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This chapter provides an overview of the procedures and methods employed for coring operations and in the shipboard laboratories of the R/V JOIDES Resolution during International Ocean Discovery Program (IODP) Expedition 397. The laboratory information applies only to shipboard work described in the Expedition Report section of the Expedition 397 Proceedings of the International Ocean Discovery Program volume that includes the shipboard sample registry, imaging and analytical instruments, core description tools, and the Laboratory Information Management System (LIMS) database. The shipboard workflow followed standard IODP procedures (as previously described by, e.g., Huber et al., 2019; Winckler et al., 2021; Planke et al., 2023), with revisions and refinements as described in this chapter. Methods used by investigators for shore-based analyses of Expedition 397 data will be documented in separate publications. All shipboard scientists contributed to this volume with the following primary responsibilities (authors are listed in alphabetical order; see Expedition 397 scientists for contact information): Summary chapter: Expedition 397 Scientists Methods and site chapters: Background and objectives: F. Abrantes, D. Hodell Operations: C.A. Alvarez Zarikian, K. Grigar Lithostratigraphy: H.L. Brooks, J.M. Link, J. McManus, C. Pallone, X. Pang, E. Salgueiro, V. dos Santos Rocha, J. Yu Biostratigraphy: C.A. Alvarez Zarikian, W. Clark, J.-A. Flores, M. Peral, K. Verma Paleomagnetism: L. Dauchy-Tric, C. Xuan Geochemistry: S. Hines, B. Mitsunaga, L. Nana Yobo, J. Wu Physical properties and downhole measurements: H.-H.M. Huang, H. Ikeda, J. Kuroda, S. Sanchez Stratigraphic correlation: T. Herbert, H.-H.M. Huang, S. Kaboth-Bahr This introductory section provides an overview of drilling and coring operations, core handling, curatorial conventions, depth scale terminology, and the sequence of shipboard analyses. Subsequent sections of this chapter document specific laboratory instruments and methods in detail. 

During International Ocean Discovery Program Expedition 397, we recovered a total of 6176.7 m of core (104.2% recovery) at four sites (U1586, U1587, U1385, and U1588) from the Promontório dos Príncipes de Avis, a plateau located on the Portuguese continental slope that is elevated above the Tagus Abyssal Plain and isolated from the influence of turbidites. The drill sites are arranged along a bathymetric transect (4692, 3479, 2591, and 1339 meters below sea level [mbsl], respectively) to intersect each of the major subsurface water masses of the eastern North Atlantic. Multiple holes were drilled at each site to ensure complete spliced composite sections, which will be further refined postcruise by a campaign of X-ray fluorescence core scanning. At Site U1586 (4692 mbsl), the deepest and farthest from shore, a 350 m sequence was recovered in four holes that extend as far back as the middle Miocene (14 Ma), which is nearly twice as old as initially predicted from seismic stratigraphy. Sedimentation rates are lower (averaging 5 cm/ky in the Quaternary) at Site U1586 than other Expedition 397 sites, and a few slumped intervals were encountered in the stratigraphic sequence. Despite these limitations, Site U1586 anchors the deep end-member of the bathymetric transect and provides an important reference section to study deepwater circulation, ventilation and carbon storage in the deep eastern North Atlantic. At Site U1587 (3479 mbsl), the second deepest site along the depth transect, we recovered a 567 m sequence of late Miocene to Holocene sediments that accumulated at rates between 6.5 and 11 cm/ky. The high sedimentation rates and long continuous record at this site will permit climate reconstruction at high temporal resolution (e.g., millennial) for the past 7.8 My. The Messinian Stage (7.25–5.33 Ma) was recovered, which provides a valuable opportunity to study the Messinian Salinity Crisis in an open marine setting adjacent to the Mediterranean. Site U1385 (Shackleton site) was a reoccupation of a position previously drilled during Integrated Ocean Drilling Program Expedition 339. Expedition 339 Site U1385 has yielded a remarkable record of millennial-scale climate change for the past 1.45 My (Marine Isotope Stage 47). During Expedition 397, we deepened the site from 156 to 400 meters below seafloor, extending the record to near the base of the Pliocene (5.3 Ma). Sedimentation rates remained high, averaging between 9 and 11 cm/ky throughout the sequence. The newly recovered cores at Expedition 397 Site U1385 will permit the study of millennial climate variability through the entire Quaternary and Pliocene, prior to the intensification of Northern Hemisphere glaciation. Site U1588 is the shallowest, closest