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Expedition 325 Scientists2


This chapter documents the primary procedures and methods employed by various operational and scientific groups during the offshore and onshore phases of Integrated Ocean Drilling Program (IODP) Expedition 325. This information concerns shipboard and Onshore Science Party (OSP) methods as described in each transect chapter. Methods for postcruise research conducted on Expedition 325 samples and data will be described in individual scientific contributions to be published after the OSP. Detailed drilling and engineering operations are described in the “Operations” sections in each transect chapter.

Shipboard scientific procedures

Numbering of sites, holes, cores, and samples

Expedition numbers for IODP are sequential, starting with 301. Drilling sites are numbered consecutively, and for a European Consortium for Ocean Research Drilling (ECORD) Science Operator (ESO)–operated platform, numbering starts with Site M0001 (the “M” indicates the ESO-operated mission-specific platform). For Expedition 325, the first site was Site M0030. Multiple holes may be drilled at a single site. For all IODP drill sites, a letter suffix distinguishes each hole drilled at one site. The first hole drilled is assigned the site number with the suffix “A,” the second hole takes the site number and the suffix “B,” and so forth. For Expedition 325, in the Scientific Prospectus sites were represented as 125 m radius overlapping circles. All holes were initially given the suffix “A” even if located within the same “site” circle. This was considered the best option because of the close proximity of some of the proposed holes and the requirement to differentiate between each time the seabed was penetrated. This was specified by the Great Barrier Reef Marine Park Authority (GBRMPA) in the permit citing a maximum number of drilled “holes” allowed. Where attempts were made to drill secondary holes at the same coordinates, consecutive letters were used, following the IODP naming convention (for example, Holes M0030A and M0030B).

The cored interval is measured in meters below seafloor (mbsf). Depth below seafloor is determined by subtracting the initial drill pipe measurement obtained when the seabed was tagged from the total drill pipe measurement (i.e., the drilling depth below seafloor depth scale [DSF-A]). For Expedition 325, the cored interval normally consisted of the entire drilled section, but in some cases some intervals were drilled without coring (e.g., when drilling in open hole down to the previous cored depth in Hole M0052C).

Recovered core is split into sections with a maximum length of 1.5 m and numbered sequentially from the top, starting at 1 (Fig. F1). By convention, material recovered from the core catcher of a sedimentary core is treated as a separate section labeled “CC” (core catcher) and placed below the last section recovered in the liner. The core catcher is assigned to the top of the cored interval if no other material is recovered. When recovered core is shorter than the cored interval, the top of the core, by convention, is equated to the top of the cored interval to achieve consistency in reporting depth in core.

A soft to semisoft sediment core from less than a few hundred meters below seafloor can expand upon recovery (typically 10%–15%), so the recovered interval may not match the cored interval. In addition, a coring gap typically occurs between cores (i.e., some cored interval was lost during recovery or was never cut). Thus, a discrepancy exists between the drilling meters below seafloor and the curatorial meters below seafloor. For example, the curatorial depth of the base of a core can be deeper than the top of the subsequent core for an expanding sediment.

Any sample removed from a core is designated by the distance measured in centimeters from the top of the section to the top and bottom of the sample removed. A full identification number for a sample consists of the following information: expedition, site, hole, core number, core type, section number, piece number (for hard rock), and interval in centimeters measured from the top of section. For example, a sample identification of “325-M0030A-3R-2, 35–40 cm,” represents a sample removed from the interval 35–40 cm below the top of Section 2 of Core 3R-2 (“R” designates that this core was taken using the rotary core barrel), from Hole M0030A during Expedition 325 (Fig. F1). All IODP core identifiers indicate core type. For Expedition 325, the following abbreviations are used:

  • X = extended nose core barrel (EXN; equivalent to IODP’s extended core barrel),
  • R = rotary core barrel (alien corer [ALN]; equivalent to IODP’s rotary core barrel).

The mbsf depth of a sample is calculated by adding the depth of the sample below the section top and the lengths of all higher sections in the core to the core-top datum measured with the drill string.

Core handling during the offshore phase of Expedition 325

As soon as a core was retrieved on deck, it was immediately curated by the ESO curators. This involved marking and cutting the core into sections with a maximum length of 1.5 m. Each section was sealed at the top and bottom by attaching color-coded plastic caps: blue to identify the top of a section and clear at the bottom. A yellow cap was placed on section ends where a whole-round sample was removed for microbiology. Core section liners were permanently labeled with an engraving tool. The lengths of the core in each section and the core catcher sample were measured to the nearest centimeter; this information was logged into ESO’s Offshore Drilling Information System (OffshoreDIS). No core splitting took place during the offshore phase of Expedition 325.

