The Laboratory for the Microbial Ecology of River Systems Transformed by Human Activity is used for work on the BELCA (biological and ecological disruptors linked to chemical contamination caused by humans) research theme.
Its research concentrates on studying aquatic microbial communities in environments subject to anthropogenic pressure.

The team’s work focuses on the influence of microbial communities (algae, bacteria and fungi) on the ecological performance of aquatic systems subject to anthropogenic pressure. The team examines the on-site and in vitro effects of chemical stress (toxic and trophic) and/or physical stress on microbial communities (in terms of the functioning and diversity of communities), including communities’ resilience, alterations to their ecological roles as diversity changes, spatial and temporal variation on site and the consequences of changes in terms of the self-purification of aquatic environments. The two main study models concern sediments and periphyton.


  • Gas chromatography
  • Fluorimetry
  • Spectrophotometry
  • Microscopy (FISH)
  • PCR-DGGE, PCR-RISA and qPCR           
  • Sediment and biofilm processing
  • Pigment characterisation and photosynthetic activity (PhytoPAM)


  • Workshop site in Ardières-Morcille (department 69), part of the Rhone Basin Workshop Area: http://www.graie.org/zabr/  
  • Outdoor lotic mesocosms
  • Fitted experimental part (pilots, microcosms)     


The team benefits from close collaborations with the laboratory for the physico-chemical analysis of aquatic environments in the MALY (ecology and pollution of aquatic environments) research unit and the quality dynamic of aquatic environments team of the REBX (water supply systems, purification and quality) research unit.

  • Other French partners:

CNRS joint research unit 5023, Lyon I; CNRS joint research unit 6023, Clermont II; INRA (Thonon Hydrobiology Plant and MSE Dijon joint research unit) and ENTPE (National Engineering School of State Public Works).

  • European partners:

University of Girona, Spain

Research programmes

  • National Research Agency (ANR) – Contaminants-Ecosystems-Health (2010-2012): Sendefo (sensitivity of bacterial communities to fungicide and capacities to break it down) programme
  • ANR – Global environmental changes (2010-2012): programme WETCHANGE (biodiversity and the functions of wet areas in response to acute low water levels caused by global changes) programme
  • PestExpo internal programme (2008-2011): evaluation of the chemical and biological quality of watercourses and the salience, assets, limitations and validity of a range of on-site sampling methods
  • IRSTEA-ONEMA convention (since 2009): evaluation and remediation of the effects of pesticides.
  • IRSTEA- RM&C water agency (2008-2011): study of the effects of the physical and chemical restoration of the River Vistre (in Gard)
  • APR – pesticides of the Ministry of Ecology, Sustainable Development, Transport and Housing (2010-2012): Impalac (predicting the impact of mixed herbicides on planktonic algal and benthic limnic communities)
  • INRA Incentive Action Programme – Microbial Degradation of Kepone (2011-2013): BIODECHLOR Programme


Make-up of the team

  • Team leader
    Stéphane Pesce
  • Scientists
    Stephane Pesce, research officer
    Gilles Armani (CDD)
    Bernard Motte, TR, appui technique aux essais (terrain et laboratoire)
    Marc Neyra
    Christophe Rosy, TR, microbiologie
    Bernadette Volat, IE, écologie microbienne et biologie moléculaire
  • Doctoral students
    Anne-Sophie LAMBERT

Most recent publications (2015 - 2014)



Diouf F, Diouf D, Klonowska A, Le Queré A, Bakhoum N, Fall D, Neyra M, Parrinello H, Diouf M, Ndoye M, Moulin M, 2015. Genetic and Genomic Diversity Studies of Acacia Symbionts in Senegal Reveal New Species of Mesorhizobium with a Putative Geographical Pattern. PLoS ONE 10, e0117667.

Foulquier A, Morin S, Dabrin A, Margoum C, Mazzella N, Pesce S, 2015.. Effects of mixtures of dissolved and particulate contaminants on phototrophic biofilms: new insights from a PICT approach combining toxicity tests with passive samplers and model substances. Environ. Sci. Pollut. Res. 22, 4025-4036.

Lambert AS, Pesce S, Foulquier A, Gahou J., Coquery M, Dabrin A, 2015. Improved short-term toxicity test protocol to assess metal tolerance in phototrophic biofilms: Toward standardization of PICT approaches. Environ. Sci. Pollut. Res. 22, 4037-4045.

Mermillod-Blondin F, Winiarski T, Foulquier A, Perrissin A, Marmonier P (in press). Links between sediment structures and ecological processes in the hyporheic zone: Ground-penetrating radar as a non-invasive tool to detect subsurface biologically active zones. Ecohydrology

Tlili A, Bérard A, Blanck H, Bouchez A, Cassio F, Eriksson M, Morin S, Montuelle B, Navarro E, Pascoal C, Pesce S, Schmitt-Jansen M, Behra R (in press) Pollution Induced Community Tolerance (PICT): Towards an ecologically relevant risk asessment of chemicals in aquatic systems. Freshwater Biol.


Artigas J, Pascault N, Bouchez A, Chastain J, Debroas D, Leloup J, Tadonleke R, Ter Halle A, Humbert JF, Pesce S,  2014. Comparative sensitivity to the fungicide tebuconazole of biofilm and planktonic microbial communities in freshwater ecosystems.  Sci. Total Environ. 468–469, 326–336.

Bonet B, Corcoll N, Tlili A, Morin S, Guasch H, 2014. Antioxidant enzyme activities in biofilms as biomarker of Zn pollution in a natural system: An active bio-monitoring study. Ecotox. Environ. Safety 103, 82-90

Devers-Lamrani M, Pesce S, Rouard N, Martin-Laurent F., 2014. Evidence for cooperative mineralization of diuron by Arthrobacter sp. BS2 and Achromobacter sp. SP1 isolated from a mixed culture enriched from diuron exposed environments. Chemosphere 117, 208-215

Foulquier A, Dehedin A, Piscart C, Montuelle B, Marmonier P, 2014. Habitat heterogeneity influences the response of microbial communities to severe low-flow periods in alluvial wetlands. Freshwater Biol. 59, 463-476

Ghiglione JF, Martin-Laurent F, Stachowski-Haberkon S, Pesce S, Vuillemier S, 2014. The coming of age of microbial ecotoxicology: report on the first two meetings in France. Environ. Sci. Pollut. Res. 21, 1241-1245

Kim Tiam S, Morin S, Pesce S, Feurtet-Mazel A, Moreira A, Gonzalez P, Mazzella N, 2014. Environmental effects of realistic pesticide mixtures on natural biofilm communities with different exposure histories.  Sci. Total Environ. 473–474, 496-506.

Kouyaté Z, Krasova Wade T, Yattara I I, Neyra M, 2014. Effects of cropping system and cowpea variety (Vigna unguiculata L. Walp) on the diversity of native cowpea bradyrhizobia and millet yield in the Sudano Sahelian zone of Mali. IRJAS, 4, 30-39.

Pascault N, Roux S, Artigas J, Pesce S, Leloup J, Debroas D, Bouchez A, Humbert JF, 2014. A high-throughput sequencing ecotoxicology study of freshwater bacterial communities and their responses to tebuconazole.  FEMS Microbiol. Ecol. 90, 563-574.

Wade TK, Le Quéré A, Laguerre G, N'Zoué A, Ndione JA, doRego F, Sadio O, Ndoye I, Neyra M, 2014. Eco-geographical diversity of cowpea bradyrhizobia in Senegal is marked by dominance of two genetic types. Sytem. Appl. Microbiol. 37, 129-139.