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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Aumont, Olivier; Rodgers, Keith;

    The repository contains the version of PISCES that was used to investigate the role played by low latitudes and the Southern Ocean at sustaining export production and PP in the low latitudes. This code is based on version 3.6 of NEMO and the repository only includes routines that have been changed with respect to this version. The code is in Fortran 90.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
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  • Authors: Haifeng Gu; Jing Zheng; Shuning Huang; Lourdes Morquecho; +5 Authors
    Phycologiaarrow_drop_down
    Phycologia
    Article . 2023 . Peer-reviewed
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      Phycologia
      Article . 2023 . Peer-reviewed
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Emilia Grypioti; Hugues Richard; Nikoleta Kryovrysanaki; Marianne Jaubert; +3 Authors

    Summary Diatoms are eukaryotic microalgae responsible for nearly half of the marine productivity. RNA interference (RNAi) is a mechanism of regulation of gene expression mediated by small RNAs (sRNAs) processed by the endoribonuclease Dicer (DCR). To date, the mechanism and physiological role of RNAi in diatoms are unknown. We mined diatom genomes and transcriptomes for key RNAi effectors and retraced their phylogenetic history. We generated DCR knockout lines in the model diatom species Phaeodactylum tricornutum and analyzed their mRNA and sRNA populations, repression‐associated histone marks, and acclimatory response to nitrogen starvation. Diatoms presented a diversification of key RNAi effectors whose distribution across species suggests the presence of distinct RNAi pathways. P. tricornutum DCR was found to process 26–31‐nt‐long double‐stranded sRNAs originating mostly from transposons covered by repression‐associated epigenetic marks. In parallel, P. tricornutum DCR was necessary for the maintenance of the repression‐associated histone marks H3K9me2/3 and H3K27me3. Finally, PtDCR‐KO lines presented a compromised recovery post nitrogen starvation suggesting a role for P. tricornutum DCR in the acclimation to nutrient stress. Our study characterized the molecular function of the single DCR homolog of P. tricornutum suggesting an association between RNAi and heterochromatin maintenance in this model diatom species.

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    New Phytologist
    Article . 2023 . Peer-reviewed
    License: CC BY
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    New Phytologist
    Article . 2023
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ New Phytologistarrow_drop_down
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      New Phytologist
      Article . 2023 . Peer-reviewed
      License: CC BY
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      New Phytologist
      Article . 2023
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    Authors: Jae-Wook Oh; Suraj Shiv Charan Pushparaj; Manikandan Muthu; Judy Gopal;

    Extensive growth of microscopic algae and cyanobacteria results in harmful algal blooms (HABs) in marine, brackish, and freshwater environments. HABs can harm humans and animals through their toxicity or by producing ecological conditions such as oxygen depletion, which can kill fish and other economically or ecologically important organisms. This review summarizes the reports on various HABs that are able to bring about marine fish kills. The predominant HABs, their toxins, and their effects on fishes spread across various parts of the globe are discussed. The mechanism of HAB-driven fish kills is discussed based on the available reports, and existing mitigation methods are presented. Lapses in the large-scale implementation of mitigation methods demonstrated under laboratory conditions are projected. Clay-related technologies and nano-sorption-based nanotechnologies, although proven to make significant contributions, have not been put to use in real-world conditions. The gaps in the technology transfer of the accomplished mitigation prototypes are highlighted. Further uses of remote sensing and machine learning state-of-the-art techniques for the detection and identification of HABs are recommended.

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    Plants
    Article . 2023 . Peer-reviewed
    License: CC BY
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    Plants
    Article . 2023
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    Plants
    Article . 2023
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      Plants
      Article . 2023 . Peer-reviewed
      License: CC BY
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      Plants
      Article . 2023
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      Plants
      Article . 2023
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Hyung-Eun An; Min-Ho Mun; Chang-Bae Kim;

