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doi:10.2204/iodp.proc.347.102.2015 Methods1T. Andrén, B.B. Jørgensen, C. Cotterill, S. Green, E. Andrén, J. Ash, T. Bauersachs, B. Cragg, A.-S. Fanget, A. Fehr, W. Granoszewski, J. Groeneveld, D. Hardisty, E. Herrero-Bervera, O. Hyttinen, J.B. Jensen, S. Johnson, M. Kenzler, A. Kotilainen, U. Kotthoff, I.P.G. Marshall, E. Martin, S. Obrochta, S. Passchier, N. Quintana Krupinski, N. Riedinger, C. Slomp, I. Snowball, A. Stepanova, S. Strano, A. Torti, J. Warnock, N. Xiao, and R. Zhang2Introduction and coringThis chapter documents the primary operational, curatorial, and analytical procedures and methods employed during the offshore and onshore phases of Integrated Ocean Drilling Program (IODP) Expedition 347. This information concerns only shipboard and Onshore Science Party (OSP) methodologies and data as described in the site chapters. Methods for postexpedition research conducted on Expedition 347 samples and data will be described in individual scientific contributions published after the OSP. Detailed drilling and engineering operations are described in “Operations” within each site chapter and “Operational strategy” in the “Expedition 347 summary” chapter (Andrén et al., 2015). The information in this chapter will enable future identification of data and samples for further scientific investigation by interested parties. Site locationsAll Expedition 347 sites (Fig. F1) were positioned using GPS coordinates supplied by the proponents and based on previous site surveys. As a number of holes were proposed at each site for different uses (e.g., paleoenvironment and microbiology), a central hole position was taken from the proponent-supplied coordinates (Hole A), and then additional positions were calculated radiating out from this position at 20 m intervals, with Holes B and C on either side of Hole A, running along the site survey seismic lines, and Holes D and E perpendicular to this orientation, again on either side of Hole A (Fig. F2). The spacing interval of 20 m between holes was chosen to limit drilling disturbance between holes while maintaining a close enough proximity to correlate between them, enabling the formation of a composite recovery and lithologic splice. Selected positions were relayed to the Hydrographic Surveyor from Geocean, and the Greatship Manisha was settled into position using a dynamic positioning (DP) system. To maintain station accurately within the required tolerance of <1 m for shallow-water sites, the DP system ran for 30–40 min at each location to build a reliable DP model, after which permission was granted to commence operations. Geocean supplied two transponder systems that were used during coring operations as backup for the DP system should there be a failure in the differential GPS (DGPS) signal because of satellite angles, particularly in the river estuary sites, or malfunction. The primary transponder was fitted to the seabed frame (Fig. F3). The secondary transponder was either deployed on the seabed frame or over the side of the vessel. Adjustments to the vessel position of <100 m at each site (e.g., when moving or “bumping over” between hole locations) were performed using the existing DP model, as it was considered representative of hydrodynamic conditions over such distances, thereby reducing the waiting time before drilling operations could commence in the new hole. Drilling platformFor Expedition 347, the maximum required depth of boreholes was 275 meters below seafloor (mbsf) in water depths ranging between 34 and 451 m. Therefore, a multipurpose offshore vessel fitted with a drilling derrick and coring system was selected to carry out the offshore operations. The drilling platform, chosen by Island Drilling and inspected by the European Consortium for Ocean Research Drilling (ECORD) Science Operator (ESO), was the Greatship Manisha, a 93 m long offshore vessel with DP (Class 2) capability (Fig. F4). The Greatship Manisha had the capacity in terms of provisions and accommodation to support 24 h operations for 45 days. A midterm port call for resupply was therefore required. Located on the aft deck were 12 ESO containers and an additional container supplied by Island Drilling (Fig. F5) containing the following:
