- Dates & Times
Laboratory
according to individual program, begin Monday, November 26
Lectures
Thursday morning 08.15 to 09.45, begin Thursday, November 29
Exercises
Thursday morning 10.15 to 12.00, begin Thursday, November 29
Seminars
Friday morning 08.30 to 10.00, begin Friday, November 30
Library Tour
Monday, November 26 at 09.15, with Sophie Fritschi
Paper presentations
Friday morning 10.15 to 11.30, begin Friday, November 30
Computer courses
Thursday evening 18.00 to 20.00, begin Thursday, November 29
Field trips
See special program
Minisymposium
Friday, December 21, all day, oral reporting
Course reports
The written reports will have to be turned in to the advisor of the laboratory experiments no later than January 11
Christmas party
Friday afternoon, December 21, 16.15, after the Minisymposium
- Program week 48 microeco
No
Time
Date
Title Reading * 1
08.15
Mon 26/11
In
Introduction and repetition
1 to 5 and 15
09.15
Library Tour with Sophie Fritschi
2
08.15
Thu 29/11
Le 1
3
09.15
Thu 29/11
Le 2
4
10.15
Thu 29/11
Ex I
Simulation of ecological determinants for the cultivation of microorganisms
5
11.15
Thu 29/11
Ex II
6
18.00
Thu 29/11
Introduction to the Internet, Literature Searches
7
08.30
Fri 30/11
Mathias Höchli, University of Zürich, Central Electron Microscope Laboratory Möglichkeiten und Grenzen der Konfokalen Lichtmikroskopie".
8
10.15
Fri 30/11
Pa
Student groups 1 and 2
- Abbreviations:
- Introduction (In) / Laboratory (La) / Lecture (Le) / Exercises (Ex) / Seminar (Se) / Computer course (Co) / Paper presentation (Pa) / Field trip (Ft)
- * Please consult approriate chapters in Madigan M.T., J.M. Martinko and J. Parker: "Brock - Biology of Microorganisms", 9th Edition, (BBOM, International Edition), Prentice Hall, 1999. ISBN: 0-13-085264-3.
- Program week 49 microeco
No
Time
Date
Title Reading * 9
08.15
Thu 06/12
Le 3
10
09.15
Thu 06/12
Le 4
11
10.15
Thu 06/12
Ex III
Microbially dominated ecosystems and concepts in microbial ecology
12
11.15
Thu 06/12
Ex IV
13
18.00
Thu 06/12
- Genomic and proteomic data collections and phylogenetic tree building
14
08.30
Fri 07/12
Se
Janine Kessi, University of Zürich, Institute of Plant Biology / Microbiology. Selenite resistance in purple non-sulfur bacteria: Physiological and biochemical aspects".
15
10.15
Fri 07/12
Pa
Student groups 4 and 5
- Abbreviations:
- Introduction (In) / Laboratory (La) / Lecture (Le) / Exercises (Ex) / Seminar (Se) / Computer course (Co) / Paper presentation (Pa) / Field trip (Ft)
- * Please consult approriate chapters in Madigan M.T., J.M. Martinko and J. Parker: "Brock - Biology of Microorganisms", 9th Edition, (BBOM, International Edition), Prentice Hall, 1999. ISBN: 0-13-085264-3.
- Program week 50 microeco
No
Time
Date
Title Reading * 16
08.15
Thu 13/12
Le 5
17
09.15
Thu 13/12
Le 6
18
10.15
Thu 13/12
Ex V
19
11.15
Thu 13/12
Ex VI
20
18.00
Thu 13/12
- Priciples for thermodynamic modelling of microbial reactions, with examples
21
08.30
Fri 14/12
Thomas Thurnheer, University of Zürich, Dental School, Institute of Oral Microbiology and General Immunology, Center for Dentistry, Oral Medicine and Maxillo Facial Surgery. "Diffusionsstudien und drei-dimensionale Organisation in einem in vitro Biofilm-Modell".
22
10.15
Fri 14/12
Pa
Student group 3
23
16.15 Fri 14/12 Se Eviatar Nevo, University of Haifa, Haifa "Ecological Genomics and Evolution". Plant Biology Forum
- Abbreviations:
- Introduction (In) / Laboratory (La) / Lecture (Le) / Exercises (Ex) / Seminar (Se) / Computer course (Co) / Paper presentation (Pa) / Field trip (Ft)
- * Please consult approriate chapters in Madigan M.T., J.M. Martinko and J. Parker: "Brock - Biology of Microorganisms", 9th Edition, (BBOM, International Edition), Prentice Hall, 1999. ISBN: 0-13-085264-3.
