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1 Coggon, R.M., Teagle, D.A.H., Sylvan, J.B., Reece, J., Estes, E.R., Williams, T.J., Christeson, G.L., Aizawa, M., Albers, E., Amadori, C., Belgrano, T.M., Borrelli, C., Bridges, J.D., Carter, E.J., D'Angelo, T., Dinarès-Turell, J., Doi, N., Estep, J.D., Evans, A., Gilhooly, W.P., III, Grant, L.J.C., Guérin, G.M., Harris, M., Hojnacki, V.M., Hong, G., Jin, X., Jonnalagadda, M., Kaplan, M.R., Kempton, P.D., Kuwano, D., Labonte, J.M., Lam, A.R., Latas, M., Lowery, C.M., Lu, W., McIntyre, A., Moal-Darrigade, P., Pekar, S.F., Robustelli Test, C., Routledge, C.M., Ryan, J.G., Santiago Ramos, D., Shchepetkina, A., Slagle, A.L., Takada, M., Tamborrino, L., Villa, A., Wang, Y., Wee, S.Y., Widlansky, S.J., Yang, K., Kurz, W., Prakasam, M., Tian, L., Yu, T., and Zhang, G., 2024. Expedition 390/393 methods. In Coggon, R.M., Teagle, D.A.H., Sylvan, J.B., Reece, J., Estes, E.R., Williams, T.J., Christeson, G.L., and the Expedition 390/393 Scientists, South Atlantic Transect. Proceedings of the International Ocean Discovery Program, 390/393: College Station, TX [International Ocean Discovery Program]. //doi.org/10.14379/iodp.proc.390393.102.2024

1. Introduction

This section provides an overview of operations, depth conventions, core handling, curatorial procedures, and analyses performed on the R/V JOIDES Resolution during the International Ocean Discovery Program [IODP] South Atlantic Transect [SAT] Expeditions 390C, 395E, 390, and 393. This information applies only to shipboard work described in the Expedition reports section of the SAT Proceedings of the International Ocean Discovery Program volume. Methods used by investigators for shore-based analyses of expedition samples and data will be described in separate individual postexpedition research publications.

1.1. Site locations

GPS coordinates [WGS84 datum] from preexpedition site surveys were used to position the vessel at SAT expedition sites. A Knudsen CHIRP 3260 subbottom profiler with SounderSuite software was used to monitor seafloor depth during the approach to each site and to confirm the seafloor depth once on site. Once the vessel was positioned at a site, the thrusters were lowered and the position maintained via dynamic positioning. Dynamic positioning control of the vessel used navigational input from the GPS weighted by the estimated positional accuracy [Figure F1]; no beacons were deployed. The final hole position was the mean position calculated from the GPS data collected over a significant portion of the time during which the hole was occupied.

Figure F1. IODP naming convention.

1.2. Drilling and logging operations

To successfully drill both soft and indurated sediments as well as crustal material of varying age and alteration, all four standard coring tools available on JOIDES Resolution were deployed during the SAT expeditions: the advanced piston corer [APC], half-length APC [HLAPC], extended core barrel [XCB], and rotary core barrel [RCB] systems. Operations took place in international waters in water depths of ~3000–5000 m.

The APC and HLAPC systems cut soft-sediment cores with minimal coring disturbance relative to other IODP coring systems. After the APC/HLAPC core barrel is lowered through the drill pipe and lands above the bit, the drill pipe is hydraulically pressurized until the two shear pins that hold the inner barrel attached to the outer barrel fail. The inner barrel then advances into the formation and cuts the core [Figure F2]. The driller can detect a successful cut, or "full stroke," by observing the pressure gauge on the rig floor because the excess pressure accumulated prior to the stroke drops rapidly.

Figure F2. APC system.

APC refusal is conventionally defined in one of two ways: [1] the piston fails to achieve a complete stroke [as determined from the pump pressure and recovery reading] because the formation is too hard, or [2] excessive force [>60,000 lb] is required to pull the core barrel out of the formation. For APC cores that do not achieve a full stroke, the next core can be taken after advancing to a depth determined by the recovery of the previous core [advance by recovery] or to the depth of a full APC core [typically 9.5 m]. When a full stroke is not achieved, one or more additional attempts are typically made, and each time the bit is advanced by the length of the core recovered [note that for these cores, this results in a nominal recovery of ~100%]. When a full or partial stroke is achieved but excessive force is not able to retrieve the barrel, the core barrel can be “drilled over,” meaning that after the inner core barrel is successfully shot into the formation, the drill bit is advanced to total depth to free the APC barrel.

The standard APC system uses a 9.5 m long core barrel, whereas the HLAPC system uses a 4.7 m long core barrel. In most instances, the HLAPC system is deployed after the standard APC system has repeated partial strokes and/or the core liners are damaged. During use of the HLAPC system, the same criteria are applied in terms of refusal as for the APC system. Use of the HLAPC system allowed for significantly greater APC sampling depths to be attained than would have otherwise been possible. For the SAT expeditions, the HLAPC system was only deployed as time allowed.

The XCB system is a rotary system with a small cutting shoe that extends below the large rotary APC/XCB bit [Figure F3]. The smaller bit can cut a semi-indurated core with less torque and fluid circulation than the main bit, potentially improving recovery. It is primarily used in sediment but can core short intervals of hard rock, such as sills, or for capturing the sediment/basement interface. The XCB system is used when the APC/HLAPC system has difficulty penetrating the formation and/or damages the core liner or core. The XCB system can also be used to either initiate holes where the seafloor is not suitable for APC coring or it can be interchanged with the APC/HLAPC system when dictated by changing formation conditions. The XCB system is used to advance the hole when HLAPC refusal occurs before the target depth is reached or when drilling conditions require it. The XCB cutting shoe typically extends ~30.5 cm ahead of the main bit in soft sediments, but a spring allows it to retract into the main bit when hard formations are encountered. Shorter XCB cutting shoes can also be used. The SAT expeditions relied on polycrystalline diamond compact [PDC] XCB cutting shoes, which improved recovery across the sediment/basement interface.

Figure F3. XCB system.

The bottom-hole assembly [BHA] used for APC and XCB coring is typically composed of an 11⁷⁄₁₆ inch [~29.05 cm] roller cone drill bit, a bit sub, a seal bore drill collar, a landing saver sub, a modified top sub, a modified head sub, 8¼ inch control length drill collars, a tapered drill collar, two stands of 5½ inch transition drill pipe, and a crossover sub to the drill pipe that extends to the surface [Figure F4].

Figure F4. Typical APC/XCB and RCB BHAs.

The RCB system is a rotary system designed to recover firm to hard sediments and basement rocks. The BHA, including the bit and outer core barrel, is rotated with the drill string while bearings allow the inner core barrel to remain stationary [Figure F5].

Figure F5. RCB system.

A typical RCB BHA includes a 9⅞ inch drill bit, a bit sub, an outer core barrel, a modified top sub, a modified head sub, a variable number of 8¼ inch control length drill collars, a tapered drill collar, two stands of 5½ inch drill pipe, and a crossover sub to the drill pipe that extends to the surface. Figure F4 depicts a typical BHA for each coring system.

Nonmagnetic core barrels were used for all APC, HLAPC, and RCB coring. APC cores were oriented with the Icefield MI-5 core orientation tool when coring conditions allowed. Formation temperature measurements were taken with the advanced piston corer temperature [APCT-3] tool [see ]. Information on recovered cores, drilled intervals, downhole tool deployments, and related information are provided in the Operations, Paleomagnetism, and Downhole measurements sections of each site chapter.

1.3. IODP depth conventions

The primary depth scales used are defined by the length of the drill string deployed [e.g., drilling depth below rig floor [DRF] and drilling depth below seafloor [DSF]], the depth of core recovered [e.g., core depth below seafloor [CSF] and core composite depth below seafloor [CCSF]], and the length of logging wireline deployed [e.g., wireline log depth below rig floor [WRF] and wireline log depth below seafloor [WSF]] [see IODP Depth Scales Terminology for sediments at //www.iodp.org/policies-and-guidelines/142-iodp-depth-scales-terminology-april-2011/file]. In cases where multiple logging passes are made, wireline log depths are mapped to one reference pass, creating the wireline log matched depth below seafloor [WMSF] scale. All units are expressed in meters. The relationship between scales is defined either by protocol, such as the rules for computation of CSF depth from DSF depth, or by user-defined correlations, such as core-to-log correlation. The distinction in nomenclature should keep the reader aware that a nominal depth value in different depth scales usually does not refer to the exact same stratigraphic interval.

Depths of cored intervals are measured from the drill floor based on the length of drill pipe deployed beneath the rig floor [DRF scale]. The depth of the cored interval is referenced to the seafloor [DSF scale; Figure F1] by subtracting the seafloor depth of the hole [i.e., water depth] from the DRF depth of the interval. Standard depths of cores in meters below seafloor [core depth below seafloor, Method A [CSF-A], scale] are determined based on the assumption that [1] the top depth of a recovered core corresponds to the top depth of its cored interval [on the DSF scale] and [2] the recovered material is a continuous section even if sediment core segments are separated by voids when recovered. Standard depths of samples and associated measurements [CSF-A scale] are calculated by adding the offset of the sample or measurement from the top of its section and the lengths of all higher sections in the core to the top depth of the core.

1.3.1. Sediment core depth scales

If a core has 100% [the length of the recovered core exceeds that of the cored interval], the CSF depth of a sample or measurement taken from the bottom of a core will be deeper than that of a sample or measurement taken from the top of the subsequent core [i.e., the data associated with the two core intervals overlap on the CSF-A scale]. This overlap can happen when a soft to semisoft sediment core recovered from a few hundred meters below the seafloor expands upon recovery [typically by a few percent to as much as 15%]. In this case, the core depth below seafloor, Method B [CSF-B], scale can be employed, where the core is [digitally] linearly compressed to fit within the cored interval. Where core recovery is 90%].

Figure F9. Bioturbation intensity.

2.1.4. Biogenic sedimentary structures

During Expedition 393, a new Bioturbation tab was added to the DESClogik template to describe in detail intervals with biogenic mottling and distinct biogenic sedimentary structures. In addition to characterizing bioturbation intensity [as described in above], Expedition 393 shipboard scientists specified the four most common trace fossils observed [as the 1st, 2nd, 3rd, and 4th dominant ichnofossils], defined ichnofossil diversity as the total number of identified ichnofossils, measured the maximum trace fossil diameter, and added comments in an Ichnofossil comment column for extra observations and details. The most common trace fossils, namely Zoophycos, Chondrites, Planolites, Palaeophycus, Thalassinoides, Skolithos, Nereites/Cosmorhaphe, Phycosiphon, and rarely Arenicolites, Cylindrichnus, and Spirophyton, were defined based on various atlases, books, and scientific papers devoted to ichnological analysis of cores from modern marine sediments [Bromley and Ekdale, 1984; Buatois and Mángano, 2011; Dorador et al., 2020; Ekdale and Bromley, 1984, 1991; Pemberton et al., 2009; Rodríguez-Tovar and Dorador, 2015; Wetzel et al., 2010].

2.1.5. Lithology sedimentary structures

The locations and types of sedimentary structures that are not a result of drilling disturbance observed on the surfaces of the section halves were selected in the Sedimentary structure column in DESClogik and assigned to, for example [commonly used], cross-lamination/stratification, interlamination/stratification, trends in grain size [coarsening or fining upward], ripple, lens or pods, or "trails, tracks, and burrows" for trace fossils. Additionally, the terms "mottling" or "indistinct mottling" were used where identification of individual ichnotaxa was not possible but the media had a bioturbated and mottled appearance. The abundance of the sedimentary structures is quantitatively expressed by the frequency parameters in Table T1. When mottling was present, both a sedimentary structure abundance [Table T1] and a bioturbation index were assigned in DESClogik, assuming mottling was due to bioturbation, unless otherwise noted [e.g., "sediment mottling"].

2.1.6. Lithologic contacts and consolidation state

We described bottom contact geometry for every distinct lithologic interval recorded and entered in DESClogik using these terms: bioturbated, gradational, erosive, planar, irregular, and sharp. Also, the attitude of the lithologic bottom contacts was described as curved, horizontal, subhorizontal, inclined, or steeply dipping [>45°]. For comparison, the lithologic contact that marks the top/bottom limit of a unit/subunit is defined as a "boundary." We reported the degree of lithification of the sediments as unconsolidated, moderately consolidated, or lithified.

2.1.7. Drilling disturbance

We recorded drilling-related sediment disturbances for each core [see Disturbance column; Figures F8, F10]. The type of drilling disturbance for soft [unconsolidated] and firm [moderately consolidated] sediment were described using these terms:

• Fall-in: out of place material at the top of a core that fell downhole onto the cored surface.
• Bowed: bedding contacts slightly–moderately deformed but still subhorizontal and continuous.
• Uparching: material retains coherency; material closest to the core liner bent downward.
• Void: empty space in the cored material [e.g., caused by gas or sediment expansion during core retrieval]. To the extent possible, voids were closed on the core receiving platform by pushing the recovered intervals toward the top of the core before cutting the sections. The space left at the bottom of the core below all the recovered material due to incomplete recovery was not described as a void.
• Flow-in, coring/drilling slurry, or along-core gravel/sand contamination: soft-sediment stretching and/or compressional shearing structures when severe.
• Soupy or mousse-like: water-saturated intervals that have lost all aspects of original bedding.
• Biscuit: sediment of intermediate stiffness with vertical variations in the degree of disturbance, whereas firmer intervals are relatively undisturbed.
• Cracked or fractured: firm sediment broken during drilling; not displaced or rotated significantly.
• Fragmented or pulverized: firm sediment pervasively broken by drilling; may be displaced or rotated.
• Drilling breccia: core is crushed and broken into many small and angular pieces; original orientation and stratigraphic position are affected.

Figure F10. Symbols used for sediment VCDs.

Each instance of drilling disturbance was assigned a degree of severity:

• Slight: core material is in place but broken or otherwise disturbed.
• Moderate: core material is in place or partly displaced, but original orientation is preserved or recognizable.
• Severe: core material is probably in the correct stratigraphic sequence, but original orientation is lost.
• Destroyed: core material is in the incorrect stratigraphic sequence, and original orientation is lost. In the case of voids, core material is absent.