    Fishes are ecologically important organisms that have long lifespans, high mobilities, and diverse trophic levels. Due to their importance, fishes are used as bioindicators for monitoring aquatic environments. One method for monitoring fishes is based on environmental DNA (eDNA), which are the deoxynucleic acids released by organisms into the environment. However, there has been a problem with false positives because eDNA is relatively stable in the environment and could even likely represent dead or non-inhabiting organisms. To address this weakness, environmental RNA (eRNA), which degrades more rapidly than eDNA in the environment, can be utilized to complement eDNA. But, to date, few studies have used eRNA for freshwater fish monitoring. In this study, to determine the relative usefulness of eDNA and eRNA metabarcoding in freshwater fishes, we performed eDNA and eRNA metabarcoding on 12S rRNA targeting fish using water samples that were collected from three locations in the Han River. We then calculated the sensitivity and positive predictivity of this approach by comparing our data to the previous specimen capture survey (PSCS) data from the last six years. The results showed that 42 species were detected by eDNA and 19 by eRNA at the three locations. At all locations, compared to the PSCS data, the average sensitivity was higher for eDNA (46.1%) than for eRNA (34.6%), and the average positive predictivity was higher for eRNA (31.7%) than for eDNA (20.7%). This confirmed that eDNA metabarcoding has the advantage of broadly determining species presence or absence (including those that are no longer present or dead), but it also generates false positives; meanwhile, eRNA metabarcoding reports living fish species, but detects fewer species than eDNA. Combining eDNA and eRNA therefore emphasizes their advantages and compensates for their disadvantages, and conducting this may therefore be useful for identifying false positives and monitoring the fish species that are actually present in the environment. This metabarcoding technique can be used in the future to provide insights into the aquatic environment and the monitoring of fisheries.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Fishesarrow_drop_down
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    Fishes
    Article . 2023
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    Fishes
    Article . 2023 . Peer-reviewed
    License: CC BY
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Fishesarrow_drop_down
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      Fishes
      Article . 2023
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      Fishes
      Article . 2023 . Peer-reviewed
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  • image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    Authors: Magdalena Niedziałkowska; Kamila Plis; Barbara Marczuk; Johannes Lang; +25 Authors

    Abstract Although the European Roe Deer (Capreolus capreolus) is one of the most common and widespread ungulate species in Europe and inhabiting a variety of habitats, few studies have addressed its population structure at a large spatial scale using nuclear genetic data. The aims of our study were to: (i) investigate genetic diversity, level of admixture, and genetic structure across European Roe Deer populations; (ii) identify barriers to gene flow; and (iii) reveal factors that have impacted the observed pattern of population genetic structure. Using 12 microsatellite loci, we analyzed 920 European Roe Deer samples from 16 study sites from northern, southern, central, and eastern Europe. The highest genetic diversity was found in central and eastern sites, and lowest in the northern and southern sites. There were 2 main groups of genetically related populations in the study area—one inhabiting mainly Fennoscandia, and the second in the continental part of Europe. This second population was further divided into 3 to 5 spatially distributed genetic clusters. European Roe Deer belonging to the Siberian mitochondrial DNA clade, inhabiting large parts of eastern Europe, were not identified as a separate population in the analysis of microsatellite loci. No isolation by distance (IBD) was detected between roe deer from the fennoscandian and the continental study sites, but the Baltic Sea was inferred to be the main barrier to gene flow. Only weak IBD was revealed within the continental population. Three lower-level genetic barriers were detected in the western, southern, and eastern parts of the study area. The main factors inferred as shaping the observed genetic diversity and population structure of European Roe Deer were postglacial recolonization, admixture of different populations of the species originating from several Last Glacial Maximum refugial areas, and isolation of several study sites.

    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Journal of Mammalogyarrow_drop_down
    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    Journal of Mammalogy
    Article . 2023 . Peer-reviewed
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      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Journal of Mammalogyarrow_drop_down
      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
      Journal of Mammalogy
      Article . 2023 . Peer-reviewed
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    Authors: Jae Hoon Choi; Jun Hyung Ryu; Seung Pyo Gong;

    Although testicular organoids have remarkable potential as testicular models in vitro, there have been few studies about testicular organoids in teleost fish. As a first step to establish a stable culture system for fish testicular organoids, we investigated the efficient conditions for an aggregate culture of dispersed testicular cells from adult marine medaka (Oryzias dancena) by evaluating the effects of culture methods and media composition on an aggregate culture. As the results, we found that culturing dispersed testicular cells in an ultra-low attachment 96 well without Matrigel was most effectively able to induce the formation of testicular cell aggregates among the five different methods tested. Subsequently, through media testing, we confirmed that the modified ESM2 was more optimal for this aggregate culture than the media conventionally used in porcine, human, and rat testicular aggregate cultures. Furthermore, we demonstrated that three supplements in the modified ESM2 including fish serum (FS), basic fibroblast growth factor (bFGF), and embryo extracts (EE) did not influence the number and size of the testicular aggregates formed, but fetal bovine serum and other supplements including β-mercaptoethanol, non-essential amino acids, sodium pyruvate, and sodium selenite were affected significantly. Nevertheless, the removal of three supplements (FS, bFGF, and EE) during culture negatively affected scp3 and sox9a expression levels, indicating their necessity. Finally, we identified that the sperms derived from in vitro cultured testicular aggregates were able to produce offspring after fertilization with naturally matured oocytes. The results from this study will provide fundamental information to develop the techniques for fish testicular organoid culture, which will eventually contribute to the development of reproductive biotechnology for aquaculture and the conservation of endangered fish species.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Journal of Marine Sc...arrow_drop_down
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    Journal of Marine Science and Engineering
    Article . 2023 . Peer-reviewed
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      Journal of Marine Science and Engineering
      Article . 2023 . Peer-reviewed
      License: CC BY
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    Authors: K.-S. Yun; K.-S. Yun; A. Timmermann; A. Timmermann; +7 Authors

