2008 Course Syllabus

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Week 1 Theme I: What defines the ocean as a microbial habitat?

  • Visiting Faculty: A. Michaels, R. Letelier, K. Johnson
    UH Faculty: Church, Karl, Steward

Monday, June 2

 

 

0830-0930

Welcome

HIG 110

1000-1200

Lab / Chemical Safety Training

MSB 315

1400-1500

K. Doggett “Radiation safety”

MSB 315

1500-

Student Defense
Reception to follow

MSB 100

Tuesday, June 3

An introduction to microbial oceanography

HIG 110

0900-1200

D. Karl “An introduction to microbial oceanography”

Reading (PDF):

  1. Microbial oceanography: paradigms, processes and promise

R. Letelier “Microbial photoautrophy”

Lecture (9.2 MB PowerPoint):

 

1230-1400

Faculty brownbag lunch: Karl / Letelier (Campus Center)

1430-1600

P. Kemp ”What is knowable about microbes and how do we learn it?“

Lecture (PowerPoint):

 

1630-

Course instructors and staff meet to discuss cruise

MSB 315

Wednesday, June 4

The ocean as a microbial habitat

HIG 110

0900-1200

K. Johnson “Where do nutrients come from? Physical and biological supply terms”

Reading (PDF):

  1. Diatom vertical migration to acquire iron

Lecture (5.9 MB PDF):

K. Johnson “Iron and the HNLC condition”

Lecture (7 MB PDF):

 

1230-1400

Faculty brownbag lunch: K. Johnson (Campus Center, Executive Dining Room)

1430-1600

R. Letelier “Philosophy of science / ethics lecture”

Readings (PDFs):

  1. Strong Inference
  2. The Weakness of Strong Inference
  3. On the Evolution of Ecological Ideas: Paradigms and Scientific Progress

Lecture (4.1 MB PowerPoint):

 

1630-1800

M. Church “Introduction to the research cruise objectives and plans”

MSB 315

Thursday, June 5

The ocean as a habitat continued (microscale to basin scale)

HIG 110

0900-1200

G. Steward “Perspectives from the microscale”

R. Letelier “Mesoscale microbial dynamics”

Lecture (12.2 MB PowerPoint):

 

1230-1400

Faculty brownbag lunches: Steward, Church (Campus Center 203A/B)

1430-1600

K. Johnson “Drifting toward metabolic balance”

Readings (PDFs):

  1. Net production of oxygen in the subtropical ocean
  2. Ocean metabolism observed with oxygen sensors on profiling floats in the South Pacific

Lecture (3.4 MB PDF):

 

Friday, June 6

Student Research Talks
All day student research symposium

Reading (Word doc):

  1. Student Symposium, June 6th, 2008

 

Saturday, June 7

All Day Symposium: “Ocean carbon cycling in a changing climate”
Matt Church, host.

University
of Hawai‘i
William Richardson School of Law (Classroom 3)

0830-0900

Coffee

0900-1600

Speakers include:

Download the flyer PDF.

Reception to follow

Sunday, June 8

Free Day for students to explore O‘ahu

 

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Week 2 Theme II: What controls microbial activity and organic matter dynamics in the sea?

  • Visiting Faculty: A. Michaels, D. Repeta, C. Carlson, D. Bronk, H.J. Tripp
    UH Faculty: Church, Rappé, Steward

Monday, June 9

Introduction to DOM

HIG 110

0900-1200

D. Bronk “The cycling of nitrogen and phosphorus in the ocean”

Additional Resources:

Readings (PDFs):

  1. Nitrogen Cycling in the Ocean: New Perspectives on Processes and Paradigms
  2. The Oceanic Phosphorus Cycle

Additional Readings (PDFs):

  1. Uptake of new and regenerated forms of nitrogen in primary productivity
  2. Nitrogen fixation by Trichodesmium spp.: An important source of new nitrogen to the tropical and subtropical North Atlantic Ocean
  3. Particulate organic matter flux and planktonic new production in the deep ocean
  4. Photochemical release of biologically available nitrogen from aquatic dissolved organic matter
  5. Atmospheric inputs of dissolved organic nitrogen stimulate estuarine bacteria and phytoplankton
  6. Depth related amino acid uptake by Prochlorococcus cyanobacteria in the Southern Atlantic tropical gyre
  7. Unicellular cyanobacteria fix N2 in the subtropical North Pacific Ocean
  8. Bioavailability of dissolved organic nitrogen and carbon from nine rivers in the eastern United States
  9. Sources and delivery of carbon, nitrogen, and phosphorus to the coastal zone: An overview of Global Nutrient Export from Watersheds (NEWS) models and their application
  10. Contribution of dissolved organic nitrogen from rivers to estuarine eutrophication

Lecture (PDF):

D. Repeta “Dissolved organic matter I - reservoirs, cycling and residence time”

Readings (PDFs):

  1. Deep-ocean gradients in the concentration of dissolved organic carbon
  2. A major biopolymeric component to dissolved organic carbon in surface sea water
  3. Radiocarbon in dissolved organic matter in the central Pacific Ocean
  4. Production and utilization of dissolved organic carbon during an experimental diatom bloom
  5. Two Chemically Distinct Pools of Organic Nitrogen Accumulate in the Ocean

Lecture (PPT):

 

1230-1400

Faculty brownbag lunch: Repeta (Campus Center Executive Dining Room)

1430-1600

C. Carlson “Temporal and Spatial Variability of Oceanic DOM: Assessing Various Scales of Turnover and Its Implications”

Readings (PDFs):

  1. Dissolved Organic Matter in the Ocean: Comments on a Controversy
  2. Marine Dissolved Organic Matter and the Carbon Cycle

Lecture (PDF):

A. Michaels “Life choices: Changing climate, changing future”

 

Tuesday, June 10

Microbial control of DOM

HIG 110

0900-1200

D. Repeta “Dissolved organic matter II - composition and reactivity towards microbial respiration”

Lecture (PPT):

D. Bronk “DON sources and sinks”

Reading (PDF):

  1. Dissolved organic nitrogen: a dynamic participant in aquatic ecosystems

Additional Readings (PDFs):

  1. The Oceanic Phosphorus Cycle
  2. Bioavailability of Organic Nitrogen from Treated Wastewater
  3. Upper ocean ecosystem dynamics and iron cycling in a global three-dimensional model
  4. High rates of N2 fixation by unicellular diazotrophs in the oligotrophic Pacific Ocean
  5. Gross and net nitrogen uptake and DON release in the euphotic zone of Monterey Bay, California
  6. Dissolved organic nitrogen: a dynamic participant in aquatic ecosystems
  7. A 15N tracer method for the measurement of dissolved organic nitrogen release by phytoplankton
  8. Marine microorganisms and global nutrient cycles

Lecture (PDF):

 

1230-1400

Faculty brownbag lunch: D. Bronk (Campus Center Executive Dining Room)

1430-1600

C. Carlson “Controls on bacterial growth and remineralization efficiency”

Readings (PDFs):

  1. Bacterial growth efficiency in natural aquatic systems
  2. Microbes and the Dissipation of Energy and Respiration: From Cells to Ecosystems
  3. Natural Assemblages of Marine Proteobacteria and Members of the Cytophaga-Flavobacter Cluster Consuming Low- and High- Molecular-Weight Dissolved Organic Matter

Lecture (PDF):

MSB 315

1630-1800

Steward “Tutorial on molecular techniques in marine ecology”

MSB 315

Wednesday, June 11

Faculty seminars

HIG 110

0900-1200

C. Carlson “Response of specific bacterial lineages to convective mixing in the Sargasso Sea”

C. Carlson “Controls on bacterial growth and remineralization efficiency”

Reading (PDF):

  1. Temporal and spatial response of bacterioplankton lineages to annual convective overturn at the Bermuda Atlantic Time-series Study site

Lecture (PDF):

D. Repeta “Iron binding organic ligands in seawater. Are microbial siderophores part of the mix?”

Lecture (PPT):

 

1230-1400

Faculty brownbag lunch: C. Carlson (HIG courtyard)

 

1430-1600

D. Bronk “So much for paradigms: nitrogen cycling in river plumes”

Readings (PDFs):

  1. Archaeal dominance in the mesopelagic zone of the Pacific Ocean
  2. Long-term changes in plankton communitystructure and productivityin the North Pacific Subtropical Gyre: The domain shift hypothesis
  3. Quantifying archaeal community autotrophy in the mesopelagic ocean using natural radiocarbon
  4. Isotope dilution models of uptake and remineralization of ammonium by marine plankton
  5. The Problem With Phosphorus…
  6. Nitrogen Uptake, Dissolved Organic Nitrogen Release, and New Production
  7. Dynamics of DON (Part 1)
  8. Dynamics of DON (Part 2)
  9. Inorganic and organic nitrogen cycling in the Southern California Bight

Lecture (PDF):

 

1600-1800

H.J. Tripp “Web-based tools for exploring microbial diversity”

Readings (PDFs):

  1. Reconstructing the metabolic network of a bacterium from its genome
  2. Artemis Reference
  3. The impact of next-generation sequencing technology on genetics

 

Thursday, June 12

 

MSB 315

0900-1200

Lab: Genome annotation workshop (H.J. Tripp)

 

1230-1400

Faculty brownbag lunch: H.J. Tripp (HIG courtyard)

 

1430-

Pre cruise meeting / Cruise planning discussions, sampling logistics

 

Friday, June 13

 

MSB 315

0900-1200

Lab: Genome annotation workshop (H.J. Tripp)

 

1230-1400

Lunch (HIG courtyard)

 

1430-

Cruise packing, preparations (Doggett, Björkman, Clemente)

 

Saturday, June 14

Cruise preparations (AM) (Doggett, Björkman, Clemente)

 

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Week 3: Research Cruise

June 15–23

Research Cruise

 

Sunday, June 15

Depart for research cruise aboard R/V Kilo Moana

Faculty and Staff for research cruise include:
Church, Rappé, Steward, Doggett, Björkman, Clemente, Watkins, Updyke

Students to check out of dorm rooms by 0830 and take taxis to UH marine center. Begin loading R/V Kilo Moana at 1000.

Activities while at sea will include tutorials and hands-on labs to measure: primary & secondary production; microscopy/flow cytometry for enumerating/sorting viruses and picoplankton; sDNA/RNA extractions; the PCR & RT-PCR; cloning; measuring microbial biomass (Chl, ATP, direct counts). Samples will also be collected for nutrients (inorganic and organic); particulates; C/N/P/Si export.

 

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Week 4 Theme III: How do we detect microbial distributions, activity, and biomass?

  • Visiting Faculty: M. Sieracki, J. Cullen, K. Casciotti, D. Siegel;
    UH Faculty: Church, Rappé, Steward

Monday, June 23

 

 

0900-1200

Offload vessel

 

1200-

Check into dorms, afternoon free

 

Tuesday, June 24

Autonomous sensors and platforms

HIG 110

0900-1200

J. Cullen “Measurements and models of primary productivity”

Reading (PDF):

  1. Primary Production Methods

Lecture (17 MB PDF):

D. Siegel “Colored Dissolved Organic Matter in the Open Sea: Distribution, Dynamics & Implications”

Lecture (5 MB PPT):

 

1230-1400

Faculty brownbag lunch: D. Siegel (Campus Center 203A/B)

 

1430-1600

M. Sieracki “Flow and imaging cytometry for studying ocean microbes”

Reading (PDF):

  1. An imaging-in-flow system for automated analysis of marine microplankton

Lecture (15.7 MB PDF):

 

1630-

Student lab analyses (Doggett, Björkman, Clemente)

 

Wednesday, June 25

From single cells to whole communities

HIG 110

0900-1200

M. Sieracki “Single cell analysis of bacteria: activity and genomics”

Readings (PDFs):

  1. Flow Cytometric Analysis of 5-Cyano-2,3-Ditolyl Tetrazolium Chloride Activity of Marine Bacterioplankton in Dilution Cultures
  2. Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time

Lecture (3.3 MB PDF):

 

 

K. Casciotti “Stable isotope approaches to studying microbial biogeochemistry (Part 1): Introduction to stable isotopes and applications using tracer-level enrichments.”

Reading (PDF):

  1. Nitrogen Isotopes in the Ocean

Lecture (PPT):

 

1230-1400

Faculty brownbag lunch: M. Sieracki (Campus Center Executive Dining Room)

1430-1600

K. Casciotti “Stable isotope approaches to studying microbial biogeochemistry (Part 2): Isotopic fractionation and variations at the natural abundance level: implications and interpretations.”

Lecture (PPT):

1630-1800

Panel discussion on proposal development (M. Sieracki and D. Siegel)

 

Thursday, June 26

Modeling microbial dynamics

HIG 110

0900-1200

J. Cullen “Measurement and interpretation of chlorophyll fluorescence: a most dangerous game ”

Lecture (7.4 MB PDF):

D. Siegel “Modeling Microbial Population Dynamics: Are Individuals Important?”

Reading (PDF):

  1. Resource competition in a discrete environment: Why are plankton distributions paradoxical?

Lecture (PPT):

 

1200-1400

Faculty brownbag lunch: K. Casciotti (Campus Center Executive Dining Room)

1400-1700

Lab tutorial: Measuring phosphorus pools in the sea (Björkman)

MSB 315

Friday, June 27

Controls on microbial distributions in the ocean

HIG 110

0900-1200

M. Sieracki “Distributions of aerobic, anoxygenic phototrophic (AAP) bacteria in the ocean”

Reading (PDF):

  1. Distribution of planktonic aerobic anoxygenic photoheterotrophic bacteria in the northwest Atlantic

Lecture (PDF):

J. Cullen “Behavior, physiology and the niche of marine phytoplankton”

Lecture (PDF):

 

1230-1400

Faculty brownbag lunch: J. Cullen (Campus Center 203A/B)

 

1430-1600

Colloquium: Navigating career choices in science (M. Sieracki)

 

Saturday, June 28

All Day Symposium: “Sensing microbes in a dynamic sea”
Grieg Steward, host

Asia Room, East-West Center, University
of Hawai‘i

0830-0900

Coffee

0900-1600

Speakers include: 

Download the flyer PDF.

Reception to follow

Sunday, June 29

Free Day for students to explore O‘ahu

 

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Week 5 Theme IV: How does plankton diversity control ecosystem function?

  • Visiting Faculty: J. Zehr, A. Worden, S. Dyhrman, G. Tyson
    UH Faculty: Church, Rappé, Steward

Monday, June 30

Cultivation dependent insight into microbial physiology

HIG 110

0900-1200

A. Worden “The Wild Side of Life: The challenges of genomic and metagenomic technologies”

S. Dyhrman “Past, present and future: Coccolithophores in a changing ocean”

Lecture: (49.2 MB PDF)

  1. Past, present, and future: Coccolithophores in a changing ocean

 

1230-1400

Faculty brownbag lunch: A. Worden, G. Tyson (Campus Center Executive Dining Room)

1430-1600

J. Zehr “From genomes to the environment: Genomics, transcriptomics and activities of model organisms in the environment—the Crocosphaera story”

MSB 315

1630-1800

Lab tutorial: Bioinformatic tools for analyzing metagenomic data (G. Tyson)

Lecture: (11.7 MB PDF)

  1. Introduction to Metagenomics

MSB 315

Tuesday, July 1

Cultivation independent insights

HIG 110

0900-1200

A. Worden “The cultured side of life: Evolution of eukaryotic algae and heterotrophic protists ”

J. Zehr “Probing physiology of uncultivated microorganisms with molecular tools: from genes to biogeochemical cycles”

 

1230-1400

Faculty brownbag lunch: S. Dyhrman (Campus Center 203A/B)

 

1430-1600

Lab tutorial: Bioinformatic tools for analyzing metagenomic data—continued (G. Tyson)

Lecture: (3.3 MB PDF)

  1. Bioinformatic tools for metagenomic data analysis

MSB 315

1630-1800

S. Dyhrman “Phosphorus cycling in the sea: new stories and enduring questions”

Lecture: (45.1 MB PDF)

  1. Phosphorus cycling in the sea: new stories and enduring questions

 

Wednesday, July 2

Faculty seminars

HIG 110

0900-1200

S. Dyhrman “The genomics of niche adaptation in the harmful alga Aureococcus”

Lecture: (41.3 MB PDF)

  1. The genomics of niche adaptation in the harmful alga Aureococcus anophagefferens

A. Worden

 

1230-1400

Faculty brownbag lunch: J. Zehr (Campus Center 203A)

 

1430-1700

J. Zehr “Distributions and dynamics of cyanobacterial nitrogen fixers, the evolving story of nitrogen fixation in the world’s oceans”

G. Tyson “Metatranscriptomics: measuring microbial genome expression in the ocean”

Lecture: (9.9 MB PDF)

  1. Metatranscriptomics: Measuring microbial gene expression in the ocean

 

Thursday, July 3

All Day: Students work in labs analyzing samples collected on research cruise

 

Friday, July 4

Free day for students to explore O‘ahu

 

Saturday, July 5

All Day: Students work on analyzing samples from research cruise (Doggett, Björkman, Clemente)

 

Sunday, July 6

Morning: Students work on analyzing samples from research cruise (Doggett, Björkman, Clemente)

 

 

Afternoon free to explore O‘ahu

 

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Week 6 Theme V: Current and Shifting paradigms in Microbial Oceanography

  • Visiting Faculty: C. Duarte, M. Pace, E. DeLong
    UH Faculty: Church, Rappé, Steward

Monday, July 7

All Day: Students working in labs on sample analyses

 

Tuesday, July 8

Comparative ecosystem analyses

HIG 110

0900-1200

C. Duarte “Comparative approaches to microbial oceanography”

Readings: (PDFs)

  1. The role of experimental approaches in marine microbial ecology.
  2. Comparative analyses in aquatic microbial ecology: How far do they go? (PDF)

Lecture: (6.1 MB PPT)

  1. Comparative analyses of marine microbial systems: searching for pattern

M. Pace “Comparative approaches to ecosystem analysis”

Readings (PDFs):

  1. Emergent Biogeography of Microbial Communities in a Model Ocean
  2. Ecosystem size determines food-chain length in lakes

Lecture: (9.8 MB PPT)

  1. Comparative approaches to ecosystem analysis

 

1230-1400

Faculty brownbag lunch: M. Pace (Campus Center 203A/B)

 

1400-1530

Student discussion of cruise data

 

1530-1830

Student working groups on data analyses

 

Wednesday, July 9

The role of experiments in microbial ecology

HIG 110

0900-1200

M. Pace “Large scale experiments: why and how”

Reading (PDF):

  1. The Need for Large-Scale Experiments to Assess and Predict the Response of Ecosystems to Perturbation

Lecture: (23.6 MB PPT)

  1. Large Scale Experiments / Manipulations

C. Duarte “Too close, yet so far: Exploring Microbial Ecology in the Top Meter of the Ocean”

Readings: (PDFs)

  1. High Atmosphere-Ocean Exchange of Organic Carbon in the NE Subtropical Atlantic.
  2. Control of air-sea CO2 disequilibria in the subtropical NE Atlantic by planktonic metabolism under the ocean skin.
  3. Aerosol inputs enhance new production in the subtropical northeast Atlantic

Lecture: (9.1 MB PPT)

  1. Too close, yet so far: Exploring Microbial Ecology in the Top Meter of the Ocean

 

1230-1400

Faculty brownbag lunch: C. Duarte (Campus Center 203A/B)

 

1430-1530

Student preparation for presentations

 

Thursday, July 10

Student Symposium

HIG 110

0800-1300

Student working groups to prepare presentations

 

1430-1600

C. Duarte “The role of publication in the scientific process”

Lecture: (2.4 MB PPT)

  1. The role of Publication in the Scientific Process

 

1630-

Distribution of course evaluations

 

Friday, July 11

All Day Symposium: “The Future of Microbial Oceanography: A research prospectus for the next decade, and beyond…”
Dave Karl, host

Koi Room,
East-West Center, University
of Hawai‘i

0800

Coffee

0830-1030

Student Presentations

Videos of presentations:

  1. Part One
  2. Part Two

1100-1600

Speakers include:

Download the flyer PDF.

1800-2100

Farewell Gala at The Willows (RSVP to Sharon Sakamoto by July 08)

 

Saturday, July 12

Free day to explore O‘ahu

 

Sunday, July 13

Students check out of dorms

 

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