2.2. Microscopic descriptions

2.2.1. Smear slide descriptions

We estimated sediment constituent size, composition, and abundance microscopically using smear slides. Smear slide samples of the main lithologies were collected from the archive-half sections. Additional samples were collected from areas of interest, such as distinct intervals [e.g., organic-rich layers or diatom or foraminiferal oozes].

For each smear slide, a small amount of sediment was removed from the section half using a flat wooden toothpick and put on a 25 mm × 75 mm glass slide. A drop of deionized water was added to the sediment, and the sediment was homogenized with the toothpick and evenly spread across the glass slide. The dispersed sample was dried on a hot plate at a low setting [110°–120°C]. A drop of adhesive [Norland optical adhesive Number 61] was added as a mounting medium for a glass coverslip, which was carefully placed on the dried sample to prevent air bubbles from being trapped in the adhesive. The smear slide was then fixed in a UV light box for 5–10 min to cure the adhesive.

Smear slides were examined with a transmitted-light petrographic microscope [Carl Zeiss AXIO with a HAL 100 halogen lamp] equipped with a standard eyepiece micrometer and a SPOT Insight FireWire digital camera. Biogenic and mineral components were identified following standard petrographic techniques as described in the Rothwell [1989], Marsaglia et al. [2013, 2015], Scholle and Ulmer-Scholle [2003], and Ulmer-Scholle et al. [2015] reference manuals and books. Several fields of view were examined at 10×, 20×, and 40× to assess the abundance of detrital [e.g., quartz, feldspar, clay minerals, mica, and heavy minerals], biogenic [e.g., nannofossils, other calcareous bioclasts, diatoms, foraminifera, and radiolarians], and authigenic [e.g., carbonate, iron sulfide, iron oxides, and glauconite] components. The average grain size of clay [63 µm] was estimated for siliciclastic, carbonate, biogenic, and volcaniclastic material. The relative percent abundances of the sedimentary constituents were visually estimated using the techniques of Rothwell [1989]. The texture of siliciclastic lithologies [i.e., relative abundance of sand-, silt-, and clay-sized grains] and the proportions and presence of biogenic and mineral components were recorded in the smear slide worksheet of the microscopic DESClogik template. Components observed in smear slides were categorized according to their abundance as shown in Table T1.

2.3. Sediment and sedimentary rock classification

Sediment and sedimentary rock types were entered in the lithology columns of the macroscopic DESClogik worksheet. Corresponding patterns and colors were defined on the graphic core summaries and hole summaries during the core descriptions accomplished during Expeditions 390 and 393.

2.3.1. Sedimentary lithologic classes

Following prior IODP expeditions [e.g., Röhl et al., 2022; Sutherland et al., 2019] and the Handbook for Sedimentologists [Mazzullo and Graham, 1988], three main sedimentary lithologic classes [Figure F11] were defined based on the primary origin of the sediment constituents [but not the depositional processes]:

• Biogenic: >50% carbonate, chemical, undifferentiated calcareous bioclasts, and calcareous microfauna and microflora.
• Siliciclastic: >50% siliciclastic particles, 75% of volcanic clasts and grains, whereas tuffaceous sediments contain 75%–25% volcanic clasts and grains mixed with nonvolcanic particles [either nonvolcanic siliciclastic, biogenic, or both]. The definition of the term "tuffaceous" [25%–75% volcanic particles] was modified from Fisher and Schmincke [1984]. Note that the term "volcaniclastic" was used following Fisher [1961] and therefore includes both volcanic and tuffaceous lithologies.

Figure F11. Sedimentary lithology naming conventions.

These three lithologic classes formed the basis of the principal name of the described sediments and sedimentary rocks, with appropriate prefixes and suffixes that could be chosen for mixed lithologies [see below].

2.3.2. Principal names and modifiers

The principal name was based on the most abundant sediment class [Figure F11]. Principal names for the siliciclastic class were adapted from the grain size classes of Wentworth [1922], whereas principal names for the volcaniclastic class were adapted from the grain size classes of Fisher and Schmincke [1984]. Thus, the Wentworth [1922] and Fisher and Schmincke [1984] classifications were used to refer to particle type [siliciclastic versus volcanic, respectively] and the maximum size of the particles. For the biogenic sediment class, commonly used terms were applied [e.g., ooze and chalk] and did not have a separate size or texture notation because those aspects are inherent in the fossil groups that make up the sediment. For example, nannofossil and foraminiferal ooze imply a dominant grain size corresponding to clay and sand, respectively. For each principal name, both a lithified and a nonconsolidated term exist that are mutually exclusive [e.g., clay or claystone; ash or tuff].

For all lithologies, the principal lithologic name was modified by prefixes and/or suffixes representing secondary components as follows:

• Prefixes describe a secondary component with abundance of 25%–50% [corresponding to "abundant" in smear slide descriptions] [Table T1].
• Suffixes are secondary or tertiary components with abundances of 10%–25% [corresponding to "common" in smear slide descriptions] and are indicated by the suffix "with" [e.g., with clay or with radiolarians] in order of decreasing abundance.

For example, an unconsolidated sediment containing 45% nannofossils, 30% clay, 15% foraminifera, and 10% radiolarians is described as clayey nannofossil ooze with foraminifera and radiolarians.

The degree of lithification was expressed in the principal name using terms common in geology:

• Siliciclastic class:
  • If the sediment could be deformed with a gloved finger, no lithification term was applied [e.g., clay].
  • If the sediment could not be deformed with a gloved finger or scratched with a fingernail, the suffix "-stone" was added to the grain size identifier [e.g., claystone].
• Biogenic class:
  • If the sediment could be deformed easily with a gloved finger, the unconsolidated term "ooze" was used in conjunction with the most abundant component [e.g., nannofossil ooze or radiolarian ooze].
  • If the source of the calcareous sediment was unclear [fragments of carbonate bioclasts 10% [by volume] phenocrysts and the dominant phenocryst is olivine with lesser amounts of plagioclase. The minerals named include all of the phenocryst phases in the rock, as long as the total content is >1%.

    The term "glass" was reserved for a homogeneous, isotropic material free of quench crystals, with 2 mm].

  Vesicles were described by their abundance, size, and shape/roundness [low, moderate, high, and highly elongate]. Vesicles were noted as filled or unfilled, but the nature of filling minerals was detailed during alteration logging [see ]. The following abundance categories were used:

  • Nonvesicular [5%–20%], and
  • Highly vesicular [>20%].

  Groundmass grain size designations during Expedition 393 were typically defined by the modal grain size of groundmass plagioclase or, more rarely, olivine microlites as assessed by binocular microscope. Consequently, a basalt with abundant microcrystalline groundmass plagioclase laths but cryptocrystalline interstitial clinopyroxene was classified as microcrystalline. Where described intervals encompass one or more lava flows, the logged groundmass grain size for that interval refers to that of the flow interior, not the cryptocrystalline to glassy chilled margins, the presence of which was noted in the groundmass comments and glass columns. Primary crystals present in flow interiors but not in the glassy margins were assumed to have crystallized in situ and were considered as part of the groundmass, not as phenocrysts. However, the distinction between phenocryst and groundmass phases becomes somewhat blurred in more coarsely crystallized or seriate textures typical of massive flows greater than ~3 m thick.

  3.5. Rock structure

  Igneous structure was determined by whether the rock is massive, sheeted, pillowed, hyaloclastic, brecciated, scoriaceous, or tuffaceous. These terms provide a picture of the style of magmatism and the environmental setting in which they occur by identifying features that are diagnostic of specific physical processes.

  • Massive basalts: distinguished by long [50–60 cm] continuous core pieces that are relatively unaffected by drilling, and by their uniform texture.
  • Pillow basalts: characterized by chilled pillow margins that are mostly curved or inclined, radial fracture patterns, and V-shaped piece outlines. They are also typically cryptocrystalline to microcrystalline and associated with the presence of hyaloclastic breccias.
  • Sheet flows: characterized by parallel, closely spaced [1 cm] crosscutting feature formed by injection of magma; dikes typically have 1–2 chilled margins. In the absence of distinguishing features, samples were labeled as lava flows.
  • Basaltic rubble: distinguished by pieces with semirounded shapes having multiple weathered surfaces that were not cut by the drill. Usually rubble can be recognized as originating from pillow basalts, based on the criteria above.
  • Chilled margins: typically composed of an outer 1–10 mm glassy rind that grades through a discrete spherulitic zone into a coalesced spherulitic zone followed by variolitic textures. The variolitic zones are usually identifiable in hand specimen because the mesostasis is altered to a light brown color, highlighting the variolitic texture. Many of the glassy rims have attached veneers or crosscutting veins of interpillow sediment that is carbonate or clay rich. Sediments may be present as fracture fill or as a cement for basaltic breccias.

  In contrast to Expedition 390 but similar to previous Expedition 309/312 [Expedition 309/312 Scientists, 2006], sheet flows during Expedition 393 were recognized and defined as single lava flows 3 m thick, with gradational grain size changes and fine- to medium-grained flow interiors used to establish continuity across pieces and sections [following Expedition 309/312 Scientists [2006]]. Note that this contrasts with the 0.5 m threshold used during Expedition 390.

  3.6. Breccias

  Breccias were entered into the main igneous log but described in further detail collaboratively between the igneous and alteration petrology teams using a separate breccias sheet. They were divided principally into the following:

  • Magmatic breccias: containing glass or quench textures such as pillow breccia, primary matrix minerals [or sediments];
  • Hyaloclastites: as above with >30% glass;
  • Hydrothermal breccias: with secondary matrix or vein minerals;
  • Tectonic breccias: such as cataclasites and fault gouges in which the matrix consists of the same material as the host rock; and
  • Sedimentary breccias: characterized by matrix filling composed entirely of sedimentary materials such as clays and carbonate.

  Breccia characteristics such as clast lithology, volume, size, sorting, alteration, and shape, as well as matrix and cement composition were recorded.

  We defined matrix as anything granular consisting of fragments of rocks or minerals and cements as anything crystalline that precipitated in situ to fill void space. Thus, a magmatic breccia might have no cement, and a hydrothermal breccia might have no matrix. The method adopted was as follows:

  1. Assign breccia type [see Breccia type, below] and define whether clast or matrix supported.
  2. Estimate clast volume proportion [percentage], clast size range [minimum/maximum, in millimeters], and sorting [see Breccia sorting].
  3. Record clast lithology [see Clast/matrix composition], alteration [see Clast/matrix alteration], shape [see Clast/matrix shape], grain size [see Clast/matrix internal grain size], and internal structure [see Clast internal structure].
  4. Estimate matrix volume proportion [percentage], identify matrix composition [same values as Clast/matrix composition] and alteration [same values as Clast/matrix alteration], and record any internal structure [same values as Clast/matrix internal grain size].
  5. Identify cement mineral composition, and estimate volume proportion [percentage].
  6. Record any further details as a comment.

  Definitions for breccia descriptions noted above include the following:

  • Breccia type: magmatic breccia, hyaloclastite, hydrothermal breccia, tectonic breccia, and sedimentary breccia.
  • Breccia sorting: poorly, moderately, moderately well, well, very well, and bimodal.
  • Clast/matrix composition: glass, basalt, dolerite, gabbro, peridotite, serpentinite, chert, mudstone, siltstone, limestone, sandstone, sediment—siliceous, sediment—calcareous, and sediment—undifferentiated.
  • Clast/matrix alteration:
    • Fresh/unaltered = 10%–50% alteration.
    • High = >50%–95% alteration.
    • Complete = >95%–100% alteration.
  • Clast shape: angular, subangular, subrounded, rounded
  • Clast/matrix internal grain size: cryptocrystalline, microcrystalline, fine grained, medium grained, coarse grained, glassy.
  • Clast internal structure: none, veined, glassy, crystalline, vesicular, aphyric, sparsely phyric, moderately phyric, highly phyric.

  To allow quantitative recalculation of different breccia components, during Expedition 393 the areal proportion of breccia on the cut surface of the archive half of the logged breccia interval was recorded as a percentage under Breccia comments. The percentage of different clast or matrix types were similarly recorded as areal percentages of the cut core surface under Clast comments and Matrix comments.

  3.7. Intermingled and interlayered sediment

  Intermingled or interlaying of thin [meta]sediment with igneous rock was included in the igneous rock description upon encountering magma/sediment contacts or mixing [e.g., from fragmentation of igneous material or injection of sediment into igneous rock]. Thicker and more coherent intervals of sediment were described as part of the sedimentary section.

  During Expedition 393, discrete sediment layers were generally described under their own interval, and in several cases even relatively thin [~5–10 cm] layers were split in lithologic [sub]units in order to promote assessment of changing lava compositions over these possible volcanic hiatuses. The catch-all nongenetic term "indurated calcareous sediment" was used to identify indurated intervolcanic materials, which could include materials derived from sedimentary and/or volcanic sources [e.g., volcanic glasses], some exhibiting recrystallization and/or hydrothermal alteration.

  3.8. Igneous contacts

  Glassy margins, chilled margins, and contact boundaries were inserted individually for the top and bottom of each interval where they could be determined. Contacts may be sharp or gradational.

  The following contact types were defined:

  • Baked contact: boundary to sediments overprinted [baked] by proximity of magma.
  • Bottom or top chilled contact: chilled contact with sediments, with or without glass adjacent to sediments.
  • Bottom or top chilled margin: chilled contact without sediments, without glass, defined by cryptocrystalline groundmass, and typically found quenched next to the chilled contact.
  • Chilled contact: a magma or lava that has clearly chilled against another rock or sediment.
  • Chilled margin: a rapidly chilled margin, for example with a cryptocrystalline, or incomplete variolitic to glassy selvage.
  • Glassy margin: a rapidly chilled margin with preserved glass.
  • Grain size: units on either side have markedly different grain sizes.
  • Modal boundary or contact: units on either side have markedly different mineral proportions.
  • Brecciated flow top: consists of angular, scoriaceous to vesicular fragments of basaltic rubble.
  • Contact not recovered.

