2011 Course Syllabus

Week 1: THE OCEAN AS A MICROBIAL HABITAT

• Visiting Faculty: Craig Carlson, David Kirchman, Ken Nealson, Carlos Pedrós-Alió, Dan Repeta

Sunday 29 May and Monday 30 May

Students arrive and check into Frear Hall at the University of Hawai‘i at Mānoa

UH Mānoa

Tuesday 31 May

Introduction / Orientation
See the videos of the day’s lectures here.

C-MORE Hale

0830-0915

Introductions

Auditorium

0915-1030

Dave Karl: “Microbial Oceanography: A Sea of Opportunities”

Readings (PDFs):

• “The trophic tapestry of the sea”
• “The Light-Driven Proton Pump Proteorhodopsin Enhances Bacterial Survival during Tough Times”
• “Microbial oceanography: paradigms, processes and promise”
• “The genomic basis of trophic strategy in marine bacteria”
• “Cramming more components onto integrated circuits”
• “Marine Habitats”
• “From Molecular Biology to Geology: A Surprising Trajectory”

Auditorium

1030-1045

Coffee Break

1045-1145

University Biosafety Training

Auditorium

1145-1300

Lunch (Campus Center 203E) Self introductions

1300-1415

University Laboratory Safety Training

Auditorium

1415-1430

Break

1430-1630

University Radiation Safety Training

Auditorium

1630-1800

Informal Mixer

Courtyard / Lanai

Wednesday 01 June

Daily Theme: “The nature of microbial cells”
See the videos of the day’s lectures here.

C-MORE Hale

0900-1015

Ken Nealson: “Energetics behind microbial life?”

Auditorium

1015-1045

Break

1045-1200

David Kirchman: “Black Box Microbial Oceanography 101”

Readings (PDFs):

• Processes in Microbial Ecology, Chpt. 5
• Processes in Microbial Ecology. Chpt. 6

Auditorium

1215-1345

Lunch (Campus Center 203E) Kirchman and Pedrós-Alió introductory chat

1400-1515

Carlos Pedrós-Alió: “Seeking the perfect desert”

1515-1800

Student research talks (Part 1)

1800-

Group Dinner (to be organized by students)

TBD

Thursday 02 June

Daily Theme: “Microbial control of ocean carbon and nutrients”
See the videos of the day’s lectures here.

C-MORE Hale

0830-0945

Dave Karl: “Elemental stoichiometry of life and death in the sea”

Readings (PDFs):

• “Marine microorganisms and global nutrient cycles”
• “The limits to growth”
• “Biological stoichiometry of plant production: metabolism, scaling and ecological response to global change”
• “Stoichiogenomics: the evolutionary ecology of macromolecular elemental composition”
• “Evolution of the nitrogen cycle and its influence on the biological sequestration of CO2 in the ocean”
• “Nutrient dynamics in the deep blue se”a
• “Optimal nitrogen-to-phosphorus stoichiometry of phytoplankton”
• “The origins of the Redfield nitrogen-to-phosphorus ratio are in a homoeostatic protein-to-rRNA ratio”
• “Redfield revisited : variability of C:N:P in marine microalgae and its biochemical basis”

Auditorium

0945-1000

Break

1000-1100

Craig Carlson: “Dissolved organic matter: Controversies and new insights”

Auditorium

1100-1200

Dan Repeta: “Distributions and characterization of dissolved organic matter in the sea”

Auditorium

1215-1345

Lunch (Campus Center 203E) Carlson, Kirchman, and Repeta introductory chat

1400-1500

David Kirchman: “Opening the black box: Linking microbes to DOM flux”

Auditorium

1500-1515

Break

1515-1730

Student Research Talks (Part 2)

Friday 03 June

Daily Theme: “Resources supporting microbial growth and metabolism”
See the videos of the day’s lectures here.

C-MORE Hale

0900-1015

Ken Nealson: “Extracellular electron transport: Implications for microbial metabolism”

Auditorium

1015-1045

Break

1045-1200

Craig Carlson: “Reactivity of dissolved organic matter: From Bottles to Basins”

Auditorium

1200-1330

Lunch in small groups

1400-1515

Dan Repeta: “Substrate specificity in microbial carbon utilization”

Auditorium

1530-1645

Carlos Pedrós-Alió: “Light and Marine Bacteroidetes”

Auditorium

Saturday 04 June

Symposium 1:
“Microbial Physiology and Oceanography”

Moderated by Dave Karl

CMORE Hale Auditorium

0830-1700

Speakers:

• Ken Nealson
• David Kirchman
• Carlos Pedrós-Alió
• Dan Repeta
• Craig Carlson

Coffee service begins at 8:30 am; presentations begin at 8:45 am. Lunch will be provided. Please RSVP to Sharon Sakamoto by Wednesday 01 June. Lunch will be provided; reception to follow.