Coring rigThe vessel was equipped with a large (6 m × 5.3 m) moonpool and a Geoquip GMTR 120 with a heave-compensated system coring rig (Fig. F6). The top drive had a 120 metric ton capacity, 0–200 rpm with 23,000 ft/lb of torque, and through-bore of 4.125 inches for deployment of in-hole tools. This rig has a combined borehole and water depth capacity of 2000 m when using a standard geotechnical drill string of 7 × 4 drill collars and 5.5 inch drill pipe. Pipe handling was carried out using a proprietary semiautomated handling system utilizing a pipe handling crane with grab, a remotely operated iron roughneck, and a proprietary catwalk system. This system was capable of handling two pipes at once with minimum manual intervention and hence improved safety. A 4 m stroke passive heave compensation (semiactive under development) was achieved using nitrogen gas as a compensation buffer with Olmsted valve slingshot protection. The rig was used in association with a 12 metric ton seabed template, fitted with clamps and seabed transponder, to provide the reaction force for in-hole tools. Wireline coringFive methods of wireline coring were employed in addition to open-hole drilling using a noncoring assembly. Identifying letters in parentheses after each coring type show the letters used in the operations table in each site chapter to identify the coring method for each core run. Piston corer system (H)The piston corer system (PCS) is designed to operate primarily in soft muddy to clayey formations. The PCS operated by advancing the core barrel into the formation through hydraulic pushing. The PCS was set up by fully retracting the core barrel into the core barrel housing, which was then held in place using two shear pins. The pins used were either brass or steel or a combination of the two, depending on the expected strength of the lithology to be cored. The core barrel housing was then lowered into the bottom-hole assembly (BHA) at the base of the drill string. Drill mud/water was pumped into the drill string, pressurizing the closed system and producing a force that overcame the strength of the shear pins, typically in the region of 50–130 bar. When the pins sheared, the corer was forced into the sediment by the pressure of the drill fluid. The number and type of shear pins inserted dictated the pressure at which the core barrel was released and, consequently, the force at which the barrel was pushed into the formation. During Expedition 347, the PCS was the primary tool, as the lithologies were expected to be clayey material. However, it was also utilized in silty and sandy formations in an attempt to collect undisturbed cores. After each core was taken, the hole was advanced by drilling to the next sample point. This was carried out either by “advance by recovery” or “advance by barrel stroke.” When advancing by recovery, the depth of the next core run was dictated by the length of core recovered, which was not known until the core was back on deck. To reduce the cycle time, “advance by barrel stroke” was occasionally used, meaning the hole was advanced without knowing the true recovery of the last run. On other occasions, some PCS runs were taken every 3 m regardless of the core length recovered. Piston coring is slower than conventional drilling, as each section has to be cored with the PCS and then drilled out before the next sample can be taken. Different core catcher combinations were used to optimize core retention with minimal core disturbance. Typically, a flapper catcher was used. However, basket catchers were added if necessary. Although these catchers are stiffer and can cause disturbance in clay cores (e.g., circumference scoring), they are more successful in retaining or assisting to retain very soft clay and sands than a flapper catcher. Extended coring system (X)The extended coring system (ECS) is designed to sample unconsolidated and noncohesive formations that are too dense for piston coring but too friable for rotary coring with direct circulation at the bit. A conventional cutting shoe is generally utilized with this system. However, a polycrystalline diamond (PCD) bit can also be used to assist recovery in more granular formations. The ECS barrel is locked into the BHA and advanced through rotation and flushing in a similar way to diamond rotary coring. The difference is that the end of the core barrel protrudes ahead of the main cutting bit by as far as 12 cm. One of a series of drill bits was used (chosen when considering the lithology encountered or expected), including tungsten, surface set, impregnated diamond, or PCD, all of which minimize flushing at the point where the core enters the core barrel to reduce undercutting and washing away. Nonrotating core barrel (N)The nonrotating core barrel (NRCB) is equivalent to a standard diamond rotary core barrel and is designed to core in hard formations. The assembly is a tribarrel construction. The outer barrel locks into and rotates with the BHA, and the inner barrel metal tube hangs from a bearing assembly at the top of the outer barrel, which removes the rotation of this tube. The final barrel is the plastic liner in which the core is collected and stored. The NRCB is advanced by rotary coring, with flushing occurring at the point where the core enters the core barrel. Normally, a conventional core spring is used to retain the core, but if the formation is soft or fractured and hence easily washed away, then an additional basket catcher is utilized to assist retention of the material even if the catcher undercuts the core as it passes through the catcher tines. The core cutting bit on the NRCB is retrieved with each core run so the cutting ability can be optimized for each formation encountered. Push