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5. Ecological assessment of combined sewer overflow management practices through the analysis of benthic and hyporheic sediment bacterial assemblages from an intermittent stream

Author

Pozzi, Adrien C.M., primary, Petit, Stéphanie, additional, Marjolet, Laurence, additional, Youenou, Benjamin, additional, Lagouy, Mickaël, additional, Namour, Philippe, additional, Schmitt, Laurent, additional, Navratil, Oldrich, additional, Breil, Pascal, additional, Branger, Flora, additional, and Cournoyer, Benoit, additional

Published
2023
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7. Evidence of Bacterial Community Coalescence between Freshwater and Discharged tpm-Harboring Bacterial Taxa from Hospital and Domestic Wastewater Treatment Plants among Epilithic Biofilms

Author

Bouchali, Rayan, primary, Marjolet, Laurence, additional, Mondamert, Leslie, additional, Chonova, Teofana, additional, Ribun, Sébastien, additional, Laurent, Elodie, additional, Bouchez, Agnès, additional, Labanowski, Jérôme, additional, and Cournoyer, Benoit, additional

Published
2023
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8. RAPPORT D'ACTIVITÉ SCIENTIFIQUE OTHU 2017/2021 / NOVEMBRE 2021

Author

Bacot, Laetitia, Barraud, Sylvie, Branger, Flora, Braud, Isabelle, Breil, Pascal, Bonneau, Jeremie, Cherqui, Frederic, Chatain, Vincent, Couvidat, Julien, Cournoyer, Benoit, Coquery, Marina, Lassabatere, Laurent, Lipeme Kouyi, Gislain, Masson, Mathieu, Marmonier, Pierre, Marjolet, Laurence, Meynier Pozzi, Adrien, Mermillod-Blondin, Florian, Namour, Philippe, Navratil, Oldrich, Riviere, Nicolas, Walcker, Nicolas, Wiest, Laure, Groupe de Recherche Rhône Alpes sur les Infrastructures et l'Eau (GRAIE), Déchets Eaux Environnement Pollutions (DEEP), Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA), RiverLy - Fonctionnement des hydrosystèmes (RiverLy), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Équipe 5 - Impact des Aménagements et des Polluants sur les HYdrosystèmes (IAPHY), Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés (LEHNA), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS), Équipe 3 - Écologie, Évolution, Écosystemes Souterrains (E3S), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Environnement, Ville, Société (EVS), École normale supérieure de Lyon (ENS de Lyon)-École des Mines de Saint-Étienne (Mines Saint-Étienne MSE), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université Lumière - Lyon 2 (UL2)-Université Jean Moulin - Lyon 3 (UJML), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Jean Monnet - Saint-Étienne (UJM)-École Nationale des Travaux Publics de l'État (ENTPE)-École nationale supérieure d'architecture de Lyon (ENSAL)-Centre National de la Recherche Scientifique (CNRS), Hôpital Haut-Lévêque [CHU Bordeaux], CHU Bordeaux [Bordeaux], TRACES - Technologie et Recherche en Analyse Chimique pour l'Environnement et la Santé, Institut des Sciences Analytiques (ISA), Université de Lyon-Université de Lyon-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), and OTHU (Observatoire de Terrain en Hydrologie Urbaine)

Subjects
ZABR - OBSERVATOIRE OTHU, [SDE]Environmental Sciences
Published
2021

10. The tpm metabarcoding DNA sequence database for taxonomic allocations using the Mothur and DADA2 bio-informatic tools (Version 2.0.1)

Author

Pozzi, Adrien, Bouchali, Rayan, Marjolet, Laurence, Cournoyer, Benoit, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
[SDE]Environmental Sciences, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2021

11. Spatio-temporal variations in chemical pollutants found among urban deposits match changes in thiopurine S-methyltransferase-harboring bacteria tracked by the tpm metabarcoding approach

Author

Aigle, Axel, Bourgeois, Emilie, Marjolet, Laurence, Houot, Sabine, Patureau, Dominique, Doelsch, Emmanuel, Cournoyer, Benoit, Galia, Wessam, Colin, Yannick, Bouchali, Rayan, Marti, Romain, Ribun, Sébastien, Pozzi, Adrien C.M., Misery, Boris, Colinon, Céline, Bernardin-Souibgui, Claire, Wiest, Laure, Blaha, Didier, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), TRACES - Technologie et Recherche en Analyse Chimique pour l'Environnement et la Santé, Institut des Sciences Analytiques (ISA), Institut de Chimie du CNRS (INC)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), This work was partly funded by the French national research program for environmental and occupational health of ANSES under the terms of project 'Iouqmer' EST 2016/1/120, l'Agence Nationale de la Recherche through the ANR-17-CE04-0010 (Infiltron) project, by Labex IMU (Intelligence des Mondes Urbains), the MITI CNRS project named Urbamic, the Greater Lyon Urban Community, and the French water agency for the Rhône, Mediterranean and Corsica areas through the Desir and DOmic projects., ANR-17-CE04-0010,INFILTRON,Dispositif INFILTRON pour une évaluation des fonctions infiltration & filtration des sols urbains dans un contexte de gestion des eaux pluviales(2017), and ANR-11-IDEX-0007,Avenir L.S.E.,PROJET AVENIR LYON SAINT-ETIENNE(2011)

Subjects
Chrysene, Geologic Sediments, Pollutants, Environmental Engineering, 010504 meteorology & atmospheric sciences, DADA2, mothur, 010501 environmental sciences, Ecotoxicology, 01 natural sciences, Sediments, chemistry.chemical_compound, Spatio-Temporal Analysis, Mothur, 11. Sustainability, Gammaproteobacteria, DNA Barcoding, Taxonomic, [CHIM]Chemical Sciences, Environmental Chemistry, Waste Management and Disposal, 0105 earth and related environmental sciences, Pollutant, Bacteria, biology, Pseudomonas, Sediment, Methyltransferases, biology.organism_classification, Pollution, 6. Clean water, Urban ecology, chemistry, 13. Climate action, Environmental chemistry, [SDE]Environmental Sciences, tpm metabarcoding, [SDV.TOX.ECO]Life Sciences [q-bio]/Toxicology/Ecotoxicology, Water Pollutants, Chemical, Environmental Monitoring
Abstract

Authors thank the OTHU network for technical assistance and financial supports, the School of Integrated Watershed Sciences H2O'LYON (ANR 17-EURE-0018), and the Urban School of Lyon (ANR-17-CONV-0004) for their advices and supports in the elaboration of this multi-disciplinary research initiative.; International audience; The bTPMT (bacterial thiopurine S-methyltransferase), encoded by the tpm gene, can detoxify metalloid-containing oxyanions and xenobiotics. The hypothesis of significant relationships between tpm distribution patterns and chemical pollutants found in urban deposits was investigated. The tpm gene was found conserved among eight bacterial phyla with no sign of horizontal gene transfers but a predominance among gamma proteobacteria. A DNA metabarcoding approach was designed for tracking tpm-harboring bacteria among polluted urban deposits and sediments recovered for more than six years in a detention basin (DB). This DB recovers runoff waters and sediments from a zone of high commercial activities. The PCR products from DB samples led to more than 540,000 tpm reads after DADA2 or MOTHUR bio-informatic manipulations that were allocated to more than 88 and less than 634 sequence variants per sample. The tpm community patterns were significantly different between the recent urban deposits and those that had accumulated for more than 2 years in the DB, and between those of the DB surface and the DB settling pit. These groups of samples had distinct mixture of priority pollutants. Significant relationships between tpm ordination patterns, sediment accumulation time periods and location, and concentrations in PAH, chlorpyrifos, and 4-nonylphenols (NP) were observed. These correlations matched the higher occurrences of, among others, Aeromonas, Pseudomonas, and Xanthomonas tpm-harboring bacteria in recent urban DB deposits more contaminated with chrysene and alkylphenol ethoxylates. Highly significant drops in tpm reads allocated to Aeromonas species were recorded in the oldest DB sediments accumulating naphthalene and metallic pollutants. Degraders of urban pollutants such as P. aeruginosa and P. putida showed conserved distribution patterns over time but P. syringae phytopathogens were more abundant in the oldest sediments. TPMT-harboring bacteria can be used to assess the incidence of high risk priority pollutants on environmental systems.

