Ring-hydroxylating dioxygenase (RHD) expression in a microbial community during the early response to oil pollution
The early functional response of a bacterial community from the sediments of a chronically oil-polluted retention basin located at the Etang de Berre (France) was investigated just after petroleum addition. After removing hydrocarbon compounds by natural abiotic and biotic processes, the sediments were maintained in microcosms and Vic Bilh petroleum was added. The diversity and the expression of genes encoding ring-hydroxylating dioxygenases (RHD) were examined just after the petroleum addition until 14 days focussing on the first hours following the contamination. RHD gene copy numbers and diversity were maintained throughout all the incubation period; however, transcripts were detected only during the first 2 days. One dominant RHD gene, immediately and specifically expressed in response to petroleum contamination, was related to RHD gene carried by a plasmid found in Pseudomonas spp. The expression of the RHD genes was correlated with high biodegradation levels observed for low molecular weight PAHs at 7 days of incubation. The study shows that the bacterial metabolism induced just after the oil input is a key stage that could determine the bacterial community structure changes. Monitoring the expression of RHD genes, key genes involved in hydrocarbon degradation, may provide useful information for managing bioremediation processes. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.
(FEMS Microbiology Ecology. vol. 80, n° 0168-6496, pp. 77-86, 26/06/2026)
IPREM, UPPA, INC-CNRS, CNRS, EEM, IPREM, UPPA, INC-CNRS, CNRS, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS
Colonisation et utilisation des habitats estuariens par les poissons migrateurs thalassotoques : approche comparative Seine-Gironde
Ce travail vise à comparer de quelles manières les trois espèces de poissons migrateurs thalassotoques (i.e. qui se reproduisent en mer et vont grandir dans les bassins versants) fréquentant la façade Atlantique : le mulet porc, l'anguille européenne et le flet, colonisent les estuaires de la Seine et de la Gironde et effectue leur croissance. L'hypothèse principale était que leur comportement pouvait être influencé par le niveau de contamination et de pressions anthropiques des estuaires. La démarche retenue pour aborder ces différentes échelles de manière comparative (entre les espèces et entre deux sites situées de manière similaire en Seine et en Gironde) a consisté à examiner : i) la phase de colonisation initiale à un stade très jeune par une approche expérimentale en mésocosme ; ii) la phase de croissance par un suivi en télémétrie acoustique en période estivale ; ii) l'ensemble du cycle vital par une analyse rétrospective à l'aide de la microchimie des otolithes des différents compartiments halins utilisés. Les trois niveaux d'analyse effectués avec des méthodes différentes permettent de dégager des patrons spécifiques (colonisation initiale, phase de croissance, cycle de vie) mais les différences entre les sites ne sont vraiment claires qu'à l'échelle très globale de l'utilisation des différents compartiments. Contrairement à notre hypothèse de départ les jeunes migrateurs thalassotoques parviennent à adopter un comportement spécifique en phase avec un rythme de type circadotidal ou nycthéméral y compris dans une ambiance de type Seine (très chargée en contaminants). Leur comportement est d'ailleurs peu différent dans les ambiances Seine ou Gironde. Il est donc tout à fait possible qu'ils ne soient pas extrêmement perturbés par les contaminants issus des sédiments que ce soit en Seine ou en Gironde. On notera toutefois que les civelles ont construit moins de terriers dans le sédiment de l'ambiance Seine que dans celui de l'ambiance Gironde, on peut imaginer que la plus forte contamination du sédiment de Seine les en dissuade. La fonctionnalité de corridor écologique ne semble donc pas empêchée par la contamination des sédiments. Durant leur phase de croissance en zone tidale d'eau douce les espèces étudiées utilisent des habitats différents selon des patrons temporels spécifiques (par exemple les mulets porcs utilisent les zones intertidales et les bras morts lors des flots de jours ; durant le jour les anguilles demeurent à l'abri dans des enrochements grossiers tandis que durant la nuit elles se déplacent dans des zones profondes à la recherche de leurs proies). Les résultats obtenus sur la Seine sont cohérent avec ceux obtenus sur la Gironde, ainsi dans les deux cas les flets recherchent de zones fraiches (ombre en Gironde, embouchures d'affluents plus frais en Seine), les anguilles présentent une activité principalement nocturne. La réaction des espèces au stress du marquage est très différente selon les espèces. Les mulets quittent très vite le secteur tandis que les anguilles et les flets sont au contraire extrêmement immobiles en "attendant" que leur condition s'améliore. Un épisode hypoxique observé en fin d'été sur la Seine a coïncidé avec un immobilisme des anguilles laissant penser que leur réaction à un stress environnemental pourrait se traduire par le même type de comportement que leur réaction au marquage. Les mulets de la Seine semblent moins inféodés à l'estuaire saumâtre que les mulets de la Gironde, ceci pourrait s'expliquer par la plus grande dimension de l'estuaire de la Gironde. Les anguilles de la Seine et de la Gironde présentent une grande variabilité d'histoires de vie mais on ne peut pas dégager de différences d'utilisation notables des habitats entre la Seine et la Gironde. Chez les flets la contribution des mères ayant utilisé l’eau douce est relativement plus importante en Seine qu'en Gironde. On en déduit une utilisation plus importante des habitats d’eau douce par les flets de Seine en comparaison avec les flets de la Gironde. Il en ressort globalement que les habitats dulcaquicoles de la Seine (trés diversifiés : bathymétrie, substrat, ripisylve…) sont proportionnellement plus utilisés par les espèces thalassotoques que ceux de Gironde. Cela peut s'expliquer par une moindre attractivité (ou une moindre capacité d'accueil) de l'estuaire saumatre de la Seine ou au contraire par une plus grande attractivité (ou une plus grande capacité d'accueil) de l'estuaire dulcaquicole de la Seine. Les comportements mis en évidence sur ces secteurs pourraient servir de référence pour des opérations de restauration.
(pp. 117, 26/06/2026)
UR EPBX, IRSTEA, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS, UR HBAN, IRSTEA, CSLN
Use of optical and radar data in synergy for mapping intertidal flats and coastal salt-marshes (Arcachon lagoon, France)
This paper explores the potential of high-resolution spaceborne Synthetic Aperture Radar data for mapping intertidal coastal areas as a complement of high-resolution optical imagery (e.g. SPOT, Formosat-2). Classification algorithms based on optical imagery alone fail to accurately discriminate a series of relevant habitats, in particular seabeds of benthic fauna (oysters), low-density Zostera noltii seabeds and salt-marsh vegetation species. Firstly, the paper addresses the benefits from TerraSAR-X data by investigating SAR signatures over intertidal wetlands which have been poorly described in the literature. Secondly, a supervised classification algorithm is run based on the fused SAR-optical bands. A statement of the mapping performance is finally carried out using field observations.
(pp. 4, 26/06/2026)
IRSTEA, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS, UMR TETIS, Cirad, IRSTEA
Les cartes auto-organisantes de Kohonen appliquées à l’étude des communautés de micro-algues des cours d’eau
Depuis une quinzaine d’années, les diatomées sont utilisées en routine afin d'évaluer l'état écologique des hydrosystèmes. Toutefois les indices diatomiques classiques ne permettent pas de diagnostiquer finement les différents types de pollution, et intègrent mal les variations naturelles, temporelles ou spatiales des communautés. Le but de ce travail est donc d'utiliser de nouvelles méthodologies biomathématiques et de tester leur pertinence dans un diagnostic de qualité écologique.
(pp. 43, 26/06/2026)
UR REBX, IRSTEA, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS
Occurrence of priority and emerging organic compounds in fishes from the Rhone River (France)
The main objective of this study was to collect new data on the occurrence and levels of priority and emerging organic compounds in freshwater fishes sampled in the Rhone River. The 34 studied contaminants included alkylphenols (AP), bisphenol A (BPA), polybromodiphenylethers (PBDE), perfluorinated compounds (PFC), hexabromocyclododecanes (HBCD), hexachloro-benzene (HCB) and hexachloro-butadiene (HCBD). About 50 fish samples (individual specimens or pooled fishes) were collected from 3 sites located upstream and downstream of the Lyon metropolitan area in the Rhone River (France). Four species were caught at each site, namely: the barbel (Barbus barbus), the common bream (Abramis brama), the white bream (Blicca bjoerkna) and the chub (Squalius cephalus). Some contaminants were quantified in all the 32 fish samples analysed: 4-nonylphenol, Α-HBCD, the 6 PBDE congeners (28, 47, 99, 100, 153, 154), perfluorooctanesulfonate (PFOS) and perfluorodecanoic acid. And 23 of the 32 samples had concentration of PFOS above the Environmental Quality Standards (up to 6 times higher the EQS); and all the 32 samples had concentrations of PBDE above the EQS (up to 4000 times higher, with the sum of 6 PBDE varying from 4.5 to 182 ng/g dw). Clearly, the interest to consider PFOS and HBCD as new priority substances is confirmed. In contrast, the pertinence of a priority status for HCBD, which was never quantified in our study, might have to be reconsidered in the future.
(Analytical and Bioanalytical Chemistry. vol. 404, n° 1618-2642, pp. p. 2721 - p. 2735, 26/06/2026)
UR MALY, IRSTEA, SISYPHE, UPMC, EPHE, PSL, PSL, CNRS, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS, LABERCA, INRA, Oniris VetAgroBio, IFREMER, EHF, UCBL, CNRS
Quantitative reconstruction of sea-surface conditions over the last ∼150 yr in the Beaufort Sea based on dinoflagellate cyst assemblages: the role of large-scale atmospheric circulation patterns
Dinoflagellate cyst (dinocyst) assemblages have been widely used over the Arctic Ocean to reconstruct sea-surface parameters on a quantitative basis. Such reconstructions provide insights into the role of anthropogenic vs natural forcings in the actual climatic trend. Here, we present the palynological analysis of a dated 36 cm-long core collected from the Mackenzie Trough in the Canadian Beau-fort Sea. Dinocyst assemblages were used to quantitatively reconstruct the evolution of sea-surface conditions (temper-ature, salinity, sea ice) and freshwater palynomorphs fluxes were used as local paleo-river discharge indicators over the last ∼ 150 yr. Dinocyst assemblages are dominated by au-totrophic taxa (68 to 96 %). Cyst of Pentapharsodinium dalei is the dominant species throughout most of the core, except at the top where the assemblages are dominated by Op-erculodinium centrocarpum. Quantitative reconstructions of sea-surface parameters display a series of relatively warm, lower sea ice and saline episodes in surface waters, alternately with relatively cool and low salinity episodes. Variations of dinocyst fluxes and reconstructed sea-surface conditions may be closely linked to large scale atmospheric circulation patterns such as the Pacific Decadal Oscillation (PDO) and to a lesser degree, the Arctic Oscillation (AO). Positive phases of the PDO correspond to increases of dinocyst fluxes, warmer and saltier surface waters, which we associate with upwelling events of warm and relatively saline water from Pacific origin. Freshwater palynomorph fluxes increased in three phases from AD 1857 until reaching maximum values in AD 1991, suggesting that the Mackenzie River discharge followed the same trend when its discharge peaked between AD 1989 and AD 1992. The PDO mode seems to dominate the climatic variations at multi-annual to decadal timescales in the western Canadian Arctic and Beaufort Sea areas.
(Biogeosciences. vol. 9, n° 1726-4170, pp. 5391 - 5406, 26/06/2026)
ISMER, UQAR, LOCEAN, IPSL, ENS-PSL, PSL, UVSQ, UPMC, CEA, INSU - CNRS, X, IP Paris, CNES, CNRS, MNHN, IRD, UPMC, INSU - CNRS, CNRS, PALEOPROXUS, LOCEAN, IPSL, ENS-PSL, UVSQ, UPMC, CEA, INSU - CNRS, X, CNES, CNRS, MNHN, IRD, UPMC, INSU - CNRS, CNRS, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS, ULaval, INSU - CNRS, CNRS
Spatial and long-term changes in the functional and structural phytoplankton communities along the French Atlantic coast
Spatial and interannual variations of phytoplankton diversity were characterized along the French Atlantic Coast in relation to physical factors and large-scale climatic indices using phytoplankton surveys conducted from 1993 to 2010 in four geographical areas. This study relates phytoplankton diversity to oyster recruitment success by comparing a 'specific' versus a 'functional' diversity approach. Functional diversity was represented by functional groups of different phytoplanktonic functional traits (size, shape, toxicity), relevant for oyster feeding during growth, reproduction and larval development. Phytoplankton diversity patterns along the French Atlantic coast corresponded to a geographical distribution mainly driven by a latitudinal gradient and hydrodynamic features as confirmed by the functional characteristics of the indicator species recorded for each geographical area (C-S-R strategies of Reynolds, specific habitat). This geographical typology was less clear for functional diversity. Only few functional groups were explained by physical factors: the non-toxic small and solitary cells were in particular related to temperature, with high densities observed in the southern areas. Even if temporal variation was less important in explaining the phytoplankton diversity patterns, the main drivers explaining the interannual pattern were the large-scale climatic indices, mainly the Atlantic Multidecennal Oscillation. Functional groups were readily explained by climatic indices than species even if the relationships cannot be applied generally because of the non-linearity of the correlations (local and temporal variations). However, the potentially toxic, small and linear phytoplankton were anticorrelated to NAO. The functional approach thus brings constructive elements concerning the relationships between the prey assemblage of oysters and their physical drivers. Redundancy and co-inertia analyses appeared as complementary analyses in investigating phytoplankton pattern of variation, being particularly useful in analyzing geographical and temporal diversity fluctuation, respectively. © 2012.