    Driven primarily by variations in the earth's axis wobble, tilt, and orbit eccentricity, our planet experienced massive glacial/interglacial reorganizations of climate and atmospheric CO2 concentrations during the Pleistocene (2.58 million years ago (Ma)–11.7 thousand years ago (ka)). Even after decades of research, the underlying climate response mechanisms to these astronomical forcings have not been fully understood. To further quantify the sensitivity of the earth system to orbital-scale forcings, we conducted an unprecedented quasi-continuous coupled general climate model simulation with the Community Earth System Model version 1.2 (CESM1.2, ∼3.75∘ horizontal resolution), which covers the climatic history of the past 3 million years (3 Myr). In addition to the astronomical insolation changes, CESM1.2 is forced by estimates of CO2 and ice-sheet topography which were obtained from a simulation previously conducted with the CLIMBER-2 earth system model of intermediate complexity. Our 3 Ma simulation consists of 42 transient interglacial/glacial simulation chunks, which were partly run in parallel to save computing time. The chunks were subsequently merged, accounting for spin-up and overlap effects to yield a quasi-continuous trajectory. The computer model data were compared against a plethora of paleo-proxy data and large-scale climate reconstructions. For the period from the Mid-Pleistocene Transition (MPT, ∼1 Ma) to the late Pleistocene we find good agreement between simulated and reconstructed temperatures in terms of phase and amplitude (−5.7 ∘C temperature difference between Last Glacial Maximum and Holocene). For the earlier part (3–1 Ma), differences in orbital-scale variability occur between model simulation and the reconstructions, indicating potential biases in the applied CO2 forcing. Our model-proxy data comparison also extends to the westerlies, which show unexpectedly large variance on precessional timescales, and hydroclimate variables in major monsoon regions. Eccentricity-modulated precessional variability is also responsible for the simulated changes in the amplitude and flavors of the El Niño–Southern Oscillation. We further identify two major modes of planetary energy transport, which played a crucial role in Pleistocene climate variability: the first obliquity and CO2-driven mode is linked to changes in the Equator-to-pole temperature gradient; the second mode regulates the interhemispheric heat imbalance in unison with the eccentricity-modulated precession cycle. During the MPT, a pronounced qualitative shift occurs in the second mode of planetary energy transport: the post-MPT eccentricity-paced variability synchronizes with the CO2 forced signal. This synchronized feature is coherent with changes in global atmospheric and ocean circulations, which might contribute to an intensification of glacial cycle feedbacks and amplitudes. Comparison of this paleo-simulation with greenhouse warming simulations reveals that for an RCP8.5 greenhouse gas emission scenario, the projected global mean surface temperature changes over the next 7 decades would be comparable to the late Pleistocene glacial-interglacial range; but the anthropogenic warming rate will exceed any previous ones by a factor of ∼100.

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    Climate of the Past
    Article . 2023
    Data sources: DOAJ
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    Climate of the Past (CP)
    Article . 2023 . Peer-reviewed
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      Climate of the Past
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      Climate of the Past (CP)
      Article . 2023 . Peer-reviewed
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    Authors: Luisa R. Abucay; Patricia Sorongon-Yap; Kathleen Kesner-Reyes; Emily C. Capuli; +22 Authors

    Available information and potential data gaps for non-fish marine organisms (cnidarians, crustaceans, echinoderms, molluscs, sponges, mammals, reptiles, and seabirds) covered by the global database SeaLifeBase were reviewed for eight marine ecosystems (Adriatic Sea, Aegean Sea, Baltic Sea, Bay of Biscay/Celtic Sea/Iberian Coast , Black Sea, North Sea, western Mediterranean Sea, Levantine Sea) across European Seas. The review of the SeaLifeBase dataset, which is based on published literature, analyzed information coverage for eight biological characteristics (diet, fecundity, maturity, length-weight relationships, spawning, growth, lifespan, and natural mortality). These characteristics are required for the development of ecosystem and ecological models to evaluate the status of marine resources and related fisheries. Our analyses revealed that information regarding these biological characteristics in the literature was far from complete across all studied areas. The level of available information was nonetheless reasonably good for sea turtles and moderate for marine mammals in some areas (Baltic Sea, Bay of Biscay/Celtic Sea/Iberian Coast , Black Sea, North Sea and western Mediterranean Sea). Further, seven of the areas have well-studied species in terms of information coverage for biological characteristics of some commercial species whereas threatened species are generally not well studied. Across areas, the most well-studied species are the cephalopod common cuttlefish ( Sepia officinalis) and the crustacean Norway lobster ( Nephrops norvegicus ). Overall, the information gap is narrowest for length-weight relationships followed by growth and maturity, and widest for fecundity and natural mortality. Based on these insights, we provide recommendations to prioritize species with insufficient or missing biological data that are common across the studied marine ecosystems and to address data deficiencies. International audience