Curation procedures for HQ cores

Coring with the HQ system used metal (stainless steel) split liner halves instead of plastic liners. This required additional steps in the curation procedure to transfer the “open core” into a standard IODP butyrate liner as follows:

  1. Uncover the top metal half.

  2. Take an empty liner with a precut slit on one side.

  3. Carefully pull the liner over the core (the liner slit faces down under the metal half).

  4. Turn everything by 180° (metal half is on top now).

  5. Pull the metal half out, making sure to hold the core inside the liner by covering the open liner end.

  6. Leave the transferred core on the core bench for 5–10 min with the split facing down to allow any remaining drilling fluids to drain.

  7. Seal the split liner with heavy-duty tape and put on the blue and clear end caps, sealing with acetone.

All cores that were transferred from metal splits were identified in the drilling information system’s core-section input form under the “remarks” field.

After curation, the core proceeded through a sequence of processing steps. Geochemists and microbiologists were given access to the cores to sample for interstitial water (IW) and microbiology. This generally required 5–10 cm whole rounds to be taken, although Rhizon syringes for IW collection were employed if core material was suitable. With the exception of IW, microbiology, and preliminary dating, no additional sampling of the cores or core catchers was undertaken during the offshore phase of Expedition 325.

The core catcher, or a sample of the core catcher, was given to the sedimentologists and coral specialists for initial description. Shipboard sedimentologists also took the opportunity to describe core sections through the clear plastic liners, although drilling fluid and mud caking often made this difficult or impossible. Subsamples of core catcher material were taken for preliminary dating using 14C or U-series analysis prior to the OSP, where the results would be presented as if they were “shipboard data.” These samples were identified by the Co-Chief Scientists and were located at the top, middle, and toward the base of each hole where suitable core catcher materials were available.

Core sections were allowed to equilibrate to “container” temperature before they were run through the multisensor core logger (MSCL).

Core handling during the Expedition 325 Onshore Science Party

After being taken out of refrigerated storage, cores were split lengthwise into a working half and an archive half. Sections containing significant lengths or well-preserved smaller sections of massive coral were treated differently (see “Specialist sampling of massive corals”). Harder cores were split with a diamond saw. Softer cores, less common during this expedition with the exception of the forereef slope site (Hole M0058A), were split with a wire or saw, depending on the degree of induration. Wire-cut cores were split from bottom to top, so investigators should be aware that older material could have been dragged up the core on the split face of each half.

Digital high-resolution images of archive halves were made with a digital imaging system, followed by discrete color reflectance measurements. Archive halves were then described visually. Total organic carbon (TOC) and X-ray diffraction (XRD) samples were taken from the cores when requested by the science party during the core description phase. If required for illustrations of particular features by the scientists, close-up crops of the high-resolution line scan images were made.

The working half of the core was sampled for both the OSP and postcruise studies. Each sample was logged into the OffshoreDIS by hole, core, section, depth, sample request number, and the name of the lead investigator receiving the sample. Samples were sealed in vials, cubes, or bags; labeled; and stored as appropriate. Samples were routinely taken for physical properties and magnetic susceptibility measurements, which are described below.

Following initial description, sampling, and measuring, both halves of the cores were wrapped in plastic to prevent rock pieces from vibrating out of order during transit. Both halves were then placed in labeled D-tubes, sealed, and transferred to refrigerated storage at the Bremen Core Repository (BCR; Germany).

Operations equipment

Site locations

At all Expedition 325 sites, GPS coordinates from precruise site surveys were used as a guide for positioning. The final coordinates and coring targets were selected from within the IODP-agreed 125 m radius around the original Scientific Prospectus positions by the Co-Chief Scientists. Selected positions were relayed to the European Geological Survey (EGS) hydrographic surveyors onboard, and the Greatship Maya was then settled on position using a dynamic positioning (DP) system. In order to maintain station accurately at each site, the DP system ran for 20–30 min prior to coring at each site to build a reliable footprint model. Where adjustments to the vessel position of <1 km were made under DP, the time required to build a suitable DP model was significantly reduced. The final site position was calculated by the surveyors, using the calculated mean position of 30 readings taken every second over the first 30 s period on station after the drill pipe had tagged the seabed.