to shore, and youngest site drilled during Expedition 397 and is also the one with the highest sedimentation rate (20 cm/ky). The base of the 412.5 m sequence is 2.2 Ma, providing an expanded Pleistocene sequence of sediment deposited under the influence of the lower core of the Mediterranean Outflow Water (MOW). Together with other Expedition 339 sites, Site U1588 will be important for determining how the depth and intensity of the MOW has varied on orbital and millennial timescales. In addition, it also provides a marine reference section for studying Quaternary climate variability at very high temporal resolution (millennial to submillennial). A highlight of the expedition is that sediment at all sites shows very strong cyclicity in bulk sediment properties (color, magnetic susceptibility, and natural gamma radiation). Particularly remarkable are the precession cycles of the Pliocene that can be correlated peak-for-peak among sites. These cyclic variations will be used to derive an orbitally tuned timescale for Expedition 397 sites and correlate them into classic Mediterranean cyclostratigraphy. The cores recovered during Expedition 397 will form the basis of collaborative postcruise research to produce benchmark paleoclimate records for the late Miocene through Quaternary using the widest range of proxy measurements. It will take many years to complete these analyses, but the records will lead to major advances in our understanding of millennial and orbital climate changes and their underlying causes and evolving contextuality. Outreach during Expedition 397 was highly productive, reaching a record number of students and the general public across the world through several diverse platforms, including live ship-to-shore events, webinars, social media, videos, radio pieces, blog posts, and in-person activities. 

Site U1587 is the second farthest from shore drilled during Expedition 397 and located at a water depth of 3479 meters below sea level (mbsl) (Figures F1, F2, F3). It is the second deepest site along the bathymetric transect and is bathed today by a mixture of ~75% North Atlantic Deep Water (NADW) and 25% Lower Deep Water (LDW) sourced from the Southern Ocean (Figure F4) (Jenkins et al., 2015). The mixing ratio of these water masses and their vertical position in the water column has changed in the past, which has implications for ventilation and carbon storage in the deep Atlantic Ocean. The location of Site U1587 was motivated by the clear expression of millennial climate variability in proxy records of oxygen isotopes and sea-surface temperature in nearby Piston Core MD95-2042 (Shackleton et al., 2000, 2004; Bard et al., 2000; Pailler and Bard, 2002; Davtian and Bard, 2023). Isotopic, organic biomarker, and pollen results from this core demonstrated the potential of correlating Iberian margin sediments with ice cores from Greenland and Antarctica and with European terrestrial sequences (e.g., Sánchez-Goñi et al., 2000; Margari et al., 2010, 2014, 2020). The sediment record from Site U1587 provides the opportunity to develop sediment proxy records for the Greenland and Antarctic ice cores to the base of the Quaternary and beyond. The piston core (JC089-04-2P) recovered near Site U1587 is 10.7 m long and has a sedimentation rate of 17 cm/ky (Figure F5). Ca/Ti and Zr/Sr show strong evidence of millennial variability during the last glacial cycle. The objective for Site U1587 is to study such variability for older glacial cycles throughout the Quaternary. Site U1587 is located at the intersection of Seismic Lines JC089-6 and JC089-7 (Figure F6). Although mass transport deposits or disturbed intervals are developed nearby, the continuity of reflections is good at Site U1587 (Figures F7, F8). The Upper Miocene to Quaternary sequence at Site U1587 is expanded relative to Site U1586 and is more than 500 m thick. Sedimentation rates are estimated to average ~10 cm/ky at Site U1587, or about twice that of Site U1586. We had permission from the Environmental Protection and Safety Panel (EPSP) to drill to 500 meters below seafloor (mbsf), but we requested and were granted permission to drill an additional 50 m to extend the record well into the late Miocene. Site U1587 provides an expanded sequence of late Miocene to Quaternary sediments with which to address the following objectives: Document how millennial climate variability evolved during the glacial cycles of the Quaternary and Pliocene as boundary conditions changed with the progressive intensification of Northern Hemisphere glaciation (NHG). Reconstruct the history of changing local dominance of northern-sourced versus southern-sourced deep water, as well as ventilation and carbon storage in the deep Atlantic Ocean. Determine interhemispheric phase relationships (leads/lags) by comparing the timing of proxy variables that monitor surface (Greenland) and deepwater (Antarctic) components of the climate system. Investigate climate during past interglacial periods, including the warm Pliocene period prior to the intensification of NHG. Link terrestrial, marine, and ice core records by analyzing pollen and terrestrial biomarkers that are delivered to the deep-sea environment of the Iberian margin. Recover a complete record of the time leading up to, during, and following the Messinian Salinity Crisis, which complements objectives of International Ocean Discovery Program (IODP) Expedition 401 (Flecker et al., 2023) and will permit evaluation of the causes and consequences of this remarkable event in Earth's history. Develop an orbitally-tuned age model for Site U1587 by correlating physical properties to eccentricity-modulated precession and tying them into the record of Mediterranean cyclostratigraphy. 

Site U1586 is the deepest (4692 meters below sea level [mbsl]) and farthest site from shore (170 km) drilled during Expedition 397 (Figures F1, F2, F3). It is located near the toe of the Promontório dos Príncipes de Avis at Common Midpoint (CMP) 1330 on Cruise JC89 Seismic Line 2 near the intersection of Cruise JC089 Line 3 (Figures F4, F5, F6). The continental slope environment is prone to failure and mass transport deposits (MTDs), and large disturbances are recognizable features on seismic profiles. For example, Site U1586 is between two MTDs or disturbed intervals at about 6.3 and 6.5 s two-way traveltime (TWT) on Cruise JC089 Seismic Line 2 near CMPs 1170–1250 and around CMP 1350 (Figure F5). Site U1586 is located where there is good continuity of reflectors to avoid these MTDs, but disturbances may still occur on a shorter length scale than the resolution of the seismic profiles. The target drilling depth of 350 meters below seafloor (mbsf) corresponds to the top of a package of chaotic high-amplitude reflections at 6.6 s TWT that was initially estimated to be late Miocene (~7 Ma) but was later determined biostratigraphically to be middle Miocene (~14 Ma) on the basis of shipboard micropaleontological analyses. The primary scientific objective of Site U1586 was to recover a deep distal record from a water depth of ~4690 mbsl. The sediment thickness thins toward the toe of the Promontório dos Príncipes de Avis owing to lower sedimentation rates with increased distance from shore. Interpretation of the seismic profiles suggests the sequence spans the late Miocene to Quaternary with an average sedimentation rate of 5 cm/ky. Recovery of late Miocene sediment at this site will complement sequences to be drilled during International Ocean Discovery Program (IODP) Expedition 401 to study the exchange between the Mediterranean and Atlantic for the period before, during, and after the Messinian Salinity Crisis (5.96–5.33 Ma) (Flecker et al., 2023). The sediments will also provide a history of surface and deepwater conditions through the Pliocene, including the mid-Pliocene warm period, when atmospheric CO2 was similar to today (400 ppm). Sediments recovered at Site U1586 will also be useful for studying how surface and deep oceanographic conditions responded to the intensification of Northern Hemisphere glaciation in the late Pliocene (~2.9 Ma). Site U1586 is under the influence of Lower Deep Water (LDW), which consists of Antarctic Bottom Water whose properties have been modified significantly from its origin in the high-latitude South Atlantic (Figure F7). This site's great depth may result in carbonate microfossil dissolution, although a 7.45 m piston core (JC089-5-3P) and 4.68 m kasten core (JC089-5-3K) recovered at the same location show continuous preservation of foraminifers during the last glacial stage and Holocene. Results from shipboard analyses during Expedition 397 further show that carbonate preservation and abundance of calcareous microfossils extends back to the Miocene (see Biostratigraphy). Sedimentation rates in the piston core average 11 cm/ky. The Ca/Ti and Zr/Sr measured using core scanning X-ray fluorescence (XRF) show distinct millennial events (Channell et al., 2018), with particularly notable peaks in Zr/Sr marking each of the Heinrich stadials of the last glacial period (Figure F8). Study of Site U1586 cores will permit the reconstruction of changes in ventilation and carbon storage in the deepest Atlantic on glacial–interglacial and millennial timescales with potential implications for atmospheric CO2 changes. Preservation of terrestrial biomarkers and pollen will permit reconstruction of vegetation changes in Europe. Lastly, it should be possible to correlate physical properties at Site U1586 into the Mediterranean cyclostratigraphy, thereby permitting regional climate change to be placed into a global context. 