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    CNR ExploRA
    Article . 2023
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    Frontiers in Marine Science
    Article . 2023
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    ISTI Open Portal
    Article . 2023
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      CNR ExploRA
      Article . 2023
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      Frontiers in Marine Science
      Article . 2023
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      ISTI Open Portal
      Article . 2023
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    Authors: Tim DeVries; Kana Yamamoto; Rik Wanninkhof; Nicolas Gruber; +31 Authors

    TD acknowledges support from the US National Science Foundation through Grant OCE-1948955. RW and BR are supported by funding from NOAA's Global Ocean Monitoring and Observations (GOMO) Program. The CICOES and PMEL contributions to this work are numbers 2023-1260 and 5497, respectively. JDM, LG, and NG acknowledge support from the European Union's Horizon 2020 research and innovation programme under Grant agreement no. 821003 (project 4C) and no. 820989 (project COMFORT). JH acknowledges funding from the Initiative and Networking Fund of the Helmholtz Association (Helmholtz Young Investigator Group Marine Carbon and Ecosystem Feedbacks in the Earth System (MarESys), Grant VH-NG-1301) and from ERC-2022-STG OceanPeak, Grant agreement 101077209. DC acknowledges support from the NASA Carbon Cycle and Ecosystems (CCE) program under Grant 80NSSC22K0154. SCD acknowledges support from the NSF Center for Chemical Currencies of a Microbial Planet (C-CoMP) (NSF Award 2019589). SAH was supported by a European Research Council Consolidator Grant (GOCART, agreement number 724416). PL was supported by Research Foundation Flanders (FWO) contract I001821N. CN acknowledges funding from the European Union's Horizon 2020 research and innovation programme under Grant agreement No 820989 (project COMFORT). LP acknowledges funding from the project PA 3075/2-1 by the German Research Foundation and the North German Supercomputing Alliance (HLRN) for providing computing power for the experiments. FFP was supported by the BOCATS2 project (PID2019-104279GB-C21) funded by MCIN/AEI/10.13039/501100011033. KBR was supported by the Institute for Basic Sciences (IBS), Republic of Korea, under IBS-R028-D1. JS acknowledges funding from the Research Council of Norway (Grant 270061) and computational/storage resources provided by UNINET/sigma2 (nn/ns2980k). JTH was funded by the Woods Hole Oceanographic Institution Postdoctoral Scholar Program, the European Union's Horizon 2020 research and innovation program under grant agreement 821003 (project 4C, Climate-Carbon Interactions in the Current Century), and the Swiss National Science Foundation under Grant 200020_200511. CLQ acknowledges funding from the European Union project 4C (Grant 821003) and the Royal Society (Grant RP\R1\191063), and support from UEA’s High Performance Computing services. TTTC and MG acknowledge financial support by the European Copernicus Marine Environment Monitoring Service (CMEMS) MOB-TAC project for the joint development with F. Chevallier of the CMEMS-LSCE-FFNN model This contribution to the RECCAP2 (REgional Carbon Cycle Assessment and Processes) assessment analyzes the processes that determine the global ocean carbon sink, and its trends and variability over the period 1985–2018, using a combination of models and observation-based products. The mean sea-air CO2 flux from 1985 to 2018 is −1.6 ± 0.2 PgC yr−1 based on an ensemble of reconstructions of the history of sea surface pCO2 (pCO2 products). Models indicate that the dominant component of this flux is the net oceanic uptake of anthropogenic CO2, which is estimated at −2.1 ± 0.3 PgC yr−1 by an ensemble of ocean biogeochemical models, and −2.4 ± 0.1 PgC yr−1 by two ocean circulation inverse models. The ocean also degasses about 0.65 ± 0.3 PgC yr−1 of terrestrially derived CO2, but this process is not fully resolved by any of the models used here. From 2001 to 2018, the pCO2 products reconstruct a trend in the ocean carbon sink of −0.61 ± 0.12 PgC yr−1 decade−1, while biogeochemical models and inverse models diagnose an anthropogenic CO2-driven trend of −0.34 ± 0.06 and −0.41 ± 0.03 PgC yr−1 decade−1, respectively. This implies a climate-forced acceleration of the ocean carbon sink in recent decades, but there are still large uncertainties on the magnitude and cause of this trend. The interannual to decadal variability of the global carbon sink is mainly driven by climate variability, with the climate-driven variability exceeding the CO2-forced variability by 2–3 times. These results suggest that anthropogenic CO2 dominates the ocean CO2 sink, while climate-driven variability is potentially large but highly uncertain and not consistently captured across different methods 32 pages, 3 tables, 7 figures.-- This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License Peer reviewed

