2013 Course Syllabus

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Week 1: The Ocean as a Habitat

• Faculty: Ginger Armbrust, John Cullen, Ken Johnson, Dan Repeta
• All Lectures in the Moore Conference Center, Daniel K. Inouye C-MORE Hale.
• Click on the lecture title to download the PowerPoint or PDF (where available).

Saturday, May 26 thru Monday, May 28

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

Tuesday, May 28

Welcome and laboratory safety training (Lab_lecture_v2 8MB .ppt)

0830–0915

Welcome (3MB .ppt)

0915–1030

David Karl: An Introduction to Microbial Oceanography (47MB .ppt)

Readings (PDFs):

• DeLong and Béjà, 2010. “The Light-Driven Proton Pump Proteorhodopsin Enhances Bacterial Survival during Tough Times”
• Karl, 2002. “Nutrient dynamics in the deep blue sea”
• Karl, 2007. “Microbial oceanography: paradigms, processes and promise”
• Karl and Letelier, 2009. “Marine Habitats”
• Lauro, et al., 2009. “The genomic basis of trophic strategy in marine bacteria”
• McFall-Ngai, et al., 2013. “Animals in a bacterial world, a new imperative for the life sciences”
• Moore, 1965. “Cramming more components onto integrated circuits”
• Nair, 2012. “Woese and Fox: Life, rearranged”
• Pedrós-Alió, 2012. “The Rare Bacterial Biosphere”
• Steindler, et al., 2011. “Energy Starved Candidatus Pelagibacter Ubique Substitutes Light-Mediated ATP Production for Endogenous Carbon Respiration”
• Woese and Fox, 1977. “Phylogenetic structure of the prokaryotic domain: The primary
  kingdoms”

1030–1045

Coffee break

1045–1145

Lab safety training

1145–1315

Lunch

1315–1415

Biosafety training

1415–1430

Break

1430–1630

Radiation safety training

1630–

Welcome Mixer

Wednesday, May 29

Processes and patterns in microbial carbon and nutrient cycles

0900–1015

John Cullen: Light, nutrients, and primary productivity (10MB PDF)

Readings (PDFs):

• Cullen, 2001. “Primary Production Methods”
• Cullen, et al., 2002. “Physical Influences on Marine Ecosystem Dynamics”
• Follows and Dutkiewicz, 2011. “Modeling Diverse Communities of Marine Microbes”

1015-1030

Coffee break

1030–1145

Dan Repeta: The marine carbon cycle: pools, inventories, fluxes (2MB .ppt)

Readings (PDFs):

• Hansell, et al., 2009. “Dissolved Organic Matter in the Ocean”
• Hansell et al., 2012. “Net removal of major marine dissolved organic carbon fractions in the subsurface ocean”
• Sarmento and Gasol, 2012. “Use of phytoplankton-derived dissolved organic carbon by different types of bacterioplankton”
• Williams and Druffel, 1987. “Radiocarbon in dissolved organic matter in the central North Pacific Ocean”

1145-1330

Lunchtime Brown Bags (Campus Center Room 203A)

1330–1445

David Karl: Ocean nutrient cycling: Distributions, processes, and fluxes (39MB .pptx)

Readings (PDFs):

• Arrigo, 2005. “Marine microorganisms and global nutrient cycles”
• Dyhrman, et al., 2007. “Microbes and the Marine Phosphorus Cycle”
• Elser, et al., 2011. “Stoichiogenomics: the evolutionary ecology of macromolecular elemental composition”
• Francis, et al., 2007. “New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation”
• Gruber, 2008. “The Marine Nitrogen Cycle: Overview and Challenges”
• Karl, et al., 2008. “The Nitrogen Cycle in the North Pacific Trades Biome: An Evolving Paradigm”
• Ulloa, et al., 2012. “Microbial oceanography of anoxic oxygen minimal zones”

1445–1600

Ginger Armbrust: Earth's history, evolution and the emergence of eukaryotic phytoplankton

1600–1615

Break

1615–1730

Ken Johnson: Observing ocean biogeochemistry in the 21st century with robotic systems: patterns and processes of microbial nutrient cycling, production and remineralization, Part 1 (30MB .pptx)

Readings (PDFs):

• Johnson, et al., 2010. “Nitrate supply from deep to near-surface waters of the North Pacific subtropical gyre”
• Riser and Johnson, 2008. “Net production of oxygen in the subtropical ocean”
• Williams, et al., 2013. “The Oligotrophic Ocean Is Autotrophic”

Thursday, May 30

Plankton productivity, diversity, and biogeochemistry (Part I)

0900–1015

John Cullen: Measures and models of ocean productivity (12MB PDF)

1015–1030

Coffee break

1030–1145

Ginger Armbrust: Functional and taxonomic diversity of phytoplankton

1200–1330

Lunchtime Brown Bags (Campus Center Room 203A)

1330–1445

Ken Johnson: Observing ocean biogeochemistry in the 21st century with robotic systems: patterns and processes of microbial nutrient cycling, production and remineralization, Part 2