Site U1588 lies on the broad, gently inclined middle-slope region of the Promontório dos Príncipes de Avis (PPA) on the southwestern Iberian margin (Figures F1, F2, F3, F4). It is the shallowest (1339 meters below sea level [mbsl]) and the closest site to the coast drilled during Expedition 397. Seismic data indicate the location is part of an extensive plastered sediment drift deposit formed under the influence of Mediterranean Outflow Water (MOW) that extends from the Gulf of Cádiz along the Portuguese margin (Hernández-Molina et al., 2003, 2006; Llave et al., 2006). Site U1588 is positioned on Seismic Line TGS-NOPEC PD00-613 (Figures F5, F6) about 8 km northeast of the intersection with Seismic Line TGS-NOPEC PD00-510 (Figure F7), where the distal part of the contourite depositional system occurs as a highly expanded sedimentary record (Hernández-Molina et al., 2014). The combination of Site U1588 (1339 mbsl) and the intermediate, MOW-influenced sites drilled during Expedition 339 (560–1073 mbsl) span the full depth range of the MOW. The record of Site U1588 will be compared with the deeper sites of Expedition 397 (2591–4692 mbsl), which are removed from contourite input and are under the influence of Northeast Atlantic Deep Water (NEADW) and Lower Deep Water (LDW) (Figure F4). Expedition 339 and 397 sites will constitute a bathymetric transect from 560 to 4691 mbsl to be used for paleoconductivity-temperature-depth (paleo-CTD) studies. The record at Site U1588 is expected to be similar to that of Integrated Ocean Drilling Program Site U1391, which was drilled 70 km south–southeast of Site U1588 at a water depth of 1085 mbsl (Figure F2). Three holes were cored and drilled to a total depth of 672 mbsf, spanning the middle Pliocene to Holocene with sedimentation rates of 13–17 cm/ky (Expedition 339 Scientists, 2013). We expected similarly high sedimentation rates at Site U1588. The high accumulation rates associated with contourite deposition provide an expanded sedimentary record to reconstruct millennial climate variability (MCV) with a resolution of a hundred years. In addition, the shallow depth of Site U1588 compared to other Expedition 397 sites is expected to yield excellent preservation of carbonate microfossils. The primary objective of Site U1588 was to drill to 500 mbsf and recover an expanded Pliocene–Pleistocene sedimentary succession formed under the influence of lower MOW (Hernández-Molina et al., 2014). The sediments of Site U1588 and those collected during Expedition 339 provide valuable material for studying how the depth and intensity of the MOW has varied on orbital and millennial timescales. Site U1588 will also provide a marine reference section for studying Quaternary climate variability at high stratigraphic resolution. Surface temperature proxies of Site U1588 will document MCV well beyond the base of the polar ice core. Because Site U1588 is closest to the coast, we expect preservation of terrestrial pollen and biomarkers that will allow linkage of the continental and marine records. Site U1588 should also preserve an MCV record of coastal upwelling along the Portuguese margin.