OC 542 / 442 – Estuarine Ecology– Syllabus – Spring 2007
OC 542/ 442 Estuarine Ecology
Dr. Anthony D'Andrea
Burt 204
College of Oceanic and Atmospheric Sciences
541-737-8079
dandrea@coas.oregonstate.edu
http://oregonstate.edu/~dandreaa/Index.html
Overview
This course is designed to provide students with an integrated view of the ecologic processes in
estuarine environments, with a special emphasis on how these processes impact the
biogeochemical cycling of carbon and nitrogen. The major topics of the course include:
introduction to estuarine systems including the geomorphology, physical oceanography and
chemistry of estuaries; abiotic and biotic controls on estuarine nutrient cycling; primary
production by phytoplankton, benthic micro- and macroalgae, and macrophytes; detrital food
webs and carbon cycling; secondary production by benthos, plankton, and nekton; and carbon
and nitrogen cycling in salt marsh, seagrass, open tideflat, and oyster reefs. Particular emphasis
will be placed throughout the course in identifying key differences in ecological processes
between Pacific west coast estuaries and East and Gulf coast estuaries. Class discussions and
current literature will also be used to encourage students to integrate lecture topics and achieve a
comprehensive understanding of how the physical, chemical, and biological properties of
estuaries regulate ecological processes.
Class meetings: There will be 20, each lasting 80-120 minutes. They will generally follow a
lecture format, but I welcome questions and discussion points raised by students. Each of you
has your own knowledge, your own scientific perspective and your own interests. The group is a
small one. We encourage each of you to ask questions, to add things you know from other work
you’ve done and to try to answer questions raised by others.
Learning Outcomes:
•
•
•
All students (graduate and undergraduate) are expected to develop an understanding of the
ecological processes in estuarine systems, demonstrate how these processes affect the cycling
of carbon and nitrogen, and apply these concepts to questions and problems (e.g. nutrient
loading, eutrophication, restoration) in different estuarine systems.
Graduate students taking this course are expected to develop the ability to critically read and
understand papers from the literature, evaluate potential flaws in past or current estuarine
paradigms, articulate ideas, and distinguish prospective future research directions in estuarine
ecology. They also will lead all of the discussion sessions. In addition, they are expected to
integrate information from the course and formulate linkages between estuarine ecosystem
processes and the student’s research (or management) project and/or interests.
Undergraduate students in the course will also develop the ability to critically read and
understand papers from the literature, and actively participate in the discussion sessions.
However, undergraduates will be paired with graduate students during discussion sessions
rather than leading them directly.
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OC 542 / 442 – Estuarine Ecology– Syllabus – Spring 2007
Textbook and other resources
Primary Textbook:
Mann K. H. (2000) Ecology of Coastal Waters: With Implications for Management, Blackwell
Science
Secondary source for selected readings (copies in Patullo Library):
Day, J. W., Jr., C. A. S. Hall, W. M. Kemp, & A. Yanez-Arancibia (1989) Estuarine Ecology.
Wiley, 558 pp. (ISBN 0-471-06263-4) [2 copies in reserve section]
Other good estuarine resources (I have copies in my office):
Alongi, D. (1997) Coastal Ecosystem Processes, CRC Press, 419 pp.
Knox G. A. (1986) Estuarine Ecosystems: A Systems Approach, Vol I. CRC Press
Knox G. A. (1986) Estuarine Ecosystems: A Systems Approach, Vol II. CRC Press
Little C. (2000) The Biology of Soft Shores and Estuaries, Oxford University Press
Valiela, I. (1995) Marine Ecological Processes, 2nd edition, Springer
Bianchi, T. (2006) Biogeochemistry of Estuaries, Oxford University Press [I have a spare copy]
The class will be supplemented by both classic papers covering topics in the course as well as
selected papers dealing with contemporary issues in estuarine ecology.
Readings
Assigned readings will consist of selected chapters from the Mann (2001) textbook, selected
chapters from the Day et al. (1989) textbook on reserve in Patullo, selected chapters from other
books, and journal articles. These assigned readings will be very important. Much of the
factual content of the course is in the readings, so it is imperative that you do them, and that you
do not get behind.
