Trophic interaction networks are notoriously difficult to understand and to diagnose (i.e., to identify contrasted network functioning regimes). Such ecological networks have many direct and indirect connections between species, and these connections are not static but often vary over time. These topological changes, as opposed to a dynamic on a static (frozen) network, can be triggered by natural forcings (e.g., seasons) and/or by human influences (e.g., nutrient or pollution inputs). Aquatic trophic networks are especially dynamic and versatile, thus suggesting new approaches for identifying network structures and functioning in a comprehensive manner.In this study, a qualitative model was devised for this purpose. Applying discrete-event models from theoretical computer science, a mechanistic and qualitative model was developed that allowed computation of the exhaustive dynamics of a given trophic network and its environment. Once the model definition is assumed, it provides all possible trajectories of the network from a chosen initial state. In a rigorous and analytical approach, for the first time, we validated the model on one theoretical and two observed trajectories recorded at freshwater stations in the La Rochelle region (Western France). The model appears to be easy to build and intuitive, and it provides additional relevant trajectories to the expert community. We hope this formal approach will open a new avenue in identifying and predicting trophic (and non-trophic) ecological networks.

While the preindustrial ocean was assumed to be in equilibrium with the atmosphere, the modern ocean is a carbon sink, resulting from natural variability and anthropogenic perturbations, such as fossil fuel emissions and changes in riverine exports over the past two centuries. Here we use a suite of sensitivity experiments based on the ECCO-Darwin global-ocean biogeochemistry model to evaluate the response of air-sea CO2 flux and carbon cycling to present-day lateral fluxes of carbon, nitrogen, and silica. We generate a daily export product by combining point-source freshwater discharge from JRA55-do with the Global NEWS 2 watershed model, accounting for lateral fluxes from 5171 watersheds worldwide. From 2000 to 2019, carbon exports increase CO2 outgassing by 0.22 Pg C yr-1 via the solubility pump, while nitrogen exports increase the ocean sink by 0.17 Pg C yr-1 due to phytoplankton fertilization. On regional scales, exports to the Tropical Atlantic and Arctic Ocean are dominated by organic carbon, which originates from terrestrial vegetation and peats and increases CO2 outgassing (+10 and +20%, respectively). In contrast, Southeast Asia is dominated by nitrogen from anthropogenic sources, such as agriculture and pollution, leading to increased CO2 uptake (+7%). Our results demonstrate that the magnitude and composition of riverine exports, which are determined in part from upstream watersheds and anthropogenic perturbations, substantially impact present-day regional-to-global-ocean carbon cycling. Ultimately, this work stresses that lateral fluxes must be included in ocean biogeochemistry and Earth System Models to better constrain the transport of carbon, nutrients, and metals across the land-ocean-aquatic-continuum.

Intertidal mudflats colonized by sediment-dwelling microphytobenthos deliver a wide range of ecosystem services. Here we simulate the response of microphytobenthos, located on a temperate tidal mudflat along the French Atlantic coast in Northwestern Europe, exposed to changes in light, temperature, and sea level conditions predicted by the Intergovernmental Panel on Climate Change. Without sea level rise, microphytobenthos benefit from the balancing effect of net primary production fluctuations, experiencing an increase in winter and a decrease in summer. Under the worst emissions scenario, microphytobenthos bloom up to 14 days earlier in spring and 5 days later in fall, thereby extending the low-level microphytobenthos biomass period by an additional 3 weeks in summer. Sea level rise reduces light exposure leading to a pronounced decline in microphytobenthos under the medium-low emissions and worst emissions scenarios. We provide evidence that the anticipated warmer climate and sea level rise will have an impact on microphytobenthos, potentially triggering cascading effects across the entire food web and disrupting ecosystem services. Under the worst-case emission scenario, benthic microalgae from temperate mudflats are projected to bloom earlier in spring and later in the fall, and lack of light due to sea level rise may lead to overall decline, according to a coupled physical-biological model and climate scenarios.

Microphytobenthos (MPB) are a key primary producer of intertidal mudflats. MPB face strong variability in incident irradiance during low tides. Despite photoprotection and photoacclimation, such variations can translate into the photoinhibition of MPB cells. This study explores the effect of photoinhibition on MPB primary production (PP) over a large and productive temperate mudflat (Brouage mudflat, NW France). We used a regional and high-resolution tri-dimensional hydrodynamic model coupled to an MPB model with or without photoinhibition. Photoinhibition leads to a 20% (-0.79 x 103 t C) decrease of the simulated MPB PP over the entire mudflat. As the upper shore is exposed to light more frequently and longer than the lower shore, the decrease of MPB PP is higher on the upper shore (-29%) than on the lower shore (-5%). With the highest photosynthetically active radiation cumulated over the mudflat, the decrease of MPB PP due to photoinhibition is the highest during spring and spring tides (-22% and -23%, respectively). The model suggests MPB photoinhibition is sensitive to the photoacclimation status of MPB cells through the light saturation parameter. This first modeling attempt to account for MPB photoinhibition is highly constrained by our current theoretical knowledge and limitations on the MPB growth physiology, but it suggests that this process can have a substantial impact on the MPB PP. As such, assessing the MPB photosynthetic response to the highly variable environmental conditions that prevail in large and productive intertidal mudflats is a real challenge for quantifying MPB PP from a synoptic to inter-annual time scale.

