Environmental Microbial Genomics Group

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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 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, and the importance of nitrous oxide from the nitrogen cycle in climate change.

A central technological approach employed to answer different questions relies on the use of metagenomic methods and next generation sequencing (both 2nd and 3rd generation). Metagenomic techniques access total microbial genomes in environments in order to avoid biases associated with culture-dependent approaches (Metagenomic 2008 presentation). Production and screening of clone libraries, use of phylogenetic microarrays and functional gene quantification with Real-time PCR and DNA and RNA (cDNA) sequencing (our lab has an Illumina MiSeq and an Oxford Nanopore sequencer) are commonly used methods. Metagenomic approaches are used to resolve scientific questions in the above research areas as well as the microbial ecology of diverse environments such as the human digestive tract, human skin and mercury-impacted Arctic snow (see video).

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) and ecological engineering.

 

 

Latest News and Events

  • 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
 

ANR projets: EVASOL HYBIOX SOLAO ULTRABIO APTITUDE ALIMINTEST SEPTANTE METASOIL PLOBEN
European proects OSIRIS METAEXPLORE TRANSBAC
CNRS projets BIOPILOTE BIOPILE MFC GENEFISH Rhône-Alpes région METAGENE

 


21 March 2016