Bacteria, Archaea, prokaryotic diversity, classification

The course is part of the Biodiverstiy cluster in the Master program Biology. The compulsory course General Microbiology from the bachelor program Biology and the part on prokaryote taxonomy in the course Practical Taxonomy in Master 1 form a good basis for this course.

The aim is to provide an overview of the known diversity of Bacteria and Archaea. In a phylogenetic framework, for both groups, firstly, the most important ways of life are discussed as the basis for the diversity and, secondly, an overview is provided of the most important known groups.

Competences: M1.1, M1.3, M1.4, M2.2, M2.4, M4.1, M.4.2, M5.1

The course is based on chapters12 and 17 in "Brock Biology of microorganisms"

1. Introduction
   Brief overview of the phylogenetic and classification principles in bacteriology + Bergey´s Manual of Systematic bacteriology. Metabolic diversity is not always linked to phylogenetic diversity.
2. Diverse ways of life:
   Different ways of life are covered. In each case ecological and biotechnological aspects are mentioned but not elaborated on. Occurrence in different groups is mentione, but these groups are discussed in more detail later in the course.
   • The aerobic way of life:
     This was discussed in a general way in the course General Microbiology. Here we will focus on the role of oxygen as ultimate means of decomposing special substrates (complex carbon compounds, methylotrophy, methanotrophy).
   • The phototrophic way of life:
     This is no repetition of what has been seen previously, but rather the emphasis will be on the differences between anaerobic and aerobic systems in terms of pigments, accessory pigments, location in the cell, electron donors and acceptors. The different ways to fix CO2 (Calvin cycle is considered as previously covered and known)
   • Chemolithotrophy: energy from oxidation of inorganic electron donors:
     Hydrogen oxidation, oxidation od reduced sulfur compounds, iron oxidation, nitrification and Anammox are discussed in detail.
   • Anaeribic ways of life: anaerobic respirations:
     The concept anaerobic respiration vs aerobic respiration at a molecular and biochemical level, Nitrate reduction and the process of denitrification, sulfate reduction, acetogenesis, methanogenesis, iron, manganese, chlorate and organic electron acceptors.
   • Anaerobic ways of life: fermentations:
     The concept of fermentation: energy and redox considerations, the fermentative diversity with examples of sugar fermentations by Enterobacteriaceae, clostridia and the lactic acid bacteria. Protein fermentation by clostridia.
   • Symbiotic associations with eukaryotes:
     Many eukaryotes host endosymbiotic prokaryotes (e.g. protists, sponges, various insects, algae, higher plants and animals) that they depend on for several, sometimes vital functions. We provide an overview of the most important functions and a few detailed examples.
3. Overview of the role of bacteria in the cycles of the elements:
   Role in carbon cycle, nitrogen cycle, sulfur cycle, iron cycle.
4. Overview of bacterial diversity:
   Using a phylogenetic tree of the phyla of Bacteria, the most important known groups of bateria are discussed (way of life, occurrence, diversity). Based on chapter 12 of Brock´s Biology of Micro-organinisms. Important ecological functions end/or biotechnological applications of some groups are mentioned but not discussed in detail.
5. Overview of archaeal diversity:
   Using a phylogenetic tree comprising the four phyla of Archaea, the most important known groups of Archaea are discussed (way of life, occurrence, diversity). Important differences between Archaea en Bacteria have been studied in General Microbiology and will be refreshed were relevant (e.g. adaptations to thermofilic life in membranes, DNA and proteins). Based on chapter 13 of Brock´s Biology of Micro-organinisms.
6. In workseminars and PGO-tutorials the following topics will be adressed:
   
   • How is the microbial diversity in an environment studied experimetnally ? (for example, the microbial community in the rhizosphere of a plant or the intestinal tract of an animal)
   • How are bacteria identified?

De students have a good general knowledge of microbiology and biochemitry based on the courses in the bachelor training Biology.

The student has a good grasp of the metabolic diversity of prokaryotes and knows the mechanisms of phototrophy, chemolithotrophy, anaerobic respiration, fermentation, the breakdown pf organic molecules with oxygen and nitrogen fixation. (M1.1, M1.4)

The student understand the role of micro-organisms in the cycles of the main elements. (M1.1, M1.4, M5.1)

The student has a good understanding of bacterial classification and the important groups of known bacteria. (M1.1)

The student is familiar with the ways of life, the occurrence and the diversity of the main groups of Archaea. (M1.1)

The student knows the most widely used techniques to study prokaryotic diversity and metabolism and for identification of prokaryotes. (M1.1, M1.4, M2.2)

Cost: 15.0 EUR
Presentations and pdf files of relevant scientific publications are available electronically.

Brock Biology of Micro-organisms, 11^th ed. 2006. M.T. Madigan & J.M. Martinko, Pearson Prentice Hall.

Bergey´s Manual of Systematic Bacteriology, 1st and 2nd edition. Springer.

The Prokaryotes, 2^nd ed. 4 Vol. Balows, A. H.G. Trüper, M. Dworkin, W. Harder and K.-H. Schleifer (eds). 1991. Springer-Verlag. A new (electronic) edition (2001) at http://www.prokaryotes.com

Questions can be discusses during and after classes and workseminars. Teachers are also available to personally answer questions or discuss problems by e-mail or after appointment.

Lectures using mainly powerpoint presentations.

Work seminars and PGO-tutorials

Periodical evaluation

Written exam, open questions and oral review of the answers.