Properties of seawater and particulate matter from a WETLabs ALFA hyperspectral laser spectrofluorometer mounted on the continuous surface water sampling system during the Tara Oceans expedition 2009-2013

The Tara Oceans Expedition (2009-2013) sampled the world oceans on board a 36 m long schooner, collecting environmental data and organisms from viruses to planktonic metazoans for later analyses using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data set provides continuous measurements made with an Aquatic Laser Fluorescence Analyzer (ALFA) (Chekalyuk et al., 2014), connected in-line to the TARA flow through system during 2013. The ALFA instrument provides dual-wavelength excitation (405 and 514 nm) of laser-stimulated emission (LSE) for spectral and temporal analysis. It offers in vivo fluorescence assessments of phytoplankton pigments, biomass, photosynthetic yield (Fv/Fm), phycobiliprotein (PBP)-containing phytoplankton groups, and chromophoric dissolved organic matter (CDOM) (Chekalyuk and Hafez, 2008; 2013A). Spectral deconvolution (SDC) is used to assess the overlapped spectral bands of aquatic fluorescence constituents and water Raman scattering (R). The Fv/Fm measurements are spectrally corrected for non-chlorophyll fluorescence background produced by CDOM and other constituents (Chekalyuk and Hafez, 2008). The sensor was cleaned weakly following the manufacturer recommended protocol.

Properties of seawater (partial pressure of carbon dioxide (pCO2)) from a ProOceanus CO2-Pro sensor mounted on the continuous surface water sampling system during the Tara Oceans expedition 2009-2013

The Tara Oceans Expedition (2009-2013) sampled the world oceans on board a 36 m long schooner, collecting environmental data and organisms from viruses to planktonic metazoans for later analyses using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data set provides continuous measurements of partial pressure of carbon dioxide (pCO2), using a ProOceanus CO2-Pro instrument mounted on the flowthrough system. This automatic sensor is fitted with an equilibrator made of gas permeable silicone membrane and an internal detection loop with a non-dispersive infrared detector of PPSystems SBA-4 CO2 analyzer. A zero-CO2 baseline is provided for the subsequent measurements circulating the internal gas through a CO2 absorption chamber containing soda lime or Ascarite. The frequency of this automatic zero point calibration was set to be 24 hours. All data recorded during zeroing processes were discarded with the 15-minute data after each calibration. The output of CO2-Pro is the mole fraction of CO2 in the measured water and the pCO2 is obtained using the measured total pressure of the internal wet gas. The fugacity of CO2 (fCO2) in the surface seawater, whose difference with the atmospheric CO2 fugacity is proportional to the air-sea CO2 fluxes, is obtained by correcting the pCO2 for non-ideal CO2 gas concentration according to Weiss (1974). The fCO2 computed using CO2-Pro measurements was corrected to the sea surface condition by considering the temperature effect on fCO2 (Takahashi et al., 1993). The surface seawater observations that were initially estimated with a 15 seconds frequency were averaged every 5-min cycle. The performance of CO2-Pro was adjusted by comparing the sensor outputs against the thermodynamic carbonate calculation of pCO2 using the carbonic system constants of Millero et al. (2006) from the determinations of total inorganic carbon (CT ) and total alkalinity (AT ) in discrete samples collected at sea surface. AT was determined using an automated open cell potentiometric titration (Haraldsson et al. 1997). CT was determined with an automated coulometric titration (Johnson et al. 1985; 1987), using the MIDSOMMA system (Mintrop, 2005). fCO2 data are flagged according to the WOCE guidelines following Pierrot et al. (2009) identifying recommended values and questionable measurements giving additional information about the reasons of the questionability.

Registry of all samples from the Tara Oceans Expedition (2009-2013)

The Tara Oceans Expedition (2009-2013) sampled the world oceans on board a 36 m long schooner, collecting environmental data and organisms from viruses to planktonic metazoans for later analyses using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. Data sets in this collection provide methodological and environmental context to all samples collected during the Tara Oceans Expedition (2009-2013).

Environmental context of all samples from the Tara Oceans Expedition (2009-2013), about depth specific features

The Tara Oceans Expedition (2009-2013) sampled the world oceans on board a 36 m long schooner, collecting environmental data and organisms from viruses to planktonic metazoans for later analyses using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data set provides environmental context to all samples from the Tara Oceans Expedition (2009-2013), including calculated averages of mesaurements made concurrently at the sampling location and depth, and calculated averages from climatologies (AMODIS, VGPM) and satellite products.

Environmental context of all samples from the Tara Oceans Expedition (2009-2013), about mesoscale features

The Tara Oceans Expedition (2009-2013) sampled the world oceans on board a 36 m long schooner, collecting environmental data and organisms from viruses to planktonic metazoans for later analyses using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data set provides environmental context to all samples from the Tara Oceans Expedition (2009-2013), about mesoscale features related to the sampling date, time and location. Includes calculated averages of mesaurements made concurrently at the sampling location and depth, and calculated averages from climatologies (AMODIS, VGPM) and satellite products.