- Program week 51 microeco
No
Time
Date
Title Reading * 24
08.15
Thu 20/12
Le 7
Levels of abstraction applied to the study of microbial ecology
25
09.15
Thu 20/12
Le 8
26
10.15
Thu 20/12
Ex VII
Adaptation to material and energy gradients in microbial mats and biofilms
27
11.15
Thu 20/12
Ex VIII
18.00
Thu 20/12
No evenig activities scheduled. Preparations for Minisymposium
28
09.15
Fri 21/12
MINISYMPOSIUM on "Current Aspects of Environmental and Ecological Microbiology"
29
16.15
Fri 21/12 Christmas Party. End of course
- Abbreviations:
- Introduction (In) / Laboratory (La) / Lecture (Le) / Exercises (Ex) / Seminar (Se) / Computer course (Co) / Paper presentation (Pa) / Field trip (Ft)
- * Please consult approriate chapters in Madigan M.T., J.M. Martinko and J. Parker: "Brock - Biology of Microorganisms", 9th Edition, (BBOM, International Edition), Prentice Hall, 1999. ISBN: 0-13-085264-3.
- During the research sections students will carry out small research projects. This year's projects focus on microbial community analyses, survival strategies and metal mobilization.
- Please consult the project descriptions below and choose a project in which you would like to be involved in.
Advisors:
- Christine Lehmann (Group 1: 2 places)
- Munti Yuhana (Group 2: 2 places)
- Thomas Horath (Group 3: 3 places)
- Marion Stagars( Group 4: 2 places)
- Helmut Brandl (Group 5: 2 places)
- Project 1
- TITLE: Phenotypic and genotypic characterization of metal corroding biofilms
- Investigators: Fabrizio Gorla and Otto-Martin Willy
- Advisor: Christine Lehmann
- Project 2
- TITLE: Molecular anlaysis of biofilm-forming bacteria from cold, oligotrophic habitats
- Investigators: Kati Seidl and Sebastian Zurbriggen
- Advisor: Munti Yuhana
- Project 3
- TITLE: Endolithic microbial communities in dolomite rocks
- Investigators: Naim Matasci and Hans-Caspar Hürlimann
- Advisor: Thomas Horath
- Project 4
- TITLE: Mobilization of metals from metal-containing solids using cyanogenic microorganisms
- Investigators: Christine Kägi and Tobias Rosenberger
- Advisor: Marion Stagars
- Project 5
- TITLE: Survival strategies of microorganisms: The formation of reserve polymers in Bacillus megaterium
- Investigators: Stephan Bänziger and Nadja Tobler
- Advisor: Helmut Brandl
- The exercise sessions will take place every Thursday morning at 10:15
Date
- Exercise
- No.
Title
Nov. 29
I
Simulation of ecological determinants for the cultivation of microorganisms
Nov. 29
II
Dec. 06
III
Microbially dominated ecosystems and concepts in microbial ecology
Dec. 06
IV
Dec. 13
V
Dec. 13
VI
Dec. 20
VII
Adaptation to material and energy gradients in microbial mats and biofilms
Dec. 20
VIII
- Computer Applications in
- Microbial Ecology, Phyolgeny, Ecological Thermodynamics, Geomicrobiology and Bio-informatics
- OnThursday evening, 6 to 8 p.m., we offer a 2-hour evening course in the e-learning lab. These courses are not mandatory parts of the MICROBIAL ECOLOGY course. Signing-up is required, however, since there are only 6 computer work stations (MAC) available. Participants should have basic working skills using internet browsers, word processing programs (e.g. Microsoft Word or equivalent) and spread sheet calculation programs (e.g. Excel or equivalent).
- On Thursday, November 29, we offer an introductory course to practice the use of the Internet. Students who feel they need a refresher on how to use the Internet should participate. Please sign up during the introductory session on Monday morning, November 26.
- The courses can be repeated if there are more applicants than computer work stations
- All courses will take place in the computer lab of the e-learning center located on the first floor of the Carriage House, Zollikerstreet 115.
