Differentiating estuarine dissolved organic matter composition by unsupervised and supervised machine learning
Differentiating the composition of Dissolved Organic Matter (DOM) in estuaries is a major environmental concern, as the DOM characteristics are closely linked to biogeochemical and ecological considerations (e.g. water properties and trophic cycling). However, tracing the spatiotemporal variations of estuarine DOM is challenging due to multiple sources and complex transformation processes. Here, we investigate the dynamics of estuarine DOM by analyzing the optical properties of DOM through UV-Visible absorbance and fluorescence spectroscopy, while also capturing the variability of DOM using machine learning algorithms and explainable artificial intelligence. To this aim, we collected sub-surface water samples (n = 249) from a human-impacted estuary with intense industrialization and urbanization in France (Seine Estuary) across distinct land use characteristics in contrasting hydrological conditions. We then applied unsupervised and supervised machine learning techniques to analyze the optical properties of DOM, which were determined by UV-Visible absorbance and Excitation-Emission Matrix (EEM) fluorescence spectroscopy combined with parallel factor analysis (PAR-AFAC). Our results show that unsupervised machine learning (K-means clustering) captures the spatial variabilities of DOM, identifying three distinct estuarine zones based on pronounced spatial variations of several DOM optical parameters. Supervised machine learning (Light Gradient Boosted Machine, LightGBM) further validates the rationality of the defined zonation. Subsequently, explainable artificial intelligence based on SHapley Additive exPlanations (SHAP) analysis shows that DOM in each zone has specific characteristics. Our model indicates that DOM in the Seine Estuary is primarily influenced by high molecular weight materials and autochthonous contributions in the upper estuary (Zone I). The dominant contribution to DOM in the mid-estuary (Zone II) comes from autochthonous and aromatic material as well as transformation and (photo)degradation products. Lower estuary (Zone III) is mainly characterized by aromatic DOM (subject to photodegradation), low molecular weight compounds, autochthonous DOM, as well as transformation and (photo)degradation products. Overall, this study presents a workflow for differentiating the composition of DOM, tracing the variability and dynamics of DOM along the land-to-sea continuum, and elucidating the involved processes. The approach developed in the Seine Estuary has significant implications for environmental management and can be adapted to other land-sea continuums.
(Water Research. vol. 284, n° 0043-1354, pp. 123900, 11/07/2026)
METIS, EPHE, PSL, INSU - CNRS, SU, CNRS, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS
Tidal Pumping, Alkalinity Production and Export: An Overlooked Carbon Sequestration Process in Salt Marshes
(11/07/2026)
EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS
Digital PCR (dPCR) vs. Quantitative PCR (qPCR) approaches for quantification of two Perkinsus species within clam tissue samples
The parasite Perkinsus olseni (Perkinsea, Alveolata), the etiological agent of Perkinsosis, infects a wide range of bivalves and gastropods, including clams, particularly in Europe. This parasite coexists in sympatry with another Perkinsus species, P. chesapeaki, which, as opposed to P. olseni, has not been directly associated to mortality events. Accurate detection and quantification of Perkinsus infections, even at low infection intensities, are crucial for monitoring clam population health and assessing risks associated with emerging diseases. In this study, we compared molecular methodologies based on duplex real-time quantitative PCR (qPCR) and digital PCR (dPCR) in order to develop effective host resource management strategies. We first evaluated detection capabilities and the impact of potential inhibitors using both methodologies across varying DNA concentrations. Subsequently, we applied these methods to two contrasting French environments: Noirmoutier, characterized by low prevalence and infection intensity, and Arcachon Bay, which exhibits high prevalence and infection intensity. Our results demonstrate that dPCR should be prioritized for detecting and quantifying parasites at low infection intensities (101 -102 cp.µL-1), as it might minimize false-negative results compared to qPCR. Notably, dPCR provided new insights and revealed cryptic infections, demonstrating greater efficiency in detecting P. chesapeaki in lightly infected sites such as Noirmoutier. Conversely, infection intensity was underestimated with dPCR relative to qPCR for clams with moderate to high Perkinsus infection levels (103 cp.µL-1 or higher), proving the latter more suitable for medium to heavily infected areas like Arcachon Bay. These findings are important as they represent the first in situ monitoring of both Perkinsus species using culture-free methodologies. This work provides essential tools for resource management and conservation strategies to address emerging diseases.
