Functional and Molecular Marine Microbiology

Marine bacteriology

After a short review of basic "general" microbiology, I describe, according to the most recent data, the biodiversity of marine microorganisms and the methods used to access information about marine bacteria (techniques, marine environment specificity, biomass, internal and external control of bacteria metabolism, metabolic potentials, N, C, P and S cycles ...). The course also reviews some very special microbiocenoses mainly focussed on symbiosis (hydrothermal vents microbiocenoses and bacterial symbiosis in coral reefs).

Molecular approaches to the diversity of marine microorganisms

About 20 years ago, it became apparent that the study of the diversity of marine microorganisms cannot be conducted without a molecular approach, given that only a fraction of them can be isolated and cultured. In addition, as for the microorganisms that can be observed through a microscope, genetic diversity is larger than that which is determined on the basis of phenotypical characteristics (morphology....). The determination of diversity at the genetic level also allows us to understand ecological characteristics (geographical distribution, endemism, etc.).

Marine bacteriology

To give an integrated scheme of bacterial impact in the ocean functioning

Molecular approaches to the diversity of marine microorganisms

To give to the students the knowledge that will allow them, on one hand, to understand and read in a critical manner the literature concerning the diversity of marine microorganisms, and on the other hand, to use molecular techniques in order to solve problems concerning the molecular diversity and ecology on which they may be working (master thesis, PhD, etc).

Marine bacteriology

Bases of microbiology are quickly reviewed at the begin of the course.

Molecular approaches to the diversity of marine microorganisms

Having basic knowledge of genetic material: DNA, RNA, proteins. If this prerequisite is not met, part of the course may be devoted to a review.

Marine bacteriology

Biomass estimations by several approaches, metabolic activities characterization, use of specific simulation softwares.

Molecular approaches to the diversity of marine microorganisms

Practical work in a laboratory on a small problem involving diversity of marine microorganisms (often cyanobacteria).

Marine bacteriology

5 times 3 hours (theory), 5 days practicals

Molecular approaches to the diversity of marine microorganisms

Face-to-face teaching, in 1st quadrisemester 1) Definitions 2) Why? 3) Molecular markers of diversity 4) Molecular techniques 5) Phylogenetic analyses and tree reconstructions 6) How  the genetic diversity is generated? 7) Examples of applications in molecular microbial ecology
8) Practical training in extraction of genomic DNA from cyanobacterial strains, PCR, electrophoresis, sequencing, phylogenetic analysis of the generated sequences

Marine bacteriology

French written syllabus.
Reference book : "Microbial Ecology of the oceans", D.L. Kirchman, Ed. Wiley-Liss Inc.

Molecular approaches to the diversity of marine microorganisms

Copies of transparencies used in class

Marine bacteriology

Oral exam with notes (2 questions).

Molecular approaches to the diversity of marine microorganisms

2) Exam on the theory

Marine bacteriology

Mathieu Poulicek - Tél 04 366 50 67 - Email: mpoulicek@ulg.ac.be

Molecular approaches to the diversity of marine microorganisms

A. Wilmotte, CIP, Chimie B6, Phone : 04/366.33.87/38.56, e-mail : awilmotte@ulg.ac.be

Molecular approaches to the diversity of marine microorganisms

Corrected sequence files 3 strains
This is the result of manual edition to remove wrong bases

Exercice of phylogenetic analysis of 3 cyanobacterial strains
Phylogenetic analysis of the 3 strains used for the practical work

Module on Microbial Systematics
Microbial Systematics and taxonomic tools

Module on Phylogenetic Analysis
Module on Phylogenetic Analysis

module on the generation of genetic diversity
module on the generation of genetic diversity

processed sequences (contigs, individual 16S and ITS)
after processing

RAW Sequences
Files rRNA sequences of the 3 strains studied during the TP

TP
Practical training