The maximum required depth of the deepest boreholes was originally 100 mbsf. Initial approval was granted by the IODP Environmental Protection and Safety Panel (EPSP) to drill to a maximum total depth of 40 mbsf on the reef sites and 100 mbsf on the forereef sites. However, these depths were amended by the EPSP to 160 m below present sea level at one chosen site on each transect (to be identified when operational offshore) in order to capture the lowest possible sea level minimum during the last glacial period.

Drilling platform

The water depth at all the sites is relatively shallow (42.27–167.14 m lowest astronomical tide). The drilling platform, chosen by the contractor and inspected by ESO, was the Greatship Maya, an IMO Class II dynamically positioned vessel complete with geotechnical coring capability (Figs. F2, F3). The Greatship Maya had sufficient capacity by way of food, water, and accommodation for 50 days of continuous operation, so there was no requirement for a port call for resupply. However, because the operational period was extended as a result of weather downtime due to Cyclone Ului, resupply of the vessel did occur.

Coring rig

The vessel was equipped with a large moonpool and a Bluestone TT150 derrick and Foremost Hydraulic top drive (Fig. F4). The compact top drive onboard the Greatship Maya was a 150 ton Canadian-built system (Foremost Industries) that is both rugged and powerful. The design of this top drive system has been adapted to make it ideal for geotechnical or scientific drilling, sampling, and coring activities. The derrick had a mast capable of handling 9 m string lengths (Fig. F5). Wireline operation of the core barrel was conducted through the top drive. Deployment of the wireline logging tools was conducted through the mud valve at the top of the top drive, from the rooster box.

Coring methodology

For efficient drilling/coring it is essential to apply a steady weight onto the drill bit. Vessel heave can reduce or apply excessive weight to the drill bit; therefore, the drilling system onboard was heave compensated to allow vessel movement. The drill string was suspended below the top drive and the drill string compensator. The fast line ran over a relative motion–compensating heave (2.5 m stroke cylinders) and was connected to the drawworks winch. The deadline similarly ran to the anchor point at the drill floor. Compensator loading is ~80 metric tons.

Seawater was intended as the primary drilling medium, but because of the conditions encountered (loose sand at the seabed surface and caving lithological formations downhole), it was necessary to use a biodegradable drilling mud (guar gum). Biodegradable plastic bags containing fluorescent microspheres were attached to the core barrel for the first run of each borehole and at specified sites of interest to assist the evaluation of contamination of samples for later microbiology studies.

The drillstring available included 77 joints of nominal 9.2 m long American Petroleum Institute (API) drill pipe, 5½ inch with 5½ inch full hole tool joints with a 4 inch bore inner diameter; five API drill collars, nominal length 9.2 m; and an assortment of short (pup) joints. In addition, there were four available bottom-hole assemblies (BHAs), two each API and HQ; 84 lengths of 3 m Longyear HQ drill rods; and a selection of drill bits.

Two BHAs were used, as dictated by the expected lithological conditions and core recovery rates. The API core barrel is a versatile BHA for the API drillstring that enables rock coring to be conducted using wireline coring techniques (see “Coring with an API BHA”) and can be used with an ALN and an EXN. The EXN is deployed to recover loose sediments. It is a nonrotating core barrel that protrudes from the drive tube. This configuration allows for a push sample–like core to be collected. As with the EXN, the ALN locks into the BHA but does not have a bearing on the core barrel allowing it to rotate. Instead, the entire assembly rotates to core a hard rock sample. Both corers may be run without altering the BHA, which allows quick change-over as required. Both are recovered to deck on a wireline.

The second BHA used was a mining-type HQ-size wireline core barrel, deployed on a mining drillstring, which fit inside the API drill string and used the API drillstring as a conductor or casing (see “Coring with an HQ string”).

Initially, a camera was deployed through the API pipe to assess the seabed character and the presence of live coral. Where no live coral was identified, drillers proceeded to spud in with the API pipe. This acted like a stinger and reduced the seabed footprint, minimizing potential impacts on the seabed environment. Following coring operations at each site, the aim was to deploy the camera again to photograph any impact from the coring operation on the seabed. On a number of occasions at Hydrographer’s Passage, the postcoring camera survey proved unsuccessful because of strong seabed currents pushing the drillstring off the vertical once it was raised above the seabed. The GBRMPA was advised of this and was satisfied on those occasions that the precoring survey to ensure that no live corals were cored was sufficient.

