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R.D. Norris, P.A. Wilson, P. Blum, A. Fehr, C. Agnini, A. Bornemann, S. Boulila, P.R. Bown, C. Cournede, O. Friedrich, A.K. Ghosh, C.J. Hollis, P.M. Hull, K. Jo, C.K. Junium, M. Kaneko, D. Liebrand, P.C. Lippert, Z. Liu, H. Matsui, K. Moriya, H. Nishi, B.N. Opdyke, D. Penman, B. Romans, H.D. Scher, P. Sexton, H. Takagi, S.K. Turner, J.H. Whiteside, T. Yamaguchi, and Y. Yamamoto2


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 342. This information applies only to shipboard work described in the Expedition Reports of the Expedition 342 Proceedings of the Integrated Ocean Drilling Program volume. Methods for shore-based analyses of Expedition 342 samples and data will be described in individual scientific contributions to be published in the open literature or in the Expedition Research Results section of this volume.

Authorship of site chapters

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

Newfoundland Ridge sections

  • Background and objectives: R.D. Norris, P.A. Wilson

  • Operations: P. Blum, S. Midgley, R.D. Norris, P.A. Wilson

  • Paleontology: C. Agnini, P.R. Bown, O. Friedrich, C.J. Hollis, K. Moriya, H. Nishi, P. Sexton

  • Core description: A. Borneman, S. Boulila, A.K. Ghosh, P.M. Hull, C.K. Junium, H. Matsui, B.N. Opdyke, D. Penman, B. Romans, H. Takagi

  • Geochemistry: K. Jo, M. Kaneko, Z. Liu, H.D. Scher, J.H. Whiteside

  • Paleomagnetism: P.C. Lippert, Y. Yamamoto

  • Physical properties: P. Blum, C. Cournede, T. Yamaguchi

  • Stratigraphic correlation: D. Liebrand, S. Kirtland Turner

  • Downhole logging: A. Fehr

Motion Decoupled Hydraulic Delivery System sections

  • P.B. Flemings, T.L. Pettigrew, P.J. Polito


Site locations

GPS coordinates from precruise site surveys were used to position the vessel at all Expedition 342 sites. A SyQuest Bathy 2010 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 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.

Coring and drilling operations

The coring strategy for Expedition 342 consisted of advanced piston corer (APC) and extended core barrel (XCB) coring to total depths of ~200–400 meters below seafloor (mbsf), depending on stratigraphic targets recovered. Two or three holes were drilled at each site to build a composite depth scale and a stratigraphic splice for continuous subsampling after the cruise (see “Sample depth calculation” and “Stratigraphic correlation”).

The APC cuts soft sediment cores with minimal coring disturbance relative to other IODP coring systems and is suitable for the upper portion of each hole. 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 at high speed 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 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 could not be achieved, one or two 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. 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.

Nonmagnetic core barrels were used during all APC deployments. Most APC cores recovered during Expedition 342 were oriented using the FlexIT tool (see “Paleomagnetism”). Formation temperature measurements were made to obtain temperature gradients and heat flow estimates (see “Downhole logging”).

The XCB system was used to advance the hole when 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 sediments but retracts into the main bit when hard formations are encountered.

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 = 11 inches), 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 collect downhole logs without dropping the bit when APC/XCB coring.

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. 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. Drilling disturbances are described in “Lithostratigraphy” in each site chapter and are graphically indicated on the graphic core summary reports, also referred to as visual core descriptions (VCDs), in “Core descriptions.”

Core handling and analysis

Cores recovered during Expedition 342 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 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. The curated length was set equal to the created length and very rarely had to be modified. Depth in hole calculations are based on the curated length. Headspace samples were taken from selected section ends (typically 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. Core catcher samples were taken for biostratigraphic analysis. When catwalk sampling was complete, liner caps (blue = top; colorless = bottom) were glued with acetone onto liner sections and the sections were placed in core racks in the laboratory for analysis.

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 the core section. For example, a sample identification of “342-U1403A-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 U1403 during Expedition 342. The “U” preceding the hole number indicates that the hole was drilled by the United States Implementing Organization (USIO) platform, the JOIDES Resolution.

Sample depth calculations

Sample depth calculations are based on the methods described in IODP Depth Scales Terminology v.2 at Depths of samples and measurements were calculated at the applicable depth scale either by fixed protocol or by combinations of protocols with user-defined correlations as summarized below. 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 were measured from the drill floor based on the length of drill pipe deployed beneath the rig floor and referred to as drilling depth below rig floor (DRF). The depth of the cored interval was referenced to the seafloor by subtracting the seafloor depth from the DRF depth of the interval. The seafloor referenced depth of the cored interval is referred to as the drilling depth below seafloor (DSF). In most cases, the seafloor depth was the length of pipe deployed minus the length of the mudline core recovered. In some cases the seafloor depth was adopted from a previous hole drilled at the site.

Depths of samples and measurements in each core are computed 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. These depths are referred to as core depth below seafloor, method A (CSF-A). Voids in the core were closed by pushing core segments together, if possible, during core handling. This convention was also applied when a core had 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 when analyzing data associated with the core material. Depths of subsamples and associated measurements at the CSF-A scale were calculated by adding the offset of the subsample 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-A 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). The core depth below sea floor, method B (CSF-B), depth scale is a solution to the overlap problem. This method scaled the recovered core length back into the interval cored, from >100% to exactly 100% recovery. If cores had <100% recovery to begin with, they were not scaled. When downloading data using the IODP-USIO Laboratory Information Management System (LIMS) Reports pages at, depths for samples and measurements are by default presented at both CSF-A and CSF-B scales. The CSF-B depth scale is primarily useful for data analysis and presentations in single-hole situations.