(Appendix) Oxygen isotope record and carbonate mineralogy of the top part of ODP Hole 101-633A

Hole 633A was drilled in the southern part of Exuma Sound on the toe-of-slope of the southeastern part of Great Bahama Bank during ODP Leg 101. The top 55 m, collected as a suite of six approximately 9.5-m-long hydraulic piston cores, represents a Pliocene-Pleistocene sequence of periplatform carbonate ooze, a mixture of pelagic calcite (foraminifer and coccolith tests), some pelagic aragonite (pteropod tests), and bank-derived fine aragonite and magnesian calcite. A 1.6-m.y.-long hiatus was identified at 43.75 mbsf using calcareous nannofossil biostratigraphy and magnetostratigraphy. The 43.75-m-thick periplatform sequence above the hiatus is a complete late Pliocene-Quaternary record of the past 2.15 m.y. The d18O curve, primarily based on Globigerinoides sacculifera, clearly displays high-frequency/low-amplitude cycles during the early Pleistocene and low-frequency/high-amplitude cycles during the middle and late Pleistocene. Variations in aragonite content in the fine fraction of the periplatform ooze show a cyclic pattern throughout the Pleistocene, as previously observed in piston cores of the upper Pleistocene. These variations correlate well with the d18O record: high aragonite corresponds to light interglacial d18O values, and vice versa. Comparison of the d18O record and the aragonite curve helps to identify 23 interglacial and glacial oxygen-isotope stages, corresponding to 10.5 aragonite cycles (labeled A to K) commonly established during the middle and late Pleistocene (0.9 Ma-present). Strictly based on the aragonite curve, another 11 aragonite cycles, labeled L to V, were identified for the early Pleistocene (0.9 to 1.6 Ma). Mismatches between the d18O record and the aragonite curve occur mainly at some of the glacial-to-interglacial transitions, where aragonite increases usually lag behind d18O depletion. When one visually connects the minima on the Pleistocene aragonite curve, low-frequency (0.4 to 0.5 m.y.) supercycles seem to be superimposed on the high-frequency cycles. The timing of this supercycle roughly matches the timing of the Pleistocene carbonate preservation supercycles described in the Pacific, Indian, and Atlantic oceans. Mismatches between aragonite and d18O cycles are even more obvious for the late Pliocene (1.6 to 2.15 Ma). Irregular aragonite variations are observed for the late Pliocene, although after the onset of late Pleistocene-like glaciations in the North Atlantic Ocean 2.4 m.y. ago the d18O record has shown a mode of high-frequency/low-amplitude cycles. Initiation of climatically induced aragonite cycles occurs only at the Pliocene-Pleistocene transition, 1.6 m.y. ago. After that time, aragonite cycles are fully developed throughout the Quaternary. The 11-m-thick periplatform sequence below the hiatus represents a lower Pliocene interval between 3.75 and 4.45 Ma. The bottom half (4.25-4.45 Ma) has a fairly constant, high aragonite content (averaging 60%) and high sedimentation rates (28 m/m.y.) and corresponds to the end of the prolonged early Pliocene interglacial interval (4.1-5.0 Ma), established as a worldwide high sea-level stand. The second half (3.75-4.25 Ma), in which aragonite content decreases by successive steps, paralleled by a gradual 5180 enrichment in Globigerinoides sacculifera and low sedimentation rates (10 m/m.y), corresponds to the climatic deterioration established worldwide between 4.1 and 3.8 Ma, to a decrease of carbonate preservation observed in the equatorial Pacific Ocean, and to a global sea-level decline. Dolomite, a ubiquitous secondary component in the lower Pliocene, is interpreted as being authigenic and possibly related to diagenetic transformation of primary bank-derived fine magnesian calcite. Transformation of the primary mineralogical composition of the periplatform ooze was evidently minor, as the sediments have retained a detailed record of the Pliocene-Pleistocene climatic evolution. Clear evidence of diagenetic transformations in the periplatform ooze includes (1) the disappearance of magnesian calcite in the upper 20 m of Hole 633A, (2) the occurrence of calcite overgrowths on foraminiferal tests and microclasts at intermittent chalky core levels, and (3) the ubiquitous presence of authigenic dolomite in the lower Pliocene.