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    MPG.PuRe
    Article . 2023
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    Global Biogeochemical Cycles
    Article . 2023 . Peer-reviewed
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    Research Collection
    Article . 2023
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    MPG.PuRe
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    https://doi.org/10.48350/19396...
    Article . 2023
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      MPG.PuRe
      Article . 2023
      Data sources: MPG.PuRe
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      Global Biogeochemical Cycles
      Article . 2023 . Peer-reviewed
      License: CC BY NC
      Data sources: Crossref
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      Research Collection
      Article . 2023
      License: CC BY NC
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      MPG.PuRe
      Article . 2023
      License: CC BY
      Data sources: MPG.PuRe
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      https://doi.org/10.48350/19396...
      Article . 2023
      License: CC BY NC
      Data sources: Datacite
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      HAL-CEA
      Article . 2023
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Aumont, Olivier; Rodgers, Keith;

    The repository contains the version of PISCES that was used to investigate the role played by low latitudes and the Southern Ocean at sustaining export production and PP in the low latitudes. This code is based on version 3.6 of NEMO and the repository only includes routines that have been changed with respect to this version. The code is in Fortran 90.

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  • Authors: Haifeng Gu; Jing Zheng; Shuning Huang; Lourdes Morquecho; +5 Authors
    Phycologiaarrow_drop_down
    Phycologia
    Article . 2023 . Peer-reviewed
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      Phycologia
      Article . 2023 . Peer-reviewed
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Emilia Grypioti; Hugues Richard; Nikoleta Kryovrysanaki; Marianne Jaubert; +3 Authors

    Summary Diatoms are eukaryotic microalgae responsible for nearly half of the marine productivity. RNA interference (RNAi) is a mechanism of regulation of gene expression mediated by small RNAs (sRNAs) processed by the endoribonuclease Dicer (DCR). To date, the mechanism and physiological role of RNAi in diatoms are unknown. We mined diatom genomes and transcriptomes for key RNAi effectors and retraced their phylogenetic history. We generated DCR knockout lines in the model diatom species Phaeodactylum tricornutum and analyzed their mRNA and sRNA populations, repression‐associated histone marks, and acclimatory response to nitrogen starvation. Diatoms presented a diversification of key RNAi effectors whose distribution across species suggests the presence of distinct RNAi pathways. P. tricornutum DCR was found to process 26–31‐nt‐long double‐stranded sRNAs originating mostly from transposons covered by repression‐associated epigenetic marks. In parallel, P. tricornutum DCR was necessary for the maintenance of the repression‐associated histone marks H3K9me2/3 and H3K27me3. Finally, PtDCR‐KO lines presented a compromised recovery post nitrogen starvation suggesting a role for P. tricornutum DCR in the acclimation to nutrient stress. Our study characterized the molecular function of the single DCR homolog of P. tricornutum suggesting an association between RNAi and heterochromatin maintenance in this model diatom species.

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    New Phytologist
    Article . 2023 . Peer-reviewed
    License: CC BY
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    New Phytologist
    Article . 2023
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      New Phytologist
      Article . 2023 . Peer-reviewed
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      New Phytologist
      Article . 2023
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    Authors: Jae-Wook Oh; Suraj Shiv Charan Pushparaj; Manikandan Muthu; Judy Gopal;

    Extensive growth of microscopic algae and cyanobacteria results in harmful algal blooms (HABs) in marine, brackish, and freshwater environments. HABs can harm humans and animals through their toxicity or by producing ecological conditions such as oxygen depletion, which can kill fish and other economically or ecologically important organisms. This review summarizes the reports on various HABs that are able to bring about marine fish kills. The predominant HABs, their toxins, and their effects on fishes spread across various parts of the globe are discussed. The mechanism of HAB-driven fish kills is discussed based on the available reports, and existing mitigation methods are presented. Lapses in the large-scale implementation of mitigation methods demonstrated under laboratory conditions are projected. Clay-related technologies and nano-sorption-based nanotechnologies, although proven to make significant contributions, have not been put to use in real-world conditions. The gaps in the technology transfer of the accomplished mitigation prototypes are highlighted. Further uses of remote sensing and machine learning state-of-the-art techniques for the detection and identification of HABs are recommended.

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    Plants
    Article . 2023 . Peer-reviewed
    License: CC BY
    Data sources: Crossref
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    Plants
    Article . 2023
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    Plants
    Article . 2023
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      Plants
      Article . 2023 . Peer-reviewed
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      Plants
      Article . 2023
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      Plants
      Article . 2023
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Hyung-Eun An; Min-Ho Mun; Chang-Bae Kim;

