BOTANY 8850: Terrestrial Biogeochemical Cycling
Investigating hydrologic and elemental flow in the local,
regional, and global environment.

Course Description -

     The principal focus is on plant processes, with mention of animal and microbial processes mediating biogeochemical cycling on land. Major topics include: A survey of global element cycles, properties and functions of biologically essential elements, element acquisition by plants, internal translocation and re-translocation, leaching loss, litter fall, litter decomposition, roles of animals, roles of microorganisms, and finally methods of estimating standing stocks and transfer rates between ecosystem components. Mastery of the theory from lecture and the methodology from lab in this course coupled with report writing, essay writing, and discussion leading should enable most students to pursue most of the nutrient cycling aspects of their research with confidence.

Grading -

Grading policy: this is a points-plus course. The final grade is determined by the number of points earned. Persons aspiring to grades "C" or higher are expected to choose an out-of-the classroom, self directed study program.

Core Requirements -

• 2 midterm examinations ................................ 100 pts each .............. 200
  1 final exam, comprehensive ......................... 300 pts ...................... 300
  10 weekly quizzes ............................................ 5 pts each ..............   50
  6 lab reports..................................................  20 pts/week ............. 200
                                                                                               total ... 750
  
• Self directed study
• 5 Essays .............................................  20 pts each .............. 100
  10 readings .........................................  10 pts each .............. 100
  
• Grading schedule
• Average "C" 70% of points in core requirements (0.7 x 750 =525 ), plus essay no.1 ( 0. 7 x 20 =14)
  and 5 readings (0.7 x 50 =35). Total 574
• Excellent "B" 80% of points in core requirements (0.8 x 750 = 600 ) plus 5 essays (0.8 x 100 =80 ) and 5
  readings ( 0.8 x 50 + 40) (100+50). Total 720
• Superior "A" Achieve 90% in core requirement (0.9 x 750 = 675 ) plus 5 essays (0.9 x 100 = 90) and
  10 readings ( 0.9 x 100 = 90). Total 855
  
  So as to avoid the rush at the end of the quarter for student, teaching assistants and instructor, each student will decide which study plan he or she wishes to follow and inform the instructor by 28 August 2000.
  
• Exams - Exams will focus on problem solving. The will consist of short answer and short essay questions. Answers to some will require sketches or diagrams. Exams 1 and 2 will be designed for completion within 50 minutes and the final within 150 minutes, however, an upper time limit of 2 hours for exams 1 and 2 will be allowed and 4 hours for the final. There will be a premium on thought rather than on speed. The final exam will be 2/3 comprehensive over the entire course and 1/3 on material since exam number two.
• Quizzes will be given at beginning of class each Wednesday(Mondays on midterm weeks) in hopes of encouraging continuous learning rather than pulse learning through the quarter.
  
• Essays - The purpose is to focus your attention as individuals rather than as a group on concepts and thought processes that are important to progress in ecology. The subjects and due dates follow:

• The role of strong inference and of multiple working hypotheses in ecosystem analysis. See the following papers:
• Gullis, R. J. 1977. Statement. Nature 265:764.
• Platt, J. R. 1964. Strong Inference. Science 146:347-353
• Chamberlin, T. C. 1965. The method of the Multiple working hypothesis, Science 148:754-759.

• The role of ecosystem analysis in planning resource management (resources - your imagination).

• A critical appraisal of gaps and potential significance of gaps in our understanding of the cycling of X, where X is an element of your choice. Persons writing essays 3, 4, 5 would choose to write about 3 different elements. You may wish to design a "process level" nutrient cycling study in place of essay #5. This option will be discussed in class. The process might be related to part of your thesis or dissertation research.
  
  The upper limit is 500 words. Essays will be evaluated on scientific content for 0-10 points and on clarity and economy of expression 1-10 points. You must earn at least 10 points on a given essay before a grade will be recorded and the requirement in the self study program is met. Possible point value will depreciate at a rate of 2 per day after the due date.
  
• Outside readings
• Purpose - to familiarize the student with current developments in the biogeochemical cycling literature and to sharpen the students critical reading skills.
• Procedure - Read an article, not a research report or short note, dealing with some aspect of biogeochemical cycling. Papers will be from 1999-2000 journals. Each report will be from a different journal. The numbers of journals containing such articles are too numerous to list here. If you have any questions about suitability of an article or journal please ask the instructor. An original and a carbon or photo copy of each report will be submitted. The report format is:
• Author, Date, Title of paper, journal name, volume, page no.
• Objectives of the paper, hypothesis tested, question or questions asked.
• General methods
• Most important conclusions.
• Your critical appraisal - does the evidence support the conclusions? Is this study a significant contribution to our ecological knowledge? Does it represent your tax dollar well spent?
  
• Text and Reserve reading.
• Text: Likens, et al. 1995?. Biogeochemistry of A Forested Ecosystem. Second Edition. Springer-Verlag, N.Y. ISBN 0-387-94351.-x paper
• Text: Schlesinger, W. H.1991. Biogeochemistry: an analysis of global change. Second Edition. Academic Press. ISBN 0-12-625155-x paper
• Reserve reading: Throughout the quarter you will be referred to books and journals. The more heavily used books will be shelved in room 3524. They will remain in that room through the end of the quarter. I don't want them taken into the laboratory where the chemicals might damage them. A journal sign out sheet is present in room 3524. If you want something xeroxed, you may sign it out for an hour while you visit a copy machine. I insist on keeping library materials in room 3524 because 1) I use these materials regularly, 2) my graduate students use these materials regularly, and 3) I purchased these books and journals with my own salary money thus I can be selfish. If you want to use them in my library I am happy to share them with you.
  
  Laboratory -
• Objectives - Designed to develop practical skills in the estimation of element standing stocks (in plants and soils) and transfer rates, work will begin with sampling in small forest plots. Element fluxes in precipitation, throughfall, stem flow, stream flow and litter fall will be estimated. Soil solutions will be sampled with 2 types of lysimeters. Each student will develop proficiency in preparation of water and tissue samples for analysis. Each student will master analytical methods for determination of NH₄-N, NO₃-N, PO₄-P, and SO₄ by colorimetric means, determination of elements with atomic absorption spectrophotometer, and determination of elements in water and tissue samples with the plasma emission spectrograph. Quality control and computerized data processing will be discussed. With proficiency in analytical methods in hand, the class as a group will analyze a small number of samples. If time permits one laboratory period will be devoted to demonstration of measurement of acetylene reduction to estimate N-fixation and measurement of sulfur evolution from the forest floor.
• Schedule of operations
  Dates Operation
• 22 Aug. Field Site Selection/sampling scheme
• 29 Aug. Prepare collectors for installation
• 5 Sept.
• 12 Sept. Install collectors at field plots: rain, throughfall, stemflow surface runoff, zero tension lysimeters porous cup lysimeters, tension lysimeters.
• 19 Sept. Install collectors at field plots (cont.), Dimensions of biomass, soils samples, forest
  floor
• 15 Sept. Lab Report #1. Description of field site and sampdling
• 26 Sept. Laboratory experience to include
• 3 Oct. a) colorimetric determinations of PO₄, NH₄, NO₃,SO₄, unknowns. b) soil extractable cations, c) exchangeable H+ d) Micro-dumas nitrogen analyzer e) Kjeldahl Nitrogen
• 12 Oct. Atomic absorption spectrophotometric determinations of K and Ca: make standard
  curves, determine unknowns with and without La.
• 17 Oct. Dimensions analysis of a tree - sampling for weight and nutrients.
• 24 Oct. Tour analytical instruments Institute of Ecology, Allometry computations at Plant Sciences Bldg.
• 30 Oct. Lab. Report #3. Allomatric estimation of biomass
• 31 Oct. Lab. demo. ion specific electrodes, ph, micro-Dumas-N
• 7 Nov. Element analysis of tree - grind & ash wood, bark, leaf, root samples, orchard leaf standards for plasma emission spectrograph and Micro-dumas nitrogen analysis or Kjeldahl Nitrogen
• 10 Nov.
• 14 Nov. Analysis of water samples from field plot.
• 17 Nov. Lab Report #5 C and N content of soil. Litter, roots
• 21 Nov. Remove collectors from field site
• 28 Nov. Analysis of samples from field plot (continue)
• 5 Dec. Prepare nutrient budget models for forest plot.
• 8 Dec. is last day of classes
  
• Notebook and lab reports
• Objectives - Each student will emerge from the course with a methods reference notebook which will help them with future work. For most of the methods used, the instructor will provide the appropriate
  bibliographic citations. The student will gain practical experience at ferreting out the critical details of the methods from the original paper and at scaling up or down the quantities of reagents to suit the particular analytical situation. The test reagents will be prepared by the laboratory assistants in order to minimize expenditure of chemicals.
• Laboratory report format (numbers in parenthesis are possible points on that item)
• Title (of the particular element or analytical procedure) (2)
• Methods (3)
• operating range and expected detection limits (from literature)
• rationale or operating principle of the chemical reactions used; the chemical recipe
• rationale or operating principle of the instrument used (this needs to be written out only once for each instrument - e.g. if you use spectrophotometer for P- explain operating principle, but when you use it again for NH₄ or NO₃ don't repeat).
• Results (3)
  1. Listing of data
  2. Sample calculation given in outline form, indicating each step, with letters or words for functions. Notations are defined and all dimensions given.Numerical data for one sample calculation are substituted into the equation and results computed.
  3. Final computed results are tabulated and shown in graphic form if appropriate - this mostly means graphic presentation of standard curves.
  4. Analysis of error - how many significant figures do you have.
• Discussion (4)
  A. Meaning of results
  B. How do results relate to lectures, other labs, your reading, etc.
  C. How would you improve this study.
• Conclusions (1)
• Literature Cited (1) (at a minimum you need to list the source of the methods, in case
  you need to go back to it at a later date).
• Additional points - clarity and brevity of writing (2) and imagination in design and execution (4)
• Lab reports will be due on the Friday one week following the scheduled completion of the exercise.

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