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Expedition 333 Scientists2


This chapter documents the methods used for shipboard scientific analyses, including sample collection, preparation, and preservation for either shipboard or shore-based analysis. This information can be used to understand the means by which we arrived at preliminary conclusions and interpretations. It also provides information for those interested in ancillary analyses, shore-based sampling, or integrative investigations.

This chapter explains coring techniques, core handling, and the numbering of sites, holes, cores, sections, and samples. In most cases, this information mirrors the details described in previous volumes of the Proceedings of the Integrated Ocean Drilling Program, particularly Expedition 322. However, because of the relationship between this expedition and the other expeditions that comprise the Nankai Trough Seismogenic Zone Experiment (NanTroSEIZE) and the large number and volume of sample requests, there are significant differences that are explained below.

Site locations

Integrated Ocean Drilling Program (IODP) Expedition 333 site locations were selected based on precruise surveys and the overall goals of NanTroSEIZE. Onboard GPS satellite navigation was used to position the vessel using dynamic positioning, and acoustic beacons deployed on the seafloor provided additional means of acquiring and keeping vessel position during operations. Because the remotely operated vehicle was not deployed in the >3000 m water depth, a precise fix on the location of the borehole was not obtained upon spud-in. The ship’s position was used as the borehole position.

Drilling operations

Four coring systems were employed during Expedition 333:

  1. Hydraulic piston coring system (HPCS), equivalent to the advanced piston coring (APC) system employed on the R/V JOIDES Resolution,

  2. Extended punch coring system (EPCS) developed during IODP Expedition 316 by combining pieces from the HPCS, extended shoe coring system (ESCS), and rotary core barrel (RCB) system to extend the range of the HPCS to more consolidated sediments,

  3. ESCS, equivalent to the extended core barrel (XCB) system employed on the JOIDES Resolution, and

  4. RCB.

The cored interval is measured in meters below seafloor (mbsf) according to the core depth below seafloor, method B (CSF-B), depth scale (see IODP Depth Scale Terminology at Drilled intervals are initially referred to in drilling depth below rig floor (DRF), which is measured from the kelly bushing on the rig floor to the bottom of the drill pipe, and is later converted to core depth below seafloor (CSF). The height of the rig floor is 28.3 m above the mean sea level. During Expedition 333, all core depths below seafloor were calculated as CSF-B, and reported in this volume as “meters below seafloor” unless otherwise noted (CSF in physical properties uses Method A).

Drilling-induced core deformation

X-ray computed tomography (CT) imagery and direct inspection of split cores often reveal significant evidence for disturbance of recovered materials. For example, during RCB coring deformation results from rotation and “spiraling” of sections of cores, “biscuiting” of small sections of core and injection of either drilling mud or finely ground material produced at the drill bit into spaces between individual biscuits, or brecciation or grinding of material before collection into the core liner/core barrel. Core deformation may also result from depressurization, expansion, and thermal equilibration of the core as it travels up the drill string, during handling on deck, and during core cutting and splitting. Where possible, such core disturbance was noted in core descriptions.

Numbering of sites, holes, cores, sections, and samples

Sites drilled by the D/V Chikyu are numbered consecutively from the first site with a prefix “C.” A site refers to one or more holes drilled while the ship is positioned within 300 m of the first hole. The first hole drilled at a given site is assigned the site number modified by the suffix “A,” the second hole takes the site number and suffix “B,” and so forth. These suffixes are assigned regardless of recovery, as long as penetration takes place. Cored intervals are calculated based on an initial 9.5 m length, which is the standard core barrel length for each coring system. In addition, we specified the collection of shorter coring intervals in areas of poor recovery or slow rate of penetration. Expansion of cores in the upper sections (and sucked-in material) and gaps related to unrecovered material result in recovery percentages greater or less than 100%, respectively. Depth intervals are assigned starting from the depth below seafloor at which coring started (IODP coring depth scale calculated using Method B [CSF-B]; see IODP Depth Scales Terminology at Short cores (incomplete recovery) are all assumed to start from that initial depth by convention. Core expansion is corrected during final processing of core measurements by subtracting void spaces, subtracting exotic material, and accounting for expansion (IODP coring depth scale calculated using Method B [CSF-B]).

A recovered core is typically divided into 1.4 m long sections that are numbered serially from 1 beginning at the top. During Expedition 333, whole-round core samples were removed for interstitial water sampling and assigned their own section number in order to allow for rapid X-ray CT scanning of time-sensitive samples. Material recovered from the core catcher was assigned to a separate section, labeled core catcher (CC), and placed at the bottom of the lowermost section of the recovered core.

A full identification number for a sample consists of the following information: expedition, site, hole, core number, core type, section number, and top to bottom interval in centimeters measured from the top of the section. For example, a sample identification of “333-C0012G-2R-5, 80–85 cm,” represents a sample removed from the interval between 80 and 85 cm below the top of Section 5 of the second RCB core from Hole C0012G, during Expedition 333 (Fig. F1).

Core handling

The following sections describe in detail the flow of core from the drill floor through the laboratory. See Figure F2 for a step-by-step flow chart of the entire process.

Core cutting area

As soon as a core is retrieved on deck, the core catcher is delivered to the core cutting area. A sample is taken for paleontological analysis, and the remainder of the core catcher sample is packed into the core liner and curated. The whole core is delivered to the core cutting area and curated for recovery length. Sections for time-sensitive whole-round samples are immediately cut out of the core, curated, and delivered to the X-ray CT laboratory for CT scanning. The time-sensitive whole-round samples include those for interstitial water and/or deep biosphere analysis. Oversight by a structural geologist in the X-ray CT laboratory acting as a “watchdog” (see below) is required before the time-sensitive whole round is processed. If the watchdog finds a potentially high interest feature or the sample is considered inappropriate for it’s intended use, Co-Chief Scientists make a decision whether or not the section may be processed. If rejected, the section is returned to the regular core flow.

Remaining core is cut into sequentially numbered 1.4 m long sections in the core cutting area. If cores contain gas in void spaces, void gas samples are collected at this time. Small (5 cm3) plugs of sediment are removed from the bottom of appropriate core sections, typically adjacent to a whole-round sample for interstitial water squeezing, for headspace gas analysis.

The recovered core length and the total length of void space are measured, and core identification, length, drilling advance, and depth information are entered into the J-CORES database. Each section is then sealed at the top (blue cap, blue tape) and bottom (clear cap, white tape); yellow caps indicate removed whole-round core samples (with sample code marked on the end cap). All sections are marked and labeled, data are entered into the J-CORES database, and sections are moved to the core processing deck.

Core processing deck

All sections are scanned using X-ray CT, and each shift has a structural geologist acting as a watchdog to oversee the collection and selection of whole-round core samples, to identify sections or intervals of special interest or unique character, and to prevent destruction of any critical samples.

Following X-ray CT scanning and time-sensitive whole-round core sampling, core sections are allowed to equilibrate to ambient laboratory temperature (2–3 h, ~20°C), after which they are run through the whole-round multisensor core logger (MSCL-W). During Expedition 333, measurements of gamma ray attenuation (GRA) bulk density, P-wave velocity, resistivity, magnetic susceptibility, and natural gamma radiation were collected using the MSCL-W. Thermal conductivity measurements were also made on whole-round core sections for soft-sediment cores.

Following MSCL-W and thermal conductivity measurement, if conducted on whole-round cores, a second round of whole-round core sampling for shore-based geotechnical and hydrogeologic analyses is conducted. The number of whole-round samples collected and their locations were based on length of core recovered and extent of intact undeformed pieces from examination of the X-ray CT data.

Following completion of whole-round core sampling, sections are split axially into working and archive halves. The archive half is subjected to nondestructive color spectroscopy, digital photo image scanning, and visual core description (VCD), after which it is covered in plastic film, shrink-wrapped in plastic, and stored in either the cold-store refrigerator or the refrigerated containers at 4°C. The working half is subjected to structural analysis and sampling and measurement for physical properties (e.g., moisture and density [MAD] and velocity) and is then sampled for postcruise analyses. Following completion of sampling, these sections are also wrapped, sealed, and stored at 4°C in preparation for shipping to the core repository. All samples collected are labeled, packaged, stored, and shipped to their final destinations according to standard practice or special instructions.

Community whole-round samples

Through NanTroSEIZE expeditions, we collect substantial numbers of “community” archive samples, especially whole rounds. In some cases, these community samples will augment and/or provide redundancy for those requested by shipboard scientists. The goal is to preserve samples for a wide range of overall science objectives over the duration of the NanTroSEIZE project. This strategy, for example, will enable additional analyses of critical intervals once those zones are identified from initial shore-based laboratory tests.

During Expedition 333, each community whole-round sample was a total of 23 cm long. A community whole round was taken from each core that had sufficient recovery. The sample was cut into two pieces; one is 15 cm long, and the other is 8 cm long. These samples were shipped to Kochi Core Center (KCC) and will be made available to the NanTroSEIZE community. A “cluster” sample was associated with each community whole round.

Sample clusters

To ensure achievement of overall NanTroSEIZE scientific objectives, it is essential to collocate suites of complementary data types for integration and analysis. This must be done with appropriate and consistent sample spacing throughout each hole. During Expedition 333, sample clusters were located immediately adjacent to all whole-round intervals extracted for interstitial water geochemistry and frictional/geotechnical/hydrogeology tests, including community whole rounds. The cluster samples were taken immediately after cutting the whole-round sample. This group of samples consists of material for shipboard X-ray diffraction (XRD), MAD, carbonate analyses, X-ray fluorescence (XRF), and personal samples (e.g., grain size, fabric, and clay mineral XRD).

Routine microbiological sampling

During Expedition 333, routine microbiological sampling was conducted as per Science and Technology Panel Recommendation 0908-09 ( Whole-round samples were taken when recovery was good from an interval adjacent to a whole-round sample for interstitial water and was immediately frozen at –80°C.

Where possible, samples (~1 cm3) were removed from the top or bottom of the whole-round sample in an anaerobic glove box. The sample was put into a centrifuge tube with 9 mL of 2% paraformaldehyde fixative. After incubation at 4°C for 4–6 h, the sample was pelleted by centrifuging tubes at 3500 rotations per minute for 10 min (at 4°C) and rinsed with phosphate-buffered saline (PBS) and ethanol. The sample was stored at 4°C until it was shipped to KCC.

1 Expedition 333 Scientists, 2012. Methods. In Henry, P., Kanamatsu, T., Moe, K., and the Expedition 333 Scientists, Proc. IODP, 333: Tokyo (Integrated Ocean Drilling Program Management International, Inc.). doi:10.2204/iodp.proc.333.102.2012

2Expedition 333 Scientists’ addresses.

Publication: 18 May 2012
MS 333-102