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Total alkalinity (AT) and dissolved inorganic carbon (CT) in the oceans are important properties with respect to understanding the ocean carbon cycle and its link to global change (ocean carbon sinks and sources, ocean acidification) and ultimately finding carbon-based solutions or mitigation procedures (marine carbon removal). We present a database of more than 44 400 AT and CT observations along with basic ancillary data (spatiotemporal location, depth, temperature and salinity) from various ocean regions obtained, mainly in the framework of French projects, since 1993. This includes both surface and water column data acquired in the open ocean, coastal zones and in the Mediterranean Sea and either from time series or dedicated one-off cruises. Most AT and CT data in this synthesis were measured from discrete samples using the same closed-cell potentiometric titration calibrated with Certified Reference Material, with an overall accuracy of ±4 µmol kg−1 for both AT and CT. The data are provided in two separate datasets – for the Global Ocean and the Mediterranean Sea (https://doi.org/10.17882/95414, Metzl et al., 2023), respectively – that offer a direct use for regional or global purposes, e.g., AT–salinity relationships, long-term CT estimates, and constraint and validation of diagnostic CT and AT reconstructed fields or ocean carbon and coupled climate–carbon models simulations as well as data derived from Biogeochemical-Argo (BGC-Argo) floats. When associated with other properties, these data can also be used to calculate pH, the fugacity of CO2 (fCO2) and other carbon system properties to derive ocean acidification rates or air–sea CO2 fluxes.

Coral reefs are increasingly in jeopardy due to global changes affecting both reef accretion and bioerosion processes. Bioerosion processes dynamics in dead reef carbonates under various environmental conditions are relatively well understood but only over a short-term limiting projections of coral reef evolution by 2100. It is thus essential to monitor and understand bioerosion processes over the long term. Here we studied the assemblage of traces of microborers in a coral core of a massive Diploastrea sp. from Mayotte, allowing us to explore the variability of its specific composition, distribution, and abundance between 1964 and 2018. Observations of microborer traces were realized under a scanning electron microscope (SEM). The area of coral skeleton sections colonized by microborers (a proxy of their abundance) was estimated based on an innovative machine learning approach. This new method with 93% accuracy allowed analyzing rapidly more than a thousand SEM images. Our results showed an important shift in the trace assemblage composition that occurred in 1985, and a loss of 90% of microborer traces over the last five decades. Our data also showed a strong positive correlation between microborer trace abundance and the coral bulk density, this latter being particularly affected by the interannual variation of temperature and cumulative insolation. Although various combined environmental factors certainly had direct and/or indirect effects on microboring species before and after the breakpoint in 1985, we suggest that rising sea surface temperature, rainfall, and the loss of light over time were the main factors driving the observed trace assemblage change and decline in microborer abundance. In addition, the interannual variability of sea surface temperature and instantaneous maximum wind speed appeared to influence greatly the occurrence of green bands. We thus stress the importance to study more coral cores to confirm the decadal trends observed in the Diploastrea sp. from Mayotte and to better identify the main factors influencing microboring communities, as the decrease of their abundance in living massive stress tolerant corals may have important consequences on their resilience.

Lithogenic elements such as aluminum (Al), iron (Fe), rare earth elements (REEs), thorium (232Th and 230Th, given as Th) and protactinium (Pa) are often assumed to be insoluble. In this study, their dissolution from Saharan dust reaching Mediterranean seawater was studied through tank experiments over 3 to 4 d under controlled conditions including controls without dust addition as well as dust seeding under present and future climate conditions (+3 ∘C and −0.3 pH). Unfiltered surface seawater from three oligotrophic regions (Tyrrhenian Sea, Ionian Sea and Algerian Basin) were used. The maximum dissolution was low for all seeding experiments: less than 0.3 % for Fe, 1 % for 232Th and Al, about 2 %–5 % for REEs and less than 6 % for Pa. Different behaviors were observed: dissolved Al increased until the end of the experiments, Fe did not dissolve significantly, and Th and light REEs were scavenged back on particles after a fast initial release. The constant 230Th/232Th ratio during the scavenging phase suggests that there is little or no further dissolution after the initial Th release. Quite unexpectedly, comparison of present and future conditions indicates that changes in temperature and/or pH influence the release of Th and REEs in seawater, leading to lower Th release and a higher light REE release under increased greenhouse conditions.

