Ocean 621: Biological Oceanography

Spring 2010

(Monday, Wednesday, Friday 9:30-10:20 AM; MSB 315)

Instructors:

Matthew Church, Office: MSB 614, 956-8779, mjchurch@hawaii.edu

Karen Selph, Office: MSB 608, 956-7941, selph@hawaii.edu

Rhian Waller, Office: MSB 610, 956-7822, rwaller@hawaii.edu

Guest Lecturer:

Grieg Steward, MSB 631, 956-6775, grieg@hawaii.edu

Biological Oceanography (OCN 621) is one of several required core courses for graduate students in the Department of Oceanography at the University of Hawaii.  The course meets three times each week (MWF) from 9:30-10:20 AM.  Lectures and exams will cover fundamental concepts in biological oceanography, including topics pertinent to the study of the ecology of pelagic and benthic organisms.  Lectures will include information related to the biomass and productivity of diverse marine ecosystems, assessment of bioelemental cycling of marine organisms, and examination of environmental controls on the growth and mortality of benthic and pelagic organisms.  The course will be divided into three primary sections: 1) planktonic production and elemental cycling, 2) pelagic food web dynamics and fisheries oceanography, and 3) ecology of marine benthic habitats.

Grades will be earned based on two criteria: 1) Regular attendance and participation in weekly lectures (10%); and 2) Performance on the three written, in class exams (30% each).  Students are expected to attend all lectures having become familiar with the reading material assigned for each lecture.

Student Learning Outcomes:

1) Students should be able to define the major forms of life in the sea, describe the characteristics that distinguish these forms, and describe how these forms relate to each other ecologically.

2) Students should be able to explain how marine organisms influence cycling of bioelements.

3) Students should be able to describe prominent characteristics of the primary marine habitats.

4) Students should be able to define processes that control the biomass, growth, and productivity of organisms in the marine environment.

5) Students should be able to describe methodological approaches appropriate for evaluating the biomass, growth, and mortality of plankton, nekton, and sessile marine organisms.


Grading:

10% class participation

30% Exam I (Bioenergetics, production and respiration, biogeochemical Fluxes)

30% Exam II (Zooplankton, pelagic ecology, fisheries oceanography)

30% Exam III (Benthic oceanography and ecology)

 

There is no required textbook for this course; however, instructors will assign reading material in the form of papers or book chapters.  Students are expected to be familiar with material in these assigned readings.


Course Schedule (Jan. 11-Feb. 19, 2010)

Date

Topic

Lecturer

Reading

Monday

Jan. 11

Introduction to Biological Oceanography

Church

 

Wednesday

Jan. 13

Overview of marine food webs

Selph

 

Friday

Jan. 15

Zooplankton microscopy demo

Selph

 

Monday

Jan. 18

NO CLASS

-MLK Day

 

 

Wednesday

Jan. 20

Plankton metabolism and bioenergetics

Church

Falkowski et al. (2008)

Friday

Jan. 22

Carbon cycling and the biological pump

Church

 Ducklow et al. (2001),  Falkowski et al. (1998)

Monday

Jan. 25

Distributions of plankton biomass

Church

 Cullen et al. (2002)

Wednesday

Jan. 27

Biomass (continued)

Church

Cullen (2001)

Friday

Jan. 29

Photosynthetic production and primary production (I)

Church

 Falkowski (2002)

Monday

Feb. 1

Production (Continued) 

Church

Carlson et al. (1994), Ducklow et al. (1996)

Wednesday

Feb. 3

Plankton community metabolism and DOM

Church

 Kirchman (2003)

Friday

Feb. 5

The microbial loop and bacterial production

Church

 del Giorgio and Duarte (2002)

Monday

Feb. 8

Ocean nutrient cycling 

(part I)

Church

 Arrigo (2005)

Wednesday

Feb. 10

Ocean nutrient cycling 

(part II)

Church

 Gruber (2008)

Friday

Feb. 12

The HNLC Condition

Church

 Boyd et al. (2007)

Monday

Feb. 15

NO CLASS

-Presidents Day

 

 

Wednesday

Feb. 17

Review period

Church

 

Friday

Feb. 19

Exam 1

Church

 

 


Course Schedule (Feb. 22-April 5, 2010)

 

Date

 

Topic

 

Lecturer

 

Reading

Monday

Feb. 22

Life at the microscale

Steward

 

Wednesday

Feb. 24

Ecological role of marine viruses

Steward

 

Friday

Feb. 26

Biogeochemical implications of marine viruses

Steward

 

Monday

March 1

Pelagic Consumers-Microzooplankton

Selph

 

Wednesday 
March 3
Pelagic Consumers-
Metazoan Zooplankton
Selph Miller (Chapt 7)
Sherr and Sherr (2002)

Tillmann (2004)
Paffenhoffer et al. (2007)

Friday

March 5

Pelagic Consumers-

Fish

Selph

 

Monday

March 8

Pelagic Consumers-Energetics

Selph

 

Wednesday 

March 10

Pelagic Community Ecology-Methods

Selph

 

Friday

March 12

Pelagic Community Ecology-Diel Vertical Migration

Selph

 

Monday

March 15

Pelagic Community Ecology-Food webs 1

Selph

 Landry (2002)

Miller Chapt. 10

Wednesday

March 17

Pelagic Community Ecology-Food webs 2

Selph

 Calbet (2008)

Purcell et al. (2007)

Friday 

March 19

Fisheries Oceanography

Selph

Pomeroy (2001)

Bluhm and Gradinger (2008)
Nicol (2006)

