Overview: Each of the field and lab exercises undertaken in the core course builds upon one another.  Students begin by measuring the biomass of primary producers in both the forest and aquatic ecosystems, then spend two weeks estimating the rates of primary production in these ecosystems.  The fourth through sixth weeks are devoted to examining the fates of organic matter produced by plants and algae.  During week 4, students study the trophic structure - abundance and distribution of secondary producers in Waquoit Bay and Johns Pond, collecting samples for later analysis of food web structure.  During weeks 5-6 students examine the rates of mineralization and respiration of soils and sediments in these ecosystems, providing a basic introduction to nutrient cycling and stoichiometry of ecosystems.  During weeks 7-8, students make additional measurements of the flows of nutrients and water through the ecosystem and draw the information previously gathered together to construct a budget of nitrogen and water and estimate nutrient loading to the estuaries.

The Earth as an Ecosystem: Four Billion Years of Biogeochemistry

  • The formation of the primordial earth, atmosphere and ocean the origins of life
  • The earth today compared to the primordial Earth, Venus and Mars
  • The oxidation of the biosphere and it's consequences
Reading: Schlesinger, W.H. 1997. Biogeochemistry: An Analysis of Global Change. Chapter 1, pp. 1-14 & Chapter 2, pp. 15-45.

 How Man is Altering the Earth as an Ecosystem: The Global Carbon Cycle

  • Review of the various major ways humans are altering the earth - chemical environment, physical environment, biological structure
  • The carbon cycle as an integrating topic; the pre-industrial carbon cycle - quasi steady state
  • Effects of industrial society on carbon cycle (fossil fuel burning, land-use change)
  • Concept of conservation of mass - the missing carbon in the contemporary carbon budget
  • Mechanisms that may account for missing carbon; forest regrowth (definitions of NPP, GPP), CO2 fertilization, N fertilization, climate variability

Discussion - preliminary discussions of the links between the carbon cycle and the earth's climate.

Reading: Climate Change State of Knowledge, OSTP, October 1997.

Recommended: McNeill, J.R. 2000. Something New Under the Sun: An Environmental History of the Twentieth-Century World. W.W. Norton & Company, New York. 421 p.

Sarmiento, J. L. and Gruber, N. 2002. Sinks for Anthropogenic Carbon. Physics Today. Vol. 55 No. 8, pp. 30-36

Climate Change and the Pan-Arctic Water Balance

  • The water balance concept
  • Why focus on the arctic water cycle?
  • Contemporary baselines of climate, runoff and ocean circulation.
  • Predicted future states of the arctic hydrological system and feedbacks to global climate.

Reading: Schlesinger, W.H., 1997. Biogeochemistry: An Analysis of Global Change, chapter 10 pp. 297-307 (The Global Water Cycle).

Taylor, K. 1999. Rapid Climate Change. American Scientist 87:320-327.

 The Ecosystem Concept: What It Is and How It Came to Be

  • Define 'ecosystem'
  • Outline the development of 'ecosystem' as an organizing concept in biology
  • Identify goals and approaches of ecosystems science
  • Example of ecosystem study

Readings: Aber, J.D., & J.M. Melillo. 2001. Terrestrial Ecosystems. Chapter 1 (pp. 1-14), Chapter 3, pp. 33-50 (see especially table 3.1).

Read ONE of the following two articles:

Tansley, A.G. 1935. The use and abuse of vegetational concepts and terms. Ecology 16: 284-307.
Lindeman, R.L. 1942. The Trophic-Dynamic Aspect of Ecology. Ecology 23: 399-418.

Other recommended references (not required)

Golley, F.B. 1993. A History of the Ecosystem Concept in Ecology: More than the sum of its parts. Yale University Press, New Haven. 253 pp.

Forbes, S.A. 1887. The lake as a microcosm. Bulletin of the Peoria Scientific Association, pp. 77-87. Reprinted (1925) in Bulletin of the Illinois State Natural History Survey 15: 537-550.

Cowles, H.C. 1899. The Ecological Relations of the Vegetation on the Sand Dunes of Lake Michigan.Botanical Gazette 27: 95-117, 167-202, 281-308, 361-391.

Clements, F.E. 1936. The nature and structure of the climax. Journal of Ecology 24: 252-284.

Odum, E.P. 1969. The Strategy of Ecosystem Development. Science 164: 262-270.


Primary Production in Terrestrial Ecosystems

  • The biochemistry of photosynthesis - light and dark reactions
  • Respiration and photorespiration
  • C3, C4 and CAM pathways
  • Stomatal function - linking C and water fluxes
  • Measurement and analysis of primary production on land

Discussion - Which techniques should be used to measure the different components of the ecosystem C budget (photosynthesis (s), GPP (daily), NPP (annual) etc)?

Reading: Schlesinger, W. H. 1997. Biogeochemistry: An Analysis of Global Change, Chapter 5, pp. 127-164.
Aber and Melillo. 2001. Terrestrial Ecosystems, Chapter 6 (Energy, Water and Carbon Balances over Leaves) pp. 93-111.

 Scaling up Estimates of Primary Production in Ecosystems

  • The control of primary production by light, temperature, nutrients and grazers
  • Converting point measurements to meter square daily and annual values
  • Developing whole-ecosystem estimates of primary production

Reading: Aber and Melillo. 2001. Terrestrial Ecosystems, Chapter 7 (Canopy Structure, Light Attenuation and Total Potential Photosynthesis), pp. 113-125, Chapter 8 (Ecosystem Water Balances and Realized Photosynthesis), pp. 127-145

Recommended: S.A. Levin (1992) The problem of pattern and scale in ecology. Ecology 73: 1943-1967.

 Producer Stock Distribution in the Biosphere

  • Patterns in production, biomass and organic matter stocks vary widely
  • Importance of global environmental gradients to distributions
  • The concept of net ecosystem production

Readings: Schlesinger, W.H.,1997. Biogeochemistry: An Analysis of Global Change, Pages 134-152..

Randerson, J.T., F.S. Chapin, III, J.W. Harden, J.C. Neff, and M.E. Harmon. 2002. Net Ecosystem Production: A Comprehensive Measure of Carbon accumulation by Ecosystems. Ecological Applications 12: 937-947.

Recommended: Field, CB, Behrenfeld, MJ, Randerson, JT and Falkowski, P (1998) Primary production of the biosphere: Integrating terrestrial and oceanic components. Science 281: 237-240.

Primary Production in Aquatic Ecosystems

  • Global patterns of aquatic primary production
  • Use of photosynthetic end products to estimate rates of production (C vs. O2 in aquatic vs. terrestrial ecosystems) and the PQ
  • Review definitions GPP, NPP, NCP, NEP, RH, RA,; what we can really measure in aquatic ecosystems using DO2 in Light/Dark Bottles?
  • Introduction to P vs. I curves, the assimilation number, the Redfield Ratio concept, nutrient uptake kinetics and the cell quota.
  • Controls on primary production in aquatic systems (light, nutrients, Cinorganic availability, vertical mixing, grazing).

Discussion - Parallels & contrasts with land plants & terrestrial ecosystems

Reading: Valiela, I. Marine Ecological Processes. Chapt. 1, Pp. 3-31, Chapt. 2, pp. 36-46, 57-83.

Recommended: Day, J.W. et al. Estuarine Ecology, Chapter 4, pp. 147-187.


Litter Decomposition and Fate of Organic Matter Produced on Land

  • Describe exponential decay curve and k
  • Identify components of litter quality
  • Illustrate how climate and litter quality influence decay rate (or k)
  • Identify relationships between site quality and litter quality & quantity
  • Discuss dynamics (mineralization vs. immobilization) of limiting and non-limiting nutrients during decay.

Readings: Schlesinger, W.H.. 1997. Biogeochemistry: An Analysis of Global Change, pp. 107-116 (Soil Development); pp. 149-164 (Decomposition- The Fate of Organic Carbon).

Aber, J.D. & J.M. Melillo. 2001. Structure of Terrestrial Ecosystems (Chapter 2, pp. 15-31). Terrestrial Ecosystems.

