BIOLOGY 5801 FALL 2016
Dr. Randall E. Hicks Swenson Science Building 153C 726-8438 Email: rhicks@d.umn.edu
Tuesday 1:00 - 2:00 pm Thursday 1:00 - 2:00 pm or By Appointment
Tuesday, Thursday 11:00 - 11:50 am SSB 202
http://www.d.umn.edu/~rhicks/microeco/index.html
You should read chapters in the textbook to supplement the course lectures, which will be helpful on the course exams. In addition, you are required to read papers that will be discussed in class.
Required Textbook:
Kirchman, D. L. 2012. Processes in Microbial Ecology. Oxford University Press, Inc., New York, NY.
Required Journal Articles:
Each student is required to read papers that will be discussed in class.
Purcell, E. M. 1976. Life at low Reynolds number. Am. J. Phys.45:3-11. [pdf]
Four other papers from the primary literature: To be announced
Microbial Ecology Reading List (supplemental) :
Students can refer to journal articles in the Microbial Ecology Reading List to find more information on a topic introduced in class. These papers will give you a greater depth of understanding about many topics that may help you give better answers on exam questions.
Supplemental Books (supplemental) :
[Some of these are available from your instructor.]
Madigan, M. T., and J. M. Martinko. 2010. Brock Biology of Microorganisms, 13th Ed., Pearson Benjamin Cummings, San Francisco, CA. [Study Aid; 14th Edition that came out in Jan. 2104 is OK too].
Atlas, R. M., and R. Bartha. 1998. Microbial Ecology, 4th Ed. Benjamin/Cummings Publishing Co., Inc. Menlo Park, CA. 694 p.
Burdlage, R. S., R. Atlas, D. Stahl, G. Geesey, and G. Saylor (eds.). 1998. Techniques in Microbial Ecology. Oxford University Press, New York.
Gerhardt, P., R. G. E. Murray, W. A. Wood, and N. R. Krieg (eds.). 1994. Methods for General and Molecular Bacteriology. American Society for Microbiology. Washington, DC.
Guerrero, R., and C. Pedrós-Alió (eds). 1993. Trends in Microbial Ecology. Proceedings of the Sixth International Symposium on Microbial Ecology. Spanish Society for Microbiology. Barcelona, Spain.
Hurst, C. J., G. R. Knudsen, M. J. McInernney, L. D. Stetzenback, and M. V. Walter (eds.). 1997. Manual of Environmental Microbiology. American Society for Microbiology. Washington, DC.
Kemp, P. F., B. F. Sherr, B. Sherr, and J. J. Cole (eds.). 1993. Handbook of Methods in Aquatic Microbial Ecology. Lewis Publishers. Ann Arbor, MI.
Kirchman, D. L. (ed.). 2000. Microbial Ecology of the Oceans. John Wiley & Sons, Inc. New York, NY.
Levin, M. A., R. J. Siedler, M. Rogul (eds.). 1992. Microbial Ecology: Principles, Methods, and Applications. McGraw-Hill, Inc. New York, NY. 945 p.
Lynch, J. M., and N. J. Poole (eds.). 1979. Microbial Ecology - A Conceptual Approach. Blackwell Scientific Publications. Oxford, England.
Martins, M. T., et al. 1997. Progress in Microbial Ecology. Proceedings of the Seventh International Symposium on Microbial Ecology. Brazilian Society for Microbiology. Sao Paulo, Brazil.
McAuthur, J. V. 2006. Microbial Ecology, An Evolutionary Approach. Elsevier, Burlington, MA. 416 p.
Microbial Ecology Journals in UMD Library or Online (supplemental) :
Applied and Environmental Microbiology, Microbial Ecology, Environmental Microbiology, Limnology and Oceanography, Annual Review of Microbiology, Environmental Science and Technology, Geochim et Cosmochim Acta, Systematic and Applied Microbiology
The UMD Bulletin describes Biol 5801 as:
Microorganisms in natural environments: diversity, distribution, energetics, and growth of heterotrophic and autotrophic microbes in oxic and anoxic habitats. Roles of microbial populations and communities in biogeochemical cycling, ecosystem functioning, landscapes, and industrial, agricultural, and environmental applications.
In addition, this course strives to meet these goals:
The course will include lectures, in-class discussions, and participation in a team project. I will be happy to answer your questions about lectures, discussions, your team project, or any topic in microbial ecology. You may have to come to me for help because instructors are not always able to determine during lectures or discussions if someone is confused or having difficulty understanding a topic or concept. Please seek me out if this happens to you. I promise to be helpful and patient in answering your questions and assisting you in resolving your problems or fears.
Course grades will be assigned at the end of the semester based on the total points you accumulate. I will be glad to discuss your potential grade with you anytime during the course. Grading will be based on the following criteria:
Criteria Points Percentage of Grade Midterm Examination 100 25% Final Examination 100 25% Team Project 160 40% Participation 40 10% Examinations:
There are two examinations. They will test your knowledge of basic concepts in microbial ecology, current techniques in the field, how to design and evaluate experiments, and interpret/evaluate data. These exams will require thoughtful replies developed from knowledge you gained from lectures, textbook and required journal articles, in-class discussions, and supplemental reading. The Midterm Examination will be an in-class examination composed primarily of multiple choice and short answer questions. The Final Examination is a take-home exam and can be comprehensive because earlier material is part of the conceptual framework to understand the last topics covered. It will also be composed of multiple choice and short answer questions. Your answers will be limited in length and therefore require concise responses.
Team Project:
Teams of four students will each explore a specific topic in microbial ecology in-depth during the semester. Members of each team will be assigned by the instructor during the third week of classes based on general interests expressed by students in the class. Your group's task is to identify and research a very narrow area of this general topic in much greater depth. Early in the semester, teams will have one class period to meet, discuss their common interest in the general topic they were assigned, and determine when the group will meet again. Your team should use this time wisely and expect to meet at least weekly thereafter outside regular class periods.
The grade your tream receives for this assignment will be based on three things: (1) the scientific journal article that your team selects for the class to read and discuss, (2) development of a short PowerPoint lecture on your specific topic, and (3) leadership of a panel discussion that stimulates classroom discussion about the paper and presentation.
After researching a narrow topic in microbial ecology your group should agree upon a scientific journal article (from the primary literature) that the entire class will read and discuss. Remember that good papers to discuss are ones that propose a new concept, test a therory, or that raise more questions than they answer. Descriptive or review papers are not good papers for discussion. Your team should provide this paper for the class at least two weeks before your presentation date.
Each team will research their narrow topic in great depth, in much greater depth than the single paper that the entire class will read, and will have one class period to present a lecture and lead a discussion on this topic. All teams will develop 30-minute PowerPoint lectures that will be presented in class, which thoroughly cover their narrow topic and presens data (e.g., figures and tables) from a variety of research papers to support points being made. Presentations based solely on textbooks and/or information from the internet are not acceptable. These presentations should use data, figures, and information from scientific journal articles and cite where this information was obtained. A reference section should appear as the last slide in your team's presentation and be quite lengthy. References cited MUST follow the format of the journal, Applied and Environmental Microbiology. Prior to their presentation, each team will provide the instructor an electronic copy of their PowerPoint presentation (via email or CD).
Timing is critical. A short, superficial presentation is unacceptable and an extremely long presentation will be downgraded accordingly. Although all team members are expected to contribute to the construction of the PowerPoint presentation, lectures with multiple speakers are usually disjoint and distracting. So, only one person from your team will present the PowerPoint lecture - select the best speaker in your team and help them practice the talk. Presentations that use multiple speakers will be not improve your team's grade but instead will hurt it. Keep your presentation focused on the topic - microorganisms and their ecology. Be careful to fact check all information in the presentation - do not give misinformation to the audience. Presentations that merely describe or summarize the paper to be discussed by the entire class are not sufficient for this assignment. Presentations on broad topics are too superficial for this advanced class and will be downgraded accordingly.
All team members will participate in the panel discussion (about 20 minutes long). Your team's goals should be to stimulate classroom discussion about the paper you selected for the class to read, and to anwer questions that are raised during the discussion based on the additional research your team completed on this topic. The instructor will not actively participate in this discussion but will merely observe and evaluate.
Great weight is placed on this assignment (see grading scheme above) and so these presentations should be well researched and constructed.
Participation:
Participation is based on attendance of lectures and participation in class discussions and panel discussions. Class discussions will focus on journal articles selected by student teams. Read the papers before attending class, come prepared with questions or comments for the discussion, and expect to contribute!
It is the policy and practice of the University of Minnesota Duluth to create inclusive learning environments for all students, including students with disabilities. If there are aspects of this course that result in barriers to your inclusion or your ability to meet course requirements – such as time limited exams, inaccessible web content, or the use of non-captioned videos – please notify the instructor as soon as possible. You are also encouraged to contact the Office of Disability Resources to discuss and arrange reasonable accommodations. Please call 218-726-6130 or visit the DR website at www.d.umn.edu/access for more information.
The University of Minnesota is committed to the policy that all of its students shall have equal educational opportunities. The University expressly forbids discrimination on the basis of race, color, creed, national origin, or marital status. If you believe that your Biology instructor has not followed this policy, then you are invited to bring this to the attention of the Biology Department Head (Swenson Science Bldg. 207, 726-7271) or the Associate Dean of the College of Science & Engineering (140 Engineering Bldg., 726-7585). Your conference will be kept confidential.
Academic dishonesty tarnishes UMD's reputation and discredits the accomplishments of students. As a result, academic dishonesty is regarded as a serious offense by all members of the academic community. In keeping with this ideal, this course will adhere to UMD's Student Academic Integrity Policy, which can be found at http://www.d.umn.edu/assl/conduct/integrity. This policy sanctions students engaging in academic dishonesty with penalties up to and including expulsion from the university for repeat offenders.
The instructor will enforce and students are expected to follow the University's Student Conduct Code (http://www.d.umn.edu/assl/conduct/code). Appropriate classroom conduct promotes an environment of academic achievement and integrity. Disruptive classroom behavior that substantially or repeatedly interrupts either the instructor's ability to teach, or student learning, is prohibited.
Disruptive behavior includes inappropriate use of technology in the classroom. Examples include ringing cell phones, text-messaging, watching videos, playing computer games, doing email, or surfing the Internet on your computer instead of note-taking or other instructor-sanctioned activities.