Course Syllabus

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): Revolution in the ocean A watery arms race The ocean’s veil Mind-grasping gravity 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): Climate-driven trends in contemporary ocean productivity Controls on tropical Pacific Ocean productivity revealed… Patterns and Prediction in Microbial Oceanography Physical Influences on Marine Ecosystem Dynamics Behavior, physiology and the niche of depth-regulating phytoplankton Primary Production Methods 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): 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): Will Ocean Fertilization Work? 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): Chemical Sensor Networks for the Aquatic Environment 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
[ Top of Page ] 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): 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): Struggling with the Ill-defined Notions…
	Lecture: “Bacterioplankton single-cell activity and bioenergetics” - del Giorgio Readings (PDFs): Comparative analyses in aquatic microbial ecology… Prediction and the aquatic sciences Role of experimental approaches in marine microbial ecology Download the Powerpoint presentation (7.1 MB)
	Lecture: Sieracki Readings (PDFs): Distribution of planktonic aerobic anoxygenic photoheterotrophic bacteria in the northwest Atlantic 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
[ Top of Page ] 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
[ Top of Page ] 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): 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): 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): 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
[ Top of Page ] 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
[ Top of Page ] Jump to: [ Week 1 \| Week 2 \| Week 3 \| Week 4 \| Week 5 \| Week 6 ] [ Symposium 1 \| Symposium 2 \| Symposium 3 ]

Course Syllabus

Week 1: Overall Theme: Microbial Control of Biogeochemistry

Week 2: Overall Theme: Microbial Growth and Metabolism

Weeks 3 and 4: Research Cruise

Week 5: Biodiversity and evolution of microbial physiology

Week 6: Synthesis and dissemination of knowledge