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Expedition 329 Scientists2

Introduction, operations, and curation

Information assembled in this chapter will help the reader understand the basis for shipboard observations and preliminary conclusions of Integrated Ocean Drilling Program (IODP) Expedition 329. It will also enable the interested investigator to identify data and select samples for further analysis. Information presented here concerns only shipboard operations and analyses described in the site chapters (Sites U1365–U1371). Methods used by various investigators for shore-based analyses of Expedition 329 samples and data will be described in individual publications in various professional journals and the Expedition Research Results chapters of this Proceedings volume. This introductory section provides an overview of operations, curatorial conventions, and general core handling and analysis.

Site locations

At all Expedition 329 sites, GPS coordinates from precruise site surveys were used to position the vessel on site. The only seismic system used during the cruise was the Syquest Bathy 2010 CHIRP subbottom profiler, which was monitored on the approach to each site to confirm the seafloor depth with that from the precruise survey. 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 uses 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 the time that the hole was occupied.

Coring and drilling operations

The advanced piston corer (APC), extended core barrel (XCB), and rotary core barrel (RCB) systems were used during Expedition 329. These standard coring systems and their characteristics are summarized in Graber et al. (2002). 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 pressurized until the shear pins that attach the inner barrel 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 XCB system is deployed when the formation becomes too stiff or too hard for the APC system. The XCB cutting shoe (bit) extends as far as ~30.5 cm ahead of the main bit in soft sediments but retracts into the main bit if hard formations are encountered.

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 or partial stroke can be achieved but excessive force cannot retrieve the barrel, the core barrel can be “drilled over”; after the inner core barrel is successfully shot into the formation, the drill bit is advanced to total depth to free the APC barrel. This strategy allows a hole to be advanced much farther with the APC, the preferred coring tool. Nonmagnetic core barrels are commonly used during all conventional APC coring, but the APC drillover technique is not typically conducted in the first hole at each site if hard rock might be encountered. Standard steel core barrels are usually used for the drillover technique because they are stronger than the nonmagnetic barrels. Most APC/XCB cored intervals are ~9.5 m long, which is the length of a standard core barrel.

During Expedition 329, a pilot hole was drilled or “washed” ahead without recovering sediment at each site to identify hard lithologies (e.g., chert) and the depth of basement. Such advances were necessary to minimize potential for major operational setbacks (e.g., extra pipe trips and tool damage). Drilling without coring was also necessary to advance the drill bit to a target depth where core recovery could be resumed or to ensure that coring gaps in one hole were covered by cored intervals in adjacent holes. The amount of advance varied case by case. An alternative method to adjust the offset between holes was to raise the bit off the bottom of a hole 1–4 m before shooting the next APC core. Core operations and recovery information is given in “Operations” in each site chapter.

Some APC cores were oriented using the Flexit tool (see “Paleomagnetism”). Formation temperature measurements were usually made in Hole B of each site and repeated, if necessary for data quality, in Holes C and D (see “Downhole measurements”). Downhole logging was attempted in only one hole at two of the sites with deepest penetration.

The XCB system was used to advance the hole when APC refusal occurred in a hole before the target depth was reached and when the formation became too stiff for the APC system or when drilling hard substrate such as cemented layers and nodules or chert. The XCB is a rotary system with a small cutting shoe extending below the large rotary drill bit. The smaller bit can cut a semi-indurated core with less torque and fluid circulation than the main bit and thus optimizes recovery.

The bottom-hole assembly (BHA) is the lowermost part of the drill string. The exact configuration of the BHA is reported in “Operations” in each site chapter. 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 that we could collect downhole logs without dropping the bit when APC/XCB coring.

The RCB system was deployed to drill basaltic basement at three of the sites. The RCB is a conventional rotary drilling system and requires a dedicated RCB BHA and a dedicated RCB drilling bit (outer diameter = 9 inch). A typical BHA for RCB coring includes an RCB drill bit, a mechanical bit release (MBR), a modified head sub, an outer core barrel, a modified top sub, and a series of drill collars followed by tapered drill collar and 5½ inch drill pipe.

Curatorial procedures and sample depth calculations

Numbering of sites, holes, cores, and samples followed standard IODP procedure. Drilling sites are numbered consecutively from the first site drilled by the Glomar Challenger in 1968. IODP Expedition 301 began using the prefix “U” to designate sites occupied by the US Implementing Organization (USIO) vessel, the R/V JOIDES Resolution. For all IODP drill sites, a letter suffix distinguishes each hole cored at the same site. The first hole cored is assigned the site number modified by the suffix “A,” the second hole takes the site number and the suffix “B,” and so forth. For Expedition 329, each site has three or more cored holes (A, B, C, D, etc.). With the exception of Site U1365, all pilot holes were assigned alphabetical designations (e.g., Hole U1366A) even though no cores were taken from these holes. The reason for this designation is because pilot holes provide vital drilling information that can be stored in the IODP database for use in future drilling.

