Articles | Volume 16, issue 22
https://doi.org/10.5194/gmd-16-6701-2023
© Author(s) 2023. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/gmd-16-6701-2023
© Author(s) 2023. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Model description paper
| 
21 Nov 2023
Model description paper |
| 21 Nov 2023
| 21 Nov 2023
Implementation and assessment of a model including mixotrophs and the carbonate cycle (Eco3M_MIX-CarbOx v1.0) in a highly dynamic Mediterranean coastal environment (Bay of Marseille, France) – Part 1: Evolution of ecosystem composition under limited light and nutrient conditions
Lucille Barré
CORRESPONDING AUTHOR
Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, UM 110, 13288 Marseille, France
Frédéric Diaz
Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, UM 110, 13288 Marseille, France
deceased
Thibaut Wagener
Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, UM 110, 13288 Marseille, France
France Van Wambeke
Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, UM 110, 13288 Marseille, France
Camille Mazoyer
Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, UM 110, 13288 Marseille, France
Christophe Yohia
Aix Marseille Univ., Université de Toulon, CNRS, IRD, OSU Institut Pythéas, 13288 Marseille, France
Christel Pinazo
CORRESPONDING AUTHOR
Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, UM 110, 13288 Marseille, France
Related authors
Lucille Barré, Frédéric Diaz, Thibaut Wagener, Camille Mazoyer, Christophe Yohia, and Christel Pinazo
Geosci. Model Dev., 17, 5851–5882, https://doi.org/10.5194/gmd-17-5851-2024, https://doi.org/10.5194/gmd-17-5851-2024, 2024
Short summary
Short summary
The carbonate system is typically studied using measurements, but modeling can contribute valuable insights. Using a biogeochemical model, we propose a new representation of total alkalinity, dissolved inorganic carbon, pCO2, and pH in a highly dynamic Mediterranean coastal area, the Bay of Marseille, a useful addition to measurements. Through a detailed analysis of pCO2 and air–sea CO2 fluxes, we show that variations are strongly impacted by the hydrodynamic processes that affect the bay.
Nicolas Metzl, Jonathan Fin, Claire Lo Monaco, Claude Mignon, Samir Alliouane, Bruno Bombled, Jacqueline Boutin, Yann Bozec, Steeve Comeau, Pascal Conan, Laurent Coppola, Pascale Cuet, Eva Ferreira, Jean-Pierre Gattuso, Frédéric Gazeau, Catherine Goyet, Emilie Grossteffan, Bruno Lansard, Dominique Lefèvre, Nathalie Lefèvre, Coraline Leseurre, Sébastien Petton, Mireille Pujo-Pay, Christophe Rabouille, Gilles Reverdin, Céline Ridame, Peggy Rimmelin-Maury, Jean-François Ternon, Franck Touratier, Aline Tribollet, Thibaut Wagener, and Cathy Wimart-Rousseau
Earth Syst. Sci. Data Discuss., https://doi.org/10.5194/essd-2024-464, https://doi.org/10.5194/essd-2024-464, 2024
Preprint under review for ESSD
Short summary
Short summary
This work presents a new synthesis of 67 000 total alkalinity and total dissolved inorganic carbon observations obtained between 1993 and 2023 in the global ocean, coastal zones and the Mediterranean Sea. We describe the data assemblage and associated quality control and discuss some potential uses of this dataset. The dataset is provided in a single format and include the quality flag for each sample.
Lucille Barré, Frédéric Diaz, Thibaut Wagener, Camille Mazoyer, Christophe Yohia, and Christel Pinazo
Geosci. Model Dev., 17, 5851–5882, https://doi.org/10.5194/gmd-17-5851-2024, https://doi.org/10.5194/gmd-17-5851-2024, 2024
Short summary
Short summary
The carbonate system is typically studied using measurements, but modeling can contribute valuable insights. Using a biogeochemical model, we propose a new representation of total alkalinity, dissolved inorganic carbon, pCO2, and pH in a highly dynamic Mediterranean coastal area, the Bay of Marseille, a useful addition to measurements. Through a detailed analysis of pCO2 and air–sea CO2 fluxes, we show that variations are strongly impacted by the hydrodynamic processes that affect the bay.
France Van Wambeke, Pascal Conan, Mireille Pujo-Pay, Vincent Taillandier, Olivier Crispi, Alexandra Pavlidou, Sandra Nunige, Morgane Didry, Christophe Salmeron, and Elvira Pulido-Villena
Biogeosciences, 21, 2621–2640, https://doi.org/10.5194/bg-21-2621-2024, https://doi.org/10.5194/bg-21-2621-2024, 2024
Short summary
Short summary
Phosphomonoesterase (PME) and phosphodiesterase (PDE) activities over the epipelagic zone are described in the eastern Mediterranean Sea in winter and autumn. The types of concentration kinetics obtained for PDE (saturation at 50 µM, high Km, high turnover times) compared to those of PME (saturation at 1 µM, low Km, low turnover times) are discussed in regard to the possible inequal distribution of PDE and PME in the size continuum of organic material and accessibility to phosphodiesters.
Nicolas Metzl, Jonathan Fin, Claire Lo Monaco, Claude Mignon, Samir Alliouane, David Antoine, Guillaume Bourdin, Jacqueline Boutin, Yann Bozec, Pascal Conan, Laurent Coppola, Frédéric Diaz, Eric Douville, Xavier Durrieu de Madron, Jean-Pierre Gattuso, Frédéric Gazeau, Melek Golbol, Bruno Lansard, Dominique Lefèvre, Nathalie Lefèvre, Fabien Lombard, Férial Louanchi, Liliane Merlivat, Léa Olivier, Anne Petrenko, Sébastien Petton, Mireille Pujo-Pay, Christophe Rabouille, Gilles Reverdin, Céline Ridame, Aline Tribollet, Vincenzo Vellucci, Thibaut Wagener, and Cathy Wimart-Rousseau
Earth Syst. Sci. Data, 16, 89–120, https://doi.org/10.5194/essd-16-89-2024, https://doi.org/10.5194/essd-16-89-2024, 2024
Short summary
Short summary
This work presents a synthesis of 44 000 total alkalinity and dissolved inorganic carbon observations obtained between 1993 and 2022 in the Global Ocean and the Mediterranean Sea at the surface and in the water column. Seawater samples were measured using the same method and calibrated with international Certified Reference Material. We describe the data assemblage, quality control and some potential uses of this dataset.
Stéphanie Barrillon, Robin Fuchs, Anne A. Petrenko, Caroline Comby, Anthony Bosse, Christophe Yohia, Jean-Luc Fuda, Nagib Bhairy, Frédéric Cyr, Andrea M. Doglioli, Gérald Grégori, Roxane Tzortzis, Francesco d'Ovidio, and Melilotus Thyssen
Biogeosciences, 20, 141–161, https://doi.org/10.5194/bg-20-141-2023, https://doi.org/10.5194/bg-20-141-2023, 2023
Short summary
Short summary
Extreme weather events can have a major impact on ocean physics and biogeochemistry, but their study is challenging. In May 2019, an intense storm occurred in the north-western Mediterranean Sea, during which in situ multi-platform measurements were performed. The results show a strong impact on the surface phytoplankton, highlighting the need for high-resolution measurements coupling physics and biology during these violent events that may become more common in the context of global change.
Julie Dinasquet, Estelle Bigeard, Frédéric Gazeau, Farooq Azam, Cécile Guieu, Emilio Marañón, Céline Ridame, France Van Wambeke, Ingrid Obernosterer, and Anne-Claire Baudoux
Biogeosciences, 19, 1303–1319, https://doi.org/10.5194/bg-19-1303-2022, https://doi.org/10.5194/bg-19-1303-2022, 2022
Short summary
Short summary
Saharan dust deposition of nutrients and trace metals is crucial to microbes in the Mediterranean Sea. Here, we tested the response of microbial and viral communities to simulated dust deposition under present and future conditions of temperature and pH. Overall, the effect of the deposition was dependent on the initial microbial assemblage, and future conditions will intensify microbial responses. We observed effects on trophic interactions, cascading all the way down to viral processes.
Céline Ridame, Julie Dinasquet, Søren Hallstrøm, Estelle Bigeard, Lasse Riemann, France Van Wambeke, Matthieu Bressac, Elvira Pulido-Villena, Vincent Taillandier, Fréderic Gazeau, Antonio Tovar-Sanchez, Anne-Claire Baudoux, and Cécile Guieu
Biogeosciences, 19, 415–435, https://doi.org/10.5194/bg-19-415-2022, https://doi.org/10.5194/bg-19-415-2022, 2022
Short summary
Short summary
We show that in the Mediterranean Sea spatial variability in N2 fixation is related to the diazotrophic community composition reflecting different nutrient requirements among species. Nutrient supply by Saharan dust is of great importance to diazotrophs, as shown by the strong stimulation of N2 fixation after a simulated dust event under present and future climate conditions; the magnitude of stimulation depends on the degree of limitation related to the diazotrophic community composition.
Matthieu Bressac, Thibaut Wagener, Nathalie Leblond, Antonio Tovar-Sánchez, Céline Ridame, Vincent Taillandier, Samuel Albani, Sophie Guasco, Aurélie Dufour, Stéphanie H. M. Jacquet, François Dulac, Karine Desboeufs, and Cécile Guieu
Biogeosciences, 18, 6435–6453, https://doi.org/10.5194/bg-18-6435-2021, https://doi.org/10.5194/bg-18-6435-2021, 2021
Short summary
Short summary
Phytoplankton growth is limited by the availability of iron in about 50 % of the ocean. Atmospheric deposition of desert dust represents a key source of iron. Here, we present direct observations of dust deposition in the Mediterranean Sea. A key finding is that the input of iron from dust primarily occurred in the deep ocean, while previous studies mainly focused on the ocean surface. This new insight will enable us to better represent controls on global marine productivity in models.
Stéphanie H. M. Jacquet, Christian Tamburini, Marc Garel, Aurélie Dufour, France Van Vambeke, Frédéric A. C. Le Moigne, Nagib Bhairy, and Sophie Guasco
Biogeosciences, 18, 5891–5902, https://doi.org/10.5194/bg-18-5891-2021, https://doi.org/10.5194/bg-18-5891-2021, 2021
Short summary
Short summary
We compared carbon remineralization rates (MRs) in the western and central Mediterranean Sea in late spring during the PEACETIME cruise, as assessed using the barium tracer. We reported higher and deeper (up to 1000 m depth) MRs in the western basin, potentially sustained by an additional particle export event driven by deep convection. The central basin is the site of a mosaic of blooming and non-blooming water masses and showed lower MRs that were restricted to the upper mesopelagic layer.
Elvira Pulido-Villena, Karine Desboeufs, Kahina Djaoudi, France Van Wambeke, Stéphanie Barrillon, Andrea Doglioli, Anne Petrenko, Vincent Taillandier, Franck Fu, Tiphanie Gaillard, Sophie Guasco, Sandra Nunige, Sylvain Triquet, and Cécile Guieu
Biogeosciences, 18, 5871–5889, https://doi.org/10.5194/bg-18-5871-2021, https://doi.org/10.5194/bg-18-5871-2021, 2021
Short summary
Short summary
We report on phosphorus dynamics in the surface layer of the Mediterranean Sea. Highly sensitive phosphate measurements revealed vertical gradients above the phosphacline. The relative contribution of diapycnal fluxes to total external supply of phosphate to the mixed layer decreased towards the east, where atmospheric deposition dominated. Taken together, external sources of phosphate contributed little to total supply, which was mainly sustained by enzymatic hydrolysis of organic phosphorus.
France Van Wambeke, Vincent Taillandier, Karine Desboeufs, Elvira Pulido-Villena, Julie Dinasquet, Anja Engel, Emilio Marañón, Céline Ridame, and Cécile Guieu
Biogeosciences, 18, 5699–5717, https://doi.org/10.5194/bg-18-5699-2021, https://doi.org/10.5194/bg-18-5699-2021, 2021
Short summary
Short summary
Simultaneous in situ measurements of (dry and wet) atmospheric deposition and biogeochemical stocks and fluxes in the sunlit waters of the open Mediterranean Sea revealed complex physical and biological processes occurring within the mixed layer. Nitrogen (N) budgets were computed to compare the sources and sinks of N in the mixed layer. The transitory effect observed after a wet dust deposition impacted the microbial food web down to the deep chlorophyll maximum.
Frédéric Gazeau, France Van Wambeke, Emilio Marañón, Maria Pérez-Lorenzo, Samir Alliouane, Christian Stolpe, Thierry Blasco, Nathalie Leblond, Birthe Zäncker, Anja Engel, Barbara Marie, Julie Dinasquet, and Cécile Guieu
Biogeosciences, 18, 5423–5446, https://doi.org/10.5194/bg-18-5423-2021, https://doi.org/10.5194/bg-18-5423-2021, 2021
Short summary
Short summary
Our study shows that the impact of dust deposition on primary production depends on the initial composition and metabolic state of the tested community and is constrained by the amount of nutrients added, to sustain both the fast response of heterotrophic prokaryotes and the delayed one of phytoplankton. Under future environmental conditions, heterotrophic metabolism will be more impacted than primary production, therefore reducing the capacity of surface waters to sequester anthropogenic CO2.
