Study of aerobic and anaerobic cultivable sedimentary microbiota - Capability of isolates to produce and degrade extracellular polymeric substances and possible use in biotechnology
The thesis is part of a larger project aiming to analyze the Extracellular Polymeric Substances (EPS) contents of sediments from modern and ancient estuaries (ANR “EXODIA”). EXODIA aims to better define the composition and function of EPS in modern and ancient estuaries, and their interaction with clay and metals through diagenesis. The aim of the thesis is to isolate, characterize and identify the culturable microorganisms potentially involved in the estuarine sediment EPS cycle (anaerobic and aerobic bacteria), in particular strains able to produce high quantities of EPS and/or able to degrade EPS. A maximum of microorganisms from the most representative sediment horizons on 6-m deep cores will be isolated by a culturomics strategy relying on the use of 16 media and 2 temperatures of incubation as well as enrichment strategies to focus on EPS degrading and biofilm-forming strains. After isolation and constitution of a strain’s library, each strain will be grown as planktonic and sessile pure culture and their ability to produce EPS (mucoid character), to form biofilms and to produce EPS-modifying enzymes (DNAses, proteases, hydrolases, lyases) will be assayed. Antibiosis and antibiofilm activities of isolates against bacterial reference strains in biofilm research (Escherichia coli and Pseudomonas aeruginosa) will be carried out. All the information relative to the isolates will be listed in a publicly available database. The identification of isolates will be performed in first intention by mass spectrometry. In parallel, genomic identification of the microbiome in sediment samples will be performed. This will allow us to estimate if our isolates are representative of the global community.
(27/05/2025)
CBMN, UB, ENITAB, INC-CNRS, CNRS, ICMCB, UB, INC-CNRS, CNRS, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS
A karst rather than periglacial origin for small enclosed depressions of the Landes Triangle, southwest France
Small topographic depressions offer insight into past and present groundwater recharge processes. The Landes Triangle (SW France) is dotted with over 2,400 such depressions, whose origins and hydrogeological implications remain unclear. This paper aims to disentangle their origin, with emphasis on the Villagrains-Landiras anticline sector: a key recharge zone, which also features the highest density of depressions. We first evaluate three historical hypotheses with open GIS data at the regional scale, then detail the near-surface structure of a depression near the anticline with electrical resistivity tomographies and ground-penetrating radar. We identify two groups of depressions based on their morphology, distribution and geological context. One aligns with an aeolian origin. The other (encompassing 97% of the depressions near the anticline) suggests a karst origin, with more circular shapes and proximity to karst, streams, faults and neighbouring depressions. However, 18% of these lie outside the crypto-karst area derived from GIS references and may rather be of periglacial origin. Yet, our geophysical survey revealed subsidence but no evidence of cryogenic sediment or solifluction. We conclude that a karst origin remains the best hypothesis in the anticline area, and highlight that sole reliance on GIS references may underestimate crypto-karst extent. Further geological investigation is therefore needed to map its full extent and related water pathways near the anticline.
(Earth Surface Processes and Landforms. vol. 50, n° 0197-9337, 25/05/2025)
EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS, ULaval
LEON-BLOOM project - Origin, spatial and temporal dynamics of cyanobacteria blooms in lake Léon, France
Lake Léon (Landes) has recently experienced important cyanobacteria blooms, leading to severe restrictions on recreational activities of this popular tourist waterbody of the Atlantic coast in France. To investigate the origins of these algal blooms, the dynamics of biological patterns, and to provide management strategies for mitigation, the "Léon-Bloom" research project established a collaboration between environmental watershed managers and research scientists. The project aims to identify the potential sources of algal growth and gain a better understanding of their spatial and temporal dynamics. The project is structured in several workpackages, each investigating a potential mechanism. (1) Firstly, nutrient fluxes from the watershed are analyzed, including the use of passive phosphorus samplers. We also set up an experimental design to investigate the role temperature, light and phosphorus on the development of phytoplankton biomass. (2) Secondly, a chemical analysis of the lake’s sediments is carried out resorting to sediment coring and experimentation to measure the potential of phosphorus release under anoxic conditions. (3) Thirdly, the role of temperature and oxygen on phytoplankton composition will be assessed using a statistical modeling approach. We measured temperature and oxygen in several stations of the lake to calibrate these models using autonomous high-frequency sensors. (4) The phytoplankton community is studied both spatially and temporally, at the taxonomic and algal group level. Cyanotoxins are also regularly monitored. Finally, two modeling-based workpackages will focus on (5) analyzing the role of wind in the spatial distribution of the plankton community and physical parameters and (6) developing remote sensing methods for monitoring algal concentrations in this lake. Ultimately, we aim to decipher the relative contribution of wind, nutrients (fluxes and internal release), and environmental variables, to understand the conditions of cyanobacterial blooms emergence.