1445–1500

Break

1500–1615

Dan Repeta: Substrate specificity in microbial carbon utilization (77MB .ppt)

1615–1700

Cruise planning

Friday, May 31

Plankton productivity, diversity, and biogeochemistry (Part II)

0900–1015

Dan Repeta: Dissolved organics matter: Distributions, concentrations, reactivity (6MB .ppt)

1015–1030

Coffee break

1030–1145

John Cullen: Behavior, physiology and the niche of marine phytoplankton (26MB PDF)

1145–1330

Lunchtime Brown Bags (Campus Center Room 203A)

1330–1445

Ginger Armbrust: The influence of symbioses and interactions between organisms on nutrient utilization in the sea

1445–1500

Break

1500–1615

Ken Johnson: Nitrogen cycling in low oxygen regions: how do autonomous, sustained observations factor into the debate on the role of classical denitrification versus anammox (13MB .pptx)

Readings (PDFs):

• Dalsgaard, et al., 2012. “Anammox and denitrification in the oxygen minimum zone of the eastern South Pacific”
• Kalvelage, et al., 2013. “Nitrogen cycling driven by organic matter export in the South Pacific oxygen minimum zone”
• Lam, et al., 2009. “Revising the nitrogen cycle in the Peruvian oxygen minimum zone”
• Ward, et al., 2008. “Organic carbon, and not copper, controls denitrification in oxygen minimum zones of the ocean”

1615–1730

“Stupid questions only”

Saturday, June 01

Student Research Symposium

• Gerdhard Jessen (60MB .ppt)
• Sarah Q. Foster (31MB .pptx)
• Mónica Rouco (5MB .pptx)
• Allanah Paul (6MB .pptx)
• Susan Evans, David Green, and Angela Hatton (4MB .pptx)
• Alison Webb (2MB .pptx)
• Alyssa Kent (5MB .pptx)
• Alvaro Munoz Plominsky (6MB .ppt)
• Jaume Bibiloni Isaksson (4MB .ppt)
• Tom S. Lankiewicz (3MB .pptx)
• Brandon Satinsky (45MB .pptx)
• John Paul Balmonte (6MB .pptx)
• Alexandra (Ali) Bausch (13MB .pptx)
• Anna R. Bramucci (10MB .pptx)

0900–1015

Student research talks

1015–1030

Coffee break

1030–1200

Student research talks

1200–1315

Lunch (provided)

1315–1600

Student research talks

1600

Reception

Sunday, June 02

 Free Day to explore O‘ahu

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Week 2: Genomes to Biomes

• Faculty: Ed DeLong, Nikos Krypides, Eric Allen, Elizabeth Costello, Scott Gifford
• All Lectures in the Moore Conference Center, C-MORE Hale

Monday, June 03

Faculty Research Talks

0900–0945

Mike Rappé: Local faculty research talk: Planktonic oceanic bacteria: Who are the abundant groups? (76MB .pptx)

0945–1030

Grieg Steward: Local faculty research talk

1030–1045

Coffee break

1045–1130

Daniela Böttjer: Lecture: Diazotroph responses to elevated pCO2 at Station ALOHA (41MB .pptx)

1130–1215

Matt Church: Local faculty research talk

Readings (PDFs):

• Church, et al., 2009. “Physical forcing of nitrogen fixation and diazotroph community structure in the North Pacific subtropical gyre”
• Karl, et al., 2011. “Predictable and efficient carbon sequestration in the North Pacific Ocean supported by symbiotic nitrogen fixation”
• Keeling, C., 1998. “Rewards and Penalties of Monitoring the Earth”

1215–1330

Lunchtime Brown Bags (Campus Center Room 203E)

1330–1430

Benedetto Barone: Lecture: Optical methods for biological oceanography (11MB PDF)

1430–1445

Break

1445–1700

Cruise planning meeting

Tuesday, June 04

Introduction to Microbial Genomics

0900–1015

Ed DeLong: Lecture: Introduction to marine microbial ‘omics (26MB .pptx)

Readings (PDFs):

• Canfield, et al., 2010. “A Cryptic Sulfur Cycle in Oxygen-Minimum-Zone Waters off the Chilean Coast”
• Society for Applied Microbiology and Blackwell Publishing Ltd, 2013. “Crystal Ball”
• Delong, 2009. “The microbial ocean from genomes to biomes”
• DeLong and Karl, 2005. “Genomic perspectives in microbial oceanography”
• Pace, 1997. “A Molecular View of Microbial Diversity and the Biosphere”
• Ulloa, et al., 2012. “Microbial oceanography of anoxic oxygen minimum zones”

1015–1030

Coffee Break

1030–1200

Elizabeth Costello: Lecture: General ecological principles in microbial systems (109MB Keynote)

Readings (PDFs) in order:

1. Vellend, 2010. “Conceptual synthesis in community ecology”
2. Hanson, et al., 2012. “Beyond biogeographic patterns: processes shaping the microbial landscape”
3. Dornelas, et al., 2012. “Quantifying temporal change in biodiversity: challenges and opportunities”

