition 339 to greater depths than anticipated.

The bottom-hole assembly (BHA) is the lowermost part of the drill string. The exact configuration of the BHA is reported in the operations section in each site chapter. A typical APC/XCB BHA consists of a drill bit (outer diameter = 11inch), 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 that downhole logs could be collected without dropping the bit when APC/XCB coring.

The RCB was deployed when XCB coring rates diminished below an acceptable level or the bit was destroyed by the increasingly hard formation. The RCB is the most conventional rotary drilling system and was used during Expedition 339 to drill and core the deepest holes. The RCB requires a dedicated RCB BHA and a dedicated RCB drilling bit. The BHA used for RCB coring included a 9 inch RCB drill bit, a mechanical bit release, a modified head sub, an outer core barrel, a modified top sub, and seven control-length drill collars followed by a tapered drill collar to the 5½ inch drill pipe (Fig. F3). Most cored intervals were ~9.5 m long, which is the length of a standard core barrel and the length of a joint of drill pipe. In some cases, the drill string was drilled or “washed” ahead without recovering sediments to advance the drill bit to a target depth to resume core recovery. Such intervals were typically drilled using a center bit installed within the RCB bit.

IODP depth conventions

Primary depth scale types are based on the measurement of drill string length (e.g., drilling depth below rig floor [DRF] and drilling depth below seafloor [DSF]), length of core recovered (e.g., core depth below seafloor [CSF] and core composite depth below seafloor [CCSF]), and logging wireline (e.g., wireline log depth below rig floor [WRF] and wireline log depth below seafloor [WSF]). All units are in meters. The relationship between scales is defined either by protocol, such as the rules for computation of CSF from DSF, or user-defined correlations, such as stratigraphic correlation of cores between holes to create a common CCSF scale from the CSF scales used in each hole. The distinction in nomenclature should keep the user aware that a nominal depth value at two different depth scales usually does not refer to exactly the same stratigraphic interval (also see “Curatorial procedures and sample depth calculations”).

For editorial convenience, the depth scale type acronym was not repeated with each depth reference in the site chapters. The scale type was declared at the beginning of each section and only mentioned again if a different scale type was used.

Core handling and analysis

The coring strategy for Expedition 339 consisted of APC coring in two holes (A and B) at each site to refusal, except at Site U1385 where five holes were cored with the APC. Multiple holes allowed us to build a composite section at each site. The drillover technique was employed to maximize APC penetration where desirable. APC refusal was followed by XCB coring at each site to ~350 meters below seafloor (mbsf) (except at Site U1385 where only the APC was used to ~150 mbsf) and then by RCB coring to total depth when necessary.

Cores recovered during Expedition 339 were extracted from the core barrel in 67 mm diameter plastic liners. These liners were carried from the rig floor to the core processing area on the catwalk outside the Core Laboratory, where they were split into ~1.5 m sections. Liner caps (blue = top; colorless = bottom) were glued with acetone onto liner sections on the catwalk by the Marine Technicians. The length of each section was entered into the database as “created length” using the Sample Master application. This number was used to calculate core recovery.

As soon as cores arrived on deck, headspace samples were taken using a syringe for immediate hydrocarbon analysis as part of the shipboard safety and pollution prevention program. Core catcher samples were taken for biostratigraphic analysis. Whole-round samples were taken from some core sections for shipboard and postcruise interstitial water analyses. Rhizon interstitial water samples and syringe samples were taken from selected intervals in addition to whole rounds (see “Geochemistry”). In addition, whole-round and syringe samples were immediately taken from the ends of cut sections at three sites for shore-based microbiological analysis.

Core sections were then placed in core racks in the laboratory. When the cores reached equilibrium with laboratory temperature (typically after ~4 h), whole-round core sections were run through the Whole-Round Multisensor Logger (WRMSL; measuring P-wave velocity, density, magnetic susceptibility, and resistivity) and the Natural Gamma Radiation Logger (NGRL). Thermal conductivity measurements were typically taken at a rate of two per core (see “Physical properties”). The core sections were then split lengthwise from bottom to top into working and archive halves. Investigators should note that older material may have been transported upward on the split face of each section during splitting. The working half of each core was sampled for shipboard analysis (biostratigraphy, physical properties, carbonate, paleomagnetism, and bulk X-ray diffraction [XRD] mineralogy). The archive half of 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 visually and 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, the cores were transported from the ship to permanent cold storage at the Bremen Core Repository (BCR) at the University of Bremen, Germany. The BCR houses cores collected from the Atlantic and Arctic Oceans (north of the Bering Strait). A postexpedition sampling party was organized and carried out at the BCR from 9 to 17 June 2012 to take personal samples requested by members of the science party.