Monday

March 22

NO CLASS

-SPRING BREAK

 

 

Wednesday

March 24

NO CLASS

-SPRING BREAK

 

 

Friday

March 26

NO CLASS

-SPRING BREAK

 

 

Monday

March 29

Fisheries Oceanography – Management

Selph

 

 

Wednesday

March 31

Review session

Selph

 

Friday

April 2

NO CLASS

-GOOD FRIDAY

 

 

Monday

April 5

Exam 2

Exam Answer Key

Selph

 

 

 


Course Schedule (April 7-May 10, 2010)

Date

Topic

Lecturer

Reading

Wednesday

April 7

Benthic Generalizations

Waller

 

 Gage and Tyler (1991)

Friday

April 9

Benthic Biogeochemistry

Waller

 

 Levington Chapt. 13

Monday

April 12

Deposit Feeding

Waller

 

 

Wednesday

April 14

Suspension Feeding

Waller

 

Wildish and Kristmanson

Friday

April 16

Reproduction and recruitment

Waller

 

 Levington Chapt. 5

Monday

April 19

Distribution Patterns

Waller

 

 Levington Chapt. 17

Wednesday

April 21

Habitats – Deep sea reducing habitats

Waller

 

Van Dover et al. (2002)

Friday

April 23

Habitats – Kelps and Mangroves

Waller

 

 

Monday

April 26

Habitats – High Latitudes

Waller

 Clarke et al. (2007)

Wednesday

April 28

Habitats – Seamounts

Waller

 Samadi et al. (2007)

Friday

April 30

Habitats – Coral Reefs

Waller

 Knowlton and Jackson (2001)

Monday

May 3

Habitats – Deep Water Corals

Waller

 Roberts et al. (2006)

Wednesday

May 5

Benthic Pollution Impacts

Waller

 

Friday

May 7

No Classes

 

 

Monday

May 10

EXAM 3

Waller

 


COURSE OUTLINE AND MAJOR CONCEPTS

I. Introduction

A. Course objectives and overview

B. Habitats and ecosystems

C. Organizational details

II. Bioenergetics - transformations of energy by living organisms

1. Photosynthesis

2. Chemosynthesis

III. Plankton biomass

A. Measuring standing stocks

B. Phytoplankton biomass distributions

C.  Pelagic biogeochemical provinces

                        1. The central gyres

                        2. High latitude ecosystems

                        3. Equatorial ecosystems

IV. Plankton carbon cycling and the biological pump

            A. Pathways and fluxes of carbon

            B.  The balance of photosynthesis and respiration

C. Particle flux as a linkage between the atmosphere and deep sea

            D.  Dissolved organic matter pumping

E.  Photosynthetic production

            F.  Gross and net production

            G.  Irradiance dependent growth

            H.  Carbon and oxygen dynamics

V.  Measurements of and controls on primary production

            A. Oxygen

            B. Carbon

            C. Isotopes

D.  Controls on photosynthetic production and phytoplankton diversity

                        1.  Nutrients

                        2.  Light

                        3.  Temperature

VI. Dissolved organic matter and the microbial loop

            A.  DOM composition

            B.  Sources

            C.  Sinks

            D. Ages and reactivity

E.  The microbial loop

            F. Bacterial biomass in the sea

            G.  Bacterial production

H. Plankton Respiration and the metabolic balance

VII. Nutrient cycling and plankton dynamics

            A. Nitrogen assimilation 

B.  New production

C.  N2 fixation

D.  Dissimilatory N cycle processes

1.  Nitrification

2.  Denitrification

3.  Anammox

E.  The HNLC condition

VIII. Pelagic consumers (Diversity, energetics and behaviors)

A. Pelagic Consumers

            1.  Microzooplankton

            2.  Mesozooplankton (Metazoans)

            3.  Fish

B. Feeding rates and behaviors

1. Functional response relationships

2. Selective feeding

3. Methods used to Measure Feeding Rates

C. Carbon and energy utilization

1. Assimilation and egestion

2. Metabolism

3. Growth and reproduction

4. Elemental Stoichiometry and Grazer-Mediated Remineralization

D. Vertical migratory behavior

IX. Structure and dynamics of pelagic communities

A. Community organization

1. Food web structure

2.  Examples: Pacific Ocean Ecosystems

X. Fisheries oceanography

A. Larval ecology and survival

1. First feeding and the critical period

2. Growth and mortality

3. Larval transport and nursery grounds

4. Environmental variability and larval survival

B. Fisheries management: Case histories

1. California sardines

2. Peruvian anchovetta

3. Whales and krill

C. Global Fisheries: Current Thoughts

1. Multispecies Management

2. Global Fish Catches and Maximum Sustainable Yields

3. Marine Protected Areas

XI. Coral Reef Ecosystems

XII. Benthic ecology

A. Generalizations

B. Microbial processes and sedimentary geochemistry / redox

C. Feeding processes

1. Energy sources

2. Suspension feeding

3. Deposit feeding

D. Distributional patterns

1. Size classes

2. Sedimentary type vs community correlations

3. Pollution gradients

4. Depth zonation

E. Life history and recruitment

F. Discussion of two recent papers on selected topics (e.g., deep-sea diversity, disturbance and succession)

G. Deep-sea reducing habitats

1. Hydrothermal vents

a. Geologic setting and global distribution

b. Microbial processes

c. Macrofaunal structure and processes

2. Characteristics of other reducing habitats

a. Subduction zones

b. Petroleum seeps

c. Whale falls

3. Biogeography of reducing habitats