The Fate of Organic Matter Produced in Aquatic Ecosystems

  • Focus on RH and NEP. Forms of NEP (accumulation in biomass, burial or export).
  • Effect of system closure on NEP and sustainability: aquatic systems vs terrestrial systems
  • Food webs: grazing, detrital and the microbial loop
  • Importance of DOM in aquatic systems
  • Controls on organic matter export, burial and preservation in aquatic systems: settling, particle size, amount of primary production, mixed layer and water column depth

Reading: Valiela, I. 1995. Marine Ecological Processes. Springer-Verlag, NY. pp. 387-412.


Secondary Production and Ecological Efficiency

  • Secondary production is elaboration of organic matter by organisms that get their energy, carbon and nutrients from organic matter generated by photosynthetic organisms includes inverts, tigers and microbes.
  • Secondary production is limited by energy fixed by plants & transfers through the food web.
  • Assimilation, growth, & ecological efficiency vary with food source and animal life history.
  • Most terrestrial production goes through detrital pathways, while in many aquatic systems grazing pathways dominant. Therefore, transfer to higher trophic levels is more very efficient in aquatic.
  • P:B as a way to estimate 2nd production. Varies with size of organism and life history.

Reading: Valiela, Marine Ecological Processes, Chapter 7. (Processing of consumed energy), sections: 7.1 Overview (pp. 203-205), 7.2.1 Assimilation (pp. 205-210), 7.3 (pp. 212-216), 7.4 Growth (pp. 219-221), 7.5.3 Production (pp.234-240).

Application of Isotopes to Studies of Ecosystems

  • What are Stable Isotopes and why are they useful
  • Nature abundance and food webs
  • Use of biographical tracers

Reading: Peterson and Fry. 1987. Stable Isotopes in Ecosystems Studies. Annual Review of Ecol. Syst. 18:293-320.

Decomposer Organisms

  • Microbial processes important in ecosystem fluxes. For many questions can blackbox. Possible controls based upon presence, upon activity, upon microbial capabilities, upon species.
  • Microbes, bacteria, fungi, protozoa, are abundant, ubiquitous, significant biomass in aquatic and terrestrial systems. Microbial food webs present. Role in moving C and energy to higher forms.
  • Recycle organic compounds and nutrients to inorganic forms. In both terrestrial and aquatic systems virtually all primary production is decomposed.
  • Most primary productivity depends upon recycled N and P
  • Fix nitrogen. Half of the new nitrogen comes from nitrogen fixation by microbes. Azolla in rice paddies, legumes, alders.
  • Allow herbivores to consume poor quality food. Cattle, deer, sheep have rumens, horse has hindgut fermentation. Importance for humans is immense.
  • Give plants access to nutrients, especially those in organic form, through fungal symbiosis with roots (mycorrhizae).

Reading: J.J. Perry and J.T. Staley. 1997. Chapter 25, Beneficial symbiotic associations, p. 652-674. In Microbiology: Dynamics and Diversity. Saunders College Publishing. Fort Worth, New York, London.


Aerobic and Anaerobic Respiration and Decomposition

  • Oxidation - Reduction - what it is, how do we determine oxidation state, and why is it important to ecosystem dynamics?
  • Energy yielding processes - the importance of both substrate and mode of decomposition
  • Electron acceptor sequence (e.g. oxygen, nitrate, sulfate, etc), based upon energy yield
  • Availability of electron acceptors in the environment
  • Chemoautrophy and element cycling (focus on NH4+ and S= oxidation for e-yield)

Reading: Jorgensen, B.B. 1980. Mineralization and the Bacterial Cycling of Carbon, Nitrogen, and Sulfur in Marine Sediments, Pp. 239-250 in D.C. Ellwood, J.N. Hedges, M.J. Leatham, J.M Lynch, J.H. Slater (eds.), Contemporary Microbial Ecology, Academic Press.

Recommended: Schlesinger, W. H. 1997. Biogeochemistry: An Analysis of Global Change. Chapter 7 pp.224-241.

Fenchel, T., G.M. King and T.H. Blackburn 1998. Bacterial Biogeochemistry: The Ecophysiology of Mineral Cycling. Introduction and Chapter 1, pp. 1-25, Appendix 1 (Thermodynamics and Calculation of Energy Yields of Metabolic Processes), pp. 284-292.

Valiela, I. 1995. Marine Ecological Processes, pp 413-424.

 The Nitrogen Cycle

  • Key N cycling processes (mineralization, nitrification, denitrification, nitrate leaching, immobilization)
  • Direct vs. coupled nitrification/denitrification
  • New vs. recycled production. The f-ratio and its relation to the biological pump
  • Effect of denitrification on estuarine and continental shelf N budgets and ramifications for autotrophy and heterotrophy

Readings: Aber and Melillo. 2001. Terrestrial Ecosystems. Chapter 14 (pp. 253-270: Nutrient Cycling)

Schlesinger, W.H. 1997. Biogeochemistry: An Analysis of Global Change, Chapter 6 (pp. 189-205, Biogeochemical Cycling in Soil).

Valiela, I. 1995. Marine Ecological Processes. Springer-Verlag, NY. Chapter 14, Section on Nitrogen, pp. 433-451.

 The Phosphorus Cycle

  • Forms of P in soil, changes in forms over time, biological availability
  • P cycling in freshwater systems, the role of Fe oxides in controlling P availability
  • The oceanic P cycle
  • P vs. N limited ecosystems

Readings: All refer to pages in Schlesinger, W.H. 1997 Biogeochemistry: An Analysis of Global Change.

Pp. 90-100, 168-170, 205-207, 218-223, 396-401

Recommended: Valiela, I. Marine Ecological Processes. pp. 454-460

Howarth, R. W., et al. 1995. Transport to and Processing of P in Near-Shore and Oceanic Waters. Phosphorus in the Global Environment, Tiessen (ed) pp. 323-356.



Ecosystem Stoichiometry

  • The relative abundance of major elements in living tissues. The differences in element ratios between terrestrial and aquatic ecosystems
  • The compounds that dictate the aquatic and terrestrial ratios
  • The Redfield Hypothesis
  • An example of an element matching calculation

Reading: Redfield, A.C. (1958). The Biological Control of Chemical Factors in the Environment. American Scientist 46:205-221

Read ONE of the following three articles:

Deevey, Jr., E. S. 1970. Mineral Cycles. Scientific American 223:148-158

Elser, J. J. et al. 1996. Organism Size, Life History, and N:P Stoichiometry. BioScience Vol. 46 No. 9:674-684

Peterson, B. J. and Melillo, J. M. 1985. The Potential Storage of Carbon Caused by Eutrophication of the Biosphere. Tellus 37B, 117-127

 Acid Deposition, Ion Exchange and Charge Balance in Ecosystems

  • Causes and patterns of Acid Deposition
  • Reactions with base cations in soils and consequences of acid inputs to forests
  • Terrestrial-Aquatic linkages
  • Effects on surface waters and in-lake processing of acid inputs

Readings: Aber, J.D., & J.M. Melillo. 2001. Terrestrial Ecosystems. Chapter 10 (pp. 169-182, Weathering Products, Ion Exchange Capacities, and Base Saturation).

Driscoll, C.T. et al. 2001. Acidic deposition in the Northeastern United States: Sources and Inputs, Ecosystems Effects and Management Strategies. Bioscience 51 (3): 180-198.

Recommended: Aber, J. D., K. J. Nadelhoffer, P. A. Steudler and J. M. Melillo. 1989. Nitrogen saturation in forest ecosystems. BioScience 39:378-386.

 N Budget of Boston Harbor and Massachusetts Bay: the Sewage Outfall Controversy

  • Background - History of the Boston sewage system - issue of ocean outfalls in general
  • The nitrogen budget of an estuary - what we can measure, what we can infer by difference
  • The role of the sediments and denitrification in removing nitrogen
  • Extrapolation - is Boston Harbor typical or not - residence time issues

Readings: Kelly, J.R. 1997 . Nitrogen Flow and the Interactions of Boston Harbor with Massachusetts Bay. Estuaries 20: 365-380.

Recommended: Giblin et al. 1997. Benthic Metabolism and Nutrient Cycling In Boston Harbor, Massachusetts. Estuaries 20: 346-364.



Land-Use Changes and Their Effects on Coastal Ecosystems

  • Population growth and land use change
  • Anthropogenic activities on land and rivers that affect: 1) the timing, 2) magnitude and 3) quality of water and material runoff to the coast
  • Dams, Channelization
  • Effects of water delivery, organic matter inputs and inorganic nutrient inputs on Estuarine metabolism and Anoxia
  • Autotrophy and heterotrophy

Reading: Hopkinson, C. and J. Vallino. 1995. Relationships Among Man's Activities in Watersheds and Estuaries; a Model of Runoff Effects on Patterns of Estuarine Community Metabolism. Estuaries 18:598-621.

 Land Use in the Mississippi Drainage and Gulf of Mexico Hypoxia

  • Causes of eutrophication - contrast marine and freshwater systems
  • Sources of nutrients - point and non-point sources
  • Estuarine susceptibility to eutrophication - predicting the effects of nutrient enrichment
  • Managing eutrophication

Readings: Howarth, R.W. et al. (2000). Executive summary and Chapter 1 in Clean Coastal Water: Understanding and Reducing the Effects of Nutrient Pollution, National Research Council Report, NAS Press, Washington, DC. 405 pp.

Goolsby, D.A. and W.A. Battaglin 2000. Nitrogen in the Mississippi Basin - Estimating Sources and Predicting Flux to the Gulf of Mexico. USGS Fact Sheet 135-00, 6 pp.

 Eutrophication of Fresh Waters: The Phosphorus Mitigation Story

This is a case history study but it is good because the data used to resolve the scientific issue included process level data, time series data (P reductions in Lake Washington) as well as whole lake experiments.

  • Difficulty of clearly forming public debate over environmental issues
  • Dealing with uncertainty in science when policy issues are at stake
  • Importance of large scale experiments in resolving questions

 Group Discussion - The class will be divided into teams taking different sides in the debate over the question of whether controlling P is necessary to prevent the eutrophication of freshwaters. One team will Represent the detergent industry, and one will represent ecologists. Giblin will moderate and ask specific people to present specific issues (e.g. C vs. P limitation). Debate will take up about ¾ class time and then Giblin will recap the debate, citing results from studies by Schindler, etc. Presentations will count toward class participation grade.

Reading: Edmondson, W. T. 1991. The Uses of Ecology: Lake Washington and Beyond. Chapter 3, (The Detergent Problem) pp. 89-138 The University of Washington Press


What Species do in Ecosystems

  • Keystone species and ecological engineers
  • Measures of Diversity
  • Species effects vs. Diversity effects
  • Direct and Indirect effects on ecosystem function
  • Functional Redundancy

Readings: Loreau, M., S. Maeem, P. Inchausti, J. Bengtsson, J.P. Grime, A. Hector, D.U. Hooper, M.A. Huston, D. Rafaelli, B. Schmid, D. Tilman, and D. A. Wardle. 2001. Biodiversity and Ecosystem Functioning: Current Knowledge and Future Challenges. Science 294: 804-808.

Recommended: Naeem, S. et al. 1999. Biodiversity and Ecosystem Functioning: Maintaining Natural Life Support Processes. Issues in Ecology, volume 4, 12 pp. (Available on line at http://www.sdsc.edu/~ESA/issues.htm).

Nutrient and Predation Controls on Ecosystem Productivity

  • What is the relative importance of nutrient supply (bottom up) and predation/grazing by consumers (top down) in controlling ecosystem productivity?
  • Trophic cascades and their implications for ecosystem management
  • Introduced species: Do exotic species tend to exert top-down effects?

Readings: Hairston, Nelson G., Frederick E. Smith, & Lawrence B. Slobodkin. 1960. Community structure, population control, and competition. The American Naturalist XCIV(879):421-425.

Vitousek, P.M. 1990. Biological invasions and ecosystem properties: towards an integration of population biology and ecosystem studies: Oikos 57:7-13.

Recommended: Carpenter, Stephen R., James F. Kitchell, & James R. Hodgson. 1985. Cascading trophic interactions and lake productivity. BioScience 35(10):634-639.

 Nutrient Transport by Fishes

  • Importance of migration for N-budget of an estuary: Menhaden in the Gulf of Mexico
  • Nutrient subsidies by Anadromous fish to the forest - Salmon in the Northwest

Readings: 1993. Deegan, L. A. Nutrient and energy transport between estuaries and coastal marine ecosystems by fish migration. Canadian Journal of Fisheries and Aquatic Sciences 50:74-79.

Willson, MF; S.M. Gende, B.H. Marston. 1998. Fishes and the Forest. Bioscience 48(6):455-62.



Ecosystems Assessment of Fisheries Exploitation

  • Status of Fisheries around the world
  • What are the limits of fisheries production

Discussion - Approval for accessing sustainability

Reading: Pauly, D. et al. 2002. Towards Sustainability in World Fisheries. Nature 418:689-695.

 The Hubbard Brook Watershed Story

  • Introduction to the location and idea of HB watershed study
  • Idea of a water budget for a forested watershed (P=I+AET+DGWS+GWR), seasonality of precipitation and average annual hydrologic budget.
  • Changes to hydrologic budget after clearing
  • Change to ion export after clearing (Ca, Mg, K). Changes to NO3- export.
  • Linkage of biogeochemistry to biotic recovery
  • Acid rain and decline of Ca in forest vegetation.

Discussion - Has cleaning up the air jeopardized forest growth?

Reading: Bormann, F.H. and G. E. Likens. 1981. Pattern and Process in a Forested Ecosystem. Pages 138-163, Chapter 5, "Reorganization: Recovery of biotic regulation." Springer Verlag, NY.




Deforestation in the Tropics and the Global Carbon Budget

  • Extent and location of tropical deforestation in the world and in the Amazon.
  • Why people clear forest (population, economic opportunity, land title, role of cattle)
  • Effects on soil and atmospheric biogeochemistry.
  • Parallels to New England history.
  • Changes in C distribution in soils and vegetation along chronosequences; C balance after deforestation
  • What does the flux of carbon from deforestation mean for the global C budget? Are the tropics an annual net source of carbon or not?
  • What can we say about the future (pasteur abandonment or agricultural intensification)?

Readings: Skole, D.S. and C. Tucker. 1993. Tropical deforestation and habitat refragmentation in the Amazon: Satellite data from 1978 to 1988. Science 260:1904-1910.

Nepstad, D.C., A. Alencar, C. Nobre, E. Lima, P. Lefebvre, P. Schlesinger, C. Poter, P. Moutinho, E. Mendoza, M. Cochrane and V. Brooks. 1999. Large-scale impoverishment of Amazonian forests by logging and fire. Nature 398:505-508.

Houghton, R.A., D.L. Skole, C.A. Nobre, J.L. Hackler, K.T. Lawrence, and W.H. Chomentowski. 2000. Annual fluxes of carbon from deforestation and regrowth in the Brazilian Amazon. Nature 403:301-304.

 Human Alteration of Global Element Cycles

What are the major reservoirs and fluxes for each cycle?

  • What processes make the element biologically available (N-fixation, P-weathering, etc)
  • What is the major driver of the fluxes over short and long time scales (focusing on biological vs. chemical controls)? (I also discuss whether or not the behavior is predictable from a thermodynamic point of view.)
  • How has man altered the cycle and what percentage of the major fluxes are driven by anthropogenic activities?

Discussion: Contrast the different cycles from several perspectives and I have the class fill out a comparative table.

Readings: Schlesinger, W.H. 1997. Biogeochemistry Pp. 383-393, 396-400, 402-406.

Nriagu, J. 1996 A history of global metal pollution. Science 272:223-224.

Additional Readings

Bennett, E.M, S.R. Carpenter and N.F. Caraco 2001. Human impact on erodable phosphorus and eutrophication: A global perspective.

Galloway, J.N., W.H. Schlesinger, C. Levy, A. Michaels, and J.L. Schnoor. 1995. Nitrogen fixation: anthropogenic enhancement environmental response. Global Biogeochem. Cycles 9:235-252.

 Loss of "Ecosystem Services"

Concept of ecosystem services

  • Quantifying the value of ecosystem services in regional and global context
  • NY City watershed protection
  • Attempts at global accounting

Reading: Costanza, R., R. d'Arge, R. de Groot, S. Farber, M. Grasso,B. Hannon, K. Limburg, S. Naeem, R.V. O'Neill, J. Paruelo, R.G. Raskin, P. Sutton and M. van den Belt. 1997. The value of the world's ecosystem services and natural capital. Nature 387:253-260.

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