(Journal of Invertebrate Pathology. vol. 213, n° 0022-2011, pp. 108417, 11/07/2026)
SBR, SU, CNRS, AD2M, SU, CNRS, SBR, SU, CNRS, ASIM, IFREMER, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS
Semi-empirical forecast modelling of rip-current and shore-break wave hazards
Sandy beaches are highly attractive but also potentially dangerous environments for those entering the water as they can be exposed to physical hazards in the surf zone. The most severe and widespread natural bathing hazards on beaches are rip currents and shore-break waves, which form under different wave, tide, and morphological conditions. This paper introduces two new, simple semiempirical rip-current and shore-break wave hazard forecast models. These physics-informed models, which depend on a limited number of free parameters, can be used to compute the time evolution of the rip-current flow speed V and shore-break wave energy E sb . These models are applied to a high-energy mesotidal-macrotidal beach, La Lette Blanche, in southwest France, where intense rip-currents and shore-break wave hazards co-exist. Hourly lifeguardperceived hazards collected during patrolling hours (from 11:00 a.m. to 07:00 p.m. LT (UTC+2)) during July and August of 2022 are used to calibrate the two models. These data are also used to transform V and E sb into a five-level scale from 0 (no hazard) to 4 (hazard maximised). The model accurately predicts rip-current and shore-break wave hazard levels, including their modulation by tide elevation and incident wave conditions, opening new perspectives for forecasting multiple surf-zone hazards on sandy beaches. In addition, daily-mean hazard forecasts demonstrate even greater predictive skill, which is important for conveying straightforward messages to the general public and lifeguard managers. The approach presented here only requires a limited number of beach morphology metrics and allows for the prediction of surf-zone hazards on beaches where wave and tide forecasts are available.
(Natural Hazards and Earth System Sciences. vol. 25, n° 1561-8633, pp. 2379–2397, 11/07/2026)
EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS, UR ETTIS, INRAE, SMGBL, UR EABX, INRAE
Key concepts and a world‐wide look at plant recruitment networks
Plant–plant interactions are major determinants of the dynamics of terrestrial ecosystems. There is a long tradition in the study of these interactions, their mechanisms and their consequences using experimental, observational and theoretical approaches. Empirical studies overwhelmingly focus at the level of species pairs or small sets of species. Although empirical data on these interactions at the community level are scarce, such studies have gained pace in the last decade. Studying plant–plant interactions at the community level requires knowledge of which species interact with which others, so an ecological networks approach must be incorporated into the basic toolbox of plant community ecology. The concept of recruitment networks (RNs) provides an integrative framework and new insights for many topics in the field of plant community ecology. RNs synthesise the set of canopy–recruit interactions in a local plant assemblage. Canopy–recruit interactions describe which (“canopy”) species allow the recruitment of other species in their vicinity and how. Here we critically review basic concepts of ecological network theory as they apply to RNs. We use RecruitNet, a recently published worldwide data set of canopy–recruit interactions, to describe RN patterns emerging at the interaction, species, and community levels, and relate them to different abiotic gradients. Our results show that RNs can be sampled with high accuracy. The studies included in RecruitNet show a very high mean network completeness (95%), indicating that undetected canopy–recruit pairs must be few and occur very infrequently. Across 351,064 canopy–recruit pairs analysed, the effect of the interaction on recruitment was neutral in an average of 69% of the interactions per community, but the remaining interactions were positive (i.e. facilitative) five times more often than negative (i.e. competitive), and positive interactions had twice the strength of negative ones. Moreover, the frequency and strength of facilitation increases along a climatic aridity gradient worldwide, so the demography of plant communities is increasingly strongly dependent on facilitation as aridity increases. At network level, species can be ascribed to four functional types depending on their position in the network: core, satellite, strict transients and disturbance‐dependent transients. This functional structure can allow a rough estimation of which species are more likely to persist. In RecruitNet communities, this functional structure most often departs from random null model expectation and could allow on average the persistence of 77% of the species in a local community. The functional structure of RNs also varies along the aridity gradient, but differently in shrubland than in forest communities. This variation suggests an increase in the probability of species persistence with aridity in forests, while such probability remains roughly constant along the gradient in shrublands. The different functional structure of RNs between forests and shrublands could contribute to explaining their co‐occurrence as alternative stable states of the vegetation under the same climatic conditions. This review is not exhaustive of all the topics that can be addressed using the framework of RNs, but instead aims to present some of the interesting insights that it can bring to the field of plant community ecology.