Coring with an API BHA

A QD Tech coring system was selected to core both rock and sediments using the API string. Two types of inner barrel assemblies were available for this project: the EXN, which is used in sediments, and the ALN, which is used in rock formation. The ALN assembly has a short or long bit option. Assemblies are directly connected to the API drillstring and recovered to deck via wireline, which has the advantage over the HQ coring system of a faster total execution time. The operation of this coring tool follows a similar procedure as the HQ rod/barrel.

Alien sampler

The alien sampler is an inner tube assembly for collecting core samples in hard formations that cannot be sampled using push-style samplers. The alien sampler is deployed into the drillstring and seats, seals, and latches into the BHA at the end of the drillstring. The core sampling portion, consisting of the shoe, core lifter, inner tube, and liner, is isolated from the rotating drillstring by a swivel-bearing arrangement.

The alien sampler outer tube and coring bit rotate with the main outer bit, and flushing water is ported through the face discharge ports in the alien sampler bit. Because of the various sample types that the alien sampler may encounter, there are three core lifter types: the basket core lifter, a hard rock–style core lifter, and an integrated core lifter shoe/basket spring (a diamond coring hard rock–style core lifter with basket springs). Aluminum split liners are also available for the alien sampler. The run length of the alien sampler is as much as 3 m before recovering the inner assembly using the wireline.

Extended nose sampler

The extended nose sampler is an assembly for collecting core samples in sediment using direct push force. It is deployed into the drillstring and seats, seals, and latches into the BHA at the end of the drillstring. The core sampling portion, consisting of the core lifter case (shoe), core lifter, inner tube, and liner, is pushed into the formation by the drillstring and is isolated from the rotating drillstring by a swivel-bearing arrangement. This inner assembly also has a vertical movement of as much as 2 inches, depending on the amount of force required against a return spring to penetrate the material.

Liner tubes and aluminum split tubes can be used in the extended nose sampler. The run length of the extended nose sampler is as much as 3 m before recovering the inner assembly with the wireline.

Coring with an HQ string

In this method, API drill pipes or drillstring is used as a casing. The drillstring is lowered to the seabed with a bumper sub connected 18 m from the drill bit. The string is then washed or slowly rotated a predetermined depth into the soft overburden, and the bumper sub is opened by filling it with drill mud. The top of the API string is then hung in the elevators on the drill floor. With the casing (drillstring) in place, the HQ core barrel can be lowered through the API string and bit.

A crossover sub is used to connect the HQ rods to the top drive. The rotational speed and bit load are adjusted by the three-speed gear change and the compensator. Constant bit load is achieved by increasing and decreasing the air in the compensator. The mud flow rate is managed by controlling the revolutions per minute (rpm) of the pump.

When a single core run (maximum = 3 m) is achieved, the inner barrel is retrieved by wireline and laid on a core rack on the drill floor while a standby barrel is lowered immediately. A two-barrel setup allows coring to continue while the core is extracted from the barrel recently recovered. This barrel can then be cleaned and fitted with a fresh liner tube for the next run. This process is continued until the target depth is reached.

A supplementary method to the above can be employed when encountering sediments or sand layers by advancing the casing as coring proceeds. Advancing the casing prevents the hole from caving in, thus preventing the core barrel from getting stuck. The casing is advanced only when there is evidence of high torque during coring on the HQ rod.

The maximum core run length was 3 m. However, the length of a core run was chosen to maximize core recovery and maintain hole stability, even at the expense of overall penetration speed. In unconsolidated materials and delicate coral frameworks, the run length was reduced to 1–1.5 m to facilitate better core recovery. In some cases, coring was stopped after <1 m if increasing pressure or high torque indicated problems advancing due to lithology or a blocked bit.

Downhole logging tools

Downhole logging services were contracted and managed by the European Petrophysics Consortium (EPC). Details and results of the expedition logging program are given in the “Downhole measurements” section in each transect chapter.

Through-pipe underwater video camera

A through-pipe camera survey was conducted before and, where possible, after coring at each site to ascertain that minimal damage would be done to any living coral present at the drill site, satisfying the environmental protection requirements of GBRMPA, the EPSP, and ESO.

The British Geological Survey (BGS) provided an underwater color video camera system and a deployment frame to allow it to be lowered inside the API drill pipe (Fig. F6). It is based on diver helmet–operated systems, with an umbilical cable relaying direct feed imagery to a monitor and recording system located inside the driller’s shack on the drill floor. The system worked well, and good video coverage was obtained from a number of sites. More importantly, the video demonstrated that it is possible to drill in a reef setting with minimal disturbance to the environment.

