ESTUARINE BIOLOGY (BI
454/554, 5 credits)
See also: http://darkwing.uoregon.edu/~oimb/Academics/fall.htm
ESTUARINE
BIOLOGY (BI 454/554, 5 credits) --- class meets all day, one day each
week, and for an additional hour on Friday
Week
1 Intro. to estuaries, tides and benthic
organisms 
Week 2 Physical
properties of estuaries
Week 3 Estuarine sedimentation and a transect of the Coos estuary
Week 4 Salt Marshes
Week 5 Seagrasses,
phytoplankton, and detritus
Week 6 Benthic communities
Week 7 more on Benthic infaunal Communities
Week 8 Estuarine Sediments and Anoxia
Week 9 Fouling Communities
Week 10 Wrap up and
overviews
Final Exam is on the class day of exam week
ACTUAL and detailed SCHEDULE
from Fall 2005
PLEASE
NOTE: This is subject to change in 2007, but it will give you an idea of what
the course will include.
ESTUARINE BIOLOGY (BI
454/554, 5 credits)
Class
Schedule: Mondays, 8:30* - 17:00 and Fridays,
1:00-2:00 *See exceptions below
Week 1 Introduction to estuaries, tides and
benthic organisms
09:00* Lecture: Introduction to the class, goals.
10:00 Lecture: Overview of estuaries; lecture on tides.
13:00 Field trip: Road trip around the estuary (South Slough, Coos River)
16:00 Lecture: Types of estuaries and circulation
Sept 30 1:00 Discussion
Week 2 Benthic organisms and physical properties of an estuary
Oct 3 HLow Tide: +1.1ft @ 06:24
07:00* Field trip: Port Side mudflat/sandflat to collect fauna & intact sediments
10:00 Lecture: Estuarine circulation and sedimentation, +/- oxygen, other physical characteristics
13:15 Lab: Set up aquaria w/ sieved sediments; examine organisms, record obsv’s, place orgs.in aquaria.
Oct 7 1:00 Discussion
Week 3 Estuarine sedimentation and transect
Oct 10 LHigh Tide +4.7ft @ 07:06 HLow Tide: +3.9ft @ 11:06 HHigh Tide +6.6ft @ 17:03
08:30 Diversity and productivity
10:00 Field trip: Boat trip up Coos Estuary – sampling stations for temp salinity, sediments
16:00 Work up data from cruise (homework - make graphs from CB transect)
Oct 14 1:00 DiscussionOct 17 HLow Tide: +1.6ft @ 06.38 LLow Tide -0.9ft @ 19:32
08:30 Lecture on Salt Marshes
10:00 more on salt marshes
11:00 Mangroves & contrasts with salt marshes
15:00 Fieldtrip to Metcalf Marsh, plant identification, quantitative transects
17:30 Set out salt marsh plants, measure samples.
Oct 21 1:00 Discussion
Week 5 Seagrasses, Phtyoplankton, and Detritus
Oct 24 HLow Tide: +4.0ft @ 11:26 HHigh Tide +5.7ft @ 17:01
08:30 Estuarine Organism Quiz (on mudflat and salt marsh organisms)
9:00 Lecture: Boundary layers; Seagrass communities, importance & ecology
10:00 Lecture: Planktonic production in estuaries
11:30 Possibly work on sediment samples
13:15 Lecture: Lecture: Estuarine production, detritus and energy flows
Oct 28 1:00 Discussion
(DAYLIGHT SAVINGS TIME ENDS THIS WEEK END)
Oct 31 LLow Tide +0.2ft @ 16:56
08:30 Midterm Exam I
10:30 Lecture: Research lecture on juvenile performance along an estuarine barnacle.
13:15 Lecture: Estuarine animals & infaunal community interactions I.
14:30 Field trip to Dome House sand flat for quantitative sampling of infauna
Nov 4 1:00 Discussion
Week 7 More on Benthic Communities
Nov 7 HLow Tide +3.8ft @ 08:54
8:30 Lecture: Infaunal community interactions II.
10:00 Lecture: Infaunal community interactions III.
13:15 Laboratory: Work up data from quantitative samples AND process marsh sediment samples.
Lab examination of morning catch
Nov 11 1:00 Discussion
Week 8 Estuarine Sediments and Anoxia
Nov 14 LLow Tide: -0.8ft @ 16:52
08:30 Lecture: Decomposition, sediment chemistry and biogeochemical cycling
09:30 trip and Lab: Trawling on "RV PLUTEUS" to collect subtidal organisms of the Coos estuary
13:30 Lab examination of morning catch
Nov 18 1:00 Discussion
Week 9 Fouling Communities
Nov 21 HLow Tide: +3.9ft @ 08:50
08:30 Lecture: Estuaries: Planktonic communities and patterns
10:00 Lecture: Estuaries: Fouling communities and Introduced Species
13:00 Finalize and present data on sediment analyses
Nov 25 NO CLASS – Thanksgiving Break
Week 10 Wrap up & overviews
Nov 28 HLow Tide: +0.2ft @ 15:54
08:30 Lecture: Negative estuaries and other topics TBA
10:00 Lecture: Human impacts on estuaries
11:30 Course evaluation.
13:00: Lab clean up.
Dec 2 1:00 Discussion
Dec 5 Final Exam is Monday of exam week: 8:30 to 10:30 am in classroom.
LIST OF PAPERS FOR WEEKLY DISCUSSIONS: We meet on Friday @ 1:00
Wk 1 (Sept 30):
Odum, E.P. (1969) The strategy of ecosystem development. Science 164: 262-70.
Wk 2: (Oct 7):
1)Beamish et al. 1994. The effect of Frazier River discharge on interannual production of Pacific salmon and herring in the Strait of Georgia. Can. J. Fish. Aquat. Sci. 51: 2843-2855.
2) Roegner, G.C. and A.L. Shanks (2001) Import of coastally derived chlorophyll a to South Slough Oregon. Estuaries 24: 244-256.
Wk 3 (Oct 14):
1) Langlois, E., A. Bonis, and J.B. Bouzillé (2003) Sediment and plant dynamics in salt marshes pioneer zone: Puccinellia maritime as a key species? Estuarine Coastal & Shelf Science 56: 239-249.
2) Bertness, M.D, and S.D. Hacker (1994) Physical stress and positive associations among marsh plants. American Naturalist 144: 363-372
Wk 4 (Oct 21):
1) Ruckelshaus, M.H., R.C. Wismar and C.A. Simenstad (1993) The importance of autotroph distribution to mussel growth in a well-mixed temperate estuary. Estuaries 16: 898-912.
2) Marguillier, S. et al. (1997) Trophic relationships in an interlinked mangrove-seagrass ecosystem as traced by ∆ 13C and ∆ 15N. Mar. Ecol. Prog. Ser. 151: 115-121.
Wk 5 (Oct 28):
1) Miller, J.A. and C.A. Simenstad (1997) A comparative assessment of a natural and created estuarine slough as a rearing habitat for juvenile chinook and coho salmon. Estuaries 20: 792-806.
2) Gross, M.R. et al. 1988. Aquatic productivity and the evolution of diadromous fish migration. Science 239: 1291-1293.
Wk 6 (Nov 4):
1) Morgan, C.A. et al. (1997) Sink or swim? Copepod population maintenance in the Columbia River estuarine turbidity-maxima region. Marine Biology 129: 309-317.
2) DeVries, M.C. et al. (1994) Abundance of estuarine crab larvae is associated with tidal hydrologic variables. Marine Biology 118: 403-413.
Wk 7 (Nov 11):
1) Micheli, F.1997. Effects of predator foraging behavior on patterns of prey mortality in soft bottoms. Ecological Monographs 67: 203-224.
2) TBA
Wk 8 (Nov 18):
1) Beck, N.G. and K.W. Bruland. 2000. Diel biogeochemical cycling in a hyperventilating shallow estuarine environment. Estuaries 23: 177-187.
2) Woodin, S.A., R.L. Marinelli, and S.M. Lindsay (1998) Process-specific cues for recruitment in sedimentary environments: geochemical signals? J. Marine Research 56: 535-558.
Wk 10 (Dec 2):
1) Paerl, H.W., J.L. Pinckney, J.M. Fear, and B.L. Peierls. (1998) Ecosystem responses to internal and watershed organic matter loading: consequences for hypoxia in the eutrophying Neuse River Estuary, North Carolina, USA. Mar. Ecol. Prog. Ser. 166: 17-25.
2) Lenihan, H.S. and C.H. Peterson (1998) How habitat degradation through fishery disturbance enhances impacts of hypoxia on oyster reefs. Ecological Applications 8: 128-140.