The Assignment:
The purpose of this assignment is to force you to think like a biogeochemist. Working with data that is always incomplete and imperfect, biogeochemists must build testable models (both conceptual and mathematical) for what governs the rates, magnitudes and pool sizes of element cycles through ecosystems. Essentially, you are being challenged to scale up from many piecemeal observations (published data) to a synthetic model that is consistent with those observations.
To do this, you should use one of 4 approaches:
1) Construct a regional or global budget for an element based on the best available data and/or revise an existing budget based on new information (e.g.). I encourage you to use this assignment to revise one of the global cycles printed in your textbook by adding data published since 2013.
Examples:
2) Scale up from a small scale process to a regional or global rate. Again if you like this idea but are stumped, choose one of the global rates from your textbook and update the estimates (or reduce their uncertainty) with more recent data.
Examples:
3) Develop (or add data to) a statistical or process based model that shows how a biogeochemical rate, pool size or relationship changes along an environmental gradient (natural or experimental) (Again, there are many such figures throughout your textbook and you can choose to update these or to try something new).
Examples
4) Perform a formal metanalysis to examine whether there are consistent ecosystem responses to manipulative experiments.
Examples
In making this attempt you will be forced to deal with uncertainty, you will have to make assumptions based on the best available data at hand and you will (hopefully) thereby recognize the critical data needs for answering the question that initially motivated your analyses. Because this is a challenging assignment I will provide feedback at several points through the semester.
For your PROJECT PROSPECTUS you must select and articulate your question, write a one or two paragraph description of your proposed approach to addressing it, and provide a list of relevant citations from which you will acquire the necessary data. You are welcome to work in groups. You will receive two peer reviews in addition to reviews from both your TA and instructor within one week. I will meet with each group individually to make sure you are on the right track. Click Rubric for evaluating Synthesis Project Prospectus for detailed on what we are looking for in your project prospectus
For your DATA COMPILATION you must hand in a data compilation that should include most of the relevant data available in the literature for addressing your question. For example, if you are building a global budget for Boron (e.g. Park & Schlesinger 2002) you will want to make it clear what pools and flux data you have found, and what is missing in the literature. Alternatively, if you are looking at how an environmental variable affects an important biogeochemical rate (e.g. how does K affect plant growth, Tripler et al. 2006) you will want to provide synthesized data in tables or graphs to describe the patterns you see. Within 1 week I will provide feedback to improve your dataset and to suggest approaches to data synthesis and analysis. I will schedule one on one meetings with folks who are struggling. Click Rubric for Data Compilation Assignment for detailed instructions and grading schema.
For your FINAL SYNTHESIS PAPER there is no page requirement. I expect that you will present your question and justify your effort by describing the importance of understanding this process/budget. You will then present the data as clearly as possible, and discuss the implications.
This paper and a formal presentation of your findings will be worth 40% of your final grade.
Still need some inspiration? Check out this collection of earlier synthesis papers from previous versions of the course. Feel free to use these as a jumping off point for your own project.
The topics are intentionally open ended. In the past many students have used their synthesis projects as a chapter in their dissertation or as part of their MP. I encourage you to choose a topic near and dear to your heart. Some of you may even end up publishing your project.
Papers arising from Duke Biogeochemistry course:
Lee, M.R., E.S. Bernhardt, P. M. van Bodegom J.H.C. Cornelissen, J. Kattge, D.C. Laughlin, Ü. Niinemets, J. Peñuelas, P.B. Reich, B. Yguel, and J.P. Wright. 2017. Invasive species’ leaf traits and dissimilarity from natives shape their impact on nitrogen cycling: a meta-analysis. New Phytologist 213:128-139.
Singh, N.K., W.M. Reyes, E.S. Bernhardt, R. Bhattacharya, J.L. Meyer, J.K. Knoepp, R.E. Emanuel. 2016. Hydro-Climatological Influences on Long-Term Dissolved Organic Carbon in a Mountain Stream of the Southeastern United States. Journal of Environmental Quality 45: 1286-1295.
Carmichael, M.J., E.S. Bernhardt, S.L. Bräuer and W.K. Smith. 2014. The Role of Vegetation in Methane Flux to the Atmosphere: Should Vegetation be Included as a Distinct Category in the Global Methane Budget. Biogeochemistry 119: 1-24.
Sudduth, E.B., S.S. Perakis and E.S. Bernhardt. 2013. Nitrate in watersheds: straight from soils to streams? JGR-Biogeosciences 118: 291-302.
Cha, Y, C. Stow and E.S. Bernhardt. 2013. Dreissenid invasion impacts on chlorophyll and total phosphorus in 25 US lake ecosystems. Freshwater Biology 58: 192-206.
The purpose of this assignment is to force you to think like a biogeochemist. Working with data that is always incomplete and imperfect, biogeochemists must build testable models (both conceptual and mathematical) for what governs the rates, magnitudes and pool sizes of element cycles through ecosystems. Essentially, you are being challenged to scale up from many piecemeal observations (published data) to a synthetic model that is consistent with those observations.
To do this, you should use one of 4 approaches:
1) Construct a regional or global budget for an element based on the best available data and/or revise an existing budget based on new information (e.g.). I encourage you to use this assignment to revise one of the global cycles printed in your textbook by adding data published since 2013.
Examples:
- Park & Schlesinger 2002. Global biogeochemical cycle of boron. Global Biogeochemical Cycles 16: 1072.
- Klee and Graedel. 2004. Elemental Cycles: A status report on human or natural dominance. Ann. Rev. Environ and Resour. 29: 69-107.
- Cole et al. 2007. Plumbing the global carbon cycle: integrating inland waters into the terrestrial carbon budget. Ecosystems 10: 171-184.
2) Scale up from a small scale process to a regional or global rate. Again if you like this idea but are stumped, choose one of the global rates from your textbook and update the estimates (or reduce their uncertainty) with more recent data.
Examples:
- Tranvik et al. 2009. Lakes and reservoirs as regulators of carbon cycling and climate. Limnology and Oceanography. 54: 2298-2314.
- Keppler et al. 2006 Methane emissions from terrestrial plants under aerobic conditions. Nature 439: 187-191.**hopefully without the major mathematical error Keppler made
- [Don’t be afraid to pick something silly] Schlesinger et al. 1993. Arboreal Sprint Failure: Lizardfall in a California Oak Woodland. Ecology ,74: 2465-2467.
3) Develop (or add data to) a statistical or process based model that shows how a biogeochemical rate, pool size or relationship changes along an environmental gradient (natural or experimental) (Again, there are many such figures throughout your textbook and you can choose to update these or to try something new).
Examples
- Elser et al. 2007. Global analysis of nitrogen and phosphorus limitation of primary producers in freshwater, marine, and terrestrial ecosystems. Ecology Letters 10: 1135–1142
- Mills and Arrigo 2010. Magnitude of oceanic nitrogen fixation influenced by the nutrient uptake ration of phytoplankton. Nature Geoscience 3: 412-416.
- Cha et al. 2012. Impacts of dreissenid mussel invasions on chlorophyll and total phosphorus in 25 lakes in the USA. Freshwater Biology**this last paper was developed by Cha as her synthesis project in the 2011 version of the course
4) Perform a formal metanalysis to examine whether there are consistent ecosystem responses to manipulative experiments.
Examples
- Rustad et al. 2001. A meta-analysis of the response of soil respiration, net N mineralization, and aboveground plant growth to experimental ecosystem warming. Oecologia 126: 543-562.
- LeBauer and Treseder 2008. Nitrogen limitation of net primary productivity in terrestrial ecosystems is globally distributed. Ecology 89: 371-379.
- Wu et al. 2011. Responses of terrestrial ecosystems to temperature and precipitation change: a meta-analysis of experimental manipulation. Global Change Biology 17: 927-942.
In making this attempt you will be forced to deal with uncertainty, you will have to make assumptions based on the best available data at hand and you will (hopefully) thereby recognize the critical data needs for answering the question that initially motivated your analyses. Because this is a challenging assignment I will provide feedback at several points through the semester.
For your PROJECT PROSPECTUS you must select and articulate your question, write a one or two paragraph description of your proposed approach to addressing it, and provide a list of relevant citations from which you will acquire the necessary data. You are welcome to work in groups. You will receive two peer reviews in addition to reviews from both your TA and instructor within one week. I will meet with each group individually to make sure you are on the right track. Click Rubric for evaluating Synthesis Project Prospectus for detailed on what we are looking for in your project prospectus
For your DATA COMPILATION you must hand in a data compilation that should include most of the relevant data available in the literature for addressing your question. For example, if you are building a global budget for Boron (e.g. Park & Schlesinger 2002) you will want to make it clear what pools and flux data you have found, and what is missing in the literature. Alternatively, if you are looking at how an environmental variable affects an important biogeochemical rate (e.g. how does K affect plant growth, Tripler et al. 2006) you will want to provide synthesized data in tables or graphs to describe the patterns you see. Within 1 week I will provide feedback to improve your dataset and to suggest approaches to data synthesis and analysis. I will schedule one on one meetings with folks who are struggling. Click Rubric for Data Compilation Assignment for detailed instructions and grading schema.
For your FINAL SYNTHESIS PAPER there is no page requirement. I expect that you will present your question and justify your effort by describing the importance of understanding this process/budget. You will then present the data as clearly as possible, and discuss the implications.
This paper and a formal presentation of your findings will be worth 40% of your final grade.
Still need some inspiration? Check out this collection of earlier synthesis papers from previous versions of the course. Feel free to use these as a jumping off point for your own project.
The topics are intentionally open ended. In the past many students have used their synthesis projects as a chapter in their dissertation or as part of their MP. I encourage you to choose a topic near and dear to your heart. Some of you may even end up publishing your project.
Papers arising from Duke Biogeochemistry course:
Lee, M.R., E.S. Bernhardt, P. M. van Bodegom J.H.C. Cornelissen, J. Kattge, D.C. Laughlin, Ü. Niinemets, J. Peñuelas, P.B. Reich, B. Yguel, and J.P. Wright. 2017. Invasive species’ leaf traits and dissimilarity from natives shape their impact on nitrogen cycling: a meta-analysis. New Phytologist 213:128-139.
Singh, N.K., W.M. Reyes, E.S. Bernhardt, R. Bhattacharya, J.L. Meyer, J.K. Knoepp, R.E. Emanuel. 2016. Hydro-Climatological Influences on Long-Term Dissolved Organic Carbon in a Mountain Stream of the Southeastern United States. Journal of Environmental Quality 45: 1286-1295.
Carmichael, M.J., E.S. Bernhardt, S.L. Bräuer and W.K. Smith. 2014. The Role of Vegetation in Methane Flux to the Atmosphere: Should Vegetation be Included as a Distinct Category in the Global Methane Budget. Biogeochemistry 119: 1-24.
Sudduth, E.B., S.S. Perakis and E.S. Bernhardt. 2013. Nitrate in watersheds: straight from soils to streams? JGR-Biogeosciences 118: 291-302.
Cha, Y, C. Stow and E.S. Bernhardt. 2013. Dreissenid invasion impacts on chlorophyll and total phosphorus in 25 US lake ecosystems. Freshwater Biology 58: 192-206.