(Biological Reviews. vol. 100, n° 1464-7931, pp. 1127-1151, 11/07/2026)
UJA, NEOLAiA, IISTA-CEAMA, UGR, CIDE, CSIC, UNCOMA, UCA, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS, SYSU, CEFE, EPHE, PSL, CNRS, IRD [Occitanie], IRD, INRAE, Institut Agro, UM, UMPV
Use of solute concentration gradients in the benthic boundary layer to highlight sediment source-sink dynamics: a non-invasive in situ study
Oxygen, nutrients, and pollutants fluxes at the sediment-water interface are involved in the water quality and ecological status of shallow coastal environments. The short-term variabilities of these fluxes, in response to hydrodynamic and benthic biogeochemical processes in the field, make it difficult to assess the net balance of these fluxes. Here we evaluate the ability of using concentration gradients in the benthic boundary layer to better understand temporal variations in these fluxes. Three shallow Mediterranean coastal lagoons (Berre, Thau and Prévost lagoons), affected by deoxygenation events and depicting contrasting water quality status, were investigated. A Benthic Oxygen Gradient Observatory System (BOGOS) was set-up and deployed for two weeks in each lagoon to obtain continuous oxygen gradient time-series. In addition, concentration gradients of nutrients (Si, NH4+, PO43−) and trace elements (Fe, Mn, Co, As, Cu, Mo, MeHg) were obtained using a specifically dedicated benthic water sampler (SUSANE) deployed under contrasting oxygenation conditions (oxic, hypoxic, anoxic, euxinic) and diurnal cycles (day and night). The results enabled us firstly to better define the limits of applying the gradient method in shallow coastal areas, considering environmental conditions (water stratification, intense water mixing, low flux intensity) as well as technical limitations (concentration uncertainty). This approach then allowed to accurately capture contrasted benthic oxygen dynamics: diurnal cycles in sediments colonized by macrophytes in Prévost and Thau lagoons, and a dominant high oxygen demand in bare sediments in Berre lagoon. Benthic solute gradients in Berre lagoon indicated release of nutrients from the sediment under normoxic conditions after a long-term anoxic event, as well as release of dissolved Mn, Fe, As and Co under anoxic conditions. Under euxinic conditions, gradients reversed for most trace elements that were trapped in sediment due to (co)precipitation with sulfide minerals, while nutrient gradients indicated continuing sizeable releases to the water column. The benthic concentration gradient approach can thus be seen as a promising approach in assessing the dynamics of benthic fluxes at an appropriate time scale in highly dynamic shallow coastal lagoons. This effort should be completed by vertical turbulent diffusivity measurements, to obtain time series of turbulent fluxes of various solutes.