coring assembly (P)The push coring assembly (PCA) is a simple tube extension which protrudes 1 m (or more if required) beyond the main core bit. The PCA was lowered into the drill string on the wireline, with the drill string raised above the bottom depth of the borehole. When it was in position, the drill string was lowered until either the full stroke of the sample tube was reached or the maximum bit weight was achieved. The drill string was then raised above the length penetrated to allow easier release before recovering the tool to the deck. A similar range of core retention catchers to that used for the PCS and ECS was available for this tool. Hammer sampler (S)The hammer sampler (HS) is a rudimentary sampling tool that uses percussive force to drive a tube into the borehole base. The tool has a built-in hammer, which is raised and lowered onto an anvil by lifting and lowering the sample wire manually over a few meters distance. This tool is typically used to acquire a sample if one has not been obtained by conventional methods. It can also be used to clear the main bit if it has become blocked. The HS was lowered on the wireline to the bottom of the borehole, and the tension was taken on the wire to define the base of the hammer. A mark was made on the wire to identify this fixed point. The rope was then raised to a distance within that of the slide bar on the hammer and lowered by free fall. This action was repeated (typically >25 times) until the fixed point mark had progressed to a point that exceeded the length of the sample tube or a sufficient sample had been acquired to prove the lithology. This method was typically employed when till/diamict lithologies were encountered to acquire spot samples approximately every 3 m. Noncoring assembly (O)The noncoring assembly (NCA) uses a small tricone Rock Roller drill bit to plug the hole in the main core bit through which the other sample tools fit. The cones may be either hardened steel or tungsten carbide tips. The tungsten carbide option was used most extensively during this expedition. The NCA was lowered and picked up on the wireline, allowing advancement without the possibility of cuttings entering the drill string by utilizing washways to move cuttings away from the face of the bit. The recovery to the deck of the NCA allowed it to be examined for trapped cuttings and provided a quick visual estimation of the lithology penetrated, which facilitated subsequent coring tool selection. Rumohr coring system (L)In addition to the main drilling system, one member of the science party provided a third-party tool system that could take gravity cores of the surficial sediment to 1 mbsf (Fig. F7). As the system did not include a core catcher, it left the uppermost sediment intact (e.g., for possible varve counting and of the sediment/water interface). This system was deployed over the side of the Greatship Manisha using a winch system. Coring methodologyTo ensure efficient drilling and coring, it is essential to apply a steady weight onto the drill bit to prevent swabbing of the hole. Vessel heave can reduce or apply excessive weight onto the drill bit; therefore, the drilling system onboard was heave compensated, with clamps on the seabed template providing a reaction force. The drill string comprised a BHA, a number of drill collars (the number of which varied depending on the expected depth of the borehole), and sufficient American Petroleum Institute (API) drill pipes. This assembly was passed through a cone guide and two sets of clamps located on a seabed frame (SBF) (Fig. F8). The SBF was situated on the seabed, acting as a reentry guide for the string (in the event of having to recover the BHA to the deck) and providing a reaction force for the piston corer. The main drill bit had an outside diameter of 210 mm (8¼ inches) and a throat of 98 mm. Any tools passing through the bit were required to have an external diameter <95 mm, which corresponds to the internal diameter of the landing ring in the BHA where all inner barrels seat. The various wireline tools were lowered on the wire, with an overshot release tool employed to release the overshot carrying the sampling tool once it was in place. When taking a piston core sample, on recovery of the overshot to the rooster box, the mud valve was closed and the string pressurized by pumping drilling fluid into the string. When the strength of the pins holding the piston in place was exceeded by the pressure of the drill fluid in the string, they sheared and the core tube fired into the strata. The drill string was then raised to allow the core to break at the base, and the overshot was run again, this time to collect the tool and recover it to the deck. The drillers were able to detect whether there had been a successful “full-stroke” by the pressure gauges on the rig floor. The core collected was 62 mm in diameter. This is the standard IODP core size, and cores were collected in standard IODP transparent liners. The maximum core run length