Seabotix remotely operated vehicle

During Expedition 325, BGS also supplied a Seabotix LBV150SE Little Benthic Vehicle (LBV) rated to 150 m water depth. Two color cameras were on board the vehicle. The main camera was mounted with a switchable high-intensity LED light array on a tilt mechanism, which allowed a 270° range of view. The second camera was a fixed-focus rear-facing unit. The LBV was propelled by four powerful thrusters: one vertical, one lateral, and two horizontal. This configuration afforded four-axis maneuverability with a top speed of 3 kt and the ability to work in currents up to 2 kt. The system enabled visual inspections of the drillstring and seabed template with relation to the reef structures and seabed features to be carried out, with video imagery being relayed in real time to recording equipment on deck, thereby complementing the suite of pre- and postdrilling downpipe camera imagery. Because of the strong currents experienced at Hydrographer’s Passage, it was not possible to launch the LBV at all sites.

YSI Environmental 6600 V2-4 Sonde

The 6600 V2-4 Sonde was used to collect simultaneous measurements of conductivity (salinity), temperature, depth, pH, dissolved oxygen, and turbidity to monitor present-day oceanographic conditions at the drilling sites. In total, 40 profiles were taken (Table T1) across the four transects. Where possible, measurements were taken at various states of the tidal cycle (falling, rising, and slack water). However, in many cases, it was only possible to take one measurement because of the time on station before moving to a new location. In addition, on many occasions, especially at Hydrographer’s Passage, the currents proved too strong to safely deploy the sonde. Sensor specifications are detailed in Table T2.

Data handling, database structure, and access

Two overlapping phases of data management were used during Expedition 325. The first phase was the capture of metadata and data during the expedition (offshore and onshore). Central to this was the Expedition Drilling Information System (GBREC-DIS). The second phase was the long-term, postexpedition archiving of Expedition 325 data sets, core material, and samples. This was done by the World Data Center for Marine Environmental Sciences (WDC-MARE) and the BCR. The Publishing Network for Geoscientific and Environmental Data (PANGAEA) is the geoscience information system used by WDC-MARE, whereas the BCR uses the Curation Drilling Information System (Curation-DIS).

Offshore, the GBREC-DIS was used to capture drilling information, core and sample curation information, core catcher photographs, and primary measurement data (e.g., MSCL, downhole logging data, and additional data such as initial visual core descriptions (VCDs) of core sections (in liner) and core catchers and IW analysis. This process was replicated during the OSP, where a broader range of measurements and observations was captured (for example, line-scan images, color reflectance data, and visual core descriptions of the cut cores). Corelyzer was used to visualize the data (high-resolution line scan images and MSCL data).

Also, expedition scientists produced a variety of spreadsheet files, text documents, and graphics containing data, descriptions, and interpretations in different formats, both offshore and onshore. These files were stored in a structured file system on a file server.

Following the OSP, Expedition 325 data were transferred to WDC-MARE. This process was completed by the time this volume was published. Until the end of the moratorium period, Expedition 325 scientists could access the data through a password-protected data portal.

After the moratorium, the data are available to the public through the IODP Scientific Earth Drilling Information System (SEDIS) portal. WDC-MARE will continue to acquire, archive, and publish new results derived from Expedition 325 samples and datasets. Expedition core and sample metadata will be transferred to the BCR Curation-DIS and linked to the IODP Sample Materials Curation System (SMCS).

Hardware installation

The ExpeditionDIS was implemented in SQLServer-2000 with Microsoft-based client PCs connecting to the system through a Microsoft Access–like user interface. For the offshore phase of the expedition, the ExpeditionDIS was installed on a server on the Greatship Maya. A second server was used as a hot-standby and data back-up system. Incremental backups to the secondary server were automatically made twice per day, and additional full backups to an external hard drive were also regularly made. These backups comprised the ExpeditionDIS and the shared file server. Automated database backups where also done twice per day.

A similar setup was used during the onshore phase. Two servers were used for the installed ExpeditionDIS and for handling files. ESO laptops were set up to provide access to the ExpeditionDIS in all used offices. Networked printers were also available via a print server. Automated database and complete file server backups were also done twice per day. The expedition reports–related files were also backed up more frequently (an additional two times per day).

1Expedition 325 Scientists, 2011. Methods. In Webster, J.M., Yokoyama, Y., Cotterill, C., and the Expedition 325 Scientists, Proc. IODP, 325: Tokyo (Integrated Ocean Drilling Program Management International, Inc.). doi:10.2204/iodp.proc.325.102.2011

2Expedition 325 Scientists’ addresses.

Publication: 16 July 2011
MS 325-102