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 sand layers, sand from intervals higher in the hole 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. Both elastic rebound and gas pressure can result in a total length for each core that is longer than the interval that was cored and thus a calculated recovery of >100%. If gas expansion or other coring disturbance results in a void in any particular core section, the void can be either closed by moving material if very large, stabilized by a foam insert if moderately large, or left as is. 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. These disturbances are described in the “Lithostratigraphy” sections in each site chapter and graphically indicated on the core summary graphic reports (visual core descriptions [VCDs]). In extreme instances core material was ejected from the core barrel, sometimes violently, onto the rig floor by high pressure in the core or other coring problem. This core material was replaced in the plastic core liner by hand and should not be considered to be in stratigraphic order. Core sections so affected are marked by a yellow label marked “disturbed,” and the nature of the disturbance is noted in the coring log.

Curatorial procedures and sample depth calculations

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 interval in centimeters measured from the top of the core section. For example, a sample identification of “339-U1386A-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, “X” designates XCB cores, and “R” designates RCB cores) of Hole A of Site U1386 during Expedition 339. The “U” preceding the hole number indicates that the hole was drilled by the United States Implementing Organization (USIO) platform, the JOIDES Resolution.

Cored intervals are defined by the core top depth in DSF and the distance the driller advanced the bit and core barrel in meters. The length of the core is defined by the sum of lengths of the core sections. The CSF depth of a sample (referred to as mbsf) is calculated by adding the offset of the sample below the section top and the lengths of all higher sections in the core to the core top depth measured with the drill string (DSF). 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 recovered interval typically does not match the cored interval. In addition, a gap typically occurs between cores, as shown by composite depth construction. Thus, a discrepancy between DSF and CSF depths can exist with regard to a stratigraphic interval. Furthermore, when more than 100% of the cored interval is recovered, 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 depth scale).

If a core has incomplete recovery, all cored material is assumed to originate from the top of the drilled interval as a continuous section for curation purposes. The true depth interval within the cored interval is unknown and should be considered a sample depth uncertainty in age-depth analyses and in the correlation of core data with downhole logging data.

Authorship of site chapters

The separate sections of the site chapters and “Methods” chapter were written by the following shipboard scientists (authors are listed in alphabetical order; no seniority is implied):

  • Background and objectives: C.A. Alvarez Zarikian, F.J. Hernández-Molina, D.A.V. Stow

  • Operations: C.A. Alvarez Zarikian, R. Grout

  • Lithostratigraphy: E. Ducassou, R. Flood, S. Furota, L. Krissek, J. Kuroda, F. Nanayama, N. Nishida, C. Roque, C. Sloss, Y. Takashimizu

  • Biostratigraphy: C.A. Alvarez Zarikian, B. Balestra, J.-A. Flores, P. Grunert, B. Li, M.F. Sanchez Goñi, F.J. Sierro, A.D. Singh, A. Voelker

  • Paleomagnetism: C. Richter, C. Xuan

  • Physical properties: A. Bahr, F. Jimenez-Espejo, E. Llave

  • Geochemistry: D. Hodell, J.K. Kim, M. Miller, A. Tzanova

  • Downhole measurements: J. Lofi, T. Williams

  • Stratigraphic correlation: G. Acton, L. Lourens

1Expedition 339 Scientists, 2013. Methods. In Stow, D.A.V., Hernández-Molina, F.J., Alvarez Zarikian, C.A., and the Expedition 339 Scientists, Proc. IODP, 339: Tokyo (Integrated Ocean Drilling Program Management International, Inc.).

2Expedition 339 Scientists’ addresses.

Publication: 17 June 2013
MS 339-102