Web sites about QIIME::

• General information
• News and announcements
• Troubleshooting forum

1200–1400

Lunchtime Brown Bags (Campus Center Room 203E)

1400–1515

Eric Allen: Lecture: Genome assembly: genomics & metagenomics (26MB .pptx)

Readings (PDFs):

• Berger, et al., 2013. “Computational solutions for omics data”
• Podell, et al., 2013. “Assembly-Driven Community Genomics of a Hypersaline Microbial Ecosystem”
• Sun, et al., 2010. “Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource”

1515–1530

Break

1530–1700

Nikos Kyrpides: Lecture: Annotation of microbial genomes (16MB .pptx)

Wednesday, June 05

Metagenomics and Transcriptomics

0900–1015

Mike Rappé: Lecture: High throughput culturing & genomics of planktonic oligotrophic marine bacteria (36MB .pptx)

1015–1030

Coffee Break

1030–1200

Eric Allen: Lecture: Microbial metagenomics in extreme environments (36MB .pptx)

1200–1400

Lunchtime Brown Bags (Campus Center Room 203E)

1400–1515

Kyrpides & Allen: Lecture: Introduction to IMG and IMG/M, and CAMERA (lecture and lab)
Kyrpides 1, 6MB .pptx; Kyrpides 2, 8MB .pptx; Allen, 21MB .pptx)

1515–1530

Break

1530–1700

Elizabeth Costello: Lecture and Lab: Introduction to QIIME

Reading (PDF):

• McFall-Ngai, et al., 2013. “Animals in a bacterial world, a new imperative for the life sciences”

Thursday, June 06

Comparative Genomics

0900–1015

Elizabeth Costello: Lecture: Dynamics of host-associated microbial communities through the lens of massively parallel rRNA sequence comparisons

1015–1030

Coffee Break

1030–1200

Ed DeLong: Lecture: Dynamics of planktonic microbial communities through the lens of metatranscriptomic analysis (20MB .pptx)

1200–1400

Lunchtime Brown Bags (Campus Center Room 203E)

1400–1515

Lab: Microbial genome & community analyses (IMG, CAMERA QIIME)

1515–1530

Break

1530–1700

Lab: Microbial genome & community analyses (IMG, CAMERA QIIME)

Friday, June 07

Genome Analyses

0900–1015

Scott Gifford: Lecture: Omics & microbial ecology of coastal ecosystems (26MB .pptx)

Readings (PDFs):

• Giovannoni, et al., 2008. “The small genome of an abundant coastal ocean methylotroph”
• Griffin, et al., 2012. “Resource Partitioning and Why It Matters”
• Johnson, et al., 2006. “Niche Partitioning Among Prochlorococcus Ecotypes Along Ocean-Scale Environmental Gradients”

1015–1030

Coffee Break

1030–1200

Ed DeLong: Lecture: Integrating ‘omics, biogeochemistry and ecology: marine oxygen minimum zones, a case study (41MB .pptx)

1200–1330

Lunchtime Brown Bags (Campus Center Room 203E)

1400–1515

Lab: Microbial genome & community analyses (IMG, CAMERA QIIME)

1530–1700

Lab: Microbial genome & community analyses (IMG, CAMERA QIIME)

Saturday, June 08

Cruise Planning

Half day

Cruise planning discussion (lunch provided)

Sunday, June 09

 Free Day to explore O‘ahu

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Weeks 3 and 4: Research Cruise (and Laboratory Analyses)

Monday, June 10

Snug Harbor: Loading Kilo Moana for research cruise
Note: Closed-toed shoes required; also make sure to bring sunscreen and a hat for loading.

Tuesday, June 11 thru
Friday, June 21

Research cruise to Station ALOHA

Friday, June 21

Return to Snug Harbor, offload ship and check into dorms
Begin laboratory analyses afternoon of June 21

Saturday, June 22

Laboratory analyses

Sunday, June 23

Laboratory analyses

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Week 5: Laboratory Analyses

Monday, June 24

0900–1200

Laboratory analyses

1200–1400

Lunchtime Brown Bags (Campus Center Room 203E)

1400–1700

Laboratory analyses

Tuesday, June 25

0900–1200

Laboratory analyses

1200–1400

Lunchtime Brown Bags (Campus Center Room 203E)

1400–1700

Laboratory analyses

Wednesday, June 26

0900–1200

Laboratory analyses

1200–1400

Lunchtime Brown Bags (Campus Center Room 203E)

1400–1700

Laboratory analyses

Thursday, June 27

0900–1015

Student break out groups working on data analyses

1015–1030

Break

1030–1200

Student break out groups on data analyses

1200–1400

Lunchtime Brown Bags (Campus Center Room 203E)

1400–1700

Student break out groups — Assembling presentation

Friday, June 28

0900–1030

Student Final Presentation

1030–1100

Break

1100–1200

Student evaluations

1200–1400

Lunch (Campus Center Room 203E)

1400–1700

Student evaluations, lab check out

1800–2100

Farewell Gala at 3660 On the Rise

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