Frédéric Gazeau, Céline Ridame, France Van Wambeke, Samir Alliouane, Christian Stolpe, Jean-Olivier Irisson, Sophie Marro, Jean-Michel Grisoni, Guillaume De Liège, Sandra Nunige, Kahina Djaoudi, Elvira Pulido-Villena, Julie Dinasquet, Ingrid Obernosterer, Philippe Catala, and Cécile Guieu
Biogeosciences, 18, 5011–5034, https://doi.org/10.5194/bg-18-5011-2021, https://doi.org/10.5194/bg-18-5011-2021, 2021
Short summary
Short summary
This paper shows that the impacts of Saharan dust deposition in different Mediterranean basins are as strong as those observed in coastal waters but differed substantially between the three tested stations, differences attributed to variable initial metabolic states. A stronger impact of warming and acidification on mineralization suggests a decreased capacity of Mediterranean surface communities to sequester CO2 following the deposition of atmospheric particles in the coming decades.
Evelyn Freney, Karine Sellegri, Alessia Nicosia, Leah R. Williams, Matteo Rinaldi, Jonathan T. Trueblood, André S. H. Prévôt, Melilotus Thyssen, Gérald Grégori, Nils Haëntjens, Julie Dinasquet, Ingrid Obernosterer, France Van Wambeke, Anja Engel, Birthe Zäncker, Karine Desboeufs, Eija Asmi, Hilkka Timonen, and Cécile Guieu
Atmos. Chem. Phys., 21, 10625–10641, https://doi.org/10.5194/acp-21-10625-2021, https://doi.org/10.5194/acp-21-10625-2021, 2021
Short summary
Short summary
In this work, we present observations of the organic aerosol content in primary sea spray aerosols (SSAs) continuously generated along a 5-week cruise in the Mediterranean. This information is combined with seawater biogeochemical properties also measured continuously along the ship track to develop a number of parametrizations that can be used in models to determine SSA organic content in oligotrophic waters that represent 60 % of the oceans from commonly measured seawater variables.
Matthieu Roy-Barman, Lorna Foliot, Eric Douville, Nathalie Leblond, Fréderic Gazeau, Matthieu Bressac, Thibaut Wagener, Céline Ridame, Karine Desboeufs, and Cécile Guieu
Biogeosciences, 18, 2663–2678, https://doi.org/10.5194/bg-18-2663-2021, https://doi.org/10.5194/bg-18-2663-2021, 2021
Short summary
Short summary
The release of insoluble elements such as aluminum (Al), iron (Fe), rare earth elements (REEs), thorium (Th) and protactinium (Pa) when Saharan dust falls over the Mediterranean Sea was studied during tank experiments under present and future climate conditions. Each element exhibited different dissolution kinetics and dissolution fractions (always lower than a few percent). Changes in temperature and/or pH under greenhouse conditions lead to a lower Th release and a higher light REE release.
France Van Wambeke, Elvira Pulido, Philippe Catala, Julie Dinasquet, Kahina Djaoudi, Anja Engel, Marc Garel, Sophie Guasco, Barbara Marie, Sandra Nunige, Vincent Taillandier, Birthe Zäncker, and Christian Tamburini
Biogeosciences, 18, 2301–2323, https://doi.org/10.5194/bg-18-2301-2021, https://doi.org/10.5194/bg-18-2301-2021, 2021
Short summary
Short summary
Michaelis–Menten kinetics were determined for alkaline phosphatase, aminopeptidase and β-glucosidase in the Mediterranean Sea. Although the ectoenzymatic-hydrolysis contribution to heterotrophic prokaryotic needs was high in terms of N, it was low in terms of C. This study points out the biases in interpretation of the relative differences in activities among the three tested enzymes in regard to the choice of added concentrations of fluorogenic substrates.
Emilio Marañón, France Van Wambeke, Julia Uitz, Emmanuel S. Boss, Céline Dimier, Julie Dinasquet, Anja Engel, Nils Haëntjens, María Pérez-Lorenzo, Vincent Taillandier, and Birthe Zäncker
Biogeosciences, 18, 1749–1767, https://doi.org/10.5194/bg-18-1749-2021, https://doi.org/10.5194/bg-18-1749-2021, 2021
Short summary
Short summary
The concentration of chlorophyll is commonly used as an indicator of the abundance of photosynthetic plankton (phytoplankton) in lakes and oceans. Our study investigates why a deep chlorophyll maximum, located near the bottom of the upper, illuminated layer develops in the Mediterranean Sea. We find that the acclimation of cells to low light is the main mechanism involved and that this deep maximum represents also a maximum in the biomass and carbon fixation activity of phytoplankton.
Katixa Lajaunie-Salla, Frédéric Diaz, Cathy Wimart-Rousseau, Thibaut Wagener, Dominique Lefèvre, Christophe Yohia, Irène Xueref-Remy, Brian Nathan, Alexandre Armengaud, and Christel Pinazo
Geosci. Model Dev., 14, 295–321, https://doi.org/10.5194/gmd-14-295-2021, https://doi.org/10.5194/gmd-14-295-2021, 2021
Short summary
Short summary
A biogeochemical model of planktonic food webs including a carbonate balance module is applied in the Bay of Marseille (France) to represent the carbon marine cycle expected to change in the future owing to significant increases in anthropogenic emissions of CO2. The model correctly simulates the ranges and seasonal dynamics of most variables of the carbonate system (pH). This study shows that external physical forcings have an important impact on the carbonate equilibrium in this coastal area.
Kahina Djaoudi, France Van Wambeke, Aude Barani, Nagib Bhairy, Servanne Chevaillier, Karine Desboeufs, Sandra Nunige, Mohamed Labiadh, Thierry Henry des Tureaux, Dominique Lefèvre, Amel Nouara, Christos Panagiotopoulos, Marc Tedetti, and Elvira Pulido-Villena
Biogeosciences, 17, 6271–6285, https://doi.org/10.5194/bg-17-6271-2020, https://doi.org/10.5194/bg-17-6271-2020, 2020
Antonio Tovar-Sánchez, Araceli Rodríguez-Romero, Anja Engel, Birthe Zäncker, Franck Fu, Emilio Marañón, María Pérez-Lorenzo, Matthieu Bressac, Thibaut Wagener, Sylvain Triquet, Guillaume Siour, Karine Desboeufs, and Cécile Guieu
Biogeosciences, 17, 2349–2364, https://doi.org/10.5194/bg-17-2349-2020, https://doi.org/10.5194/bg-17-2349-2020, 2020
Short summary
Short summary
Residence times of particulate metals derived from aerosol deposition in the Sea Surface Microlayer of the Mediterranean Sea ranged from a couple of minutes (e.g., for Fe) to a few hours (e.g., for Cu). Microbial activity seems to play an important role in in this process and in the concentration and distribution of metals between diferent water layers.
Christos Panagiotopoulos, Mireille Pujo-Pay, Mar Benavides, France Van Wambeke, and Richard Sempéré
Biogeosciences, 16, 105–116, https://doi.org/10.5194/bg-16-105-2019, https://doi.org/10.5194/bg-16-105-2019, 2019
Pascale Bouruet-Aubertot, Yannis Cuypers, Andrea Doglioli, Mathieu Caffin, Christophe Yohia, Alain de Verneil, Anne Petrenko, Dominique Lefèvre, Hervé Le Goff, Gilles Rougier, Marc Picheral, and Thierry Moutin
Biogeosciences, 15, 7485–7504, https://doi.org/10.5194/bg-15-7485-2018, https://doi.org/10.5194/bg-15-7485-2018, 2018
Short summary
Short summary
The OUTPACE cruise took place between New Caledonia and French Polynesia. The main purpose was to understand how micro-organisms can survive in a very poor environment. One main source of nutrients is at depth, below the euphotic layer where micro-organisms live. The purpose of the turbulence measurements was to determine to which extent turbulence may
upliftnutrients into the euphotic layer. The origin of the turbulence that was found contrasted along the transect was also determined.
Audrey Gimenez, Melika Baklouti, Thibaut Wagener, and Thierry Moutin
Biogeosciences, 15, 6573–6589, https://doi.org/10.5194/bg-15-6573-2018, https://doi.org/10.5194/bg-15-6573-2018, 2018
Short summary
Short summary
During the OUTPACE cruise conducted in the oligotrophic to ultra-oligotrophic region of the western tropical South Pacific, two contrasted regions were sampled in terms of N2 fixation rates, primary production rates and nutrient availability. The aim of this work was to investigate the role of N2 fixation in the differences observed between the two contrasted areas by comparing two simulations only differing by the presence or not of N2 fixers using a 1-D biogeochemical–physical coupled model.
Thibaut Wagener, Nicolas Metzl, Mathieu Caffin, Jonathan Fin, Sandra Helias Nunige, Dominique Lefevre, Claire Lo Monaco, Gilles Rougier, and Thierry Moutin
Biogeosciences, 15, 5221–5236, https://doi.org/10.5194/bg-15-5221-2018, https://doi.org/10.5194/bg-15-5221-2018, 2018
Short summary
Short summary
The western tropical South Pacific was sampled along a longitudinal 4000 km transect (OUTPACE cruise) for the measurement of carbonate parameters (total alkalinity and total inorganic carbon) between the Melanesian Archipelago and the western part of the South Pacific gyre. This paper reports this new dataset and derived properties. We also estimate anthropogenic carbon distribution in the water column using the TrOCA method.
Nicholas Bock, France Van Wambeke, Moïra Dion, and Solange Duhamel
Biogeosciences, 15, 3909–3925, https://doi.org/10.5194/bg-15-3909-2018, https://doi.org/10.5194/bg-15-3909-2018, 2018
Short summary
Short summary
We report the distribution of major nano- and pico-plankton groups in the western tropical South Pacific. We found microbial community structure to be typical of highly stratified regions of the open ocean, with significant contributions to total biomass by picophytoeukaryotes, and N2 fixation playing a central role in regulating ecosystem processes. Our results also suggest a reduction in the importance of predation in regulating bacteria populations under nutrient-limited conditions.
Thierry Moutin, Thibaut Wagener, Mathieu Caffin, Alain Fumenia, Audrey Gimenez, Melika Baklouti, Pascale Bouruet-Aubertot, Mireille Pujo-Pay, Karine Leblanc, Dominique Lefevre, Sandra Helias Nunige, Nathalie Leblond, Olivier Grosso, and Alain de Verneil
Biogeosciences, 15, 2961–2989, https://doi.org/10.5194/bg-15-2961-2018, https://doi.org/10.5194/bg-15-2961-2018, 2018
Short summary
Short summary
Surface waters of the western tropical South Pacific were sampled along a longitudinal 4000 km transect during the stratified period between the Melanesian Archipelago and the western part of the South Pacific gyre. We found a significant biological carbon pump sustained almost exclusively by N2 fixation and essentially controlled by phosphate availability in the iron-rich Melanesian Archipelago waters which appears to be a net sink for atmospheric CO2 while the gyre is in a quasi-steady state.
France Van Wambeke, Audrey Gimenez, Solange Duhamel, Cécile Dupouy, Dominique Lefevre, Mireille Pujo-Pay, and Thierry Moutin
Biogeosciences, 15, 2669–2689, https://doi.org/10.5194/bg-15-2669-2018, https://doi.org/10.5194/bg-15-2669-2018, 2018
Short summary
Short summary
The western tropical South Pacific Ocean has recently been shown to be a hotspot for biological nitrogen fixation. In this study, we examined the horizontal and vertical distribution of heterotrophic prokaryotic production alongside photosynthetic rates, nitrogen fixation rates and phosphate turnover times across the western tropical South Pacific Ocean, in order to relate these fluxes to bottom–up controls (related to nitrogen, phosphate and labile C availability).
Vincent Taillandier, Thibaut Wagener, Fabrizio D'Ortenzio, Nicolas Mayot, Hervé Legoff, Joséphine Ras, Laurent Coppola, Orens Pasqueron de Fommervault, Catherine Schmechtig, Emilie Diamond, Henry Bittig, Dominique Lefevre, Edouard Leymarie, Antoine Poteau, and Louis Prieur
Earth Syst. Sci. Data, 10, 627–641, https://doi.org/10.5194/essd-10-627-2018, https://doi.org/10.5194/essd-10-627-2018, 2018
Short summary
Short summary
We report on data from an oceanographic cruise, covering western, central and eastern parts of the Mediterranean Sea. This cruise was fully dedicated to the maintenance and the metrological verification of a biogeochemical observing system based on a fleet of BGC-Argo floats.