was 3.3 m. However, the length of a core run was chosen to maximize core recovery and quality while maintaining hole stability, even at the expense of overall penetration speed. When attempting to capture a lithologic interface as defined from seismic profiles, the run lengths were often shortened by raising the corer above the bottom of the borehole by a known height prior to pressuring the drill string. In some instances, the hole was advanced by open holing—drilling ahead without recovering sediments. This was done in difficult lithologies that could not be recovered using the tools onboard to enable recovery of other lithologies beneath these intervals or when recovery (composite or from an individual hole) of an interval had already reached >90% and the scientific rationale was to try and get deeper within the time constraints. It was also employed when coring multiple holes to ensure that any gaps in recovery from one hole were recovered in another. The advance varied from a small offset of 0.5 m to ensure maximum core overlap between holes in some locations to a more regular spacing of 3 m through the till lithologies to monitor when or whether the lithology was changing. Seawater was the primary drilling medium utilized until the lithologies encountered required stabilization and increased flushing of drill cuttings. If this occurred on a paleoenvironment hole, then Guar gum, a biodegradable drilling mud, was used. On microbiology holes, however, this medium would have been detrimental to the microbial communities under investigation, and a polymer called GS550 was used as an alternative. Further, a concentrated solution of perfluorocarbon (PFC) was introduced into the seawater or GS550 drilling mud in the microbiology holes to assess potential contamination of the core samples. See “Microbiology” for further details. As per the risk assessment analysis conducted by ESO and the Natural Environment Research Council during the planning stages of Expedition 347, downpipe camera/remotely operated vehicle surveys were conducted at Sites M0060, M0064, and M0065 prior to coring operations to assess the seabed for dumped ammunitions and mines from World War II (WWII). A prerequisite for being able to commence operations was to ascertain that the seabed was clear of any obstructions. Coring of all holes at Site M0065 commenced at 2 mbsf with open holing to this depth because of the risk of chemical warfare agents dumped following WWII being recovered. To further mitigate this risk, no surface gravity Rumohr cores were conducted. Coring at Site M0062 commenced at 0.5 mbsf with open holing of the upper 50 cm because of the risk of heavy metals and other contaminants (e.g., DDT pesticide, polycyclic aromatic hydrocarbons [PAHs], hexachlorocyclohexane [HCH], and polychlorinated biphenyls [PCBs]) from nearby abandoned paper mills and industry, as identified by the Swedish Geological Survey (pers. comm., 2012). Surface gravity Rumohr cores were conducted at this site, following a reassessment of the potential risk having cored the main holes. However, the Rumohr corer and the core liners were pressure washed prior to being brought onboard to remove any contamination. In addition, all participants involved in handling these cores wore additional personal protective equipment. These gravity cores were not subsampled onboard and were only split during the OSP once satisfactory precautions were in place. Downhole logging toolsDownhole logging services were contracted from Weatherford and managed by the European Petrophysics Consortium (EPC). Details and results of the expedition logging program are given in “Downhole logging” and in each site chapter. Through-pipe underwater video cameraA through-pipe camera survey was conducted at sites designated as being in potential dumping grounds for WWII munitions as part of the risk assessment mitigation procedures. The British Geological Survey (BGS) supplied an underwater color video camera system and a deployment frame that allowed it to be lowered down inside the API drill pipe. It is based on diver helmet–operated systems, with an umbilical cable relaying direct feed imagery to a monitor located inside the drillers dog house on the drill floor. The drill pipe was run to just above the seabed (~5 m). The through-pipe camera system was then lowered down inside the pipe. Because of currents remobilizing the surface sediments, it was often necessary to lower the drill pipe and camera further down while monitoring the live video feed until the seafloor was clearly visible. Because of the positioning of the three primary holes (A, B, and C) along a transect at 20 m intervals, it was decided to run the predrilling camera survey for all holes at once while moving slowly along the transect under DP before returning to commence coring operations at Hole A. Seabotix remotely operated vehicleDuring Expedition 347, the BGS supplied a Seabotix LBV 150 SE Little Benthic Vehicle (LBV) rated to 150 m water depth (Fig. F9). Two color cameras were mounted on the vehicle. The main camera was mounted with a switchable high-intensity LED light array on a tilt mechanism that allowed a 270° range of view. The second camera was a fixed-focus rear-facing unit. The LBV was powered by four 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 inspection of the drill string and seabed template, in particular at Site M0060 after the drill pipe became stuck and had to be backed off. The LBV allowed real-time analysis of the situation, along with documentation that the situation had been rectified satisfactorily. Shipboard scientific proceduresCuratorial procedures and sample depth calculationsExpedition numbers for IODP expeditions are sequential, starting with 301. Drilling sites are numbered consecutively. For ESO platforms, numbering starts with Site M0001, with “M” indicating an ESO-operated Mission Specific Platform (MSP). For Expedition 347, the first site was Site M0059. Multiple holes may be drilled at a single site. The first hole drilled is assigned the site number with the suffix “A,” the second hole, the site number and the suffix “B,” and so on. Where shallow gravity cores were taken with the third-party Rumohr coring system, these holes were identified with the suffixes “K,” “L,” and “M” to maintain numbering consistency for the main coring holes. For Expedition 347, the cored interval normally consisted of the entire drilled section, but in some cases intervals were drilled without coring (e.g., open holing the top of Holes M0062A–M0062C and other intervals between spot cores). Recovered core is split into sections with a maximum length of 1.5 m and numbered sequentially from the top, starting at 1 (Fig. F10). 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 may expand upon recovery (typically 10%–15%), so the recovered interval may not match the cored interval. In addition, a coring gap can occur between cores (i.e., some cored interval was lost during recovery or was never cut). Thus, a discrepancy may sometimes exist between the drilled 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 if there has been significant core expansion on recovery to deck. In all of the chapters in this volume, the depths are initially quoted without adjusting for any expansion. However, some chapters also present an adjusted depth, although the science party acknowledge that applying a linear compression factor might not be representative of any nonlinear expansion that might have occurred. Therefore, care should be taken when applying the corrected depths. Any sample removed from a core is measured in centimeters from the top of the section to the top and bottom of the sample removed. An identification number for a sample comprises 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 “347-M0060A-3H-2, 35–40 cm,” represents a sample removed from the interval 35–40 cm below the top of Section 2, Core 3H (“H” indicates core type; see below), from Hole M0060A during Expedition 347 (Fig. F10). All IODP core identifiers indicate core type. For Expedition 347, the following abbreviations are used:
Descriptions of these tools are presented in “Wireline coring.” The depth of a sample in meters below seafloor 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. With regard to numbering of samples taken during the OSP for postcruise research, Expedition 347 is the first expedition within the IODP program to utilize the International Geo Sample Number (IGSN; www.igsn.org) alphanumeric system of unique identifiers. Each sample is assigned a unique code, potentially enabling the IODP core repository and investigators to track all samples accurately, even when shared between different laboratories. IGSN is similar to digital object identifiers (DOIs) for articles and data. This method will also provide a central registry for investigators in the future to be able to build on previous work as new techniques and methodologies are developed. Drilling-induced core deformationCores may be disturbed and have extraneous material in them as a result of the coring process. In formations that are unconsolidated, such as loose sands and gravel beds, material from higher intervals may have fallen to the base of the hole or been washed down by drill fluid circulation. This material may then be sampled by the next core run. Therefore, on splitting and description of the cores, the top of each core run was examined for evidence of core disturbance or anomalous material, described as “fall-in.” In addition, it is also possible that on recovery of the piston core barrel, suction can draw in soupy material—this was described as “flow-in.” Common piston coring–induced deformation includes concave deformation of horizontally laminated sediments, with the laminations appearing to have been pulled downward at the liner edges. In gaseous sediments, recovery of a core to the surface may result in expansion of the core material as the gas comes out of solution. This can significantly disturb the cores, appearing either as small cracks or by driving core segments apart within the liner tube. Pressure within the liner can be reduced by drilling holes in the end caps and/or along the length of the liner. This provides the gas with a means of escape but can also result in some sediment being extruded through the holes with the gas, causing some core disturbance. IODP depth conventionsIODP utilizes a system of depth scales (measured in meters) that are method specific. The primary scales are as follows:
During Expedition 347, the cored interval was measured offshore by the drillers in meters below seafloor, equating to drilling depth below seafloor. The depth below seafloor for any core/sample was determined by taking the depth to tagging seafloor with the drill string as the zero core datum and adding on all further advances to the target depth/maximum penetration. Where appropriate, downhole logging data and core measurements were stratigraphically correlated to improve the depth correlation between the wireline log depth below seafloor, drilling depth below seafloor, and core depth below seafloor depth scales. This process is described in more detail in “Stratigraphic correlation.” For all sites except Sites M0060 and M0063, it was possible to formulate a composite splice (see details in “Stratigraphic correlation” in each site chapter). In these instances, postcruise sampling was taken from the splice unless otherwise indicated. For ease of communication of shipboard results, depths are reported in meters below seafloor (mbsf) unless otherwise stated. Core handling offshoreAs soon as a core was recovered onto deck, it was immediately curated. This involved marking and cutting the cores into sections with a 1.5 m maximum length. Time-sensitive headspace syringe samples were taken for CH4 analysis immediately following sectioning of the core. Each section was then sealed at the top and bottom by attaching color-coded plastic caps, which were securely taped. Blue caps identify the top of a core section, and white caps indicate the bottom. A yellow cap was placed on section ends to identify where a microbiology whole-round sample had been taken. Core section liners were permanently labeled with an engraving tool. The lengths of the core in each section and the core catcher sample were entered into the Offshore Drilling Information System (Offshore DIS). In some instances where methane-rich sediments continued to de-gas and expand following recovery, holes were drilled into the end caps and along the length of the core sections to allow venting and prevent the end caps from being forced off and core material lost. No core splitting took place during the offshore phase of Expedition 347. All core material was kept in a temperature-controlled refrigerated container offshore and transported back to the IODP Bremen Core Repository (BCR), Center for Marine Environmental Sciences (MARUM; Germany), at +4°C. On arrival at the BCR, all cores were stored in the main repository, again at +4°C. In suitable sediments, core catcher samples were taken for later dating using optically stimulated luminescence (OSL). These samples were collected immediately on the drill floor in black plastic layflat sleeving, with the sleeving being held over the end of the core barrel during transference of the sediment. The samples were then double bagged in a dark environment and sealed against any light penetration, thus minimizing the risk of light contamination. Paleoenvironment cores: offshore sampling and processingAfter curation, the cores proceeded through a sequence of processing steps. Geochemists sampled for interstitial water (IW). This was predominantly achieved through the use of Rhizon samplers and syringes. However, 5–10 cm whole rounds were taken for squeezing when the core material became unsuitable for using Rhizon samplers. The core catcher or subsample of core catcher material was given to the sedimentologists and biostratigraphers for initial description after being photographed by the core curator. Shipboard sedimentologists also took the opportunity to assess the main core sections through the clear plastic liner, in particular to identify lithologic boundaries and any evidence of varved sequences. The microbiologists documented the degree of core disturbance in core sections from the first paleoenvironment hole drilled to inform their later subsampling strategy at designated microbiology holes (Sites M0059, M0060, M0063, and M0065). Core sections were allowed to equilibrate to “container” temperature before they were run through the slow-track multisensor core logger (MSCL) at a resolution of either 1 or 2 cm spacing, depending on the lithology and scientific requirements. This enabled stratigraphic correlation between different holes at the same site using magnetic susceptibility measurements, ensuring maximum stratigraphic overlap between holes. The cores were then transferred to a 4°C temperature-controlled reefer. Microbiology cores: offshore