Publications

Publications

Publications

Publications

Publications

Publications

Publications

Publications

Crises hydriques et recomposition des systèmes irrigués en zone semi-aride : le cas du périmètre Manombo–Andoharano–Mamovoky (Sud-Ouest malgache)

Martial Anjarasoa Rakotonjanahary, Frédéric Hoffmann, Félicitée Réjo-Fienena, Bénédicte Thibaud

La région Sud-Ouest de Madagascar est particulièrement vulnérable au dérèglement climatique en raison de son climat semi-aride, caractérisé par des températures élevées et des précipitations faibles et irrégulières. Le changement climatique accentue les sécheresses, provoque une forte variabilité des pluies et retarde le début des saisons pluvieuses, tout en réduisant leur durée. Les projections climatiques indiquent également une augmentation importante des températures dans cette région, ce qui aggrave la rareté de l’eau et affecte directement les ressources en eau de surface ainsi que le développement agricole. Le périmètre irrigué d’Andoharano-Mamovoky, alimenté par le fleuve Manombo via le barrage d’Andoharano, illustre ces enjeux hydrologiques et agricoles. Le débit du Manombo est très variable et la grande majorité de l’eau prélevée est destinée à l’irrigation. Cette forte dépendance à une ressource instable rend le système irrigué vulnérable aux déficits hydriques, notamment en saison sèche. Dans ce contexte, l’étude cherche à comprendre comment les changements du régime hydrologique influencent les rapports sociaux, les inégalités d’accès à l’eau et les conflits entre les usagers du périmètre irrigué. L’étude adopte une approche méthodologique combinant analyses hydrologiques et climatiques, entretiens avec les usagers et observations de terrain. Les résultats montrent une récurrence des années sèches et une baisse de la disponibilité en eau, ce qui accentue les tensions entre agriculteurs. Les communautés développent différentes stratégies d’adaptation, comme l’ajustement des calendriers agricoles et la mise en place de tours d’eau. Toutefois, ces réponses restent limitées par des infrastructures hydrauliques insuffisantes et des inégalités d’accès à l’eau, ce qui fragilise la résilience du système irrigué à long terme et souligne la nécessité de renforcer la gouvernance et les infrastructures hydrauliques.

(09/07/2026)

LAM, IEP Bordeaux, IRD, UBM, CNRS, UBM, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS

Dual clumped isotopes in foraminiferal calcite reveal kinetic bias in some species

Amelia Jane Davies, Marion Peral, Jonathan Erez, Adam Levi, David Evans, Oliver Friedrich, Thibaut Caley, Romi Nambiar, Douglas Coenen, Philip Tauxe Staudigel, Mattia Tagliavento, Miguel Bernecker, Jens Fiebig

Clumped isotope (∆ 47 ) analyses of foraminifera provide a powerful means to reconstruct upper and bottom water temperatures, independent of seawater δ 18 O and elemental composition. We show statistically significant disequilibrium in the dual (∆ 47 -∆ 48 ) clumped isotope composition of some large benthic foraminifera, while other large benthic foraminifera plot within analytical uncertainty of ∆ 47 –∆ 48 equilibrium. This deviation suggests the influence of reaction kinetics, such as kinetic effects during CO 2 absorption or a combination of ion attachment/detachment effects at the solution-crystal interface and slight DIC disequilibrium. Measured core-top, planktic and deep-sea benthic foraminifera plot within the 95% confidence level of empirical ∆ 47 -∆ 48 equilibrium, although additional measurements are required to confidently exclude kinetic ∆ 47 -∆ 48 bias. Dual clumped isotope measurements of large benthic foraminifera from the Eocene of the Paris and Hampshire basins that conform with ∆ 47 -∆ 48 equilibrium (95% confidence level) further support existing evidence for surface ocean temperatures ~12–17 °C warmer than today.