Pierre Marrec, Gérald Grégori, Andrea M. Doglioli, Mathilde Dugenne, Alice Della Penna, Nagib Bhairy, Thierry Cariou, Sandra Hélias Nunige, Soumaya Lahbib, Gilles Rougier, Thibaut Wagener, and Melilotus Thyssen
Biogeosciences, 15, 1579–1606, https://doi.org/10.5194/bg-15-1579-2018, https://doi.org/10.5194/bg-15-1579-2018, 2018
Short summary
Short summary
The objective of this study was to better understand the variability of the phytoplankton community structure in small physical structures at the surface of the ocean. After identifying such a structure in the Mediterranean Sea, we deployed cutting-edge physical and biological sensors in order to observe at a high frequency the dynamics of this structure. From these observations we described the variations of the phytoplankton community structure and how the physics controls this variability.
Ilana Berman-Frank, Dina Spungin, Eyal Rahav, France Van Wambeke, Kendra Turk-Kubo, and Thierry Moutin
Biogeosciences, 13, 3793–3805, https://doi.org/10.5194/bg-13-3793-2016, https://doi.org/10.5194/bg-13-3793-2016, 2016
Short summary
Short summary
In the marine environment, sticky sugar-containing gels, termed transparent exopolymeric particles (TEP), are produced from biological sources and physical and chemical processes. These compounds are essential vectors enhancing downward flow of organic matter and its storage at depth. Spatial and temporal dynamics of TEPs were followed for 23 days during the VAHINE mesocosm experiment that investigated the fate of nitrogen and carbon derived from organisms fixing atmospheric N2 (diazotrophs).
Marc Tedetti, Lauriane Marie, Rüdiger Röttgers, Martine Rodier, France Van Wambeke, Sandra Helias, Mathieu Caffin, Véronique Cornet-Barthaux, and Cécile Dupouy
Biogeosciences, 13, 3283–3303, https://doi.org/10.5194/bg-13-3283-2016, https://doi.org/10.5194/bg-13-3283-2016, 2016
Short summary
Short summary
In the framework of the VAHINE project, we investigated the spectral characteristics and the variability of dissolved and particulate chromophoric materials throughout a 23-day mesocosm experiment conducted in the south-west Pacific at the mouth of the New Caledonian coral lagoon. We found that the dynamics of CDOM and particulate matter absorption were strongly coupled with those of cyanobacteria Synechococcus spp. and bacterial production.
France Van Wambeke, Ulrike Pfreundt, Aude Barani, Hugo Berthelot, Thierry Moutin, Martine Rodier, Wolfgang R. Hess, and Sophie Bonnet
Biogeosciences, 13, 3187–3202, https://doi.org/10.5194/bg-13-3187-2016, https://doi.org/10.5194/bg-13-3187-2016, 2016
Short summary
Short summary
The phytoplankton is at the base of the plankton food web in large parts of oceanic "deserts" such as the South Pacific Ocean, where nitrogen sources limit activity. Mesocosms were fertilized with phosphorus to stimulate diazotrophy (atmospheric N2 fixation). Mostly diazotroph-derived nitrogen fuelled the heterotrophic bacterial community through indirect processes generating dissolved organic matter and detritus, such as mortality, lysis and grazing of both diazotrophs and non-diazotrophs.
Ulrike Pfreundt, France Van Wambeke, Mathieu Caffin, Sophie Bonnet, and Wolfgang R. Hess
Biogeosciences, 13, 2319–2337, https://doi.org/10.5194/bg-13-2319-2016, https://doi.org/10.5194/bg-13-2319-2016, 2016
Short summary
Short summary
The Southwest Pacific has one of the highest N2 fixation rates in the global ocean, yet information is scarce on the bacterioplankton interrelationships. We detected high microbial diversity in the New Caledonia lagoon and inside a 50 000 L experimental enclosure of the same water mass over 3 weeks and give evidence for previously unknown niche partitioning. Phosphate fertilization promoted the growth of efficient N2 fixing cyanobacteria triggering the growth of most heterotrophic bacteria.
K. Desboeufs, N. Leblond, T. Wagener, E. Bon Nguyen, and C. Guieu
Biogeosciences, 11, 5581–5594, https://doi.org/10.5194/bg-11-5581-2014, https://doi.org/10.5194/bg-11-5581-2014, 2014
Related subject area
Oceanography
DalROMS-NWA12 v1.0, a coupled circulation–ice–biogeochemistry modelling system for the northwest Atlantic Ocean: development and validation
A revised ocean mixed layer model for better simulating the diurnal variation in ocean skin temperature
Evaluating an accelerated forcing approach for improving computational efficiency in coupled ice sheet–ocean modelling
An optimal transformation method for inferring ocean tracer sources and sinks
PPCon 1.0: Biogeochemical-Argo profile prediction with 1D convolutional networks
Experimental design for the Marine Ice Sheet–Ocean Model Intercomparison Project – phase 2 (MISOMIP2)
Development of a total variation diminishing (TVD) sea ice transport scheme and its application in an ocean (SCHISM v5.11) and sea ice (Icepack v1.3.4) coupled model on unstructured grids
Spurious numerical mixing under strong tidal forcing: a case study in the south-east Asian seas using the Symphonie model (v3.1.2)
Modelling the water isotope distribution in the Mediterranean Sea using a high-resolution oceanic model (NEMO-MED12-watiso v1.0): evaluation of model results against in situ observations
LIGHT-bgcArgo-1.0: using synthetic float capabilities in E3SMv2 to assess spatiotemporal variability in ocean physics and biogeochemistry
HIDRA3: a robust deep-learning model for multi-point ensemble sea level forecasting
Towards a real-time modeling of global ocean waves by the fully GPU-accelerated spectral wave model WAM6-GPU v1.0
A simple approach to represent precipitation-derived freshwater fluxes into nearshore ocean models: an FVCOM4.1 case study of Quatsino Sound, British Columbia
An optimal transformation method applied to diagnose the ocean carbon budget
Implementation and assessment of a model including mixotrophs and the carbonate cycle (Eco3M_MIX-CarbOx v1.0) in a highly dynamic Mediterranean coastal environment (Bay of Marseille, France) – Part 2: Towards a better representation of total alkalinity when modeling the carbonate system and air–sea CO2 fluxes
Development of a novel storm surge inundation model framework for efficient prediction
The Ross Sea and Amundsen Sea Ice-Sea Model (RAISE v1.0): a high-resolution ocean-sea ice-ice shelf coupling model for simulating the Dense Shelf Water and Antarctic Bottom Water in the Ross Sea, Antarctica
Skin sea surface temperature schemes in coupled ocean–atmosphere modelling: the impact of chlorophyll-interactive e-folding depth
A wave-resolving 2DV Lagrangian approach to model microplastic transport in the nearshore
DELWAVE 1.0: deep learning surrogate model of surface wave climate in the Adriatic Basin
StraitFlux – precise computations of water strait fluxes on various modeling grids
Comparison of the Coastal and Regional Ocean COmmunity model (CROCO) and NCAR-LES in non-hydrostatic simulations
HOTSSea v1: a NEMO-based physical Hindcast of the Salish Sea (1980–2018) supporting ecosystem model development
Intercomparisons of Tracker v1.1 and four other ocean particle-tracking software packages in the Regional Ocean Modeling System
CAR36, a regional high-resolution ocean forecasting system for improving drift and beaching of Sargassum in the Caribbean archipelago
Implementation of additional spectral wave field exchanges in a three-dimensional wave–current coupled WAVEWATCH-III (version 6.07) and CROCO (version 1.2) configuration: assessment of their implications for macro-tidal coastal hydrodynamics
Comparison of 4-dimensional variational and ensemble optimal interpolation data assimilation systems using a Regional Ocean Modeling System (v3.4) configuration of the eddy-dominated East Australian Current system
LOCATE v1.0: numerical modelling of floating marine debris dispersion in coastal regions using Parcels v2.4.2
New insights into the South China Sea throughflow and water budget seasonal cycle: evaluation and analysis of a high-resolution configuration of the ocean model SYMPHONIE version 2.4
MQGeometry-1.0: a multi-layer quasi-geostrophic solver on non-rectangular geometries
Parameter estimation for ocean background vertical diffusivity coefficients in the Community Earth System Model (v1.2.1) and its impact on El Niño–Southern Oscillation forecasts
Great Lakes wave forecast system on high-resolution unstructured meshes
Impact of increased resolution on Arctic Ocean simulations in Ocean Model Intercomparison Project phase 2 (OMIP-2)
A high-resolution physical–biogeochemical model for marine resource applications in the northwest Atlantic (MOM6-COBALT-NWA12 v1.0)
A flexible z-layers approach for the accurate representation of free surface flows in a coastal ocean model (SHYFEM v. 7_5_71)
Ocean wave tracing v.1: a numerical solver of the wave ray equations for ocean waves on variable currents at arbitrary depths
Design and evaluation of an efficient high-precision ocean surface wave model with a multiscale grid system (MSG_Wav1.0)
Evaluation of the CMCC global eddying ocean model for the Ocean Model Intercomparison Project (OMIP2)
Barents-2.5km v2.0: an operational data-assimilative coupled ocean and sea ice ensemble prediction model for the Barents Sea and Svalbard
Open-ocean tides simulated by ICON-O, version icon-2.6.6
Using Probability Density Functions to Evaluate Models (PDFEM, v1.0) to compare a biogeochemical model with satellite-derived chlorophyll
Data assimilation sensitivity experiments in the East Auckland Current system using 4D-Var
Using the COAsT Python package to develop a standardised validation workflow for ocean physics models
Improving Antarctic Bottom Water precursors in NEMO for climate applications
Formulation, optimization, and sensitivity of NitrOMZv1.0, a biogeochemical model of the nitrogen cycle in oceanic oxygen minimum zones
Waves in SKRIPS: WAVEWATCH III coupling implementation and a case study of Tropical Cyclone Mekunu
Adding sea ice effects to a global operational model (NEMO v3.6) for forecasting total water level: approach and impact
Enhanced ocean wave modeling by including effect of breaking under both deep- and shallow-water conditions
An internal solitary wave forecasting model in the northern South China Sea (ISWFM-NSCS)
The 3D biogeochemical marine mercury cycling model MERCY v2.0 – linking atmospheric Hg to methylmercury in fish
Kyoko Ohashi, Arnaud Laurent, Christoph Renkl, Jinyu Sheng, Katja Fennel, and Eric Oliver
Geosci. Model Dev., 17, 8697–8733, https://doi.org/10.5194/gmd-17-8697-2024, https://doi.org/10.5194/gmd-17-8697-2024, 2024
Short summary
Short summary
We developed a modelling system of the northwest Atlantic Ocean that simulates the currents, temperature, salinity, and parts of the biochemical cycle of the ocean, as well as sea ice. The system combines advanced, open-source models and can be used to study, for example, the ocean capture of atmospheric carbon dioxide, which is a key process in the global climate. The system produces realistic results, and we use it to investigate the roles of tides and sea ice in the northwest Atlantic Ocean.
Eui-Jong Kang, Byung-Ju Sohn, Sang-Woo Kim, Wonho Kim, Young-Cheol Kwon, Seung-Bum Kim, Hyoung-Wook Chun, and Chao Liu
Geosci. Model Dev., 17, 8553–8568, https://doi.org/10.5194/gmd-17-8553-2024, https://doi.org/10.5194/gmd-17-8553-2024, 2024
Short summary
Short summary
Sea surface temperature (SST) is vital in climate, weather, and ocean sciences because it influences air–sea interactions. Errors in the ECMWF model's scheme for predicting ocean skin temperature prompted a revision of the ocean mixed layer model. Validation against infrared measurements and buoys showed a good correlation with minimal deviations. The revised model accurately simulates SST variations and aligns with solar radiation distributions, showing promise for weather and climate models.
Qin Zhou, Chen Zhao, Rupert Gladstone, Tore Hattermann, David Gwyther, and Benjamin Galton-Fenzi
Geosci. Model Dev., 17, 8243–8265, https://doi.org/10.5194/gmd-17-8243-2024, https://doi.org/10.5194/gmd-17-8243-2024, 2024
Short summary
Short summary
We introduce an accelerated forcing approach to address timescale discrepancies between the ice sheets and ocean components in coupled modelling by reducing the ocean simulation duration. The approach is evaluated using idealized coupled models, and its limitations in real-world applications are discussed. Our results suggest it can be a valuable tool for process-oriented coupled ice sheet–ocean modelling and downscaling climate simulations with such models.
Jan D. Zika and Taimoor Sohail
Geosci. Model Dev., 17, 8049–8068, https://doi.org/10.5194/gmd-17-8049-2024, https://doi.org/10.5194/gmd-17-8049-2024, 2024
Short summary
Short summary
We describe a method to relate fluxes of heat and freshwater at the sea surface to the resulting distribution of seawater among categories such as warm and salty or cold and salty. The method exploits the laws that govern how heat and salt change when water mixes. The method will allow the climate community to improve estimates of how much heat the ocean is absorbing and how rainfall and evaporation are changing across the globe.
