Microbial Ecology - Biology 4446/5446 (3-4)

                                                                     Spring 2004

 

Instructor: Dr. R.J.C. McLean, Dept. Biology, Texas State University

Office: SCI 364, office hours M-Th 8:15 – 9:15am, (512)245-3365 phone, (512)245-8713 fax, email: McLean@txstate.edu

 

Prerequisite: Bio 2400/3440, courses in biochemistry and/or ecology would be helpful

 

Text: R.M. Maier, I.L. Pepper, and C.P. Gerba 2000. Environmental Microbiology, Academic Press, San Diego

 

Other reference materials: (Old text) R.M. Atlas and R. Bartha. Microbial Ecology, Fundamentals and Applications, 4th. ed., 1997. Benjamin/Cummings Publishing Co. Inc., Menlo Park CA. Scientific journals including: Applied and Environmental Microbiology, Advances in Microbial Ecology, Environmental Microbiology, FEMS Microbiology Ecology, Microbial Ecology, Microbiology and Molecular Biology Reviews, Annual Review of Microbiology

 

Catalog Description: This course will illustrate the wide variety of bacteria in nature, their interactions with other organisms and environments, and their roles in global cycling of elements such as carbon, nitrogen, and sulfur. The laboratories involve a semester-long project dealing with

 

Course grading:

                                    Mid term 1       (Feb 24)           10 %

                                    Mid term 2       (April 8)           15 %

                                    Laboratory                               50 %

                                    Final take home exam               25 % (Due at 5:00 pm May 11, 2004)

                                   

The laboratory grade (50 % of course grade) is broken down as follows:

 

Laboratory quiz based on class experiments                                          10 %

            (last week of classes)

Major laboratory project (aquifer/terrestrial microbiology)                     40 %

            (research proposal 5%, oral presentation 10%, effort 5%, report 20%)

 

5446 students will be required to submit a budget containing detailed costs of all supplies at the time of their proposal.

 

As a guide, I use the following grading scheme: [A 90-100%, B 80-89%, C 70-79%, D 60-69%, F < 60%].  In situations where a student's grade is within 2% of the cutoff (e.g. 88-92), the final grade will be based on both the grade achieved, and the lab grade for effort and participation. Grade disputes must be given to Dr. McLean in writing within one week after a test is returned. This will result in the entire test being regraded and the higher or lower grade being used.

 

** Students must achieve a passing grade (at least 60%) in both the lecture (mid-term 1, mid-term 2 and final) and laboratory portions of the course in order to pass. Students dropping the course before March 8 will get an automatic W. After March 8, students must have a passing grade in order to drop with a grade of W, otherwise a grade of F will be assigned.

 

Subjects Covered:

 

A. Overview of Environmental Microbiology

            Methods employed

            Microbial Communities

            Physical and Chemical Influences

            Biological interactions

            Biogeochemical cycles

 

B. Water Microbiology and Aquatic Environments

           

C. Terrestrial and Subsurface Microbiology

 

D. Extreme Environments and Life on other worlds (exobiology)

 

Laboratory Topics:

(Many of these exercises will run over several weeks)

 

1)         Direct examination of microbial populations in the environment (bright field, dark field, fluorescence microscopy)

 

2)         In situ determination of microbial metabolism in the environment (CH4 production by sediment microorganisms)

 

3)         Enrichment culturing for selected groups of microorganisms (e.g. autotrophs, heterotrophs, aerobes, and anaerobes)

 

4)         Microcosm and mesocosm studies i.e. modelling an environment

 

5)                  Microbial Evolution (spread of antibiotic resistance in a microbial population)

 

6)                  Coliform testing

 

7)                  Major Laboratory Project.

 

            The major laboratory project will consist of students investigating some aspect of microbial ecology. In many cases, students may elect to examine the Edwards Aquifer, or alternatively another project with approval of Dr. McLean. The fascinating aspect of most of these studies is that they will represent original research. Students will work on these projects in pairs. Some possible projects include:

 

1)                  Phenotypic characterization of mutants in Myxococcus xanthus biofilms.

 

2)                  Characterization of an unidentified new aquifer isolate.

 

3)                  Estimating decomposition rates of various materials (e.g. leaves, insects, gasoline) by aquifer microorganisms.

 

4)                  Influence of artificially introduced wastewater on the aquifer microflora (fate of introduced E. coli or other organism).

 

5)                  Do aquifer bacteria assist in mineral formation or dissolution.

 

6)                  Influence of bacterial biofilms on leaf colonization by macroinvertebrates such as snails.

 

7)                  Chemotaxis response of aquifer isolates to acyl homoserine lactones (AHLs).

 

8)                  Enhancing biofilm formation in E. coli UTI strains for genomic investigation.

 

9)                  AHL antagonists in plants or invertebrates.

 

10)              Influence of organic or inorganic pollutant on aquifer bacteria - can also involve experimental estimation of bioremediation potential of aquifer bacteria.

 

11)              Isolation of unusual microorganisms (e.g. anaerobes, methylotrophs).

 

12)              Your own idea.

 

            Students working in pairs will select their topic and get approval from Dr. McLean by the end of the first week of classes. During the second week of classes (lecture and lab), students will turn in 2 page typed research proposals and present (5 min oral presentations) research proposals consisting of: problem, background, proposed strategy to be used for experimentation, data analysis techniques, and anticipated findings. Participation in discussion by all members of class is required.

 

            The final report for this project will be presented both as an oral report (10 minute presentation and 5 minute question) and as a written scientific paper (using the format for Applied and Environmental Microbiology available at http://aem.asm.org/misc/ifora.shtml). The paper is due the last day of classes (5/3/04) at 5:00 pm.