Descriptif

Microbial ecology for environmental sciences

Microorganisms are the backbone of all ecosystems. They play fundamental roles in the functioning of natural ecosystems and in biogeochemical cycles. They are also essential in various industrial bioprocesses used for depollution. In most cases, they do not live as single species but form microbial ecosystems composed of various microorganisms. The study of these intricate microbial communities is complex and requires specific tools. Numerous molecular techniques have been developed for this purpose. The aim of the “microbial ecology for environmental science” course is to present the importance of microbial communities in the environment and in bioprocesses as well as the methods classically used for their analysis. 16S ribosomal RNA based techniques will be presented as well as recent metaomics methodologies. It will provide the fundamental notions necessary to set-up and analyze a microbial ecology experiment for environmental samples. A particular focus will be given to depollution bioprocesses.

Teaching staff

Ariane Bize, Researcher, IRSTEA

Lise Fechner, Program Officer, IFREMER

Olivier Chapleur, Researcher, IRSTEA

Sébastien Lacroix, Researcher, Veolia

Jean-Jacques Pernelle, Research Director, IRSTEA

Course outline

● Microbial ecology of natural ecosystems

- What is a microorganism? What is microbial diversity?

- Role of microorganisms in the functioning of natural ecosystems and biogeochemical cycles.

● Microbial resource management

- Use of complex microbial communities for industrial processes

- Focus on biotechnologies for waste and wastewater management and valorization: activated sludge, anaerobic digestion and microbial fuel cells

● Molecular microbial ecology

- 16S ribosomal RNA based techniques

- Introduction to metaomics methodologies (metagenomics, metatranscriptomics, metaproteomics)

● Analyzing microbial dynamics in environmental samples

- Setting-up a microbial ecology experiment, experimental planning and follow-up.

- How to track changes in microbial communities over time or assess their biodiversity? Example of ARISA fingerprinting and fluorescent in-situ hybridization

- Analytical tools for big microbial ecology data sets. Hypotheses and biological interpretation.

This module includes 20 hours of courses, 8 hours of tutorial classes and 12 hours of practical work.

 --------------------------------------------

Level required: Basic knowledge in biology

Language: English

Credits ECTS: 5

Supervisor: Laurent Mazéas