Estuarine Biology

ESTUARINE BIOLOGY (BI 454/554, 5 credits)

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 Tuesday of exam week

ACTUAL and detailed SCHEDULE for Fall 2009

PLEASE NOTE: This is subject to change, but it will give you an idea of what the course will include.

ESTUARINE BIOLOGY (BI 454/554, 5 credits) Instructor: Richard Emlet, TA: Paul Dunn

Class Schedule: Tuesdays, 8:30* - 17:00 and Fridays, 13:30-14:30   *See exceptions below

Week 1

Sept 29 No class Richard & Paul will be on a research cruise

Oct 2   No discussion - Richard & Paul still on cruise

Week 2 Introduction to estuaries, tides and benthic organisms

October 8 (Thursday)* 08:48 +3.07ft low

08:30   Lecture: Introduction to the class, goals.

09:00 Lecture: Overview of estuaries – importance, distribution in space and time.

10:30   trip to floating docks to see fouling communities

11:30   discussion
13:15   Lecture on tides

14:30   Set up and deploy fouling plate study

Oct 9 13:30 Discussion

Week 3 Benthic organisms and physical properties of an estuary (we meet two full days this week)

Oct 12 (Monday)* 08:18 +6.05ft; 13:36 +3.45ft; 19:27 +6.78ft

08:30 Lecture: Types of estuaries and circulation

10:10   Field trip: Boat trip up Coos Estuary – sampling stations for temp salinity, sediments

15:00 Start work up data from cruise (homework - make graphs from CB transect)

Oct 13 (Tuesday) 14:55 +2.69ft low

08:30 Lecture: Estuarine circulation and sedimentation, +/- oxygen, other physical characteristics

10:00 Continue work on getting CTD data analyzed

13:15 Field trip: Portside mudflat/sandflat to collect fauna & sediments

16:00 Laboratory: Set up aquaria w/ sieved sediments and organisms

Oct 16 13:30 Discussion



Week 4 The estuarine environment and boundary layers

Oct 20 07:38 +2.65ft; 13:38 +8.43ft

08:30   Lecture on boundary layers

10:00   Field Field trip to measure boundary layers

14:00 Work up boundary layer data

Oct 23 13:30 Discussion

Week 5 Salt Marshes

Oct 27    08:38 +6.07ft; 14:28 +3.37ft; 20:01 +5.74ft

08:30   Estuarine Organism Quiz (on fouling and mudflat organisms)

09:30   Lecture: Saltmarshes

10:45   Lecture: Mangroves & contrasts with salt marshes

13:00 Fieldtrip to Metcalf Marsh, plant identification, quantitative transects

16:00 Begin laboratory to work up field samples

Oct 30 13:30 Discussion

(DAYLIGHT SAVINGS TIME ENDS THIS WEEK END)

Week 6 Benthic Communities

Nov 3     11:32 +8.74ft; 18:25 -1.15ft

08:30 Midterm Exam I

14:00   Lecture: Estuarine animals & infaunal community interactions I.

16:30   Field trip to Dome House sand flat for quantitative sampling of infauna

Nov 6 13:30 Discussion



Week 7 More on Benthic Communities

Nov 10   12:34 +2.89ft low

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.

Nov 13            13:30 Discussion

Week 8 Seagrasses, Phytoplankton, and Detritus

Nov 17   11:32 +8.67ft; 18:29 -1.02 low; Sunset 16:55

8:30     Lecture: Seagrass communities, importance & ecology

10:00   Possibly work on sediment samples

13:15   Lecture: Lecture: Estuarine production, detritus and energy flows

14:30 Lab: Re-weigh saltmarsh plants and sediments.

15:30   Field trip to SSNERR ?

Nov 20            13:30 Discussion

Week 9 Estuarine Sediments and Anoxia

Nov 24 11:31 +3.69ft low

08:30 Lecture: Decomposition, sediment chemistry and biogeochemical cycling

10:00   Field trip trawling on "RV PLUTEUS" to collect subtidal organisms of the Coos estuary

13:30   Lab examination of morning catch

Nov 27 NO DISCUSSION -- Thanksgiving Break

Week 10   Fouling Communities and Negative Estuaries

Dec 1 10:24 +8.99; 17:27 -1.24ft

08:30   Lecture: Fouling communities and Introduced Species

10:00   Collect fouling plate experiment and evaluate

13:00 Lecture: Negative estuaries and other topics TBA

15:00   Lab clean up.

Dec 4   13:30 Discussion

Dec 9 Final Exam is Tuesday of exam week: 8:30 to 10:30 am in classroom.

Estuarine Biology 2009, Fall Quarter OIMB

LIST OF PAPERS FOR WEEKLY DISCUSSIONS: We meet on Friday’s @ 13:30

Wk 1 (Oct 2) No Discussion

Wk 2 (Oct 9)

1) Lotze, H. K., H. S. Lenihan, et al. (2006.) Depletion, degradation, and recovery potential of estuaries and coastal seas. Science 312: 1806-1809.

2) Thrush, S. F., J. Halliday, et al. (2008). The effects of habitat loss, fragmentation, and community homogenization on resilience in estuaries. Ecological Applications 18(1): 12-21.

Wk 3 (Oct 16):

1) Roegner, G.C. and A.L. Shanks (2001) Import of coastally derived chlorophyll a to South Slough Oregon. Estuaries 24: 244-256.

2) Rand, P. S., S. G. Hinch, et al. (2006) Effects of river discharge, temperature, and future climates on energetics and mortality of adult migrating Fraser River sockeye salmon." Trans. Amer. Fish. Soc. 135(3): 655-667.

Wk 4 (Oct 23):

1) Miller, B. A. and S. Sadro (2003) Residence time and seasonal movements of juvenile coho salmon in the ecotone and lower estuary of Winchester Creek, South Slough, Oregon. Trans. Amer. Fish. Soc. 132(3): 546-559.

2) Magnuson, A. & R. Hilborn (2003) Estuarine influence on survival rates of Coho (Oncorhychus kisutch) and Chinook salmon (Oncorhynchus tshawytsha) released from hatcheries on the US Pacific coast. Estuaries 26: 1094-1103.

Wk 5 (Oct 30):

1) Hacker, S. D. and M. D. Bertness (1999). Experimental evidence for factors maintaining plant species diversity in a New England salt marsh. Ecology 80(6): 2064-2073.

2) Sala, N. M., M. D. Bertness, et al. (2008). "The dynamics of bottom-up and top-down control in a New England salt marsh." Oikos 117(7): 1050-1056.

Wk 6 (Nov 6):

1) Micheli, F.1997. Effects of predator foraging behavior on patterns of prey mortality in soft bottoms. Ecological Monographs 67: 203-224.

Wk 7 (Nov 13):

1) Lenihan, H. S., C. H. Peterson, et al. (2001). Cascading of habitat degradation: oyster reefs invaded by refugee fishes escaping stress." Ecological Applications 11(3): 764-782.

2) Altieri, A. H. (2008). Dead zones enhance key fisheries species by providing predation refuge. Ecology 89(10): 2808-2818.

Wk 8 (Nov 20):

1) 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.

2) Chanton, J. and F. G. Lewis (2002). "Examination of coupling between primary and secondary production in a river-dominated estuary: Apalachicola Bay, Florida, U.S.A. Limnol. Oceanogr. 47(3): 683-697.

Wk9 (Nov 27) No class

Wk10 (Dec 4):

1) Beck, N.G. and K.W. Bruland. 2000. Diel biogeochemical cycling in a hyperventilating shallow estuarine environment. Estuaries 23: 177-187.

2) Gribsholt, B., J. E. Kostka, et al. (2003). Impact of fiddler crabs and plant roots on sediment biogeochemistry in a Georgia saltmarsh. Marine Ecology-Progress Series 259: 237-251.