Course Syllabus

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Week 1: Overall Theme: Microbial Control of Biogeochemistry

Monday, June 25

 

 

08:00-08:30

Intro

MSB 100

09:00-11:30

Lab Safety / Bio Safety

 

13:00-16:00

Rad Safety

 

17:00-18:00

Mixer

 

Tuesday, June 26

The Ocean as a Habitat

MSB 100

08:30-11:45

Lecture: G. Steward

 

 

Lecture: M. Merrifield

 

11:30-12:45

Lunchtime brownbag - Merrifield and Steward; Campus Center 203A/B

13:00-17:00

Nutrient Lab

HIG 215

Wednesday, June 27

Food web control of elemental cycles

MSB 100

08:30-11:45

Lecture: “Wheels within wheels cycling where? Local within global, organism within ecosystem, and species within evolution in the pelagial” - V. Smetacek

Readings (PDFs):

  1. Revolution in the ocean
  2. A watery arms race
  3. The ocean’s veil
  4. Mind-grasping gravity
  5. Making sense

Download the Powerpoint presentation (59 MB)

 

 

Lecture: “The fate of marine primary productivity” - P. Boyd

Download the Powerpoint presentation (12 MB)

 

11:30-13:15

Lunchtime brownbag - Cullen; Campus Center 203A/B

13:30-16:30

Nutrient Lab

HIG 215

17:00-18:30

Colloquium: “Describing and Predicting Environmental Influences on Phytoplankton  Communities and Food Web Structure” - Cullen

Readings (PDFs):

  1. Climate-driven trends in contemporary ocean productivity
  2. Controls on tropical Pacific Ocean productivity revealed…
  3. Patterns and Prediction in Microbial Oceanography
  4. Physical Influences on Marine Ecosystem Dynamics
  5. Behavior, physiology and the niche of depth-regulating phytoplankton
  6. Primary Production Methods
  7. Modeling Ocean Ecosystems (10 MB; first page blank)

Download the Powerpoint presentation (13 MB)

 

Thursday, June 28

Modeling ocean biogeochemistry and plankton ecology

MSB 100

08:30-11:45

Lecture: “Measurements and Models of Primary Productivity” - J. Cullen

Download the Powerpoint presentation (7 MB)

 

 

Lecture: “Modeling the export of biogenic particulates from upper ocean” - P. Boyd

 

 

Lecture: “Is our mechanistic understanding of the ocean good enough to model the glacial and anthropocenec oceans?” - Smetacek

Readings (PDF):

  1. Extensive phytoplankton blooms in the Atlantic sector of the glacial Southern Ocean

 

11:30-12:45

Lunchtime brownbag - Leinen, Boyd, and Smetacek; Campus Center 203A/B

13:00-17:00

Student Introductions

 

17:30-19:00

Colloquium: V. Smetacek

 

Friday, June 29

Ecosystem Metabolism and the biological pump

MSB 100

08:30-11:45

Lecture: “Observing metabolic rates in coastal and oligotrophic waters of the ocean with autonomous sensors” - K. Johnson

Download the Powerpoint presentation (21 MB)

 

 

Lecture: “Understanding the Ocean's Biological Pump” - K. Buesseler

Readings (PDFs):

  1. Will Ocean Fertilization Work?
  2. Revisiting Carbon Flux Through the Ocean’s Twilight Zone

Download the Powerpoint presentation (63 MB)

 

11:30-13:30

Lunchtime brownbag - Johnson and Buesseler

 

15:30-17:00

Keynote Address: “The Future of Ocean Research” - M. Leinen

MSB 100

Saturday, June 30

Symposium #1: “Ocean carbon sequestration” - D. Karl, host
For complete details please download the flyer PDF.

EWC
Asia Room

08:30-11:30

Morning Speakers:

 

 

“Iron fertilization: the biogeochemical basis for carbon sequestration” - K. Johnson

Readings (PDFs):

  1. Chemical Sensor Networks for the Aquatic Environment
  2. Diel nitrate cycles observed with in situ sensors predict monthly and annual new production

View the presentation on-line

Download the Powerpoint presentation (6 MB)

 

 

“The export response to ocean iron fertilization — how to measure and why it matters” - K. Buesseler

View the presentation on-line

Download the Powerpoint presentation (27 MB)

 

 

P. Boyd

View the presentation on-line

 

11:30-13:30

Lunch

 

13:30-17:00

Afternoon Speakers:

 

 

“Iron fertilisation of the ocean in the Anthropocene” - V. Smetacek

View the presentation on-line

Download the Powerpoint presentation (42 MB)

 

 

M. Leinen

 

 

J. Cullen

View the presentation on-line

 

17:00-19:00

Pupus / drinks at the East-West Center

 

Sunday, July 1

Free day

 

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Week 2: Overall Theme: Microbial Growth and Metabolism

Monday, July 2

 

08:30-16:30

Lab: Primary production and photosynthesis - Z. Johnson

 

 

Lab: Bacterial production / microscopy - Steward / Church

 

 

Lab: ATP and Chl a

MSB 625

 

Lab: Microscopy

HIG 215

Tuesday, July 3

 

08:30-16:30

Lab: Primary production and photosynthesis - Z. Johnson

 

 

Lab: Bacterial production / microscopy - Steward / Church

 

 

Lab: ATP and Chl a

MSB 625

 

Lab: Microscopy

HIG 215

Wednesday, July 4

Free day

 

Thursday, July 5

Microbial food web dynamics

MSB 114

08:30-11:45

Lecture: “Dissolved Organic Material — from Physiology to Biogeochemistry” - Williams

Reading (Word doc):

  1. Dissolved organic material…

 

 

Lecture: del Giorgio

 

11:30-12:45

Lunchtime brownbag - Sieracki, del Giorgio; Campus Center 203A/B

13:00-15:30

Review Primary production / photosynthesis lab - Johnson

MSB 315

15:30-17:00

Colloquium: Seracki

Download the Powerpoint presentation (1.2 MB)

 

Friday, July 6

Control / regulation of microbial metabolism

MSB 114

08:30-11:45

Lecture: “Struggling with the Ill-defined Notions of Organic Stability, Lability and Resistance” - Williams

Reading (Word doc):

  1. Struggling with the Ill-defined Notions…

 

 

Lecture: “Bacterioplankton single-cell activity and bioenergetics” - del Giorgio

Readings (PDFs):

  1. Comparative analyses in aquatic microbial ecology…
  2. Prediction and the aquatic sciences
  3. Role of experimental approaches in marine microbial ecology

Download the Powerpoint presentation (7.1 MB)

 

 

Lecture: Sieracki

Readings (PDFs):

  1. Distribution of planktonic aerobic anoxygenic photoheterotrophic bacteria in the northwest Atlantic
  2. Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time

Download the Powerpoint presentation (1.9 MB)

 

11:30-12:45

Lunchtime brownbag - Williams; Campus Center 203A/B

13:00-15:00

Review: “Bacterial Production Lab / Microscopy” - Church / Steward

MSB 315

15:30-17:00

Colloquium: “Prediction, understanding and description in the aquatic sciences” - del Giorgio

Download the Powerpoint presentation (530 KB)

 

Saturday, July 7

Symposium #2: “Metabolic Balance of the Open Sea” - M. Church, host
For complete details please download the flyer PDF.

EWC
Asia Room

08:30-11:30

Morning Speakers:

 

“Overview of food web” - Sieracki

Download the Powerpoint presentation (23.6 MB)

 

 

“Photosynthesis” - Johnson

 

 

“The Fundamentals of Measuring Planktonic Respiration” - Williams

 

11:30-13:30

Lunch

 

13:30-15:30

Afternoon Speakers:

 

 

“Respiration in aquatic ecosystems: from cells to the biosphere” - del Giorgio

 

 

“Time / Space Frequencies” - Karl

 

15:30-17:30

Roundtable discussion

 

17:30-19:30

Pupus / drinks

 

Sunday, July 8

Free day

 

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Weeks 3 and 4: Research Cruise

Monday, July 9

Cruise prep all day - HIG215 / Snug harbor BEACH lab

Tuesday, July 10 to Friday, July 20

Cruise aboard Kilo Moana

 

Friday, July 20

Offload KM, students move back into Hale Manoa

Saturday, July 21

Free day

 

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Week 5: Biodiversity and evolution of microbial physiology

Sunday, July 22

 

08:30-11:45

Cruise Analyses

MSB / HIG

13:30-16:30

Cruise Analyses

MSB / HIG

Monday, July 23

 

 

08:30-11:45

Cruise Analyses

MSB / HIG

13:30-16:30

Cruise Analyses

MSB / HIG

Tuesday, July 24

Biodiversity and speciation

MSB 114

08:30-11:30

Lecture: “Marine Microbial Diversity: Dipping into the Rare Biosphere” - Pedros-Alio

Download the Powerpoint presentation (32.4 MB)

 

 

Lecture: “Fragment analysis in microbial oceanography: When is an OTU an ESU?” - Rocap

Download the Powerpoint presentation (11.8 MB)

 

11:30-12:45

Lunchtime brownbag - Worden, DeLong

MSB 315

13:30-16:45

Lecture: “Origins of diversity in the bacterioplankton: theories, observations, and evolutionary experiments” - Thompson

Reading (PDF):

  1. The Paradox of the Plankton (The American Naturalist)

Download the Powerpoint presentation (4.9 MB)

 

 

Lecture: “Non-oxygenic microbial photophysiologies in the ocean: rhodopsin and bacteriochlorophyll based systems ” - DeLong

Download the Powerpoint presentation (13.3 MB)

 

18:00-19:30

Colloquium: Worden

Reading (PDF):

  1. Crystal Ball (Environmental Microbiology)

Download the Powerpoint presentation (15.8 MB)

 

Wednesday, July 25

Cultivated microorganisms as model systems

MSB 114

08:30-11:45

Lecture: “Diversity of stramenopile algae as seen through chloroplast genomics” - Rocap

Download the Powerpoint presentation (23.2 MB)

 

 

Lecture: “The cultured-side of life\85insights on diversity” - Worden

Download the Powerpoint presentation (16 MB)

 

11:30-12:45

Lunchtime brownbag - Pedros-Alio, Rocap

MSB 315

13:30-16:45

Student cruise data analyses

MSB 315

16:00-17:30

Colloquium: “The Scientific Presentation as Theater” - Pedros-Alio

Download the Powerpoint presentation (16.9 MB)

 

Thursday, July 26

Application of environmental -omics in microbial oceanography

MSB 114

08:30-11:45

Lecture: “The evolving field of environmental genomics: problems and prospects” - DeLong

Download the Lecture Powerpoint presentation (26.5 MB)

Download the Lab Powerpoint presentation (3.1 MB)

 

 

Lecture: Worden

 

11:30-12:45

Lunchtime brownbag - Thompson

MSB 315

13:30-15:45

Lab: CAMERA - Kravitz

MSB 314

18:00-19:30

Colloquium: “How would you study the biology of extraterrestrial seas?” - Thompson

Reading (PDF):

  1. Possible ecosystems and the search for life on Europa

Download the Powerpoint presentation (17.4 MB)

 

Friday, July 27

Symposium #3: “Biodiversity, speciation, and the ‘-omics’ of marine microorganisms” - M. Rappé, host
For complete details please download the flyer PDF.

EWC
Asia Room

08:30-11:45

Morning Speakers:

 

 

“Light and Marine Bacteroidetes” - Pedros-Alio

Download the Powerpoint presentation (22.7 MB)

 

 

“Ecology and diversity of picoeukaryotes” - Worden

Download the Powerpoint presentation (23.1 MB)

 

 

Kravitz / Gilna

Download the Gilna Powerpoint presentation (21.4 MB)

Download the Kravitz Powerpoint presentation (4.6 MB)

 

11:30-13:30

Lunch

 

13:30-15:30

Afternoon Speakers:

 

 

“In search of a meaningful species concept for bacteria… what can we learn from ‘population genomics’?” - Thompson

Download the Powerpoint presentation (8.3 MB)

 

 

“Ecotypic diversity of marine cyanobacteria: Tales from the pangenome” - Rocap

Download the Powerpoint presentation (8.2 MB)

 

 

“Exploring the marine microbial world with cultivation-independent, genomic approaches” - DeLong

 

15:30-17:30

Roundtable discussion

 

17:30-19:30

Pupus / drinks at the East-West Center

 

Saturday, July 28

Free day

 

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Week 6: Synthesis and dissemination of knowledge

Sunday, July 29

Field trip to HIMB for FISH lab — lunch / dinner at HIMB

08:30

Depart UH for HIMB

 

09:30-11:30

FISH lab

 

11:30-13:30

Lunch

 

13:30-17:00

FISH / TRFLP lab

 

17:30-19:00

Dinner at HIMB

 

Monday, July 30

Field trip to HIMB for FISH lab — lunch / dinner at HIMB

08:30

Depart UH for HIMB

 

09:30-11:30

FISH lab

 

11:30-13:30

Lunch

 

13:30-17:00

FISH / TRFLP lab

 

17:30-19:00

Dinner at HIMB

 

Tuesday, July 31

Bioinformatics and phylogenetic analyses

08:30

Lecture: Bioinformatics

 

 

“Marine virus lecture” - Alex Culley

 

13:00-15:00

ARB workshop - Rappé / Steward

MSB 314

Wednesday, Aug.1

 

08:30-16:30

Student working groups

MSB 315

Thursday, Aug. 2

Student working groups

MSB 315

Friday, Aug. 3

 

08:30-15:30

Student presentations

MSB 114

18:00-21:00

Farewell reception at the Waikiki Aquarium

 

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