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Abstract: Realistic modelling of marine ecosystems is necessary for improving our understanding of the ocean’s biogeochemical state and for predicting their response to anthropic perturbations. An essential step in achieving this task is the use of mechanistic formulations to describe the biogeochemical processes involved in the dynamics of marine pelagic ecosystems. This study provides a review on some modelling strategies for some of the key processes involved in the dynamics of phytoplankton. It encompasses the most advanced work in terms of mechanistic understanding and, therefore, mainly deals with photosynthesis (including photoacclimation and photoinhibition), respiration, and nutrient uptake (including multi-limitation of algal growth by nutrients). We highlight, that in many ecosystem models, phytoplankton processes are still described more or less empirically, mainly due to a lack of biochemical knowledge, or if a mechanistic formulation exists, the parameters are often difficult to assess experimentally. As a result of this investigation, a preliminary structure for a generic phytoplankton model is delivered in the last section of this paper. This model includes a mechanistic representation of photosynthesis/photoinhibition based on photosystem II status, as well as new formulations for photoacclimation and dissolved organic matter exudation processes. The model sensitivity analysis with regard to its parameters and a comparison with chemostat experimental data are presented in a companion paper [Baklouti, M., Faure, V., Pawlowski, L., Sciandra, A., 2006. Investigation and sensitivity analysis of a mechanistic phytoplankton model implemented in a new modular numerical tool (Eco3M) dedicated to biogeochemical modelling. Progress in Oceanography]. Finally, this new class of multi-element, multi-species phytoplankton models will provide the basis for future studies on ecosystem modelling. [Copyright &y& Elsevier]

This paper analyzes the variability of microplastics vertical distributions in the oceanic water column. Data were obtained from targeted sampling in the Bay of Marseille (France) and from a numerical simulation forced by realistic physical forcings. By fitting model and in-situ data in a simplified vertical dimension, three microplastics classes may be deduced: settling, buoyant and winter neutrally-buoyant microplastics. Buoyant microplastics are mainly concentrated at the surface but they can be mixed throughout the whole water column during episodes with strong winds and no water stratification, inducing an implicit underestimation of buoyant microplastics in surface sampling. Almost symmetrical to the distribution of buoyant microplastics, settling microplastics are mainly found at the bottom but they can sometimes reach the surface under the mixing conditions cited above. They could thus contribute to surface sampling. Winter neutrally-buoyant microplastics are more homogenously mixed during the winter but are under the stratified layers during summer., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023. Published by Elsevier Ltd.)

Benthic exchanges of oxygen and nutrient at the sediment-water interface were investigated under light and dark conditions at 5 selected sites in a sub-tropical atoll. Mean oxygen fluxes were - 1316.5 ± 242.0 μmol m -2  h -1 and mean effluxes of oxygen under light conditions were 2231.7 ± 626.4 μmol m -2  h -1 , presumably due to microphytobenthos present at the sediment-water interface. The consequences of this high related productivity was a systematic consumption of nutrients (DIN, PO 4 and Si(OH) 4 ) during almost all light incubations, contrasting with the effluxes of nutrients during dark incubations. Our results suggest that the sediments were net autotrophic and the oxygen balance in favor of microbenthic production when compared to community demand. Diurnal rates of gross benthic primary productivity were high (3423 ± 1192 μmol m -2  h -1 ) which emphasize the role of microphytobenthos in maintaining the oxygen reservoir in tropical lagoons., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

This study reports the first measurements of nitrogen uptake and new data on carbon fixation ( 15 N/ 13 C incorporation) for two size-fractionated phytoplankton (<2 μm and >2 μm), on organic matter, and phytoplankton stocks in Ahe lagoon. Data were collected between November and December 2017, during the hot season with prevailing trade winds. Ammonium and nitrate uptake data (7.58 to 39.81 and 1.80 to 21.43 μmol N m -3  h -1 , respectively) suggest a rapid turn-over of N-nutrients in the water column and show that primary production was largely sustained by recycled nitrogen providing 68% of the pelagic N demand. These results highlight the spatial heterogeneity of the measured processes linked to the local hydrodynamics, exhibiting higher regenerated production in the more exploited southwestern part of the lagoon and a higher proportion of new production in the north. Intense nutrient recycling appears to promote nanophytoplankton production which is critical for pearl oyster growth., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Four perfluoroalkyl substances (PFAS) were analyzed in 62 duplicate surface water samples from the Rhône River and Marseille Bay (France; NW Mediterranean Sea). Perfluorooctane sulfonate (PFOS) was detected in all samples and exceeded the European Environmental Quality Standard (EQS) values in over 80% of the cases. The most contaminated samples were from the Rhône River (up to 200 ng L -1 ∑ 4 PFAS), as well as those collected near a wastewater treatment plant outlet in Marseille Bay (up to 9 ng L -1 ∑ 4 PFAS). While PFOS was the predominant PFAS in Marseille Bay, remarkably high concentrations of perfluorohexanoic acid (PFHxA) were measured in the Rhône River (8-193 ng L -1 ). The relative abundances of individual compounds differed thus significantly between the Rhône River and Marseille Bay, indicating different sources. A simulation made with the MARS3D model showed that PFOS inputs from the Rhône River can enter Marseille Bay at levels > EQS., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Our study highlights the Lagrangian transport of solid particles discharged at the Marseille Wastewater Treatment Plant (WWTP), located at Cortiou on the southern coastline. We focused on episodic situations characterized by a coastal circulation pattern induced by intrusion events of the Northern Current (NC) on the continental shelf, associated with SE wind regimes. We computed, using MARS3D-RHOMA and ICHTHYOP models, the particle trajectories from a patch of 5.104 passive and conservative fine particles released at the WWTP outlet, during 2 chosen representative periods of intrusion of the NC in June 2008 and in October 2011, associated with S-SE and E-SE winds, respectively. Unexpected results highlighted that the amount of particles reaching the vulnerable shorelines of both northern and southern bays accounted for 21.2% and 46.3% of the WWTP initial patch, in June 2008 and October 2011, respectively. Finally, a conceptual diagram is proposed to highlight the mechanisms of dispersion within the bays of Marseille of the fine particles released at the WWTP outlet that have long been underestimated.