(Communications Earth & Environment. vol. 7, n° 2662-4435, pp. 580, 08/07/2026)

EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS

Last century ecological shifts of coastal dinocysts communities in an anthropized estuary: the case of the Rance estuary, North Brittany, France

Vincent Iratçabal, Clément Lambert, Aurélie Penaud, Gwendoline Gregoire, Anne Murat, Sabine Schmidt, Evelyne Goubert

Over recent decades, dinoflagellate communities have undergone significant changes, resulting in the emergence of the toxic bloom-forming species Alexandrium minutum in Brittany, as observed along most European coastlines. Reconstructing the evolution of these communities requires, high-resolution studies of coastal and estuarine sediment cores. This study focuses on the palynological analysis of two new sediment cores collected from the Rance estuary (UMR 5805 EPOC & Geo-Transfert, 2022), covering the past century. The Rance estuary is a 22 km-long inlet opening onto the English Channel, with a tidal range up to 13 m. Since the early 1900s, most of its already limited fluvial inputs have been cut off following the construction of the Châtelier Lock upstream. The estuary is also notable for hosting the world’s first tidal power plant. Constructed between 1962 and 1966, it has since profoundly altered the hydrological regime, increasing the duration of high-water slack from minutes to several hours and raising the mean water level within the basin. We use a multi-proxy approach combining sedimentological analyses (laser grain-size and calibrated XRF geochemical measurements) with palynological data (classical palynological protocol using cold HCl and HF, spiked with exotic markers). Palynomorphs identification were done by light microscopy at x400 with a focus on dinocysts, identified from genus to species level. The acquired dataset also involves non-exhaustive counts of ciliate cysts and green algae, as well as selected key pollen taxa. All those data are then compared to historical datasets ranging from meteorological data to river discharge and lands usages. Over the last century, a marked ecological shift has been observed in the dinocyst community. The Rance estuary was initially dominated by heterotrophic dinocysts, followed by an increase in Spiniferites taxa in the 1960s. In the 1990s, the dinocyst assemblage was mainly composed of Spiniferites taxa and Alexandrium spp., wich accounted for up to 50 % of the community. These shifts in planktonic community structure reflect both macro-regional drivers (e.g., climate change and catchment-scale agricultural practices) and changes in the hydro-sedimentary functioning of the study site. In this study, we demonstrate that high-resolution estuarine sediment cores allow the reconstruction of dinocyst community trajectories over the past century. Although the species involved differ, comparable trends are observed at other sites investigated at the regional scale. This study, together with others, will help improve our understanding of the driving forces behind these changes, the emergence of the toxic species Alexandrium minutum, and the relative contributions of anthropogenic and climatic forcing.

(06/07/2026)

GEO-OCEAN, UBS, IFREMER, INSU - CNRS, UBO EPE, CNRS, LUSAC, UNICAEN, NU, INTECHMER, Cnam, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS

Spatial distribution of modern dinocyst assemblages in two western France estuaries: a North (Rance) – South (Gulf of Morbihan) comparison in Brittany

Vincent Iratçabal, Clément Lambert, Aurélie Penaud, Gwendoline Gregoire, Anne Murat, Sabine Schmidt, Evelyne Goubert

European coastal ecosystems are facing unprecedented changes, resulting in an increased frequency and intensity of algal blooms, some of which may become harmful. Algal blooms are seasonally recurring phenomena resulting from massive proliferation of planktonic microorganisms, some of which may produce toxins. Dinoflagellates, one of the groups involved, can produce resting cysts that remain viable for at least a century and contribute to coastal seed banks. This study describes the ecological states, as indicated by dinocysts, of two estuaries in Brittany: one in the south, the Gulf of Morbihan (GoM), and the other in the north, the Rance Estuary (RE). These shallow embayments are characterized by ocean-like salinity, low turbidity, and limited freshwater inputs. Sampling was carried out in coves and lateral tidal flats in order to ensure the recovery of fine-grained sediments. In the GoM, 33 samples were collected in 2023. They consist of the uppermost layers of surface sediments collected using two methods: orange peel grab for subtidal zones and by foot for intertidal zone. In the RE, 18 sediment slices were retrieved from the upper 15 cm of several cores collected in 2022 by UMR 5805 EPOC and Geo-Transfert (Uwitec gravity corer, virtual top, average depth: 9 cm). All samples were processed to obtain sedimentological data (laser grain-size) and palynological data (classical palynological protocol using cold HCl and HF). Palynomorphs identification were done by light microscopy at x400 (dinocysts identified from genus to species level, non-exhaustive counts of ciliate cysts and green algae, as well as selected key pollen taxa). RE samples were also analysed for geochemical measurements (calibrated XRF). Owing to the freshness of the samples, dinocysts with preserved cellular content were counted in the sediments from both the GoM and RE, allowing the assessment of the proportion of “viable” cysts within reconstructed assemblages. In both estuaries, spatial variations in dinocyst concentrations are mainly correlated with tidal dynamics and grain size, while dinocyst assemblages (taxa percentages) are highly homogeneous at the scale of each estuary and also depend on continental shelf assemblages that are transported into the estuaries by tides. Regarding discrepancies between both estuaries, total dinocyst concentrations are three times higher on average in the GoM than in the RE. Moreover, assemblages from the GoM are strongly dominated by Lingulodinium machaerophorum (> 50%) while, in the case of the RE, assemblages are dominated by Spiniferites taxa (30–80%) and Alexandrium spp. (up to 40%). Despite lower dinocyst concentrations, the RE shows a high proportion of “viable” cysts (~44%). The proportion of “viable” cysts is unrelated to dinocyst concentrations and appears to be controlled by taphonomic processes. This study, focusing on the distribution of modern dinocysts in estuarine surface sediments, is crucial for understanding: i) dinocyst ecological preferences and the estimation of seed bank stocks, and ii) paleoecological and paleoenvironmental studies conducted in parallel on late Holocene sediment cores.

(06/07/2026)

GEO-OCEAN, UBS, IFREMER, INSU - CNRS, UBO EPE, CNRS, IUEM, IRD, INSU - CNRS, UBO EPE, CNRS, LUSAC, UNICAEN, NU, INTECHMER, Cnam, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS

PFAS Data Hub: An open data portal featuring geovisualisation

Luc Martinon, Alexis Guyot, Benjamin Lysaniuk, Emmanuel Henry, Stéphanie Vermeersch, Pierre Labadie

Per-and polyluoroalkylated substances (PFAS) are a group of man-made chemical substances used in everyday products and industry processes since the 1950s. They contain carbon-fluorine bonds, among the strongest in chemistry, resulting in intrinsic or indirect extreme environmental persistence and earning them the nickname "forever chemicals". In a context of growing awareness of PFAS toxicity and widespread pollution, the Forever Pollution Project (FPP), a cross-border journalistic investigation, compiled data on measured and estimated PFAS contamination across Europe, published as an interactive map. In this data paper we present the PFAS Data Hub (PDH), a project building upon the FPP dataset and reprocessing it using a more robust and transparent methodology. We incorporated several additional data sources, most of which are automatically updated on a monthly basis. To our knowledge, this constitutes the only compilation of PFAS contamination data at the European scale. It is intended to support research projects across a wide range of different disciplines, and to be used as a source of information by journalists, citizens and civil society organisations. The data, as well as a geovisualisation tool with filtering and export options, is available on the PDH website: https://pdh.cnrs.fr.

