Microbial Meta-omics and Ecosystem Function

Spring Semester 2011




Class time:  Friday, 12:30 - 3:00 pm

Location:   Biosciences West, Room 302

Credit hours:   2 units

Instructors:  Scott Saleska and Virginia Rich

Course Description: A gram of soil or a milliliter of water contain ~106-109 microbial cells, and there are more microbial cells in a human body than human cells. Not only numerically dominant, microbes are the drivers of planetary biogeochemistry, and ecosystem function cannot be understood in their absence. In this cross-disciplinary graduate seminar we will discuss research that uses biogeochemistry and molecular microbial ecology to address ecosystem function, while we introduce the current cutting-edge methods and thinking in each field. Methods covered range from molecular meta-genomics to the use of isotopes as biogeochemical tracers at multiple scales. Lectures will be mixed with journal club-style readings and discussions, so active participation essential. Graduate students from diverse backgrounds are welcome, and advanced undergraduates are welcome with instructor permission.

By the end of this course, you will be comfortable reading primary literature in both fields and be familiar with the jargon and major methods of each, including environmental metagenomics, -transcriptomics, and proteomics, micrometeorological methods, isotope ratios as tracers of biogeochemical cycling, and as probes of microbial function (stable isotope probing).  Some topic areas: understanding the role of microbes in the local and global cycles of carbon, nitrogen and water, in processes in the soil, oceans, the biota, and the atmosphere.  Your critical reading and discussion skills will be honed within the interdisciplinary setting of mixed backgrounds (i.e., you will get better at critically evaluating materials about which you know less than your normal fare). In addition, you will have an overview of some of the research being done at the fields’ intersection, and have developed opinions about its strengths, weaknesses, and future trajectories.

Organization and requirements:

(1) Ecology 596L will be run largely as a seminar. The first meeting will be organizaional, but all other class meetings will be run as a discussion. The instructor and each student will lead one discussion, but everyone is expected to participate in all discussions. You are strongly encouraged to ask questions if you do not understand something -- the class participants will likely come from several disciplines and what is obvious in one discipline is not necessarily obvious to others. But come prepared, both by reading the material and doing the writing assignment (see below).

(2) The readings for this class consist of readings from the primary literature. Each week all students will bring a concise (e.g. 1 paragraph) summary of each assigned paper, along with a list of at least 3 questions they had about the work.

(3) Once or twice during the semester, each student will lead a discussion on a topic and readings -- either from the suggested list, or a topic of their choosing, selected in consultation with the instructors. Students will conduct a literature search on the chosen topic and make two or three key references available to the entire group at least one week in advance of the presentation. These papers will form the basis of a general discussion and will be available as pdf files on the class website. Each student should meet with the instructors at least once before their presentation (ideally two weeks in advance) to discuss and clarify the readings and scope of the topic.

(4) When leading a discussion, students should prepare an overview of the general topic (in the nature of a tutorial to explain necessary background to those who may be in the class from other disciplines) as well as an overview of the specific papers. This overview (e.g. in the form of a powerpoint presentation) should include an outline of key points, tables or illustrations, a bibliography of relevant papers, and a list of questions to generate discussion.

(5) Grading
Your final grade will be determined by total number of points accumulated from the weekly write-ups, the presentation, and class participation (there are no exams or final paper).





Class Participation






Grade Scale
A: 90-100 %
B: 80-89 %
C: 70-79 %
D: 60-69 %
E (fail): 0-59 %


None required.

Honors Students

Honors students will be admitted with permission from the instructor, and their additional assignment(s) will be negotiated individually based on their backgrounds and goals.

Policy on Expected Classroom Behavior
Due to the interdisciplinary nature of this seminar, a good classroom attitude is critical – come ready to learn and to share your own knowledge graciously. Vigorous collegial debate is encouraged, and expected. Laptops are allowed in class but checking email is not. Each student is expected to attend every class session; however, all holidays or special events observed by organized religions will be honored for those students who show affiliation with that particular religion, and absences pre-approved by the UA Dean of Students (or Dean's designee) will be honored.

Policy Against Plagiarism

Policy Against Threatening Behavior

Academic Integrity
Integrity is expected of every student in all academic work. The guiding principle of academic integrity is that a student's submitted work must be the student's own. This principle is furthered by the Student Code of Conduct and disciplinary procedures established by ABOR Policies 5-308 - 5-403, all provisions of which apply to all University of Arizona students. For further information, please see:

Special Needs and Accommodations Statement
Students who need special accommodation or services should contact the SALT (Strategic Alternatives Learning Techniques), the Center for Learning Disabilities (SALT Center, Old Main, PO Box 210021, Tucson, Arizona 85721-0021, (520) 621-1242, FAX (520) 621-9448, TTY (520) 626-6072),, and/or the Disability Resources Center, 1540 E. 2nd Street, PO Box 210064, Tucson, Arizona 85721-0064, (520) 621-3268, FAX (520)621-9423, The appropriate office must document the need for accommodations.