  During Expedition 393, contacts were differentiated as "within-unit" and "upper unit" contacts using the same value lists as Expedition 390 to facilitate easy location and extraction of unit contact information.

  3.9. Unit alteration

  A qualitative assessment of alteration was included along with the description of the igneous petrology to record the overall extent of alteration in that igneous unit/subunit. Separate detailed alteration and vein logs were made, and the associated methods are described in . Qualitative alteration categories were as follows:

  • Fresh/unaltered = 10%–50% alteration.
  • High = >50%–95% alteration.
  • Complete = >95%–100% alteration.

  3.10. Thin section descriptions

  Thin section investigation was used to complement and refine macroscopic core observations for igneous rocks. All thin section observations were entered into the LIMS database through a DESClogik thin section template. Thin section descriptions include both primary [igneous] rock-forming minerals [including phenocrysts, groundmass, etc.] and secondary [alteration] mineral phases [in veins, vesicles, groundmass, etc.]. Their mineralogy, abundance [modal volume percentages], sizes, shapes, habits, textural relationships, inclusions, alteration [color, intensity, and style], veins [type and number], and vesicles [type and fillings] were determined, enabling verification of macroscopic observations. When time permitted, the estimated volume percentages of the original primary mineral phases, groundmass, and vesicles were also included when entering mineral abundances in DESClogik.

  Thin section descriptions include the following information:

  • Sample domain: because thin sections are often taken from intervals that contain more than one lithologic feature, it is necessary in the thin section description log to identify which feature [i.e., domain] is being described. In this case, where there is more than one domain represented in the slide, each domain is described separately. For example, a slide that shows a large secondary vein [25% of the slide] in a basaltic matrix [75% of the slide] is given two descriptions: one being the "vein" and the other the "host rock." Other possible domains include clast, glass, halo, and xenolith.
  • Lithology prefix modifier and lithology prefix for the described sample domain, following the nomenclature for rock classification described in .
  • Principal lithology: refers only to the lithology of the described sample domain and follows the nomenclature for rock classification [see ].
  • Overall rock texture/crystallinity of the domain described [i.e., holohyaline, holocrystalline, hypohyaline, hypocrystalline].
  • Interpretation of the rock structure/mode of emplacement: pillow lava, sheet flow, massive flow, dike, pyroclastic rock, rubble.
  • Average groundmass grain size modal name following Neuendorf et al. [2005]. Note that because of time constraints, groundmass grain sizes were not determined for most thin section descriptions during Expedition 390:
    • Glassy,
    • Cryptocrystalline [2 mm].
  • Maximum and minimum groundmass grain size modal name. Because of time constraints, grain sizes were not determined for most thin section descriptions during Expedition 390.
  • Groundmass texture: intergranular, intersertal, granular, felty, ophitic, subophitic, trachytic, microlitic, graphic, vitrophyric, eutaxitic, skeletal, spherulitic, variolitic, dendritic, fibrous.
  • Mineral phenocryst shape: the dominant [>50% of crystals] shape of the olivine, plagioclase, clinopyroxene, orthopyroxene, and spinel crystals in euhedral, subhedral, and anhedral.
  • Mineral phenocryst habit: the dominant [>50% of crystals] habit of olivine, plagioclase, clinopyroxene, orthopyroxene, and spinel crystals divided into elongate, equant, subequant, tabular, acicular, dendritic, skeletal, variolitic, spherulitic, sheaf, plumose, and glomeroporphyritic.
  • Plagioclase phenocryst zoning type: continuous, discontinuous, oscillatory, patchy, unzoned.
  • Clinopyroxene and orthopyroxene phenocryst exsolution: blebs, lamellae.
  • Vesicle size, shape, and abundance.
  • Proportion of groundmass phases.
  • Additional features such as dissolution/resorption textures, sieve textures, and inclusions are noted in the comments sections.

  Modal data were visually estimated by reference to standard charts. Crystal sizes were measured using a micrometer scale; generally, these measurements are more precise than hand-specimen estimates.

  3.10.1. Expedition 393 modifications

  Two minor modifications were made for the Expedition 393 thin section igneous petrography descriptions, captured on the 393_microscopic template in DESClogik:

  • Where necessary, thin sections were divided into domains based on both primary igneous and secondary alteration criteria. These domain types may coincide spatially but not necessarily. For example, a single igneous domain may be covered by multiple alteration domains, and vice versa. Igneous domains were selected from chilled margin, glassy margin, flow interior, breccia clast, and breccia matrix, and any additional information was provided as a comment.
  • All thin sections were screened in reflected light for primary and secondary oxide and sulfide minerals, with particular emphasis on locating any primary sulfide blebs in glasses.

  To visually calibrate micro- and macroscopic modal abundance estimates of phenocrysts and vesicles across the hard rock core description team, a digital areal abundance exercise was undertaken following approaches used during Integrated Ocean Drilling Program Expeditions 309/312 and 327 [Expedition 309/312 Scientists, 2006; Expedition 327 Scientists, 2011]. A set of Expedition 390 thin sections were selected to cover different abundance ranges. Full page images of the thin sections were printed, and the phenocrysts and vesicles were traced onto an overlay using different colors. This overlay was scanned, and using the threshold function in Adobe Photoshop, each phase was separated. The area represented by each phase was then determined by using the histogram function, where the number of pixels of each color was divided by the total number of pixels in the image to calculate a percent abundance of each phase.

  3.11. Expanded depths and unit thicknesses [Expedition 393]

  3.11.1. Expanded depths

  The incomplete recovery of basement cores remains a reality of scientific ocean drilling, and recoveries for individual basement cores ranged from 0% to >90% along the SAT. Immediately after recovery, the pieces from each core were curated into bins, each separated by 1–2 cm, starting from the top of the core. For cores with near 100% recovery, this spacing may lead to curated lengths in excess of the drill-advanced length over which that core was cut. In the far more common case of 95%–100% alteration.

4.1.2. Vein and mineral fill log

Detailed logs of vein, vesicles, and breccias were produced, allowing the precise interval of their occurrence to be recorded independent of the larger scale alteration log and enabling accurate quantification and plotting of different mineral occurrences downhole.

The vein and mineral fill log records the presence, location, width, crosscutting relationships, shape, and composition percent along with color, and width of associated halos of each vein. The fill texture, connectivity, and morphology of veins was described. Structural measurements on veins were not undertaken during Expedition 390.

A detailed log was made of the relative proportions and abundance of minerals filling void spaces. This principally recorded veins but also included vein networks, vesicles, breccia cements, and secondary minerals [of indeterminate geometry] in rubble bins. This allowed easy quantification and plotting of the abundance of filling minerals downhole. Using the width and geometry of these veins, the area and subsequently volume of each vein was calculated and used to determine the volume percent of the core filled by secondary minerals in veins [e.g., see Figure in the Site U1559 chapter [Coggon et al., 2024b]] normalized for core recovery.

Filling minerals [and their relative proportions] were assessed based on color, texture, and habit and confirmed by analysis of thin sections and/or XRD where necessary.

Halos surrounding veins or vesicles were described by their half-width and color. Secondary mineral assemblages were noted where distinguishable in macroscopic core.

Features were not logged across pieces to simplify normalizing the abundance of secondary minerals to recovery using the piece log. Continuous occurrences of breccia were logged piece by piece. In rare cases, a long vein crossing two pieces may have been logged as two veins. Where pieces logged for breccia cement [or in the piece log] had tapered or irregular ends, the top and bottom interval of the piece were chosen to approximate a square end piece of full width core [e.g., for a planar tapered end this would be halfway up the tapered interval].

For each secondary mineral-filled feature logged, the proportion of the area filled [as opposed to open void] was also recorded. This allowed the quantification of the open voids/macroporosity as a proportion of the total rock downhole.

Each feature was described as following:

• Filling type: vein, vein net, vesicles, cemented breccia, sediment, rubble.
• Vein section interval [in centimeters]: measured upper and lower intersections with the margin of the split face of the archive half of the core or the greatest upper and lower extent of a vein [Figure F16] and mean perpendicular width. This allows the area percent of specific veins and their mineral fills to be calculated.
• Other fill type interval: measured upper and lower interval and estimate the total proportion of secondary minerals in the interval resulting in data comparable to veins.
• Vein generation: if distinguishable, via crosscutting or other relationships.
• Qualitative vein dip:
  • Vertical: vein extends across 50% of core width.
• Vein texture [schematic illustrations of vein textures, connectivity, and morphologies described are provided in Figure F17]: massive, cross-fiber [antitaxial], oblique-fiber, vuggy, polycrystalline, crack-seal [syntaxial], crack-seal [stretching], sheared, patchy, overgrowth, cemented breccia [hydrothermal, tectonic].
• Vein connectivity: Isolated, single, branched, network, en echelon, crosscutting, ribbon, parallel, anastomosing, overlapping.
• Vein morphology: planar, curved, irregular, vein tip, tension gash, cemented fault breccia.
• Fill color and Munsell color code [Expedition 390 only].
• Estimated relative abundance of each secondary mineral: including clay, carbonate, zeolite, Fe oxyhydroxides, other clay, green clay, sulfides, amorphous silica, quartz, and chlorite; for Expedition 393: unknown 1, unknown 2, and unknown 3 were used primarily for variations in sediment fill].
• XRD results, if any, for comparison.
• Orientation of major veins [Expedition 393 only; see below for core reference frame [CRF]].
• Associated halo half-width: if halo is zoned, use width 1 [and color 1, etc.] for the inner zone and width 2 for the outer zone.
• Assign color and Munsell color code to halo/zones.
• Pyrite fronts associated with the halo.
• Further details as comments.

Figure F16. Intervals and width measured for veins.

Figure F17. Vein fill textures, morphologies, and connectivities.

4.1.3. Breccia log

Breccias were recorded separately to allow, among other things, detailed characterization of each clast type, matrix, and cement. This was carried out collaboratively between the igneous and alteration petrologists, and the method is described in . Where breccias were encountered, they were first logged in detail and then a piece-by-piece estimate of secondary mineral abundances in the breccia cement was made in the vein_halos_fill log. This enables downhole quantification of secondary minerals in a consistent way for veins, vesicles, and breccias, whereas the breccia log allows other relevant details to be recorded.

4.1.4. Piece log

The length and, if less than 5.7 cm, width of each recovered piece of hard rock core was logged to calculate the cut surface area of the core to normalize the results of vein and alteration logging to recovery within each section and thereby accurately quantify the volume proportion of altered rock and secondary minerals within the core [see Figure F18].

Figure F18. Hard rock sample bins and piece length measurement.

The curated length is usually slightly longer than the true piece length because there must be some room left to allow the removal and inspection of core pieces. These gaps may be up to a few centimeters, which may be significant for shorter pieces of core and when core recovery is low.

To produce the piece log, curated details of the core, including upper and lower curated bin depths in the core, were exported. Within each bin, the core piece[s] were pushed to the top of the bin and their lower interval in the core was measured. The piece length was calculated from the difference between the top bin interval and the bottom piece interval measured. The piece logs are available in ALTPET in .

4.2. Thin sections

To complement and refine macroscopic descriptions of the alteration and structural features of the core, thin sections of igneous rocks were studied in transmitted and reflected polarizing light microscopy. Thin section samples were selected typically once per igneous unit, often coincident with a bulk geochemistry sample, and generally positioned to include multiple features of interest.

Alteration was characterized in thin section by division of the sample into one or more alteration domains [e.g., background, vein, or halo; see Figure F19] and listing the secondary minerals identified in each, together with their estimated abundance and what features of the rock they replaced or filled. During Expedition 390 when only one alteration petrologist was able to sail, only a free-text summary description was produced and included in the thin section reports in the visual core descriptions.

Figure F19. Approach taken to defining alteration domains.

Thin section descriptions are included in and are also available from the LIMS database. Digital photomicrographs were taken during the expedition to document features described in the thin sections; these can be obtained from the IODP data librarian.

4.3. Structures

This section outlines the techniques used for macroscopic and microscopic description of structural features observed in hard rock basement cores. Conventions for structural studies established during previous hard rock drilling expeditions [e.g., ODP Legs 118, 140, 147, 148, 153, 176, 206, and 209; Integrated Ocean Drilling Program Expeditions 304/305 and 335; IODP Expeditions 357 and 360; and the Oman Drilling Project] were generally followed during Expedition 393, but these descriptions were not undertaken during Expedition 390 because of a lack of personnel.

All material from both working and archive halves was examined. The most representative structural features in the cores recovered during Expeditions 390 and 393 are summarized on the VCD form [see ].

4.4. X-ray diffraction analysis

To refine identification of secondary alteration minerals, selected veins, vesicles, and breccia cement minerals were analyzed by XRD. Minerals were separated from the working half of the core using a stainless steel spatula or a dremel tool to abrade or chip off small [~10–50 mg] samples with minimal damage to the core. In addition, whole-rock geochemistry powders [see ] were also analyzed by XRD.

Samples for XRD analysis were freeze-dried for 12 h prior to being crushed and powdered using an agate mortar and pestle. Diffraction data were generated on the shipboard Bruker D4 Endeavor X-ray diffractometer, which is equipped with a Cu source and uses a generator voltage of 35 kV and current of 40 mA. Depending on the rate of core recovery and scientific objectives, the XRD operated under two different protocols. For routine analyses to aid core description and deliver essentially qualitative analyses, the operating conditions were set to step scans of 4°–75°2θ for 3750 steps at a rate of 1 s/step [the typical setting used on the ship during previous expeditions]. For high-precision XRD analyses capable of quantitative analysis via Rietveld-based full-pattern fitting techniques using small amounts of sample, acquisition occurred at step scans of 4°–120°2θ for 5800 steps at a rate of 2 s/step. Diffraction results were evaluated against powder diffraction files for a large database of natural and synthetic minerals using the HighScore software package. The results of this evaluation included matched mineral species [see XRD files in ALTPET in ].

4.5. Expedition 393 alteration petrology

During Expedition 393, the same observations were made and recorded using DESClogik as those made during Expedition 390 to allow for comparability along the SAT. The data were captured in the following DESClogik templates: 393_macroscopic and 393_microscopic. To ensure efficiency of core flow, the sequence in which observations were made was slightly modified and some additional observations made. These changes are set out below.

