Instructors: Drs. Michael Lomas and Peter Sedwick, BIOS
Description: This course focuses on the fundamental principles of biological oceanography as they
relate to different marine ecosystems (e.g., pelagic ocean systems, deep-sea vents). Knowledge of
these fundamental principles is applied to the study of nutrient and energy flows within contemporary
marine foodwebs. Practical laboratory exercises are designed to reinforce and integrate
the principles in class. These include field observations in the near shore environment, an oceanographic
cruise to the Hydrostation 'S' Time-series Station, and controlled laboratory experiments.
All exercises are geared to provide exposure to modern biological oceanographic research techniques.
Text: 'Biological Oceanography' by Charles Miller. Other texts on reserve in library.
There will be additional readings from the primary literature that delve into greater detail on relevant
topics through out the course. These are listed in the course syllabus along with the relevant
pages from Lalli and Parsons. It is imperative that these readings be done in advance of the appropriate
lecture to provide the background. The lectures themselves are the forum for the more
in depth examples and discussion of the concepts. Hopefully, this format will promote a more
positive question/answer atmosphere within the class. There are also a number of books that have
been put on reserve in the library, that go into still further detail about specific lecture topics. I encourage
you to use these resources.
Course Requirements:The course is designed for a 14-week period, with two 1.5 hr lectures and
one 3-4 hr lab per week. Grades are based on class participation, laboratory assignments, exams
and an oral presentation based on literature research.
- Exams: Three exams are spaced throughout the course, with the final being a cumulative
exam.
- Lab Reports: You are required to keep a lab notebook for some of the laboratory exercises,
while others will require a more formal lab report format. Both of these formats will be
evaluated as part of your final grade in this course. The formal lab reports should be computer
generated and should include graphs or data tables as appropriate. They will follow
standard scientific format and include the following sections: Introduction (or context for
experiment), Materials and Methods, Results and Discussion, and Conclusions.
- Participation: Group participation and free discussion are the underpinnings of advancing
scientific understanding. Therefore, it is expected that you will get involved in the several
sessions that we have planned for group discussion and oral presentation of your individual
projects.
- Grading: Your final grades will be determined based on the following categories and
percentages.
Exams 50%
Lab (notebook and reports) 40%
Participation (including oral presentation) 10%
WEEK 1
Lecture Period 1&2.
Introduction to Oceanography
Origin of the Earth and Life
Geological Setting of the Ocean
Properties and Composition of Seawater
Ocean Circulation
History of Oceanography
LAB 1. Introduction to the BIOS library -
choose research topic for final oral presentation.
WEEK 2
Lecture Period 3&4.
What is a Phytoplankton ‘Bloom’?
Uncoupling of production and loss processes
Sverdrup - critical depth/compensation depth
Anatomy of a Phytoplankton Bloom -
How does it grow - species succession
How does it end - fates, termination
LAB 2. Microscopy and plankton
quantitation
WEEK 3
Lecture Period 5.
Who are the organisms that bloom
Phytoplankton taxonomy -concept of
functional groups
HAB’s
Lecture Period 6. Primary Production - controls (1)
Light in the sea - Ocean Optics
Phytoplankton pigments
Photoecology
LAB 3: Phytoplankton pigment analysis
WEEK 4
Lecture Period 7&8.
Primary production - controls (2)
Nutrient uptake/Redfield Ratios -
N, P, Si, C, Fe, etc.
N vs. P debate - timescales
New vs. regenerated production
Inorganic vs. organic nutrition
DOP/DON work - contrast with microbial
loop.
Temperature - Eppley Q10
LAB 4: Effect of antifoulants on
phytoplankton growth
WEEK 5
Lecture Period 9. MID-TERM EXAM #1
Lecture Period 10. Marine Microbial Loop
Who, what, where
Bacteria, viruses, Bacterial growth -
How, efficiency, DOC transfer - fate of
spring bloom
Coupling/uncoupling
Controls on bacteria - grazing, viral lysis
LAB 4 - continued: Effects of antifoulants on
phytoplankton growth
WEEK 6
Lecture Period 11. Zooplankton Taxonomy
Methodologies
Morphologies
Lecture Period 12. Zooplankton Feeding
Ecology (1)
Rates and controls
Methodology
LAB 5: Bacteria and virus enumeration
laboratory.
WEEK 7
Lecture Period 13. Zooplankton Feeding Ecology (2)
Species - specific grazing rates (loss of food)
Quantifying Secondary Production (fitting
into models)
Rates and controls
Lecture Period 14. Zooplankton Population Biology
Population Biology
Growth, reproduction
Vertical migration
LAB 6: Zooplankton grazing dilution
experiment
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WEEK 8
Lecture Period 15&16. Regional-Scale Case studies:
Southern Ocean and the Fe hypothesis
JGOFS Process Studies -
LAB 6 - continued: Zooplankton grazing
dilution experiment - completion
WEEK 9
Lecture Period 17. MIDTERM EXAM #2
All day Lecture/Lab. Cruise to hydrostation S;
start iron-nutrient growout experiment
LAB 7 - continued: sampling (t = 1 day)
LAB 7 - continued: sampling (t = 2 day)
WEEK 10
Lecture Period 19&20. The surface ocean at the global
scale.
Satellite oceanography - Ocean view at the
global scale
AVHRR, SeaWiFS, MODIS, etc.
Compare/contrast - the ocean’s biogeographic
and biogeochemical provinces
LAB 7 - continued: Chl analysis for growout
experiment
WEEK 11
Lecture Period 21. Concepts in fisheries
oceanography
Lecture Period 22. Deep-sea biology (1)
Who lives there
Study methods
LAB 8: Biogeochemistry of Mangrove Bay
WEEK 12
Lecture Period 23. Deep-sea biology (2)
Adaptations
Food and energy sources
Lecture Period 24. Climate Change
Principles
Global - El Nino/La nina
Regional/Basin - NAO/PDO
Case Study:Arctic Research
LAB 8 - continued: Biogeochemistry of Man
grove Bay
WEEK 13
Lecture Period 25.Modelling in Biological
Oceanography
1-D/3-D models
NPZD models
Functional group models
Lecture Period 26. The future of Biological
Oceanography - molecular biology
LAB 9: Free period to finalize oral
presentations, complete lab reports, etc.
WEEK 14
Lecture Period 27. Student presentation of oral
reports
Lecture Period 28. FINAL EXAM
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