Core composite depth scales (CCSF) were constructed for each site, 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 logging data, and for some intervals postcruise XRF scanning data, core depths in adjacent holes at a site were vertically shifted to maximize the correlation of the data from cores recovered in adjacent holes. The correlation process resulted in affine tables, indicating the vertical shift of cores at the CCSF scale relative to the CSF-A scale. Once the CCSF scale was constructed, a splice was defined that best represented the stratigraphy of a site by utilizing and splicing the best core intervals from each hole at a site. Because of core expansion, the CCSF depths of stratigraphic intervals are typically 10%–15% deeper than their CSF-A depths (see “Stratigraphic correlation”). CCSF construction also revealed that coring gaps on the order of 1 m typically occur between cores in each hole, despite the apparent >100% recovery.

More on sample depth terminology

IODP Depth Scales Terminology v.1, adopted in June 2007, established the above summarized framework to distinguish between and refer to the different depth scale types used in scientific ocean drilling. Unfortunately, that document lacked clear directives for the use of the terminology in the editorial context, which resulted in rather inconsistent use since its implementation. IODP Depth Scales Terminology v.2 (April 2011), following a number of workshops and panel meetings, attempted to clarify this issue with the following directive:

  1. A detailed description of the depth scales used during operations and data collection must be presented in the “Methods” chapter of reports and publications. The description in the “Methods” chapter should include designation of default depth terminology for use in the publication or report, to be used in all cases where depth was determined using the specified method.

  2. The terms “meters below seafloor” or “meters below rig floor” and abbreviations “mbsf” and “mbrf” should be used throughout the report or publication in both text and figures where the depth being referenced was determined using the depth scale specified as the default depth scale for that report or publication in the “Methods” chapter.

  3. If depth being referenced was not determined using the depth scale specified as the default depth scale for that report or publication, the abbreviation of the actual method should be used in both text (e.g., 12.34 m CCSF) and figure labels (e.g., Depth CCSF [m]).

  4. The relationship between the default depth scale and the depth scale used in more specific investigations should, where possible, be clearly documented in the “Methods” chapter (e.g., the relationship between mbsf and CCSF as used in 3. above). If it is not possible to establish such a relationship, this should be stated in the “Methods” chapter.

These guidelines, aimed at continuing some of the old terminology that the new framework meant to differentiate and replace, resulted in a hybrid nomenclature recommendation including pieces of the old and the new concepts and names. For example, we now have statements such as “mbsf to CCSF growth rates” rather than “CSF-A to CCSF growth rates.” Furthermore, the directive required that each science party designate one particular depth scale type as the “default,” with the assumption that in most cases the CSF-A scale type would be designated the default scale.

During Expedition 342, we used the IODP depth scales DRF, DSF, CSF-A, and CCSF, and all depths were consistently expressed in terms of these four scale types throughout text, tables, and figures of the expedition Preliminary Report. After the expedition, in an attempt to make the reports more compatible with the above cited nomenclature directive, Publications Staff replaced all occurrences of “m CSF-A” in all text, figure and table documents with “mbsf.”

Shipboard core analysis

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), which measures P-wave velocity, density, and magnetic susceptibility, and the Natural Gamma Radiation Logger (NGRL). Thermal conductivity measurements were also taken before the cores were split lengthwise from bottom to top into working and archive halves. Investigators should note that older material might 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 Image 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 working section halves were transported from the ship to permanent cold storage at the Bremen Core Repository (BCR) at the University of Bremen, Germany. Archive section halves were divided into three batches and shipped directly to the Scripps Institution of Oceanography (SIO), the Gulf Coast Repository at Texas A&M University (TAMU), and the BCR for X-ray fluorescence (XRF) scanning. Most of the archive section halves measured at the SIO and TAMU were shipped to the BCR in February 2013 to be available for U-channel sampling at the 18 February–3 March postexpedition sampling party at the BCR, during which >30,000 samples were taken for studies in the investigators’ laboratories.

1 Norris, R.D., Wilson, P.A., Blum, P., Fehr, A., Agnini, C., Bornemann, A., Boulila, S., Bown, P.R., Cournede, C., Friedrich, O., Ghosh, A.K., Hollis, C.J., Hull, P.M., Jo, K., Junium, C.K., Kaneko, M., Liebrand, D., Lippert, P.C., Liu, Z., Matsui, H., Moriya, K., Nishi, H., Opdyke, B.N., Penman, D., Romans, B., Scher, H.D., Sexton, P., Takagi, H., Turner, S.K., Whiteside, J.H., Yamaguchi, T., and Yamamoto, Y., 2014. Methods. In Norris, R.D., Wilson, P.A., Blum, P., and the Expedition 342 Scientists, Proc. IODP, 342: College Station, TX (Integrated Ocean Drilling Program). doi:10.2204/iodp.proc.342.102.2014

2Expedition 342 Scientists’ addresses.

Publication: 3 March 2014
MS 342-102