Instructor:  Brent C. Christner
Office:  282b Life Sciences Building
Phone:  (225) 578-1734
Email:  xner@lsu.edu
Office hours:  W 11:00–12:00 or by appointment
Course website:  http://www.brent.xner.net/BIOL4800/index.htm

Prerequisites:
BIOL 2051 – General Microbiology
BIOL 2153 – Principles of Genetics

Course objective:
The goal of this course is to provide a framework for understanding the relationship between and biogeochemical role of microorganisms in natural communities.  Course topics are structured to demonstrate the linkages between microbial ecology, diversity, and evolution. The specific objectives of this course are to expose students to the following topics:
·   Role of microbial life in the evolution and ecology of the biosphere.
·   Application of classical ecological concepts to microbial populations and communities.
·   Underlying principles that drive microbial population structure in the environment.
·   Community function and dynamics at both the molecular and the organismal level.
·   Abiotic and biotic interactions within microbial communities.
·   Ecophysiology and thermodynamic constraints on microbial community structure.
·   Molecular and genomic tools for understanding the physiology and ecology of microbial communities.
·   Microbial metabolism and biogeochemical cycling.

Text:
Strongly Recommend: Madigan, M.T., J.M. Martinko, P.V. Dunlap, and D.P. Clark. 2009. Brock: Biology of Microorganisms (12th or current eds.), Prentice Hall. Amazon – 12^th ed. (new - $170; used - $143 and up); 11^th ed. (new - $135; used - $19 and up).
Tepidly Recommend: Atlas, R.M., and R. Bartha. 1997. Microbial Ecology: Fundamentals and Applications, Benjamin Cummings.  Amazon (new - $137; used - $31 and up).

Scientific literature:
Readings from the text will be supplemented with scientific research papers and reviews that will be available on the course website (http://www.brent.xner.net/BIOL4800/index.htm).  For many students, these papers will be their first exposure to scientific literature.  Reading a scientific paper is not like reading a text book.  One goal of this course is to develop your ability to digest the content of and critically evaluate scientific literature.  On two occasions during the semester (11 September and 18 November), the class period will be dedicated to open discussions of current scientific literature covering “hot topics” in microbial ecology.  Student participation in these discussion sessions will be graded.

Grading:
Exams: There will be 2 exams.  Regular exams consist of multiple choice (60%), short answer (30%), and essay (10%) questions. If a student misses the mid-term exam for any reason, there will be one opportunity to makeup the exam at the end of the course.  The makeup exam will cover the same material but will be in essay format.  There will be no early or late finals administered.  The only exception is if a student has 3 or more final exams scheduled in 24 hours and a request is submitted to the Office of the University Registrar (http://appl003.lsu.edu/slas/registrar.nsf/index) by the specified university deadline.

Research paper:  A research paper is required for this course.  Papers are to be written in the style of a published minireview (e.g., Applied and Environmental Microbiology).  Paper length should be 10 double-spaced, 12-pt Times New Roman pages not counting illustrations and citations (15 pages for graduate students).  You are encouraged to explore topics in microbial ecology not covered in the lecture or assigned readings.  Each student must prepare an outline and meet with the instructor prior to final approval of a research paper topic. The deadline for submitting a research paper topic and outline is 9 October.  Submit a hard copy of your paper to me in class on 13 November.  DO NOT place your paper in my mailbox or under the door of my office.  In addition to the hard copy, you must also submit an electronic version of your paper.  Email this file to xner@lsu.edu with the file named using your first initial and last name in the file name (e.g. BChristner_BIO4800ResPaper.doc). The penalty for late turn in of a research paper is deduction of 10 percentage points per day.  See the research paper handout for specific directions on content and requirements.

Oral presentation: All students will present their paper topics during one of the final class sessions.  Each presentation should be 12 minutes in length, allowing 3 minutes for questions.  The deliverables are the oral presentation and a hard copy of your slides for the instructor and class.  PowerPoint presentations are fine but not required.  Students are responsible for all material covered in these talks.

Class participation:  Student participation in class discussions will be graded.  Attendance may affect your participation grade.

