Unit 6.1 - Biogeochemical Modeling Framework
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This page first made public: May 15, 2017
In this unit, students will learn about the dynamic movement of nutrients among and within ecosystems primarily through the reading and discussion of scientific literature. This unit is generally subdivided into three sections: (1) allochthonous inputs (2) the role of organisms in biogeochemical cycles and how ecological theory can be applied to biogeochemistry and (3) how biogeochemical processes can assist in creating solutions for humanity's grand challenges. This unit is designed to provide students with the opportunity to develop their reading and interpretation of scientific literature. Students will also become familiar with the utility of isotopic techniques and their use in biogeochemistry through readings and data analysis of carbon and nitrogen isotopic data sets. Chosen scientific articles are provided, each with their own set of reading questions. Additionally, short introductory materials are provided to introduce students to some of the general concepts and processes in the study of biogeochemistry.
- Increase student proficiency in the reading and interpretation of scientific literature.
- Increase student understanding of how scientific hypotheses are developed and tested.
- Enhance student understanding of how biogeochemical processes are linked over space and time by studying biogeochemical processes at multiple spatial and temporal scales and exploring the role of organisms in nutrient transformations.
Specific Biogeochemistry Learning Goals:
- Introduce students to general biogeochemical concepts, processes, theory and specifically the carbon and nitrogen cycles.
- Students will be able to describe and provide examples of how allochthonous inputs support ecosystems at global and local scales.
- Students will be able to describe the role of organisms in biogeochemical processes.
- Students will be able to describe how forest age and biodiversity affects nutrient uptake and retention within ecosystems.
- Students will be able to describe how organisms can play a key role in solving humanity's grand challenges.
- Students will become familiar with the use of stable isotopes in biogeochemistry and how to interpret stable isotope data.
- Students will be able to identify scientific questions and hypotheses from peer-reviewed scientific literature.
Context for Use
This week-long unit explores biogeochemical processes. It is outlined with the framework of three 75 minutes classes but can be rearranged to fit other class schedules. It is intended to serve as an introduction to the study of biogeochemistry, emphasizing the biological component of the Critical Zone and provides a series of readings form the scientific literature highlighting the dynamic nature of the field. The primary mode of instruction is student-led discussions of classic and contemporary scientific articles. Material and resources are also provided for a series of brief lectures to provide students the required background biological and ecological knowledge needed to understand the nature and motivation behind the questions asked in the example literature. These additional resources have been developed assuming students have had no to little training in the biological sciences. Material and activities are designed for a class size of approximately 20 students and for upper-level undergraduates. Instructors are encouraged to adapt material for students more familiar with the biological sciences and biogeochemical processes and/or larger and smaller class sizes. Minimal resources are needed for this unit.
This unit primarily uses the scientific literature as a teaching and learning tool. Students will use the scientific literature to develop a scientific frame of mind, including identifying certain aspects of the scientific method and thinking critically about results. This objective will be achieved by using different examples of biogeochemical research that will challenge students to think about Critical Zone processes at different spatial and temporal scales while integrating the role of organisms into biogeochemical processes. Carbon and nitrogen isotopic data is also provided. These data, which are based on real studies, can be used for data analysis activities. The application of biogeochemistry toward contemporary and global grand challenges will be explored including climate change and environmental stability.
Description and Teaching Materials
The general design of this unit is built around the reading and analysis of the scientific and biogeochemical literature. Students are expected to arrive to class sections (if taught in person) with the assigned papers read. If reading questions have been assigned these should also be completed prior to class. Questions on the general scientific nature and the specific biogeochemical issues are provided.
The strength of isotopes as a method to measure biogeochemical processes is a pervasive theme throughout this unit with multiple readings demonstrating the utility of isotopic techniques. To provide more experience with isotopic techniques, two Excel-based data sets and teacher notes/extensions are available below. These activities can serve as either an in-class or out-of-class assigment so that students can work with and interpret both carbon and nitrogen isotopic-data. These activities may work particularly well with the Helfield and Naiman (2001) paper on nitrogen isotopes.
Due to the introductory nature of the material, it is highly recommended that a review of the "General Biogeochemistry" slides occurs prior to in-depth discussion. This review could be either an out-of-class assignment prior to the first class session or could be presented on the first day of the unit. The PowerPoint slides are intended to serve as a very general introduction to the four main biogeochemical cycles, to emphasize the multiple compartments that elements cycle through, and the significant role that microorganisms such as bacteria and fungi serve in these cycles. Some slides include brief notes highlighting the main take-home points.
Example lesson: "Borne on the wind and ocean: Gioda et al. (2013) and McDowell (1998). An examination of the relationship between cloud-, rain and dust-derived solutes and nutrients in a tropical rainforest from afar and the effect on local watershed processes. At the Luquillo Mountain CZO, for example, approximately 50% of the Na washed from the watershed in stream flow is from in situ weathering of bedrock, whereas the other 50% is derived from marine aerosols carried to the watershed through the atmosphere. For phosphorus, the largest input is from African dust, and a clear impact of African dust on the Ca and NO3 concentrations in rainfall can be demonstrated. This topic has the advantage of measuring cross-connections between some of the other modules in the curriculum and emphasizes the interconnections of the Earth System at the global scale, and how they affect local-scale phenomena. Additionally, these papers could be used together with McDowell and Fisher (1976) that examines the influence of leaf litter inputs as a source of organic matter and nutrients to streams. The use of these three papers together would demonstrate the role of allochthonous (originating from outside the system) inputs at multiple scales from global to forest-stream ecosystems.
Instructors should select papers according to relevance of topics. It is suggested that each assignment and discussion includes at least 2 papers. Outline below is provided as example. Readings and assigned questions for Day 1 should be assigned during previous class session and likewise for subsequent classes. The readings/assignments have been subdivided into four general categories. Multiple readings have been provided for each section and instructors are encouraged to select the combination of articles that best suits their expertise and the interests of the students.
General Scientific Habits of Mind Question (Can be used with all reading/assignment outlined below): This attachment is found here in the assessment section. These 8 questions are geared at helping students think scientifically about research and literature and can be used with any of the articles listed below. Questions ask students to identify the different components of the scientific method within each paper (e.g. research question, hypotheses) and what components of the Critical Zone are being researched. Questions can be assigned as out-of-class work and/or used in-class to stimulate discussion.
- General Scientific Reading Questions (Microsoft Word 2007 (.docx) 13kB Dec25 16)
Unit 6.1 - Day 1 (75 min total)
Introductory Biogeochemistry Lecture Slides (PowerPoint 2007 (.pptx) 1.4MB May30 17) (30 minutes)
Reading Discussion #1: Read and discuss first set of papers (45 min). Have students submit answers to assigned questions.
Allochthonous Inputs: Borne on the wind and oceans - To highlight how nutrients are introduced into ecosystems the concept of allochthony (from outside the system) is used to demonstrate how biogeochemistry requires an integrated approach over space and time and includes components of scale. This includes wind-borne inputs from the Sahara Desert and marine ecosystems to neo-tropical rain forests, the role of Pacific salmon in delivering marine-derived nitrogen to terrestrial forests and stream ecosystems, and the influence of riparian leaf litter in stream ecosystems.
- Gioda, A. et al. 2013. Chemical constituents in clouds and rainwater in the Puerto Rican rainforest: potential sources and seasonal drivers. Atmospheric Environment. 68:208-220.
- Link to abstract: http://www.sciencedirect.com/science/article/pii/S1352231012010643
- Gioda_etal_Reading_Questions (Microsoft Word 2007 (.docx) 13kB Dec25 16)
- McDowell, W.H. 1998. Internal nutrient fluxes in a Puerto Rican rainforest. Journal of Tropical Ecology. 14: 521-536
- Link to abstract: https://www.cambridge.org/core/journals/journal-of-tropical-ecology/article/internal-nutrient-fluxes-in-a-puerto-rican-rain-forest/63A4085A805EB6078092D252F240FF8F
- McDowell_Reading_Questions (Microsoft Word 2007 (.docx) 13kB Dec25 16)
- McDowell, W.H. and S.G. Fisher. 1976. Autumnal processing of dissolved organic matter in a small woodland stream ecosystem. Ecology. 57: 561-569.
- Link to abstract: http://onlinelibrary.wiley.com/doi/10.2307/1936440/full
- McDowell_Fisher_Reading_Questions (Microsoft Word 2007 (.docx) 13kB Dec25 16)
Unit 6.1 - Day 2 (75 min total)
Reading Discussion #2: Read and discuss second set of papers (45 minutes). Have students submit answers to assigned questions.
The Role of Organisms in Biogeochemistry - The role of organisms in transforming nutrients within ecosystems is explored including how the presence of a top-predator (wolves) influences nitrogen dynamics across the landscape and how marine derived nutrients can be delivered to forests via salmon.
- Bump, J.K. et al. 2009. Wolves modulate soil nutrient heterogeneity and foliar nitrogen by configuring the distribution of ungulate carcasses. Ecology. 90: 3159-3167.
- Link to abstract: http://onlinelibrary.wiley.com/doi/10.1890/09-0292.1/full
- Bump etal. Reading Questions (Microsoft Word 2007 (.docx) 15kB Dec25 16)
- Helfield, J.M. and R.J. Naiman. 2001. Effects of salmon-derived nitrogen on riparian forest growth and implications for stream productivity. Ecology. 82:2403-2409.
- Link to abstract: http://onlinelibrary.wiley.com/doi/10.1890/0012-9658(2001)082%5B2403:EOSDNO%5D2.0.CO;2/full
- Helfield_Naiman_Reading_Questions (Microsoft Word 2007 (.docx) 15kB Dec25 16)
Activity 6.1 - Day 2: Carbon and Nitrogen Isotopes:
Introduce carbon and nitrogen isotope activity (30 minutes)
Isotopic-based techniques are becoming an increasingly powerful and popular tool in biogeochemical research. Two data and Excel-based activities are provided here to give students experience with and interpreting isotopic data and additional experience creating and interpreting graphs. The first activity includes "made-up" 12C and 13C data to look at the effects of precipitation and drought on two different species of trees. The second activity uses 15N data based on Marks et al. (2009) to study the effects of invasive fish species on the structure of aquatic food webs. Below instructors can find an introductory handout with follow-up and extension questions and the associated Excel sheets.
Unit 6.1 - Day 3 (75 min total)
Reading Discussion #3: Read and discuss third set of papers (45 minutes). Have students submit answers to assigned questions.
Ecological Theory, Biodiversity and Biogeochemistry - The effect of forest age and the effect of biological diversity on nutrient retention and ecosystem stability is explored using examples from two Long Term Ecological Research (LTER) sites: Hubbard Brook Experimental Forest (New Hampshire) and Cedar Creek (Minnesota). The Vitousek and Rainers (1975) paper on forest age/succession and nutrient uptake also provides a nice example of classic scientific literature in which the impact is still felt nearly 40 years later.
- Vitousek, P.M. and W. A. Rainers. 1975. Ecosystem succession and nutrient retention: a hypothesis. Bioscience. 25: 376-381
- Link to abstract: http://bioscience.oxfordjournals.org/content/25/6/376.short
- Vitousek_Reiners_Reading_Questions (Microsoft Word 2007 (.docx) 15kB Dec25 16)
- Tilman D. et al. 1996. Productivity and sustainability influenced by biodiversity in grassland ecosystems. Nature. 379: 718-720.
- Link to abstract: http://www.nature.com/nature/journal/v379/n6567/abs/379718a0.html
- Tilman et al. Reading Questions (Microsoft Word 2007 (.docx) 13kB Dec25 16)
Grand Challenges - Examples from the scientific literature demonstrate how biogeochemical theory can be useful in creating solutions for humanity's grand challenges. Examples include the role of nitrogen in global climate change and how excess nutrients may be removed from ecosystems.
- Hungate et al. 2003. Nitrogen and climate change. Science. 302: 1512.
- Link to abstract: http://science.sciencemag.org/content/302/5650/1512
- Hungate_etal_Reading Questions (Microsoft Word 2007 (.docx) 15kB Dec25 16)
- Mulholland et al. 2008. Stream denitrification across biomes and its response to anthropogenic nitrate loading. Nature. 452: 202-205.
- Link to abstract: http://www.nature.com/nature/journal/v452/n7184/abs/nature06686.html
- Mulholland et al. Reading Questions (Microsoft Word 2007 (.docx) 16kB Dec25 16)
Review/discuss carbon and nitrogen isotope activity (30 minutes).
Experimental Design Presentation (Optional: See Assessment Section Below): Students design a scientific experiment using stable isotopic techniques that is a follow-up study to one of the research articles used in class. Students, individually or in small groups, present their ideas in a PowerPoint format to their classmates highlighting their research questions, scientific hypotheses, experimental techniques, and why their research question is important for the understanding of Critical Zone processes. Students should be encouraged to ask questions of their peers after each presentation. The provided rubric outlines 8 scientific metrics and 8 presentation metrics to evaluate each student and their presentation. Individual point values have been omitted from the rubric so that each instructor can assign point values to elements that they believed should be stressed and to appropriately complement the design of their course. A Word document outlining some general PowerPoint tips is also provided.
Scientific Presentation Rubric (Microsoft Word 2007 (.docx) 16kB Dec25 16)
General PowerPoint Tips (Microsoft Word 2007 (.docx) 16kB Dec25 16)
Teaching Notes and Tips
It is not expected that all papers provided are used. The unit was developed so that a diverse array of literature was provided for the instructor to select from based on their expertise and the interest of the student.
Although all students are expected to read all articles, it is recommended that students be assigned into small groups to lead each discussion. Leaders are also expected to bring to class a series of thought-provoking questions (~5 questions) to stimulate class discussion. These questions could also be submitted in advance and assigned as an out-of-class graded assignment to be completed prior to discussion.
Some papers have complicated and very detailed methods likely outside the scope of an introductory Critical Zone course. For these particular papers, students should be encouraged to read through each methods section with the objective of understanding the larger idea of what the scientists did to test their hypotheses and what they measured as opposed to the details of how variables were measured.
The carbon and nitrogen isotopic data sets also provide a good opportunity to reinforce or introduce Excel skills. These data sets can be used to introduce basic Excel manipulations and calculations (e.g. means, standard error), graph building, and simple statistical analyses (e.g. Student's ttests) for basic hypothesis testing. The associated Word document complementing the two Excel data sheets provides basic isotopic introductory material, sets of instructions, and multiple follow-up questions for discussion and lesson extension.
Three assessment tools are outlined here.
1) General Scientific Habits of Mind Question: This attachment is found here in the assessment section. These 8 questions are intended to help students think scientifically about research and literature and can be used with any of the articles listed below. Questions ask students to identify the different components of the scientific method within each paper (e.g. research question, hypotheses) and what components of the Critical Zone are being researched. Questions can be assigned as out-of-class work and/or used in-class to stimulate discussion.
2) Specific Reading Questions: For each paper a series of 5-6 questions are offered with brief bullet-pointed answers. These assignments are located under the link for each individual paper in the "References and Resources" section. Questions ask students to think more critically about each paper with respect to the biogeochemical and Critical Zone research that the paper exemplifies. Questions can be assigned as out-of-class work and/or used in-class to stimulate discussion.
3) Activity 6.1 - Carbon and Nitrogen Isotopes: Isotopic-based techniques are becoming an increasingly powerful and popular tool in biogeochemical research. Two data and Excel-based activities are provided here to give students experience with and interpreting isotopic data and additional experience creating and interpreting graphs. The first activity includes "made-up" 12C and 13C data to look at the effects of precipitation and drought on two different species of trees. The second activity uses 15N data based on Marks et al. (2009) to study the effects of invasive fish species on the structure of aquatic food webs. Below instructors can find an introductory handout with follow-up and extension questions and the associated Excel sheets.
4) Capstone (Optional): If the instructor is interested in using a larger capstone-like activity for the Biogeochemistry section, one activity is briefly outlined below. This capstone activity will extend the Biogeochemistry section beyond the original three 75 minute class periods. Thus the incorporation of these capstone activities are the instructor's prerogative and should be based on student interest. Presenting science publicly in an oral format is also an important scientific skill. The associated rubric scores students on their development of a scientific idea as well as their development and presentation of the science. The instructor should emphasize to the students the characteristics of a good PowerPoint presentation and well-received public speaking. Giving an example presentation is an excellent way for students to understand the elements of a good scientific talk. It is recommended that the instructor proceed through a talk completely followed by a second time illustrating and highlighting the individual components of the talk. This activity stresses that good science doesn't just happen in the field; rather, it begins, and even requires, the ability to develop interesting, important, and creative ideas and question.
References and Resources
- Weiss, S.B. 1999. Cows, cars, and checkerspot butterflies: nitrogen deposition and management of nutrient-poor grasslands for a threatened species. Conservation Biology. 13: 1476-1486
- Link to abstract: http://onlinelibrary.wiley.com/doi/10.1046/j.1523-1739.1999.98468.x/full
- McClain, M.E. et al. 2003. Biogeochemical hot spots and hot moments at the interface of terrestrial and aquatic ecosystems. Ecosystems. 6: 301-312.
- Link to abstract: http://www.jstor.org/stable/3659030?seq=1#page_scan_tab_contents
- Zak, D.R. et al. 2006: A Molecular Dawn for Biogeochemistry. Trends in Ecology and Evolution. 21: 288-295.
- Link to abstract: http://www.sciencedirect.com/science/article/pii/S0169534706001273
- Swap, R. et al. 1992. Saharan dust in the Amazon Basin. Tellus. 44B: 133-149.
- Link to abstract: http://onlinelibrary.wiley.com/doi/10.1034/j.1600-0889.1992.t01-1-00005.x/abstract
- Lavery, T.J. et al. 2010. Iron defecation by sperm whales stimulates carbon export in the Southern Ocean. Proceedings of the Royal Society B: Biological Sciences. 277: 3527-3531.