Pre-class readings. Each of these will be associated with a particular class meeting date. The
pre-class readings for the course are listed in the syllabus along with the topics. You should read
these book chapters and journal articles before you come to the corresponding class meeting, and
preferably only a short time beforehand so that the material is fresh in your mind when you come
in.
In addition to the assigned readings, I plan to hand out supplemental reading lists from time to
time during the course (approximately weekly). These are not assignments. You can learn a lot
about the subject of estuarine ecology, and do very well in this course, without reading any of
them. These supplemental papers are not required readings. They are intended to flesh out
information from the lectures, and give you an avenue into the literature on things that may be of
particular interest to you, either during the term or later on.
Access to assigned readings.
Assigned reading is available in three different ways:
1. As PDF files on the College of Oceanic and Atmospheric Sciences (COAS) ‘Terra Firma’
system and the OSU ‘Blackboard’ system. You can save the files or print copies of the
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OC 542 / 442 – Estuarine Ecology– Syllabus – Spring 2007
readings so that you have your own copies. I plan to have readings for a given week posted
by the Friday preceding that week’s lectures. Obviously this will not be possible for week
one.
2. The old-fashioned way, by looking them up. For example, the Day et al. (1998) readings are
accessible from the copies in the reserve section of the Patullo Library (in the Ocean Admin
building). For journal articles, I will give you the full citation for each reading assignment.
All are in textbooks or journals that are readily available, and many are in journals that are
available electronically through the Valley Library. So if you prefer to go to the library and
look them up (either in person or using a computer) it should be easy to do so.
3. By way of the Instructor. If you have any difficulty at all getting hold of these readings by the
methods described above please call, e-mail or see me. This may be particularly useful to
those of you who are not students in COAS. I can show you how to navigate Terra Firma or
Blackboard or, if all else fails, e-mail you a PDF file of any assigned reading. I will also have
hard copies of the readings in a folder in the Reserve section of the Patullo Library in the
COAS Admin building.
Handouts during class meetings.
Before or within a day of each class I will make all the visual materials we used available as PDF
files in the ‘Lecture materials’ folder for that class date on both Terra Firma and Blackboard.
This is so that you can have clean copies of these materials even if you mark up your hard copies
extensively during class (which is encouraged). It will also give you color copies of the slides
presented in color (photographs, maps, conceptual diagrams, etc.) which sometimes lose
considerable information when copied in black and white. As was the case for the reading
assignments, please get hold of me if you would like PDF files of the visual materials shown in
class but have any trouble accessing them off the COAS Terra Firma or OSU Blackboard
systems.
Grading
Grades will be based on a take-home midterm exam, active participation in discussion sessions, a
written research topic paper, a special topics presentation, and overall participation in class
activities.
Take-Home Midterm
30%
Discussion Sessions
20%
Research Topic Paper
25%
Presentation
20%
Participation
5%
Caveats and Small Print
All materials generated for this class, which include but are not limited to syllabi, in-class
materials, and exams, are copyrighted. You do not have the right to distribute these without
written consent of the instructor.
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OC 542 / 442 – Estuarine Ecology– Syllabus – Spring 2007
Plagiarism: As commonly defined, plagiarism consists of passing off as one's own the ideas,
words, writings, etc., which belong to another. In accordance with this definition, you are
committing plagiarism if you copy the work of another person and turn it in as your own, even if
you should have the permission of that person. Plagiarism is one of the worst academic sins, for
the plagiarist destroys the trust among colleagues without which research cannot be safely
communicated. This is a grievous offense and will not be tolerated. Individuals guilty of
plagiarism will be severely penalized.
The American with Disabilities Act (ADA) is a federal anti-discrimination statute that provides
comprehensive civil rights protection for persons with disabilities. Among other things, this
legislation requires that all students with disabilities be guaranteed a learning environment that
provides for reasonable accommodation of their disabilities. If you believe you have a disability
requiring accommodation, please contact the instructor.
Discussion Sessions
There will be three, two-hour discussion sessions during the course. These sessions will involve
themes, current questions, and management issues in estuarine ecology. For each discussion
session, students will read papers from the current literature and be given a list of thought
questions to help guide the discussion. Each discussion session will be led by a group of students
in the class. The purpose is to encourage and train students to critically read the literature,
introduce them to the state of current research, articulate ideas, and recognize potential future
directions in estuarine ecology. Keep in mind that a large part of your grade for these sessions
will be based on active participation in the discussion.
Example:
Discussion 1: Atlantic vs. Pacific: can east coast studies be readily applied to Pacific small river
estuaries?
Discussion 2: Salt marsh: the pulsing and source-sink paradigms
Discussion 3: Eutrophication in estuaries: A case study of Chesapeake Bay
Research Topic Paper
The purpose of this assignment will be to place your research interests or topic within the context
of estuarine ecosystem processes and evaluate your ability to critically read the literature. The
narrative should emphasize an ecosystem perspective and be composed in the following general
format:
Introduction: Briefly explain your research topic. This should be written so a general reader will
know what you are working on and why.
Thesis statement: A formal statement of the primary hypothesis or hypotheses you will be
testing.
Narrative: Three to five pages of text, single-spaced (excluding figures and references), that
explain the linkages between your topic and estuarine processes. I will be looking for how well
you can: (1) synthesize information from the course as it applies to your research (or
management) interests and (2) put your research in an ecosystem perspective. I encourage the
use of figures and illustrations but do NOT include figures handed out during the class.
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OC 542 / 442 – Estuarine Ecology– Syllabus – Spring 2007
The end product of this paper will help you integrate information from the course and hopefully
be useful when you write your research proposal, project report, or thesis.
Group Presentation
The last 2-4 class sessions will be set aside for student lectures on estuarine topics of interest
which were not explicitly covered in the class. The purpose of this is two-fold: (1) have students
integrate information from the course into topics relevant to their interests, and (2) improve the
public speaking and presentation skills of the students. Each student or group will meet with the
instructor to discuss the topics of their presentation, develop a reading list and assign readings,
concisely present the topic in 20-30 minutes, and field questions on the topic and presentation.
example topics can include (but are not limited to):
Eutrophication
Pollution
Salt marsh restoration
Hypoxia
Harmful algal blooms
Estuarine habitat and salmonid life cycles
Management/policy of estuarine systems
Estuarine Fisheries
Non-native species in estuaries
Shellfisheries of estuarine systems
Role of birds in estuarine food webs
Mangrove ecosystems
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OC 542 / 442 – Estuarine Ecology– Syllabus – Spring 2007
OC542 / 442 – Estuarine Ecology– Spring 2007 - Schedule
Date
Lecture
Topic
April 3
April 5
April 10
1
2
3
Overview of course; Intro to estuaries
Estuarine classification
Estuarine physics
April 12
4
Estuarine sediments and sediment properties
April 17
5
Estuarine chemistry and nitrogen cycling
April 19
6
Denitrification in estuarine systems
April 19?
April 24
April 26
May 1
7
8
9
May 3
10
May 8
11
May 10
12
May 10?
May 15
13
May 17
14
May 22
15
May 24
16
May 29
17
May 31
May 31?
18
June 5
June 7
19
20
DISCUSSION 1: Atlantic vs. Pacific: can
east coast studies be readily applied to
Pacific small river estuaries?
Carbon cycle and organic matter in estuaries
Primary production: Phytoplankton
Primary production: Microphytobenthos and
Macroalgae
Primary Production: Macrophytes of salt
marsh and seagrass systems
Relative importance of primary producers in
estuaries
Detritus, microbial processes, and detrital
food webs
Consumers I: Benthos, benthic feeding
types, secondary production, and the
“benthic effect”
DISCUSSION 2: Salt marsh function: the
pulsing and source-sink paradigms
Consumers II: Overview of zooplankton and
nekton in estuaries
Ecosystem processes in salt marshes
Ecosystem processes of seagrass
communities
Ecosystem processes on open tideflats and
oyster reefs
Nitrogen in PNW small river estuaries:
Yaquina Bay case study
Net ecosystem metabolism in estuaries
DISCUSSION 3: Eutrophication in
estuaries: A case study of Chesapeake Bay
STUDENT PRESENTATIONS
STUDENT PRESENTATIONS
Readings
Mann 2001, Ch.1, pp. 1-15
Elliot & McClusky 2002
Kjerve 1989, in Day et al. 1989, Ch 2,
pp. 47-78
Open University 1999, excerpts from
Waves, Tides and Shallow-Water
Processes, Ch. 3 Sediments of shallow
water environments, Ch. 4 Principles
and processes of sediment transport,
Ch. 6 Estuaries
Kemp 1989, in Day et al. 1989,
Ch 3, pp. 79-96,
104-133
Herbert 1999
Seitzinger 1988
see details of assignment
Valiela 1995, Ch 13, pp. 385-424
Mann 2001, Ch 7, pp. 94-100
MacIntyre et al. 1996
Pregnall & Rudy 1985
Mann 2001, Ch 3, pp. 18-30
Mann 2001, Ch 5, pp. 64-78
Mann 2001, Ch 6, pp. 79-92
Mann 2001, Ch 8, pp. 118-135
see details of assignment
Mann 2001, Ch 7, pp. 103-117
Teal 1962
Dame 1989
Williams and Heck 2000
Herman et al. 1999
Newell 2004
Hopkinson & Smith 2005
see details of assignment
to be determined
to be determined
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OC 542 / 442 – Estuarine Ecology– Syllabus – Spring 2007
Detailed References for Assigned Reading
Dame, R. F. 1989. The importance of Spartina alterniflora to Atlantic Coast estuaries. Crit. Rev.
Aquat. Sci. 1: 639-660.
Elliot, M. & D. S. McClusky. 2002. The need for definitions in understanding estuaries. Est.
Coast. Shelf Sci. 55: 815-827.
Herbert, R. A. 1999. Nitrogen cycling in coastal marine ecosystems. FEMS Microbiol. Rev. 23:
563-590.
Herman, P. M. J., J. J. Middelburg, J. Van de Koppel, & C. H. R. Heip. 1999. Ecology of
estuarine macrobenthos. Adv. Ecol. Res. 29: 195-240.
Hopkinson, C. S., Jr. & E. M. Smith. 2005. Estuarine respiration: an overview of benthic,
pelagic, and whole system respiration, p. 122-146. In P. J. le B. Williams and P. A. del
Giorgio [eds.], Respiration in Aquatic Ecosystems. Oxford Univ. Press.
Kemp, W. M. 1989. Ch 3, Estuarine Chemistry, p. 79-144. In J. W. Day, Jr., C. A. S. Hall, W.
M. Kemp and A. Yáñez-Arancibia [eds.], Estuarine Ecology. Wiley.
Kjerve, B. 1989. Ch 2, Estuarine geomorphology and physical oceanography, p. 47-78. In J. W.
Day, Jr., C. A. S. Hall, W. M. Kemp and A. Yáñez-Arancibia [eds.], Estuarine Ecology.
Wiley.
McIntyre, H. L., R. J. Geider, & D. C. Miller. 1996. Microphytobenthos: The ecological role of
the "Secret Garden" of unvegetated, shallow-water marine habitats. I. Distribution,
abundance, and primary production. Estuaries 19: 186-201.
Newell, R. I. E. 2004. Ecosystem influences of natural and cultivated populations of suspensionfeeding bivalve molluscs: A review. J. Shellfish Res. 23: 51-61.
Open_University. 1999. Waves, Tides, and Shallow-Water Processes, excerpts from Ch 2, 3, 4,
6. Open University.
Pregnall, A. M. & P. P. Rudy. 1985. Contribution of green macroalgal mats (Enteromorpha spp.)
to seasonal production in an estuary. Mar. Ecol. Prog. Ser. 24: 167-176.
Seitzinger, S. P. 1988. Denitrification in freshwater and coastal marine systems: Ecological and
geochemical significance. Limnol. Oceanogr. 33: 702-724.
Teal, J. M. 1962. Energy flow in the salt marsh ecosystem of Georgia. Ecology 43: 614-624.
Valiela, I. 1995. Chapter 13: The carbon cycle: Production and transformations of organic
matter, p. 385-424. In I. Valiela [ed.], Marine Ecological Processes. Springer.
Williams, S. L. & K. L. Heck, Jr. 2001. Ch 12, Seagrass Community Ecology, p. 317-337. In M.
D. Bertness, S. D. Gaines and M. E. Hay [eds.], Marine Community Ecology. Sinauer.
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