    Fishes are ecologically important organisms that have long lifespans, high mobilities, and diverse trophic levels. Due to their importance, fishes are used as bioindicators for monitoring aquatic environments. One method for monitoring fishes is based on environmental DNA (eDNA), which are the deoxynucleic acids released by organisms into the environment. However, there has been a problem with false positives because eDNA is relatively stable in the environment and could even likely represent dead or non-inhabiting organisms. To address this weakness, environmental RNA (eRNA), which degrades more rapidly than eDNA in the environment, can be utilized to complement eDNA. But, to date, few studies have used eRNA for freshwater fish monitoring. In this study, to determine the relative usefulness of eDNA and eRNA metabarcoding in freshwater fishes, we performed eDNA and eRNA metabarcoding on 12S rRNA targeting fish using water samples that were collected from three locations in the Han River. We then calculated the sensitivity and positive predictivity of this approach by comparing our data to the previous specimen capture survey (PSCS) data from the last six years. The results showed that 42 species were detected by eDNA and 19 by eRNA at the three locations. At all locations, compared to the PSCS data, the average sensitivity was higher for eDNA (46.1%) than for eRNA (34.6%), and the average positive predictivity was higher for eRNA (31.7%) than for eDNA (20.7%). This confirmed that eDNA metabarcoding has the advantage of broadly determining species presence or absence (including those that are no longer present or dead), but it also generates false positives; meanwhile, eRNA metabarcoding reports living fish species, but detects fewer species than eDNA. Combining eDNA and eRNA therefore emphasizes their advantages and compensates for their disadvantages, and conducting this may therefore be useful for identifying false positives and monitoring the fish species that are actually present in the environment. This metabarcoding technique can be used in the future to provide insights into the aquatic environment and the monitoring of fisheries.

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    Fishes
    Article . 2023
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    Fishes
    Article . 2023 . Peer-reviewed
    License: CC BY
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      Fishes
      Article . 2023
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      Fishes
      Article . 2023 . Peer-reviewed
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  • image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    Authors: Magdalena Niedziałkowska; Kamila Plis; Barbara Marczuk; Johannes Lang; +25 Authors

    Abstract Although the European Roe Deer (Capreolus capreolus) is one of the most common and widespread ungulate species in Europe and inhabiting a variety of habitats, few studies have addressed its population structure at a large spatial scale using nuclear genetic data. The aims of our study were to: (i) investigate genetic diversity, level of admixture, and genetic structure across European Roe Deer populations; (ii) identify barriers to gene flow; and (iii) reveal factors that have impacted the observed pattern of population genetic structure. Using 12 microsatellite loci, we analyzed 920 European Roe Deer samples from 16 study sites from northern, southern, central, and eastern Europe. The highest genetic diversity was found in central and eastern sites, and lowest in the northern and southern sites. There were 2 main groups of genetically related populations in the study area—one inhabiting mainly Fennoscandia, and the second in the continental part of Europe. This second population was further divided into 3 to 5 spatially distributed genetic clusters. European Roe Deer belonging to the Siberian mitochondrial DNA clade, inhabiting large parts of eastern Europe, were not identified as a separate population in the analysis of microsatellite loci. No isolation by distance (IBD) was detected between roe deer from the fennoscandian and the continental study sites, but the Baltic Sea was inferred to be the main barrier to gene flow. Only weak IBD was revealed within the continental population. Three lower-level genetic barriers were detected in the western, southern, and eastern parts of the study area. The main factors inferred as shaping the observed genetic diversity and population structure of European Roe Deer were postglacial recolonization, admixture of different populations of the species originating from several Last Glacial Maximum refugial areas, and isolation of several study sites.

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    Journal of Mammalogy
    Article . 2023 . Peer-reviewed
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      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Journal of Mammalogyarrow_drop_down
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      Journal of Mammalogy
      Article . 2023 . Peer-reviewed
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    Authors: Jae Hoon Choi; Jun Hyung Ryu; Seung Pyo Gong;

    Although testicular organoids have remarkable potential as testicular models in vitro, there have been few studies about testicular organoids in teleost fish. As a first step to establish a stable culture system for fish testicular organoids, we investigated the efficient conditions for an aggregate culture of dispersed testicular cells from adult marine medaka (Oryzias dancena) by evaluating the effects of culture methods and media composition on an aggregate culture. As the results, we found that culturing dispersed testicular cells in an ultra-low attachment 96 well without Matrigel was most effectively able to induce the formation of testicular cell aggregates among the five different methods tested. Subsequently, through media testing, we confirmed that the modified ESM2 was more optimal for this aggregate culture than the media conventionally used in porcine, human, and rat testicular aggregate cultures. Furthermore, we demonstrated that three supplements in the modified ESM2 including fish serum (FS), basic fibroblast growth factor (bFGF), and embryo extracts (EE) did not influence the number and size of the testicular aggregates formed, but fetal bovine serum and other supplements including β-mercaptoethanol, non-essential amino acids, sodium pyruvate, and sodium selenite were affected significantly. Nevertheless, the removal of three supplements (FS, bFGF, and EE) during culture negatively affected scp3 and sox9a expression levels, indicating their necessity. Finally, we identified that the sperms derived from in vitro cultured testicular aggregates were able to produce offspring after fertilization with naturally matured oocytes. The results from this study will provide fundamental information to develop the techniques for fish testicular organoid culture, which will eventually contribute to the development of reproductive biotechnology for aquaculture and the conservation of endangered fish species.

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    Journal of Marine Science and Engineering
    Article . 2023 . Peer-reviewed
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      Journal of Marine Science and Engineering
      Article . 2023 . Peer-reviewed
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    Authors: K.-S. Yun; K.-S. Yun; A. Timmermann; A. Timmermann; +7 Authors

    Driven primarily by variations in the earth's axis wobble, tilt, and orbit eccentricity, our planet experienced massive glacial/interglacial reorganizations of climate and atmospheric CO2 concentrations during the Pleistocene (2.58 million years ago (Ma)–11.7 thousand years ago (ka)). Even after decades of research, the underlying climate response mechanisms to these astronomical forcings have not been fully understood. To further quantify the sensitivity of the earth system to orbital-scale forcings, we conducted an unprecedented quasi-continuous coupled general climate model simulation with the Community Earth System Model version 1.2 (CESM1.2, ∼3.75∘ horizontal resolution), which covers the climatic history of the past 3 million years (3 Myr). In addition to the astronomical insolation changes, CESM1.2 is forced by estimates of CO2 and ice-sheet topography which were obtained from a simulation previously conducted with the CLIMBER-2 earth system model of intermediate complexity. Our 3 Ma simulation consists of 42 transient interglacial/glacial simulation chunks, which were partly run in parallel to save computing time. The chunks were subsequently merged, accounting for spin-up and overlap effects to yield a quasi-continuous trajectory. The computer model data were compared against a plethora of paleo-proxy data and large-scale climate reconstructions. For the period from the Mid-Pleistocene Transition (MPT, ∼1 Ma) to the late Pleistocene we find good agreement between simulated and reconstructed temperatures in terms of phase and amplitude (−5.7 ∘C temperature difference between Last Glacial Maximum and Holocene). For the earlier part (3–1 Ma), differences in orbital-scale variability occur between model simulation and the reconstructions, indicating potential biases in the applied CO2 forcing. Our model-proxy data comparison also extends to the westerlies, which show unexpectedly large variance on precessional timescales, and hydroclimate variables in major monsoon regions. Eccentricity-modulated precessional variability is also responsible for the simulated changes in the amplitude and flavors of the El Niño–Southern Oscillation. We further identify two major modes of planetary energy transport, which played a crucial role in Pleistocene climate variability: the first obliquity and CO2-driven mode is linked to changes in the Equator-to-pole temperature gradient; the second mode regulates the interhemispheric heat imbalance in unison with the eccentricity-modulated precession cycle. During the MPT, a pronounced qualitative shift occurs in the second mode of planetary energy transport: the post-MPT eccentricity-paced variability synchronizes with the CO2 forced signal. This synchronized feature is coherent with changes in global atmospheric and ocean circulations, which might contribute to an intensification of glacial cycle feedbacks and amplitudes. Comparison of this paleo-simulation with greenhouse warming simulations reveals that for an RCP8.5 greenhouse gas emission scenario, the projected global mean surface temperature changes over the next 7 decades would be comparable to the late Pleistocene glacial-interglacial range; but the anthropogenic warming rate will exceed any previous ones by a factor of ∼100.

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    Climate of the Past
    Article . 2023
    Data sources: DOAJ
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    Climate of the Past (CP)
    Article . 2023 . Peer-reviewed
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      Climate of the Past
      Article . 2023
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      Climate of the Past (CP)
      Article . 2023 . Peer-reviewed
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    Authors: Luisa R. Abucay; Patricia Sorongon-Yap; Kathleen Kesner-Reyes; Emily C. Capuli; +22 Authors

    Available information and potential data gaps for non-fish marine organisms (cnidarians, crustaceans, echinoderms, molluscs, sponges, mammals, reptiles, and seabirds) covered by the global database SeaLifeBase were reviewed for eight marine ecosystems (Adriatic Sea, Aegean Sea, Baltic Sea, Bay of Biscay/Celtic Sea/Iberian Coast , Black Sea, North Sea, western Mediterranean Sea, Levantine Sea) across European Seas. The review of the SeaLifeBase dataset, which is based on published literature, analyzed information coverage for eight biological characteristics (diet, fecundity, maturity, length-weight relationships, spawning, growth, lifespan, and natural mortality). These characteristics are required for the development of ecosystem and ecological models to evaluate the status of marine resources and related fisheries. Our analyses revealed that information regarding these biological characteristics in the literature was far from complete across all studied areas. The level of available information was nonetheless reasonably good for sea turtles and moderate for marine mammals in some areas (Baltic Sea, Bay of Biscay/Celtic Sea/Iberian Coast , Black Sea, North Sea and western Mediterranean Sea). Further, seven of the areas have well-studied species in terms of information coverage for biological characteristics of some commercial species whereas threatened species are generally not well studied. Across areas, the most well-studied species are the cephalopod common cuttlefish ( Sepia officinalis) and the crustacean Norway lobster ( Nephrops norvegicus ). Overall, the information gap is narrowest for length-weight relationships followed by growth and maturity, and widest for fecundity and natural mortality. Based on these insights, we provide recommendations to prioritize species with insufficient or missing biological data that are common across the studied marine ecosystems and to address data deficiencies. International audience