(Estuarine, Coastal and Shelf Science. vol. 323, n° 0272-7714, pp. 109432, 11/07/2026)
CHROME, UNIMES, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS, UAG, INSU - CNRS, UM, CNRS, CEREGE, IRD, AMU, CdF (institution), INSU - CNRS, CNRS, INRAE, UMR Marbec - Station Sète, UMR MARBEC, IRD, IFREMER, CNRS, UM, MIO, IRD, AMU, INSU - CNRS, UTLN, CNRS, LCE, AMU, INC-CNRS, CNRS, HSM, IRD, INSU - CNRS, CNRS, UM, CCEM, IFREMER
Rapport intermédiaire du projet Vigie-Lacs
L’objectif du projet est d’acquérir des connaissances scientifiques indispensables à la préservation des communautés de plantes aquatiques des lacs et étangs du littoral aquitain fortement menacées par les activités humaines et le changement climatique. Ce projet pluridisciplinaire fait appel à plusieurs domaines scientifiques complémentaires, telles que l’écologie des communautés, l’autécologie, la biogéochimie, les biostatistiques, la génétique ou encore l’hydrogéologie.
(pp. 24, 11/07/2026)
UR EABX, INRAE, ECLA, USMB [Université de Savoie] [Université de Chambéry], INRAE, OFB, BioGeCo, UB, INRAE, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS
Contamination des sols français par les résidus de pesticides
La contamination de l’environnement par les résidus de pesticides est une préoccupation croissante par les acteurs publics au vu de leur omniprésence dans tous les milieux et leurs impacts directs et indirects sur la biodiversité et la santé humaine. Cependant, les études traitant de la contamination des sols par les résidus de pesticides sont très peu nombreuses, témoignant du manque de connaissance sur l’état de la contamination des sols et les impacts potentiels sur la biodiversité. Le projet Phytosol, financé entre 2018 et 2022 par l’Anses et coordonné par INRAE a permis d’acquérir des données inédites de 111 substances sur 47 sols prélevés dans le cadre du Réseau de mesures de la qualité des sols (RMQS). Les résultats de cette étude, détaillés dans le rapport suivant et publiés en 2023 dans la revue Environmental Science Technology, démontrent ainsi que 98% des sols prélevés contiennent au moins un résidu de pesticides, y compris des sites sans traitements phytosanitaires tels que les prairies permanentes, les sols forestiers ou encore des sols de parcelles en agriculture biologique. L’évaluation des risques indique également un risque modéré à fort pour les vers de terre notamment dans les sols de grandes cultures. Enfin, la confrontation avec les applications de produits phytosanitaires a mis en évidence la présence de certaines substances bien au-delà de leur temps de dégradation théorique et à des concentrations supérieures à celles attendues. Le déroulement de l’étude (mise en place, méthodologie) ainsi que les résultats détaillés sont présentés dans ce rapport.
(11/07/2026)
Info&Sols, INRAE, LPTC, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS
Modification des régimes de sédimentation en rade de Brest en réponse aux pressions climatiques et humaines
(11/07/2026)
LUSAC, UNICAEN, NU, INTECHMER, Cnam, GEO-OCEAN, UBS, IFREMER, INSU - CNRS, UBO EPE, CNRS, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS, SHOM, LEMAR, IRD, IFREMER, UBO EPE, CNRS
Hourly valve opening data of oysters Ostrea edulis measured during a one-year semi-controlled experiment
This dataset shows the hourly valve behavioral data of the 32 oysters Ostrea edulis throughout the year of the experiment as well as the temperature recorded by each HFNI valvometer. The oyster valve behavior is characterized by 3 parameters: the Valve Opening Amplitude (VOA, the percentage of the valve opening relative to maximum opening), the Valve Opening Duration (VOD, the percentage of time that an oyster spends with its valves open), and the VOA/VOD. For each parameter, the data are presented for each oyster and as a group average for each condition. Missing data correspond to the death of oysters or the stopping of recording by a HFNI valvometer.
(11/07/2026)
EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS