ESTUARINE BIOLOGY (BI 454/554, 5 credits)

This course will be taught in Fall 2012 @ OIMB by R. Emlet.

See also:



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 an estuary (circulation and sedimentation)

Week 3   Salt Marshes started

Week 4   Salt Marshes continued & Mangrove comparisons

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 Tuesday Dec 7 of exam week


ACTUAL and detailed SCHEDULE from Fall 2011

PLEASE NOTE: This is subject to change on 2012, but it will give you an idea of what the course will include.


ESTUARINE BIOLOGY (BI 454/554, 5 credits)

Class Schedule:  Tuesday, 8:30* - 17:00 and Fridays, 11:00-12:00   *See exceptions below


Week 1  Introduction to estuaries, tides and benthic organisms

Sept 27   06:21 +0.36 ft hLow

*07:20 Field trip to Portside mudflat - collect infaunal organisms

  09:45 Lecture: Introduction to the class, goals.

  10:15 Lecture: Overview of estuaries – importance, distribution in space and time.

  11:15 Sieve mud and set up aquaria of sediment

  13:15 Finish sieving and settling up aquaria with organisms

  14:15 Field trip to floating docks to see fouling communities/introduced species/water movement

  16:00 Discuss, plan, set-up, and deploy fouling plate study…

Sept 30 11:00  Discussion


Week 2   Benthic organisms and physical properties of an estuary

October 4   07:21  +5.85 ft lHigh (sunrise: 07:18)      12:36 +3.35 ft hLow

08:30   Lecture: Types of estuaries and circulation

10:00   Field trip: Boat trip up Coos Estuary – sampling stations for temp salinity, sediments

            Group 1 depart at 10:00 am

            Group 2 meet at x and arrive at exchange site at x

16:00   Lecture: Tides

Oct 7   11:00 Discussion


Week 3 

Oct 11    06:15 +1.80 ft hLow  12:21 +7.7 ft hHigh; 18:50 +0.47 ft lLow

08:30   Lecture:  Estuarine sedimentation AND gradients, +/- oxygen, other physical characteristics

10:00   Start work up data from cruise (homework - make graphs from CB transect)

            Sometime today: talk about the CB CTD transect and Secchi data

Oct 14 11:00 Discussion


Week 4 Saltmarshes

Oct 18   10:19 +3.81 ft hLow 16:13 +6.91 ft hHigh

08:30   Lecture: Saltmarshes

10:00   Fieldtrip to Metcalf Marsh, plant identification, quantitative transects

13:15   Begin laboratory to work up field samples

16:00   Lecture: Mangroves - replacement of salt-marsh in the tropics

Oct 21 11:00 Discussion


Week 5 The estuarine environment and boundary layers 

Oct 25             11:15 +8:58 ft hHigh  17:53 -0.76 ft lLow

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

09:30   Lecture on boundary layers

11:00   Laboratory: Process samples salt marsh samples.

13:15   Field trip to measure boundary layers

15:30   Work up boundary layer data

Oct 28 11:00 Discussion        


Week 6 Benthic Communities

Nov 1     11:06  +3.34 ft hLow     16:53 +7.12 ft hHigh
08:30   Midterm Exam I

10:30   Lecture: Larval biology in estuaries.

11:30   Laboratory - weigh sediment and plant samples  

13:15   Lecture: Estuarine animals & infaunal community interactions I.

14:30   Bring in settlement plates and evaluate 6 week outcome.

Nov 4  11:00 Discussion




Week 7 More on Benthic Communities 

Nov 8     16:54  +0.37 ft lLow   (sunset 17:00)

8:30     Lecture: Infaunal community interactions  II.

10:00   Lecture: Infaunal community interactions  III.

15:15   Field trip to Dome House sand flat for quantitative sampling of infauna.         

Nov 11            11:00 Discussion


Week 8  Seagrasses, Phytoplankton and Detritus Estuarine

Nov 15   08:18 +3.78 ft  hLow  14:02 +7.46 ft hHigh

08:30   Lecture: Seagrass communities, importance & ecology

10:00   Lecture: Estuaries: Planktonic communities and patterns

1100   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 or plankton sampling?

Nov 18            11:00 Discussion


Week 9  Sediments and Anoxia

Nov 22   08:55 +8.5 ft hHigh   15:50 -0.48 ft lLow  (sunset 16:47)

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

13:15      Convene in lab, look at and key out organisms collected on morning dredge trip. 
Nov 25 No discussion (Thanksgiving)


Week 10  Fouling Communities and Negative Estuaries

Nov 29  08:46 +3.15 hLow 

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 2   11:00 Discussion


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





Estuarine Biology 2011, Fall Quarter OIMB



Wk 1(Sept 30)

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

2) Elliott, M. and A. K. Whitfield (2011) Challenging paradigms in estuarine ecology and management. Estuarine, Coastal

       and Shelf Science 94: 306-314. (pdf)


Wk 2 (Oct 7):

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

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: 655-667. (pdf)


Wk 3 (Oct 14):

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: 546-559. (pdf)

2) Hering, D.K., D.L. Bottom, E.F. Prentice, K.K. Jones, and I.A. Fleming (2010) Tidal movements and residency of subyearling Chinook salmon (Oncorhynchus tshawytscha) in an Oregon salt marsh channel.  Can. J. Fish. Aquatic. Sci. 67:524-533 (pdf)


Wk 4 (Oct 21):

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: 2064-2073. (pdf)

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: 1050-1056. (pdf)


Wk 5 (Oct 28):

1) Woodin, S.A., D.S. Wethey, and N. Volkenborn (2010) Infaunal hydraulic ecosystem engineers: cast of characters and impacts.  Integr. Comp. Biol. 50: 176-187.  (pdf)


Wk 6 (Nov 4):

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


Wk 7 (Nov 11):

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: 764-782. (pdf)

2) Seitz, R.D., D.M. Dauer, R.J. Llansó and W.C. Long. (2009) Broad-scale effects of hypoxia on benthic community structure

       in Chesapeake Bay, USA. Journal of Experimental Marine Biology and Ecology 381, Supplement: S4-S12. (pdf)


Wk 8 (Nov 18):

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. (pdf)

2) Howe, E. and C. Simenstad (2011)  Isotopic determination of food web origins in restoring and ancient estuarine wetlands of the San Francisco Bay and Delta. Estuaries and Coasts 34: 597-617. (pdf)


Wk 9  (Nov 25) Thanksgiving break - No class


Wk10 (Dec 2):

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

2) Paerl, H. W., L. M. Valdes, et al. (2006) Anthropogenic and climatic influences on the eutrophication of large estuarine ecosystems. Limnology and Oceanography 51(1): 448-462. (pdf)