List of size fractionated eukaryotic plankton community samples and associated metadata (Database W1)

The present data set provides an Excel file in a zip archive. The file lists 334 samples of size fractionated eukaryotic plankton community with a suite of associated metadata (Database W1). Note that if most samples represented the piconano- (0.8-5 µm, 73 samples), nano- (5-20 µm, 74 samples), micro- (20-180 µm, 70 samples), and meso- (180-2000 µm, 76 samples) planktonic size fractions, some represented different organismal size-fractions: 0.2-3 µm (1 sample), 0.8-20 µm (6 samples), 0.8 µm - infinity (33 samples), and 3-20 µm (1 sample). The table contains the following fields: a unique sample sequence identifier; the sampling station identifier; the Tara Oceans sample identifier (TARA_xxxxxxxxxx); an INDSC accession number allowing to retrieve raw sequence data for the major nucleotide databases (short read archives at EBI, NCBI or DDBJ); the depth of sampling (Subsurface - SUR or Deep Chlorophyll Maximum - DCM); the targeted size range; the sequences template (either DNA or WGA/DNA if DNA extracted from the filters was Whole Genome Amplified); the latitude of the sampling event (decimal degrees); the longitude of the sampling event (decimal degrees); the time and date of the sampling event; the device used to collect the sample; the logsheet event corresponding to the sampling event ; the volume of water sampled (liters). Then follows information on the cleaning bioinformatics pipeline shown on Figure W2 of the supplementary litterature publication: the number of merged pairs present in the raw sequence file; the number of those sequences matching both primers; the number of sequences after quality-check filtering; the number of sequences after chimera removal; and finally the number of sequences after selecting only barcodes present in at least three copies in total and in at least two samples. Finally, are given for each sequence sample: the number of distinct sequences (metabarcodes); the number of OTUs; the average number of barcode per OTU; the Shannon diversity index based on barcodes for each sample (URL of W4 dataset in PANGAEA); and the Shannon diversity index based on each OTU (URL of W5 dataset in PANGAEA).

Total V9 rDNA information organized at the metabarcode level (Database W4)

The present data set provides a tab separated text file compressed in a zip archive. The file includes metadata for each TaraOceans V9 rDNA metabarcode including the following fields: md5sum = unique identifier; lineage = taxonomic path associated to the metabarcode; pid = % identity to the closest reference barcode from V9_PR2; sequence = nucleotide sequence of the metabarcode; refs = identity of the best hit reference sequence(s); TARA_xxx = number of occurrences of this barcode in each of the 334 samples; totab = total abundance of the barcode ; cid = identifier of the OTU to which the barcode belongs; and taxogroup = high-taxonomic level assignation of this barcode. The file also includes three categories of functional annotations: (1) Chloroplast: yes, presence of permanent chloroplast; no, absence of permanent chloroplast ; NA, undetermined. (2) Symbiont (small partner): parasite, the species is a parasite; commensal, the species is a commensal; mutualist, the species is a mutualist symbiont, most often a microalgal taxon involved in photosymbiosis; no the species is not involved in a symbiosis as small partner; NA, undetermined. (3) Symbiont (host): photo, the host species relies on a mutualistic microalgal photosymbiont to survive (obligatory photosymbiosis); photo_falc, same as photo, but facultative relationship; photo_klep, the host species maintains chloroplasts from microalgal prey(s) to survive; photo_klep_falc, same as photo_klep, but facultative; Nfix, the host species must interact with a mutualistic symbiont providing N2 fixation to survive; Nfix_falc, same as Nfix, but facultative; no, the species is not involved in any mutualistic symbioses; NA, undetermined. For example, the collodarian/Brandtodinium symbiosis is annotated: Chloroplast, "no"; Symbiont (small), "no"; Symbiont (host), "photo", for the collodarian host; and: Chloroplast, "yes"; Symbiont (small), "mutualist"; Symbiont (host), "no", for the dinoflagellate microalgal endosymbiont.chloroplast = "yes", "no" or "NA"; symbiont.small = "parasite", "commensal", "mutualist", "no" or "NA"; symbiont.host = "photo", "photo_falc", "photo_klep", "Nfix", no or NA; benef = "Nfix", "no" or "NA"; trophism = Metazoa , heterotroph , NA , photosymbiosis , phototroph according to the previous fields.

Strontium and boron geochemistry of ODP sites at Hydrate Ridge, eastern Pacific Ocean

ODP Leg 204, which drilled at Hydrate Ridge, provides unique insights into the fluid regime of an accretionary complex and delineates specific sub-seafloor pathways for fluid transport. Compaction and dewatering due to smectite-illite transition increase with distance from the toe of the accretionary prism and bring up fluids from deep within the accretionary complex to sampled depths (<= 600 mbsf). These fluids have a distinctly non-radiogenic strontium isotope signature indicating reaction with the oceanic basement. Boron isotopes are also consistent with a deep fluid source that has been modified by desorption of heavy boron as clay minerals change from smectite to illite. One of three major horizons serves as conduit for the transport of mainly fluid. Our results enable us to evaluate fluid migration pathways that play important roles on massive gas hydrate accumulations and seepage of methane-rich fluids on southern Hydrate Ridge.