(21/05/2025)
UR EABX, INRAE, ECLA, USMB [Université de Savoie] [Université de Chambéry], INRAE, OFB, OFB - DRAS, OFB, UMR ISPA, Bordeaux Sciences Agro, INRAE, RECOVER, AMU, INRAE, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS, OFB Service EcoAqua, OFB - DRAS, OFB
Rescuelog : Collecte numérique et reporting des interventions de sauveteurs à l’océan avec (ru)ODK, Shiny et SK8
Les plages du Sud-Ouest de la France présentent des risques élevés de noyades, nécessitant des dispositifs de surveillance efficaces. Le projet Rescuelog modernise la collecte et l’analyse des données sur les interventions de sauveteurs grâce à un workflow entièrement intégré dans l’écosystème R. Les interventions sont enregistrées via des tablettes Android utilisant ODK Collect, les données étant ensuite extraites avec ruODK (Mayer 2020) et structurées dans une base PostgreSQL après validation. Des données environnementales, incluant les prévisions météo et marines, sont enrichies via l’API de Météo-France grâce au package httr2 (Wickham 2023). Ces données alimentent un modèle prédictif, construit avec tidymodels (Kuhn and Wickham 2020), permettant d’anticiper les jours à haut risque de noyade. Ce modèle est versionné et stocké grâce au package vetiver (Silge 2023), puis exploité par une application Shiny déployée via le service sécurisé SK8 (SK8 Team 2024) d’INRAE. Cette solution démontre la capacité des outils R à proposer des workflows robustes, sécurisés et scalables pour des problématiques opérationnelles critiques comme la prévention des noyades.
(18/05/2025)
UR EABX, INRAE, UR ETTIS, INRAE, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS
Detailed characterization of a LNAPL-contaminated soil using X-ray microtomography and gas chromatography
The effectiveness of remediation strategies for soils contaminated by light non-aqueous hydrocarbons (LNAPL) depends on a detailed understanding of their geological and hydrodynamic properties, as well as their spatial distribution. In this work, 3D X-ray microtomography (μ-CT) and gas chromatography (GC) are combined to characterize porosity, permeability, LNAPL saturation (S n ), and van Genuchten parameters (α and N) at a LNAPLcontaminated site. Moreover, a novel μ-CT-based method is presented to quantify LNAPL ganglia connectivity-an essential factor in understanding their spatial distribution and migration dynamics. The data obtained using this approach were employed to calculate LNAPL transmissivity. This technique, referred to as the μ-CT/GC method, was compared with LNAPL transmissivity values derived from the API-LRDM 2 hydrodynamic model (based on literature data) and from baildown test results, revealing significant discrepancies. However, the transmissivity obtained through μ-CT/GC method was more closely aligned with values measured during insitu tests (baildown test). These findings underline the limitations of conventional transmissivity prediction approaches and pave the way for developing more effective remediation strategies. Moreover, the results highlight the significant impact of the site's strong hydrodynamic heterogeneity on pollutant retention and mobility.
