Back to search form

Adaptation to chlorinated pollutants of the microbial compartment of multi-contaminated soils

Research unit

UMR 7156 - Génétique Moléculaire, Génomique et Microbiologie (GMGM)
Institut de Botanique, 28, rue Goethe, 67083 STRASBOURG

Group

Name: Adaptations et interactions microbiennes dans l'environnement

Group leader: VUILLEUMIER Stéphane - vuilleumier@unistra.fr

Group leader's phone: 0368852022

Website: Visit website

Group organization:
- Chercheurs: 3
- ITA: 2
- Doctorants: 2
- Post-Docs: 0
- Autres: 1

Publications of the team linked to the topic (3 last years):
1) Elsayed O, Maillard E, Vuilleumier S, Nijenhuis I, Richnow HH, Imfeld G (2014). Using compound specific isotope analysis to assess the degradation of chloroacetanilide herbicides in lab-scale wetlands. Chemosphere 99, 89-95.
2) Farhan Ul Haque M, Nadalig T, Bringel F, Schaller H, Vuilleumier S (2013). Fluorescence-based bacterial bioreporter for specific detection of methyl halide emissions in the environment. Appl. Environ. Microbiol. 79, 6561-6567.
3) Imfeld G, Vuilleumier S (2012). Measuring the effects of pesticides on bacterial communities in soil: a critical review. Eur. J. Soil Biol. 49, 22-30.

About PhD

PhD Director: VUILLEUMIER Stéphane - vuilleumier@unistra.fr

Phone: 0368852022

Junior advisor: NADALIG Thierry

Co-tutely: non

Co-Director: BRINGEL Françoise
University of Co-Director: Université de Strasbourg

About PhD topic :

Title: Adaptation to chlorinated pollutants of the microbial compartment of multi-contaminated soils

Project: The microbial degradation of chlorinated pollutants represents the domain of expertise of the host laboratory. The main objective of the PhD project will be to characterise the dynamics and the diversity of microbial communities during reactive and mass transfer of selected chlorinated pollutants in soil microcosms.
With billions of cells per gram which may belong to millions of different species, surface soils likely represent the terrestrial compartment with the highest microbial diversity. Exposure of soils to toxic contaminants, and to chlorinated pollutants in particular, has marked effects on their microbial diversity. However, these still need to be characterised globally and in detail at the molecular level.
In this PhD project, microbial populations will be investigated in soil microcosms by DNA analyses involving PCR and sequencing. On the basis of sequence information available in databases and also obtained in the project, the PhD candidate will strive to define a suite of genetic biomarkers associated with the bacterial degradation of chlorinated pollutants and with resistance to such compounds.
In the laboratory, the degradation of selected chlorinated pollutants in column microcosms of a multicontaminated soil under different experimental conditions will be investigated. The technique of « stable isotope probing » (SIP), which leads to the selective incorporation of C13-labelled compounds in the DNA of physiologically active populations, will be developed. This will allow an in-depth investigation of the functional potential of the soil microbial compartment associated with dehalogenation.
At the field scale, an industrial multicontaminated site will also be investigated using the same approaches, in the context of a collaborative pilot project for biological containment of various pollutants.
Experiments that will be carried out in the PhD project will include
- isolation of DNA from multicontaminated soils and interstitial water;
- development of PCR and qPCR assays for biomarker genes in order to probe the structure (e.g. 16S rrnA (bacteria, Archaea) ; 18S rrnA
(eucaryotes)) and the function (genes for the degradation of pollutants, genes for key soil functions) of microbial populations;
- analysis of populations active in the degradation of chlorinated pollutants (stable isotope probing);
- genotyping analyses by T-RFLP and D-HPLC of structural and functional genes;
- high-throughput random or targetted sequencing (454, Illumina);
- biostatistical analyses of microbial diversity.
The project will thereby contribute to answer the following questions:
- What are the proportion and the diversity of bacteria associated with the degradation of chlorinated pollutants in the investigated soils?
- How is soil microbial diversity affected by exposure to pollutants or by the addition of pollutant-degrading bacteria?
- To what extent does the coupling of molecular biological and analytical chemical approaches allow the definition of innovative and reliable bioindication tools to monitor cleanup of polluted soils?
In summary, the work to be performed in the PhD project will contribute to better evaluate the potential of environmental genomics approaches, currently under rapid development, to accompany the remediation of polluted sites, and to assess the functional status of ecosystems and of their potential for resistance, resilience and adaptation to environmental contaminants.

Wished skills: - Master in biological sciences, or at the interface with chemistry or environmental sciences
- Good knowledge of microbiology and molecular biology; fundamentals in analytical chemistry, biochemistry, and genomics
- Ability to work independently and to participate in team efforts
- Good oral / written communication and presentation skills
- Creativity
- Interest to develop collaborations with partners from both industry and academia
- Strong interest for environmental questions

Expertises which will be acquired during the training: - Quantitative follow-up of gene expression using qPCR
- Environmental genomics (stable isotope probing (SIP), sequencing)
- Bioinformatic analysis
- Analysis of volatile compounds by gas and liquid chromatography