Gloria Pietropolli, Luca Manzoni, and Gianpiero Cossarini
Geosci. Model Dev., 17, 7347–7364, https://doi.org/10.5194/gmd-17-7347-2024, https://doi.org/10.5194/gmd-17-7347-2024, 2024
Short summary
Short summary
Monitoring the ocean is essential for studying marine life and human impact. Our new software, PPCon, uses ocean data to predict key factors like nitrate and chlorophyll levels, which are hard to measure directly. By leveraging machine learning, PPCon offers more accurate and efficient predictions.
Jan De Rydt, Nicolas C. Jourdain, Yoshihiro Nakayama, Mathias van Caspel, Ralph Timmermann, Pierre Mathiot, Xylar S. Asay-Davis, Hélène Seroussi, Pierre Dutrieux, Ben Galton-Fenzi, David Holland, and Ronja Reese
Geosci. Model Dev., 17, 7105–7139, https://doi.org/10.5194/gmd-17-7105-2024, https://doi.org/10.5194/gmd-17-7105-2024, 2024
Short summary
Short summary
Global climate models do not reliably simulate sea-level change due to ice-sheet–ocean interactions. We propose a community modelling effort to conduct a series of well-defined experiments to compare models with observations and study how models respond to a range of perturbations in climate and ice-sheet geometry. The second Marine Ice Sheet–Ocean Model Intercomparison Project will continue to lay the groundwork for including ice-sheet–ocean interactions in global-scale IPCC-class models.
Qian Wang, Yang Zhang, Fei Chai, Y. Joseph Zhang, and Lorenzo Zampieri
Geosci. Model Dev., 17, 7067–7081, https://doi.org/10.5194/gmd-17-7067-2024, https://doi.org/10.5194/gmd-17-7067-2024, 2024
Short summary
Short summary
We coupled an unstructured hydro-model with an advanced column sea ice model to meet the growing demand for increased resolution and complexity in unstructured sea ice models. Additionally, we present a novel tracer transport scheme for the sea ice coupled model and demonstrate that this scheme fulfills the requirements for conservation, accuracy, efficiency, and monotonicity in an idealized test. Our new coupled model also has good performance in realistic tests.
Adrien Garinet, Marine Herrmann, Patrick Marsaleix, and Juliette Pénicaud
Geosci. Model Dev., 17, 6967–6986, https://doi.org/10.5194/gmd-17-6967-2024, https://doi.org/10.5194/gmd-17-6967-2024, 2024
Short summary
Short summary
Mixing is a crucial aspect of the ocean, but its accurate representation in computer simulations is made challenging by errors that result in unwanted mixing, compromising simulation realism. Here we illustrate the spurious effect that tides can have on simulations of south-east Asia. Although they play an important role in determining the state of the ocean, they can increase numerical errors and make simulation outputs less realistic. We also provide insights into how to reduce these errors.
Mohamed Ayache, Jean-Claude Dutay, Anne Mouchet, Kazuyo Tachikawa, Camille Risi, and Gilles Ramstein
Geosci. Model Dev., 17, 6627–6655, https://doi.org/10.5194/gmd-17-6627-2024, https://doi.org/10.5194/gmd-17-6627-2024, 2024
Short summary
Short summary
Water isotopes (δ18O, δD) are one of the most widely used proxies in ocean climate research. Previous studies using water isotope observations and modelling have highlighted the importance of understanding spatial and temporal isotopic variability for a quantitative interpretation of these tracers. Here we present the first results of a high-resolution regional dynamical model (at 1/12° horizontal resolution) developed for the Mediterranean Sea, one of the hotspots of ongoing climate change.
Cara Nissen, Nicole S. Lovenduski, Mathew Maltrud, Alison R. Gray, Yohei Takano, Kristen Falcinelli, Jade Sauvé, and Katherine Smith
Geosci. Model Dev., 17, 6415–6435, https://doi.org/10.5194/gmd-17-6415-2024, https://doi.org/10.5194/gmd-17-6415-2024, 2024
Short summary
Short summary
Autonomous profiling floats have provided unprecedented observational coverage of the global ocean, but uncertainties remain about whether their sampling frequency and density capture the true spatiotemporal variability of physical, biogeochemical, and biological properties. Here, we present the novel synthetic biogeochemical float capabilities of the Energy Exascale Earth System Model version 2 and demonstrate their utility as a test bed to address these uncertainties.
Marko Rus, Hrvoje Mihanović, Matjaž Ličer, and Matej Kristan
EGUsphere, https://doi.org/10.5194/egusphere-2024-2068, https://doi.org/10.5194/egusphere-2024-2068, 2024
Short summary
Short summary
HIDRA3 is a novel deep-learning model for predicting sea levels and storm surges, offering significant improvements over previous models and numerical simulations. It utilizes data from multiple tide gauges, enhancing predictions even with limited historical data and during sensor outages. With its advanced architecture, HIDRA3 outperforms the current state-of-the-art models by achieving up to 15 % lower mean absolute error, proving effective for coastal flood forecasting in diverse conditions.
Ye Yuan, Fujiang Yu, Zhi Chen, Xueding Li, Fang Hou, Yuanyong Gao, Zhiyi Gao, and Renbo Pang
Geosci. Model Dev., 17, 6123–6136, https://doi.org/10.5194/gmd-17-6123-2024, https://doi.org/10.5194/gmd-17-6123-2024, 2024
Short summary
Short summary
Accurate and timely forecasting of ocean waves is of great importance to the safety of marine transportation and offshore engineering. In this study, GPU-accelerated computing is introduced in WAve Modeling Cycle 6 (WAM6). With this effort, global high-resolution wave simulations can now run on GPUs up to tens of times faster than the currently available models can on a CPU node with results that are just as accurate.
Krysten Rutherford, Laura Bianucci, and William Floyd
Geosci. Model Dev., 17, 6083–6104, https://doi.org/10.5194/gmd-17-6083-2024, https://doi.org/10.5194/gmd-17-6083-2024, 2024
Short summary
Short summary
Nearshore ocean models often lack complete information about freshwater fluxes due to numerous ungauged rivers and streams. We tested a simple rain-based hydrological model as inputs into an ocean model of Quatsino Sound, Canada, with the aim of improving the representation of the land–ocean connection in the nearshore model. Through multiple tests, we found that the performance of the ocean model improved when providing 60 % or more of the freshwater inputs from the simple runoff model.
Neill Mackay, Taimoor Sohail, Jan David Zika, Richard G. Williams, Oliver Andrews, and Andrew James Watson
Geosci. Model Dev., 17, 5987–6005, https://doi.org/10.5194/gmd-17-5987-2024, https://doi.org/10.5194/gmd-17-5987-2024, 2024
Short summary
Short summary
The ocean absorbs carbon dioxide from the atmosphere, mitigating climate change, but estimates of the uptake do not always agree. There is a need to reconcile these differing estimates and to improve our understanding of ocean carbon uptake. We present a new method for estimating ocean carbon uptake and test it with model data. The method effectively diagnoses the ocean carbon uptake from limited data and therefore shows promise for reconciling different observational estimates.
Lucille Barré, Frédéric Diaz, Thibaut Wagener, Camille Mazoyer, Christophe Yohia, and Christel Pinazo
Geosci. Model Dev., 17, 5851–5882, https://doi.org/10.5194/gmd-17-5851-2024, https://doi.org/10.5194/gmd-17-5851-2024, 2024
Short summary
Short summary
The carbonate system is typically studied using measurements, but modeling can contribute valuable insights. Using a biogeochemical model, we propose a new representation of total alkalinity, dissolved inorganic carbon, pCO2, and pH in a highly dynamic Mediterranean coastal area, the Bay of Marseille, a useful addition to measurements. Through a detailed analysis of pCO2 and air–sea CO2 fluxes, we show that variations are strongly impacted by the hydrodynamic processes that affect the bay.
Xuanxuan Gao, Shuiqing Li, Dongxue Mo, Yahao Liu, and Po Hu
Geosci. Model Dev., 17, 5497–5509, https://doi.org/10.5194/gmd-17-5497-2024, https://doi.org/10.5194/gmd-17-5497-2024, 2024
Short summary
Short summary
Storm surges generate coastal inundation and expose populations and properties to danger. We developed a novel storm surge inundation model for efficient prediction. Estimates compare well with in situ measurements and results from a numerical model. The new model is a significant improvement on existing numerical models, with much higher computational efficiency and stability, which allows timely disaster prevention and mitigation.
Zhaoru Zhang, Chuan Xie, Chuning Wang, Yuanjie Chen, Heng Hu, and Xiaoqiao Wang
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2024-128, https://doi.org/10.5194/gmd-2024-128, 2024
Revised manuscript accepted for GMD
Short summary
Short summary
A coupled fine-resolution ocean-ice model is developed for the Ross Sea and adjacent regions in Antarctica, a key area for the formation of global ocean bottom water — the Antarctic Bottom Water (AABW) that affects the world ocean circulation. The model has high skills in simulating sea ice production driving the AABW source water formation and water mass properties when assessed against observations. A model experiment shows significant impact of ice shelf melting on the AABW characteristics.
Vincenzo de Toma, Daniele Ciani, Yassmin Hesham Essa, Chunxue Yang, Vincenzo Artale, Andrea Pisano, Davide Cavaliere, Rosalia Santoleri, and Andrea Storto
Geosci. Model Dev., 17, 5145–5165, https://doi.org/10.5194/gmd-17-5145-2024, https://doi.org/10.5194/gmd-17-5145-2024, 2024
Short summary
Short summary
This study explores methods to reconstruct diurnal variations in skin sea surface temperature in a model of the Mediterranean Sea. Our new approach, considering chlorophyll concentration, enhances spatial and temporal variations in the warm layer. Comparative analysis shows context-dependent improvements. The proposed "chlorophyll-interactive" method brings the surface net total heat flux closer to zero annually, despite a net heat loss from the ocean to the atmosphere.
Isabel Jalón-Rojas, Damien Sous, and Vincent Marieu
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2024-100, https://doi.org/10.5194/gmd-2024-100, 2024
Revised manuscript accepted for GMD
Short summary
Short summary
This study presents a novel modeling approach for understanding microplastic transport in coastal waters. The model accurately replicates experimental data and reveals key transport mechanisms. The findings enhance our knowledge of how microplastics move in nearshore environments, aiding in coastal management and efforts to combat plastic pollution globally.
Peter Mlakar, Antonio Ricchi, Sandro Carniel, Davide Bonaldo, and Matjaž Ličer
Geosci. Model Dev., 17, 4705–4725, https://doi.org/10.5194/gmd-17-4705-2024, https://doi.org/10.5194/gmd-17-4705-2024, 2024
Short summary
Short summary
We propose a new point-prediction model, the DEep Learning WAVe Emulating model (DELWAVE), which successfully emulates the Simulating WAves Nearshore model (SWAN) over synoptic to climate timescales. Compared to control climatology over all wind directions, the mismatch between DELWAVE and SWAN is generally small compared to the difference between scenario and control conditions, suggesting that the noise introduced by surrogate modelling is substantially weaker than the climate change signal.
Susanna Winkelbauer, Michael Mayer, and Leopold Haimberger
Geosci. Model Dev., 17, 4603–4620, https://doi.org/10.5194/gmd-17-4603-2024, https://doi.org/10.5194/gmd-17-4603-2024, 2024
Short summary
Short summary
Oceanic transports shape the global climate, but the evaluation and validation of this key quantity based on reanalysis and model data are complicated by the distortion of the used modelling grids and the large number of different grid types. We present two new methods that allow the calculation of oceanic fluxes of volume, heat, salinity, and ice through almost arbitrary sections for various models and reanalyses that are independent of the used modelling grids.
Xiaoyu Fan, Baylor Fox-Kemper, Nobuhiro Suzuki, Qing Li, Patrick Marchesiello, Peter P. Sullivan, and Paul S. Hall
Geosci. Model Dev., 17, 4095–4113, https://doi.org/10.5194/gmd-17-4095-2024, https://doi.org/10.5194/gmd-17-4095-2024, 2024
Short summary
Short summary
Simulations of the oceanic turbulent boundary layer using the nonhydrostatic CROCO ROMS and NCAR-LES models are compared. CROCO and the NCAR-LES are accurate in a similar manner, but CROCO’s additional features (e.g., nesting and realism) and its compressible turbulence formulation carry additional costs.
Greig Oldford, Tereza Jarníková, Villy Christensen, and Michael Dunphy
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2024-58, https://doi.org/10.5194/gmd-2024-58, 2024
Revised manuscript accepted for GMD
Short summary
Short summary
We developed a physical ocean model called the Hindcast of the Salish Sea (HOTSSea) that recreates conditions throughout the Salish Sea from 1980 to 2018, filling in the gaps in patchy measurements. The model predicts physical ocean properties with sufficient accuracy to be useful for a variety of applications. The model corroborates observed ocean temperature trends and was used to examine areas with few observations. Results indicate that some seasons and areas are warming faster than others.
Jilian Xiong and Parker MacCready
Geosci. Model Dev., 17, 3341–3356, https://doi.org/10.5194/gmd-17-3341-2024, https://doi.org/10.5194/gmd-17-3341-2024, 2024
Short summary
Short summary
The new offline particle tracking package, Tracker v1.1, is introduced to the Regional Ocean Modeling System, featuring an efficient nearest-neighbor algorithm to enhance particle-tracking speed. Its performance was evaluated against four other tracking packages and passive dye. Despite unique features, all packages yield comparable results. Running multiple packages within the same circulation model allows comparison of their performance and ease of use.
Sylvain Cailleau, Laurent Bessières, Léonel Chiendje, Flavie Dubost, Guillaume Reffray, Jean-Michel Lellouche, Simon van Gennip, Charly Régnier, Marie Drevillon, Marc Tressol, Matthieu Clavier, Julien Temple-Boyer, and Léo Berline
Geosci. Model Dev., 17, 3157–3173, https://doi.org/10.5194/gmd-17-3157-2024, https://doi.org/10.5194/gmd-17-3157-2024, 2024
Short summary
Short summary
In order to improve Sargassum drift forecasting in the Caribbean area, drift models can be forced by higher-resolution ocean currents. To this goal a 3 km resolution regional ocean model has been developed. Its assessment is presented with a particular focus on the reproduction of fine structures representing key features of the Caribbean region dynamics and Sargassum transport. The simulated propagation of a North Brazil Current eddy and its dissipation was found to be quite realistic.
Gaetano Porcile, Anne-Claire Bennis, Martial Boutet, Sophie Le Bot, Franck Dumas, and Swen Jullien
Geosci. Model Dev., 17, 2829–2853, https://doi.org/10.5194/gmd-17-2829-2024, https://doi.org/10.5194/gmd-17-2829-2024, 2024
Short summary
Short summary
Here a new method of modelling the interaction between ocean currents and waves is presented. We developed an advanced coupling of two models, one for ocean currents and one for waves. In previous couplings, some wave-related calculations were based on simplified assumptions. Our method uses more complex calculations to better represent wave–current interactions. We tested it in a macro-tidal coastal area and found that it significantly improves the model accuracy, especially during storms.
Colette Gabrielle Kerry, Moninya Roughan, Shane Keating, David Gwyther, Gary Brassington, Adil Siripatana, and Joao Marcos A. C. Souza
Geosci. Model Dev., 17, 2359–2386, https://doi.org/10.5194/gmd-17-2359-2024, https://doi.org/10.5194/gmd-17-2359-2024, 2024
Short summary
Short summary
Ocean forecasting relies on the combination of numerical models and ocean observations through data assimilation (DA). Here we assess the performance of two DA systems in a dynamic western boundary current, the East Australian Current, across a common modelling and observational framework. We show that the more advanced, time-dependent method outperforms the time-independent method for forecast horizons of 5 d. This advocates the use of advanced methods for highly variable oceanic regions.
Ivan Hernandez, Leidy M. Castro-Rosero, Manuel Espino, and Jose M. Alsina Torrent
Geosci. Model Dev., 17, 2221–2245, https://doi.org/10.5194/gmd-17-2221-2024, https://doi.org/10.5194/gmd-17-2221-2024, 2024
Short summary
Short summary
The LOCATE numerical model was developed to conduct Lagrangian simulations of the transport and dispersion of marine debris at coastal scales. High-resolution hydrodynamic data and a beaching module that used particle distance to the shore for land–water boundary detection were used on a realistic debris discharge scenario comparing hydrodynamic data at various resolutions. Coastal processes and complex geometric structures were resolved when using nested grids and distance-to-shore beaching.
Ngoc B. Trinh, Marine Herrmann, Caroline Ulses, Patrick Marsaleix, Thomas Duhaut, Thai To Duy, Claude Estournel, and R. Kipp Shearman
Geosci. Model Dev., 17, 1831–1867, https://doi.org/10.5194/gmd-17-1831-2024, https://doi.org/10.5194/gmd-17-1831-2024, 2024
Short summary
Short summary
A high-resolution model was built to study the South China Sea (SCS) water, heat, and salt budgets. Model performance is demonstrated by comparison with observations and simulations. Important discards are observed if calculating offline, instead of online, lateral inflows and outflows of water, heat, and salt. The SCS mainly receives water from the Luzon Strait and releases it through the Mindoro, Taiwan, and Karimata straits. SCS surface interocean water exchanges are driven by monsoon winds.
Louis Thiry, Long Li, Guillaume Roullet, and Etienne Mémin
Geosci. Model Dev., 17, 1749–1764, https://doi.org/10.5194/gmd-17-1749-2024, https://doi.org/10.5194/gmd-17-1749-2024, 2024
Short summary
Short summary
We present a new way of solving the quasi-geostrophic (QG) equations, a simple set of equations describing ocean dynamics. Our method is solely based on the numerical methods used to solve the equations and requires no parameter tuning. Moreover, it can handle non-rectangular geometries, opening the way to study QG equations on realistic domains. We release a PyTorch implementation to ease future machine-learning developments on top of the presented method.
Zheqi Shen, Yihao Chen, Xiaojing Li, and Xunshu Song
Geosci. Model Dev., 17, 1651–1665, https://doi.org/10.5194/gmd-17-1651-2024, https://doi.org/10.5194/gmd-17-1651-2024, 2024
Short summary
Short summary
Parameter estimation is the process that optimizes model parameters using observations, which could reduce model errors and improve forecasting. In this study, we conducted parameter estimation experiments using the CESM and the ensemble adjustment Kalman filter. The obtained initial conditions and parameters are used to perform ensemble forecast experiments for ENSO forecasting. The results revealed that parameter estimation could reduce analysis errors and improve ENSO forecast skills.
Ali Abdolali, Saeideh Banihashemi, Jose Henrique Alves, Aron Roland, Tyler J. Hesser, Mary Anderson Bryant, and Jane McKee Smith
Geosci. Model Dev., 17, 1023–1039, https://doi.org/10.5194/gmd-17-1023-2024, https://doi.org/10.5194/gmd-17-1023-2024, 2024
Short summary
Short summary
This article presents an overview of the development and implementation of Great Lake Wave Unstructured (GLWUv2.0), including the core model and workflow design and development. The validation was conducted against in situ data for the re-forecasted duration for summer and wintertime (ice season). The article describes the limitations and challenges encountered in the operational environment and the path forward for the next generation of wave forecast systems in enclosed basins like the GL.
Qiang Wang, Qi Shu, Alexandra Bozec, Eric P. Chassignet, Pier Giuseppe Fogli, Baylor Fox-Kemper, Andy McC. Hogg, Doroteaciro Iovino, Andrew E. Kiss, Nikolay Koldunov, Julien Le Sommer, Yiwen Li, Pengfei Lin, Hailong Liu, Igor Polyakov, Patrick Scholz, Dmitry Sidorenko, Shizhu Wang, and Xiaobiao Xu
Geosci. Model Dev., 17, 347–379, https://doi.org/10.5194/gmd-17-347-2024, https://doi.org/10.5194/gmd-17-347-2024, 2024
Short summary
Short summary
Increasing resolution improves model skills in simulating the Arctic Ocean, but other factors such as parameterizations and numerics are at least of the same importance for obtaining reliable simulations.
Andrew C. Ross, Charles A. Stock, Alistair Adcroft, Enrique Curchitser, Robert Hallberg, Matthew J. Harrison, Katherine Hedstrom, Niki Zadeh, Michael Alexander, Wenhao Chen, Elizabeth J. Drenkard, Hubert du Pontavice, Raphael Dussin, Fabian Gomez, Jasmin G. John, Dujuan Kang, Diane Lavoie, Laure Resplandy, Alizée Roobaert, Vincent Saba, Sang-Ik Shin, Samantha Siedlecki, and James Simkins
Geosci. Model Dev., 16, 6943–6985, https://doi.org/10.5194/gmd-16-6943-2023, https://doi.org/10.5194/gmd-16-6943-2023, 2023
Short summary
Short summary
We evaluate a model for northwest Atlantic Ocean dynamics and biogeochemistry that balances high resolution with computational economy by building on the new regional features in the MOM6 ocean model and COBALT biogeochemical model. We test the model's ability to simulate impactful historical variability and find that the model simulates the mean state and variability of most features well, which suggests the model can provide information to inform living-marine-resource applications.
Luca Arpaia, Christian Ferrarin, Marco Bajo, and Georg Umgiesser
Geosci. Model Dev., 16, 6899–6919, https://doi.org/10.5194/gmd-16-6899-2023, https://doi.org/10.5194/gmd-16-6899-2023, 2023
Short summary
Short summary
We propose a discrete multilayer shallow water model based on z-layers which, thanks to the insertion and removal of surface layers, can deal with an arbitrarily large tidal oscillation independently of the vertical resolution. The algorithm is based on a two-step procedure used in numerical simulations with moving boundaries (grid movement followed by a grid topology change, that is, the insertion/removal of surface layers), which avoids the appearance of very thin surface layers.
Trygve Halsne, Kai Håkon Christensen, Gaute Hope, and Øyvind Breivik
Geosci. Model Dev., 16, 6515–6530, https://doi.org/10.5194/gmd-16-6515-2023, https://doi.org/10.5194/gmd-16-6515-2023, 2023
Short summary
Short summary
Surface waves that propagate in oceanic or coastal environments get influenced by their surroundings. Changes in the ambient current or the depth profile affect the wave propagation path, and the change in wave direction is called refraction. Some analytical solutions to the governing equations exist under ideal conditions, but for realistic situations, the equations must be solved numerically. Here we present such a numerical solver under an open-source license.
Jiangyu Li, Shaoqing Zhang, Qingxiang Liu, Xiaolin Yu, and Zhiwei Zhang
Geosci. Model Dev., 16, 6393–6412, https://doi.org/10.5194/gmd-16-6393-2023, https://doi.org/10.5194/gmd-16-6393-2023, 2023
Short summary
Short summary
Ocean surface waves play an important role in the air–sea interface but are rarely activated in high-resolution Earth system simulations due to their expensive computational costs. To alleviate this situation, this paper designs a new wave modeling framework with a multiscale grid system. Evaluations of a series of numerical experiments show that it has good feasibility and applicability in the WAVEWATCH III model, WW3, and can achieve the goals of efficient and high-precision wave simulation.
Doroteaciro Iovino, Pier Giuseppe Fogli, and Simona Masina
Geosci. Model Dev., 16, 6127–6159, https://doi.org/10.5194/gmd-16-6127-2023, https://doi.org/10.5194/gmd-16-6127-2023, 2023
Short summary
Short summary
This paper describes the model performance of three global ocean–sea ice configurations, from non-eddying (1°) to eddy-rich (1/16°) resolutions. Model simulations are obtained following the Ocean Model Intercomparison Project phase 2 (OMIP2) protocol. We compare key global climate variables across the three models and against observations, emphasizing the relative advantages and disadvantages of running forced ocean–sea ice models at higher resolution.
Johannes Röhrs, Yvonne Gusdal, Edel S. U. Rikardsen, Marina Durán Moro, Jostein Brændshøi, Nils Melsom Kristensen, Sindre Fritzner, Keguang Wang, Ann Kristin Sperrevik, Martina Idžanović, Thomas Lavergne, Jens Boldingh Debernard, and Kai H. Christensen
Geosci. Model Dev., 16, 5401–5426, https://doi.org/10.5194/gmd-16-5401-2023, https://doi.org/10.5194/gmd-16-5401-2023, 2023
Short summary
Short summary
A model to predict ocean currents, temperature, and sea ice is presented, covering the Barents Sea and northern Norway. To quantify forecast uncertainties, the model calculates ensemble forecasts with 24 realizations of ocean and ice conditions. Observations from satellites, buoys, and ships are ingested by the model. The model forecasts are compared with observations, and we show that the ocean model has skill in predicting sea surface temperatures.
Jin-Song von Storch, Eileen Hertwig, Veit Lüschow, Nils Brüggemann, Helmuth Haak, Peter Korn, and Vikram Singh
Geosci. Model Dev., 16, 5179–5196, https://doi.org/10.5194/gmd-16-5179-2023, https://doi.org/10.5194/gmd-16-5179-2023, 2023
Short summary
Short summary
The new ocean general circulation model ICON-O is developed for running experiments at kilometer scales and beyond. One targeted application is to simulate internal tides crucial for ocean mixing. To ensure their realism, which is difficult to assess, we evaluate the barotropic tides that generate internal tides. We show that ICON-O is able to realistically simulate the major aspects of the observed barotropic tides and discuss the aspects that impact the quality of the simulated tides.
Bror F. Jönsson, Christopher L. Follett, Jacob Bien, Stephanie Dutkiewicz, Sangwon Hyun, Gemma Kulk, Gael L. Forget, Christian Müller, Marie-Fanny Racault, Christopher N. Hill, Thomas Jackson, and Shubha Sathyendranath
Geosci. Model Dev., 16, 4639–4657, https://doi.org/10.5194/gmd-16-4639-2023, https://doi.org/10.5194/gmd-16-4639-2023, 2023
Short summary
Short summary
While biogeochemical models and satellite-derived ocean color data provide unprecedented information, it is problematic to compare them. Here, we present a new approach based on comparing probability density distributions of model and satellite properties to assess model skills. We also introduce Earth mover's distances as a novel and powerful metric to quantify the misfit between models and observations. We find that how 3D chlorophyll fields are aggregated can be a significant source of error.
Rafael Santana, Helen Macdonald, Joanne O'Callaghan, Brian Powell, Sarah Wakes, and Sutara H. Suanda
Geosci. Model Dev., 16, 3675–3698, https://doi.org/10.5194/gmd-16-3675-2023, https://doi.org/10.5194/gmd-16-3675-2023, 2023
Short summary
Short summary
We show the importance of assimilating subsurface temperature and velocity data in a model of the East Auckland Current. Assimilation of velocity increased the representation of large oceanic vortexes. Assimilation of temperature is needed to correctly simulate temperatures around 100 m depth, which is the most difficult region to simulate in ocean models. Our simulations showed improved results in comparison to the US Navy global model and highlight the importance of regional models.
David Byrne, Jeff Polton, Enda O'Dea, and Joanne Williams
Geosci. Model Dev., 16, 3749–3764, https://doi.org/10.5194/gmd-16-3749-2023, https://doi.org/10.5194/gmd-16-3749-2023, 2023
Short summary
Short summary
Validation is a crucial step during the development of models for ocean simulation. The purpose of validation is to assess how accurate a model is. It is most commonly done by comparing output from a model to actual observations. In this paper, we introduce and demonstrate usage of the COAsT Python package to standardise the validation process for physical ocean models. We also discuss our five guiding principles for standardised validation.
Katherine Hutchinson, Julie Deshayes, Christian Éthé, Clément Rousset, Casimir de Lavergne, Martin Vancoppenolle, Nicolas C. Jourdain, and Pierre Mathiot
Geosci. Model Dev., 16, 3629–3650, https://doi.org/10.5194/gmd-16-3629-2023, https://doi.org/10.5194/gmd-16-3629-2023, 2023
Short summary
Short summary
Bottom Water constitutes the lower half of the ocean’s overturning system and is primarily formed in the Weddell and Ross Sea in the Antarctic due to interactions between the atmosphere, ocean, sea ice and ice shelves. Here we use a global ocean 1° resolution model with explicit representation of the three large ice shelves important for the formation of the parent waters of Bottom Water. We find doing so reduces salt biases, improves water mass realism and gives realistic ice shelf melt rates.
Daniele Bianchi, Daniel McCoy, and Simon Yang
Geosci. Model Dev., 16, 3581–3609, https://doi.org/10.5194/gmd-16-3581-2023, https://doi.org/10.5194/gmd-16-3581-2023, 2023
Short summary
Short summary
We present NitrOMZ, a new model of the oceanic nitrogen cycle that simulates chemical transformations within oxygen minimum zones (OMZs). We describe the model formulation and its implementation in a one-dimensional representation of the water column before evaluating its ability to reproduce observations in the eastern tropical South Pacific. We conclude by describing the model sensitivity to parameter choices and environmental factors and its application to nitrogen cycling in the ocean.
Rui Sun, Alison Cobb, Ana B. Villas Bôas, Sabique Langodan, Aneesh C. Subramanian, Matthew R. Mazloff, Bruce D. Cornuelle, Arthur J. Miller, Raju Pathak, and Ibrahim Hoteit
Geosci. Model Dev., 16, 3435–3458, https://doi.org/10.5194/gmd-16-3435-2023, https://doi.org/10.5194/gmd-16-3435-2023, 2023
Short summary
Short summary
In this work, we integrated the WAVEWATCH III model into the regional coupled model SKRIPS. We then performed a case study using the newly implemented model to study Tropical Cyclone Mekunu, which occurred in the Arabian Sea. We found that the coupled model better simulates the cyclone than the uncoupled model, but the impact of waves on the cyclone is not significant. However, the waves change the sea surface temperature and mixed layer, especially in the cold waves produced due to the cyclone.
Pengcheng Wang and Natacha B. Bernier
Geosci. Model Dev., 16, 3335–3354, https://doi.org/10.5194/gmd-16-3335-2023, https://doi.org/10.5194/gmd-16-3335-2023, 2023
Short summary
Short summary
Effects of sea ice are typically neglected in operational flood forecast systems. In this work, we capture these effects via the addition of a parameterized ice–ocean stress. The parameterization takes advantage of forecast fields from an advanced ice–ocean model and features a novel, consistent representation of the tidal relative ice–ocean velocity. The new parameterization leads to improved forecasts of tides and storm surges in polar regions. Associated physical processes are discussed.
Yue Xu and Xiping Yu
Geosci. Model Dev., 16, 2811–2831, https://doi.org/10.5194/gmd-16-2811-2023, https://doi.org/10.5194/gmd-16-2811-2023, 2023
Short summary
Short summary
An accurate description of the wind energy input into ocean waves is crucial to ocean wave modeling, and a physics-based consideration of the effect of wave breaking is absolutely necessary to obtain such an accurate description, particularly under extreme conditions. This study evaluates the performance of a recently improved formula, taking into account not only the effect of breaking but also the effect of airflow separation on the leeside of steep wave crests in a reasonably consistent way.
Yankun Gong, Xueen Chen, Jiexin Xu, Jieshuo Xie, Zhiwu Chen, Yinghui He, and Shuqun Cai
Geosci. Model Dev., 16, 2851–2871, https://doi.org/10.5194/gmd-16-2851-2023, https://doi.org/10.5194/gmd-16-2851-2023, 2023
Short summary
Short summary
Internal solitary waves (ISWs) play crucial roles in mass transport and ocean mixing in the northern South China Sea. Massive numerical investigations have been conducted in this region, but there was no systematic evaluation of a three-dimensional model about precisely simulating ISWs. Here, an ISW forecasting model is employed to evaluate the roles of resolution, tidal forcing and stratification in accurately reproducing wave properties via comparison to field and remote-sensing observations.
Johannes Bieser, David J. Amptmeijer, Ute Daewel, Joachim Kuss, Anne L. Soerensen, and Corinna Schrum
Geosci. Model Dev., 16, 2649–2688, https://doi.org/10.5194/gmd-16-2649-2023, https://doi.org/10.5194/gmd-16-2649-2023, 2023
Short summary
Short summary
MERCY is a 3D model to study mercury (Hg) cycling in the ocean. Hg is a highly harmful pollutant regulated by the UN Minamata Convention on Mercury due to widespread human emissions. These emissions eventually reach the oceans, where Hg transforms into the even more toxic and bioaccumulative pollutant methylmercury. MERCY predicts the fate of Hg in the ocean and its buildup in the food chain. It is the first model to consider Hg accumulation in fish, a major source of Hg exposure for humans.
Cited articles
Agawin, N. S. R., Duarte, C. M., and Agusti, S.: Nutrient and temperature control of the contribution of picoplankton to phytoplankton biomass and production, Limnol. Oceanogr., 45, 591–600, https://doi.org/10.4319/lo.2000.45.3.0591, 2000.
Allen, J. I., Holt, J. T., Blackford, J., and Proctor, R.: Error quantification of a high-resolution coupled hydrodynamic-ecosystem coastal ocean model: Part 2. Chlorophyll-a, nutrients, and SPM, J. Mar. Syst., 68, 381–404, https://doi.org/10.1016/j-jmarsys.2007.01.005, 2007.
Auger, P. A., Diaz, F., Ulses, C., Estournel, C., Neveux, J., Joux, F., Pujo-Pay, M., and Naudin, J. J.: Functioning of the planktonic ecosystem on the Gulf of Lions shelf (NW Mediterranean) during spring and its impact on the carbon deposition: a field data and 3-D modelling combined approach, Biogeosciences, 8, 3231–3261, https://doi.org/10.5194/bg-8-3231-2011, 2011.
Baklouti, M., Diaz, F., Pinazo, C., Faure, V., and Queguiner, B.: Investigation of mechanistic formulations depicting phytoplankton dynamics for models of marine pelagic ecosystems and description of a new model, Prog. Oceanogr., 71, 1–33, https://doi.org/10.1016/j.pocean.2006.05.002, 2006a.
Baklouti, M., Faure, V., Pawlowski, L., and Sciandra, A.: Investigation and sensitivity analysis of a mechanistic phytoplankton model implemented in a new modular numerical tool (Eco3M) dedicated to biogeochemical modelling, Prog. Oceanogr., 71, 34–58, https://doi.org/10.1016/j.pocean.2006.05.003, 2006b.
Banaru, D., Diaz, F., Verley, P., Campbell, R., Navarro, J., Yohia, C., Oliveros-Ramos, R., Mellon-Duval, C., and Shin, Y. J.: Implementation of an end-to-end model of the Gulf of Lions ecosystem (NW Mediterranean Sea). I. Parametrization, calibration and evaluation, Ecol. Model., 401, 1–19, https://doi.org/10.1016/j.ecolmodel.2019.03.005, 2019.
Barré, L., Diaz, F., Wagener, T., Van Wambeke, F., Mazoyer, C., Yohia, C., and Pinazo, C.: Eco3M_MIX-CarbOx (v1.0), Zenodo [code], https://doi.org/10.5281/zenodo.7669658, 2022.
Barré, L., Diaz, F., Wagener, T., Mazoyer, C., Yohia, C., and Pinazo, C.: Implementation and assessment of a model including mixotrophs and the carbonate cycle (Eco3M_MIX-CarbOx v1.0) in a highly dynamic Mediterranean coastal environment (Bay of Marseille, France) (Part. II): Towards a better representation of total alkalinity when modelling the carbonate system and air-sea CO2 fluxes, Geosci. Model Dev. Discuss. [preprint], https://doi.org/10.5194/gmd-2023-34, in review, 2023.
Barrier, N., Petrenko, A. A., and Ourmières, Y.: Strong intrusions of the Northern Mediterranean Current on the eastern Gulf of Lion: insights from in-situ observations and high-resolution numerical modelling, Ocean Dynam., 66, 313–327, https://doi.org/10.1007/s10236-016-0921-7, 2016.
Bernard, C. and Rassoulzadegan, F.: Seasonal variations of mixotrophic ciliates in the northwest Mediterranean Sea, Mar. Ecol. Prog. Ser., 108, 295–301, 1994.
Burkholder, J. M., Glibert, P. M., and Skelton, H. M.: Mixotrophy, a major mode of nutrition for harmful algal species in eutrophic waters, Harmful Algae, 8, 77–93, https://doi.org/10.1016/j.hal.2008.08.010, 2008.
Campbell, R., Diaz, F., Hu, Z., Doglioli, A., Petrenko, A., and Dekeyser, I.: Nutrients and plankton spatial distributions induced by a coastal eddy in the Gulf of Lion. Insights from a numerical model, Prog. Oceanogr., 109, 47–69, https://doi.org/10.1016/j.pocean.2012.09.005, 2013.
Christaki, U., Van Wambeke, F., and Dolan, J. R.: Nanoflagellates (mixotrophs, heterotrophs and autotrophs) in the oligotrophic eastern Mediterranean: standing stocks, bacterivory and relationships with bacterial production, Mar. Ecol. Prog. Ser., 181, 297–307, 1999.
Christaki, U., Courties, C., Karayanni, H., Giannakourou, A., Maravelias, C., Kormas, K., and Lebaron, P.: Dynamic characteristics of Prochlorococcus and Synechococcus consumption by bacterivorous nanoflagellates, Microb. Ecol., 43, 341–352, 2002.
Christaki, U., Courties, C., Joux, F., Jeffrey, W. H., Neveux, J., and Naudin, J. J.: Community structure and trophic role of ciliates and heterotrophic nanoflagellates in Rhone River diluted mesoscale structures (NW Mediterranean Sea), Aquat. Microb. Ecol., 57, 263–277, https://doi.org/10.3354/ame01339, 2009.
Djaoudi, K., Van Wanbeke, F., Barani, A., Nunige, S. H., Sempere, R., and Pulido-Vilena, E.: Atmospheric fluxes of soluble organic C, N, and P to the Mediterranean Sea: Potential biogeochemical implications in the surface layer, Prog. Oceanogr., 163, 59–69, https://doi.org/10.1016/j.pocean.2017.07.008, 2018.
Dolan, J. R.: Mixotrophy in ciliates: a review of Chlorella symbiosis and chloroplast retention, Marine Microbial Food Webs, 6, 115–132, 1992.
Dolan, J. R. and Perez, M. T.: Costs, benefits, and characteristics of mixotrophy in marine oligotrichs, Freshwater Biol., 45, 227–238, 2000.
Duhamel, S., Van Wambeke, F., Lefevre, D., Benavides, M., and Bonnet, S.: Mixotrophic metabolism by natural communities of unicellular cyanobacteria in the western tropical South Pacific Ocean, Environ. Microbiol., 20, 2743–2756, https://doi.org/10.1111/1462-2920.14111, 2018.