Download the advertisement flyer PDF.
See the videos of the presentations here.

Sunday 05 June

Free Day for students to explore O‘ahu

Free Day

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Week 2: THE MICROBIAL OCEAN VIEWED THROUGH THE LENS OF GENES & GENOMES

• Visiting Faculty: Eric Allen, Ed DeLong, Nikos Kyrpides, Mary Ann Moran, Alexandra Worden

Monday 06 June

Daily Theme: “Introduction to marine microbial genomics ”
See the videos of the day’s lectures here.

C-MORE Hale

0900-1015

Ed DeLong: “Introduction: Marine microbes and genomics”

Readings (PDFs):

• “Trends between gene content and genome size in prokaryotic species with larger genomes”
• “A Molecular View of Microbial Diversity and the Biosphere”
• “Genomic perspectives in microbial oceanography”
• “Evolutionary Origins of Genomic Repertoires in Bacteria”

Auditorium

1015-1045

Break

1045-1200

Mary Ann Moran: “Physiology, ecology & genomics of the ubiquitous marine Roseobacter clade”

Readings (PDFs):

• “Genome characteristics of a generalist marine bacterial lineage”
• “Transporter genes expressed by coastal bacterioplankton in response to dissolved organic carbon”
• “Novel pathway for assimilation of dimethylsulphoniopropionate widespread in marine bacteria”

Auditorium

1200-1330

Faculty brownbag lunch (Campus Center 203E) Moran and Worden faculty introductory chat)

1330-1500

Alex Worden: “Microbial genomes and HGT”

TED lecture:

• Bonnie Bassler now bacteria “talk”

Readings (PDFs):

• “Smallest Algae Thrive As the Arctic Ocean Freshens”
• “The eukaryotic tree of life: endosymbiosis takes its TOL”
• “Protists are microbes too: a perspective”

Ed DeLong: “Introduction: Marine microbes and genomics”

Auditorium

1500-1530

Break

1530-1700

Mike Rappé: “Culturing the uncultivated: A Roseobacter case study”

Readings (PDFs):

• “Complete genome sequence of strain HIMB100, a cultured representative of the SAR116 clade of marine Alphaproteobacteria”

Auditorium

1800-

Group Dinner (to be organized by students)

TBD

Tuesday 07 June

Daily Theme: “Comparative genomics—theory & applications”
See the videos of the day’s lectures here.

C-MORE Hale

0900-1015

Nikos Kyrpides: “Annotation of microbial genomes”

Auditorium

1015-1045

Break

1045-1200

Eric Allen: “Genome assembly: genomics & metagenomics”

Readings (PDFs):

• “Application of ‘next-generation’ sequencing technologies to microbial genetics”
• “Going deeper: Metagenome of a hadopelagic microbial community”
• “Community Genomics in microbial ecology and evolution”

Auditorium

1200-1330

Faculty brownbag lunch (Campus Center 203E) Kyrpides and Allen faculty introductory chat

1330-1700

Lecture & Computer Lab I “Genomic and metagenomic web-based analytical tools”

1330-1500

Nikos Kyrpides: “Introduction to IMG and IMG/M”
Lab: Logging in and Surfing around IMG

1500-1700

Eric Allen: “Introduction to CAMERA”
Lab: Logging in and Surfing around CAMERA

Wednesday 08 June

Daily Theme: “Metagenomics & metaranscriptomics”
See the videos of the day’s lectures here.

C-MORE Hale

0900-1015

Alex Worden: “Eukaryotic phytoplankton genomes and metagenomics”

Auditorium

1015-1030

Break

1030-1200

Ed DeLong: “Integrating microbial ‘omics’, physiological, ecology and biogeochemistry”

Readings (PDFs):

• “Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea”
• “The microbial ocean from genomes to biomes”
• “A Cryptic Sulfur Cycle in Oxygen-Minimum-Zone Waters off the Chilean Coast”
• “Bacterial Rhodopsin: Evidence for a New Type of Phototrophy in the Sea”

Auditorium

1200-1330

Faculty brownbag lunch (Campus Center 203E) DeLong and Rappé faculty introductory chat

1330-1700

Computer Lab II “Genomic and metagenomic analysis using IMG, IMG/M and CAMERA”
Kyrpides: “Annotating a new microbial genome using IMG”
Allen: “Analyzing metagenomic datasets using CAMERA”

Readings (PDFs):

• “The dynamic genetic repertoire of microbial communities”
• “De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities”

Thursday 09 June

Daily Theme: “Metagenomics & metaranscriptomics (cont’d)”
See the videos of the day’s lectures here.