(Estuarine, Coastal and Shelf Science. vol. 108, n° 0272-7714, pp. 37--51, 26/06/2026)
EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS, IFREMER, LIENSs, INSU - CNRS, ULR, CNRS, DYNECO, IFREMER, BOREA, UNICAEN, NU, MNHN, IRD, SU, CNRS, UA, CNRS, UNICAEN, NU, NU
Development of q-PCR approaches to assess water quality: Effects of cadmium on gene expression of the diatom Eolimna minima
This study was undertaken to develop molecular tools to assess water quality using diatoms as the biological model. Molecular approaches were designed following the development of a rapid and easy RNA extraction method suited to diatoms and the sequencing of genes involved in mitochondrial and photosystem metabolism. Secondly the impact of cadmium was evaluated at the genetic level by q-PCR on 9 genes of interest after exposure of Eolimna minima diatom populations cultured in suspension under controlled laboratory conditions. Their growth kinetics and Cd bioaccumulation were followed.Population growth rates revealed the high impact of Cd at 100μg/L with total inhibition of growth. These results are linked to the high bioaccumulation values calculated after 14 days of exposure, 57.0±6.3μg. Cd/g. dw and 734.1±70μg. Cd/g. dw for exposures of 10 and 100μg. Cd/L respectively.Genetic responses revealed the impact of Cd on the mitochondrial metabolism and the chloroplast photosystem of E. minima exposed to 10 and 100μg. Cd/L with induction of cox1, 12S, d1 and psaA after 7 days of exposure for the concentration of 100μg. Cd/L and of nad5, d1 and psaA after 14 days of exposure for both conditions.This is the first reported use of q-PCR for the assessment of toxic pollution on benthic river diatoms. The results obtained presage interesting perspectives, but the techniques developed need to be optimized before the design of new water quality diagnosis tools for use on natural biofilms.
(Water Research. vol. 46, n° 0043-1354, pp. 934-942, 26/06/2026)
UR REBX, IRSTEA, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS
Comparison of kernel density estimators with assumption on number of modes
(26/06/2026)
LMBA, UBS, UBO EPE, CNRS, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS, CQFD, IMB, UB, Bordeaux INP, CNRS, Inria, IMB, UB, Bordeaux INP, CNRS
Evaluation of advanced tertiary treatments for the reduction of refractory micropollutants in treated wastewater
Some refractory micropollutants remain in treated wastewater after secondary treatments. In order to reduce their concentration in treated water, tertiary treatments can be used such as advanced oxidation processes and activated carbon. The efficiency of granular activated carbon in a long term is not well known and advanced oxidation processes have mostly been studied at laboratory scale. Advanced oxidation processes and granular activated carbon pilots were studied in two different wastewater treatment plants in order to determine their efficiency on numerous micropollutants. Both processes were efficient (>90%) on beta blockers and other drugs. The removal of alkylphenols was not complete with UV and hydrogen peroxide. Activated carbon was still efficient after six months functioning 24/24.
(pp. 4, 26/06/2026)
IRSTEA, IRSTEA, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS, UR MALY, IRSTEA