Epstein, S. S., Burkovsky, I. V., and Shiaris, M. P.: Ciliate grazing on bacteria, flagellates, and microalgae in a temperate zone sandy tidal flat: ingestion rates and food niche partitioning, J. Exp. Mar. Biol. Ecol., 165, 103–123, https://doi.org/10.1016/0022-0981(92)90292-I, 1992.
Esteban, G. F., Fenchel, T., and Finlay, B. J.: Mixotrophy in ciliates, Protists, 161, 621–641, https://doi.org/10.1016/j.protis.2010.08.002, 2010.
Faure, V., Pinazo, C., Torréton, J. P., and Jacquet, S.: Modelling the spatial and temporal variability of the SW lagoon of New Caledonia I: A new biogeochemical model based on microbial loop recycling, Mar. Pollut. Bull., 61, 465–479, https://doi.org/10.1016/j.marpolbul.2010.06.041, 2010a.
Faure, V., Pinazo, C., Torréton, J. P., and Douillet, P.: Modelling the spatial and temporal variability of the SW lagoon of New Caledonia II: Realistic 3D simulations compared with in situ data, Mar. Pollut. Bull., 61, 480–502, https://doi.org/10.1016/j.marpolbul.2010.06.040, 2010b.
Fisher, N. L. and Halsey, K. H.: Mechanisms that increase the growth efficiency of diatoms in low light, Photosynth. Res., 129, 183–197, 2016.
Flynn, K. J. and McGillicuddy, D. J.: Modeling marine harmful algal blooms: Current status and future prospects, Harmful Algal Blooms: A Compendium Desk Reference, 115–134, https://doi.org/10.1002/9781118994672.ch3, 2018.
Flynn, K. J., Stoecker, D. K., Mitra, A., Raven, J., Glibert, P. M., Hansen, P. J., Graneli, E., and Burkholder, J. M.: Misuse of the phytoplankton–zooplankton dichotomy: the need to assign organisms as mixotrophs within plankton functional types, J. Plankton Res., 35, 3–11, https://doi.org/10.1093/plankt/fbs062, 2012.
Fraysse, M., Pinazo, C., Faure, V. M., Fuchs, R., Lazzari, P., Raimbault, P., and Peyraud, I.: Development of a 3D Coupled Physical-Biogeochemical Model for the Marseille Coastal Area (NW Mediterranean Sea): What Complexity Is Required in the Coastal Zone?, PLoS ONE, 8, e80012, https://doi.org/10.1371/journal.pone.0080012, 2013.
Fraysse, M., Pairaud, I., Ross, O. N., Faure, V. M., and Pinazo, C.: Intrusion of Rhone River diluted water into the Bay of Marseille: Generation processes and impacts on ecosystem functioning, J. Geophys. Res.-Oceans, 119, 119, 6535–6556, https://doi.org/10.1002/2014JC010022, 2014.
Garcia, F. and Raimbault, P.: Panache du Rhône: Suivi des eaux du Rhône en zone côtière par mesure haute fréquence de la salinité de surface, MIO UMR 7294 CNRS [data set], https://doi.org/10.34930/79C421C5-9335-4957-88FA-804FB4AE4B43, 2022.
Garcia, N., Gregori, G., Lafont, M., Lagadec, V., Nunige, S., and Raimbault, P.:SOMLIT-Frioul time series (French Research Infrastructure ILICO): long-term core parameter monitoring in the Bay of Marseille, SEANOE [data set], https://doi.org/10.17882/96252, 1997.
Gatti, J., Petrenko, A., Devenon, J. -L., Leredde, Y., and Ulses, C.: The Rhone River dilution zone present in the northeastern shelf of the Gulf of Lion in December 2003, Cont. Shelf Res., 26, 1794–1815, https://doi.org/10.1016/j.csr.2006.05.012, 2006.
Gaudy, R. and Thibault-Botha, D.: Metabolism of Centropages species in the Mediterranean Sea and the North Atlantic Ocean, Prog. Oceanogr., 72, 151–163, https://doi.org/10.1016/j.pocean.2007.01.005, 2007.
Gehlen, M., Gangstø, R., Schneider, B., Bopp, L., Aumont, O., and Ethe, C.: The fate of pelagic CaCO3 production in a high CO2 ocean: a model study, Biogeosciences, 4, 505–519, https://doi.org/10.5194/bg-4-505-2007, 2007.
Geider, R.: Algal photosynthesis, Vol. 2, Springer Science & Business Media, ISBN 1475721536, 2013.
Geider, R., MacIntyre, H. L., and Kana T. M.: A dynamic regulatory model of phytoplanktonic acclimation to light, nutrients, and temperature, Limnol. Oceanogr., 43, 679–694, 1998.
Ghyoot, C., Flynn, K. J., Mitra, A., Lancelot, C., and Gypens, N.: Modeling Plankton Mixotrophy: A Mechanistic Model Consistent with the Shuter-Type Biochemical Approach, Frontiers in Ecology and Evolution, 5, 5–78, https://doi.org/10.3389/fevo.2017.00078, 2017.
Gibson, R. N., Atkinson, R. J. A., and Gordon, J. D. M.: Review of three-dimensional ecological modelling related to the North Sea shelf system, Part II: Model validation and data needs, Oceanogr. Mar. Biol., 44, 1–60, 1420006398, 2006.
Glibert, P. M. and Legrand, C., The Diverse Nutrient Strategies of Harmful Algae: Focus on Osmotrophy, Ecology of Harmful Algae, 163–175, https://doi.org/10.1007/978-3-540-32210-8_13, 2006.
Glibert, P. M., Al-Azri, A., Allen, J. I., Bouwman, A. F., Beusen, A. H. W., Burford, M. A., Harrison, P. J., and Zhou, M.: Key Questions and Recent Research Advances on Harmful Algal Blooms in Relation to Nutrients and Eutrophication, Global Ecology and Oceanography of Harmful Algal Blooms, Ecol. Stud., 232, 229–258, https://doi.org/10.1007/978-3-319-70069-4_12, 2018.
Gorsky, G., Dallot, S., Sardou, J., Fenaux, R., Carré, C., and Palazzoli, I.: C and N composition of some northwestern Mediterranean zooplankton and micronekton species, J. Exp. Mar. Biol. Ecol., 124, 133–144, https://doi.org/10.1016/0022-0981(88)90116-5, 1988.
Guillemain, D.: Données de température à la station Planier-Souquet (5m), Regional temperature observation network T-MEDNet [data set], https://t-mednet.org/request-data (last access: 7 November 2023), 2021.
Graneli, E., Carlsson, P., and Legrand, C.: The role of C, N and P in dissolved and particulate organic matter as a nutrient source for phytoplankton growth, including toxic species, Aquat. Ecol., 33, 17–27, 1999.
Hartmann, M., Grob, C., Tarran, G. A., Martin, A. P., Burkill, P. H., Scanlan, D. J., and Zubkova, M. V.: Mixotrophic basis of Atlantic oligotrophic ecosystems, P. Natl. Acad. Sci. USA, 109, 5756–5760, https://doi.org/10.1073/pnas.1118179109, 2012.
Johansson, M., Gorokhova, E., and Larsson, U. L. F.: Annual variability in ciliate community structure, potential prey and predators in the open northern Baltic Sea proper, J. Plankton Res., 26, 67–80, https://doi.org/10.1093/plankt/fbg115, 2004.
Jost, C., Lawrence, C. A., Campolongo, F., Van de Bund, W., Hill, S., and DeAngelis, D. L.: The effects of mixotrophy on the stability and dynamics of a simple planktonic food web model, Theor. Popul. Biol., 66, 37–51, https://doi.org/10.1016/j.tpb.2004.02.001, 2004.
Kempton, J. W., Lewitus, A. J., Deeds, J. R., Law, J. M., and Place, A. R.: Toxicity of Karlodinium micrum (Dinophyceae) associated with a fish kill in a South Carolina brackish retention pond, Harmful Algae, 1, 233–241, https://doi.org/10.1016/S1568-9883(02)00015-X, 2002.
Kirchman, D. L. and Gasol, J. M.: Microbial Ecology of the Oceans, John Wiley & Sons, ISBN 1119107199, 2018.
Lacroix, G. and Grégoire, M.: Revisited ecosystem model (MOD-ECOGeL) of the Ligurian Sea: seasonal and interannual variability due to atmospheric forcing, J. Marine Syst., 37, 229–258, https://doi.org/10.1016/S0924-7963(02)00190-2, 2002.
Lajaunie-Salla, K., Diaz, F., Wimart-Rousseau, C., Wagener, T., Lefèvre, D., Yohia, C., Xueref-Remy, I., Nathan, B., Armengaud, A., and Pinazo, C.: Implementation and assessment of a carbonate system model (Eco3M-CarbOx v1.1) in a highly dynamic Mediterranean coastal site (Bay of Marseille, France), Geosci. Model Dev., 14, 295–321, https://doi.org/10.5194/gmd-14-295-2021, 2021.
Leblanc, K., Quéguiner, B., Diaz, F., Cornet, V., Michel-Rodriguez, M., Durrieu de Madron, X., Bowler, C., Malviva, S., Thyssen, M., Grégori, G., Rembauville, M., Grosso, O., Poulain, J., de Vargas, C., Pujo-Pay, M., and Conan, P.: Nanoplanktonic diatoms are globally overlooked but play a role in spring blooms and carbon export, Nat. Commun., 9, 953–964, https://doi.org/10.1038/s41467-018-03376-9, 2018.
Leles, S. G., Bruggeman, L. P. J., Blackford, J., Ciavatta, S., Mitra, A., and Flynn, K. J.: Modelling mixotrophic functional diversity and implications for ecosystem function, J. Plankton Res., 40, 627–642, https://doi.org/10.1093/plankt/fby044, 2018.
Lewitus, A. J: Osmotrophy in marine microalgae, Algal cultures, analogues of blooms and applications, Volume 1, Subba Rao D. V., Science publishers Inc., USA, ISBN 1578083923, 2006.
Livanou E., Lagaria, A., Santi, I., Mandalakis, M., Paylidou, A., Lika, K., and Psarra, S.: Pigmented and heterotrophic nanoflagellates: Abundance and grazing on prokaryotic picoplankton in the ultra-oligotrophic Eastern Mediterranean Sea, Deep-Sea Res. Pt. II, 164, 100–111, https://doi.org/10.1016/j.dsr2.2019.04.007, 2019.
Livanou, E., Oikonomou, A., Psarra, S., and Konstadia, L.: Role of mixotrophic nanoflagellates in the Eastern Mediterranean microbial food web, Mar. Ecol. Prog. Ser., 672, 15–32, https://doi.org/10.3354/meps13782, 2021.
Marechal, D.: A soil-based approach to rainfall-runoff modelling in ungauged catchments for England and Wales, PhD thesis, Cranfield University, 157 pp., 2004.
Margalef, R.: Life-forms of phytoplankton as survival alternatives in an unstable environment, edited by: Gauthier-Villars, Oceanol. Acta, 1, 493–509, https://archimer.ifremer.fr/doc/00123/23403/ (last access: July 2023), 1978.
Marty, J.-C., Chiavérini, J., Pizay, M.-D., and Avril, B.: Seasonaland interannual dynamics of nutrients and phytoplankton pigments in the western Mediterranean Sea at the DYFAMED time series station (1991–1999), Deep-Sea Res. Pt. II, 49, 1965–1985, https://doi.org/10.1016/S0967-0645(02)00022-X, 2001.
McGillicuddy Jr., D. J.: Models of harmful algal blooms: conceptual, empirical, and numerical approaches, J. Marine Syst., 83, 105, 2010.
Mella-Flores, D., Mazard, S., Humily, F., Partensky, F., Mahé, F., Bariat, L., Courties, C., Marie, D., Ras, J., Mauriac, R., Jeanthon, C., Mahdi Bendif, E., Ostrowski, M., Scanlan, D. J., and Garczarek, L.: Is the distribution of Prochlorococcus and Synechococcus ecotypes in the Mediterranean Sea affected by global warming?, Biogeosciences, 8, 2785–2804, https://doi.org/10.5194/bg-8-2785-2011, 2011.
Millet, B., Pinazo, C., Banaru, D., Pagès, R., Guiart, P., and Pairaud, I.: Unexpected spatial impact of treatment plant discharges induced by episodic hydrodynamic events: Modelling lagrangian transport of fine particles by Northern Current intrusions in the Bays of Marseille (France), Édité par João Miguel Dias, PLoS ONE, 13, e0195257, https://doi.org/10.1371/journal.pone.0195257, 2018.
Millette, N. C., Pierson, J. J., Aceves, A., and Stoecker, D. K.: Mixotrophy in Heterocapsa rotundata: a mechanism for dominating the winter phytoplankton, Limnol. Oceanogr., 62, 836–845, https://doi.org/10.1002/lno.10470, 2017.
Millot, C.: The Golf of Lions' hydrodynamic, Cont. Shelf Res., 10, 885–894, 1990.
Mitra, A. and Flynn, K. J.: Modelling mixotrophy in harmful algal blooms: More or less the sum of the parts?, J. Marine Syst., 83, 158–169, https://doi.org/10.1016/j.jmarsys.2010.04.006, 2010.
