- We continue using the text by Madigan, M.T., J.M. Martinko and J. Parker, "BROCK, BIOLOGY OF MICROORGANISMS", 9th ed. 1999, Prentice Hall. The publisher offers a website (http://www.prenhall.com/brock) which gives short summaries of each chapter and which allows the student to review and self-test his/her basic knowledge in microbiology. This is the mandatory text on which part of the exams will be based.
- The student is expected to read the chapters listed as "Reading Assignments" in the Program and to test himself/herself by trying to answer the Test Questions. The answers to Multiple Choice Questions can be sent in for correction and the corrected test results will be returned to the student within a few seconds.
- The book contains more than what will be covered during the course. Students who need to repeat some of the material from earlier courses will find it useful to look through the corresponding chapters at the beginning of the book and there is a wealth of information for those who would like to know more.
- Contents of chapters 1 to 5 and 15 are prerequisites for the MICROBIAL ECOLOGY course. These contents are discussed in the introductory courses in biochemistry, microbiology and cellbiology. Students should review these chapters again as a preparation for the MICROBIAL ECOLOGY course.
- Contents of chapters 6 to 11 will not be discussed in this course since most of the material covered there forms the contents of the molecular biology and genetics courses. Knowledge outlined in those chapters will be required, however, to solve problems dealing with molecular aspects of the genetic evolutionary driving forces, which are offered as part of the MICROBIAL ECOLOGY course exercises.
Other recommended texts
- The Physiology and Biochemistry of Prokaryotes, 2nd ed. David White. Oxford University Press, 2000. ISBN0-19-508439-X.
- Biology of the Prokaryotes. J.W.Lengeler, G.Drews, H.G.Schlegel (eds). Thieme Stuttgart, 1999. ISBN: 3-13-108411-1.
- The key contents of the MICROBIAL ECOLOGY course are contained in chapters 12 to 14, 16, 17, 19 and 21 of Madigan, M.T., J.M. Martinko and J. Parker, "BROCK, BIOLOGY OF MICROORGANISMS", 9th ed. 1999, Prentice Hall. The READING ASSIGNMENTS focus mainly on these chapters.
- Supplementary information to the topics of the course can be found in chapters 29 to 32 of the book by Lengeler J.W., G. Drews & H.G. Schlegel (eds.), Biology of the Prokaryotes.
- Reference copies of the follwing books are available in the reading room of the library at the Botanical Garden where they may be consulted. The books may not be removed from the library.
- Brock - Biology of Microorganisms. Madigan M.T., J.M. Martinko and J. Parker (eds.). 9th edition, (BBOM, International Edition), Prentice Hall, 1999. ISBN: 0-13-085264-3.
- The Physiology and Biochemistry of Prokaryotes. White David. 2nd edition, Oxford University Press, 2000. ISBN: 0-19-508439-X.
- Biology of the Prokaryotes. Lengeler J.W., G.Drews, H.G.Schlegel (eds.). Thieme Stuttgart, 1999. ISBN: 3-13-108411-1.
- Research papers specifically relating to the practical course projects are listed in the project descriptions and are available from the advisor of your experiment.
- These tests are based on the microbiology courses
- Physiology of Prokaryotes (4th semester) and
- Diversity of Microorganisms (3rd semester)
- They should be fulfilled by the participants before the "Microbial Ecology Course" starts.
- In order to obtain maximal credits, course participants are expected to
- actively participate in all aspects of the cours (lectures, exercises and labs),
- show that they are able to work up the Reading Assignments,
- deliver a written report describing the outcome of the group research project(s)*
- prove their skills in solving the problems offered as exercises and
- presenting the essence of a scientific paper related to the student's field of interest in microbial ecology in 15 minutes in English and being able to respond to questions related to it (Minisymposium).
* For comparison you might consult last year's reports.