The gross primary production (GPP) of intertidal mudflat microphytobenthos supports important ecosystem services such as shoreline stabilization and food production, and it contributes to blue carbon. However, monitoring microphytobenthos GPP over a long-term and large spatial scale is rendered difficult by its high temporal and spatial variability. To overcome this issue, we developed an algorithm to map microphytobenthos GPP in which the following are coupled: (i) NDVI maps derived from high spatial resolution satellite images (SPOT6 or Pleiades), estimating the horizontal distribution of the microphytobenthos biomass; (ii) emersion time, photosynthetically active radiation (PAR), and mud surface temperature simulated from the physical model MARS-3D; (iii) photophysiological parameters retrieved from Production-irradiance (P-E) curves, obtained under controlled conditions of PAR and temperature, using benthic chambers, and expressing the production rate into mg C h(-1) m(-2) ndvi(-1). The productivity was directly calibrated to NDVI to be consistent with remote-sensing measurements of microphytobenthos biomass and was spatially upscaled using satellite-derived NDVI maps acquired at different seasons. The remotely sensed microphytobenthos GPP reasonably compared with in situ GPP measurements. It was highest in March with a daily production reaching 50.2 mg C m(-2) d(-1), and lowest in July with a daily production of 22.3 mg C m(-2) d(-1). Our remote sensing algorithm is a new step in the perspective of mapping microphytobenthos GPP over large mudflats to estimate its actual contribution to ecosystem functions, including blue carbon, from local and global scales.

In situ data along with input/output files and code of the model used in the manuscript by Savelli et al. submitted to Journal of Geophysical Research: Biogeosciences Savelli, R., Bertin, X., Orvain, F., Gernez, P., Dalle, A., Coulombier, T., Pineau, P., Lachaussée, N., Polsenaere, P., Dupuy, D., Le Fouest, V., submitted. Impact of chronic and massive resuspension mechanisms on the microphytobenthos dynamics in a temperate intertidal mudflat. Journal of Geophysical Research: Biogeosciences See the readme.txt file for explicit details on the repository.

Microphytobenthos (MPB) resuspension is a key mechanism in the transfer of organic matter from productive intertidal mudflats to terrestrial and marine systems. In this study, we infer on the contribution of physical and biological factors involved in the MPB resuspension. We use a physical‐biological coupled model forced by realistic meteorological and hydrodynamical forcings to simulate chronic (without any concomitant sediment resuspension) and massive (driven by bed failure) resuspension over a year. The model simulates mud surface temperature, MPB growth, and grazing by the gastropod Peringia ulvae. The model suggests that MPB resuspension is the highest in spring tides and at the flood beginning due to high current velocity and low water heights that promote waves‐sea bottom interactions. The seasonal export of MPB biomass is the highest in spring, up to threefold higher than in summer when the export is the lowest. The simulated seasonal dynamics of MPB resuspension results from the MPB biomass concentration in the sediment, physical disturbances, and the bioturbation activity by P. ulvae. Annually, 43% of the simulated MPB primary production is resuspended. The MPB resuspension (60.8 g C·m−2·yr−1) exceeds the loss by P. ulvae grazing (41.1 g C·m−2·yr−1). The model suggests that chronic and massive resuspension events are important in the synoptic to seasonal MPB dynamics in temperate intertidal mudflats. Accounting for such processes in the carbon budget assessment in the land‐ocean interface could bring new insights to our understanding of the role played by MPB in the coastal carbon cycle.

Microphytobenthos (MPB) from intertidal mudflats are key primary producers at the land–ocean interface. MPB can be more productive than phytoplankton and sustain both benthic and pelagic higher trophic levels. The objective of this study is to assess the contribution of light, mud temperature, and gastropod Peringia ulvae grazing pressure in shaping the seasonal MPB dynamics on the Brouage mudflat (NW France). We use a physical–biological coupled model applied to the sediment first centimetre for the year 2008. The simulated data compare to observations, including time-coincident remotely sensed and in situ data. The model suggests an MPB annual cycle characterised by a main spring bloom, a biomass depression in summer, and a moderate fall bloom. In early spring, simulated photosynthetic rates are high due to mud surface temperature (MST) values close to the MPB temperature optimum for photosynthesis and because increasing solar irradiance triggers the onset of the MPB spring bloom. Simulated peaks of high P. ulvae grazing (11 days during which ingestion rates exceed the primary production rate) mostly contribute to the decline of the MPB bloom along with the temperature limitation for MPB growth. In late spring–summer, the MPB biomass depression is due to the combined effect of thermo-inhibition and a moderate but sustained grazing pressure. The model ability to infer biotic and abiotic mechanisms driving the seasonal MPB dynamics could open the door to a new assessment of the export flux of biogenic matter from the coast to the open ocean and, more generally, of the contribution of productive intertidal biofilms to the coastal carbon cycle.