C-MORE Hale

0900-1015

Eric Allen: “Metagenomics in extreme environments (acid mine, hypersaline)”

Auditorium

1015-1030

Break

1030 -1200

Mary Ann Moran: “Experimental Microbial Metatranscriptomics”

Auditorium

1200-1330

Lunch (Campus Center 203E)

1330-1700

Computer Lab II “Genomic and metagenomic analysis using IMG, IMG/M and CAMERA”
Kyrpides: “Annotating a new microbial genome using IMG”
Allen: “Analyzing metagenomic datasets using CAMERA”

Friday 10 June

Symposium 2:
“The Microbial Ocean Viewed Through the Lens of
Genes and Genomes”

Moderated by Grieg Steward

CMORE Hale Auditorium

0830-1200

Speakers:

• Mary Ann Moran: “Genomic Insights into Sulfur Cycling in the Surface Ocean”
• Eric Allen: ”The Fats of Life: Secondary Lipid Biosynthesis Potential in Diverse Microbial Lineages“
• Alex Worden: “Genomics of Marine Picoeukaryote Populations”

Coffee service begins at 8:30 am; presentations begin at 8:45 am. Lunch will be provided. Please RSVP to Sharon Sakamoto by Wednesday 08 June. Lunch will be provided; reception to follow.

Download the advertisement flyer PDF.
See the videos of the presentations here.

Saturday 11 June
1200-1700

 Loading Research Vessel Kilo Moana

Snug Harbor

Sunday 12 June

BEGIN RESEACH CRUISE

0800

Students check out of dorm rooms in Frear Hall; take cabs to Snug Harbor

UH Mānoa

1030

Depart Snug Harbor for research cruise aboard the R/V Kilo Moana

Snug Harbor

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Week 3 & 4: RESEARCH CRUISE IN THE SUBTROPICAL NORTH PACIFIC OCEAN

Sunday 12 June – Wednesday 22 June

RESEARCH CRUISE

R/V Kilo Moana

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Week 4: LABORATORY AND GENOME ANALYSES

Wednesday 22 June

Return to Honolulu

0800

Return to Snug Harbor, offload research vessel

Snug Harbor

1100-1200

Return to UH Mānoa campus; students check into Frear Hall

UH Mānoa

1400-1700

UH laboratory analyses

C-MORE Hale

Wednesday 22 June
0900-1700

UH laboratory analyses

C-MORE Hale

Thursday 23 June
0900-1700

UH laboratory analyses

Friday 24 June
0900-1700

UH laboratory analyses

Saturday 25 June
0900-1700

UH laboratory analyses

Sunday 26 June

Free Day for students to explore O‘ahu

Free Day

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Week 5: MICROBIAL OCEANOGRAPHY IN THE 21ST CENTURY

• Visiting Faculty: John Cullen, Ken Johnson, Ricardo Letelier, Oscar Schofield

Monday 27 June

UH lab analyses…

Readings (PDFs):

• “Plastics-Irradiated-Etched: The Nuclepore® Filter Turns 45 Years Old”
• “Microbial Ecology at Sea: Sampling, Subsampling, and Incubation Considerations”

C-MORE Hale

0900-1200

UH laboratory analyses and genome annotation

1300-1700

Discussion of laboratory analyses and methods

Tuesday 28 June

Daily Theme: “Technologies for sensing the sea”
See the videos of the day’s lectures here.

C-MORE Hale

0900-1015

John Cullen: “Optical observations of the ocean”

Auditorium

1015-1045

Break

1045-1200

Ricardo Letelier: “Satellite remote sensing of plankton”

Auditorium

1230-1330

Lunch (Campus Center 203E) Cullen and Letelier introductory chats

1400-1515

Oscar Schofield: “Mobile assets, capabilities and available sensors for detecting plankton”

Readings (PDFs):

• “Resolving the Impacts and Feedback of Ocean Optics on Upper Ocean Ecology”

Auditorium

1530-1645

Ken Johnson: “Observing microbial processes at the global scale with profiling floats with chemical sensors”

Readings (PDFs):

• “Observing Biogeochemical Cycles at Global Scales with Profiling Floats and Gliders”
• “The Argo-Oxygen Program” (2.4MB)

Auditorium

Wednesday 29 June

Daily Theme: “Measurements and models of plankton productivity”
See the videos of the day’s lectures here.

C-MORE Hale

0900-1015

John Cullen: “Measurements and models of phytoplankton biomass and productivity”

Readings (PDFs):

• “Primary Production Methods”
• “Marine Primary Production in Relation to Climate Variability and Change” (2.5MB)

Auditorium

1015-1045

Break

1045-1200

Oscar Schofield: “Tools for sensing phytoplankton biomass and physiology”

Readings (PDFs):

• “Diel variations in optical properties of Micromonas pusilla (Prasinophyceae)”
• “The Slocum Mission” (2.5MB)

Auditorium

1230-1330

Lunch in small groups

1400-1515

Ricardo Letelier: “Satellite-based measurements of ocean productivity”

Auditorium

1530-1645

Ken Johnson: “Linking nutrient acquisition and community metabolism at HOT and BATS using profiling floats with chemical sensors”

Readings (PDFs):

• “Nitrate supply from deep to near-surface waters of the North Pacific subtropical gyre”
• “Net production of oxygen in the subtropical ocean”

Auditorium

18:00-

Group dinner (to be organized by the students)

TBD

Thursday 30 June

Daily Theme: “The ocean as a microbial habitat”
See the videos of the day’s lectures here.

C-MORE Hale

0900-1015

John Cullen: “Behavior, physiology and the niche of marine phytoplankton”

Readings (PDFs):

• “Chapter 8. Physical Influences on Marine Ecosystem Dynamics”
• “Behavior, physiology and the niche of depth-regulating phytoplankton”
• “Using Cultures to Investigate the Physiological Ecology of Microalgae” (10MB)
• “Modeling Diverse Communities of Marine Microbes” (2.4MB)

Auditorium

1015-1045

Break

1045-1200

Ricardo Letelier: “Climate and biology in the North Pacific Subtropical Gyre”

Auditorium

1230-1330

Lunch (Campus Center 203E) Johnson and Schofield introductory chats

1400-1515

Oscar Schofield: “Hot days in polar seas”

Auditorium

1530-1645

Ken Johnson: “Iron: the other limiting nutrient”

Readings (PDFs):

• “Mesoscale Iron Enrichment Experiments 1993-2005: Synthesis and Future Directions”

Auditorium

Friday 01 July

Symposium 3:
“Using 21st Century Technology to Address
the Big Questions of 20th Century Oceanography”

Moderated by Dave Karl

CMORE Hale Auditorium

0830-1700

Speakers:

• John Cullen, Dalhousie University
• Ken Johnson, Monterey Bay Aquarium Research Institute
• Readings (PDFs):
• “Observing Biogeochemical Cycles at Global Scales with Profiling Floats and Gliders”
• “The Argo-Oxygen Program”
• “Nitrate supply from deep to near-surface waters of the North Pacific subtropical gyre”
• “Net production of oxygen in the subtropical ocean”
• “Mesoscale Iron Enrichment Experiments 1993-2005: Synthesis and Future Directions”
• Ricardo Letelier, Oregon State University
• Oscar Schofield, Rutgers University
• Dave Karl, closing remarks

Coffee service begins at 8:30 am; presentations begin at 9:00 am. Lunch will be provided. Please RSVP to Sharon Sakamoto by Wednesday 29 June. Lunch will be provided; reception to follow.

Download the advertisement flyer PDF.
See the videos of the presentations here.

Saturday 02 July
0900-1700

UH laboratory analyses and genome annotation

C-MORE Hale

Sunday 03 July

Free day to explore O‘ahu

Free day

Monday 04 July
Independence Day

Free day to explore O‘ahu

Free day

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Week 6: SYNTHESIS AND INTEGRATION

Tuesday 05 July

Complete UH laboratory analyses and genome annotation

C-MORE Hale

0900-1000

Grieg Steward

Auditorium

1015-1115

Matt Church

Auditorium

1130-1230

Mike Rappé

Readings (PDFs):

• “New Threshold and Confidence Estimates for Terminal Restriction Fragment Length Polymorphism Analysis of Complex Bacterial Communities”

Auditorium

Wednesday 06 July
0900-1700

Synthesis of cruise/genome data, preparing final presentations

C-MORE Hale

Thursday 07 July
0900-1700

Synthesis of cruise/genome data, preparing final presentations

C-MORE Hale

Friday 08 July

Symposium and End of Course

C-MORE Hale

1000-1200

Student Research Symposium

See the videos of their presentations here.

Auditorium

1200-1330

Lunch

1330-1430

Course evaluations

Auditorium

1730-2000

Farewell gala – End of course

Waikiki Aquarium

Saturday 09 July

Free day to explore O‘ahu

Free day

Sunday 10 July

Students check out of Frear Hall

UH Mānoa

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Jump to:  [ Week 1 | Week 2 | Week 3 | Week 4 | Week 5 | Week 6 ]  [ Symposium 1 | Symposium 2 | Symposium 3 ]