4.5.1. Alteration description

During Expedition 390, an alteration type designated as "mottled gray area%" was used to describe a characteristic alteration style associated with chilled margins. During Expedition 393, this was clarified in DESClogik to "Chilled margin mottled gray area%" and was counted toward the proportion of background alteration rather than as its own category of alteration. In addition to estimating the area percentage represented by different alteration types [as identified by dominant color and appearance], during Expedition 393 the intensity of alteration [expressed as percent alteration] was also estimated for each alteration type. These estimations were calibrated against thin section observations and are generally correlated with color intensity, where the more intense colors are associated with higher degrees of alteration. The inclusion of this estimation allows the total alteration percentage to be weighted by the proportion and intensity of the different alteration types. During Expedition 390, alteration intensity was estimated only for background alteration.

Modifications to the observation sequence were made in relation to the logging of veins-halos-fills. During Expedition 393, these observations were separated into veins-halos and vesicle-other fills with breccia cement fills moved to the Breccias tab. These are mechanical changes to aid the description core flow and do not reflect changes in what was observed and recorded.

4.5.2. Thin section description

The following additions and clarifications were added for the Expedition 393 thin section alteration petrography descriptions captured in the 393_microscopic template in DESClogik:

• Where necessary, thin sections were divided into domains based on both primary igneous and secondary alteration criteria. These two domain types may coincide spatially but not necessarily. For example, a single igneous domain may be covered by multiple alteration domains and vice versa. Alteration domains were selected from "background," "vein halo," and "other halo," and any additional information was provided as a description.
• Vesicle fill and veins were also described on separate tabs in the 393_microscopic template that are slightly modified from the macroscopic versions of these tabs. New to the microscopic template is the specific recording of the sequence of fills in the fill sequence column. This column has a standard format of reporting minerals from rim to center [e.g., a vein lined with brown clay and filled with carbonate would be listed as brown clay–carbonate].
• Breccia cements were described in the vesicle tab.

4.5.3. Structure description

The orientation of veins [width > 0.1 mm] were measured by the Expedition 393 hard rock core description team. These methods follow conventions for structural studies established during previous hard rock drilling projects [e.g., Legs 118, 140, 147, 148, 153, 176, 206, and 209; Expeditions 304/305, 335, 357, and 360; and the Oman Drilling Project].

Measurements of vein-related structural features were undertaken on the archive-half cores in accordance to the standard IODP core reference frame [CRF] [Figure F20]. The plane normal to the axis of the borehole is referred to as the horizontal plane. On this plane, a 360° net is used with a pseudosouth [180°] pointing into the archive half and a pseudonorth [0°] pointing out of the archive half and perpendicular to the cut surface of the core. The cut surface of the core, therefore, is a vertical plane striking 90°–270°. Apparent dip angles [0°–90°] and dip direction [0°–360°] of planar structures were measured on the split cores. True dip angles and dip directions were obtained from a second apparent dip angle and dip direction measurement and calculated using a macro in Microsoft Excel [Oman Drilling Project [Kelemen et al., 2020]].

Figure F20. Reference frame and measuring orientation of planar feature.

4.5.4. X-ray diffraction

Whole-rock powders and picked mineral separates were analyzed for their mineralogical composition by powder XRD following the same analytical protocol as that detailed for Expedition 390. Mineralogical compositions were determined by semiquantitative, standardless Rietveld analysis using Panalytical HighScore Plus software and both the Panalytical Example Database and PDF-4/Axiom 2019 database.

The background of the XRD spectra was first fitted in the software using a bending factor selected by the user to preserve all measured peaks. Peak positions were then automatically located by the software, with the minimum significance defined by the user for each spectrum such that all detected peaks were recognized. Library mineral diffraction patterns that matched the measured data were then searched in three steps prior to Rietveld analysis. Firstly, a broad pass search of all minerals in the database identified the dominant mineral phases. Multiple possible patterns for different mineral solid solutions were added to the pattern list at this stage. Secondly, a restricted search was made of just clay family minerals. Thirdly, a restricted search was made of just zeolite family minerals. From the clay and zeolite family searches, any minerals that had a reasonable possibility of being present in oceanic crust and scored a match were added to the pattern list. Rietveld fitting analysis then reduced this large list of possible minerals and mineral solid solutions down to a best-fit set of minerals and estimated abundances that could explain all the diffraction peaks. This multistep pattern search was found to better locate potential matches for low-abundance secondary clay and zeolite phases recognized but not exactly identified by thin section petrography.

5. Biostratigraphy

Calcareous nannofossils [also called calcareous nannoplankton] and planktic foraminifera were examined to provide preliminary age constraints for recovered sediment, and benthic foraminifera were analyzed to provide preliminary estimates of paleodepth. Biostratigraphic and paleodepth analyses were performed on the core catcher [CC] samples, and additional samples were taken from split sections as needed to further refine the stratigraphic position of key datums.

Core catcher samples from Expeditions 390C and 395E [Holes U1556A, U1557B, U1558A, U1559A, U1560A, and U1561A] were sent to the Expedition 390/393 paleontologists for shore-based analyses at their home institutions. Only the archive halves of these cores were made available on JOIDES Resolution during Expeditions 390 and 393, so no additional section samples were available for planktic or benthic foraminiferal analyses. However, additional calcareous nannoplankton smear slide samples were taken from the archive halves to refine the age model at critical intervals. Whole-round cores spanning the sediment/basement interface from Holes U1556A, U1557B, and U1559A were split shipboard during Expedition 390, and whole-round cores spanning the sediment/basement interface from Holes U1558F, U1583C, and U1560C were split shipboard during Expedition 393. These cores were sampled for both calcareous nannoplankton and planktic foraminifera as needed [at least one sample per section] to determine the age of the sediment/basement interface. Thin section samples from indurated calcareous sediments in basement rocks were taken as needed [generally one or two samples per site] for planktic foraminiferal biostratigraphy of interflow sediments.

Biostratigraphic age assignments were based on identification of calcareous nannoplankton and planktic foraminiferal lowest occurrences [base [B]] and highest occurrences [top [T]]. Biozone boundaries were placed at the midpoint between the sample containing the marker species and the sample below [for lowest occurrences] or above [for highest occurrences] without the marker species. The ages of the calcareous nannoplankton and planktic foraminiferal biozonation schemes used during Expedition 390/393 followed Gradstein et al. [2020] as modified by King et al. [2020] for Neogene planktic foraminifera. Calcareous nannoplankton and planktic foraminiferal biozone marker species and other useful biostratigraphic datums are illustrated in Figure F21.

Figure F21. Microfossil datums.

Calcareous nannoplankton and foraminiferal occurrences, preservation, abundance, and zonal assignments were entered into the LIMS database using the DESClogik software package, with the exception of benthic foraminifera for Site U1557, which samples were analyzed at the end of Expedition 390/393. Biostratigraphic data are reported in tables summarizing recorded datums, distribution charts, qualitative abundance plots, and preservation summaries for each site. Both onshore analysis of Expeditions 390C and 395E core catchers and shipboard Expedition 390/393 biostratigraphic analyses largely focused on the presence of age- and depth-diagnostic species, and therefore distribution data do not represent the complete microfossil assemblage. Qualitative notes about the overall abundance and preservation state were made for calcareous nannoplankton and planktic and benthic foraminifera in each sample analyzed. Observations regarding other notable sedimentary material [e.g., fish teeth, echinoderm spines, and diatoms] were also included.

5.1. Calcareous nannofossils

5.1.1. Calcareous nannofossil taxonomy and biostratigraphy

Nannofossil taxonomy primarily follows Bown [1998, 2005] and Perch-Nielsen [1985] as compiled in the online database Nannotax3 [Young et al., 2022]. The zonal scheme of Martini [1971] [zonal code numbers NP and NN] were used for Cenozoic calcareous nannofossil biostratigraphy. Additional biohorizons from the Paleogene scheme of Agnini et al. [2014] [zonal code numbers CNP, CNE, and CNO] and the Neogene/Quaternary scheme of Backman et al. [2012] [zone numbers CNM and CNPL] are also included. The compilation of Raffi et al. [2006] was also partially used to provide additional information on the reliability, definition, and timing of Quaternary bioevents. These zonations represent a general framework for the biostratigraphic classification of middle- to low-latitude nannofossil assemblages and are presented in Figure F21.

The genus Gephyrocapsa dominates Pleistocene assemblages. However, this group demonstrates a large range of variation in size and morphology, which causes problems in identification [e.g., Samtleben, 1980; Su, 1996; Bollmann, 1997]. Size variations in Gephyrocapsa spp. are commonly used as biostratigraphic markers in the Pleistocene, and several studies confirm the reliability of these biometric subdivisions as biostratigraphic markers [e.g., Raffi et al., 1993, 2006; Young, 1998; Raffi, 2002; Lourens et al., 2004; Maiorano and Marino, 2004]. We elected to use this biometric classification with the following divisions applied for shipboard identification of Gephyrocapsa:

• Gephyrocapsa spp. 50 cm long] were run on the NGRL.
• Core sections were thermally equilibrated to ambient room temperature [~20°C] for ~4 h.
• Whole-round core sections were run on the WRMSL: GRA bulk densitometer, magnetic susceptibility pass-through loop system [loop magnetic susceptibility [MSL]], and PWL.
• Whole-round core sections were passed to geochemistry and microbiology teams for dissolved O2 measurements and Rhizon sampling [see and ].
• Thermal conductivity [TCON] was measured once per core.
• Cores were split lengthwise into archive and working halves.
• Samples for MAD analyses were collected from the working half, generally two per core in representative lithologies, and analyzed for MAD properties.
• Discrete compressional velocity measurements were made on the working half using the Section Half Measurement Gantry [SHMG].
• Strength measurements were made on the working half using the automated vane shear [AVS] and pocket penetrometer [soft sediments only].
• The archive half of the core sections was passed through the SHIL for imaging and the SHMSL for RSC and MSP measurements.

Expedition 393 followed a slightly modified workflow for sediment cores. During this expedition, dissolved O2 measurements were made by the geochemistry and microbiology group on whole-round core sections immediately after STMSL logging. Thermal conductivity was measured on section halves after splitting. Additionally, the archive halves were run on the X-ray Imaging Logger just after splitting or after full completion of the hole, before storing the sections in the reefer.

Hard rock cores followed a slightly different sequence:

1. Core sections were shaken out onto the core cutting table, and pieces were oriented where possible. At this point, discrete pieces were removed for microbiological work [see ].
2. Discrete pieces of a given recovered hard rock section were shaken into a sterile split liner in the core splitting room for examination by a petrologist and/or a structural geologist, who determined the splitting line for obtaining working and archive halves from each whole-round piece. The core pieces were then put back into a full core section liner with plastic spacers between curated pieces [see ].
3. Core sections were thermally equilibrated to ambient room temperature [~20°C] for ~4 h.
4. NGRL measurements [for sections >50 cm in length] and X-ray imaging, neither of which were sensitive to temperature, were made on whole-round sections during this equilibration time.
5. After equilibration, whole-round core sections were run on the WRMSL with the GRA bulk densitometer and MSL [PWL was turned off].
6. Whole-round core exteriors were imaged on a DMT digital color CoreScan3 system.
7. Cores were split into archive and working halves along the previously marked splitting lines.
8. The archive half of the cores was passed through the SHIL for imaging and SHMSL for RSC and MSP.
9. Oriented, discrete cube samples [~8 cm3] were taken from the working-half cores for P-wave velocity and MAD analyses, generally two per core, in representative lithologies. These cubes were also used for paleomagnetic measurements [see ] to minimize the material removed from the core. The samples were placed in seawater under vacuum for 4–12 h for resaturation before measurement. Discrete samples were measured for P-wave velocity in three orthogonal directions and then processed for MAD analyses.
10. Selected pieces of core sections were also resaturated for 4 h under vacuum and measured for thermal conductivity. This analysis was nondestructive; pieces were returned to the core following measurement.

During Expedition 393, the whole-round sections were usually run through DMT imaging before NGRL or WRMSL, and selected sections were run on the X-ray imager after the NGRL.

A subset of the physical properties measurements were made during Expeditions 390 and 393 on cores recovered from Expeditions 390C and 395E [Estes et al., 2021; Williams et al., 2021]. Only archive halves of the Expedition 390C and 395E sediment cores were available during Expeditions 390 and 393; therefore, only nondestructive SHMSL and SHIL measurements were made.

Hard rock [lithified sediment and igneous basement] core sections associated with the sediment/basement interfaces that were recovered during Expeditions 390C and 395E received the full array of hard rock core measurements listed above.

8.2. Whole-round core section measurements

Whole-round cores were used to collect measurements of NGR, MS, compressional wave velocity, thermal conductivity, and digital images.

8.2.1. Special Task Multisensor Logger

The STMSL is run during sediment coring on whole-round sections immediately after laser engraving. The recovery of a complete stratigraphic section relies on the rapid hole-to-hole stratigraphic correlation of incoming sediment cores. The STMSL was used to measure GRA and MS at a sampling interval of 10 cm [see below]. The data were used for real-time stratigraphic correlation [see ]. Higher resolution GRA and MS data were later measured using the WRMSL after the core sections had thermally equilibrated to ambient room temperature.

8.2.2. Natural Gamma Radiation Logger

Natural gamma rays occur primarily as the result of the decay of 238U, 232Th, and 40K isotopes. Because radioactive decay and the resultant gamma ray emissions are not sensitive to temperature, the whole-round cores could be run through the NGRL before equilibrating to room temperature. The NGRL detector unit was calibrated using 137Cs and 60Co sources and identifying the peaks at 662 [137Cs] and 1330 keV [60Co].

Counts were summed over the range of 100–3000 keV during Expeditions 390 and 393 to be compatible with data collection from Expeditions 390C and 395E and for direct comparison with downhole logging data. Background gamma radiation measurements of an empty core liner counted for 21,600 s [6 h] were made prior to measuring core sections. The background signal is then automatically subtracted from the measured values of the core sections. A new background gamma radiation measurement is only necessary when the ship moves ≥2° latitude, which made quantification of background gamma radiation only necessary once during Expedition 390 and once during Expedition 393.

A single NGRL run consisted of two sets of measurements taken by eight sensors, each spaced 20 cm apart. The two sets of measurements were offset by 10 cm, which yielded a total of 16 measurements equally spaced 10 cm apart over a 150 cm long section of core. The quality of the energy spectrum measured in a core depends on the concentration of radionuclides in the sample and on the counting time, with higher times yielding more clearly defined spectra. Each set of measurements for a single NGRL run were counted for 300 s. Core sections 25 cm they were scanned in multiple frames. Additional blue lines were marked at 20 cm intervals along the exterior of the core in this case to enable images to be cropped and reconstructed using a dedicated Python script [see ] [Figure F25]. Finally, any highly fractured core that still fit together to form a cylinder was secured using rubber bands or shrink-wrapped prior to scanning, though this was a last resort because the wrapping creates interference in the image because of spurious reflectance.

Figure F25. Examples of how to scan each bin type.

Default settings for the CoreScan3 software were customized to ensure minimal correction by the software to ensure a consistent brightness across the data set. These settings are imperative for accurate manipulation by the Python program and include the following:

• Disabling Auto-adjust exposure;
• Selecting No core detection, no selection; and
• Choosing the Slightly lighter exposure setting

During Expedition 393, an X-Rite ColorChecker balance chart was imaged every 12 h during imaging periods to standardize colors across each unwrapped core image scan.

8.3.1. Core image processing

Each core piece scanned on the DMT CoreScan3 was saved both as DMT and BMP files and named using the following convention: Expedition of core recovery-Site-Hole-Core-Section-Bin.Extension [e.g., 390C-U1556A-2R-1-Pc1.DMT]. If a bin contained multiple subpieces that were scanned separately, each piece's file name was appended with a numbered identifier followed by an x [e.g., 390C-U1556A-2R-1-Pc1-1x.DMT]. Similarly, if a long piece [or multiple continuous pieces] were scanned together but in separate frames, each filename is also appended with a numbered identifier followed by an x [e.g., 390C-U1556A-2R-1-Pc1-1x.DMT; 390C-U1556A-2R-1-Pc1-2x.DMT] [for examples see Figure F25].

Individual image frames were stitched together to reconstruct bins >25 cm to provide a single high-resolution image per whole-round core section. Image processing was carried out using a Python program to allow comparison between full section DMT and SHIL data sets that will be made available postexpedition.

Because the DMT's computer was not able to be connected to the ship's server, a 1 TB external solid-state hard drive was strapped to the desk to avoid knocking and all images were saved directly onto it. These images were then exported manually to another hard drive before being copied onto the backup servers aboard the ship at the end of each shift.

8.4. Thermal conductivity

TCON is the coefficient of proportionality relating conductive heat flow to a thermal gradient [Blum, 1997]. Thermal conductivity was measured using the transient needle probe method in whole- or half-space geometry [Von Herzen and Maxwell, 1959], using a Teka Bolin TK04 system.

For a minority of sediment cores, thermal conductivity was measured after whole-round core sections had equilibrated to room temperature but prior to the cores being split. The needle probe method was used in full-space configuration for soft sediments [Von Herzen and Maxwell, 1959]. The needle probe was inserted into the unconsolidated sediment through 2 mm holes drilled into the core liner roughly once per core, generally in locations determined using MS data gathered on the WRMSL. In general, MS is lower in carbonate-rich intervals and higher in clay-rich intervals. Both kinds of intervals were targeted in order to assess thermal conductivity in these end-member lithologies.

For the majority of sediment cores, thermal conductivity was measured with a half-space needle puck [similar to the method used for hard rock] because the needle probe method was found to result in poor data quality. The needle puck was pressed gently against a split core section of the working half to measure thermal conductivity.

For hard rock material, TCON measurements were taken from pieces that were at least 10 cm long after splitting. If the split face of the piece was significantly rough, a lap plate and grit were used to smooth the sample face for better connection to the probe. The split samples were first saturated in ambient-temperature seawater for 4 h with a vacuum pump to aid in the full saturation of pore space. A puck with the measurement probe was attached to the split face and secured with a strap or rubber band. Three steps of heating–cooling cycles were used, and the final TCON value was the mean of the three cycles, although data from each of the cycles are also recorded in the LIMS database.

8.5. Split core section-half and discrete measurements

Once cores were split, samples for discrete petrophysical measurements were taken for MAD analysis, as well as P-wave velocity in the case of hard rock. For soft rocks, discrete samples were taken for MAD analysis; however, shear strength and P-wave velocity measurements were made directly on the cut surface of the working half. Meanwhile, the archive half was used for nondestructive SHMSL measurements and half-round imaging of the split core surface on the SHIL.

8.5.1. X-ray image logger [Expedition 393]

During Expedition 393, X-ray images were recorded on the archive half of each section of sediment recovered to evaluate bioturbation intensity, drilling disturbance, or any structures or features that could produce a recognizable density signature. X-ray imaging was also attempted on selected sections of basement but produced underwhelming results. The X-ray imager is composed of a Teledyne ICM CP120B X-ray generator and a detector unit. The generator works with a maximum voltage of 120 kV and a tube current of 1 mA, and the focal spot is 0.8 mm × 0.5 mm. The generator produces a directional cone at a beam angle of 50° × 50°. The detector unit is located 65 cm from the source and consists of a Go-Scan 1510 H system composed of an array of complementary metal oxide semiconductor [CMOS] sensors arranged to offer an active area of 102 mm × 153 mm and a resolution of 99 µm. Core sections were run through the imaging area at 12 cm intervals, providing images of 15 cm onto the detector with an overlap of 3 cm.

Tests were conducted to obtain the best image resolution for determining the internal structure of the cores, beginning with a standard 80 kV voltage and 1.0 mA current, 60 ms exposure time, and stack of 20 images for all cores. Some adjustments were made during the course of the expedition to improve the image quality in different lithologies. Separate routines were developed for basement and sediment cores, where both used a 300 ms exposure time and a stack of 20 images. Basement core images were acquired using a 100 kV voltage and 0.6 mA current, whereas sediment cores were scanned using 80 kV and 0.5 mA. Image processing parameters were set to a range of 0–1 for basement cores and 0–2 for sediment cores, with a 1% mask threshold for both.

The raw images were collected as 16-bit images and were processed with the IODP in-house processing utility in the IMS software. The software applies corrections for the detector [gain and offset corrections], compensates for core shape and thickness, and adjusts the image contrast. The Savitzky-Golay finite impulse response [FIR] filter is used to smooth images. The resulting processed images include a masked background, the depth scale of the section, and the acquisition parameters. The software applies different processing to APC or rotary cores.

The X-ray imager was not run during Expedition 390 because of time and staffing limitations.

8.5.2. Section-Half Multisensor Logger

8.5.2.1. Point magnetic susceptibility

MSP was measured on archive-half sections using a Bartington Instruments MS2E point sensor at a higher spatial resolution than MS measured by the WRMSL on whole-round cores. Flush contact between the probe and the archive halves was needed; thus, the sediment section halves were covered with plastic wrap to avoid contamination. The instrument takes and averages three measurements made at 1 s intervals to an accuracy of 5%. Before each measurement, the probe was zeroed in air and a background magnetic field was measured and removed from the data. MSP measurements were conducted at a resolution of 2.5 cm for sediment and hard rock sections. A built-in laser surface analyzer aided in the recognition of irregularities in the split core surface [e.g., cracks and voids] and provided an independent check on the fidelity of SHMSL measurements [e.g., Expeditions 301, 371, and 378 [Expedition 301 Scientists, 2005; Sutherland et al., 2019; Röhl et al., 2022]].

The Bartington Instruments MS2E point sensor that is used for MSP measurements uses a higher frequency than the WRMSL [2 kHz]. This could introduce small differences in values measured on the two systems if superparamagnetic grains displaying frequency-dependent magnetic susceptibility are present [Dearing et al., 1996]. Further differences may also arise from averaging point measurements compared to continuous measurements. Because it is difficult to isolate these different factors, absolute differences between the two magnetic susceptibility systems should be interpreted with caution.

8.5.2.2. Reflectance spectroscopy and colorimetry

The reflectance of visible light from the archive halves of sediment cores was measured using an Ocean Optics USB4000 spectrophotometer mounted on the automated SHMSL. Measurements were taken at 2.5 cm spacing to provide a high-resolution stratigraphic record of color variation for visible wavelengths. Empty intervals, voids, and gaps were skipped to avoid spurious measurements. Intervals where the top of the flat hard rock surface was below the level of the core liner were lifted by adding support matting or foam beneath each hard rock piece to ensure good contact with the sensor. Each measurement was recorded in 2 nm wide spectral bands from 400 to 700 nm. Colorimetry and reflectance data were reported using the L*a*b* color system, in which L* is lightness, a* is redness [positive] versus greenness [negative], and b* is yellowness [positive] versus blueness [negative]. The color reflectance spectrometer calibrates on two spectra, pure white [reference] and pure black [dark]. Color calibration was conducted approximately once every 6 h [twice per shift].

8.5.3. Pocket penetrometer and vane shear strength

Both pocket penetrometer and vane shear strength quantify the effective shear strength [σm] of the lithology by applying a known compressive and shear stress, respectively.

The pocket penetrometer [PEN] is an unconfined compression strength test and was measured on every core. At a prescribed stress, the shear strength of a material or yield [τf] is related to the compressive strength [Δσf] by

τf=Δσf/2.

The penetrometer uses a 6.4 mm diameter probe, which is gently pushed into the core below the split core section surface to a marked line on the probe. The selected probe location must be where core section surfaces are smooth. The mechanical scale is in kilograms per square centimeter, and the maximum value measurable by the pocket penetrometer is 4.5 kg/cm2. The data were uploaded to the LIMS database in kg/cm2 and can be converted to kPa as follows:

2τf kPa=981×2τf kg/cm2.

The vane shear strength [AVS] test is an undrained shear strength test, implying that the quantified shear strength is the effective shear strength, which corresponds to the applied stress minus the intergranular pore fluid pressure [ρf]:

σ′m=σm-Pf,

where

σm=σ1-σ3/2.

The Giesa AVS system is suited for measuring the shear strength of very soft to relatively stiff marine sediments and is especially useful for analyzing undisturbed clay- or silt-rich samples. The system consists of a controller and a gantry for shear vane insertion. A four-bladed miniature vane was pushed carefully into the sediment of the working halves until the top of the vane was level with the core surface. The vane was then rotated to determine the torque required to cause the core material to shear [failure torque]. All vane shear strength measurements were obtained using a 12.7 mm vane. Failure torque was determined by measuring the rotation of a torsional spring using a spring-specific relation between rotation angle and torque.

Vane shear strength [Su[V]] can be determined as described by Blum [1997]:

SuV=T/Kv=Δ/B/Kv,

where

• T = torque required to induce material failure [in N·m],
• Kv = constant, depending on vane dimensions [in m3],
• Δ = maximum torque angle [in degrees] at failure, and
• B = spring constant that relates the deflection angle to the torque [in °/N·m]

We performed one measurement per sediment core section until the recovered material became too stiff for vane insertion. Measurements were conducted in regions considered to be the most representative of the core lithology. Shear and compressional strength measurements should be considered approximations of the true sediment strength, as these experiments do not account for pore pressure changes in the cores after splitting.

8.5.4. Moisture and density

Two discrete samples were taken per core from the working half [~10 cm3 samples in sediment and ~8 cm3 samples in hard rock], with additional samples taken at notable lithologic boundaries. The aim was to have at least one sample characterizing each lithologic unit. In indurated sediment and hard rock, discrete samples were extracted for MAD analyses as well as P-wave velocity measurements and paleomagnetism where possible. MAD samples were used to measure wet and dry bulk density, grain density, water content, and porosity following methods presented in Blum [1997], which are briefly outlined below. In hard rocks, MAD samples are typically taken from rock pieces appearing cohesive enough to withstand being cut into cubes, which may bias the data toward higher density values than any surrounding more heterogeneous intervals. During Expedition 393, the initial mass was also measured prior to saturation.

Preweighed and numbered 16 mL Wheaton glass vials were used to process and store the sediment samples. Following measurement of wet mass, samples were dried in a convection oven for at least 24 h at 105° ± 5°C. Dried samples were then cooled in a desiccator for at least 2 h before the dry mass and volume were measured. For hard rock, the procedure included resaturation with seawater for 4–12 h under vacuum before the wet mass measurement was conducted.

Wet and dry sample masses were measured to a precision of 0.005 g using dual-Mettler Toledo [XS204] electronic balances, with one acting as a reference. A standard with a comparable mass to each sample was placed on the reference balance and the computer averaging system compensated for the ship's motion by taking multiple measurements—typically 300 per sample.

Dry sample volumes were determined using a hexapycnometer system of a six-celled custom-configured Micrometrics AccuPyc 1330TC helium-displacement pycnometer. The system measures dry sample volume using pressurized He-filled chambers, where the precision of each cell was 1% of the full-scale volume. Volume measurements were preceded by three purges of the sample chamber with helium. For each measurement, five unknown cells and one cell that contained two stainless steel calibration spheres with a total volume of ~10 cm3 were run. Calibration spheres were sequentially cycled through the cells to identify any systematic error and/or instrument drift. The volumes occupied by the numbered Wheaton vials were calculated before the expedition by multiplying each vial's weight against the average density of the vial glass. The fundamental relation and assumptions for the calculations of all physical properties parameters, such as wet bulk density [ρwet], dry bulk density [ρdry], sample grain density [ρsolid], porosity [ϕ], and void ratio [VR] were included in the MADMax shipboard program set with the "Method C" calculation process [Blum, 1997].

8.5.5. Discrete P-wave velocity

Triaxial P-wave velocity was measured using the P-wave gantry system on discrete samples generally twice but at least once per core. When lithologies of interest were identified visually, additional measurements were taken. Velocity was measured using Panametrics-NDT Microscan delay line transducers transmitting at 0.5 MHz. The signal received through the section half or discrete sample was recorded by the Velocity Gantry 2.0.5.0 IODP software, where the peak of the first P-wave arrival is either automatically or manually chosen. In case of a weak signal, manual picking of the first arrival was performed.