- COMPUTER COURSE 1 (November 29)
- a) Introduction to the Internet
- Searching on the Internet, search machines, making use of the links offered on the microeco homepage.
- b) Literature Searches
- Literature searches on data banks, libraries and journals. Search strategies and information processing.
- COMPUTER COURSE 2 (December 6)
- a) Genomic and proteomic data collections
- Molecular records of the biosphere: databases containing genome and protein sequences.
- Functional bioinformatics: genomics, proteomics.
- b) Phylogenetic tree building
- Biological databases for the study of microbial evolution: physiology, phylogeny, taxonomy.
- The three domains (kingdoms) of organisms: Bacteria, Archaea and Eukarya.
- Criteria for defining evolutionary relatedness: what distignuishes the three domains (kingdoms) of life ?
- Phylogenetic trees based on 16S-rRNA, backgrounds and construction.
- Environmental genomics, defining novel organisms
- COMPUTER COURSE 3 (December 13)
- a) Priciples for thermodynamic modelling of microbial reactions
- Application of a simple calculation model (Excel spread sheet).
- Thermodynamic laws and the calculation of free energies.
- Range of applicability of thermodynamic principles in microbial energetics.
- Free energies of reactions: terms, definitions and abbreviations.
- Application of thermodynamics in ecological processes:
- Direction and probability of reactions, exergonic and endergonic reactions,
- Alterations of DGr by microbially mediated processes,
- Influence of pH and temperature on DGr,
- Microbial activities which change the ion activity product and the solubility of minerals,
- Activities which alter redox conditions (Dpe).
- b) Examples
- Aerobic and anaerobic oxidation of ammonia.
- The missing link: ammonia-based photosynthesis.
- Acetogenic and sulfidogenic methanol utilization.
- Chemolithoautotrophic growth with reduced S-compounds & nitrate as electron acceptor: Thioploca sp.
- Interactions in anaerobic communities: a thermodynamic perspective.
- Syntrophobacter wolinii in association with hydrogenotrophs: predictions based on thermodynamics.
- Thermochemical energy yield from substrate oxidation with different oxidants.
- Anaerobic methane oxidation: a missing organism ?
- Growth efficiency of methanogens.
- Alteration of halogenated hydrocarbons through halorespiration.
- THE VIDEOS ARE AVAILABLE AT THE LIBRARY OF THE BOTANICAL INSTITUTE WHERE THEY MAY BE VIEWED INDIVIDUALLY DURING LIBRARY OPENING HOURS.
- Please ask for the headphones at the library office desk
- "Unseen Life on Earth" is an introduction to microbiology which gives biology students a unique opportunity to dynamically learn complex topics and enhance their understanding of the microbial world. The series is designed for students who have had introductory biology and chemistry coursework. The background information to the individual programs in the series may be found in the microbiology textbook (BBOM 9th ed.) and we are making reference to particular videos during the course.
- The video series consists of 12 half-hour programs that cover various aspects of microbiology. They contain much more information than we will ever cover during the lectures; and they might stimulate you to become informed about the many facets of the most exciting fields of microbiology.
- Contents of the 12 series:
- MICROBIAL CELL BIOLOGY
- 1. The Microbial Universe
- 2. The Unity of Living Systems
- 3. Metabolism
- Microbial Cell Biology
- 1. The Microbial Universe
- An overview of the world of microorganisms; how a group of scientists identified a previously unknown microbe; basic laboratory techniques and microbial genetic codes.
- 2. The Unity of Living Systems
- Similiarities among procaryotic and eukaryotic organisms; diverse patterns of cell assembly; the relationship of cell types to non-cell entities such as viruses.
- 3. Metabolism
- Production of energy and transformation of the environment by microbial metabolism; construction and use of molecules by microorganisms.
- Microbial Genetics
- 4. Reading the Code of Life
- The central role of DNA in carrying and replicating information; mutations; microbial regulation of genetic products to conserve energy and adapt to new environments.
- 5. Genetic Transfer
- Genetic diversity through horizontal gene transfer; conjugation, transformation and transduction; exploitation of these processes through recombinant DNA.
- Integrating Themes
- 6. Microbial Evolution
- New theories of evolution and the relationships among organisms; development of genetic techniques using molecular sequences to trace phylogenetic relationships of microbial life.
- 7. Microbial Diversity
- Relationships between bacteria, archaea, and eukaryote branches of life; impact of diversity in natural habitats and the laboratory.
- Microorganisms in the Environment
- 8. Microbial Ecology
- Microorganisms as processors of oxygen, nutrients and waste; important environments dominated by microbes; the essential role of microbes in human life.
- 9. Microbial Control
- Controlling microbes in special situations, e.g., food safety and hospitals; strategies used in microbial control.
- Microorganisms and Human Life
- 10. Microbial Interactions
- Symbiotic relationships among microbes; relationships between microbes and higher organisms.
- 11. Human Defenses
- Strategies used by invading microbial pathogens; exploration of the coordinated human defense system
- through visual analogy, animation and examples of specific diseases.
- 12. Microbes and Human Diseases
- Microbial and human encounters that result in disease; factors in disease outbreaks; current efforts to track infectious diseases and control disease worldwide.
- Objectives and Scope
- Students of the Microbial Ecology Course 2001 will present their course research results and advisors of the course will briefly introduce the kind of research they are themselves involved in. The contributions will provide a better understanding of the groups research topics and the results obtained during the course.
- We hope that these presentations will inspire interest in research with ecological perspectives; research which in turn might provide new solutions to current environmental problems. The contributions will also broaden the often narrow focus of the every-day research work and offer students and established investigators an ecological approach to answering environmental and geobiological questions.
- Discussion after each presentation; the times given in the program include the discussion period. Sessions are chaired by the course participants who will introduce the speakers, keep the time schedule and assure the proper functioning of the room infrastructure.
- PROGRAM
08.30 |
Kurt Hanselmann |
Introduction |
08.40 |
Guest Lecture by Janine Kessi |
Selenite resistance in purple non-sulfur bacteria: Physiological and biochemical aspects |
09.30 |
INTERMISSION |
|
Session 1: |
Interactions of cyanogenic microbes with metals |
|
chaired by Naim Matasci and Hans-Caspar Hürlimann |
||
10.00 |
Christine Kägi and Tobias Rosenberger |
Mobilization of metals from metal-containing solids using cyanogenic microorganisms |
10.20 |
Marion Stagars |
How cyanogenic microorganisms recycle electronic waste |
Session 2: |
Microbes in metal-corroding biofilms |
|
chaired by Kati Seidl and Sebastian Zurbriggen |
||
10.45 |
Otto Martin Willy and Fabrizio Gorla |
Genotypic identification of biofilm-forming bacteria on stainless steel: tracking the stainless steel stainers |
11.05 |
Christine Lehmann |
Tracing microbial activities in sediments of Lake Cadagno |
11.30 |
LUNCH |
|
Session 3: |
Reserve polymers in Bacillus megaterium |
|
chaired by Otto Martin Willy and Fabrizio Gorla |
||
13.00 |
Nadja Tobler and Stephan Bänziger |
Formation of storage polymers in Bacillus megaterium |
13.20 |
Helmut Brandl |
Biodegradation of plastics |
Session 4: |
Endolithic microbes in dolomite rocks |
|
chaired by Christine Kägi and Tobias Rosenberger |
||
13.45 |
Naim Matasci and Hans-Caspar Hürlimann |
How many of the eight 16S rRNA gene sequences found in Piora Dolomite represent new organisms ? |
14.05 |
Thomas Horath |
Endolithic prokaryotes from Piora Dolomite: Isolation and sequencing of bacterial 16S rRNA gene fragements |
14.25 |
INTERMISSION |
|
Session 5: |
Biofilm-formimg bacterial communities in high-mountain lakes |
|
chaired by Nadja Tobler and Stefan Bänziger |
||
14.45 |
Kati Seidl and Sebastian Zurbriggen |
Molecular analysis of biofilm-formimg bacteria from Jöri lake XIII |
15.05 |
Munti Yuhana |
Assessing the diversity of psychrophilic bacteria in low-nutrient aquatic habitats |
15.30 |
Kurt Hanselmann |
Summary |
15.45 |
End of Minisymposium |
|
16.00 |
Christmas Party |
Small Lecture Hall |
- Here, we summarize how a manuscript should be structured, what the different sections should contain and how the literature should be cited. The course reports should be structured accordingly. The outline below can be downloaded as a pdf file file.
- 1. Title page: It contains the title (only proper nouns or acronyms are capitalized), lists authorship, address of institution, key words, running title, corresponding author's address, phone, fax and e-mail.
- 2. Abstract: Begin the abstract with your most significant finding. The abstract summarizes the paper's intent, methods, results, and the significance of the findings. It is of prime importance since it is used by the reader for guidance about the subject, how it is treated and how the significans of the results can be valued. The quality and readability of the abstract will determine how much attention a reader will devote to the rest of the report. The abstract , therefore, summarize the contents accurately and be understandable independent of the text of the rest of the manuscript. It should contain no equations, figures or illustrations and it should be brief.
- 3. Executive Summary: This will be one of the last sections written. It should be able to stand by itself, be concise and right to the point. Like the abstract, the executive summary summarizes the content and contains brief statements which serve as: introduction, objectives, methodlogy, main results, conclusions and recommendations. (Scientific papers submitted for publication do not contain executive summaries.)
- 4. Introduction: It should make the "story" of your work clear and interesting to the reader. An introduction contains a section on the significance of the subject matter, reviewing the most pertinent literature as background information and introducing the methodologicial approach. It provides the reader with the information necesssary to comprehend the topic and to understand how and why you formulated the problem the way you did. It briefly states subject, goals, purposes, importance, methods, audience and anticipated form of the results. The last paragraph should be a definition of the question addressed and a description of how your study attempts to answer that question.
- 5. Procedures, methods, materials: This chapter, one of the most important of the report, must present your methods of analysis in a way that will allow the reader to replicate your efforts under similar conditions. The procedure or methodology is the general, conceptual flow chart of the problem solving approach. You must provide a rationale for all procedures you elected to use.
- In conducting your work you may have had to modify the procedures you first intended to use. Explain what modifications you made and why.
- 6. Results: This chapter contains the presentation of the finding of your investigation. When appropriate, summarize your findings in tables and graphs. Tables and graphs should supplement not simply duplicate the text. In the text you should tell the reader what to look for in the table or graph. Do not use a table or graph to take the place of text (e.g. do not say: results see table..).
- Each table and graph should be numbered (Figure 1) and have a title. Readers should be able to understand the table or graph without further explanation. In the text, refer to tables and graphs by their number.
- 7. Discussion: This chapter contains an analysis of your results with reference to the questions you originally addressed. Do not neglect to analyse data which does not support your original hypothesis. As a researcher you have an obligation to report and analyse all relevant data. Finding lack of support for a theory or stating that the evidence is inconclusive is as important as finding supporting evidence.
- Be sure that all your conclusions are consistent with and follow from an analysis of your data. Everything in this section must grow logically from what you have presented in earlier sections. In closing you may want to mention new directions, questions and experiments which emerge from your results.
- Conclude your discussion with a summary of your most important findings and discoveries.
- 8. Appendices: They might contain information which is not necessarily needed to understand the results, but which is difficult to compile again.
- 9. References: You are responsible for supplying complete bibliographic information but do not mention less relevant references. All references cited in the text appear in the References, and vice versa.
- Literature citations in the text are given in chronological followed by alphabetical order and are formatted like these examples: "Campbell (1983, 1987b )" or "(Smith et al. 1984; Karl and Craven 1988; Korobi 1997, 1998)."
- The References are listed in alphabetical, then chronological order. Each citation is complete, according to the following examples (since these rules might vary between journals, one should consult the journals instructions for authors):
- Article: Fenchel, T. 1986. Protozoan filter feeding. Prog. Protistol. 1: 65-113.
- Book: Stumm, W. and J. Morgan. 1981. Aquatic chemistry, 2nd ed. Wiley.
- Chapter: Codispoti, L. A. 1983. Nitrogen in upwelling systems, p. 513-564. In E. J. Carpenter and G. Capone [eds.], Nitrogen in the marine environment. Academic Press.
- Spelling of author(s) name(s) and years of publication need to be double-checked before submission. Citations of personal communications, manuscripts in preparaton, unpublished thesis, and other less easily accessible sources are kept to a minimum in the References. All entries need to be verified against original sources; check especially journal titles, accents, and spelling in languages other than English.
- 10. Acknowledgements: In this section one specifically acknowledges the assistance or involvement of particular people and one mentions the granting agencies and the project grants which supported the study financially.
- 11. Tables and Figures:
- All figures and tables are cited in the text and numbered in the order that they appear.
- Figures:
- Graph axes on all figures are labeled using a single font (Times Roman preferred) and are sized so that they will be similar after final reduction.
- The labels are at least 1/8 inch (0.71 cm) from all lines in the figure.
- Lines and symbols are of proper thickness and size to be successfully reduced.
- The final height of all type (after reduction) is at least 8 points (0.1 inch, 2.8 mm).
- Scale bars are on the figure, NOT in the figure legend.
- Figures are numbered in Arabic numerals in the order of their citation in the text.
- Figure legends (one paragraph per figure) explain all panels (A, B, ...a, b, c,...) of a figure. Symbols used in the figure (e.g., circles, squares, ...) are explained in a key on the figure itself rather than in the legend.
- The maximum size for a figure is 18.4x23.2 cm.
- For figures taken from published work one needs copyright permision and the figures need to be acknowledged.
- Maps include reference to latitude and longitude and are bounded by a fine border.
- Tables: Contain a title and explanatory legends if necessary. Omit fancy table formats.
- 12. Abbreviations and acronyms: Abbreviations are used sparingly. Periods are used after all abbreviations except for metric measures, compass directions, and time (min, h, d, yr). All acronyms are spelled out upon first use. When dates are given, three-letter month abbreviations are used (Jan, Feb, Nov, ...), except for months with four letters, which are spelled out in full (June, July).
- 13. Selecting a journal: Chose a journal which publishes original articles about aspects of your research. The journal should have a broad readership and be regarded highly by the research community.
- Submissions are judged mainly on the originality of their data, interpretations, and ideas, and on the degree to which these can be generalized beyond the particular experiments reported on. In microbial ecology, laboratory studies, modeling, and methodological studies must demonstrate relevance to natural environments. Manuscripts are edited for brevity and clarity. All submissions to a journal must be formatted according to the specifications outlined in the journal's "instructions for manuscripts" or "instructions to authors".
- Editors place high priority on the susceptibility of results to independent verification. If a paper contains results obtained using a strain of microbe isolated from nature and not available yet from a public collection, the author is expected to honor in a reasonable time all requests for samples of the culture or to deposit specimens in a public culture collection.
- Authors reporting on results that includes new nucleotide or amino acid sequences must submit the sequence information to a publicly accessible archive (e.g., GenBank or EMBL) and provide the accession number(s) in the part of the manuscript that describes the research methods. Manuscripts that use existing sequences from GenBank/EMBL must cite accession numbers and original literature references to them (if they exist).
- 14. Report / Manuscript Checklist:
- - The General style: concise
- - Title page: complete
- - Abstract: brief
- - (Executive summary: informative)
- - Introduction: concise
- - Methods: precise
- - Results: clearly structured
- - Discussion: logical
- - References: selective
- - Tables: inclusive
- - Figures: graphically appealing
- - Appendices: helpful and informative
- - Abbreviations and acronyms: complete
- - Acknowledgements: polite
- 15. Using Microsoft Correction Tools
- The student reports will become available in January as pdf files
- Project No. 1:
- Title: Phenotypic and genotypic characterization of metal corroding biofilms
- Investigators: Fabrizio Gorla and Otto-Martin Willy
- Advisor: Christine Lehmann
- Project No. 2:
- Title: Molecular anlaysis of biofilm-forming bacteria from cold, oligotrophic habitats
- Investigators: Kati Seidl and Sebastian Zurbriggen
- Advisor: Munti Yuhana
- Project No. 3:
- Title: Endolithic microbial communities in dolomite rocks
- Investigators: Naim Matasci and Hans-Caspar Hürlimann
- Advisor: Thomas Horath
- Project No. 4:
- Title: Mobilization of metals from metal-containing solids using cyanogenic microorganisms
- Investigators: Christine Kägi and Tobias Rosenberger
- Advisor: Marion Stagars
- Project No. 5:
- Title: Survival strategies of microorganisms: The formation of reserve polymers in Bacillus megaterium
- Investigators: Stefan Bänziger and Nadja Tobler
- Advisor: Helmut Brandl