Literature summary:  A 250-word literature summary is required at the beginning of class on 11 September.  In your own words, summarize one of the assigned scientific readings for this date (see “Course Calendar”) and turn in a hard copy of this document at the beginning of class.  Late assignments will not be accepted.

Problem set:  There will be a problem set handed out during the semester. You are not permitted to collaborate with other students on the problem set.  The problem set is due on 4 November at the beginning of the lecture because the answers will be reviewed during that lecture.  Late problem sets will not be accepted.

Additional requirements for graduate credit: Graduate student exams will be different (multiple choice 40%, short answer 30%, and essay 30%) and will be graded on different standards from those designed for undergraduate students.  Graduate students are also required to submit a more substantial 15 page research paper.  As with exams, graduate student research papers and oral presentations will be evaluated separately from the rest of the class.  Grades for graduate students will be straight scale, meaning there will be NO adjustment of the final grade.  To obtain a passing grade (i.e., C or higher), graduate students must accrue at least 70% of the possible points in the course.

Other course information:
Email and internet access are required for the course.  Students should check the course site and read their email regularly.

Lecture slides:  The instructor will supply a hard copy of the lecture slides for each class.  An electronic copy (pdf version) of these notes will be made available on the course website (http://www.brent.xner.net/BIOL4800/index.htm).

Attendance will be documented but is not directly factored into the final grade.

Study hint:  The LSU Center for Academic Success (CAS; http://appl003.lsu.edu/slas/cas.nsf/index) exists to help students do well in their classes.  At their web site, consider taking their “Test Your Learning Style” to see how you learn best.

Code of Student Conduct:
Students are expected to adhere to the Code of Student Conduct, which can be accessed at: http://appl003.lsu.edu/slas/dos.nsf/$Content/Code+of+Conduct?OpenDocument.  University regulations on academic misconduct will be strictly enforced and violators will be referred immediately to the Dean of Students. Plagiarism examples and information on proper and improper student writing.

Students with disabilities:
If a student has a disability which may require accommodation, you should immediately contact the Office of Disability Services (http://appl003.lsu.edu/slas/ods.nsf/index) to officially document the needed accommodation.  The instructor must be presented with this documentation during the first week of class.

To make our time together as valuable as possible:
·   Attend all scheduled classes and arrive on time.
·   Come prepared to discuss the material.
·   Please turn off cell phones and refrain from sending text messages, checking email, or any other behavior that might be disruptive to other students.
·   If you have trouble concentrating on the lecture because of a distraction, quietly ask those responsible for the distraction to stop. If the distraction continues, please let me know.
·   Please contact me immediately if you have any problem which is preventing you from performing satisfactorily in this class.

course calendar
(Subject to change)

 ^† Unless specified, readings from chapters in Brock Biology of Microorganisms 12^th ed (11^th ed).
* Indicates dates for open discussions of “hot topics” in microbial ecology.           

Disclaimer: the copyright of the respective articles are with the corresponding publishers and the files are provided for academic use only.
Supplemental readings:
^a Cohan, F.M. (2002) What are bacterial species? Annu. Rev. Microbiol. 56:457-87.
^b Ward, D.M. (2006) A macrobiological perspective on microbial species. Microbe 1:269-278.
^c Pace, N.R. (1997) A molecular view of microbial diversity and the biosphere. Science 276:734-740.
^d Connon, S.A., and S.J. Giovannoni. (2002) High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates. Appl. Environ. Microbiol. 68:3878-3885.
^e Zengler, K. et al. (2002) Cultivating the uncultured.  Proc. Natl. Acad. Sci. 99:15681-15686.
^f Ferrari, B.C. et al. (2005) Microcolony cultivation on a soil substrate membrane system selects for previously uncultured soil bacteria. Appl. Environ. Microbiol. 71:8714-8720.
^g Handelsman, J. (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol. Mol. Biol. Rev. 68:669-685.
^h Hallam, S.J. et al. (2004) Reverse methanogenesis: testing the hypothesis with environmental genomics. Science 305:1457-1462.
ⁱ Tringe, S.G. et al. (2005) Comparative metagenomics of microbial communities. Science, 308:554-557.