Biology 528 Microbial Ecology

 

Instructor: David Lipson

Office: PS241C (inside PS241B Lab, inside PS241 hallway)

Phone: (619) 594-4460

Email: dlipson@sciences.sdsu.edu

Office hours: TBA.

 

Prerequisites: upper division standing in the Biology or Microbiology Major, or graduate standing in a biological science.  Required courses: Biology 352, 354.  Recommended courses: Biology 350, 366

 

Grading criteria:

Lecture (midterms and final exam)                             300 points

Laboratory:                                                                                    150 points

 

Lab point breakdown:

Attendance/participation                                   40

Lab notebook/handouts                                      40

Group projects/oral presentation                 25

Research paper                                                         45

 

 

Examinations:

                  The three midterm and final examinations will each be worth 100 points, and will include short answer, multiple choice, and essay questions.  Students will be allowed to drop one exam grade.  The final exam will be cumulative.  No make-up exams will be given, but you may miss any one exam, including the final.

 

Laboratory

                  A three hour lab section is scheduled each week.  Students will use enrichment and dilution cultures to isolate microorganisms from various aquatic and terrestrial environments.  Microscopic and biochemical methods will be used to characterize these isolates and the microbial communities, as a whole.  Molecular techniques will be used to identify and/or enumerate these microbes.  Generally speaking, you will have fun. 

 

Attendence is required.  Not only does attendance and class participation account for almost 10% of the grade, but each class missed beyond the second absence will result in the lowering of the final grade by a letter grade. 

 

Please note: cleaning up after yourself is required, and counts in your participation grade.

 

Laboratory notebooks: Each student will keep a lab notebook, in which all methods and results are recorded during each lab session.  The goal is to produce a complete and accurate record of your activities, not necessarily an orderly, easy-to-read document. So, DO NOT re-copy your daily scribbles, just turn in the original, stains, mistakes, and all.

 

Group projects:

                  Students will work in groups of three or four on a simple microbial ecology study.  The group will prepare a 15-20 minute oral presentation, in which student will speak for about 5 minutes. 

 

Research paper:

Each individual student will prepare an original written report reviewing a topic in microbial ecology, preferably related to the group project.  The most successful and interesting papers do the following: (1) focus on a central thesis or question, (2) synthesize scientific work to support your thesis or answer your question. 

 

Formatting issues: 4-5 pages, not including references, 12-point font, double-spaced.  Web pages are generally not to be used as references.  References should generally be from peer-reviewed scientific journals, only.  The references may include published reviews, however, your papers should refer to at least 2 studies from the primary literature.  Students will be allowed an opportunity to revise thier drafts after receiving feedback from the instructor.

 

A note about plagiarism: DON”T DO IT!  Your written work must be original, and all sources must be cited properly.  See www.sa.sdsu.edu/htc/Plagiarism.pdf, and http://its.sdsu.edu/turnitin/pdf/Plagiarism_AcadSen.pdf for more information on definitions of plagiarism, how to avoid it, and what terrible things can happen to you if you do it.

 

Text for lecture:

Required: Atlas and Bartha, Microbial Ecology: Fundamentals and Applications, 4th Ed.

 

(Supplemental reading from other sources will also be assigned.)

 

Text for Lab:

Handouts will be provided as needed.

 

Supporting materials will generally be available on the class Blackboard site.

 

Learning Objectives for Microbial Ecology

 

After taking this course, students should be able to:

 

Describe the diversity of all microbial life in terms of the three domains, knowing major characteristics of each.

 

Understand the importance of microbes in the early evolution of the earth and the atmosphere

 

Relate metabolic reactions carried out by microbes to global biogeochemical cycling of elements: understand these reactions in terms of chemistry, microbial physiology, and the importance in the environment.

 

Appreciate the vast genetic and physiological diversity of microbes, and classify microbes into basic categories based on their metabolic fueling reactions (e.g. chemoheterotrophy, photoautotrophy, etc.)

 

Define the various forms of interactions (competition, predation, mutualism, etc.) among and between microbial populations

 

Understand the factors that regulate interactions between microbes

 

Understand the importance of these interactions in structuring microbial communities

 

Define horizontal gene transfer, and explain its implications for microbial ecology and evolution

 

Relate general principles of microbial ecology to role of microbes in human disease

 

Understand how the specific environmental properties of soils, oceans and biofilms affect microbial communities therein.

 

Appreciate the extraordinary resistance of microbes to environmental stress, know examples of stress-resistant microbial species, and explain the strategies employed by microbes to cope with various environmental stresses.

 

Describe how microbes are useful in biotechnological and environmental applications such as sewage treatment, bioremediation, etc.  Relate the physiology of microbes to their role in these processes.