Published
2021

12. Relative weight of organic waste origin on compost and digestate 16S rRNA gene bacterial profilings and related functional inferences

Author

Aigle, Axel, Bourgeois, Emilie, Marjolet, Laurence, Houot, Sabine, Patureau, Dominique, Doelsch, Emmanuel, Cournoyer, Benoit, Galia, Wessam, Aigle, Axel, Bourgeois, Emilie, Marjolet, Laurence, Houot, Sabine, Patureau, Dominique, Doelsch, Emmanuel, Cournoyer, Benoit, and Galia, Wessam

Abstract

Even though organic waste (OW) recycling via anaerobic digestion (AD) and composting are increasingly used, little is known about the impact of OW origin (fecal matters and food and vegetable wastes) on the end products' bacterial contents. The hypothesis of a predictable bacterial community structure in the end products according to the OW origin was tested. Nine OW treatment plants were selected to assess the genetic structure of bacterial communities found in raw OW according to their content in agricultural and urban wastes and to estimate their modifications through AD and composting. Two main bacterial community structures among raw OWs were observed and matched a differentiation according to the occurrences of urban chemical pollutants. Composting led to similar 16S rRNA gene OTU profiles whatever the OW origin. With a significant shift of about 140 genera (representing 50% of the bacteria), composting was confirmed to largely shape bacterial communities toward similar structures. The enriched taxa were found to be involved in detoxification and bioremediation activities. This process was found to be highly selective and favorable for bacterial specialists. Digestates showed that OTU profiles differentiated into two groups according to their relative content in agricultural (manure) and urban wastes (mainly activated sludge). About one third of the bacterial taxa was significantly affected by AD. In digestates of urban OW, this sorting led to an enrichment of 32 out of the 50 impacted genera, while for those produced from agricultural or mixed urban/agricultural OW (called central OW), a decay of 54 genera over 60 was observed. Bacteria from activated sludge appeared more fit for AD than those of other origins. Functional inferences showed AD enriched genera from all origins to share similar functional traits, e.g., chemoheterotrophy and fermentation, while being often taxonomically distinct. The main functional traits among the dominant genera in activated s

Published
2021

14. INFILTRON package for assessing infiltration & filtration functions of urban soils

Author

Jeremie Bonneau, Benoit Cournoyer, Rafael Angulo-Jaramillo, Veronica Rodriguez-Nava, Paola Concialdi, Yannick Colin, Marjolet Laurence, Matteo Martini, Laurent Lassabatere, Cédric Louis, Sofia Bouarafa, Anne-Cécile De Giacomoni, Simone Di Prima, Pierre-Emmanuel Peyneau, Emmanuelle Bergeron, Arthur Marais, Wessam Galia, Axel Aigle, Thanh Huong Lai, and Gislain Lipeme Kouyi

Subjects
Infiltration (hydrology), Soil water, Environmental engineering, Environmental science
Abstract

The extension of urban and peri-urban areas and the related artificialization of soils drastically impacts the water cycle as well as biogeochemical cycles. In particular, the sealing of soils with impervious surfaces such as roads increases runoff and decreases concomitant infiltration. At the catchment scale, more significant amounts of stormwater must be collected and managed to prevent from flooding urban areas and mitigate discharge to the environment. Sustainable Urban Drainage Systems (SUDS) were developed to alleviate these problems. These systems allow the restoration of one of the main functions of urban and peri-urban soils, i.e., infiltrating stormwater. They simultaneously reduce the risk of flooding and increase groundwater recharge. Another essential service must be ensured and optimized: the removal of pollutants from infiltrating water by the soil, to avoid the degradation of the quality of the groundwater.The INFILTRON project aims to design a methodology for the assessment of infiltration and filtration of pollutants by SUDS. The project is a collaboration of many partners, with expertise in soil physics, urban hydrology, nanoparticle engineering, and modeling, to engineer a specific device for the simultaneous monitoring of water infiltration and pollutant filtration. This infiltration device both infiltrates water and injects nanoparticles (NPs) into the soil. It was sized to account for preferential flow, which is known to have a significant impact on infiltration and pollutant transfer. The engineered NPs were designed to be detectable in the ground using ground-penetrating radar (GPR) and to mimic the transfer of nano-pollutants (emerging pollutants, bacteria, etc.) commonly found in real stormwater. An infiltration-filtration model was developed to interpret the experimental data and to quantify two indicators for the assessment of water infiltration and pollutant filtration. INFILTRON will provide a very interesting toolbox for practitioners and stakeholders for the evaluation of the infiltration and filtration functions of not only SUDS within the framework of stormwater management, but also anthropized soils within the management of urban and peri-urban areas.

Published
2020

15. Coalescence of bacterial groups originating from urban runoffs and artificial infiltration systems among aquifer microbiomes

Author

Colin, Yannick, primary, Bouchali, Rayan, additional, Marjolet, Laurence, additional, Marti, Romain, additional, Vautrin, Florian, additional, Voisin, Jérémy, additional, Bourgeois, Emilie, additional, Rodriguez-Nava, Veronica, additional, Blaha, Didier, additional, Winiarski, Thierry, additional, Mermillod-Blondin, Florian, additional, and Cournoyer, Benoit, additional

Published
2020
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16. Supplementary material to "Coalescence of bacterial groups originating from urban runoffs and artificial infiltration systems among aquifer microbiomes"

Author

Colin, Yannick, primary, Bouchali, Rayan, additional, Marjolet, Laurence, additional, Marti, Romain, additional, Vautrin, Florian, additional, Voisin, Jérémy, additional, Bourgeois, Emilie, additional, Rodriguez-Nava, Veronica, additional, Blaha, Didier, additional, Winiarski, Thierry, additional, Mermillod-Blondin, Florian, additional, and Cournoyer, Benoit, additional

Published
2020
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18. Human-Driven Microbiological Contamination of Benthic and Hyporheic Sediments of an Intermittent Peri-Urban River Assessed from MST and 16S rRNA Genetic Structure Analyses

Author

Marti, Romain, Ribun, Sebastien, Aubin, Jean-baptiste, Colinon, Celine, Petit, Stephanie, Marjolet, Laurence, Gourmelon, Michele, Schmitt, Laurent, Breil, Pascal, Cottet, Marylise, Cournoyer, Benoit, Marti, Romain, Ribun, Sebastien, Aubin, Jean-baptiste, Colinon, Celine, Petit, Stephanie, Marjolet, Laurence, Gourmelon, Michele, Schmitt, Laurent, Breil, Pascal, Cottet, Marylise, and Cournoyer, Benoit

Abstract

Rivers are often challenged by fecal contaminations. The barrier effect of sediments against fecal bacteria was investigated through the use of a microbial source tracking (MST) toolbox, and by Next Generation Sequencing (NGS) of V5-V6 16S rRNA gene (rrs) sequences. Non-metric multi-dimensional scaling analysis of V5-V6 16S rRNA gene sequences differentiated bacteriomes according to their compartment of origin i.e., surface water against benthic and hyporheic sediments. Classification of these reads showed the most prevalent operating taxonomic units (OTU) to be allocated to Flavobacterium and Aquabacterium. Relative numbers of Gaiella, Haliangium, and Thermoleophilum OTU matched the observed differentiation of bacteriomes according to river compartments. OTU patterns were found impacted by combined sewer overflows (CSO) through an observed increase in diversity from the sewer to the hyporheic sediments. These changes appeared driven by direct transfers of bacterial contaminants from wastewaters but also by organic inputs favoring previously undetectable bacterial groups among sediments. These NGS datasets appeared more sensitive at tracking community changes than MST markers. The human-specific MST marker HF183 was strictly detected among CSO-impacted surface waters and not river bed sediments. The ruminant-specific DNA marker was more broadly distributed but intense bovine pollution was required to detect transfers from surface water to benthic and hyporheic sediments. Some OTU showed distribution patterns in line with these MST datasets such as those allocated to the Aeromonas, Acinetobacter, and Pseudomonas. Fecal indicators (Escherichia coli and total thermotolerant coliforms) were detected all over the river course but their concentrations were not correlated with MST ones. Overall, MST and NGS datasets suggested a poor colonization of river sediments by bovine and sewer bacterial contaminants. No environmental outbreak of these bacterial contaminants was dete

Published
2017
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20. Human-Driven Microbiological Contamination of Benthic and Hyporheic Sediments of an Intermittent Peri-Urban River Assessed from MST and 16S rRNA Genetic Structure Analyses

Author

Marti, Romain, primary, Ribun, Sébastien, additional, Aubin, Jean-Baptiste, additional, Colinon, Céline, additional, Petit, Stéphanie, additional, Marjolet, Laurence, additional, Gourmelon, Michèle, additional, Schmitt, Laurent, additional, Breil, Pascal, additional, Cottet, Marylise, additional, and Cournoyer, Benoit, additional

Published
2017
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21. Incidence des organisations urbaines sur le microbiote des eaux de ruissellement et la dissémination de formes pathogènes

Author

Marti, Romain, Michalon, Jérôme, Jean-Yves, Toussaint, LIPEME KOUYI, Gislain, Marjolet, Laurence, Gleizal, Audrey, Claire, Bernardin, Blaha, D., Barraud, Sylvie, Ribun, S, Aubin, Jean-Baptiste, Sophie, Vareilles, COURNOYER, Benoit, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Centre Max Weber (CMW), École normale supérieure - Lyon (ENS Lyon)-Université Lumière - Lyon 2 (UL2)-Université Jean Monnet [Saint-Étienne] (UJM)-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA), Laboratoire de Génie Civil et d'Ingénierie Environnementale (LGCIE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Déchets Eaux Environnement Pollutions (DEEP), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA), Probabilités, statistique, physique mathématique (PSPM), Institut Camille Jordan [Villeurbanne] (ICJ), École Centrale de Lyon (ECL), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Jean Monnet [Saint-Étienne] (UJM)-Centre National de la Recherche Scientifique (CNRS)-École Centrale de Lyon (ECL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Jean Monnet [Saint-Étienne] (UJM)-Centre National de la Recherche Scientifique (CNRS), Environnement Ville Société (EVS), École normale supérieure - Lyon (ENS Lyon)-École des Mines de Saint-Étienne (Mines Saint-Étienne MSE), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université Lumière - Lyon 2 (UL2)-Université Jean Moulin - Lyon 3 (UJML), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Jean Monnet [Saint-Étienne] (UJM)-École Nationale des Travaux Publics de l'État (ENTPE)-École nationale supérieure d'architecture de Lyon (ENSAL)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure de Lyon (ENS de Lyon)-Université Lumière - Lyon 2 (UL2)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), Institut Camille Jordan (ICJ), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS)-École Centrale de Lyon (ECL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), Environnement, Ville, Société (EVS), École normale supérieure de Lyon (ENS de Lyon)-École des Mines de Saint-Étienne (Mines Saint-Étienne MSE), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Jean Monnet - Saint-Étienne (UJM)-École Nationale des Travaux Publics de l'État (ENTPE)-École nationale supérieure d'architecture de Lyon (ENSAL)-Centre National de la Recherche Scientifique (CNRS), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-École nationale supérieure d'architecture de Lyon (ENSAL)-École des Mines de Saint-Étienne (Mines Saint-Étienne MSE), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-École Nationale des Travaux Publics de l'État (ENTPE)-Université Jean Monnet [Saint-Étienne] (UJM)-Université Jean Moulin - Lyon 3 (UJML), Université de Lyon-Université Lumière - Lyon 2 (UL2)-École normale supérieure - Lyon (ENS Lyon), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Centre Max Weber ( CMW ), École normale supérieure - Lyon ( ENS Lyon ) -Université Lumière - Lyon 2 ( UL2 ) -Université Jean Monnet [Saint-Étienne] ( UJM ) -Centre National de la Recherche Scientifique ( CNRS ), Institut National des Sciences Appliquées de Lyon ( INSA Lyon ), Université de Lyon-Institut National des Sciences Appliquées ( INSA ), Laboratoire de Génie Civil et d'Ingénierie Environnementale ( LGCIE ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon ( INSA Lyon ), Université de Lyon-Institut National des Sciences Appliquées ( INSA ) -Institut National des Sciences Appliquées ( INSA ), VetAgro Sup ( VAS ), Microbiologie, adaptation et pathogénie ( MAP ), Université de Lyon-Institut National des Sciences Appliquées ( INSA ) -Institut National des Sciences Appliquées ( INSA ) -Centre National de la Recherche Scientifique ( CNRS ), Déchets Eaux Environnement Pollutions ( DEEP ), Université de Lyon-Institut National des Sciences Appliquées ( INSA ) -Université de Lyon-Institut National des Sciences Appliquées ( INSA ), Institut Camille Jordan [Villeurbanne] ( ICJ ), École Centrale de Lyon ( ECL ), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Institut National des Sciences Appliquées de Lyon ( INSA Lyon ), Université de Lyon-Institut National des Sciences Appliquées ( INSA ) -Institut National des Sciences Appliquées ( INSA ) -Université Jean Monnet [Saint-Étienne] ( UJM ) -Centre National de la Recherche Scientifique ( CNRS ), Environnement Ville Société ( EVS ), and École normale supérieure - Lyon ( ENS Lyon ) -Université Lumière - Lyon 2 ( UL2 ) -Université Jean Moulin - Lyon III-Université Jean Monnet [Saint-Étienne] ( UJM ) -École Nationale des Travaux Publics de l'État ( ENTPE ) -Ecole Nationale Supérieure des Mines de Saint-Etienne-École nationale supérieure d'architecture de Lyon ( ENSAL ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut National des Sciences Appliquées de Lyon ( INSA Lyon )