A full curatorial identifier for a sample 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 and also the sampling tools and volumes taken. For example, in sediment, a sample identification of “329-U1365A-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 U1365 during Expedition 329. For hard rocks, a sample identification of “329-U1365E-3R-8 (Piece 1, 4–7 cm)” indicates a 3 cm sample of Piece 1 removed from the interval between 4 and 7 cm below the top of Section 8 of Core 3 (“R” designates that this core was taken with the RCB) in Hole A at Site U1365. For cores taken with the XCB, the core type is indicated by an “X” after the core number. During Expedition 329, some of the sediment was drilled without coring in holes where hard chert horizons were encountered or in holes where the target recovery was underlying basement rock. Drilled intervals are assigned double-digit numbers, and the cores recovered after a drilled interval are assigned the following number in combination with the corresponding letter for drilling/coring system. For example, the drilled interval in Hole U1365E was designated 329-U1365E-11, where the first “1” indicates drilled interval 1 and the second “1” indicates the first section of that interval that was drilled. The first core recovered in Hole U1365E after the drilled interval was designated 329-U1365E-2R (“R” for rotary core barrel).

The cored interval is measured in meters below seafloor (mbsf) according to the core depth below seafloor, method A (CSF-A), depth scale (see IODP Depth Scale Terminology at In general, the depth below seafloor is determined by subtracting the water depth estimated from the initial drill pipe measurement to the seafloor from the total drill pipe measurement. The depth interval assigned to an individual core begins with the depth below seafloor at which coring began and extends to the depth that coring advanced. Each coring interval is generally ~9.5 m, which is the length of a core barrel; however, coring intervals may be shorter.

During Expedition 329, unless otherwise noted, all core depths below seafloor were calculated as CSF-A and all downhole wireline depths calculated as wireline depth below seafloor, method A (WSF-A). For ease of communication of shipboard results, all depths are reported in this volume as “mbsf” unless otherwise noted.

Core handling and analysis

A diverse core flow scheme was formulated for Expedition 329. Cores from the first hole at each site (typically Hole B) were dedicated for dissolved oxygen analyses (see “Biogeochemistry”), routine Core Laboratory analyses (see “Lithostratigraphy, igneous petrology, alteration, and structural geology,” “Paleontology and biostratigraphy,” “Physical properties,” and “Paleomagnetism”), and sampling table processing. This hole was designated for the stratigraphic backbone for the site.

As soon as cores arrived on deck, they 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, where they were cut into ~1.5 m sections. Liner caps (blue indicating top, colorless indicating bottom) were placed onto liner sections on the catwalk by the curator. Hard rock pieces were pushed to the top of the liner sections and the total rock length was measured. The length was entered into the database using the SampleMaster application as “created” length. Created length is used to calculate recovery. Headspace samples were taken from each core catcher in Hole B using a syringe for immediate hydrocarbon analysis as part of the shipboard safety and pollution prevention program. Typically this procedure is followed in the first hole drilled at a site, but because methane was not expected at the sites drilled during Expedition 329, the Environmental Protection and Safety Panel (EPSP) and the Texas A&M University Safety Panel approved our proposal to first drill a pilot hole at each site.

The first core from each hole (i.e., Core 1H) was sampled for bottom water if a mudline was recovered and seawater was present inside the top of the core liner. The bottom seawater was used for comparative studies of microbial communities between seawater and subseafloor habitats.

Cores from the first hole cored at each site were quickly processed on the catwalk, and the 1.5 m whole-round core sections were transferred immediately to the Cold Room adjacent to the Microbiology Laboratory for dissolved oxygen measurements (see “Biogeochemistry”). The whole-round cores were subsequently brought back to the Core Laboratory for routine core processing.

Cores from subsequent holes (typically Holes C and D, but sometimes E and F depending on core conditions), were processed on the catwalk and the whole-round sections were transferred immediately to the core reefer on the Hold Deck of the JOIDES Resolution for a wide range of geochemical and microbiological subsampling. Once the subsampling was completed, the remaining pieces of the whole-round core sections were brought back to the Core Laboratory for routine core processing. If core quality allowed, Hole C was sampled primarily for geochemistry and Hole D was sampled primarily for microbiology. When Hole D was cored by APC/XCB, it was primarily used to fill lithostratigraphic gaps of previous holes. Interstitial water samples were taken with Rhizon samplers at selected intervals (see “Biogeochemistry” and “Microbiology”).

Basalt cores were processed on the catwalk and immediately taken to the core reefer on the Hold Deck for cold storage and preliminary lithostratigraphic description. The cores were visually examined by the shipboard microbiologists and petrologists, and potential samples for microbiological studies were identified, discussed by the Sample Allocation Committee, and subsequently aseptically collected by the microbiologists. Once the samples were taken, the hard rock core sections were brought to the Core Laboratory for routine core processing.

As described in “Lithostratigraphy, igneous petrology, alteration, and structural geology,” “Physical properties,” and “Paleomagnetism,” routine core processing in the Core Laboratory included whole-round logging of core sections on the Whole Round Multisensor Logger (WRMSL) and splitting into working and archive halves. Archive-half sections were imaged on the Section Half Imaging Logger (SHIL), logged with the Section Half Multisensor Logger (SHMSL), and visually described for lithologic and petrologic properties. The working halves were sampled for shipboard analyses and postexpedition research.

In the Core Laboratory, whole-round sections were split lengthwise in the core splitting room to expose the core. For hard rock cores, oriented pieces of core were marked on the bottom with a red wax pencil to preserve orientation, either before they were extracted from the core barrel or when they were removed from the split core liner. In some cases, pieces were too small to be oriented. Adjacent but broken core pieces that could be fit together along fractures were curated as single pieces. The petrologist on shift confirmed piece matches, corrected any errors, and marked the split line on the pieces, which defined how the pieces were cut in two equal halves. The aim was to maximize the expression of dipping structures on the cut face of the core while maintaining representative features in both archive and working halves. A plastic spacer was secured to the split core liner with acetone between individual pieces or reconstructed contiguous groups of subpieces. These spacers may represent a substantial interval of no recovery. The length of each section of core, including spacers, was entered into the curation database as “curated” length. Curated length commonly differs by a few to several centimeters from the created length measured on the catwalk. The database recalculates the assumed depth of each piece based on the curated length.

Sampling for shipboard analyses and personal research was done onboard. Both halves of the core were shrink-wrapped, put into labeled plastic tubes, sealed, and transferred to cold storage space aboard the ship. At the end of the expedition, the cores and samples were transferred from the ship to refrigerated containers and shipped to cold storage at the IODP Gulf Coast Repository in College Station, Texas (USA).

Drilling-induced core deformation

Cores may be significantly disturbed and contain extraneous material as a result of the coring and core handling process. Therefore, the top 10–50 cm of each core must be carefully examined for potential “fall-in” during description. Common coring-induced deformation includes concave-downward appearance of originally horizontal bedding. In APC cores, the motion of the piston may result in fluidization (flow-in) at the bottom of the cores. Retrieval from depth to the surface may result in elastic rebound. Observed core disturbances are described in “Lithostratigraphy” and other sections in each site chapter and graphically indicated on the core standard graphic reports (visual core descriptions [VCDs]; see “Lithostratigraphy, igneous petrology, alteration, and structural geology”).

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):

  • Operations: C. Alvarez Zarikian, S. Midgley
  • Background and objectives: S. D’Hondt, F. Inagaki
  • Lithostratigraphy: B. Hoppie, F. Shiraishi, G. Uramoto
  • Paleomagnetism: H. Evans, T. Shimono
  • Igneous petrology: C. Smith-Duque, G. Zhang
  • Paleontology and biostratigraphy: C. Alvarez Zarikian
  • Biogeochemistry: N. Dubois, T. Ferdelman, B. Gribsholt, J.-H. Hyun, S. Mitsunobu, R.W. Murray, D.C. Smith, A. Spivack, M. Szpak, Y. Yamaguchi, W. Ziebis
  • Microbiology: T. Engelhardt, J. Kallmeyer, J. Lynch, Y. Morono, D.C. Smith, B.O. Steinsbu, Y. Suzuki, L. Toffin, X.-H. Zhang
  • Physical properties: R. Harris, J. Kim
  • Downhole measurements: H. Evans

1 Expedition 329 Scientists, 2011. Methods. In D’Hondt, S., Inagaki, F., Alvarez Zarikian, C.A., and the Expedition 329 Scientists, Proc. IODP, 329: Tokyo (Integrated Ocean Drilling Program Management International, Inc.). doi:10.2204/iodp.proc.329.102.2011

2Expedition 329 Scientists’ addresses.

Publication: 13 December 2011
MS 329-102