Terrestrial inputs (natural and anthropogenic) from rivers, the atmosphere and physical processes strongly impact the functioning of coastal pelagic ecosystems. The objective of this study was to develop a tool for the examination of these impacts on the Marseille coastal area, which experiences inputs from the Rhone River and high rates of atmospheric deposition. Therefore, a new 3D coupled physical/biogeochemical model was developed. Two versions of the biogeochemical model were tested, one model considering only the carbon (C) and nitrogen (N) cycles and a second model that also considers the phosphorus (P) cycle. Realistic simulations were performed for a period of 5 years (2007-2011). The model accuracy assessment showed that both versions of the model were able of capturing the seasonal changes and spatial characteristics of the ecosystem. The model also reproduced upwelling events and the intrusion of Rhone River water into the Bay of Marseille well. Those processes appeared to greatly impact this coastal oligotrophic area because they induced strong increases in chlorophyll-a concentrations in the surface layer. The model with the C, N and P cycles better reproduced the chlorophyll-a concentrations at the surface than did the model without the P cycle, especially for the Rhone River water. Nevertheless, the chlorophyll-a concentrations at depth were better represented by the model without the P cycle. Therefore, the complexity of the biogeochemical model introduced errors into the model results, but it also improved model results during specific events. Finally, this study suggested that in coastal oligotrophic areas, improvements in the description and quantification of the hydrodynamics and the terrestrial inputs should be preferred over increasing the complexity of the biogeochemical model.

Coral reef lagoons are under the growing influence of anthropogenic activities, leading to increasing loads of nutrients and various contaminants. Modelling approaches are a useful tool for studying such a complex coastal environment. In this study, we carried out the development of a three-dimensional coupled hydrodynamical-biogeochemical model of the south-west lagoon of New Caledonia. The biogeochemical model presented in Faure et al. (2006, 2010) was dynamically coupled with a hydrodynamical model (MARS3D) in order to study the short-term variability of the ecosystem. Two simulations (in winter and summer) were then performed from measured initial conditions using realistic wind and irradiance conditions and river inputs. Examinations of the biogeochemical response to these transient meteorological conditions were presented and compared with temporal field data corresponding to the considered periods. Results highlighted the ecosystem functioning, based on the balance of hydrodynamical and biogeochemical processes. Influence of urban and terrigeneous inputs were limited to the coastal zone. The model accurately reproduced the measured Chl.a and bacterial production, highlighting the improvement made on the biogeochemical model. However, the underestimation of some variables in model outputs, in particular nutrients, led us to focus on different inputs, such as sediment inputs which were not taken into account or properly estimated. Moreover, the role of boundary waters appeared crucial and suggested a calibration effort. Last, the final aim of our modelling study will help the development of a useful tool for studying the key processes of the ecosystem of the south-west lagoon of New Caledonia, as well as the examination of the biogeochemical response under different scenarios., (Copyright (c) 2010 Elsevier Ltd. All rights reserved.)

This work is an extension and improved version of the biogeochemical model of the South-West lagoon of New Caledonia, presented by Bujan et al. (2000) and Pinazo et al. (2004). This new ecological model was developed to include an explicit description of the microbial loop. Additional variables included bacterial production and dissolved organic matter and a better description of organic matter recycling. A particular effort was made to calibrate parameters of the model for the studied area, using representative field measurements and experiments. The biogeochemical model described the nitrogen and carbon cycles relating the variable stoichiometry of the elements in each biological compartment. Several lagoon surveys demonstrated that, on average, the water column is nearly homogenous. We chose therefore to present in this paper non dimensional model outputs in order to study the behaviour of the new model. The addition of a microbial loop modified the simulated functioning of the lagoon and the fluxes of carbon and nitrogen between the different compartments: it allowed a better description of the recycling of organic matter, recognized as important processes in oligotrophic ecosystems like in the SW lagoon of NC. A sensitivity analysis was performed in order to identify the most sensitive parameters and variables of the model. The different results emphasised the importance of the dissolved inorganic and organic compartment. Preliminary comparisons with field data showed that the model reproduced realistic values. However, the next important step of this work was to dynamically couple this new biogeochemical model in a 3D hydrodynamical model in order: (1) to perform a realistic validation with in situ data (2) to achieve an analysis of the spatial and temporal variability of the ecosystem. This study is presented in the companion paper (Faure et al., 2010)., (Copyright (c) 2010 Elsevier Ltd. All rights reserved.)

Numerous experimental studies showed that the phytoplankton Chla-to-Carbon ratio (Chla:C) is highly variable, whereas most of the marine ecosystem models use a constant ratio. In this work, we tested three different formulations for computing the modelled Chla in a 3D coupled hydrodynamical-biogeochemical model of the Southwest lagoon of New Caledonia. The first formulation considers a constant Chla:C ratio. In the second one, Chla is a diagnostic variable related to the variable phytoplankton nitrogen-to-carbon ratio. In the last formulation, Chla is a state variable of the model, which is dynamically simulated. Results showed important differences between the formulations, the first leading to overestimate the Chla concentration in low nutrients conditions. Thus, this study strengthens the importance of the Chla modelling in a coupled model in order to better estimate a crucial variable for validation of ecosystem models.