The distance between transducers was measured with a built-in linear voltage displacement transformer [LVDT]. Calibration was performed daily with a series of acrylic cylinders of differing thicknesses and a known P-wave velocity of 2750 ± 20 m/s. The system time delay determined from calibration was subtracted from the picked arrival time to give a traveltime of the P-wave through the sample. The thickness of the sample [calculated by the LVDT, in meters] was divided by the traveltime [in seconds] to calculate P-wave velocity in meters per second. A clean first P-wave arrival can be difficult to pick depending on the material; therefore, distilled water was applied to the contacts between sample cube and calipers to improve the coupling and resulting reading.

For soft-sediment cores, P-wave velocity measurements were performed on the working half along the x-axis. Different positions with respect to lithology were chosen to generate viable data. Discrete measurements were chosen to target intact pieces and avoid the drilling mud from XCB coring, which is significantly softer. Given the instrument uncertainties, the higher discrete P-wave value was always considered likely to be the better representation of the true P-wave velocity.

Measurements of hard rock P-wave velocity were made using the 2 cm × 2 cm × 2 cm cubes also used for MAD analysis and paleomagnetism measurements. The P-wave measurement was taken on the seawater-saturated cube [see ] to best represent in situ conditions. The hard rock measurements were conducted after orienting the sample [Blum, 1997] and placing it on the gantry that measures P-wave velocity in three orthogonal directions [x-, y-, and z-directions]. P-wave anisotropy ratios could be calculated from these multidirectional analyses.

One of the factors affecting the measurements is the less than perfect shape of the cubes, which are cut by hand using an electric double-bladed trimming saw from the working half. Despite all the care taken, they can have slightly nonparallel or irregular surfaces that will affect the velocity measurement. Considering that any such imperfection can only decrease the velocity [by introducing spaces between the pieces and the transducers], we consider the fastest measurement for each sample [regardless of its direction] to be the most representative of the formation at that depth.

8.6. Data filtering procedure

WRMSL and SHMSL data contained spurious values measured at gaps in the core section [empty intervals], cracks in core pieces, and, for bulk volumetric measurements [WRMSL], due to reduced volume of material [departure from a continuous cylindrical core] in the vicinity of the sensor. Filtering out these spurious data points provides a data set more suitable for quantitative analysis. In the case of full-diameter continuous core recovery, only a minor amount of filtering was required, for example for fall-in material at the top of some APC cores. Valid measurement intervals were identified from the SHMSL laser profile data, which detects gaps and cracks between pieces. The SHMSL and WRMSL MS data were filtered based on those data. Additional manual editing was required in specific intervals where the SHMSL laser could not detect gaps.

8.7. Comparison to ODP Hole 896A

During Expedition 393, the discrete physical properties measurements on basement [MAD, VP, and TCON] were compared to the same type of data from ODP Hole 896A [Shipboard Scientific Party, 1993; Table T6]. Hole 896A is located ~1 km from the deep ocean crust reference ODP Hole 504B and was drilled 290 m into heavily sedimented basalts [~179 m of overburden] that formed at ~6.9 Ma at the intermediate-spreading Costa Rica Rift. The Hole 896A data provide a convenient benchmark to compare physical properties measurements from across the SAT. The full data set from Hole 896A was used for comparison, and encompasses the range of basalt alteration levels that were sampled from these cores. Because the sediment cover is different between the sites from Expedition 393 and Hole 896A, we compared the data as a function of basement depth rather than depth below seafloor.

8.8. Stratigraphic correlation

The paleoceanographic scientific objectives of the SAT expeditions are best addressed when there is recovery of complete stratigraphic sections for all sites. However, recovery of a continuous section from a single IODP hole is technically impossible, even with up to 100% or greater nominal recovery [e.g., Ruddiman et al., 1987; Hagelberg et al., 1995; Lisiecki and Herbert, 2007], because core recovery gaps occur between successive APC and XCB cores in a single hole. Additionally, tides, ship heave, drilling disturbance, and missing material [through whole-round sampling] generally preclude complete recovery of the sediment package in a single drilled hole. Therefore, construction of a complete stratigraphic section requires multiple holes at a given site referenced to a composite depth scale. The SAT composite depth and splice construction methodology followed previous expeditions [e.g., Integrated Ocean Drilling Program Expedition 342 and Expeditions 371 and 378 [Norris et al., 2014; Sutherland et al., 2019; Röhl et al., 2022]]. By offsetting the recovery depth of cores below seafloor between each hole, it was possible to maximize the probability that adjacent holes recover most core gaps encountered in previous holes. Then, stratigraphic intervals from two or more holes cored at the same site can be combined into a splice. Where there are two holes at a site, stratigraphic gaps often remain.

The STMSL was used to provide rapid measurements of MS and GRA density for real-time correlation. Correlating the first and second holes, core by core, allows tracking of the depth of coring gaps in both holes to prevent coinciding core gaps. This required coordination with the drill floor toolpushers throughout drilling, where we either maintained the drill shot depth, pulled up the drill string, or advanced the drill string, thus altering the projected depth of the core gap in the second hole.

Subsequently, once thermal equilibration was reached and WRMSL and SHMSL measurements were completed, the raw physical properties data and core images were downloaded using the Correlation Downloader software or directly from the LIMS database. One exception was GRA density, where we filtered and removed data 100% recovery. During the process of constructing the composite section, the CCSF depth becomes systematically deeper than that of the CSF-A depth for equivalent horizons. This expansion has four main causes:

• Decompression of the sediment as it is brought to atmospheric pressure;
• Pore-space gases coming out of solution, warming, and expanding;
• Stretching that occurs as part of the coring process; and/or
• Recovering borehole wall sediment that fell downhole and was cored.

8.8.2. Splice

For each site a splice was generated, where core sections from adjacent holes were combined to minimize coring gaps for each site [Figure F26]. The placement of splice tie points was inherently subjective, but we used the following guidelines for splice construction:

• The top and bottom 1 m of cores, where drilling disturbance was more likely, were typically avoided.
• Caution was taken during compositing and splicing within the uppermost 2 cores at every site to avoid artifacts caused by entrainment and duplication of loose sediment at the top of the hole because of imperfect alignment of the "shot" core barrels.
• We routinely attempted to avoid intervals of cores from holes where whole-round samples for IW, microbiological, and geochemistry samples were taken to maximize the possibility of still generating a spliced continuous sediment record for postexpedition sampling.
• We attempted to select portions of core that were the most representative of the stratigraphic section using all the physical properties data sets and core images at our disposal.

8.9. Downhole measurements

The downhole measurements made during the SAT expeditions included formation temperature measurements during APC coring operations at all sites, as well as downhole logging in most of the basement holes.

Downhole logs are measurements used to assess the physical, chemical, and structural properties of the formation surrounding a borehole that are made by lowering sondes with an electrical wireline in the hole after completion of drilling. The data are continuously acquired with depth [at vertical sampling intervals ranging from 2.5 mm to 15 cm] and measured in situ. Downhole logs measure formation properties on a scale that is intermediate between those obtained from laboratory measurements on core samples and those from geophysical surveys. They are useful in calibrating the interpretation of geophysical data and provide a link for the integrated understanding of physical properties on a wide range of scales.

Downhole logs can be interpreted in terms of the stratigraphy, lithology, mineralogy, magnetic characteristics, and geochemical composition of the penetrated formation. They also provide information on the condition, shape, and size of the borehole and on possible deformation induced by drilling or formation stress. In intervals where core recovery is incomplete or disturbed, log data may provide the only way to characterize the formation and can be used to determine the actual thickness of individual units or lithologies when contacts are not recovered, to pinpoint the actual depth of features in cores with incomplete recovery, or to identify and characterize intervals that were not recovered. Where core recovery is good, log and core data complement one another and may be interpreted jointly.

8.9.1. Wireline logging operations

During wireline logging operations, logs are recorded with a variety of tools combined into tool strings, which are lowered into the hole after completion of coring operations. Three primary tool strings were used during Expeditions 390 and 393 [Figure F27]: the Triple combination [triple combo], which measures spectral and natural gamma radiation, porosity, density, resistivity, and magnetic susceptibility; the Formation MicroScanner [FMS]-sonic string, which provides high-resolution resistivity images of the borehole wall and sonic velocities; and the Ultrasonic Borehole Imager [UBI], which provides acoustic images of the borehole wall. Each tool string also contains a telemetry cartridge for communicating through the wireline to the Schlumberger data acquisition system on the drillship. Individual tools, measurements, and units are listed in Tables T7 and T8.

Figure F27. Wireline tool strings.

In preparation for logging, the boreholes were flushed of debris by circulating viscous drilling fluid and filled with seawater or seawater-based logging gel [sepiolite mud mixed with seawater and weighted with barite; approximate density = 10.5 lb/gal or 1.258 g/cm3] to help stabilize the borehole walls. After completion of coring, the bottom of the drill string was set high enough above the bottom of the casing for the longest tool string to fit inside the casing before entering the open hole. The tool strings were then lowered downhole on a seven-conductor wireline cable during sequential deployments. The gamma ray tool and in some cases the sonic tool are the only tools that provide meaningful data inside the drill pipe or casing [mostly qualitative]. Such data are used primarily to identify the depth of seafloor and the sediment/basement boundary but can also be used for stratigraphic characterization.

Each tool string deployment is a logging run, starting with the assembly of the tool string and any necessary calibrations. The tool string is then lowered to the bottom of the hole while recording a partial set of data, and then it is pulled up at a constant speed [typically 250–500 m/h] to record the main data. During each run, tool strings can be lowered down and pulled up the hole several times for repeatability or to try to improve the data quality. Each lowering or raising of a tool string while collecting data constitutes a pass. During each pass the incoming data are recorded and monitored in real time on the surface minimum configuration multitasking acquisition and imaging system [MAXIS]. A logging run is complete once a tool string has been recovered to the rig floor and disassembled. A wireline heave compensator [WHC] was employed to minimize the effect of ship's heave on the tool string's position in the borehole [see below].

8.9.2. Logged properties and tool measurement principles

The primary logging measurements recorded during Expeditions 390 and 393 are listed in Table T7. The logged properties and the principles used in the tools that measure them are briefly described below. More detailed information on individual tools and their geologic applications may be found in Serra [1984, 1986, 1989], Schlumberger [1989, 1994], Rider [1996], Goldberg [1997], Lovell et al. [1998], and Ellis and Singer [2007]. A complete online list of acronyms for the Schlumberger tools and measurement curves is available at //www.apps.slb.com/cmd.

8.9.2.1. Natural radioactivity

The Hostile Environment Natural Gamma Ray Sonde [HNGS] was used on all tool strings to measure natural radioactivity in the formation. The HNGS uses two bismuth germanate scintillation detectors and five-window spectroscopy to determine concentrations of potassium [in weight percent], thorium [in parts per million], and uranium [in parts per million] from the characteristic gamma ray energies of isotopes in the 40K, 232Th, and 238U radioactive decay series, which dominate the natural radiation spectrum. The computation of the elemental abundances uses a least-squares method of extracting U, Th, and K elemental concentrations from the spectral measurements. The HNGS filters out gamma ray energies below 500 keV, eliminating sensitivity to bentonite or KCl in the drilling mud and improving measurement accuracy. The HNGS also provides a measure of the total spectral gamma ray [HSGR] emission measured in American Petroleum Institute gamma radiation units [gAPI]. The HNGS response is influenced by the borehole diameter, and therefore HNGS data are corrected for borehole diameter variations during acquisition.

The Enhanced Digital Telemetry Cartridge [EDTC; see ], a telemetry cartridge used primarily to communicate data to the surface, includes a sodium iodide scintillation detector that also measures the total natural gamma ray [NGR] emission. It is not a spectral tool but it provides high-resolution total gamma ray for each pass, which allows precise depth match processing between logging runs and passes.

8.9.2.2. Porosity

Formation porosity was measured with the Accelerator Porosity Sonde [APS]. The sonde includes a minitron neutron generator that produces fast [14.4 MeV] neutrons and five neutron detectors [four epithermal and one thermal] positioned at different spacing from the minitron. The tool's detectors count neutrons that arrive at the detectors after being scattered and slowed by collisions with atomic nuclei in the formation.

The highest energy loss occurs when neutrons collide with hydrogen nuclei, which have practically the same mass as the neutron [the neutrons bounce off heavier elements without losing much energy]. If the hydrogen [i.e., water] concentration is low, as in low-porosity formations, neutrons can travel farther before being captured and the count rates increase at the detector. The opposite effect occurs in high-porosity formations where the water content is high. The raw porosity value is often an overestimate because hydrogen bound in minerals such as clays or in hydrocarbons also contributes to the measurement.

Upon reaching thermal energies [0.025 eV], the neutrons are captured by the nuclei of Cl, Si, B, and other elements, resulting in a gamma ray emission. This neutron capture cross section [Σf] is also measured by the tool.

8.9.2.3. Density

Formation density was measured with the Hostile Environment Litho-Density Sonde [HLDS]. The sonde contains a radioactive cesium [137Cs] gamma ray source [622 keV] and far- and near-gamma ray detectors mounted on a shielded skid, which is pressed against the borehole wall by a hydraulically activated decentralizing arm. Gamma rays emitted by the source undergo Compton scattering, where gamma rays are scattered by electrons in the formation. The number of scattered gamma rays that reach the detectors is proportional to the density of electrons in the formation, which is in turn related to bulk density. Porosity may also be derived from this bulk density if the matrix [grain] density is known.

The HLDS also measures the photoelectric effect [PEF], a measure of the photoelectric absorption of low-energy gamma radiation. Photoelectric absorption occurs when gamma ray energy falls below 150 keV as a result of being repeatedly scattered by electrons in the formation. Because PEF depends on the atomic number of the elements in the formation [heavier elements have higher PEF], it also varies according to the chemical composition of the minerals.

Good contact between the tool and borehole wall is essential for good HLDS logs. Poor contact results in underestimation of density values. Both the density correction and caliper measurement of the hole are used to check the contact quality.