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    CNR ExploRA
    Article . 2023
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    Frontiers in Marine Science
    Article . 2023
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    ISTI Open Portal
    Article . 2023
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      CNR ExploRA
      Article . 2023
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      Frontiers in Marine Science
      Article . 2023
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      ISTI Open Portal
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    Authors: Tim DeVries; Kana Yamamoto; Rik Wanninkhof; Nicolas Gruber; +31 Authors

    TD acknowledges support from the US National Science Foundation through Grant OCE-1948955. RW and BR are supported by funding from NOAA's Global Ocean Monitoring and Observations (GOMO) Program. The CICOES and PMEL contributions to this work are numbers 2023-1260 and 5497, respectively. JDM, LG, and NG acknowledge support from the European Union's Horizon 2020 research and innovation programme under Grant agreement no. 821003 (project 4C) and no. 820989 (project COMFORT). JH acknowledges funding from the Initiative and Networking Fund of the Helmholtz Association (Helmholtz Young Investigator Group Marine Carbon and Ecosystem Feedbacks in the Earth System (MarESys), Grant VH-NG-1301) and from ERC-2022-STG OceanPeak, Grant agreement 101077209. DC acknowledges support from the NASA Carbon Cycle and Ecosystems (CCE) program under Grant 80NSSC22K0154. SCD acknowledges support from the NSF Center for Chemical Currencies of a Microbial Planet (C-CoMP) (NSF Award 2019589). SAH was supported by a European Research Council Consolidator Grant (GOCART, agreement number 724416). PL was supported by Research Foundation Flanders (FWO) contract I001821N. CN acknowledges funding from the European Union's Horizon 2020 research and innovation programme under Grant agreement No 820989 (project COMFORT). LP acknowledges funding from the project PA 3075/2-1 by the German Research Foundation and the North German Supercomputing Alliance (HLRN) for providing computing power for the experiments. FFP was supported by the BOCATS2 project (PID2019-104279GB-C21) funded by MCIN/AEI/10.13039/501100011033. KBR was supported by the Institute for Basic Sciences (IBS), Republic of Korea, under IBS-R028-D1. JS acknowledges funding from the Research Council of Norway (Grant 270061) and computational/storage resources provided by UNINET/sigma2 (nn/ns2980k). JTH was funded by the Woods Hole Oceanographic Institution Postdoctoral Scholar Program, the European Union's Horizon 2020 research and innovation program under grant agreement 821003 (project 4C, Climate-Carbon Interactions in the Current Century), and the Swiss National Science Foundation under Grant 200020_200511. CLQ acknowledges funding from the European Union project 4C (Grant 821003) and the Royal Society (Grant RP\R1\191063), and support from UEA’s High Performance Computing services. TTTC and MG acknowledge financial support by the European Copernicus Marine Environment Monitoring Service (CMEMS) MOB-TAC project for the joint development with F. Chevallier of the CMEMS-LSCE-FFNN model This contribution to the RECCAP2 (REgional Carbon Cycle Assessment and Processes) assessment analyzes the processes that determine the global ocean carbon sink, and its trends and variability over the period 1985–2018, using a combination of models and observation-based products. The mean sea-air CO2 flux from 1985 to 2018 is −1.6 ± 0.2 PgC yr−1 based on an ensemble of reconstructions of the history of sea surface pCO2 (pCO2 products). Models indicate that the dominant component of this flux is the net oceanic uptake of anthropogenic CO2, which is estimated at −2.1 ± 0.3 PgC yr−1 by an ensemble of ocean biogeochemical models, and −2.4 ± 0.1 PgC yr−1 by two ocean circulation inverse models. The ocean also degasses about 0.65 ± 0.3 PgC yr−1 of terrestrially derived CO2, but this process is not fully resolved by any of the models used here. From 2001 to 2018, the pCO2 products reconstruct a trend in the ocean carbon sink of −0.61 ± 0.12 PgC yr−1 decade−1, while biogeochemical models and inverse models diagnose an anthropogenic CO2-driven trend of −0.34 ± 0.06 and −0.41 ± 0.03 PgC yr−1 decade−1, respectively. This implies a climate-forced acceleration of the ocean carbon sink in recent decades, but there are still large uncertainties on the magnitude and cause of this trend. The interannual to decadal variability of the global carbon sink is mainly driven by climate variability, with the climate-driven variability exceeding the CO2-forced variability by 2–3 times. These results suggest that anthropogenic CO2 dominates the ocean CO2 sink, while climate-driven variability is potentially large but highly uncertain and not consistently captured across different methods 32 pages, 3 tables, 7 figures.-- This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License Peer reviewed

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    https://doi.org/10.48350/19396...
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