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The relationship between water quality and the microbial virulome and resistome in urban streams in Brazil
2024
Guedes Stehling, Eliana | Rueda Furlan, João Pedro | Lopes, Ralf | Chodkowski, John | Stopnisek, Nejc | Angelino Savazzi, Eduardo | Shade, Ashley | Universidade de São Paulo = University of São Paulo (USP) | Michigan State University [East Lansing] ; Michigan State University System | Slovenia National Laboratory of Health, Environment and Food [Ljubljana, Slovenia] (NLZOH) | 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) | United States National Science Foundation CAREER #1749544
International audience | Urban streams that receive untreated domestic and hospital waste can transmit infectious diseases and spread drug residues, including antimicrobials, which can then increase the selection of antimicrobial-resistant bacteria. Here, water samples were collected from three different urban streams in the state of São Paulo, Brazil, to relate their range of Water Quality Indices (WQIs) to the diversity and composition of aquatic microbial taxa, virulence genes (virulome), and antimicrobial resistance determinants (resistome), all assessed using untargeted metagenome sequencing. There was a predominance of phyla Proteobacteria, Actinobacteria, and Bacteroidetes in all samples, and Pseudomonas was the most abundant detected genus. Virulence genes associated with motility, adherence, and secretion systems were highly abundant and mainly associated with Pseudomonas aeruginosa. Furthermore, some opportunistic pathogenic genera had negative correlations with WQI. Many clinically relevant antimicrobial resistance genes (ARGs) and efflux pump-encoding genes that confer resistance to critically important antimicrobials were detected. The highest relative abundances of ARGs were β-lactams and macrolide-lincosamide-streptogramin. No statistically supported relationship was detected between the abundance of virulome/resistome and collection type/WQI. On the other hand, total solids were a weak predictor of gene abundance patterns. These results provide insights into various microbial outcomes given urban stream quality and point to its ecological complexity. In addition, this study suggests potential consequences for human health as mediated by aquatic microbial communities responding to typical urban outputs.
Show more [+] Less [-]The use of copper as plant protection product contributes to environmental contamination and resulting impacts on terrestrial and aquatic biodiversity and ecosystem functions
2024
Pesce, Stéphane | Mamy, Laure | Sanchez, Wilfried | Artigas, Joan | Bérard, Annette | Betoulle, Stéphane | Chaumot, Arnaud | Coutellec, Marie-Agnès | Crouzet, Olivier | Faburé, Juliette | Hedde, Mickael | Leboulanger, Christophe | Margoum, Christelle | Martin-Laurent, Fabrice | Morin, Soizic | Mougin, Christian | Munaron, Dominique | Nélieu, Sylvie | Pelosi, Céline | Leenhardt, Sophie | RiverLy - Fonctionnement des hydrosystèmes (RiverLy) ; Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) | Ecologie fonctionnelle et écotoxicologie des agroécosystèmes (ECOSYS) ; AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) | Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER) | Laboratoire Microorganismes : Génome et Environnement (LMGE) ; Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA) | Environnement Méditerranéen et Modélisation des Agro-Hydrosystèmes (EMMAH) ; Avignon Université (AU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) | Stress Environnementaux et BIOsurveillance des milieux aquatiques (SEBIO) ; Institut National de l'Environnement Industriel et des Risques (INERIS)-Université de Reims Champagne-Ardenne (URCA)-Université Le Havre Normandie (ULH) ; Normandie Université (NU)-Normandie Université (NU)-SFR Condorcet ; Université de Reims Champagne-Ardenne (URCA)-Centre National de la Recherche Scientifique (CNRS)-Université de Reims Champagne-Ardenne (URCA)-Centre National de la Recherche Scientifique (CNRS) | Dynamique et durabilité des écosystèmes : de la source à l’océan (DECOD) ; Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut Agro Rennes Angers ; Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro) | Service santé de la faune et fonctionnement des écosystèmes agricoles (OFB Service Santé Agri) ; Direction de la recherche et de l’appui scientifique (OFB - DRAS) ; Office français de la biodiversité (OFB)-Office français de la biodiversité (OFB) | Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols) ; Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier ; Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro) | MARine Biodiversity Exploitation and Conservation - MARBEC (UMR MARBEC ) ; Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM) | Agroécologie [Dijon] ; Université de Bourgogne (UB)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Dijon ; Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro) | Ecosystèmes aquatiques et changements globaux (UR EABX) ; Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) | Direction de l'Expertise scientifique collective, de la Prospective et des Etudes (DEPE) ; Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) | OFB (Plan Ecophyto)
International audience | Copper-based plant protection products (PPPs) are widely used in both conventional and organic farming, and to a lesser extent for non-agricultural maintenance of gardens, greenspaces, and infrastructures. The use of copper PPPs adds to environmental contamination by this trace element. This paper aims to review the contribution of these PPPs to the contamination of soils and waters by copper in the context of France (which can be extrapolated to most of the European countries), and the resulting impacts on terrestrial and aquatic biodiversity, as well as on ecosystem functions. It was produced in the framework of a collective scientific assessment on the impacts of PPPs on biodiversity and ecosystem services in France. Current science shows that copper, which persists in soils, can partially transfer to adjacent aquatic environments (surface water and sediment) and ultimately to the marine environment. This widespread contamination impacts biodiversity and ecosystem functions, chiefly through its effects on phototrophic and heterotrophic microbial communities, and terrestrial and aquatic invertebrates. Its effects on other biological groups and biotic interactions remain relatively under-documented.
Show more [+] Less [-]The use of copper as plant protection product contributes to environmental contamination and resulting impacts on terrestrial and aquatic biodiversity and ecosystem functions
2024
Pesce, Stéphane | Mamy, Laure | Sanchez, Wilfried | Artigas, Joan | Bérard, Annette | Betoulle, Stéphane | Chaumot, Arnaud | Coutellec, Marie-agnès | Crouzet, Olivier | Faburé, Juliette | Hedde, Mickael | Leboulanger, Christophe | Margoum, Christelle | Martin-laurent, Fabrice | Morin, Soizic | Mougin, Christian | Munaron, Dominique | Nélieu, Sylvie | Pelosi, Céline | Leenhardt, Sophie
Copper-based plant protection products (PPPs) are widely used in both conventional and organic farming, and to a lesser extent for non-agricultural maintenance of gardens, greenspaces, and infrastructures. The use of copper PPPs adds to environmental contamination by this trace element. This paper aims to review the contribution of these PPPs to the contamination of soils and waters by copper in the context of France (which can be extrapolated to most of the European countries), and the resulting impacts on terrestrial and aquatic biodiversity, as well as on ecosystem functions. It was produced in the framework of a collective scientific assessment on the impacts of PPPs on biodiversity and ecosystem services in France. Current science shows that copper, which persists in soils, can partially transfer to adjacent aquatic environments (surface water and sediment) and ultimately to the marine environment. This widespread contamination impacts biodiversity and ecosystem functions, chiefly through its effects on phototrophic and heterotrophic microbial communities, and terrestrial and aquatic invertebrates. Its effects on other biological groups and biotic interactions remain relatively under-documented.
Show more [+] Less [-]