Environmental Microbial Genomics Group

Logos Genomenviron and Ampere
Laboratoire Ampere
Ecole Centrale de Lyon . France
Université de Lyon
(33) 472 18 60 92
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The Environmental Microbial Genomics Group in the Laboratoire Ampère at the Ecole Centrale de Lyon (Université de Lyon; "University of Lyons") examines a range of research topics from fundamental mechanisms of microbial adaptation (Archaea (see film here), Bacteria, Fungi) such as horizontal gene transfer, nitrogen cycle and de novo gene synthesis to environmental perturbations due to anthropogenic activities such as nickel mining and environmental pollution. Important society based questions are also addressed such as the fate of transgenes from transgenic plants, drug discovery, impact of anthropogenic extreme environments, fate of REACH chemicals, the bioremediation of contaminated soils and water (environmental bioengineering) and the importance of climate change. Other scientific questions include the microbial ecology of diverse environments such as the human digestive tract, human skin and mercury-impacted Arctic snow (see video).

A central technological approach employed to answer different questions relies on combining the use of 'omic methods and next generation sequencing (both 2nd and 3rd generation) with classical environmental microbiology. Metagenomic techniques access total microbial genomes in environments in order to avoid biases associated with culture-dependent approaches. Production and screening of clone libraries, use of phylogenetic microarrays and functional gene quantification with Real-time PCR and DNA and RNA (cDNA) sequencing (an Illumina MiSeq and an Oxford Nanopore sequencer) are commonly used methods. A range od bioinformatics and modeling approaches are used including microbial ecology networks.

This group also benefits from close ties with electrical engineers for the exploration of the effect of lightning on gene transfer, possible lightning related soil bioremediation techniques, and the production of electricity from microbial fuel cells.

This range of research can be alternatively referred to as microbial ecology, environmental microbiology (click for intro in French ) and ecological engineering.



Latest News and Events

  • Dr Agathe Paitier defended her thesis entitled "Microbial Fuel Cell (MFCs) Scale-Up: Current collectors and Hydrodynamics" on the 17th of November 2017. The external members of her committee included Prof Giuliano Premier (University of South Wales), Dr Théodore Bouchez (IRSTEA) and Dr Wafa Achouak (CNRS.)
  • Dr David Royet defended his thesis entitled "Nouvelle approche de décryptage de la diversité bactérienne environnementale par capture magnétique de populations spécifiques de bactéries au sein de microbiotes complexes " on the 16th of March 2017. The external members of his committee were Dr Florence Ploetze (Institut de biologie
    moléculaire des plantes), Prof. Pierre Peyret (Université Clermont Auvergne), Prof. Mike DuBow (Université Paris Sud), and Dr. Florence Razan (ENS Rennes).
  • Dr Christoph Keuschnig defended his thesis entitled "Multi-scale spatial analysis of microbial distribution in soil and sediment" on the 6th of December 2016. The external members of his committee were Prof Kirstin Hofmockel(Iowa State University and Pacific Northwest National Lab, USA), Prof Leif Kledtmesson (University of Goteborg, Sweden), Prof. Sophie Zekmeister (University of Vienna, Austria) and Dr Sine Ngando (Université Blaise Pascal , Clermont-Ferrand, France).
  • Dr Jean-Sebastien Beaulne defended his thesis entitled "Multi-scale spatial analysis of microbial distribution in soil and sediment" on the 20th of November 2015. The external members of his committee were Prof Josh Schimel (University of California at Santa Barbara, USA), Prof Soren Sorenson (University of Copenhagen, Denmark) and Dr Alban Ramette (University of Bern, Switzerland).
  • Dr Laura Sanguino-Casado defended her thesis entitled " EXPLORING ENVIRONMENTAL VIRUS-HOST INTERACTIONS AND THEIR RELEVANCE TO MICROBIAL ADAPTATION USING CRISPRs" on the 10th of November 2015. The external members of her committee were Prof Matthew Sullivan (Ohio State University, USA), Prof Alex Anesio (University of Bristol, UK), Prof Francisco Rodríguez Valera (Universidad Miguel Hernández, Alicante, Spain) and Prof Michael Schloter (Helmholtz Zentrum München, Germany).
  • Dr. Lorrie Maccario defended her thesis entitled "SNOW ECOSYSTEM: MICROBIAL COMMUNITY STRUCTURE AND FUNCTION IN ARCTIC SNOWPACKS" on the 18th of September 2015. The external members of her committee were Prof Jody Deming (University of Washington, Seattle, USA), Prof Carsten Jacobsen (Aarhus University, Denmark), Prof Mohamed Jebbar (University of Brest, France) and Dr Aurélien Dommergues (University of Grenoble, France).


Nature Reviews Microbiologyy Cover 200904



19 November 2017