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Outline of the Course

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Outline of the Course

I. Introduction to the course and a description of marine environments (Class 1 )

A. Course logistics

B. Definitions of terms and some concepts

C. Survey of discussion topics


II. Chapter 1 Introduction to benthic organisms & feeding guilds (Class 2 )

A. Case studies

  1. Jumars & Fauchald’s 1977 classification of feeding guilds
  2. Cammen’s (1980) model of ingestion rate

B. Classifications of marine benthic organisms

  1. Macrofauna, meiofauna, and microfauna
  2. Benthic Feeding Guilds & Functional groups

III. Chapter 2 Microphytobenthos & benthic primary production (Class 3 )

A. Case studies

1. Savin Hill Cove

a. Gould & Gallagher (1990)

2. Ems Dollard

a. Admiraal et al. (1982)
b. Admiraal (1984)

B. Benthic diatoms

Chapter 3 Bioturbation (Class 4 )
A. Case Studies
  1. Cammen (1980)
  2. Boudreau (1998)
  3. Shull (2001)
B. What is Bioturbation? C. Why is it important? D. How is it measured? E. Effects of the benthic infauna on sediment geochemistry F. Pelletization
Chapter 4 Benthic population processes (Class 5 )

A. Case studies

  1. Gallagher et al. (1990)
  2. Competition

B. Predation

C. Amensalism

VI. Chapter 5 General patterns of community structure (Class 6 )

A. Case studies

1. Jumars & Gallagher (1982)

B. Methods to describe community structure

  1. Diversity indices
  2. Classification
  3. Ordination
  4. Canonical Analysis

C. Factors controlling community structure

  1. Biogeography
  2. Environmental Factors
  3. Biological interactions

D. Examples

  1. The intermediate disturbance hypothesis
  2. Succession in the Skagit flats
  3. EMAP Virginian Province data

E. Deep-sea community structure and patterns of marine biodiversity (Class 9)

F. Case studies

G. Patterns of deep-sea community structure

H. Sanders’ stability-time hypothesis

I. Other hypotheses for patterns of deep-sea diversity.

VII. Chapter 6 Effects of pollution on marine benthic communities (Class 10)

A. Case studies

  1. Organic enrichment gradients Rhoads et al. (1978)
  2. The West Falmouth oilspill, Grassle & Grassle (1974)

B. General Principles

C. Effects on communities

D. Effects on individuals

E. Statistical models for monitoring and assessing the effects of pollution

F. Chapter 7 Effects of pollution in East Coast Benthos

1. Case studies

a.The EMAP program
b.Boston Harbor: Gallagher & Keay (1998)
c.New Bedford Harbor

G. EPA’s EMAP program & patterns of east coast community structure: salinity effects dominate

H. Effects of pollution on Boston Harbor, New Bedford Harbor, and MA Bay benthos

ECOS 630 Biol. Ocean. Processes Syllabus, P. 15 of 34.


VIII. Chapter 8 P, B, and ì: the fundamental units of phytoplankton ecology (Class 11)

A. Readings

  1. Eppley (1972)
  2. Lorenzen (1966)
  3. Gallagher’s Chapter 1

B. Distinguishing among B, P, and ì: Biomass, production and specific growth rate

C. C:Chl a ratios Gallegos & Vant (1996)

D. The effects of temperature on ìmax Ahlgren (1987)

Chapter 9 The C-14 & oxygen methods (Class 12)
A. Readings 1. Peterson (1980) Estimating primary production using the 14C and O2 methods. B. The great productivity debate
Chapter 10 Environmental factors controlling primary production: Light (Class 13)

A. Readings

1. Required:

a. Harrison et al. (1985)
b. Falkowski & Raven (1997)

B. What is photosynthesis?

C. P vs. I curves

  1. simulated in situ incubations.
  2. Jassby-Platt equation
  3. Estimating primary production using the P vs. I approach in MA Bay.

D. Diel and vertical patterns of production.

E. Photoadaptation & photoinhibition

F. Importance of light quality

XI. Chapter 11 Environmental factors controlling primary production: Nutrient limitation (Class 11 )

A. Readings

  1. Howarth (1988)
  2. Liebig’s Law of the minimum and Brandt’s denitrification hypothesis

B. Phytoplankton growth & the nitrogen cycle

C. Chemostats in oceanography

1. Coupling N uptake and growth with Michaelis-Menten style equations

a.The Droop equation & the cell quota
b.Caperon & Meyer’s equation
c.growth kinetics

2. Goldman’s relative growth rate and the Redfield ratio

D. Other nutrients: P, Si, metals (Fe and Zn)

XII. Chapter 12 The spring and fall blooms (Class 12 )

A. Readings

1. Required

a. Sverdrup (1953)

ECOS 630 Biol. Ocean. Processes Syllabus, P. 16 of 34.

b. Townsend & Spinrad (1986)

2. Recommended: Parsons et al. (1966)

B. Sverdrup’s critical depth concept

  1. Non-dimensional critical depth
  2. The vernal bloom in the North Pacific and North Atlantic.
    1. The spring bloom in MA Bay
      1. Nelson & Smith’s (1991) explanation for the lack of an Antarctic bloom
      2. The timing of the MA Bay bloom

C. The fall bloom

XIII. Chapter 13 Upwellling & El Niño (Class 13 )

A. Case studies

  1. Ryther et al. (1971)
  2. Mann & Lazier (1996)

B. The physics of upwelling

  1. The role of wind stress
  2. Ekman spiral, Ekman mass transport
  3. coastal upwelling
  4. Equatorial divergences

C. Succession at upwelling centers

D. Upwelling and fish production

E. Upwelling and bottom-water anoxia off New Jersey

F. El Niño and La Niña

XIV. Chapter 14 Production in the coastal zone (Class 14 )

A. Case studies

  1. Riley (1967)
  2. Eppley et al. (1979)

B. Why Nitrogen is the key limiting nutrient in the sea

C. The advection-diffusion equation, and the importance of horizontal and vertical eddy diffusive fluxes of nitrate

D. Box and Markov models of nitrogen transport

E. The role of vertical stability and the importance of horizontal nutrient transport

XV. In class midterm examination (10/24/06 Tu, Class 15 )

XVI. Chapter 15 Production in Harbors and Bays, especially MA Bay (Class 16 )

A. Case studies

  1. Cole & Cloern (1987)
  2. McGillicuddy et al. (2003)
  3. Boston Harbor

a. Adams et al. (1992)

B. Types of estuaries and fronts

C. The seasonal cycle of production in MA Bay

D. The N cycle in the Gulf of Maine, MA Bay, Boston Harbor

E. Edmondson’s definition of eutrophication

F. Effects of light and nutrients and the Cole-Cloern/ Platt relationship.

G. The vertical distribution of phytoplankton & the subsurface chlorophyll maximum

H. Effects of the MWRA outfall

  1. Importance of vertical stratification
  2. Secondary treatment and phytoplankton biochemical oxygen demand
  3. Upwelling & hypoxia in NJ

XVII. Chapter 16 Primary production in the oceanic gyres (Class 17 )

A. Case studies

  1. Platt et al. (1989)
  2. Rates of production in gyres.
  3. Problems with the 14C method.
  4. Indirect measures of primary production

B. Models of gyre production.

  1. Are the gyres analogous to a chemostats?
  2. Goldman et al.’s (1978) micro-nutrient patch hypothesis
  3. The two-layer hypothesis
  4. The role of mesoscale phenomena

XVIII. Chapter 17 Satellite remote sensing of Chl a and primary production (Class 18 )

A. Case studies

  1. Platt & Sathyendranath (1986)
  2. Behrenfield & Falkowski (1997)

B. Types of satellites and their sensors

C. The CZCS algorithm to estimate Chl a

D. Estimating primary production from space.


XIX. Chapter 11 Zooplankton grazing mechanisms (Class 19 )

A. Case studies

1. Koehl & Strikler (1981)

B. Life at Low Reynolds number

C. Frost’s empirical relationships between grazing and phytoplankton

D. Interaction between phytoplankton size and grazing

E. How to measure zooplankton grazing rates.

F. Are noxious phytoplankton blooms in the coastal zone due to lack of grazing, eutrophication, or both?

XX. Chapter 12 Predation on zooplankton (Class 20 )

A. Case studies

1. Brooks & Dodson (1965)

B. Brooks and Dodson’s (1965) ‘Size-efficiency hypothesis’

C. The role of invertebrate predation

D. The trophic-cascade hypothesis

  1. Carpenter’s whole-lake experiments
  2. Critical analysis of the design

XXI. Chapter 13 Vertical migration of zooplankton ( Class 21 )

A. Case studies

1. Ohman et al. (1983)

B. Zooplankton life histories

C. Demography

D. Demographic analysis of the adaptive value of vertical migration

E. Game theoretic analysis of vertical migration

XXII. Chapter 14 Heterotrophic microbial processes (Class 22 )

A. Case studies

1. Azam et al. (1983)

B. Methods for determining microbial standing stocks & production

C. What limits bacterial production?

D. The microbial loop hypothesis

  1. sources of dissolved organic matter (DOM)
  2. Control of bacterial standing stock and production
  3. Nutrient regeneration
  4. transfer of DOM to macrozooplankton and fish

E. Microbial biodiversity (Class 23 )

XXIII. Chapter 15 : The Ecological Implications of Body Size (Class 24 )

XXIV. Chapter 16 Factors controlling primary and secondary production HNLC regions, the subarctic Pacific and Southern Ocean. (Class 25 )

A. Case studies

  1. Martin & Fitzwater (1988)
  2. Boyd et al. (2000)

B. The North Pacific

  1. The Major-grazer paradigm
  2. Refutation/Revolution: the micrograzer paradigm
  3. Martin’s iron limitation hypothesis
  4. New paradigm: the ecumenical iron hypothesis

C. The Southern Ocean

D. 2

Chapter 17 Oceanographic production and atmospheric CO (Class 26 )

  1. Martin’s Geritol solution to global warming: Fe limitation
  2. IronEx II & III
  3. Southern ocean: Fe or light limitation?

XXV. Ecosystem Modeling ( Class 27 )

A. Chapter 18

  1. Readings: TBA
    1. Recommended
      1. Steele (1974)
      2. Evans & Parslow (1985)
        1. Steele’s North Sea Ecosystem Model
        2. (1) the standard run & Landry’s modifications
      1. Model stability: the role of refuges and predation

B. Chapter 19 Coastal marine ecosystem modeling (Class 28 )

1. Case studies

a. Kremer & Nixon (1978)
b.MA Bay model

2. Kremer and Nixon’s Narragansett Bay Model

a.Physical model
b.Phytoplankton growth
c.Zooplankton growth
e.Benthic-pelagic coupling

3. Predicting the effects of man’s activities: DiToro’s Hydroqual model of MA Bay

XXVI. Final Examination during the scheduled final exam period.