(Journal of Contaminant Hydrology. vol. 273, n° 0169-7722, 18/05/2025)
EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS, UB
Biomonitoring of azole fungicides in free-living blackbird plasma using on-line solid-phase extraction coupled to liquid chromatography-tandem mass spectrometry (SPE HPLC-MS/MS)
In this study, a rapid and sensitive method using on-line solid-phase extraction (SPE) coupled to liquid chromatography - tandem mass spectrometry (SPE HPLC-MS/MS) was developed to analyse 15 azole fungicides currently used in vineyards in blackbird plasma samples. The monitored fungicides included 13 triazoles (cyproconazole, difenoconazole, epoxiconazole, fenbuconazole, flusilazole, flutriafol, metconazole, penconazole, propiconazole, tebuconazole, tetraconazole, triadimefon, triadimenol) and 2 imidazoles (imazalil and prochloraz). After a rapid preparation step by protein precipitation with acetonitrile on 25 µL of plasma samples, final extracts diluted with Milli-Q water were analyzed by on-line SPE-LC-MS/MS in positive electrospray mode (ESI+) using the dynamic multi-reaction monitoring mode (dMRM). Following optimization, method validation was achieved through studies of linearity, sensitivity, accuracy, precision, and sample extract conservation. The limits of quantification (LOQs) obtained for a low volume of plasma (25 µL) ranged from 0.01 to 0.43 ng g−1 plasma, except for triadimenol (1.37 ng g−1). Finally, the validated method was successfully applied to 34 Eurasian blackbird plasma samples, with blackbirds from different habitats (city, forest, vineyards) submitted to contrasted azole pressures. Five of them were detected, tebuconazole and tetraconazole being the predominant ones. As expected, azoles concentrations were more elevated in blackbirds sampled in vineyards where most of these fungicides are used.
(Journal of Chromatography A. vol. 1748, n° 0021-9673, pp. 465725, 10/05/2025)
EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS, CEBC, ULR, CNRS, INRAE
Molecular characterization of organic aerosols in urban and forested areas of Paris using high-resolution mass spectrometry
In order to study aerosols in environments influenced by anthropogenic and biogenic emissions to variable extents, PM1 samples were collected during summer 2022 in the greater Paris area (ACROSS campaign, Atmospheric Chemistry Of the Suburban Forest, 14 June to 25 July) at two locations that represent the urban Paris and the suburban forested areas. They were analyzed using high-resolution mass spectrometry (HRMS) together with total carbon (TC) with a thermo-optical method. Both sites are compared here to explore differences in aerosol composition from urban and forested environments. The TC analysis shows similar organic carbon (OC) concentrations at both sites (3.2 ± 1.8 µg m−3 for Paris and 2.9 ± 1.5 µg m−3 for Rambouillet) and higher elemental carbon (EC) values in the urban area. Both OC and EC concentrations did not show significant variations for daytime and nighttime conditions. This work highlights the influence of anthropogenic inputs on the chemical composition of urban and forested areas, derived from the presence of CHO and CHON compounds but also the detection of two sulfur-containing compounds (C5H12SO7 and C10H17NSO7), which could be tentatively assigned as organosulfates. A smaller number of aromatic compounds were observed for clean periods that better represent the local biogenic and anthropogenic contributions in Rambouillet and Paris, respectively.
(Atmospheric Chemistry and Physics. vol. 25, n° 1680-7316, pp. 4885-4905, 09/05/2025)
LISA (UMR_7583), INSU - CNRS, UPEC UP12, CNRS, UPCité, CAM, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS, INERIS
Atmospheric stability of six particulate biogenic secondary organic aerosol markers towards photolysis, hydroxyl radicals and ozone
This study aimed to investigate the kinetics of the heterogeneous reactions of six biogenic secondary organic aerosol (BSOA) markers of atmospheric interest, i.e. the terebic, terpenylic, cis-pinonic, pinic, 3-methyl-1,2,3-butanetricarboxylic (MBTCA) and β-caryophyllinic acids. For this purpose, these compounds were individually adsorbed onto silica model particles and exposed either to solar irradiation, hydroxyl radicals, or ozone. Marker concentrations extracted from particles were subsequently analyzed by liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (LC-QTOF/MS). Pseudo-first-order rate constants were derived from simulations (using either exponential functions or the tangent slope at t0) of particulate marker concentration decays as a function of exposure time to different oxidants or light. Second-order rate constants were calculated considering the oxidant concentrations under different experimental conditions. The overall atmospheric lifetime of each marker was calculated, revealing that β-caryophyllinic acid is the most reactive compound studied, with a lifetime of <14.3 min, followed by cis-pinonic acid (8.6 h), MBTCA (19 h), pinic acid (>2.8 days), terpenylic acid (>4.8 days), and terebic acid (>5.8 years).This work confirms that the atmospheric stability of some BSOA markers is insufficient, to justify their relevance as tracers of particle formation or aging processes.
(Chemosphere. vol. 380, n° 0045-6535, pp. 144453, 09/05/2025)
EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS
Predicting individual’s decision to enter the water at a high-energy recreational surf beach in France
Objectives To predict beachgoer decision to enter the water at a high-energy surf beach, in southwest France. Methods We built a unique multidisciplinary database combining data collected by an on-site beachgoers survey, weather stations, marine buoys and tidal reconstruction. Human, weather and meteocean factors were considered as potentially predictive of beachgoer behaviour. We employed a logistic regression analysis to predict beachgoers’ decision to enter the water on any given day at a high-energy recreational beach. Results We demonstrated that both environmental and human factors influence a beachgoer’s decision to enter the water. Daily mean wave height and daily mean insolation duration were significant predictors at the p<0.001 level, while age, place of residence and self-confidence in swimming out of a rip current were significant at the p<0.05 level or higher. Beachgoers were more likely to enter the water on sunny days with lower waves. Younger individuals, those living outside the Landes département, and those who declared themselves to be ‘confident’ or ‘uncertain’ about their ability to swim out of a rip current expressed a higher propensity to enter the water. Our model has an accuracy, F-Score, precision and recall of 71%, 73%, 86%, 79%, respectively. Conclusions Beachgoer exposure on any given day can ultimately be predicted by coupling our model with beach attendance models. This would allow for the design of rescue and preventive operations on days with high expected exposure. While models based solely on environmental factors can be used to forecast beach risks, incorporating human factors into the model provides valuable insight for crafting prevention messages. In this regard, lifeguards could engage more actively with beach users to deliver appropriate safety messages.
(Injury Prevention, n° 1353-8047, pp. ip-2024-045574, 08/05/2025)
UR ETTIS, INRAE, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS
Management of groundwater resources in the coastal aquifers of the Magdalen Islands (Canada) using decision support models
Freshwater resources are scarce on islands surrounded by seawater, where groundwater lenses are often the only sources of fresh water. These resources are highly sensitive to climate variability and human activities, requiring specialized management approaches. Here, groundwater flow models that account for climate and parameter uncertainty are used to guide groundwater resource management on the Magdalen Islands (Quebec, Canada). An island-wide groundwater flow model was developed for four islands of the archipelago using MODFLOW-2005 and the sharp interface seawater intrusion package SWI2, driven by a spatially distributed SWB2 recharge model. Parameter estimation was then conducted using PEST_HP, producing island-wide maps of the freshwater lenses and water budgets. Transient simulations were run to determine the percent rise of the freshwater-seawater interface below pumping wells relative to the onset of pumping. The model was then combined with PESTPP-OPT and climate change projections to conduct pumping optimization under climate and parameter uncertainty, and with MODPATH to delineate zones for groundwater protection. The modeling results indicate that groundwater resources will be sufficient to meet the future water demand on the islands as projected through 2050. While some wellfields can provide more fresh water, others cannot, and certain wells may be at risk of saltwater intrusion in the future. Climate change is unlikely to impact overall groundwater resource availability, but it will reduce the volume of freshwater that can be withdrawn from existing wellfields. The scripted, open-source modeling approach used here can be applied to similar environments to address common management challenges encountered in island aquifer settings.
(Hydrogeology Journal. vol. 33, n° 1431-2174, pp. 801 - 824, 07/05/2025)
ULaval, BRGM, UMR G-EAU, Cirad, BRGM, IRD, INRAE, Institut Agro, UM, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS