7.47    BIOLOGICAL OCEANOGRAPHY
Spring 2007
Course Description and Syllabus

PLEASE NOTE: MOST LINKS NO LONGER WORK FROM THIS WEBPAGE

Ver. 10 May 2007

Instructors:
Stace Beaulieu (macro-biology), Blake 203, x3536, stace@whoi.edu, Stace's homepage

Stefan Sievert (micro-biology), Watson 207, x2305, ssievert@whoi.edu, Stefan’s homepage

Teaching Assistant:
Stacy DeRuiter, MRF 225, x3254, sderuiter@whoi.edu, Stacy’s homepage

Class Meetings:
Tuesdays 12:45 - 2:15 PM and Thursdays 1 - 2:30 PM
Weeks 1 - 7 (6 Feb - 20 Mar), Redfield 204
Weeks 7 - 11 (22 Mar - 19 Apr), Watson Conf. Room
Weeks 12 - 15 (24 Apr - 17 May), Redfield 204
Recitation   Thursdays 11 - 12 noon, Redfield 204

Course website (password protected):
http://www.whoi.edu/science/B/people/sbeaulieu/teaching/BO_Spr2007/

General course description:
This course is designed to present an intensive overview of biological oceanography. Major biological paradigms and processes in the ocean will be discussed, and the dependence of biological processes on physical and chemical aspects of the environment will be examined.  The course will survey the diversity of marine habitats and the major groups of taxa inhabiting those habitats.  The course will emphasize processes rather than individual taxa, including the production, consumption, and remineralization of organic material in the ocean, as well as the factors controlling those processes.  The structure of marine food webs and the flow of energy within different marine habitats will be detailed and contrasted.

General course format:
The course will be primarily lecture and associated discussions combined with recitation led by the TA.  One class period will involve a student debate on a current topic in biological oceanography.  There will also be a laboratory/field component held mainly during recitation. One class period will be devoted to a hands-on plankton lab.  This is a graded course (not 'pass/fail').  Two problem sets will be assigned, covering the first 1/3 and second 1/3 of the course, respectively.  Students will also conduct a semester-long writing assignment, proposing a research project in biological oceanography.  A final exam will be held in the second to last class period, with the final class period devoted to a review of student proposals.

Evaluation criteria:
Students will receive letter grades for the course, determined by performance in 4 areas:
- Proposal and proposal review (35%),
- Final Exam (30%),
- Problem sets (20%)
- Class participation, including debate and field component (15%).

Reading assignments:
Reading assignments will come from the primary literature and will be posted to the course website, prior to the lecture.
Suggested background readings will come from the following textbooks:
- Biological Oceanography.  By C. Miller (2004) Blackwell Publishing.
- Biological Oceanography: An introduction.  2nd ed. by C. Lalli and T. Parsons (1997) Butterworth-Heinemann.
- Marine Community Ecology. Eds. M.D. Bertness, S.D. Gaines, M.E. Hay (2000) Sinauer Associates.
- Microbial Ecology of the Oceans. Ed. by D. Kirchman (2000) Wiley.
- Biology of the Prokaryotes. Ed. by Lengeler, J.W. et al. (1999) Blackwell Science.

In addition to the above, copies of the following books will be reserved in the Redfield 204 reading room:
- Biological Oceanographic Processes.  3rd ed. by T. Parsons, M. Takahashi, and B. Hargrave (1984) Pergamon.
- Concepts in Biological Oceanography: An Interdisciplinary Primer. By P. Jumars (1993) Oxford UP.
- Dynamics of Marine Ecosystems: Biological-Physical Interactions in the Oceans. 2nd ed. by K. Mann and J. Lazier (1996) Blackwell Science (Note: 3rd ed. published 2006).
- Ecological Geography of the Sea. By A. Longhurst (1998) Academic (Note: new ed. published 2006).
- Fluid Mechanics for Marine Ecologists. By S. Massel (1999) Springer.
- Marine Ecological Processes. 2nd ed. by I. Valiela (1995) Springer.
- Marine Ecosystems and Climate Variation. Ed. by N. Stenseth et al. (2004) Oxford UP.
- Ocean Biogeochemical Dynamics. By J. Sarmiento and N. Gruber (2006) Princeton UP.

Research proposal:
Each student will write a proposal on a topic of his or her choosing.  These proposals should identify an intriguing question and offer reasonable approaches to solving it and can be related to planned thesis work.  Topics should be approved by the instructors early in the term, and a general outline and preliminary bibliography will be due in early March.  The TA will have copies of past students’ proposals and of instructors’ NSF proposals for you to use as examples.

Guidelines.  We expect the text of these proposals to be 10 pages in length (12 pt Times New Roman Font, double spaced) and no longer, this includes figures and tables.  Citations to appropriate literature are required, and are in addition to the 10 pages. Required components are similar to the NSF grant format, including the following section subheadings:  Project summary, Background and rationale, Proposed work (Approach, experimental design, and methods), and Significance (or Broader impacts). The project summary should be no longer than one page and should effectively summarize the motivation, research plan, and broader impacts.  The rest of the sections can be can be of varying lengths depending on the project being proposed.  Please limit your proposed work to a total of 3 years, with total expenses less than $100,000 (not including salary).  We would like you to submit a brief budget justification (1 paragraph, to follow your references).  If your proposal is submitted without following the above guidelines (e.g. over page limit), there will be a grade reduction.

For grading of these proposals, both content and writing quality (style, clarity, organization, etc.) will be evaluated and weighted equally.  Drafts will be reviewed by the instructors and returned for revision 2 weeks prior to the due date for final versions. As part of the assignment, final proposals will be reviewed by peers and instructors, and all students will participate in a mock NSF review panel in the final class period.

Teaching Assistant and Recitation:
The TA, Stacy DeRuiter, will lead the recitation sessions. If you have a question to raise in recitation, please email it to the TA in advance of the session.  Although attendance is optional, the recitation session gives the TA an opportunity to explain material from lecture and readings, present supplementary material, and answer students’ questions about assignments. The TA will be involved in grading assignments.
Throughout the semester, we will be collecting plankton and sediment samples (alternating each week) for you to look at under a microscope during the recitation sections.  Observations of the weekly samples will be used in our plankton lab class on 15 March and will be considered when developing the final exam.
Real-time data for local waters:
- Nantucket Sound Ferry (temperature, chlorophyll)
- Martha's Vineyard Coastal Observatory (temperature, solar radiation)

Field Trip:
We will have one field trip near the end of the semester (we'll choose May 1, 2, 3, or 4 at 1 - 4PM), to provide you with an overview of coastal habitats as well as sampling methods in biological oceanography.  Due to tides, the field trip must be held outside of class hours (thus, attendance is optional).  We will go to Woodneck Beach and marsh, and groups will be assigned exploratory projects to conduct during the field trip.  Concepts pertinent to the field trip will be considered when developing the final exam.

Schedule	Tues 12:45 - 2:15 PM			Thurs 1 - 2:30 PM			Thurs 11 - 12 noon
Week #	Date	Class #	Instructor/ Subject/ Topics/ ASSIGNMENTS/ Readings	Date	Class #	Instructor/ Subject/ Topics/ ASSIGNMENTS/ Readings	Recitation
1	6 Feb	1	Beaulieu/ Introduction 1/ Introduction, history, and recent achievements in Bio Oce/ Lecture PDF, refs Barber and Hilting (2000) "Achievements in biological oceanography" Background reading: L&P Chap. 1.	8 Feb	2	Beaulieu/ Introduction 2/ Physical context and introduction to marine ecosystem model/ Lecture PDF, refs Werner et al. (2004) "Modelling marine ecosystems and their environmental forcing" Background reading: L&P Chap. 2, Miller Chap. 4.	NO RECITATION
2	13 Feb	3	Beaulieu/ Phytoplankton 1/ Photosynthesis, primary production, and the spring bloom/ Lecture PDF, refs Behrenfeld et al. (2005) Global Biogeochemical Cycles Background reading: L&P Chap. 3, Miller Chaps. 1 & 3.	15 Feb	4	Guest: Dyhrman/ Phytoplankton 2/ Phytoplankton diversity/ Lecture PDF, refs Riebessell et al. (2000) Nature Background reading: Miller Chap. 2.	Plankton sample #1
3	20 Feb		NO CLASS: HOLIDAY	22 Feb	5	Beaulieu/ Phytoplankton 3/ New production, export, and the biological pump/ PROPOSAL IDEA DUE/ Lecture PDF, refs Eppley and Peterson (1979) Nature Background reading: L&P Chap. 5, Miller Chap. 16.	Benthic sample #1 (start microbial column experiment)
4	27 Feb	6	Beaulieu/ Zooplankton 1/ Zooplankton diversity and patchiness/ Lecture PDF, refs Haury et al. (1978) "Patterns and processes in the time-space scales of plankton distributions" Folt and Burns (1999) TREE Background reading: L&P Chap. 4, Miller Chap. 6.	1 Mar	7	Beaulieu/ Zooplankton 2/ Zooplankton in the marine ecosystem model, with focus on grazing and diel vertical migration/ Lecture PDF, refs Franks (2002) Journal of Oceanography Steinberg et al. (2000) DSRI Background reading: Miller Chaps. 7 & 8.	Plankton sample #2 Discuss Problem Set #1
5	6 Mar	8	Beaulieu/ Zooplankton 3/ Larval ecology, with focus on biological-physical interactions/ PROBLEM SET 1 DUE/ Lecture PDF, refs Shanks and Brink (2005) MEPS Background reading: BGH Chap. 7.	8 Mar	9	Beaulieu/ Nekton 1/ Fish larvae to fisheries oceanography/ Lecture PDF, refs Thorrold et al. (2001) Science Pauly et al. (2002) Nature Background reading: L&P Chap. 6, Miller Chap. 15.	Benthic sample #2 Follow-up to Problem Set #1
6	13 Mar	10	Beaulieu and DeRuiter/ Nekton 2/ Apex predators and marine mammals/ PROPOSAL OUTLINE AND REFERENCES DUE/ Apex predators: PDF, refs Marine mammals: PDF Block et al. (2005) Nature Tuna-Dolphin Issue, NOAA webpage	15 Mar	11	Beaulieu/ PLANKTON LAB (Plankton sample #3)	Additional follow-up to Problem Set #1
7	20 Mar	12	DEBATE	22 Mar	13	Sievert/ Microbes 1/ Introduction to Marine Microbiology/ Lecture PDF (large file) Pomeroy (1974) BioScience Background reading: Kirchman Ch. 1, Miller Ch. 5.	Benthic sample #3
8	27 Mar		NO CLASS: SPRING BREAK	29 Mar		NO CLASS: SPRING BREAK	NO RECITATION
9	3 Apr	14	Sievert/ Microbes 2/ The Microbial World: Nutrition, Metabolic Diversity and Microbial Ecology/ Lecture PDF (large file) Fuchs et al. (2007) Background reading: Kirchman Chaps. 2 and 4, Azam and Worden (2004).	5 Apr	15	Sievert/ Microbes 3/ Microbial control of element cycles: Overview/ PROPOSAL FULL DRAFT DUE/ Lecture PDF (black/white) Deutsch et al. (2007) Background reading: Lengeler et al. Chaps. 30 and 32, Kirchman  Chap. 15.	Plankton sample #4
10	10 Apr	16	Sievert/ Microbes 4/ Water column processes, including the microbial loop/ Lecture PDF (black/white) DeLong et al. (2006) Background reading: Kirchman Chaps. 3 and 5, Cho and Azam (1988), Smith et al. (1992).	12 Apr	17	Sievert/ Ecological geography/ Biomes/ PROBLEM SET 2 DUE (Friday)/ Lecture PDF Follows et al. (2007) Background reading: Miller Chap. 10, Paul: Chap. 2.	Benthic sample #4, Discuss Problem Set #2
11	17 Apr		NO CLASS: HOLIDAY	19 Apr	18	Sievert/ Microbes 5/ Sediment microbiology/ Lecture PDF (large file) Biddle et al. (2006) PNAS Background reading: Jorgensen and D'Hondt (2006); Banfield and Nealson: Chap. 1.	Assess microbial column experiment, Follow-up to Problem Set #2
12	24 Apr	19	**back to Redfield 2-04** Beaulieu/ Benthic 1/ Intertidal habitats/ FINAL PROPOSALS DUE/ Lecture PDF, refs Barry et al. (1995) Science Silliman et al. (2005) Science Background reading: BGH Chaps. 9 & 11; L&P Chap. 8.1-8.2.	26 Apr	20	Beaulieu/ Benthic 2/ Soft-bottom subtidal habitats, with focus on the benthic boundary layer/ Lecture PDF, refs Rhoads (1974) OMBAR Background reading: BGH Chap. 10, Miller Chap. 13.	Plankton sample #5 (last sample), Classic papers in rocky intertidal ecology: Connell (1961) Paine (1966) Sousa (1979)
13	1 May	21	Guest: Tarrant/ and Beaulieu/ Benthic 3/ Corals reefs and marine protected areas/ Lecture PDF Mumby et al. (2006) Science Palumbi (2002) Pew Oceans Commission report Background reading: BGH Chap. 15.	3 May	22	Beaulieu/ Benthic 4/ Myths of the deep sea/ Lecture PDF, refs Grassle and Maciolek (1992) American Naturalist Background reading: BGH Chap. 14, L&P Chap. 8.8, Miller Chap. 12.	Last year's BBL problem set; Guidance for proposal review; Benthic sample #5 = Field Trip, Friday, 4 May, 1:30 - 4:30 PM, Woodneck Beach
14	8 May	23	Sievert/ Microbes 6/ e.g. Hydrothermal vents and cold seeps: I. Microbes/ PROPOSAL REVIEW DUE/ Lecture PDF (large file) Reysenbach et al. (2006) Nature Background reading: Van Dover: Chaps. 5 & 6.	10 May	24	Beaulieu/ Benthic 5/ Hydrothermal vents and cold seeps: II. Macrofauna/ Lecture PDF, refs VanDover and Lutz (2004) JEMBE Background reading: L&P Chap. 8.9, Miller Chap. 14.	Prep. for final exam
15	15 May	25	FINAL EXAM Click for last year's exam	17 May	26	PROPOSAL PANEL REVIEW