8.9.2.4. Electrical resistivity

The High-Resolution Laterolog Array [HRLA] provides six electrical resistivity measurements with different depths of investigation [including the borehole, or mud, resistivity and five measurements of formation resistivity with increasing penetration into the formation]. The sonde sends a focused current into the formation and measures the intensity necessary to maintain a constant drop in voltage across a fixed interval, providing direct resistivity measurements. The array has one central source electrode and six electrodes above and below it, which serve alternatively as focusing and returning current electrodes. By rapidly changing the role of these electrodes, a simultaneous resistivity measurement at six penetration depths is achieved. The tool is designed to ensure that all signals are measured at exactly the same time and tool position and to reduce the sensitivity to "shoulder bed" effects when crossing sharp beds thinner than the electrode spacing. The HRLA needs to be run centralized in the borehole for optimal results, so knuckle joints were used to centralize the HRLA while allowing the density and porosity tools that are often on the same tool string to maintain good contact with the borehole wall.

Typically, minerals found in sedimentary and crustal rocks are electrical insulators, whereas ionic solutions like pore water are conductors. In most rocks, electrical conduction occurs primarily by ion transport through pore fluids and is strongly dependent on the porosity, the types of pores and connectivity, the permeability, and the pore fluid.

8.9.2.5. Magnetic susceptibility

The Magnetic Susceptibility Sonde [MSS] is a nonstandard wireline tool designed by Lamont-Doherty Earth Observatory [LDEO]. It measures the ease with which formations are magnetized when subjected to a magnetic field. The ease of magnetization, or susceptibility, is ultimately related to the concentration and composition [size, shape, and mineralogy] of magnetic minerals in the formation. These measurements provide one of the best methods for investigating stratigraphic changes in mineralogy and lithology because the measurement is quick, repeatable, and nondestructive and because different lithologies often have strongly contrasting susceptibilities. The data can be compared to the susceptibility measurements made on the recovered core by the WRMSL and the MSP measurements of the SHMSL [see ].

The MSS dual-coil sensor provides ~40 cm resolution measurements with ~20 cm depth of horizontal investigation. The MSS was run as the lowermost tool in the triple combo tool string using a specially developed data translation cartridge to enable the MSS to be run in combination with the Schlumberger tools. MSS data are plotted as uncalibrated units and are affected by temperature and borehole size. For quality control and environmental correction, the MSS also measures internal tool temperature, z-axis acceleration, and low-resolution borehole conductivity.

8.9.2.6. Acoustic velocity

The Dipole Shear Sonic Imager [DSI] measures the transit times between sonic transmitters and an array of eight receivers. The waveforms are then used to calculate the sonic velocity in the formation. The omnidirectional monopole transmitter emits high frequency [5–15 kHz] pulses to extract the compressional velocity [VP] of the formation, as well as the shear velocity [VS] when it is faster than the sound velocity in the borehole fluid. It combines replicate measurements, thus providing a direct VP measurement through sediments that is relatively free from the effects of formation damage or an enlarged borehole [Schlumberger, 1989]. The same transmitter can be fired in sequence at a lower frequency [0.5–1 kHz] to generate Stoneley waves that are sensitive to fractures and variations in permeability. Along with the monopole transmitters found on most sonic tools, the DSI also has two crossed-dipole transmitters that allow an additional VS measurement.

8.9.2.7. Acoustic images

Acoustic images of the borehole wall were generated from measurements taken by the UBI. The UBI features a high-resolution transducer, which emits ultrasonic pulses at a frequency of 250 and 500 kHz [low and high resolution, respectively] that are reflected by the borehole surface and then received by the same transducer recording the amplitude and traveltime of the reflected signal. Continuous rotation of the transducer combined with the upward motion of the tool result in a 360° image of the borehole wall. The amplitude of the signal depends on the reflection coefficient of the borehole fluid/borehole wall interface, the position of the UBI tool in the borehole, the shape of the borehole, and the roughness of the borehole wall. Modulation of the reflected signal is dependent on the borehole wall roughness. Therefore, fractures or other changes in the character of the drilled formation [e.g., grain size and texture] can be recognized in the amplitude image. The recorded traveltime image gives detailed information about the cross-sectional shape of the borehole, which allows calculation of one caliper value [radius] of the borehole from each traveltime measurement. These amplitude and traveltime measurements are recorded in combination with an azimuthal measurement [from the General Purpose Inclinometry Tool [GPIT]], permitting orientation of these images. The full coverage of UBI measurements make the images a useful tool for core orientation and for stress analysis [Paillet and Kim, 1987].

8.9.2.8. Microresistivity images

The FMS provides high-resolution electrical resistivity–based images of the borehole walls that can be used for detailed lithostratigraphic or structural interpretation. The tool has four orthogonally oriented arms, each with 16 button electrodes that are pressed against the borehole walls during logging. The electrodes are arranged in two diagonally offset rows of 8 electrodes each. A focused current is emitted from the button electrodes into the formation, with a return electrode near the top of the tool. Resistivity of the formation at the button electrodes is derived from the intensity of current passing through the button electrodes.

Processing transforms the resistivity measurements into oriented high-resolution images that reveal geologic structures of the borehole wall based on their conductivity. Features such as bedding, stratification, fracturing, slump folding, and bioturbation can be resolved [Luthi, 1990; Salimullah and Stow, 1992; Lovell et al., 1998]. Because the images are oriented to magnetic north, further analysis can provide measurement of the dip and direction [azimuth] of planar features in the formation. In addition, when the corresponding planar features can be identified in the recovered core samples, individual core pieces can be reoriented with respect to true north.

The maximum extension of the FMS caliper arms is 40.6 cm [16 inches]. In holes with a diameter greater than this maximum, the pad contact at the end of the caliper arms will be inconsistent and the FMS images may appear out of focus and too conductive. Irregular [rough] borehole walls will also adversely affect the images if contact with the wall is poor. Approximately 30% of a borehole with a diameter of 25 cm is imaged during a single pass. Standard procedure is to make two full uphole passes with the FMS to maximize the borehole coverage with the pads.

8.9.2.9. Acceleration and inclinometry

The GPIT makes three-component acceleration and magnetic field measurements. The primary purpose of this tool is to determine the acceleration and orientation of the tool string in which it is deployed. Tool orientation is defined by three parameters: tool deviation, tool azimuth, and relative bearing. The GPIT uses a three-axis inclinometer and a three-axis fluxgate magnetometer to record the orientation of the logging tool as the magnetometer records the magnetic field components [Fx, Fy, and Fz]. The resulting data can be used to facilitate corrections for irregular tool motion and to provide oriented image data from the FMS and UBI tools. Corrections for cable stretching and/or ship heave using GPIT acceleration data [Ax, Ay, and Az] allow precise determinations of log depths.

8.9.2.10. Auxiliary logging equipment

The Schlumberger logging equipment head [LEH, or cablehead] measures tension at the very top of the wireline tool string, which diagnoses difficulties in running the tool string up or down the borehole or when exiting or entering the drilling string or casing.

Telemetry cartridges are used in each tool string to allow transmission of the data from the tools to the surface. The EDTC also includes a sodium iodide scintillation detector to measure the total natural gamma ray emission of the formation. This gamma ray log was used to match the depths between the different passes and runs. In addition, it includes an accelerometer, and that data can be used in real time to evaluate the efficiency of the WHC.

Because the tool strings combine tools of different generations and with various designs, they include several adapters and joints between individual tools to allow communication, provide isolation, avoid interferences [mechanical, acoustic], terminate wirings, or to position the tool properly in the borehole. The knuckle joints, in particular, were used to allow some of the tools such as the HRLA to remain centralized in the borehole, whereas the overlying HLDS was pressed against the borehole wall.

All these additions are included and contribute to the total length of the tool strings in Figure F27.

8.9.3. Log data quality

The condition of a borehole is the principal factor contributing to log data quality. The ideal conditions for logging include a consistent borehole diameter of the size of the bit with no washouts or bridges. Oversized borehole diameters can have a significant impact on measurements, especially those that require tool eccentering [e.g., HLDS] or tool centralization [e.g., FMS and UBI]. The measurement principles of the eccentered tools, as well as the centralized FMS, means that direct contact with the formation is essential for the acquisition of high-quality data. The UBI is a noncontact tool, but data quality is best when the tool is actively centered in the borehole. Deep investigation measurements such as gamma radiation, resistivity, and sonic velocity, which do not require contact with the borehole wall, are generally less sensitive to borehole conditions, although data are optimized in boreholes where the tools can be centralized [up to ~20 inch diameter].

If the borehole diameter varies over short intervals because of washouts of softer material or ledges of harder material, the logs from tools that require good contact with the borehole wall [i.e., FMS, density, and porosity tools] may be degraded. Bridged sections, where the borehole diameter is significantly less than the bit size, will also cause irregular log results. The quality of the borehole can be improved by minimizing the circulation of drilling fluid while drilling, flushing the borehole to remove debris prior to logging, and logging as soon after drilling and conditioning as possible.

The quality of the wireline depth determination depends on several factors. The depth of the logging measurements is determined from the length of the cable spooled out from the winch on the ship. Uncertainties in logging depth occur because of ship heave, cable stretch, cable slip, and tidal changes. To minimize the wireline tool motion caused by ship heave, a hydraulic WHC was used to adjust the wireline depth for rig motion during wireline logging operations [see ]. The seafloor is identified on the gamma ray log by the abrupt reduction in gamma ray count at the water/sediment interface [mudline], an important reference datum for matching logging depths and providing depth consistency across all logging data. Discrepancies between the drilling core depth and wireline logging depth may occur because of core expansion, incomplete core recovery, incomplete heave compensation, and drill pipe stretch. Reconciling the differences between the two data sets is possible through comparison of the common data sets acquired in situ and on core [e.g., magnetic susceptibility and NGR].

8.9.4. Wireline heave compensator

During wireline logging operations, the up-and-down motion of the ship [heave] causes a similar motion of the downhole logging tools. If the amplitude of this motion is large, depth discrepancies can be introduced into the logging data. The risk of damaging downhole instruments is also increased. A WHC system was designed to compensate for the vertical motion of the ship and maintain a steady motion of the logging tools to ensure high-quality logging data acquisition [Iturrino et al., 2013; Liu et al., 2013]. The WHC uses a vertical accelerometer [motion reference unit [MRU]] positioned under the rig floor near the ship's center of gravity to calculate the vertical motion of the ship with respect to the seafloor. It then adjusts the length of the wireline by varying the distance between two sets of pulleys through which the cable passes in order to minimize downhole tool motion.

8.9.5. Logging data flow and depth scales

Data for each wireline logging run were monitored in real time and recorded using the Schlumberger surface acquisition system. Data were shortly thereafter transferred onshore to LDEO for standardized data processing, formatting for the online logging database, and archiving. Processed data were returned to the ship and made available to the shipboard scientists within a few days of logging.

The processing included several stages. First, using the gamma ray logs recorded by every tool string, a visually interactive program was used to match the depths of recognizable features across all the passes to a reference curve, commonly the gamma ray log of the longest upward pass. Image data [FMS and UBI] were also processed to correct the effects of irregular tool motion using the acceleration data from the GPIT. After depth matching, all the logging depths were shifted from the rig floor depth reference [in which they were initially recorded] to a seafloor depth reference, based on the seafloor as identified by the step in gamma radiation at the sediment/water interface. All the processed data were made available in ASCII and DLIS formats for most logs and in GIF for the images.

8.10. In situ temperature measurements

During all SAT expeditions, in situ formation temperature measurements were made at selected depths in the sediments at all sites to assess the thermal structure of the sedimentary section along the transect and measure the regional heat flow.

The APCT-3 tool fits directly into a modified coring shoe of the APC and consists of a battery pack, data logger, and a platinum resistance-temperature device calibrated over a temperature range of 0°–30°C. Before entering the borehole, the tool is stopped at the seafloor for 5–10 min to thermally equilibrate with bottom water. However, the lowest temperature recorded during the run down is preferred to the average temperature at the seafloor as an estimate of bottom water temperature because [1] this measurement is more repeatable and [2] the bottom water is expected to have the lowest temperature in the profile. After the APC penetrated the sediment, it was held in place for ~10 min as the APCT-3 tool recorded the temperature of the cutting shoe every second. When the APC was fired into the formation, there was typically an instantaneous temperature rise due to frictional heating. The heat gradually dissipated into the surrounding sediment as the temperature at the APCT-3 tool equilibrated toward the temperature of the sediment.

The equilibrium temperature of the sediment was estimated by applying a mathematical heat-conduction model to the temperature decay record [Horai and Von Herzen, 1985]. The synthetic thermal decay curve for the APCT-3 tool is a function of the geometry and thermal properties of the probe and the sediment [Bullard, 1954; Horai and Von Herzen, 1985]. The equilibrium temperature must be estimated by applying a fitting procedure in the TP-Fit software [Heesemann et al., 2006]. However, when the APC system did not achieve a full stroke or when ship heave pulled up the APC system from full penetration, the temperature equilibration curve was disturbed and temperature determination was less accurate. The nominal accuracy of the APCT-3 tool temperature measurements is ±0.05°C.

8.11. Heat flow

A simple estimation of the vertical conductive heat flow at each site can be made by calculating a least-squares linear fit of the measured formation temperature as a function of depth. The slope of this linear fit is the temperature gradient, and the local vertical conductive heat flow is the product of this gradient with the mean thermal conductivity measured in the sediments from this site.

Another measure of the heat flow in a conductive regime can be established with a Bullard plot [Bullard, 1939]. If the vertical heat flow [q] is assumed constant with depth, such as in a predominantly conductive regime, the temperature at depth z can be calculated by a simple integration:

T=T0+q⋅∫0zdzKz,

where T0 is the temperature at the seafloor and K[z] the thermal conductivity at a depth z. The value in the integral is the thermal resistance of the interval between the seafloor and z. If the heat flow is constant with depth, as in a conductive regime, this defines a linear relationship between temperature and thermal resistance, and its slope is the conductive heat flow [Bullard, 1939].