Mitra, A., Flynn, K. J., Burkholder, J. M., Berge, T., Calbet, A., Raven, J. A., Granéli, E., Glibert, P. M., Hansen, P. J., Stoecker, D. K., Thingstad, F., Tillmann, U., Våge, S., Wilken, S., and Zubkov, M. V.: The role of mixotrophic protists in the biological carbon pump, Biogeosciences, 11, 995–1005, https://doi.org/10.5194/bg-11-995-2014, 2014.
Mitra, A., Flynn, K. J., Tillmann, U., Raven, J. A., Caron, D., Stoecker, D. K., Not, F., Hansen, P. J., Hallegraeff, G., Sanders, R., Wilken, S., McManus, G., Johnson, M., Pitta, P., Våge, S., Berge, T., Calbet, A., Thingstad, F., Jin Jeong, H., Burkholder, J. -A., Glibert, P. M., Granéli, E., and Lundgren, V.: Defining planktonic protist functional groups on mechanisms for energy and nutrient acquisition: Incorporation of diverse mixotrophic strategies, Protist, 167, 106–120, https://doi.org/10.1016/j.protis.2016.01.003, 2016.
Montagnes, D. J.: Growth responses of planktonic ciliates in the genera Strobilidium and Strombidium, Mar. Ecol. Prog. Ser., 130, 241–254, https://doi.org/10.3354/meps130241, 1996.
Morel, A. and André, J. -M.: Pigment distribution and primary production in the western Mediterranean as derived and modelled from coastal zone colour scanner observations, J. Geophys. Res.-Oceans, 96, 12685–12698, https://doi.org/10.1029/91JC00788, 1991.
Nielsen, L. P., Christensen, P. B., Revsbech, N, P., and Sorensen, I.: Denitrification and photosynthesis in stream sediment studied with microsensor and wholecore techniques, Limnol. Oceanogr., 35, 1135–1144, https://doi.org/10.4319/lo.1990.35.5.1135, 1990.
Oikomonou, A., Livanou, E., Mandalakis, M., Ligaria, A., and Psarra, S.: Grazing effect of flagellates on bacteria in response to phosphate addition in the oligotrophic Cretan Sea, NE Mediterranean, FEMS Microbiol. Ecol., 96, fiaa086, https://doi.org/10.1093/femsec/fiaa086, 2020.
Oursel, B., Garniera, C., Zebracki, M., Durrieu, G., Pairaud, I., Omanovic, D., Cossab, D., and Lucas, Y.: Flood inputs in a Mediterranean coastal zone impacted by a large urban area: Dynamic and fate of trace metals, Mar. Chem., 167, 44–56, https://doi.org/10.1016/j.marchem.2014.08.005, 2014.
Pitta, P. and Giannakourou, A.: Planktonic ciliate in the oligotrophic Eastern Mediterranean: vertical, spatial distribution and mixotrophy, Mar. Ecol. Prog. Ser., 194, 269–282, 2000.
Platt, T. G. C. L., Gallegos, C. L., and Harrison, W. G.: Photoinhibition of photosynthesis in natural assemblages of marine phytoplankton, J. Mar. Res., 38, 1525, 1980.
Polovina, J. J., Howell, E. A., and Abecassis, A.: Ocean's least productive waters are expanding, Geophys. Res. Lett., 35, L03618, https://doi.org/10.1029/2007GL031745, 2008.
Pratt, J. R. and Cairns, J.: Functional groups in the protozoa, Roles in differing ecosystems, J. Protozool. Res., 32, 415–423, 1985.
Price, R. W. and Turner, J. T.: Ecology of planktonic ciliates in marine food webs, Rev. Aquat. Sci., 6, 139–181, 1992.
Ptacnik, R., Sommer, U., Hansen, T., and Martens, V.: Effects of microzooplankton and mixotrophy in an experimental planktonic food web, Limnol. Oceanogr., 49, 1435–1445, 2004.
Ptacnik, R., Gomes, A., Royer, S-J., Berger, S. A., Calbet, A., Nejstgaard, J. C., Gasol, J. M., Isari, S., Moorthi, S. D., Ptacnikova, R., Striebel, M., Sazhin, A. F., Tsagaraki, T. M., Zervoudaki, S., Altoja, K., Dimitriou, P. D., Laas, P., Gazihan, A., Martinez, R. A., Schabhuttl, S., Santi, I., Sousoni, D., and Pitta, P.: A light-induced shortcut in the planktonic microbial loop, Sci. Rep., 6, 29286, https://doi.org/10.1038/srep29286, 2016.
Pujo-Pay, M., Conan, P., Oriol, L., Cornet-Barthaux, V., Falco, C., Ghiglione, J.-F., Goyet, C., Moutin, T., and Prieur, L.: Integrated survey of elemental stoichiometry (C, N, P) from the western to eastern Mediterranean Sea, Biogeosciences, 8, 883–899, https://doi.org/10.5194/bg-8-883-2011, 2011.
Putt, M.: Metabolism of photosynthate in the chloroplast-retaining ciliate Laboea strobila, Mar. Ecol. Prog. Ser., Oldendorf, 60, 271–282, 1990.
Raven, J. A.: Phagotrophy in phototrophs, Limnol. Oceanogr., 42, 198–205, 1997.
Razzak, S. A., Ilyas, M., Ali, S. A. M., and Hossain, M. M.: Effects of CO2 Concentration and pH on Mixotrophic Growth of Nannochloropsis oculate, Appl. Biochem. Biotech., 176, 1290–1302, https://doi.org/10.1007/s12010-015-1646-7, 2015.
Riemann, B., Havskum, H., Thingstad, F., and Bernard, C.: The role of mixotrophy in pelagic environments, Molecular Ecology of Aquatic Microbes, NATO ASI Series, 38, Joint, I. Springer, Berlin, Heidelberg, https://doi.org/10.1007/978-3-642-79923-5_6, 1995.
Ross, O. N., Fraysse, M., Pinazo, C., and Pairaud, I.: Impact of an intrusion by the Northern Current on the biogeochemistry in the Eastern Gulf of Lion, NW Mediterranean, Estuar. Coast. Shelf S., 170, 1–9, 2016.
Sanders, R.: Mixotrophic Protists in Marine and Freshwater Ecosystems, J. Protozool., 38, 76–81, 1991.
Sarthou, G., Timmerman, K. R., Blain, S., and Tréguer, P.: Growth physiology and fate of diatoms in the ocean: a review, J. Sea Res., 53, 25–42, https://doi.org/10.1016/j.seares.2004.01.007, 2005.
Schaeffer, A., Molcard, A., Forget, P., Fraunié, P., and Garreau, P.: Generation mechanisms for mesoscale eddies in the Gulf of Lions: radar observation and modelling, Ocean Dynam., 61, 1587–1609, https://doi.org/10.1007/s10236-011-0482-8, 2011.
Sherr, B. F., Sherr, E. B., Caron, D. A., Vaulot, D., and Worden, A. Z.: Oceanic protists, Oceanography, 20, 130–134, https://doi.org/10.5670/oceanog.2007.57, 2007.
Stickney, H. L., Hood, R. R., and Stoecker, D. K.: The impact of mixotrophy on planktonic marine ecosystems, Ecol. Model., 125, 203–230, https://doi.org/10.1016/S0304-3800(99)00181-7, 2000.
Stoecker, D. K.: Mixotrophy among Dinoflagellates 1, J. Eukaryot. Microbiol., 46, 397–401, 1999.
Stoecker, D. K. and Capuzzo, J. M.: Predation on protozoa: its importance to zooplankton, J. Plankton Res., 12, 891–908, 1990.
Stoecker, D. K., Silver, M. W., Michaels, A. E., and Davis, L. H.: Obligate mixotrophy in Laboea strobila, a ciliate which retains chloroplasts, Mar. Biol., 99, 415–423, 1988.
Stoecker, D. K., Li, A., Coats, D. W., Gustafson, D. E., and Nannen, M. K.: Mixotrophy in the dinoflagellate Prorocentrum minimum, Mar. Ecol. Prog. Ser., 152, 1–12, 1997.
Stoecker, D. K.: Conceptual models of mixotrophy in planktonic protists and some ecological and evolutionary implications, Eur. J. Protistol., 34, 281–290, https://doi.org/10.1016/S0932-4739(98)80055-2, 1998.
Stoecker, D. K., Hansen, P. J., Caron, D. A., and Mitra, A.: Mixotrophy in marine plankton, Annu. Rev. Mar. Sci., 9, 11–35, https://doi.org/10.1146/annurev-marine-010816-060617, 2017.
Tett, P.: A three-layer vertical and microbiological processes model for shelf seas, Report No. 14, Proudman Oceanographic Laboratory, Birkenhead, UK, 85, https://nora.nerc.ac.uk/id/eprint/3877/1/ir14.pdf (last access: 7 November 2023), 1990.
Thingstad, T. F., Hagström, A., and Rassoulzadegan, F.: Accumulation of degradable DOC in surface waters: Is it caused by a malfunctioning microbialloop?, Limnol. Oceanogr., 42, 398–404, https://doi.org/10.4319/lo.1997.42.2.0398, 1997.
Timmermans, K. R., van der Wagt, B., Veldhuis, M. J. W., Maatman, A., and de Baar, H. J. W.: Physiological responses of three species of marine pico-phytoplankton to ammonium, phosphate, iron and light limitation, J. Sea Res., 53, 109–120, https://doi.org/10.1016/j.seares.2004.05.003, 2005.
Thornley, J. H. M. and Cannell, M. G. R.: Modelling the component of plant respiration: Representation and realism, Ann. Bot.-London, 85, 55–67, https://doi.org/10.1006/anbo.1999.0997, 2000.
Unrein, F., Gasol, J. M., and Massana, R.: Dinobryon faculiferum (Chrysophyta) in coastal Mediterranean seawater: presence and grazing impact on bacteria, J. Plankton Res., 32, 559–564, https://doi.org/10.1093/plankt/fbp150, 2010.
Verity, P. G. and Paffenhofer, G. A.: On assessment of prey ingestion by copepods, J. Plankton Res., 18, 1767–1779, 1996.
Vrede, K., Heldal, M., Norland, S., and Bratbak, G.: Elemental Composition (C, N, P) and Cell Volume of Exponentially Growing and Nutrient-Limited Bacterioplankton, American Society for Microbiology Journal, 68, 2965–2971, https://doi.org/10.1128/AEM.68.6.2965-2971.2002, 2002.
Wanninkhof, R.: Relationship between wind speed and gas exchange over the ocean revisited, Limnol. Oceanogr.-Meth., 12, 351–362, https://doi.org/10.4319/lom.2014.12.351, 2014.
Ward, B. A. and Follows M. J.: Marine mixotrophy increases trophic transfer efficiency, mean organism size, and vertical carbon flux, P. Natl. Acad. Sci. USA, 113, 2958–2963, https://doi.org/10.1073/pnas.1517118113, 2016.
Wilken, S., Huisman, J., Naus-Wiezer, S., and Van Donk, E.: Mixotrophic organisms become more heterotrophic with rising temperature, Ecol. Lett., 16, 225–233, https://doi.org/10.1111/ele.12033, 2013.
Xueref-Remy, I., Lefèvre, D., Nathan, B., Milne, M., Piazzola, J., Yohia, C., Armengaud, A., Blanc, P. E. Mevy, J.-P., Reiter, I., Paya, A., Lajaunie-Salla, K., Wimart-Rousseau, C., Diaz, F., Pinazo, C., and Wagener, T.: Aix-Marseille Carbon Pilot Study (AMC), https://www.otmed.fr/research-projects-and-results/result-2449 (last access: 7 November 2023), 2016.
Yacobi, Y. Z., Zohary, T., Kress, N., Hecht, A., Robarts, R. D., Waiser, M., Wood, A. M., and Li, W. K. W.: Chlorophyll distribution throughout the southeastern Mediterranean in relation to the physical structure of the water mass, J. Marine Syst., 6, 179–190, https://doi.org/10.1016/0924-7963(94)00028-A, 1995.
Yohia, C.: Genèse du mistral par interaction barocline et advection du tourbillon potentiel, Climatologie, 13, 24–37, https://doi.org/10.4267/climatologie.1182, 2017.
Zubkov, M. V. and Tarran, G. A.: High bacterivory by the smallest phytoplankton in the North Atlantic Ocean, Nature, 455, 224–226, https://doi.org/10.1038/nature07236, 2008.
Short summary
While several studies have shown that mixotrophs play a crucial role in the carbon cycle, the impact of environmental forcings on their dynamics remains poorly investigated. Using a biogeochemical model that considers mixotrophs, we study the impact of light and nutrient concentration on the ecosystem composition in a highly dynamic Mediterranean coastal area: the Bay of Marseille. We show that mixotrophs cope better with oligotrophic conditions compared to strict auto- and heterotrophs.
While several studies have shown that mixotrophs play a crucial role in the carbon cycle, the...