Subjects
[SHS.SOCIO]Humanities and Social Sciences/Sociology, Contamination, [ SHS.SOCIO ] Humanities and Social Sciences/Sociology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2015

22. Évaluation de la diversité des espèces du genre Pseudomonas par meta-taxogénomique : Contexte d'un bassin versant industriel

Author

Marti, Romain, Michalon, Jérôme, Ribun, S, Marjolet, Laurence, Gleizal, A., Tilly, B., Jean-Yves, Toussaint, Sophie, Vareilles, COURNOYER, Benoit, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Centre Max Weber (CMW), École normale supérieure - Lyon (ENS Lyon)-Université Lumière - Lyon 2 (UL2)-Université Jean Monnet [Saint-Étienne] (UJM)-Centre National de la Recherche Scientifique (CNRS), Unite de Microbiologie Alimentaire et Previsionnelle, Ecole Nationale Vétérinaire de Lyon (ENVL), Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA), Environnement Ville Société (EVS), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-École nationale supérieure d'architecture de Lyon (ENSAL)-École des Mines de Saint-Étienne (Mines Saint-Étienne MSE), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-École Nationale des Travaux Publics de l'État (ENTPE)-Université Jean Monnet [Saint-Étienne] (UJM)-Université Jean Moulin - Lyon 3 (UJML), Université de Lyon-Université Lumière - Lyon 2 (UL2)-École normale supérieure - Lyon (ENS Lyon), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), École normale supérieure - Lyon (ENS Lyon)-École des Mines de Saint-Étienne (Mines Saint-Étienne MSE), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université Lumière - Lyon 2 (UL2)-Université Jean Moulin - Lyon 3 (UJML), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Jean Monnet [Saint-Étienne] (UJM)-École Nationale des Travaux Publics de l'État (ENTPE)-École nationale supérieure d'architecture de Lyon (ENSAL)-Centre National de la Recherche Scientifique (CNRS), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Centre Max Weber ( CMW ), École normale supérieure - Lyon ( ENS Lyon ) -Université Lumière - Lyon 2 ( UL2 ) -Université Jean Monnet [Saint-Étienne] ( UJM ) -Centre National de la Recherche Scientifique ( CNRS ), Ecole Nationale Vétérinaire de Lyon ( ENVL ), Institut National des Sciences Appliquées de Lyon ( INSA Lyon ), Université de Lyon-Institut National des Sciences Appliquées ( INSA ), Environnement Ville Société ( EVS ), École normale supérieure - Lyon ( ENS Lyon ) -Université Lumière - Lyon 2 ( UL2 ) -Université Jean Moulin - Lyon III-Institut National des Sciences Appliquées de Lyon ( INSA Lyon ), Université de Lyon-Institut National des Sciences Appliquées ( INSA ) -Université de Lyon-Institut National des Sciences Appliquées ( INSA ) -Université Jean Monnet [Saint-Étienne] ( UJM ) -École Nationale des Travaux Publics de l'État ( ENTPE ) -Ecole Nationale Supérieure des Mines de Saint-Etienne-École nationale supérieure d'architecture de Lyon ( ENSAL ) -Centre National de la Recherche Scientifique ( CNRS ), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure de Lyon (ENS de Lyon)-Université Lumière - Lyon 2 (UL2)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), Environnement, Ville, Société (EVS), École normale supérieure de Lyon (ENS de Lyon)-École des Mines de Saint-Étienne (Mines Saint-Étienne MSE), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Jean Monnet - Saint-Étienne (UJM)-École Nationale des Travaux Publics de l'État (ENTPE)-École nationale supérieure d'architecture de Lyon (ENSAL)-Centre National de la Recherche Scientifique (CNRS), and Michalon, Jérôme

Subjects
[SHS.SOCIO]Humanities and Social Sciences/Sociology, Contamination, [SHS.SOCIO] Humanities and Social Sciences/Sociology, [ SHS.SOCIO ] Humanities and Social Sciences/Sociology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2015

23. Serotypes A1 and A2 of Mannheimia haemolytica are susceptible to genotypic, capsular and phenotypic variations in contrast to T3 and T4 serotypes of Bibersteinia (Pasteurella) trehalosi

Author

Villard-Marjolet, Laurence, Gauthier, D., Maurin, Françoise, Borges, E., Richard, Y., Abadie, G., Kodjo, A., Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Lyon 1, Depot 1, and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL)

Subjects
[SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2008

24. Spatio-temporal variations in chemical pollutants found among urban deposits match changes in thiopurine S-methyltransferase-harboring bacteria tracked by the tpm metabarcoding approach.

Author

Aigle A, Colin Y, Bouchali R, Bourgeois E, Marti R, Ribun S, Marjolet L, Pozzi ACM, Misery B, Colinon C, Bernardin-Souibgui C, Wiest L, Blaha D, Galia W, and Cournoyer B

Subjects
DNA Barcoding, Taxonomic, Environmental Monitoring, Geologic Sediments, Methyltransferases, Spatio-Temporal Analysis, Bacteria enzymology, Bacteria genetics, Water Pollutants, Chemical analysis
Abstract

The bTPMT (bacterial thiopurine S-methyltransferase), encoded by the tpm gene, can detoxify metalloid-containing oxyanions and xenobiotics. The hypothesis of significant relationships between tpm distribution patterns and chemical pollutants found in urban deposits was investigated. The tpm gene was found conserved among eight bacterial phyla with no sign of horizontal gene transfers but a predominance among gammaproteobacteria. A DNA metabarcoding approach was designed for tracking tpm-harboring bacteria among polluted urban deposits and sediments recovered for more than six years in a detention basin (DB). This DB recovers runoff waters and sediments from a zone of high commercial activities. The PCR products from DB samples led to more than 540,000 tpm reads after DADA2 or MOTHUR bio-informatic manipulations that were allocated to more than 88 and less than 634 sequence variants per sample. The tpm community patterns were significantly different between the recent urban deposits and those that had accumulated for more than 2 years in the DB, and between those of the DB surface and the DB settling pit. These groups of samples had distinct mixture of priority pollutants. Significant relationships between tpm ordination patterns, sediment accumulation time periods and location, and concentrations in PAH, chlorpyrifos, and 4-nonylphenols (NP) were observed. These correlations matched the higher occurrences of, among others, Aeromonas, Pseudomonas, and Xanthomonas tpm-harboring bacteria in recent urban DB deposits more contaminated with chrysene and alkylphenol ethoxylates. Highly significant drops in tpm reads allocated to Aeromonas species were recorded in the oldest DB sediments accumulating naphthalene and metallic pollutants. Degraders of urban pollutants such as P. aeruginosa and P. putida showed conserved distribution patterns over time but P. syringae phytopathogens were more abundant in the oldest sediments. TPMT-harboring bacteria can be used to assess the incidence of high risk priority pollutants on environmental systems., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Published
2021
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