- The Microbial Ecology Course will be part of the final Diploma exam. Contents of the exam (40 minutes) are
- the chapters and papers given as reading assignments
- the material discussed in lectures seminars and exercises
- the laboratory work
- Students interested in MICROBIAL ECOLOGY and the study of the DIVERSITY OF MICROORGANISMS should have solid knowledge in the basic subjects of the natural sciences. Some of the contents which are essential are listed below. Students will profit most if they review the material before the MICROBIAL ECOLOGY course.
- General Prerequisites
- A few key words describing the contents most applicable to MICROBIAL ECOLOGY are listed below for
- Chemistry
- Biochemistry
- Physics
- Mathematics
- Plant Physiology
- Molecular Biology
- Structural Biology
- Genetics
- Microbiology
- These subject are taught in the undergraduate courses of the 1st to the 4th semester.
- Chemistry
- Recalling a few chemical principles
- Structure of atoms, molecules, ions, isotopic distribution,
- Oxidation states of the elements, exchange of electrons, electronegativity & electronaffinity,
- The nature of chemical bonds,
- Stoechiometries and yields of reactions,
- Dynamic equilibria (solubility, redox, protonation/deprotonation, dissociation, sorption/desorption, complexation), reaction kinetics,
- Thermodynamic functions, electrochemical potentials & electromotive forces,
- Chemical reactivities of solid surfaces.
- Biochemistry
- Bio-macromolecules and their monomers;
- Enzymes and coenzymes in metabolic processes;
- Membrane translocation, transport of electrons and protons within and across membranes, electrochemical potential,
- Oxidative phosphorylation, energy-rich bonds, group translocation reactions
- Basic metabolic routes and enzymatic mechanisms
- Energetic processes in mitochondria
- Thermodynamic concepts applied to bioenergetics
- Physics
- Recalling a few physical principles
- Characteristics & behavior of gases and liquids (water),
- Measurement and characteristics of electromagnetic radiation, absorption, reflexion, fluorescence, changes of the radiation spectrum in water, in the atmosphere;
- Ecologically important geophysical determinants: heat flow, temperature, pressure, magnetic field,
- Transformation of energy
- Calculation of electrochemical potential differences, electron currents
- Mathematics
- Mathematical description of growth in static and continous culture as differential equations and their solutions
- Plant Physiology: Photosynthesis and Bioenergetics
- Architecture and pigment composition of the photosynthetic membrane,
- Stoichiometry and energetics of biomass formation during assimilation;
- Light dependent reactions in photosynthetic membranes,
- Mechanisms of light driven energy transfer and electron flow from electron sources to sinks,
- CO2-fixation reactions
- Prokaryotic Molecular Biology taught as part of the Molecular Biology and Genetics courses during the 2nd and 3rd semester
- Genetic elements; regulation of information processing on the molecular level; mutation, recombination and rearrangement of genetic information; energy conversion mechanisms
- Structural Microbiology taught as part of the Cell Biology courses during the 2nd semester
- Architecture and function of biological membranes and subcellular structures
- Genetics taught as part of Biology II during the 2nd semester
- Molecular and cytological basics and terms of heredity,
- Mutagenesis, types and induction of mutations,
- Parasexuality in prokaryotes, bacteriophages and viruses,
- Molecular mechanisms of gene expression
- Microbiology taught as parts of Biology-III and Biochemistry-II
- Basic Microbiology
- Biological innovations by prokaryotes
- Basic concepts in microbial evolution
- Isolation, cultivation and characterization of bacteria and archaea
- Growth, growth kinetics and growth prevention of microbes
- Expressions of microbial growth in aggregates, biofilms and other community structures
- Metabolic versatility and diversity
- Microbial interactions in food webs
- Industrially produced microbial products
- Biochemistry and Physiology of Prokaryotes
- Basic principles of bacterial and archaeal metabolisms
- Diversity of phototrophic bacteria and their photosynthetic processes
- Pathways which allow for C-Autotrophy
- Biochemistry of Chemolithotrophy
- Thermodynamics and energetics of chemolithotrophs in extreme habitats
- Common themes in anaerobic respiration
- Versatility of fermenters
- Degradation of xenobiotics