Principles of Ecosystem Ecology

Fall Semester 2009

PCB 5338, section 2551

Instructor: Michelle Mack




Welcome to Ecosystem Ecology. I hope that you will come away from this course with a better understanding of the basic principles that govern structure and function across all ecosystems.  At the same time, I hope that you will come away with a better appreciation of the unique nature of the ecosystems where you work and live.  My goal is to give you the conceptual tools that will help you understand both the processes that underlie similarities among all ecological systems, and the processes that generate unique aspects of individual systems.  We will also tackle some of the grand challenges of our time:  global warming, rising atmospheric CO2, loss of biodiversity, invasions by non-native species, pollution of lakes, rivers, and coastal waters–and how these environmental problems affect ecological systems. My goal for the course is not necessarily to turn all of you into ecosystem ecologists (although that would be great!).  Rather, I hope to provide you with a basic understanding of the principles of ecosystem ecology that will help you progress in your own studies of ecological systems.


The course is roughly divided into halves over the course of the semester. The first half will provide some background on the history of ecosystem ecology and on climate and soils, but will focus primarily on element cycling, particularly carbon and nutrient cycles. We will examine the energy base of ecosystems–what controls carbon fixation by plants and what is the fate of that fixed carbon. We will also study nutrient inputs to, cycling through, and losses from ecosystems. The second half will focus on interactions and perturbations, including those resulting from human-induced global changes. We will examine transfers of energy from primary producers to higher trophic levels and how herbivory and disturbances such as fire affect primary production and nutrient cycling. We will examine how elevated atmospheric CO2, changing climate, increased atmospheric nitrogen deposition, biological invasions, and losses of biodiversity alter ecosystem processes. We will also discuss human dependence on ecosystems and how our activities are altering systems at local, regional, and global scales.


This semester, the course is scheduled for two periods on Tuesday (6-7) and one on Thursday (6).  On Tuesday, I will lecture for the first period, and then there will be a student-led discussion of the primary literature during the second period.  I will lecture on Thursday.  The purpose of the student-led discussion is to expose you to a wide range of literature and to give you the opportunity to practice your class leadership skills.  Each week, a team of students will be responsible for giving the class a brief overview of the papers, and then leading the discussion.  Leaders will be graded on their preparation, their understanding of the papers and their ability to engage the group in discussion.


You will need a basic understanding of ecology and college-level chemistry and biology as background for this course.  If you are unsure if your course background is adequate please discuss this with the instructor.


The goals of the course are:


• to teach you the basic principles and concepts of ecosystem ecology


• to introduce you to current uncertainties and controversies in ecosystem ecology


• to increase your awareness of human-induced global changes and how they are affecting ecosystem processes


• to increase your awareness of human dependency on ecosystem processes


• to motivate you to at least keep informed about global environmental problems; at most take some action to try and solve some of these problems.






The required text for the course is a textbook written by F. Stuart Chapin, Pamela Matson, and Harold A. Mooney, Principles of Ecosystem Ecology. Readings from this text are required.


There will also be required readings from the primary literature that will supplement lecture materials.  These will be posted on the web. The purpose of these papers is to expose you to both classic and current ideas and to promote your understanding of ideas through discussion.


The course web site URL is  I will post Powerpoint slides on the web before each lecture. However, reading these notes alone cannot take the place of coming to lectures. I will emphasize certain things in lectures that cannot be emphasized in the printed form. You can also find other announcements and assignments on the web site.






In class participation: You will be graded on (1) the discussion presentation that you lead, and (2) your participation in class discussions.  My expectation is that you will keep abreast of text book readings, readings from the primary literature, and lecture materials, and you will come to each class prepared with questions and a mindset that will enable you to participate in discussions.



Problem Sets: There will be 2 graded problem sets given during the semester. The purpose of these problem sets is to keep you up to date on the material and help you prepare for the exams.


Mid-Term Exams: There will be two mid-terms that will test your knowledge of material covered in the lectures and readings. Both exams will be structured as a combination of short-answer questions, short-essay questions, and calculations. Essay questions will require approximately a paragraph-length answer. Complete, well-structured paragraphs are unnecessary, however. Rather, phrases, sentences or "bullet points" that show what you know about a topic are sufficient. Possible kinds of questions that might be included on an exam are "What are the major factors that control rates of X in an ecosystem?" or "Given what you know about the controls over process X, how would you expect that process to differ in Ecosystem A and Ecosystem B?" or "How and why do you expect elevated CO2 (or some other environmental perturbation) to affect productivity in Ecosystem A versus Ecosystem B?"


Final exam:  The final exam will cumulative: it will encompass material from the entire course, including the lecture, text book, and discussion readings.  The format of the final exam will consist of short-answer questions that you will receive on Thursday, December 4 so that you will be able to contemplate your answers prior to the exam on December 9.   You will not be allowed to bring notes to the exam.  The purpose of this format is to guide your review of the material.





Discussion leadership


Discussion participation


Problem sets (2)

100 (50 each)

Mid-term exams (2)

200 (100 each)

Final exam







Grades will be assigned as follows based on the total number of points possible, weighted as shown above: 90-100% A, 80-89% B, 70-79% C, 60-69% D, 0-59% F. I may lower grading criteria at the end of the quarter if assignments or exams are more difficult than intended.


Important dates are indicated on the lecture/discussion schedule.


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