sampling and processingFollowing the initial cutting of cores into sections on the drill floor, syringe samples were immediately taken from the bottom of Section 1 and the top of Section 2 when required for time-sensitive measurements such as headspace samples, PFC contamination, and DNA testing. The cores were then curated as previously described, with the exception of permanent engraving. Following initial curation, the core sections were then taken immediately to the Fast-track MSCL, where they were run through magnetic susceptibility loops at 2 cm resolution without allowing any time for temperature equilibration to minimize microbiological degradation prior to sampling, fixing, and storage. These data were then used to stratigraphically correlate the microbiology cores with the paleoenvironment cores, which facilitated real-time drilling decisions. The cores were then taken into a core reception container where they were subsampled for further microbiology and IW analyses, which consisted of taking a combination of syringe samples and whole rounds (see “Microbiology”). After subsampling, the remaining cores were returned to curation for final labeling and permanent engraving. The cores were then sampled for additional IW, using Rhizon syringes where necessary to acquire the required volume of pore water, and allowed to reach container temperature. Finally, core sections >15 cm in length were run through the slow-track MSCL to acquire the full suite of petrophysical information and then transferred to a 4°C temperature-controlled reefer. Samples taken offshore for IW were analyzed for salinity, pH, alkalinity, ammonium, sulfide, and methane while offshore to aid microbiological sampling at geochemical boundaries/transitions. See “Geochemistry” for further details. Offshore core flow is summarized in Figure F11. Core handling at the Onshore Science PartyThe OSP was held at the BCR from 22 January to 20 February 2014. Before splitting, all cores were measured for thermal conductivity and natural gamma radiation (NGR). See “Physical properties” for further details. After removal from refrigerated storage, cores were split lengthways into working and archive halves. Cores were split from top to bottom. Therefore, investigators should be aware that younger material could have been transported downward on the split face of each core. The core splitters have horizontal and vertical wire cutters, steel plates to keep soupy material in place during splitting, and a diamond saw for more indurated material at their disposal. However, most cores were able to be split using wire cutters. The archive half of the core was taken immediately for high-resolution digital line scanning (see SLABCORESCAN in “Supplementary material”). The core was then described by the sedimentologists, aided by thin sections and smear slides (see “Lithostratigraphy” for further details). Following description, the archive halves were wrapped and put back into the core repository reefer. The working half of the core was first taken for color reflectance measurements. See “Physical properties” for further detail. Following this, and on completion of core description, the working halves were sampled. The first samples taken were for IODP minimum measurements, encompassing biostratigraphic analyses, paleomagnetism analysis on discrete cubes, physical property measurements, and total organic carbon measurements. See “Physical properties,” “Paleomagnetism,” “Biostratigraphy,” and “Lithostratigraphy” for further details. Following these measurements, sampling for postcruise research was undertaken. The working halves were then wrapped and put back into the core repository reefer. Each sample taken was logged into the Expedition Drilling Information System (Expedition DIS). Samples taken from the cores offshore for IW were analyzed for cations (major and trace elements) and anions (chlorinity, bromide, sulfate, and phosphate) during the OSP. See “Geochemistry” for further details. Onshore core flow is summarized in Figure F12. Data handling, database structure, and AccessData management during the offshore and onshore phases of Expedition 347 had two stages. The first stage was the capture of metadata and data during the offshore and onshore parts of the expedition. Central to this was the Expedition DIS, which stored information about drilling, core curation, sampling, and primary measurements. The second stage was the longer term postexpedition archiving of Expedition 347 data sets, core material, and samples. This function was performed by the World Data Center for Marine Environmental Sciences (PANGAEA) and the BCR. The Expedition DIS is a flexible and scalable database system originally developed for the International Continental Drilling Program (ICDP) and adapted for ESO. The underlying data model for the Expedition DIS is compatible with those of the other IODP implementing organizations and ICDP. For the specific expedition platform configuration and workflow requirements of Expedition 347, the Expedition DIS data model, data import pumps, and user interfaces were adapted to form the Baltic Sea Expedition DIS. This also included some new functionality, such as setting up predefined series for quicker entry of microbiology samples and IW subsamples and tools for the handling of Fast-track MSCL data. The Expedition DIS was implemented in SQLServer-2008 R2 installed on a central server with Microsoft-based client PCs connecting to the system through a Microsoft Access 2010 user interface. It was the first time the new version of the DIS was used for an MSP expedition, though much of the user interfaces such as input forms remain similar to the previous version. The work on DIS development is carried out by Smartcube. Offshore, the Expedition DIS was used to capture metadata related to core and sample curation, store core catcher photographs and downhole logging data, and print section, sample, and subsample labels. In addition, the database also stored primary measurements data:
Expedition scientists and ESO staff also generated a variety of spreadsheet files, text documents, and graphics containing operations and scientific data, geological descriptions, and interpretations. Therefore, in addition to the structured metadata and data stored in the Expedition DIS, all data files were stored in a structured file system on a shared file server. Backups of the Expedition DIS and the file server were made continuously and also replicated on the backup server. The EPC was responsible for the capture and processing of MSCL and downhole logging data. During the offshore phase, the Corewall Correlator application was used to view and correlate MSCL data (particularly magnetic susceptibility data) from different holes and against downhole logging data. On completion of the offshore phase of the expedition, the Expedition DIS database and the file system were transferred to the BCR to continue data capture during the OSP. Onshore, additional data types were captured in the Expedition DIS: core close-up images, high-resolution line-scan images, color reflectance data, thin section data, NGR data, smear slide data, and full visual core descriptions of the split cores. All other data, including spreadsheets and preliminary results, were loaded onto a shared file server. The Expedition DIS was backed up daily, and the file server was backed up twice daily. During the onshore phase, line-scan images and MSCL, NGR, and downhole logging data were loaded into the Corewall Corelyzer and Correlator applications for visualization and core correlation purposes. After the expedition, the sampling and core curation data were exported from the Expedition DIS to Curation DIS, the long-term BCR core curation system. In the second stage, all Expedition 347 data were transferred to the PANGAEA information system. PANGAEA is a member of the International Council of Scientific Unions World Data Center system. It has a flexible data model that reflects the information processing steps in earth science fields and can handle any related analytical data (Diepenbroek et al., 1999, 2002). It is used for processing, long-term storage, and publication of georeferenced data related to earth sciences. PANGAEA’s data management functions include quality checking, data publication, and metadata dissemination that follows international standards. The data captured in the Baltic Sea Expedition DIS and the data stored in the shared file server were transferred to PANGAEA following initial validation procedures. The data transfer process was completed by the time of publication of the Expedition reports section of this volume. Until the end of the moratorium period, data access was restricted to the expedition scientists through unique usernames and passwords. However, following the moratorium, all data except the downhole wireline data will be published online (www.PANGAEA.de). PANGAEA will continue to acquire, archive, and publish new results derived from Expedition 347 samples and data sets. Downhole wireline data are archived at brg.ldeo.columbia.edu/logdb with a link from PANGAEA. IODP MSP data are downloadable from the MSP data portal (iodp.wdc-mare.org). Core, section, and sample curation using the Baltic Sea Expedition DISExpedition 347 followed IODP protocols and naming conventions (see “Curatorial procedures and sample depth calculations”). The Expedition DIS captured the curation metadata and printed the appropriate labels, also to IODP standards. The curation metadata comprise
Because of expanding sediments, recovery often exceeded 100%. No corrections were made within the Expedition DIS for this, with top and bottom depths of sections (in meters below seafloor) calculated on the basis of the core-top depth. However, the operations summary table (see T1 in the “Expedition 347 summary” chapter [Andrén et al., 2015]) shows adjusted recovery percentages for holes with >100% suggested recovery. |
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