Abstract Excess 231Pa and 230Th (231Paxs and 230Thxs) can be used to reconstruct past oceanic sedimentation (230Th‐normalized flux) and circulation changes ((231Pa/230Th)xs,0, hereafter Pa/Th). These quantities are determined by computing the detrital and authigenic contributions from bulk sediment measurement. The method relies on the use of a chosen constant value of the detrital (238U/232Th) activity ratio (hereafter (U/Th)det). In this study, we have extracted the detrital fraction of the sediments from North Atlantic deep‐sea core SU90‐08 (43°03′1N, 30°02′5W, 3,080m) and determined its (U/Th)det value over the last 40 ky. We find that (U/Th)det varied significantly through time with a minimum value of 0.4 during the Holocene and a maximum value of 0.7 during the Last Glacial Maximum (LGM). The sensitivity of sedimentary 230Th‐normalized flux and Pa/Th is tested for our study site and for other North Atlantic sites. We show that the sensitivity is highly dependent on the core location and its terrigenous material supply. The 230Th‐normalized flux and Pa/Th signals are very robust in cores with low detrital contributions, whereas they are very sensitive to (U/Th)det changes in cores with higher detrital contribution. In the latter case, changes in 230Th‐normalized flux and Pa/Th due to the choice of a constant (U/Th)det can largely exceed the uncertainty on the 230Th‐normalized flux and Pa/Th, inducing potential biases in the amplitude and temporal variability of reconstructed sedimentation and ocean circulation changes.

We present the neodymium isotopic composition (εNd) of mixed planktonic foraminifera species from a sediment core collected at 622 m water depth in the Balearic Sea, as well as εNd of scleractinian cold-water corals (CWC; Madrepora oculata, Lophelia pertusa) retrieved between 280 and 442 m water depth in the Alboran Sea and at 414 m depth in the southern Sardinian continental margin. The aim is to constrain hydrological variations at intermediate depths in the western Mediterranean Sea during the last 20 kyr. Planktonic (Globigerina bulloides) and benthic (Cibicidoides pachyderma) foraminifera from the Balearic Sea were also analyzed for stable oxygen (δ18O) and carbon (δ13C) isotopes. The foraminiferal and coral εNd values from the Balearic and Alboran seas are comparable over the last ∼ 13 kyr, with mean values of −8.94 ± 0.26 (1σ; n = 24) and −8.91 ± 0.18 (1σ; n = 25), respectively. Before 13 ka BP, the foraminiferal εNd values are slightly lower (−9.28 ± 0.15) and tend to reflect higher mixing between intermediate and deep waters, which are characterized by more unradiogenic εNd values. The slight εNd increase after 13 ka BP is associated with a decoupling in the benthic foraminiferal δ13C composition between intermediate and deeper depths, which started at ∼ 16 ka BP. This suggests an earlier stratification of the water masses and a subsequent reduced contribution of unradiogenic εNd from deep waters. The CWC from the Sardinia Channel show a much larger scatter of εNd values, from −8.66 ± 0.30 to −5.99 ± 0.50, and a lower average (−7.31 ± 0.73; n = 19) compared to the CWC and foraminifera from the Alboran and Balearic seas, indicative of intermediate waters sourced from the Levantine basin. At the time of sapropel S1 deposition (10.2 to 6.4 ka), the εNd values of the Sardinian CWC become more unradiogenic (−8.38 ± 0.47; n = 3 at ∼ 8.7 ka BP), suggesting a significant contribution of intermediate waters originated from the western basin. We propose that western Mediterranean intermediate waters replaced the Levantine Intermediate Water (LIW), and thus there was a strong reduction of the LIW during the mid-sapropel ( ∼ 8.7 ka BP). This observation supports a notable change of Mediterranean circulation pattern centered on sapropel S1 that needs further investigation to be confirmed.

The boron isotopic composition (δ11B) of marine carbonates (e.g. corals) is increasingly utilised as a proxy for paleo-pH, with the strong correlation between δ11B of marine calcifiers and seawater pH now well documented. However, the potential roles of other environmental parameters that may also influence both the boron isotopic composition and boron concentration into coral aragonite are poorly known. To overcome this, the tropical scleractinian coral Acropora sp. was cultured under 3 different temperatures (22, 25 and 28 °C) and two light conditions (200 and 400 μmol photon m−2 s−1). The δ11B indicates an increase in internal pH that is dependent on the light conditions. Changes in light intensities from 200 to 400 μmol photon m−2 s−1 seem to indicate an apparent decrease in pH at the site of calcification, contrary to what is expected in most models of light-enhanced calcification. Thus, variations in light conditions chosen to mimic average annual variations of the natural environments where Acropora sp. colonies can be found could bias pH reconstructions by about 0.05 units. For both light conditions, a significant impact of temperature on δ11B can be observed between 22 and 25 °C, corresponding to an increase of about 0.02 pH-units, while no further δ11B increase can be observed from 25 to 28 °C. This non-linear temperature effect complicates the determination of a correction factor. B / Ca ratios decrease with increasing light, consistent with the decrease in pH at the site of calcification under enhanced light intensities. When all the other parameters are constant, boron concentrations in Acropora sp. increase with increasing temperatures and increasing carbonate ion concentrations. These observations contradict previous studies where B / Ca in corals was found to vary inversely with temperature, suggesting that the controlling factors driving boron concentrations have not yet been adequately identified and might be influenced by other environmental variables and/or species-specific responses.