9. Geochemistry

Shipboard geochemistry data routinely collected during the SAT expeditions [390C, 395E, 390, and 393] included headspace analysis of hydrocarbon gases, in situ pore water oxygen measurements, IW chemistry [e.g., salinity, pH, alkalinity, major cations and anions, nutrients, major and minor elements], loss on ignition [LOI], total carbon [TC] and total inorganic carbon [TIC], and elemental compositions of basement rocks using both ICP-AES and XRF using a handheld portable instrument [pXRF]. During Expedition 390, sulfide concentrations in IW were also determined. All data generated during shipboard analyses have been uploaded to the LIMS database. This combination of analyses provides insight into biogeochemical processes including metabolic rates, abiotic diagenetic reactions, mineral alteration [e.g., authigenic mineral precipitation and water-rock interactions], and advective fluid migration.

9.1. Headspace analysis of hydrocarbon gases

During Expeditions 390C and 395E and at Site U1583 during Expedition 393, headspace hydrocarbon analyses were conducted as part of standard shipboard safety monitoring procedures, as described in Kvenvolden and McDonald [1986] and Pimmel and Claypool [2001], to prevent drilling into sediments that contain hydrocarbon concentrations above safety levels. One sample per sediment core was subjected to headspace hydrocarbon gas analysis.

The ~3–5 cm3 sediment sample was collected from the interior of a freshly exposed core directly after sectioning on the catwalk. This sample was placed in a 20 cm3 glass vial and sealed with a Teflon/silicon septum and a crimped aluminum cap. The headspace sample was typically taken at the top of Section 4 [below the IW sample], unless obvious core disturbance suggested that a different section should be selected. The sample was placed in the oven at 80°C for 30 min. A 5 cm3 aliquot of the evolved hydrocarbon gases was extracted from the headspace vial with a standard gas syringe and then manually injected into an Agilent 7890 Series II gas chromatograph [GC] equipped with a flame ionization detector [FID] set at 250°C. The column [2 mm inner diameter, 6.3 mm outer diameter] was packed with 80/100 mesh HayeSep T [Restek]. The GC oven program was set to stay at 80°C for 8.25 min with a subsequent heat-up to 150°C at 40°C/min. The total run time was 15 min.

Results were collected using the Hewlett Packard 3365 ChemStation software. The chromatographic response was calibrated using nine different gas standard analyses and checked daily. The concentration of the analyzed hydrocarbon gases was reported as parts per million by volume [ppmv]. Table T9 lists precision and detection limits for the headspace gas analyses during the SAT expeditions.

9.2. Interstitial water collection and analysis

During the SAT expeditions, IW was extracted [1] through squeezing of whole round core samples that were cut on the catwalk [all expeditions including 390C and 395E] and [2] at a higher resolution on entire sections of core using Rhizon samplers during Expeditions 390 and 393 to enable a wide range of shipboard analyses and for postexpedition research [Table T9]. The residual whole-round sediments after IW extraction [squeeze cakes] were sampled for shipboard inorganic carbon and total carbon analyses as well as for postexpedition research.

9.2.1. IW sampling from sediment squeezing

Whole round samples 5–20 cm in length for IW extraction were cut on the catwalk, immediately capped, and then transferred to the chemistry laboratory for squeezing. The surfaces of each whole-round sample were carefully scraped away under ambient laboratory conditions using stainless steel knives to remove contamination due to seawater, drilling disturbances, and/or sediment smearing along the insides of the core liners. More exterior material was removed from XCB cores because XCB coring can result in more significant physical disturbance and seawater contamination in the core liner. The remaining sediments were transferred to titanium squeezers and loaded into a Carver hydraulic laboratory press [Manheim and Sayles, 1974]. The sediments were squeezed to extract IW at pressures up to 25,000 lb [~24.3 MPa]. A minimum of 30 min of squeezing was required for all cores; up to 2 h of squeezing was required to extract sufficient IW from some XCB cores because sediments collected with the XCB system are generally more compacted. IW extracted in the squeezers was passed through a nanopure water-precleaned Whatman Number 1 filter above a titanium screen into a 60 mL high-density polyethylene [HDPE] syringe that had been acid-cleaned with 10% HCl. For Expedition 393, two stacked Whatman Number 1 filters were used to reduce the particulates passing through to the syringe. For all expeditions, a 0.45 µm polyethersulfone membrane filter was attached to the syringe tip upon collection of IW from the squeezers. The collected fluids were then filtered through a 0.2 µm polyethersulfone membrane filter into appropriate containers and processed for shipboard and postexpedition analyses. The squeeze cake residues were then subsampled for postexpedition research and shipboard carbonate and total carbon analyses. The residual squeeze cakes were stored at 4°C. Squeezers were cleaned between samples with tap water, rinsed with 18.2 MΩ deionized water, and dried with compressed air before further sample processing.

9.2.2. Interstitial water analysis

9.2.2.1. Salinity, pH, and alkalinity

Salinity, alkalinity, and pH were measured immediately on IW extracted from squeezing following the procedures in Gieskes et al. [1991]. Hole U1558D IW salinity was measured on a temperature-compensated digital refractometer [Index Instruments Ltd.] Salinity measurements for Hole U1558F were consistently offset by 1 salinity unit and were corrected to reflect this drift. The instrument began to drift to higher values and could not be recalibrated. For subsequent holes, measurements were made with a Fisher Model S66366 optical refractometer. International Association for the Physical Sciences of the Oceans [IAPSO] standard seawater [salinity = 35] and 18.2 MΩ water [salinity = 0] were used to calibrate salinity. During Expeditions 390C and 395E, salinity was also measured using a Metrohm 785 DMP chloride autotitrator; a 100 µL sample was titrated against 0.015 M silver nitrate solution. IW pH and alkalinity were determined using a Metrohm 794 Basic Titrino autotitrator with a glass pH electrode. A 3 mL sample was titrated against 0.1 M HCl at 25°C to reach an endpoint of pH = 4.2. The IAPSO standard seawater [alkalinity = 2.325 mM; certified value] and laboratory standards [5–100 mM Na2CO3 alkalinity, made by mixing different proportions of 0.7 M KCl + 0.1 M Na2CO3] were used for calibration. The IAPSO standard was analyzed at the beginning and end of the sequence and after every 10 samples. Repeated measurements of IAPSO seawater for alkalinity yielded precision better than 2.5%.

9.2.2.2. Major cations and anions

Sulfate [SO4], chloride [Cl], bromide [Br], sodium [Na], magnesium [Mg], potassium [K], and calcium [Ca] concentrations were analyzed by ion chromatography [Metrohm 850 Professional IC] using 100 µL of IW diluted by 100 times with 18.2 MΩ water. For anions [Cl, SO4, and Br], a Metrosep C6 column [100 mm long; 4 mm inner diameter] was used with 3.2 mM Na2CO3 and 1.0 mM NaHCO3 solutions as eluents, whereas a Metrosep A supp 7 column [150 mm long; 4 mm inner diameter] was used with 1.7 mM HNO3 and pyridine-2,6-dicarboxylic acid [PDCA] solutions as eluents for cations [Na, K, Mg, and Ca]. The standards were IAPSO in various dilutions [ranging from 150% to 1% IAPSO] to create a 9-point calibration curve. Reproducibility was checked on the repeated measurements of standard IAPSO and IAPSO dilution of 1:10 every 10 samples. Reproducibility [defined by standard deviation/average; relative standard deviation [RSD]] of repeated IAPSO measurements [N = 16] was better than 1.5% for Cl, SO4, Na, Mg, K, and Br, whereas for Ca2+ it was 3.5% for Expedition 390 and 60°C] by placing a long syringe needle between the stopper and the wall of the bottle. After purging, the bottle was sealed with the butyl stopper and cap. Sterile filtered sodium bicarbonate [NaHCO3] was injected through the stopper. The pH of the medium was adjusted to 7.5 by injection of sterile filtered 6.5% HCl or NaOH. Sterile filtered Na2S·9H2O was then injected through the stopper to reduce the medium. Reduction was confirmed by color loss [pink to clear] of the resazurin in solution.

Samples were prepared inside an anaerobic chamber [95:5 [v/v] N2:H2]. The outermost layer of the whole-round core and both ends were cut off with a sterile ceramic knife to remove potentially contaminated material. A cut-off syringe was used to take 5 cm3 of mud from the center of each whole round. The sediment plug was transferred to a 20 mL crimp-top vial, 5 mL of sulfate-reducing medium was added, and the vial was sealed with a nontoxic blue butyl stopper and aluminum crimp cap. The vial headspace was then flushed with N2 gas to remove surplus hydrogen. Each sample was prepared in triplicate. In the radioisotope laboratory, the vials were injected with 10 µL of 35S radiolabeled Na2SO4 [3.7 MBq] and then vigorously shaken with a vortex mixer. Samples were incubated at the in situ temperature of 4°C, as determined by APCT-3 tool measurements. After 10 days of incubation, 5 mL of 20% [w/v] zinc acetate solution was injected into each vial to trap H2S gas produced during sulfate reduction. Vials were then thoroughly shaken with a vortex mixer. The vials were opened, and the sediment slurries were quantitatively transferred to 50 mL centrifuge tubes with three rinses of 5 mL 20% zinc acetate solution. The centrifuge tubes were shaken with a vortex mixer and then frozen immediately at −20°C to stop microbial activity. The samples were shipped to a shore-based laboratory for extraction and analysis following Kallmeyer et al. [2004]. Kill controls, sediment controls, medium controls, and drilling fluid controls were taken to test for contamination or abiogenic turnover of sulfur. A kill control was prepared for approximately every other sample by injecting 5 mL of 20% zinc acetate immediately after injection of the radiotracer to stop microbial activity. Sediment controls were incubated without radiotracer. The radiotracer was added after microbial activity was stopped to check for reactions postincubation. Medium controls [5 mL of sterile medium, no sediment] and drilling fluid controls [5 mL of drilling fluid, no sediment] were prepared and incubated with radiotracer added to check for reactions in the medium and in contaminating drilling fluids. Drilling fluid was also collected after core retrieval from the gap between the core and liner, and additional samples were taken directly from the drilling fluid tank.

10.5.7. Ammonium enrichment

Ammonium enrichment incubation experiments were set up during Expedition 393. About 35–40 cm3 of rocks from the interior of the whole-round core sample were crushed using a sterile Fisher Scientific CerCo Diamonite mortar and pestle. One basement sample and one sediment sample were collected from as close as possible to the sediment/basement interface. Serum vials [50 mL] were used for this experiment, with aerobic sterile filtered seawater [SW] as the basal media for all enrichments [MacLeod et al., 2017]. To initiate enrichments, ~9–12 g of crushed rock chips were transferred to serum vials and submerged in SW to a level equivalent to 40 mL total volume [rocks plus media]. These ammonium nutrient addition experiments were coupled with bio-orthogonal noncanonical amino acid tagging [BONCAT]. For these enrichments, L-homopropargylglycine [HPG] was added to the vial at a final concentration of 50 µM. After adding NH4Cl to a final concentration of 0.4 mM, the vials were sealed with butyl stoppers and allowed to incubate for ~6 months at 4°C. Five treatments were prepared for each selected sample:

• Crushed rocks in SW and 1.5 mM NH4Cl [no HPG];
• Crushed rocks in SW, 1.5 mM NH4Cl, and HPG;
• Crushed rocks in SW, 0.5 mM NH4Cl, and HPG;
• Crushed rocks in SW and HPG [no NH4Cl]; and
• Crushed rocks in SW only.

For each sample and each of these treatments, a killed control was set up using autoclaved rocks from the outer core. Once the incubation period is completed, further analysis will be performed in the shore-based laboratory at Texas A&M University. This involves Cu[i]-catalyzed click chemistry to be applied to the BONCAT samples following methods outlined by Hatzenpichler and colleagues [Hatzenpichler et al., 2014, 2016; Hatzenpichler and Orphan, 2015]. After click-staining, the stained cells will be sorted using fluorescence-activated cell sorting [Reichart et al., 2020] and the sorted cells will be prepared for sequencing.

10.5.8. Virus-induced microbial mortality and viral production experiments

For Expedition 393, we used the dilution technique developed for surface sediments [Dell'Anno et al., 2009] to set up experiments with the goal of determining virus-induced microbial mortality and viral production rates from lytic viruses. To compare anaerobic and aerobic conditions, one set of experiments [Site U1558] was performed in a Coy anaerobic chamber installed on the tween deck flushed with N2. The other experiments were performed in the KOACH bench under sterile aerobic conditions. Sediment samples [10 cm3] were subsampled with a cut-off syringe and then diluted with autoclaved seawater. Seawater used for sample dilution was collected either from surface water, using a field-rinsed bucket attached to a rope, or near the seafloor using the Niskin bottle attached to the subsea camera system frame. Experiments were set up in duplicate in 50 mL centrifuge tubes. Samples were incubated anaerobically inside the chamber [room temperature of ~20°C]. In duplicate, 1 mL samples were taken at t = 0, 6, 12, 24, and 48 h and 7 and 14 days in sterile cryotubes. Each sample was fixed with paraformaldehyde [final concentration 2%], incubated 10 min at 4°C, and frozen at −80°C to be further processed in the shore-based laboratory [Texas A&M University at Galveston [USA]]. Cell and viral counts will be performed using epifluorescence microscopy following Pan et al. [2019]. The remaining material from the incubations was shipped to the shore-based laboratory for total DNA extraction and metagenomic sequencing.

10.5.9. Prophage induction

For Expedition 393, we induced prophages to determine the extent of lysogeny in sediment. To compare anaerobic and aerobic conditions, one set of experiments [Site U1558] was performed in a Coy anaerobic chamber installed on the tween deck flushed with N2. The other experiments were performed in the KOACH bench under sterile aerobic conditions. Samples [10 cm3] were diluted 1:1 [v/v] in autoclaved seawater supplemented with Mitomycin C [1 µg/mL final concentration in 0.02 µm prefiltered seawater]. Experiments were set up in duplicate in 50 mL Falcon tubes. In duplicate, 1 mL samples were taken at t = 0, 6, 12, 24, and 48 h and 7 and 14 days in sterile cryotubes. Each sample was fixed with paraformaldehyde [final concentration 2%], incubated 10 min at 4°C, and frozen at −80°C to be further processed in the shore-based laboratory [Texas A&M University at Galveston]. Cell and viral counts will be performed using epifluorescence microscopy following Pan et al. [2019]. The remaining material from the incubations were shipped to the shore laboratory for total DNA extraction and metagenomic sequencing.

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