(03/07/2026)

LIS, AMU, UTLN, CNRS, PRODIG (UMR_8586 / UMR_D_215 / UM_115), UP1, IRD, SU, CNRS, UPCité, IRISSO, PSL, CNRS, INRAE, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS

Effets des pratiques viticoles et de la saison sur les biofilms périphytiques : une approche multivariée

Doufoungognon Carine Estelle Koné, Mélissa Eon, Nicolas Mazzella, Aurélie Moreira, Nathalie Tapie, Hélène Budzinski, Laurence Denaix, Gaëtane Le Provost, Adrien Rusch, Chloé Bonnineau, Nicolas Creusot

L'agriculture intensive exerce une forte pression sur les écosystèmes aquatiques, mais les évaluations quantitatives de ses impacts sur les milieux naturels adjacents restent rares. Les systèmes aquatiques sont particulièrement sensibles aux changements d'occupation des sols, ce qui rend essentiel d'évaluer comment les pratiques agricoles affectent leur intégrité écologique. Les biofilms périphytiques, communautés microbiennes complexes colonisant les substrats immergés, sont largement reconnus comme des indicateurs pertinents de la biodiversité structurelle et fonctionnelle. Leur réponse rapide aux variations environnementales les rend particulièrement adaptés pour évaluer les effets des pratiques agricoles. Dans cette étude, nous avons étudié les effets des pratiques viticoles (biologique BIO, 5 sites ; conventionnel CONV, 3 sites) et de la saison (printemps et automne 2025) sur la structure et la fonction des biofilms dans des canaux drainants (Libourne, France). Les biofilms ont été colonisés sur des substrats artificiels en verre pendant quatre semaines. Onze variables (Chlorophylle a, cyanobactéries, diatomées, algues vertes, biomasse MSF (Matière Sans Filtre), indice photosynthétique, matière organique, rendement photosynthétique (RP), tolérance au cuivre (CE50), activité microbienne par métamétabolomique non ciblée et cuivre dans l'eau) ont été analysées. Une PERMANOVA brute a montré que le site était le facteur dominant (R² = 48,4 %), avec des effets plus faibles du traitement (6,7 %) et de la saison (6,6 %). Après ajustement pour les covariables paysagères afin de supprimer l'influence du paysage propre à chaque site, les résidus ont été analysés par PERMANOVA, analyse discriminante linéaire (LDA) et analyse discriminante partielle des moindres carrés (PLS DA). La PERMANOVA ajustée a révélé des effets significatifs du traitement (R² = 14,4 %), de la saison (R² = 12,5 %) et de leur interaction (R² = 5,4 %) (p < 0,01). La LDA et la PLS DA ont identifié les variables les plus discriminantes. Les pratiques agricoles et la saisonnalité exercent toutes deux des effets forts et spécifiques sur la structure et la fonction des biofilms. Les pratiques conventionnelles favorisent les cyanobactéries résistantes au cuivre. Ces sites présentent également une biomasse plus élevée, mais leur rendement photosynthétique est plus faible. Les pratiques biologiques favorisent quant à elles les diatomées et un meilleur rendement photosynthétique. La saisonnalité induit une transition de communautés dominées par la biomasse au printemps vers des communautés tolérantes au cuivre en automne. L'activité microbienne a varié selon la saison et le type de vignoble. Au printemps, les sites CONV présentaient de faibles teneurs en terpénoïdes et des teneurs élevées en polykétides, tandis que les sites BIO montraient l'inverse. En automne, les sites BIO présentaient des teneurs plus élevées en terpénoïdes, polykétides et alcaloïdes que les sites INT et CONV. Dans l'ensemble, ces résultats soulignent l'importance d'une surveillance multi-échelle pour évaluer de manière fiable l'impact écologique des pratiques agricoles.

(01/07/2026)

UR EABX, INRAE, UB, CNRS, INRAE, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS, UMR ISPA, Bordeaux Sciences Agro, INRAE, UMR SAVE, UB, Bordeaux Sciences Agro, INRAE

Effect of the microparasite Perkinsus olseni on the bioturbation activity and engineering potential of the Manila clam Ruditapes philippinarum

Héliaz Le Bayon, Elisa Chailler, Sarah Bureau, Jérôme Coudret, Caroline Broudin, Céline Houbin, Alicia Romero-Ramirez, Aurélie Chambouvet, Annabelle Dairain

Host behavioral modifications induced by parasites can have profound ecological consequences, especially when they affect ecosystem engineers such as bioturbators. While the influence of macroparasites on host behavior and, by extension, on ecosystem functioning is documented in the marine realm, the role of microparasites remains unexplored. The association between Perkinsus olseni, a widespread microeukaryotic parasite, and the Manila clam Ruditapes philippinarum, an abundant bioturbator in many coastal soft-bottom environments, is an interesting model for investigating this overlooked aspect. Infection by P. olseni has been shown to alter various physiological parameters in clams, such as immune response, metabolic activity, and reproductive performance. However, whether these internal disruptions translate into behavioral changes, such as modifications in sediment particle transports initiated by clams, remains an open question. In this study, we explore whether infection by P. olseni influences the bioturbation activity of the Manila clam, a process with significant implications for ecosystem processes, such as nutrient fluxes, in coastal environments. We did not report major changes in the engineering potential of the Manila clam when infected with non-lethal doses of Perkinsus olseni. However, we noticed a subtle increase in the magnitude of sediment transport activities, which may reflect behavioral adaptations. Given the ecological role of R. philippinarum as a driver of benthic processes, even little parasiteinduced behavioral shifts could cascade down to affect ecosystem processes such as sediment dynamics and benthic community structure. Exploring such interactions opens new perspectives on how microparasites may influence ecosystem functioning, not only through physiological disturbances but also via changes in host functional traits.

(Journal of Invertebrate Pathology. vol. 217, n° 0022-2011, pp. 108605, 01/07/2026)

ECOMAP, AD2M, SU, CNRS, SBR, SU, CNRS, EDYMAR, AD2M, SU, CNRS, SBR, SU, CNRS, AD2M, SU, CNRS, SBR, SU, CNRS, SBR, SU, CNRS, CNRS, STAMAR, INSU - CNRS, SU, CNRS, ISTerre, IRD, INSU - CNRS, USMB [Université de Savoie] [Université de Chambéry], CNRS, Fédération OSUG, UGA, FR2424, SBR, SU, CNRS, UB, Bordeaux INP, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS, CENAREST

Continuous speleothem record from central Tunisia (the Mine cave) reveals climatic events for the last 27 ka

Sahar Ben Hamida, Chedia Zaara Ben Mosbah, Walid Oueslati, Dominique Blamart, Hai Cheng, R. Lawrence Edwards, Matthieu Fournier, Dominique Genty

The Last Deglaciation, a key period punctuated by many climatic events, has been recorded in several natural archives but, it has been rarely recorded continuously on speleothems because of the presence of stops in their growth rate due to cold/dry climates. Here we present the results of a stalagmite (Min-stm2) from the Mine Cave (Oueslatia, Tunisia) that cover continuously the last 27 ka BP after a very slow growth between 120 ka to 35 ka. The time resolution, calculated with twenty-eight U/Th dating points and a 1 mm sampling space for stable isotopes, reaches 24 years during the Bølling-Allerød (BA) period, while it was the lowest (330 a/mm) during the Younger Dryas (YD). The growth rate (GR) curve reveals a sudden growth increase at 27.5 ± 0.08 ka BP, a key point in the stalagmite history, demonstrating that infiltration due to a humid and a relatively temperate climate started again at least in Tunisia. More vigorous northwesterly winds combined with the southern displacement of the ITCZ belt may explain this abrupt hydrological change. Despite of extreme cold climate that occurred N-Mediterranean area (i.e. Western Europe) during the Last Glacial Maximum (LGM) and the Oldest Dryas, the studied stalagmite kept a sustained GR showing a quite high humidity in the N-Tunisia area. The Last Deglaciation is here clearly marked by a large decrease in the calcite δ18O and δ13C between maximum values at 21.9 ka, denoting the coldest conditions, and minimum values at 8.5 ka coinciding with the warmest conditions. Even if the isotopic curves nicely mimic the ice and marine core records of the deglaciation, detailed events show some noticeable differences. For example, the stalagmite δ13C at the end of the BA is interrupted by a rapid and pronounced isotopic increase denoting colder conditions after 13.3 ± 0.1 ka BP which could be related to the IACP (Intra Allerød Cold Period). GR during the YD appears extremely slow. The Holocene onset, at about 11.7 ± 0.09 a BP, is marked by a gradual decrease in δ18O and δ13C until 8.3 ka associated with high GR suggesting increased precipitation. Despite the high time resolution during this period (better than 40 years), the 8.2 ka event is not recorded, marking a different sensitivity compared with more western and northern speleothem records. While the δ18O continuously increased after the Holocene optimum at 8.3 ka, a positive excursion occurred on the δ13C between 8.3 ka and 6.3 ka suggesting a reduction in the vegetation activity. This is likely due to increased seasonality with drier spring/summer conditions and humid autumn/winter and/or lower CO2 dissolution in the soil water during infiltration. The comparison with a former studied stalagmite from the same cave brings precious information about the local influences in recording detailed climatic variations.

(Quaternary Science Reviews. vol. 384, n° 0277-3791, pp. 109921, 01/07/2026)

LMRE, LSCE, UVSQ, INSU - CNRS, CNRS, DRF (CEA), CEA, UTM, PALEOCEAN, LSCE, UVSQ, INSU - CNRS, CNRS, DRF (CEA), CEA, IGEC, Xjtu, M2C, UNICAEN, NU, INSU - CNRS, UNIROUEN, NU, CNRS, UNIROUEN, NU, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS

Vegetation Increases CH4 Emissions and Methanotroph Diversity in Marine Sediments

Marion Dolivet‐maréchal, Carlos Palacin‐lizarbe, Henri M P Siljanen, Dhiraj Paul, Abigaïl Delort, Jonathan Gervaix, Charline Creuzé des Châtelliers, Sabine Schmidt, Mathis Cognat, David Sebag, Olivier Taugourdeau, Clara Schübert, Nathalie Labourdette, Isabelle Bertrand, Lorenzo M W Rossi, Xavier Le Roux, Agnès Richaume, Alessandro Florio

Seagrass meadows are key blue carbon (C) ecosystems, storing large amounts of organic C over centuries. Their climate benefits may be reduced by methane (CH 4 ) emissions, whose microbial and environmental descriptors in Zostera noltii meadows, dominant seagrass in North‐Western Europe, remain poorly understood. We studied CH 4 fluxes, CH 4 ‐producing and consuming microbial communities and sediment physicochemical parameters in Z. noltii meadows and adjacent bare sediments across seven sites in Arcachon Bay, France. In situ CH 4 fluxes were measured at low tide during daytime conditions, providing standardized estimates of peak emissions. Microbial communities were characterized using targeted metagenomics of three functional genes ( mcrA , mmoX , pmoA ) and quantitative PCR. CH 4 fluxes were higher in vegetated than bare sediments (24.4 ± 2.6 vs. 9.4 ± 0.7 μmol m −2 day −1 ). Mixed linear models and random forest analyses identified C accumulation rate and CO 2 flux as the strongest positive descriptors of CH 4 fluxes. Vegetated sediments hosted more diverse methanotrophs, while methanogens showed no habitat differences. Four genera ( mcrA–Methanolobus , mmoX–Methylocella , pmoA–Methylococcus , Methyloglobulus ) emerged as abundant, seagrass‐associated, correlated with CH 4 fluxes, and highlighted by models. Functional diversity, especially pmoA richness, was a stronger microbial descriptor of CH 4 fluxes than gene abundance or a specific genus. Findings indicate Z. noltii meadows enhance C burial and CH 4 emission, with methanotroph diversity potentially mitigating CH 4 emissions. Our results provide the first integrated assessment of CH 4 fluxes and their descriptors in Z. noltii meadows, based on limited temporal coverage capturing the daytime peak emission conditions, highlighting the intertwined nature of C burial and CH 4 emissions and the need to account for both in blue C climate assessments.