Here we show the use of the 210Pb-226Ra excess method to determine the growth rate of two corals from the world's largest known cold-water coral reef, Røst Reef, north of the Arctic circle off Norway. Colonies of each of the two species that build the reef, Lophelia pertusa and Madrepora oculata, were collected alive at 350 m depth using a submersible. Pb and Ra isotopes were measured along the major growth axis of both specimens using low level alpha and gamma spectrometry and trace element compositions were studied. 210Pb and 226Ra differ in the way they are incorporated into coral skeletons. Hence, to assess growth rates, we considered the exponential decrease of initially incorporated 210Pb, as well as the increase in 210Pb from the decay of 226Ra and contamination with 210Pb associated with Mn-Fe coatings that we were unable to remove completely from the oldest parts of the skeletons. 226Ra activity was similar in both coral species, so, assuming constant uptake of 210Pb through time, we used the 210Pb-226Ra chronology to calculate growth rates. The 45.5 cm long branch of M. oculata was 31 yr with an average linear growth rate of 14.4 ± 1.1 mm yr−1 (2.6 polyps per year). Despite cleaning, a correction for Mn-Fe oxide contamination was required for the oldest part of the colony; this correction corroborated our radiocarbon date of 40 yr and a mean growth rate of 2 polyps yr−1. This rate is similar to the one obtained in aquarium experiments under optimal growth conditions. For the 80 cm-long L. pertusa colony, metal-oxide contamination remained in both the middle and basal part of the coral skeleton despite cleaning, inhibiting similar age and growth rate estimates. The youngest part of the colony was free of metal oxides and this 15 cm section had an estimated a growth rate of 8 mm yr−1, with high uncertainty (~1 polyp every two to three years). We are less certain of this 210Pb growth rate estimate which is within the lowermost ranges of previous growth rate estimates. We show that 210Pb-226Ra dating can be successfully applied to determine the age and growth rate of framework-forming cold-water corals if Mn-Fe oxide deposits can be removed. Where metal oxides can be removed, large M. oculata and L. pertusa skeletons provide archives for studies of intermediate water masses with an up to annual time resolution and spanning over many decades.

The "δ11B-pH" technique was applied to modern and ancient corals Porites from the sub-equatorial Pacific areas (Tahiti and Marquesas) spanning a time interval from 0 to 20.720 calendar years to determine the amplitude of pH changes between the Last Glacial Period and the Holocene. Boron isotopes were measured by Multi-Collector – Inductively Coupled Plasma Mass Spectrometry (MC-ICPMS) with an external reproducibility of 0.25‰, allowing a precision of about ±0.03 pH-units for pH values between 8 and 8.3. The boron concentration [B] and isotopic composition of modern samples indicate that the temperature strongly controls the partition coefficient KD for different aragonite species. Modern coral δ11B values and the reconstructed sea surface pH values for different Pacific areas match the measured pH expressed on the seawater scale and confirm the calculation parameters that were previously determined by laboratory calibration exercises. Most ancient sea surface pH reconstructions near Marquesas are higher than modern values. These values range between 8.19 and 8.27 for the Holocene and reached 8.30 at the end of the last glacial period (20.7 kyr BP). At the end of the Younger Dryas (11.50±0.1 kyr BP), the central sub-equatorial Pacific experienced a dramatic drop of up to 0.2 pH-units from the average pH of 8.2 before and after this short event. Using the marine carbonate algorithms, we recalculated the aqueous pCO2 to be 440±25 ppmV at around 11.5 kyr BP for corals at Marquesas and ~500 ppmV near Tahiti where it was assumed that pCO2 in the atmosphere was 250 ppmV. Throughout the Holocene, the difference in pCO2 between the ocean and the atmosphere at Marquesas (ΔpCO2) indicates that the surface waters behave as a moderate CO2 sink or source (−53 to 20 ppmV) during El Niño-like conditions. By contrast, during the last glacial/interglacial transition, this area was a marked source of CO2 (21 to 92 ppmV) for the atmosphere, highlighting predominant La Niña-like conditions. Such conditions were particularly pronounced at the end of the Younger Dryas with a large amount of CO2 released with ΔpCO2 of +185±25 ppmV. This last finding provides further evidence of the marked changes in the surface water pH and temperature in the equatorial Pacific at the Younger Dryas-Holocene transition and the strong impact of oceanic dynamic on the atmospheric CO2 content.

With climate projections questioning the future survival of stony corals and their dominance as tropical reef builders, it is critical to understand the adaptive capacity of corals to ongoing climate change. Biological mediation of the carbonate chemistry of the coral calcifying fluid is a fundamental component for assessing the response of corals to global threats. The Tara Pacific expedition (2016-2018) provided an opportunity to investigate calcification patterns in extant corals throughout the Pacific Ocean. Cores from colonies of the massive Porites and Diploastrea genera were collected from different environments to assess calcification parameters of long-lived reef-building corals. At the basin scale of the Pacific Ocean, we show that both genera systematically up-regulate their calcifying fluid pH and dissolved inorganic carbon to achieve efficient skeletal precipitation. However, while Porites corals increase the aragonite saturation state of the calcifying fluid (Ω cf ) at higher temperatures to enhance their calcification capacity, Diploastrea show a steady homeostatic Ω cf across the Pacific temperature gradient. Thus, the extent to which Diploastrea responds to ocean warming and/or acidification is unclear, and it deserves further attention whether this is beneficial or detrimental to future survival of this coral genus., (© 2023. The Author(s).)

Tropical coral reefs are among the most affected ecosystems by climate change and face increasing loss in the coming decades. Effective conservation strategies that maximize ecosystem resilience must be informed by the accurate characterization of extant genetic diversity and population structure together with an understanding of the adaptive potential of keystone species. Here we analyzed samples from the Tara Pacific Expedition (2016-2018) that completed an 18,000 km longitudinal transect of the Pacific Ocean sampling three widespread corals-Pocillopora meandrina, Porites lobata, and Millepora cf. platyphylla-across 33 sites from 11 islands. Using deep metagenomic sequencing of 269 colonies in conjunction with morphological analyses and climate variability data, we can show that despite a targeted sampling the transect encompasses multiple cryptic species. These species exhibit disparate biogeographic patterns and, most importantly, distinct evolutionary patterns in identical environmental regimes. Our findings demonstrate on a basin scale that evolutionary trajectories are species-specific and can only in part be predicted from the environment. This highlights that conservation strategies must integrate multi-species investigations to discern the distinct genomic footprints shaped by selection as well as the genetic potential for adaptive change., (© 2023. The Author(s).)

Heat waves are causing declines in coral reefs globally. Coral thermal responses depend on multiple, interacting drivers, such as past thermal exposure, endosymbiont community composition, and host genotype. This makes the understanding of their relative roles in adaptive and/or plastic responses crucial for anticipating impacts of future warming. Here, we extracted DNA and RNA from 102 Pocillopora colonies collected from 32 sites on 11 islands across the Pacific Ocean to characterize host-photosymbiont fidelity and to investigate patterns of gene expression across a historical thermal gradient. We report high host-photosymbiont fidelity and show that coral and microalgal gene expression respond to different drivers. Differences in photosymbiotic association had only weak impacts on host gene expression, which was more strongly correlated with the historical thermal environment, whereas, photosymbiont gene expression was largely determined by microalgal lineage. Overall, our results reveal a three-tiered strategy of thermal acclimatization in Pocillopora underpinned by host-photosymbiont specificity, host transcriptomic plasticity, and differential photosymbiotic association under extreme warming., (© 2023. The Author(s).)

Coral reef science is a fast-growing field propelled by the need to better understand coral health and resilience to devise strategies to slow reef loss resulting from environmental stresses. Key to coral resilience are the symbiotic interactions established within a complex holobiont, i.e. the multipartite assemblages comprising the coral host organism, endosymbiotic dinoflagellates, bacteria, archaea, fungi, and viruses. Tara Pacific is an ambitious project built upon the experience of previous Tara Oceans expeditions, and leveraging state-of-the-art sequencing technologies and analyses to dissect the biodiversity and biocomplexity of the coral holobiont screened across most archipelagos spread throughout the entire Pacific Ocean. Here we detail the Tara Pacific workflow for multi-omics data generation, from sample handling to nucleotide sequence data generation and deposition. This unique multidimensional framework also includes a large amount of concomitant metadata collected side-by-side that provide new assessments of coral reef biodiversity including micro-biodiversity and shape future investigations of coral reef dynamics and their fate in the Anthropocene., (© 2023. The Author(s).)

Telomeres are environment-sensitive regulators of health and aging. Here,we present telomere DNA length analysis of two reef-building coral genera revealing that the long- and short-term water thermal regime is a key driver of between-colony variation across the Pacific Ocean. Notably, there are differences between the two studied genera. The telomere DNA lengths of the short-lived, more stress-sensitive Pocillopora spp. colonies were largely determined by seasonal temperature variation, whereas those of the long-lived, more stress-resistant Porites spp. colonies were insensitive to seasonal patterns, but rather influenced by past thermal anomalies. These results reveal marked differences in telomere DNA length regulation between two evolutionary distant coral genera exhibiting specific life-history traits. We propose that environmentally regulated mechanisms of telomere maintenance are linked to organismal performances, a matter of paramount importance considering the effects of climate change on health., (© 2023. The Author(s).)

The Tara Pacific expedition (2016-2018) sampled coral ecosystems around 32 islands in the Pacific Ocean and the ocean surface waters at 249 locations, resulting in the collection of nearly 58 000 samples. The expedition was designed to systematically study warm-water coral reefs and included the collection of corals, fish, plankton, and seawater samples for advanced biogeochemical, molecular, and imaging analysis. Here we provide a complete description of the sampling methodology, and we explain how to explore and access the different datasets generated by the expedition. Environmental context data were obtained from taxonomic registries, gazetteers, almanacs, climatologies, operational biogeochemical models, and satellite observations. The quality of the different environmental measures has been validated not only by various quality control steps, but also through a global analysis allowing the comparison with known environmental large-scale structures. Such publicly released datasets open the perspective to address a wide range of scientific questions., (© 2022. The Author(s).)

Endogenous viral elements (EVEs) offer insight into the evolutionary histories and hosts of contemporary viruses. This study leveraged DNA metagenomics and genomics to detect and infer the host of a non-retroviral dinoflagellate-infecting +ssRNA virus (dinoRNAV) common in coral reefs. As part of the Tara Pacific Expedition, this study surveyed 269 newly sequenced cnidarians and their resident symbiotic dinoflagellates (Symbiodiniaceae), associated metabarcodes, and publicly available metagenomes, revealing 178 dinoRNAV EVEs, predominantly among hydrocoral-dinoflagellate metagenomes. Putative associations between Symbiodiniaceae and dinoRNAV EVEs were corroborated by the characterization of dinoRNAV-like sequences in 17 of 18 scaffold-scale and one chromosome-scale dinoflagellate genome assembly, flanked by characteristically cellular sequences and in proximity to retroelements, suggesting potential mechanisms of integration. EVEs were not detected in dinoflagellate-free (aposymbiotic) cnidarian genome assemblies, including stony corals, hydrocorals, jellyfish, or seawater. The pervasive nature of dinoRNAV EVEs within dinoflagellate genomes (especially Symbiodinium), as well as their inconsistent within-genome distribution and fragmented nature, suggest ancestral or recurrent integration of this virus with variable conservation. Broadly, these findings illustrate how +ssRNA viruses may obscure their genomes as members of nested symbioses, with implications for host evolution, exaptation, and immunity in the context of reef health and disease., (© 2023. The Author(s).)

Background: Over the last decade, several coral genomes have been sequenced allowing a better understanding of these symbiotic organisms threatened by climate change. Scleractinian corals are reef builders and are central to coral reef ecosystems, providing habitat to a great diversity of species., Results: In the frame of the Tara Pacific expedition, we assemble two coral genomes, Porites lobata and Pocillopora cf. effusa, with vastly improved contiguity that allows us to study the functional organization of these genomes. We annotate their gene catalog and report a relatively higher gene number than that found in other public coral genome sequences, 43,000 and 32,000 genes, respectively. This finding is explained by a high number of tandemly duplicated genes, accounting for almost a third of the predicted genes. We show that these duplicated genes originate from multiple and distinct duplication events throughout the coral lineage. They contribute to the amplification of gene families, mostly related to the immune system and disease resistance, which we suggest to be functionally linked to coral host resilience., Conclusions: At large, we show the importance of duplicated genes to inform the biology of reef-building corals and provide novel avenues to understand and screen for differences in stress resilience., (© 2023. The Author(s).)

Coral reefs are among the most diverse ecosystems on Earth. They support high biodiversity of multicellular organisms that strongly rely on associated microorganisms for health and nutrition. However, the extent of the coral reef microbiome diversity and its distribution at the oceanic basin-scale remains to be explored. Here, we systematically sampled 3 coral morphotypes, 2 fish species, and planktonic communities in 99 reefs from 32 islands across the Pacific Ocean, to assess reef microbiome composition and biogeography. We show a very large richness of reef microorganisms compared to other environments, which extrapolated to all fishes and corals of the Pacific, approximates the current estimated total prokaryotic diversity for the entire Earth. Microbial communities vary among and within the 3 animal biomes (coral, fish, plankton), and geographically. For corals, the cross-ocean patterns of diversity are different from those known for other multicellular organisms. Within each coral morphotype, community composition is always determined by geographic distance first, both at the island and across ocean scale, and then by environment. Our unprecedented sampling effort of coral reef microbiomes, as part of the Tara Pacific expedition, provides new insight into the global microbial diversity, the factors driving their distribution, and the biocomplexity of reef ecosystems., (© 2023. The Author(s).)

Health and resilience of the coral holobiont depend on diverse bacterial communities often dominated by key marine symbionts of the Endozoicomonadaceae family. The factors controlling their distribution and their functional diversity remain, however, poorly known. Here, we study the ecology of Endozoicomonadaceae at an ocean basin-scale by sampling specimens from three coral genera (Pocillopora, Porites, Millepora) on 99 reefs from 32 islands across the Pacific Ocean. The analysis of 2447 metabarcoding and 270 metagenomic samples reveals that each coral genus harbored a distinct new species of Endozoicomonadaceae. These species are composed of nine lineages that have distinct biogeographic patterns. The most common one, found in Pocillopora, appears to be a globally distributed symbiont with distinct metabolic capabilities, including the synthesis of amino acids and vitamins not produced by the host. The other lineages are structured partly by the host genetic lineage in Pocillopora and mainly by the geographic location in Porites. Millepora is more rarely associated to Endozoicomonadaceae. Our results show that different coral genera exhibit distinct strategies of host-Endozoicomonadaceae associations that are defined at the bacteria lineage level., (© 2023. The Author(s).)

Cotton (Gossypium sp.), a plant of tropical and sub-tropical origin, appeared at several sites on the Arabian Peninsula at the end of the 1st mill. BCE-beginning of the 1st mill. CE. Its spread into this non-native, arid environment is emblematic of the trade dynamics that took place at this pivotal point in human history. Due to its geographical location, the Arabian Peninsula is connected to both the Indian and African trading spheres, making it complex to reconstruct the trans-continental trajectories of plant diffusion into and across Arabia in Antiquity. Key questions remain pertaining to: (1) provenance, i.e. are plant remains of local or imported origin and (2) the precise timing of cotton arrival and spread. The ancient site of Mleiha, located in modern-day United Arab Emirates, is a rare and significant case where rich archaeobotanical remains dating to the Late Pre-Islamic period (2nd-3rd c. CE), including cotton seeds and fabrics, have been preserved in a burned-down fortified building. To better understand the initial trade and/or production of cotton in this region, strontium isotopes of leached, charred cotton remains are used as a powerful tracer and the results indicate that the earliest cotton finds did not originate from the Oman Peninsula, but were more likely sourced from further afield, with the north-western coast of India being an isotopically compatible provenance. Identifying the presence of such imported cotton textiles and seeds in southeastern Arabia is significant as it is representative of the early diffusion of the crop in the region, later to be grown extensively in local oases.

Coral reefs are the most diverse habitats in the marine realm. Their productivity, structural complexity, and biodiversity critically depend on ecosystem services provided by corals that are threatened because of climate change effects-in particular, ocean warming and acidification. The coral holobiont is composed of the coral animal host, endosymbiotic dinoflagellates, associated viruses, bacteria, and other microeukaryotes. In particular, the mandatory photosymbiosis with microalgae of the family Symbiodiniaceae and its consequences on the evolution, physiology, and stress resilience of the coral holobiont have yet to be fully elucidated. The functioning of the holobiont as a whole is largely unknown, although bacteria and viruses are presumed to play roles in metabolic interactions, immunity, and stress tolerance. In the context of climate change and anthropogenic threats on coral reef ecosystems, the Tara Pacific project aims to provide a baseline of the "-omics" complexity of the coral holobiont and its ecosystem across the Pacific Ocean and for various oceanographically distinct defined areas. Inspired by the previous Tara Oceans expeditions, the Tara Pacific expedition (2016-2018) has applied a pan-ecosystemic approach on coral reefs throughout the Pacific Ocean, drawing an east-west transect from Panama to Papua New Guinea and a south-north transect from Australia to Japan, sampling corals throughout 32 island systems with local replicates. Tara Pacific has developed and applied state-of-the-art technologies in very-high-throughput genetic sequencing and molecular analysis to reveal the entire microbial and chemical diversity as well as functional traits associated with coral holobionts, together with various measures on environmental forcing. This ambitious project aims at revealing a massive amount of novel biodiversity, shedding light on the complex links between genomes, transcriptomes, metabolomes, organisms, and ecosystem functions in coral reefs and providing a reference of the biological state of modern coral reefs in the Anthropocene., Competing Interests: The authors have declared that no competing interests exist.

Increasing atmospheric CO 2 from man-made climate change is reducing surface ocean pH. Due to limited instrumental measurements and historical pH records in the world's oceans, seawater pH variability at the decadal and centennial scale remains largely unknown and requires documentation. Here we present evidence of striking secular trends of decreasing pH since the late nineteenth century with pronounced interannual to decadal-interdecadal pH variability in the South Pacific Ocean from 1689 to 2011 CE. High-amplitude oceanic pH changes, likely related to atmospheric CO 2 uptake and seawater dissolved inorganic carbon fluctuations, reveal a coupled relationship to sea surface temperature variations and highlight the marked influence of El Niño/Southern Oscillation and Interdecadal Pacific Oscillation. We suggest changing surface winds strength and zonal advection processes as the main drivers responsible for regional pH variability up to 1881 CE, followed by the prominent role of anthropogenic CO 2 in accelerating the process of ocean acidification.

Speleothem-like deposits that develop underground in urban areas are an archive of the environmental impact of anthropic activities that has been little studied so far. In this paper, the sulfate content in shallow groundwater from northern Paris (France) is compared with the sulfur content in two 300-year-old urban carbonate deposits that grew in a historical underground aqueduct. The present-day waters of the aqueduct have very high sulfur and calcium contents, suggesting pollution from gypsum dissolution. However, geological gypsum levels are located below the water table. Sulfur content was measured by micro-X-ray fluorescence in these very S-rich carbonate deposits (0.5 to 1% of S). A twofold S increase during the second half of the 1800s was found in both samples. These dates correspond to two major periods of urbanization above the site. We discus three possible S sources: anthropic sources (industries, fertilizers…), volcanic eruptions and input within the water through gypsum brought for urbanization above the studied site (backfill with quarry waste) since the middle of the 19th century. For the younger second half of the studied section, S input from gypsum brought during urbanization was confirmed by the study of isotopic sulfur composition (δ 34 S=+15.2‰ at the top). For the oldest part, several sulfur peaks could be related to early industrial activity in Paris, that caused high local air pollution, as reported in historical archives but also to historical gypsum extraction. This study provides information on the origin and timing of the very high SO 4 2- levels measured nowadays within the shallow groundwater, thus demonstrating the interest in using carbonate deposits in urban areas as a proxy for the history of urbanization or human activities and their impact on water bodies., (Copyright © 2016 Elsevier B.V. All rights reserved.)

Goda Buticha is a cave site near Dire Dawa in southeastern Ethiopia that contains an archaeological sequence sampling the late Pleistocene and Holocene of the region. The sedimentary sequence displays complex cultural, chronological and sedimentological histories that seem incongruent with one another. A first set of radiocarbon ages suggested a long sedimentological gap from the end of Marine Isotopic Stage (MIS) 3 to the mid-Holocene. Macroscopic observations suggest that the main sedimentological change does not coincide with the chronostratigraphic hiatus. The cultural sequence shows technological continuity with a late persistence of artifacts that are usually attributed to the Middle Stone Age into the younger parts of the stratigraphic sequence, yet become increasingly associated with lithic artifacts typically related to the Later Stone Age. While not a unique case, this combination of features is unusual in the Horn of Africa. In order to evaluate the possible implications of these observations, sedimentological analyses combined with optically stimulated luminescence (OSL) were conducted. The OSL data now extend the radiocarbon chronology up to 63 ± 7 ka; they also confirm the existence of the chronological gap between 24.8 ± 2.6 ka and 7.5 ± 0.3 ka. The sedimentological analyses suggest that the origin and mode of deposition were largely similar throughout the whole sequence, although the anthropic and faunal activities increased in the younger levels. Regional climatic records are used to support the sedimentological observations and interpretations. We discuss the implications of the sedimentological and dating analyses for understanding cultural processes in the region., Competing Interests: The authors have declared that no competing interests exist.

Rationale: Laser Ablation coupled to Multi-Collector Inductively Coupled Plasma Mass Spectrometry (LA-MC-ICPMS) is a powerful tool for the high-precision measurement of the isotopic ratios of many elements in geological samples, with the isotope ratio ((11) B/(10) B) of boron being used as an indicator of the pH of oceanic waters. Most geological samples or standards are polished and ablation occurs on flat surfaces. However, the shape and the irregularities of marine biocarbonates (e.g., corals, foraminifera) can make precise isotopic measurements of boron difficult. Even after polishing, the porosity properties and the presence of holes or micro-fractures affect the signal and the isotopic ratio when ablating the material, especially in raster mode., Methods: The effect of porosity and of the crater itself on the (11) B signal and the isotopic ratio acquired by LA-MC-ICPMS in both raster and spot mode was studied. Characterization of the craters was then performed with an optical profilometer to determine their shapes and depths. Surface state effects were examined by analyzing the isotopic fractionation of boron in silicate (NIST-SRM 612 and 610 standards) and in carbonate (corals)., Results: Surface irregularities led to a considerable loss of signal when the crater depth exceeded 20 µm. The stability and precision were degraded when ablation occurred in a deep cavity. The effect of laser focusing and of blank correction was also highlighted and our observations indicate that the accuracy of the boron isotopic ratio does not depend on the shape of the surface. After validation of the analytical protocol for boron isotopes, a raster application on a Porites coral, which grew for 18 months in an aquarium after field sampling, was carried out., Conclusions: This original LA-MC-ICPMS study revealed a well-marked boron isotope ratio temporal variability, probably related to growth rate and density changes, irrespective of the pH of the surrounding seawater. Copyright © 2015 John Wiley & Sons, Ltd., (Copyright © 2015 John Wiley & Sons, Ltd.)

The first record of urban speleothems used to reconstruct the history of heavy metal pollution of shallow groundwaters is presented. Two speleothems grew during the last 300 years in an underground aqueduct in the north-eastern part of Paris. They display high Pb, Mn V, Cu, Cd and Al concentrations since 1900 due to the urbanization of the site which triggered anthropogenic contamination of the water feeding the speleothems. Surprisingly, these heavy metal concentrations are also high in the oldest part. This early pollution could come from the use of Parisian waste as fertilizers in the orchards and vineyards cultivated above the aqueduct before urbanization. Lead isotopes were measured in these carbonates as well as in lead artifacts from the 17th-18th centuries ((206)Pb/(207)Pb=1.180+/-0.003). The mean (206)Pb/(207)Pb ratio, for one of the speleothems is 1.181+/-0.003 unvarying with time. These lead signatures are close to those of coal and old lead from northern European mines, lower than the natural background signature. It confirms that the high metal concentrations found come from anthropogenic pollution. Conversely, the lead isotopic composition of the second speleothem presents two temporal trends: for the oldest levels, the mean value (1.183+/-0.003) is similar to the first speleothem. For the youngest part, a lower value (1.172+/-0.005) is recorded, evidencing the contribution of a new lead source at the beginning of the industrial revolution. Pb isotopes were also measured in recent samples from a nearby superficial site. The first sample is a recent (AD 1975+/-15 years) deposit ((206)Pb/(207)Pb=1.148+/-0.003), and the second, a thin subactual layer ((206)Pb/(207)Pb=1.181+/-0.002). These data are compatible with the adding of anthropogenic sources (leaded gasoline and industrial lead from Rio Tinto ore)., (Copyright © 2015 Elsevier B.V. All rights reserved.)

Phloem Protein2 (PP2) is a component of the phloem protein bodies found in sieve elements. We describe here the lectin properties of the Arabidopsis (Arabidopsis thaliana) PP2-A1. Using a recombinant protein produced in Escherichia coli, we demonstrated binding to N-acetylglucosamine oligomers. Glycan array screening showed that PP2-A1 also bound to high-mannose N-glycans and 9-acyl-N-acetylneuraminic sialic acid. Fluorescence spectroscopy-based titration experiments revealed that PP2-A1 had two classes of binding site for N,N',N''-triacetylchitotriose, a low-affinity site and a high-affinity site, promoting the formation of protein dimers. A search for structural similarities revealed that PP2-A1 aligned with the Cbm4 and Cbm22-2 carbohydrate-binding modules, leading to the prediction of a beta-strand structure for its conserved domain. We investigated whether PP2-A1 interacted with phloem sap glycoproteins by first characterizing abundant Arabidopsis phloem sap proteins by liquid chromatography-tandem mass spectrometry. Then we demonstrated that PP2-A1 bound to several phloem sap proteins and that this binding was not completely abolished by glycosidase treatment. As many plant lectins have insecticidal activity, we also assessed the effect of PP2-A1 on weight gain and survival in aphids. Unlike other mannose-binding lectins, when added to an artificial diet, recombinant PP2-A1 had no insecticidal properties against Acyrthosiphon pisum and Myzus persicae. However, at mid-range concentrations, the protein affected weight gain in insect nymphs. These results indicate the presence in PP2-A1 of several carbohydrate-binding sites, with potentially different functions in the trafficking of endogenous proteins or in interactions with phloem-feeding insects.

Extensive studies of the radiocarbon (14C) distribution and transfer in the marine environment of the North-Cotentin peninsula and along the English Channel have been carried out. The main aims of these studies have been to estimate the spatial and temporal variation of the 14C concentration in seawater and to calculate 14C concentration factors for some biological species. Such information will be helpful in order to calculate precisely radiation doses to humans. First results obtained in the vicinity of the COGEMA La Hague nuclear plant (Goury) indicate a 14C labelling of the dissolved inorganic carbon (DIC) in seawater (8.0-26.2 Bq.m(-3)) and a tight relationship between the 14C in the liquid releases from the plant and the 14C concentrations in DIC. The particulate organic carbon (POC) is also labelled. The concentration factor calculations for the brown algae (Fucus serratus) sampled from Goury, and also along the English Channel, give 14C values around 3000 Bq.kg(-1) fresh weight / Bq.L(-1).

SOS, the guanine nucleotide exchange factor for Ras, becomes phosphorylated on serine and threonine residues following stimulation of cells with growth factors. These phosphorylations may play a role in negative feedback of Ras stimulation and have been shown to be mediated in part by the MAP kinases Erk-1 and Erk-2. Here we show that in addition to MAP kinase, a major mitogen activated kinase for SOS is p90 Rsk-2, a downstream target of MAP kinase. p90 Rsk-2 phosphorylates SOS in an in gel assay and also in solution in vitro. The ability of p90 Rsk-2 to phosphorylate SOS increases greatly following EGF treatment of PC12 cells and is blocked by expression of N17 Ras or treatment with the MEK inhibitor PD98059. Phosphopeptide mapping revealed that the sites phosphorylated by p90 Rsk-2 in vitro were also phosphorylated in intact cells in response to EGF treatment. Several major sites of in vivo phosphorylation correlated with p90 Rsk-2 phosphorylation sites rather than MAP kinase sites. It is therefore likely that p90 Rsk-2 plays an important role in the down regulation of the Ras activation pathway through SOS.

Phosphorylation/dephosphorylation reactions are one of the dynamic mechanisms through which cells modulate protein activity in response to environmental stimuli. The eukaryotic molecules which are responsible for the phosphorylation of serine, threonine and tyrosine residues appear to have co-ordinately evolved from simple prokaryotic enzymes which primarily respond to nutritional cues. In multicellular eukaryotes the complexity of data transfer greatly exceeds that of simple bacteria. The eukaryotic cell needs to exchange information with neighbouring and distant sister cells. Positional, nutritional and hormonal data are transmitted from the extracellular milieu across the plasma membrane and into the cytoplasm. In certain cases the signal must pass into the nucleus or other subcellular organelles where it is decoded and the proper cellular response initiated. All of these events have been shown to have a protein kinase component and it seems likely that in mammalian cells over 1,000 different kinase molecules have evolved to form the requisite signal transducing networks. In this review we describe a previously unappreciated family of protein kinases, the dual specificity or DSK kinases, which play important roles in the regulation of normal cellular growth and differentiation.