PCB 5443 Advanced Ecology II: Communities and Ecosystems 

Spring 2022

Tuesdays & Thursdays 9:30AM-10:45AM

MMC Chemistry & Physics, Room 115

Dr. John Kominoski
Office: OE-207
Office Hours: by appointment

Course Description and Purpose

Ecosystems comprise the basic unit of ecology by linking physical, chemical, and biological interactions of environments. The ecosystem concept emerged out of observations that organisms were both controlling as well as controlled by their environments. The basis of ecosystem ecology is that energy flows, limiting elements cycle, and mass balance is used to quantify stocks and fluxes of matter. Theories of ecosystem ecology are emerging that link across disciplines in ecology and expand upon patterns and trends at multiple spatial and temporal scales. This course covers historic and foundational concepts, core theories, empirical and modeling approaches, and emerging perspectives in the youngest and broadest of the fields within the discipline of ecology.  The course is divided into (i) introductory lectures to orient students to topics, (ii) reading and discussion of primary literature led by students, (iii) reflection and application of concepts through take-home exams, and (iv) analyze data to test basic ecosystem ecology questions.

Course Objectives

Students will gain the following knowledge and skills by completing this course:

  • Understand what an ecosystem is and how to measure its components relative to its whole
  • Understand global biogeochemical cycles of key elements and their drivers
  • Understand metabolic processes and their relative dependence on temperature
  • Know the foundations of the discipline – including the people, places, and institutions that helped build it – and where ecosystem ecology is expanding
  • Understand and apply the core theories that link ideas and concepts in ecosystem ecology
  • Develop mechanistic relationships linking structure and function within and among diverse ecosystems
  • Access public databases and analyze ecosystem-level data to test basic questions in ecosystem ecology

Important Information

Professional and Academic Integrity:

All students must adhere to the FIU-2501 Student Conduct and Honor Code (Links to an external site.), which demonstrates respect for themselves, their fellow students, and the educational mission of Florida International University. All students are deemed by the University to understand that if they are found responsible for academic misconduct, they will be subject to the Academic Misconduct procedures and sanctions. Academic Misconduct policies and procedures will be strictly enforced regarding cheating and plagiarism.

Accessibility and Accommodation: The Disability Resource Center (DRC) collaborates with students, faculty, staff, and community members to create diverse learning environments that are usable, equitable, inclusive and sustainable. The DRC provides FIU students with disabilities the necessary support to successfully complete their education and participate in activities available to all students. If you have a diagnosed disability and plan to utilize academic accommodations, please contact the DRC at 305-348-3532 or visit them at the Graham Center GC 190. For additional assistance please visit the website of FIU’s Disability Resource Center (Links to an external site.).

*The professor reserves the right to change or modify the syllabus at any time during the semester.

Sample Grading Scheme

A95 or aboveB83 – 86C70 – 76
A-90 – 94B-80 – 82D60 – 69
B+87 – 89C+77 – 79F59 or less

Textbooks:                                                                                                                                 Weathers, K.C., D.L. Strayer, and G.E. Likens. 2021. Fundamentals of Ecosystem Science, 2nd Edition, Elsevier. ISBN 9780128127629 http://www.sciencedirect.com/science/book/9780120887743 

Optional:                                                                                                                                        Chapin, F.S., P.A. Matson, and P.M. Vitousek. 2011. Principles of Terrestrial Ecosystem Ecology, 2nd Edition, Springer. ISBN 1441995048 http://link.springer.com/book/10.1007%2F978-1-4419-9504-9 

Coleman, D.C. 2010. Big Ecology: The Emergence of Ecosystem Science. University of California Press. ISBN 978-0-520-26475-5

Golley, F.B. 1993. A History of the Ecosystem Concept: More Than the Sum of Its Parts, Yale University Press. ISBN 0300055463

Class Schedule:

 History, Energetics, Biogeochemical Cycles  
11/13 JanCourse Overview & The Ecosystem Concept                                Tansley 1935; Odum 1969
18/20 Jan Community Development & The Ecosystem ConceptConnell & Slayter 1977; Bormann & Likens 1967;
Kominoski et al. 2018a
W1, W10

25/27 Jan Carbon Cycle (Photosynthesis, GPP, NPP)Chapin et al. 2006W6-7
Carbon Cycle (Decomposition)Tiegs et al. 2019W4-5
01/03 FebNitrogen and Phosphorus CyclesDeegan et al. 2012; Vega Thurber et al. 2014W8-9
08/10 FebEcosystem Energetics & Trophic DynamicsLindeman et al. 1942; Carpenter et al. 1985W2-3
Exam 1 Due 5PM ET 13 Feb
Foundational Theories
15/17 FebEcological Stoichiometric TheoryRedfield 1958; Hessen et al 2013
22/24 FebMetacommunity Ecology: Niche & Neutral Theories
Record et al. 2021; Tilman 1985; Hubbell 2006
01/03 MarchSpring Break (No Class) 
08/10 MarchMetabolic Theory of EcologyBrown et al. 2004; Follstad Shah et al. 2017
15/17 MarchDisturbance Ecology TheoryJentsch and White 2019; Gaiser et al. 2020; Kominoski et al. 2020
Exam 2 Due 5PM ET 20 March
Integrating Communities & Ecosystems 
22/24 MarchBiodiversity-Ecosystem FunctioningDuffy 2017; Gonzalez et al. 2020 
29/31 MarchEcosystem Connectivity & Landscape EcologyKominoski et al. 2018b; Turner et al. 2019
05/07 AprilSocial-Ecological SystemsMcPhearson et al. 2016; Hoellein and Rochman 2021W13-18
12/14 AprilEcosystem Stability & ResilienceFolke et al. 2004; McMeans et al. 2013W11-12
19/21 AprilStudent Data Synthesis Presentations (Finals Week, No Final Exam but Required Class Meeting) W19
Exam 3 Due 5PM ET 22 April

Class Notes

Purpose: Provide a common foundation of the history, concepts, theories, and applications of community and ecosystem science for graduate students training to be ecologists. Each class will address a different concept or theory. Two textbooks will be used to provide background material for lectures and discussions of current papers from the primary literature. You may also benefit by access to a general ecology textbook as a reference for things you may have forgotten from your undergraduate classes, as well as the two optional textbooks on historical and modern foundations in ecosystem ecology.

Pedagogy: Classes will contain a balance of lecture and discussion. Class time is used for answering student questions, discussions of the material, and review of core ecological concepts in ecosystems. Students will be required to graph, analyze, and interpret ecosystem data on exams.

Student responsibilities: You are expected to do the assigned reading before class and participate in class discussions throughout the term.  

Each student each week must upload to Canvas a 1-page, single-spaced overview of the assigned readings addressing the following:

  • What general ecological concepts does the readings address?
  • Are these concepts specific to particular ecosystem types or generalizable across ecosystems?  If yes, how?
  • How do the readings advance these concepts?
  • What additional knowledge gaps exist for these concepts?
  • Develop questions to test these knowledge gaps
  • Interpret data from papers

Grades: There will be three take-home exams. Your performance on these exams will account for 60% of your grade. A synthesis of publicly available ecosystem-level data (selected by the student) and presentation of results and interpretation will account for 20% of your grade. An additional 20% of your grade will be derived from your attendance, 1-page write-ups, as well as participation in readings and class discussions. 

Exams. Exams will consistent of 3-4 essay questions associated with various topics from textbooks and primary literature discussed in class. Students will be required to graph, analyze, and interpret data in order to answer some questions. Exams will be given and completed outside of class. Completed exams are due by 5PM ET the date of the exam. Exams are closed book.

Participation. Attendance in class in required and essential to obtaining a high grade. Students with excused absences must still submit a 1-page write up to Canvas for papers discussed in class on the day that the student was absent.


Bormann, F.H. and Likens, G.E., 1967. Nutrient cycling. Science155(3761), pp.424-429.

Brown, J.H., Gillooly, J.F., Allen, A.P., Savage, V.M. and West, G.B., 2004. Toward a metabolic theory of ecology. Ecology85(7), pp.1771-1789.

Carpenter, S.R., Kitchell, J.F. and Hodgson, J.R., 1985. Cascading trophic interactions and lake productivity. BioScience35(10), pp.634-639.

Chapin, F.S., Woodwell, G.M., Randerson, J.T., Rastetter, E.B., Lovett, G.M., Baldocchi, D.D., Clark, D.A., Harmon, M.E., Schimel, D.S., Valentini, R. and Wirth, C., 2006. Reconciling carbon-cycle concepts, terminology, and methods. Ecosystems, (7), pp.1041-1050.

Connell, J.H. and Slatyer, R.O., 1977. Mechanisms of succession in natural communities and their role in community stability and organization. The American Naturalist111(982), pp.1119-1144.

Deegan, L.A., Johnson, D.S., Warren, R.S., Peterson, B.J., Fleeger, J.W., Fagherazzi, S. and Wollheim, W.M., 2012. Coastal eutrophication as a driver of salt marsh loss. Nature490(7420), pp.388-392.

Duffy, J.E., Godwin, C.M. and Cardinale, B.J., 2017. Biodiversity effects in the wild are common and as strong as key drivers of productivity. Nature549(7671), pp.261-264.

Elser, J.J., Dobberfuhl, D.R., MacKay, N.A. and Schampel, J.H., 1996. Organism size, life history, and N: P stoichiometry: toward a unified view of cellular and ecosystem processes. BioScience46(9), pp.674-684.

Follstad Shah, J.J., Kominoski, J.S., Ardón, M., Dodds, W.K., Gessner, M.O., Griffiths, N.A., Hawkins, C.P., Johnson, S.L., Lecerf, A., LeRoy, C.J. and Manning, D.W., 2017. Global synthesis of the temperature sensitivity of leaf litter breakdown in streams and rivers. Global Change Biology23(8), pp.3064-3075.

Gaiser, E.E., Bell, D.M., Castorani, M.C., Childers, D.L., Groffman, P.M., Jackson, C.R., Kominoski, J.S., Peters, D.P., Pickett, S.T., Ripplinger, J. and Zinnert, J.C., 2020. Long-term ecological research and evolving frameworks of disturbance ecology. BioScience70(2), pp.141-156.

Gonzalez, A., Germain, R.M., Srivastava, D.S., Filotas, E., Dee, L.E., Gravel, D., Thompson, P.L., Isbell, F., Wang, S., Kéfi, S. and Montoya, J., 2020. Scaling‐up biodiversity‐ecosystem functioning research. Ecology Letters23(4), pp.757-776.

Hessen, D.O., Elser, J.J., Sterner, R.W. and Urabe, J., 2013. Ecological stoichiometry: an elementary approach using basic principles. Limnology and Oceanography58(6), pp.2219-2236.

Hoellein, T.J. and Rochman, C.M., 2021. The “plastic cycle”: a watershed‐scale model of plastic pools and fluxes. Frontiers in Ecology and the Environment.

Hubbell, S.P., 2006. Neutral theory and the evolution of ecological equivalence. Ecology87(6), pp.1387-1398.

Jentsch, A. and White, P., 2019. A theory of pulse dynamics and disturbance in ecology. Ecology100(7), p.e02734.

Kominoski, J.S., Gaiser, E.E., Castañeda‐Moya, E., Davis, S.E., Dessu, S.B., Julian, P., Lee, D.Y., Marazzi, L., Rivera‐Monroy, V.H., Sola, A. and Stingl, U., 2020. Disturbance legacies increase and synchronize nutrient concentrations and bacterial productivity in coastal ecosystems. Ecology, 101(5), e02988.

Kominoski, J.S., Gaiser, E.E. and Baer, S.G., 2018a. Advancing theories of ecosystem development through long-term ecological research. BioScience68(8), pp.554-562.

Kominoski, J.S., Ruhí, A., Hagler, M.M., Petersen, K., Sabo, J.L., Sinha, T., Sankarasubramanian, A. and Olden, J.D., 2018b. Patterns and drivers of fish extirpations in rivers of the American Southwest and Southeast. Global Change Biology24(3), pp.1175-1185.

Lindeman, R.L., 1942. The trophic‐dynamic aspect of ecology. Ecology23(4), pp.399-417.

McMeans, B.C., Rooney, N., Arts, M.T. and Fisk, A.T., 2013. Food web structure of a coastal Arctic marine ecosystem and implications for stability. Marine Ecology Progress Series482, pp.17-28.

McPhearson, T., Pickett, S.T., Grimm, N.B., Niemelä, J., Alberti, M., Elmqvist, T., Weber, C., Haase, D., Breuste, J. and Qureshi, S., 2016. Advancing urban ecology toward a science of cities. BioScience66(3), pp.198-212.

Odum, E.P., 1969. The strategy of ecosystem development, an understanding of ecological succession provides a basis for resolving man’s conflict with nature. Science, pp.262-270.

Record, S., Voelker, N.M., Zarnetske, P.L., Wisnoski, N.I., Tonkin, J.D., Swan, C., Marazzi, L., Lany, N., Lamy, T., Compagnoni, A. and Castorani, M.C., 2021. Novel insights to be gained from applying metacommunity theory to long-term, spatially replicated biodiversity data. Frontiers in Ecology and Evolution8, p.479.

Redfield, A.C., 1958. The biological control of chemical factors in the environment. American Scientist46(3), pp.230A-221.

Tansley, A.G., 1935. The use and abuse of vegetational concepts and terms. Ecology16(3), pp.284-307.

Tiegs, S.D., Costello, D.M., Isken, M.W., Woodward, G., McIntyre, P.B., Gessner, M.O., Chauvet, E., Griffiths, N.A., Flecker, A.S., Acuña, V. and Albariño, R., 2019. Global patterns and drivers of ecosystem functioning in rivers and riparian zones. Science Advances5(1), eaav0486.

Tilman, D., 1985. The resource-ratio hypothesis of plant succession. The American Naturalist125(6), pp.827-852.

Turner, M.G., Braziunas, K.H., Hansen, W.D. and Harvey, B.J., 2019. Short-interval severe fire erodes the resilience of subalpine lodgepole pine forests. Proceedings of the National Academy of Sciences116(23), pp.11319-11328.

Vega Thurber, R.L., Burkepile, D.E., Fuchs, C., Shantz, A.A., McMinds, R. and Zaneveld, J.R., 2014. Chronic nutrient enrichment increases prevalence and severity of coral disease and bleaching. Global Change Biology20(2), pp.544-554.

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