(Global Change Biology. vol. 32, n° 1354-1013, pp. e70989, 01/07/2026)

LEM, UCBL, ENVL, VAS, CNRS, INRAE, CEAB, CSIC, UEF, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS, Bordeaux INP, IFPEN, OASU, UB, INSU - CNRS, ULR, CNRS, INRAE, UMR Eco&Sols, Cirad, IRD, INRAE, Institut Agro, UM, UNIMI

Role of emerging contaminants in promoting horizontal transfer of antimicrobial resistance genes : a multiscale approach in environmental context

Ana Rey Sogo

The global dissemination of antimicrobial resistance (AMR) through horizontal gene transfer (HGT), and specifically through conjugative transfer, represents one of the most urgent challenges in environmental microbiology and public health. While antibiotics have long been recognized as drivers of AMR selection and spread, the role of contaminants of emerging concern (e.g., industrial chemicals, disinfectants, personal care products) as promoters of bacterial conjugation at environmentally relevant concentrations remains insufficiently understood. This thesis addresses that gap through a multiscale, integrative approach combining machine learning (ML)-based predictive modelling, in vitro experimentation across three conjugation systems, and in situ field assessment in a wastewater-influenced estuary.In the first chapter, a suite of ML models (Linear Regression, Random Forest, and XGBoost) was developed and evaluated using a curated dataset of published effects of chemical stressors on conjugation experiments. The best-performing model, XGBoost, achieved an internal validation R² of 0.719, demonstrating meaningful predictive capacity. Feature importance analysis revealed that chemical concentration, bacterial species and structural fingerprints were the dominant predictors. These findings establish a framework for HGT risk assessment and identify the boundaries of current predictive capacity, underscoring the need for larger, more homogeneous experimental datasets to extend model applicability.In the second chapter, the effects of twelve CECs from six functional groups on conjugative transfer were characterized using two intraspecies Escherichia coli mating systems sharing the same recipient HMS174 but differing in donor background and plasmid incompatibility (Inc) group (IncF/K12 and IncP/UB1637). Both systems responded to CEC exposure at 0.001–0.01 µg/mL, but the IncP system consistently showed stronger and more reproducible induction. This differential sensitivity was attributed to plasmid type and mechanistically explained by three factors: the higher basal transfer frequency of IncF, leaving less apparent fold-change induction; cell population heterogeneity; and the plasmid intrinsic regulatory system. Molecular mechanisms were further elucidated for individual CECs, demonstrating compound-specific pathways.In the third chapter, the investigation was extended to an in situ environmental context, characterizing the mobilizable plasmidome at four sampling points spanning wastewater treatment plant (WWTP) effluents and pristine receiving waters. Integration of captured plasmids, qPCR of AMR-related genes and site chemical context demonstrated that WWTP effluent discharge locations harbored high plasmid capture rates and diversity. Furthermore, exposure of the in vitro IncF/HMS174 conjugation system to WWTP effluent modulated conjugative transfer, providing a mechanistic link between complex chemical stressor mixtures and in situ HGT dynamics.Collectively, this thesis establishes that CECs at environmentally relevant concentrations constitute a modest but real risk factor for conjugation-driven AMR dissemination, whose magnitude is determined by the interplay of chemical identity, plasmid regulatory architecture, and population-level heterogeneity. The compound-specific mechanistic diversity uncovered highlights the importance of studying individual chemicals, while exposure to effluent mixtures and the in situ mobilizable plasmidome underscore that real-world risk is shaped by chemical complexity and ecological context in ways that single-compound laboratory-based experiments cannot fully capture. These findings argue for the integration of HGT-promoting potential into environmental risk frameworks, and for the development of standardized, multi-plasmid conjugation assays as regulatory tools for assessing chemical threats to the environmental resistome.

(30/06/2026)

EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS