biolutoxR: An R-Shiny package for easy performing data analysis of a toxicity test based on bacterial bioluminescence inhibition
In the 21st century, in the context of an environmental crisis, chemical pollution has become a major global concern. In addition to chemical analysis, many bioassays have been developed and have proved to be interesting tools for considerably improve our understanding of the effects of human activities on species and ecosystems. Compared with animal or plant bioassays, bacterial bioassays based on bioluminescence inhibition have the advantage of being relatively economical and reproducible. This toxicity test uses the bioluminescent metabolic response of bacteria exposed for a short time to a solution of interest in the aim of assessing and quantifying its toxicity. Although routine tools are available to pre-process the data obtained, to our knowledge no flexible research tool is available for the data analysis following these tests, which could limit the access to the results for novices or experienced people unfamiliar with data processing software. To overcome this lack of tools for this bioassay, an R-Shiny package is proposed to generalise data analysis following a toxicity test based on bacterial bioluminescence inhibition. The traditional paper-based working environment is reproduced digitally in this package, which ultimately facilitates data entry and cleaning, makes the creation of relevant dynamic graphs, and simplifies access to toxicity data (e.g. dose-response curve and median effective concentration, i.e. EC 50 ). The aim of this tool is to provide the target community with a high-performance tool that can be used to obtain toxicity test results based on the inhibition of bacterial bioluminescence.
(SoftwareX. vol. 29, n° 2352-7110, 24/01/2025)
LIENSs, INSU - CNRS, ULR, CNRS, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS, UR EABX, INRAE
Deciphering tidal signature in a fluvial-dominated delta using digital outcrop models (Roda Sandstone, Eocene, South Pyrenean Basin)
Deltaic environments are crucial depositional systems for georesources, often studied for their excellent reservoir quality in both ancient and modern contexts. However, while mixed river tide-influenced deltas are complex and important, they remain underexplored in the ancient sedimentary record. This study focuses on the Roda Sandstone, a Lower Eocene fluvial-dominated, tide-influenced delta system in the Graus-Tremp foreland basin, to address gaps in understanding the interaction between fluvial and tidal processes within these environments. Fieldwork and core analysis were conducted to investigate the Roda Sandstone. Nineteen sedimentological sections were logged, and palaeocurrents were measured in the field. A Digital Outcrop Model (DOM) was created using 11,000 drone-captured images, georeferenced with DGPS data. The Digital Outcrop Model was processed with photogrammetry and analysed using a specialised for detailed stratigraphic and facies interpretation. Additionally, five well cores, totalling 340 m, were described and integrated with the Digital Outcrop Model. The sedimentological and stratigraphic study combined with the Digital Outcrop Model interpretation led to the identification of 10 facies grouped into five facies associations and the recognising of 7 deltaic lobes, representative of fifth-order sequences. The 3D evolution of these lobes reveals variations in progradation directions and the intensity of tidal reworking. This shows a gradual shift to a tidally dominated-deflected delta front as they were prograde. This work enabled the characterization of tidal sedimentary bodies, including the dimensions of tidal dunes and bars, paleo-bathymetries, and their specific locations within both progradational and retrogradational sequences. During regressive periods, the preservation of tidal dunes and bars intercalated in the delta foresets depends on the fluvial sediment supply and autocyclic factors. Whereas the preservation of larger tidal bars on bottomsets is permitted by the lower river sediment supply during transgressive periods of fourth-order cycles. This research advances our understanding of ancient mixed deltas by providing a depositional model that clarifies the preservation of tidal features. Additionally, it underscores the value of DOMs in enhancing correlations, distinguishing different sedimentary structures generated by competing currents, and offering detailed facies mapping for improved paleoenvironmental interpretations.
(03/01/2025)
EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS, GEOPS, INSU - CNRS, CNRS, IFPEN, IUF, M.E.N.E.S.R., LIENSs, INSU - CNRS, ULR, CNRS
Crotalia jafari: a new weakly calcified holococcolithophore genus and species from the Southwest Indian Ocean
We here describe a distinctive weakly calcified holococcolithophore Crotalia jafari gen. et sp. nov. from the Southwest Indian Ocean phytoplankton. The coccospheres of Crotalia jafari measure 8–15 ?m in diameter, and possess 430–538 coccoliths, with each coccolith measuring less than 1 ?m in diameter. The coccoliths are tightly attached to each other by an organic layer. Their central area appears open. Finger-shaped extensions are present in the peripheral coccoliths, and stretch from the hexagonal surface layer towards the basal plate. The basal plate is flat and composed of irregular wall fabric. The crystallites of the coccoliths are small. These morphological features make this holococcolithophore unique among the extant and fossil coccolithophores. The described species is therefore placed into the new genus ‘Crotalia’. This study also suggests that high diversity of weakly calcified (and still undescribed) holo- and heterococcolithophores may exist in the Southern Ocean, which requires additional careful observation.
(Micropaleontology. vol. 71, n° 0026-2803, pp. 101-108, 01/01/2025)
EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS
The Late Pleistocene - Holocene meandering lower Garonne River, southwest France: Architecture of the valley fill and chronology, comparison with other European rivers
The architecture and chronology of Late Pleistocene to Holocene alluvial deposits in the lower Garonne have been studied in details based on data (boreholes, trenches, ground-penetrating radar profiles, numerical dating) collected in quarries and during archaeological surveys. The preserved alluvial bodies, dated between ca. 38 ka and present, show that the river retained a meandering or anabranching pattern throughout this period, associated with the formation of lateral accretion packages and scroll bars in the convexity of meanders. Valley incision in connection to the LGM low sea level reached up to 19 m in the study area, and occurred between ca. 26 and 18 ka. Since ca. 18 ka, the lateral migration of meanders widened the plain without any significant incision of the Oligocene marl bedrock. The Early-Middle Holocene was characterized by the development of highly sinuous meanders, while sinuosity decreased in a late phase including the Little Ice Age. Comparison with other lowland European rivers shows that the persistence of a meandering or anabranching pattern during MIS 2 is not an isolated case. The documented examples are associated with rivers typified by low valley slope, or situated in southern regions unaffected by permafrost and characterized by dense vegetation. The latter conditions would not have led to a drastic change in river discharge and bedload transport during the Last Glacial, as was the case for more northerly rivers where braiding seems to have been common.
(Geomorphology. vol. 468, n° 0169-555X, pp. 109469, 01/01/2025)
Inrap, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS, UNIROUEN, NU, IDEES, UNICAEN, NU, ULH, NU, UNIROUEN, NU, CNRS, IRIHS, UNIROUEN, NU, BRGM, LOG, INSU - CNRS, ULCO, CNRS, IRD [Ile-de-France], M2C, UNICAEN, NU, INSU - CNRS, UNIROUEN, NU, CNRS
Phases of Magmatism and Tectonics Along the Madagascar‐Comoros Volcanic Chain, and Synchronous Changes in the Kinematics of the Lwandle and Somalia Plates
This paper aims to solve the longstanding debate on the origin of the Comoros volcanic archipelago (Mozambique Channel, Indian Ocean) concerning whether it represents a hotspot trail or a boundary between the Lwandle and Somalia plates in possible connection with the East African Rift System (EARS). To achieve this goal, we analyzed rock samples from recently discovered and previously uninvestigated volcanoes and edifices by means of geochemistry and geochronology. Major-trace element analyses and radiometric dating ( 40 Ar/ 39 Ar, K-Ar, and (U-Th)/He) allow us to identify a widespread phase of Comorian volcanism initiated at 9-8 Ma, involving the Zélée, Geyser, and Leven banks, three atolls east of the Comoros. Another tectono-magmatic phase initiated at 2.5 Ma led to a N-S widening of seamount volcanism, and to the progressive development of en-échelon NW-SE structures. With this new addition of atolls and seamounts, the Comoros Archipelago becomes a ∼700 km-long, ∼200 km-wide E-W chain extending from the Cenozoic volcanoes of Madagascar to the EARS. The reactivation of this chain at 9-8 and 2.5 Ma coincides with abrupt changes in the motion of the Somalia plate relative to the Lwandle plate, and with plate boundary modifications. The en-échelon reorganization of structures also matches the kinematic evolution of Somalia relative to Lwandle, from transtension (>3 Ma) to pure dextral slip (≤3 Ma) in the northern Mozambique Channel. We conclude that the Madagascar-Comoros volcanic chain is a branch of the EARS and a plate boundary, further strengthening the link between magmatism and the Rovuma-Lwandle-Somalia plate kinematics
(Journal of Geophysical Research : Solid Earth. vol. 130, n° 2169-9313, pp. e2024JB029488, 01/01/2025)
IPG Paris, UR, LGSR, UR, IPG Paris, IPGP - UMR_7154, INSU - CNRS, IGN, UR, IPG Paris, CNRS, UPCité, GEOPS, INSU - CNRS, CNRS, LMV, IRD, INSU - CNRS, CNRS, UCA, GR, UR, INSU - CNRS, CNRS, OVSG, IPG Paris, GEO-OCEAN, UBS, IFREMER, INSU - CNRS, UBO EPE, CNRS, BRGM, SU, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS, UNIGE, GFZ, UHM
Active biomonitoring of river pollution using an ex-situ exposure system with two model species
In the context of increasing pollution pressure on aquatic ecosystems, it is essential to improve our knowledge of habitat quality and its suitability for organisms. It is particularly relevant to better integrate early life stages of fish into pollution biomonitoring programs, as they are reliable indicators of ecosystem integrity and because of their high sensitivity to pollutants. To avoid the influence of environmental parameters on their development, a lab-on-field approach, called the ex-situ exposure method, was developed. Aquatic organisms were exposed to a continuous flux of water under semi-controlled temperature, oxygen, and photoperiod conditions to avoid the influence of these confounding factors when interpreting the results. To investigate the potential role of water contamination, this active biomonitoring method was applied to the Garonne River (Southwest France), where migratory fish populations have declined. Two model species from different taxa were used: embryos of the Japanese medaka (Oryzias latipes) and adults of the crustacean Gammarus fossarum. The results showed a significant impact of water quality on embryo mortality and early hatching in two separate experiments on Japanese medaka. In addition, an induction of feeding rate was observed in exposed gammarids, but no impact on their embryo survival, suggesting differences in sensitivity between the two species selected. Chemical and biological analyses did not identify trace metals, pesticides, or microorganisms as potential sources of toxicity in medaka embryos or G. fossarum. These results raise concerns about the quality of the water in the Garonne River and its toxicity to aquatic organisms.
(Science of the Total Environment. vol. 959, n° 0048-9697, pp. 178159, 01/01/2025)
UR EABX, INRAE, RiverLy, INRAE, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS, MFP, UB, CNRS
Toxicity assessment of DMSO extracts of environmental aged beached plastics using human cell lines
Plastic products contain complex mixtures of chemical compounds that are incorporated into polymers to improve material properties. Besides the intentional chemical additives, other compounds including residual monomers and non-intentionnaly added substances (NIAS) as well as sorbed pollutants are usually also present in aged plastic. Since most of these substances are only loosely bound to the polymer via non-covalently interactions, i.e., van der Waals forces, they may leach to the surrounding environment. Although there is increasing knowledge about toxicity of weathered plastic to aquatic organisms, only little is known about how plastic associated chemicals affect human health. Seafood consumption is one of the routes of human exposure to microplastics. The aim of this study was to evaluate the ability of naturally aged plastic associated chemicals to induce harmful effects to human health via the consumption of MP-contaminated seafood. Human colorectal adenocarcinoma Caco-2 and human hepatocyte carcinoma HepG2 cells were selected as model of the colon and liver cells respectively. They are known for their high capacity to metabolize organic contaminants. Both cell lines were exposed to DMSO extracts of different plastics to investigate the effects of chemicals on cell viability, oxidative stress induction and genotoxicity. In addition, the estrogenic effects of DMSO-extracts were evaluated using an estrogen-dependent reporter gene assay in T47D-Kbluc human breast cancer cells. Chemical profiles of the DMSO extracts were polymer-dependent, with polyvinyl chloride (PVC) highly contaminated with metals while polypropylene (PP) contained the lowest concentration of metals. Organic pollutants, including polycyclic aromatic hydrocarbons, were mainly found in PVC, high density polyethylene (HDPE) and PP extracts, whereas other extracted plastics had less (PP) to no organic contamination (polyethylene terephthalate PET). PVC was the most toxic plastic inducing cytotoxicity for both cell lines. DNA damage was observed for Caco-2 cells exposure to HDPE, PVC and nylon. Reactive oxygen species were induced only with nylon extracts in intestinal cells. No toxicity was observed for PP and PET and none of the tested plastics had any estrogenic effect. Our results demonstrate that some environmental aged plastic material released a variety of known and unknown chemical compounds some of which are toxic in vitro and contribute to the knowledge on adverse human health effects of plastics.
(Ecotoxicology and Environmental Safety. vol. 289, n° 0147-6513, pp. 117604, 01/01/2025)
EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS, CBMN, UB, ENITAB, INC-CNRS, CNRS, Cedre
A new species of Diopatra (Annelida, Onuphidae) from Akanda National Park in Gabon (West Africa)
Several ecological surveys were recently conducted in the Akanda National Park in Gabon. The main objectives of this study were to assess the urban impact on the estuarine ecosystem of Libreville and to document the benthic biodiversity of this ecosystem. Among all the species collected, a new species of Diopatra was discovered in different habitats, including mangroves. This species is described and illustrated in detail, and information on 16S gene is provided. Diopatra ariasi sp. nov. is a medium-sized species and belongs to the D. neapolitana complex, having antennae with long ceratophores and ventral lobes. This species is also characterized by the presence of ceratophores with 9–12 rings on antennae, by sensory buds which are semicircular, by spiraled branchiae from chaetiger 4–5; by bidentate pseudocompound falcigers with moderately long hoods in first four chaetigers; by pectinate chaetae with 11–15 teeth from chaetiger 6–8 and by bidentate subacicular hooks from chaetiger 15–18.
(Marine Biodiversity. vol. 55, n° 1867-1616, pp. 94, 08/04/2026)
EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS, UMR MARBEC, IRD, IFREMER, CNRS, UM
Non-Stationary Model Free Parameter In Equilibrium Shoreline Modelling
The state-of-the-art equilibrium shoreline model proposed by Davidson et al. (2013) is used to hindcast shoreline evolution. A similar approach to the work of Ibaceta et al. ( 2022) is adopted, where they introduced non-stationary model free parameters to improve long term shoreline change predictions. An Ensemble Kalman Filter (EnKF) is implemented to track the temporal variability in model free parameters and explore if their evolution can be linked to the environmental forcing. A correlation between the winter wave energy and the model free parameter φ (beach memory) is identified where high energetic winters are followed by an increase in the parameter suggesting such time variation in beach memory can be parametrized.
(08/04/2026)
UB, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS, BRGM, WRL, UNSW
Role of aquatic macrophytes on diel evolution of lowland streams nutrient concentrations, pCO2 and d-13DIC
(08/04/2026)
EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS