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Week 1: The Ocean as a Habitat
- Faculty: Phil Boyd, Curtis Deutsch, Alyson Santoro, John Cullen, Dan Repeta
- All Lectures in the Moore Conference Center, Daniel K. Inouye C-MORE Hale.
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Tuesday, May 27 |
Welcome and laboratory safety training |
0830–0915 |
Welcome
|
0915–1030 |
Lecture: An Introduction to Microbial Oceanography (Karl)
Readings (PDFs):
- Moore, 1965. “Cramming more components onto integrated circuits”
- Woese and Fox, 1977. “Phylogenetic structure of the prokaryotic domain: The primary kingdoms”
- 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”
- DeLong and Béjà, 2010. “The Light-Driven Proton Pump Proteorhodopsin Enhances Bacterial Survival during Tough Times”
- Steindler, et al., 2011. “Energy Starved Candidatus Pelagibacter Ubique Substitutes Light-Mediated ATP Production for Endogenous Carbon Respiration”
- Nair, 2012. “Woese and Fox: Life, rearranged”
- Pedrós-Alió, 2012. “The Rare Bacterial Biosphere”
- McFall-Ngai, et al., 2013. “Animals in a bacterial world, a new imperative for the life sciences”
- Karl, 2014. “Solar energy capture and transformation in the sea”
- Sañudo-Wilhelmy, et al., 2014. “The Role of B Vitamins in Marine Biogeochemistry”
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1030–1045 |
Coffee break |
1045–1145 |
Lab safety (Hans Nielsen) |
1145–1315 |
Lunch |
1315–1415 |
Biosafety (Steve Case) |
1415–1430 |
Break |
1430–1630 |
Radiation safety (Irene Sakimoto) |
1630– |
Welcome Mixer |
Wednesday, May 28 |
Processes and patterns in microbial carbon and nutrient cycles |
0900–1015 |
Lecture: The marine carbon cycle: pools, inventories, fluxes (Repeta)
Readings (PDFs):
|
1015-1045 |
Coffee break |
1045–1200 |
Lecture: Processes controlling carbon and nutrient distributions and cycling (Deutsch)
|
1215-1330 |
Lunchtime introductions (Campus Center, 203E) |
1330–1445 |
Lecture: The Microbial Marine Nitrogen Cycle (Santoro)
Readings (PDFs):
|
1500–1530 |
Break |
1530–1645 |
Lecture: The ocean P cycle (Karl)
Readings (PDFs):
- VanBogelen, et al., 1996 “Global Analysis of Proteins Synthesized during Phosphorus Restriction in Escherichia coli”
- Falkowski_1997 “Evolution of the nitrogen cycle and its influence on the biological sequestration of CO2 in the ocean”
- 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”
- Martinez, et al., 2011 “Phosphite utilization by the marine picocyanobacterium Prochlorococcus MIT9301”
- Karl, 2014. “Microbially Mediated
Transformations of Phosphorus
in the Sea: New Views of an
Old Cycle”
|
1645–1845 |
Student Research Talks |
Thursday, May 29 |
Plankton productivity and organic matter production |
0830–0945 |
Lecture: Light, nutrients, and primary productivity PDF (Cullen)
Readings (PDFs):
|
0945–1015 |
Coffee break |
1015–1130 |
Lecture: Plankton community structure and the biological pump (Boyd)
Readings (PDFs):
|
1130–1300 |
Lunchtime introductions (Campus Center, 203E) |
1315–1430 |
Lecture: Plankton growth, stoichiometry and nutrients (Deutsch)
|
1430–1500 |
Break |
1500–1730 |
Student Research Talks
|
Additional Lecture |
Lecture: Microbial processes in the mesopelagic (Santoro)
Readings (PDFs):
- Anderson and Wang, 2010. “Carbon cycling and POC turnover in the mesopelagic zone of the ocean: Insights from a simple model”
- Burd et al., 2010. “Assessing the apparent imbalance between geochemical and biochemical indicators of meso- and bathypelagic biological activity: What the @$]! is wrong with present calculations of carbon budgets?”
- Gierging et al, 2014. “Reconciliation of the carbon budget in the ocean\92s twilight zone”
- Hansman et al, 2009. “The radiocarbon signature of microorganisms in the mesopelagic ocean”
- Herndl et al, 2005. “Contribution of Archaea to Total Prokaryotic Production in the Deep Atlantic Ocean”
- Herndl and Reinthaler, 2013. “Microbial control of the dark end of the biological pump”
- Reinthaler et al, 2010. “Major contribution of autotrophy to microbial carbon cycling in the deep North Atlantic\92s interior”
- Robinson et al, 2010. “Mesopelagic zone ecology and biogeochemistry \96 a synthesis”
- Steinberg et al., 2008. “Bacterial vs. zooplankton control of sinking particle flux in the ocean\92s twilight zone”
- Swan et al., 2011. “Potential for Chemolithoautotrophy Among Ubiquitous Bacteria Lineages in the Dark Ocean”
- Weinbauer et al. 2013. “Seasonal variability of microbial respiration and bacterial and archaeal community composition in the upper twilight zone”
|
1730–2000 |
Pavel Medal in Microbial Oceanography Reception |
Friday, May 30 |
Plankton ecology and biogeochemistry |
0900–1015 |
Lecture: Measures and models of ocean productivity PDF (Cullen)
|
1015–1045 |
Coffee break |
1045–1200 |
Lecture: The HNLC condition and iron biogeochemistry (Boyd)
Readings (PDFs):
|
1215–1330 |
Lunchtime introductions (Campus Center, 203E) |
1345–1500 |
Lecture: Promises and pitfalls of ocean biogeochemical models (Deutsch)
|
1530–1645 |
Lecture: Dissolved organic matter: distributions and composition (Repeta)
Readings (PDFs):
|
1700–1830 |
Introduction to Station ALOHA (Church) |
Saturday, May 31 |
Plankton ecology and biogeochemistry |
0900–1015 |
Lecture: Behavior, physiologies, and niches of marine plankton PDF (Cullen)
Readings (PDFs):
|
1015–1045 |
Break |
1045–1200 |
Lecture: Plankton biogeochemistry in a future ocean (Boyd)
Readings (PDFs):
|
1200–1330 |
Lunch (provided) |
1330–1445 |
Lecture: Ecology and physiology of planktonic archaea (Santoro)
Readings (PDFs):
|
1445–1500 |
Break |
1500–1615 |
Lecture: Organic matter reactivity and microbial substrate utilization (Repeta)
Readings (PDFs):
|
1630–1800 |
Reception |
Sunday, June 01 |
Free day to snorkel and explore with Ken |
[ Top of Page | Week 1 | Week 2 | Week 3 | Week 4 | Week 5 ]
Week 2: Microbial oceanography through the lens of genomics
- Faculty: Ginger Armbrust, Penny Chisholm (virtually), Ed DeLong, Craig Nelson, Carlos Pedros-Alio, Grieg Steward, John Eppley, Thomas Bibby
- All Lectures in the Moore Conference Center, C-MORE Hale
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Monday, June 02 |
|
0900–1015 |
Lecture: Cellular life and function (Growth, reproduction, introduction to DNA, RNA, transcription, translation, and regulation) (Steward)
|
1015–1045 |
Coffee break |
1045–1130 |
Lecture: Microbial phylogeny and genomics 101 (DeLong)
Readings (PDFs):
|
1200–1330 |
Lunchtime introductions |
1345–1500 |
Lecture: Introduction to eukaryotic marine phytoplankton (Armburst)
|
1500–1515 |
Break |
1515–1630 |
Lecture: Culture-independent approaches to studying microorganisms; plate count anomaly, 16S rRNA genes, PCR, cloning, FISH (Nelson)
|
1630–1730 |
Cruise planning meeting |
Tuesday, June 03 |
Microbial ecology and diversity |
0900–1015 |
Lecture: Introduction to major marine bacterial lineages (Pedrós-Alió)
|
1015–1045 |
Coffee Break |
1045–1200 |
Lecture: Microbial phylogeny and genomics 101 (DeLong)
Readings (PDFs):
|
1200–1400 |
Lunchtime introductions |
1400–1515 |
Lecture: Modern rRNA tag surveys and statistical analyses (Nelson)
|
1515–1545 |
Break |
1545–1700 |
Lab Practical: Computer analyses of rRNA tag sequences (Nelson)
|
Wednesday, June 04 |
Genomics and meta-omics |
0900–1015 |
Lecture: Prochlorococcus: The Power of Diversity I (Chisholm)
|
1015–1045 |
Coffee Break |
1030–1200 |
Lecture: Eukaryotic phytoplankton ecology (Armburst)
|
1200–1400 |
Lunchtime introduction |
1400–1515 |
Lecture: Marine planktonic virus ecology (Steward)
|
1515–1530 |
Break |
1530–1700 |
Lecture: The scientific presentation as theater (Pedros-Alio)
Reading (PDF): How to Give a Killer Presentation Lessons from TED by Chris Anderson
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1800– |
Group Dinner |
Thursday, June 05 |
Comparative Genomics |
0900–1015 |
Lecture: Prochlorococcus: The Power of Diversity II ( (Chisholm) |
1015–1045 |
Coffee Break |
1045–1200 |
Lecture: Genomics of marine Flavobacteria (Pedrós-Alió)
Reading (PDF): Beatriz Fernandez-Gomez et al. 2013. Ecology of marine Bacteroidetes: a comparative genomics approach. The ISME Journal 7, 10261037
|
1200–1400 |
Lunchtime introductions — Bibby (Campus Center, 203E) |
1400–1530 |
Lecture: Genomic insights into diatom ecology & physiology (Armbrust) |
1530–1545 |
Break |
1545–1700 |
Lab: Photophysiology & molecular biology of marine cyanobacteria (Bibby) |
Friday, June 06 |
|
0900–1015 |
Lecture: Integrating \91omics, biogeochemistry and ecology (DeLong)
Readings (PDFs):
|
1015–1045 |
Coffee Break |
1045–1200 |
Lecture: Statistical analyses in microbial ecology (Nelson)
|
1200–1330 |
Lunchtime introductions |
1400–1515 |
Computer Lab: Microbial metagenomic analysis tools — lab practical (DeLong/Eppley) |
1530–1545 |
Break |
1530–1700 |
Computer Lab: Microbial metagenomic analysis tools - lab practical (DeLong/Eppley) |
Saturday, June 07 |
Free Day to Explore O‘ahu |
Sunday, June 08 |
Load R/V Kilo Moana for research cruise
Note: Closed-toed shoes required; also make sure to bring sunscreen and a hat |
[ Top of Page | Week 1 | Week 2 | Week 3 | Week 4 | Week 5 ]
Weeks 3 and 4: Research Cruise
- Possible Faculty/staff: Church, Steward, Doggett, Clemente, Björkman, Searson
|
Monday, June 09 |
Depart Snug Harbor aboard R/V Kilo Moana |
Monday, June 16 |
Return to Snug Harbor, offload ship and check into dorms
Begin laboratory analyses afternoon of June 16 |
Tuesday, June 17 |
|
0800–1130 |
Biogeochemical laboratory analyses (LLN, LLP, PSi, PPO4, LLSi, PC/PN, flow cyto)
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1130–1330 |
Lunchtime introductions (TBD)
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1330–1730 |
Biogeochemical laboratory analyses (LLN, LLP, PSi, PPO4, LLSi, PC/PN, flow cyto)
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Wednesday, June 18 |
|
0800–1130 |
Biogeochemical laboratory analyses (LLN, LLP, PSi, PPO4, LLSi, PC/PN, flow cyto)
|
1130–1330 |
Lunchtime introductions (TBD)
|
1330–1730 |
Biogeochemical laboratory analyses (LLN, LLP, PSi, PPO4, LLSi, PC/PN, flow cyto)
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Thursday, June 19 |
|
0800–1130 |
Students complete biogeochemical laboratory analyses (LLN, LLP, PSi, PPO4, LLSi, PC/PN, flow cyto)
|
1130–1330 |
Lunchtime introductions (TBD)
|
1330–1730 |
Students begin molecular laboratory analyses (sequencing tutorial)
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Friday, June 20 |
|
0800–1130 |
Molecular laboratory analyses (Amplicon sequencing)
|
0130–1330 |
Lunchtime introductions (Campus Center, TBD)
|
1330–1730 |
Molecular laboratory analyses (Amplicon sequencing)
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Saturday, June 21 |
|
0800–1130 |
Molecular laboratory analyses (Metagenomics)
|
1130–1330 |
Lunchtime introductions (Campus Center, TBD)
|
1330–1730 |
Molecular laboratory analyses (Metagenomics)
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Sunday, June 22 |
Free Day to Explore O‘ahu |
[ Top of Page | Week 1 | Week 2 | Week 3 | Week 4 | Week 5 ]
Week 5: Laboratory Analyses and Synthesis |
Monday, June 23 |
|
0800–1130 |
Molecular laboratory analyses (Metagenomics)
|
1130–1330 |
Lunchtime introductions (Campus Center, TBD)
|
1330–1730 |
Molecular laboratory analyses (Metagenomics)
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Tuesday, June 24 |
|
0800–1130 |
Molecular laboratory analyses (Metagenomics)
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1130–1330 |
Lunchtime introductions (Campus Center, TBD)
|
1330–1730 |
Molecular laboratory analyses (Metagenomics)
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Wednesday, June 25 |
|
0900–1015 |
Student break out groups working on data analyses |
1015–1030 |
Break |
1030–1200 |
Student break out groups working on data analyses |
1200–1400 |
Lunchtime introductions (Campus Center, TBD) |
1400–1700 |
Student break out groups working on data analyses |
Thursday, June 26 |
|
0900–1015 |
Students working on presentations |
1015–1030 |
Break |
1030–1200 |
Students working on presentations |
1200–1400 |
Lunchtime introductions (Campus Center, TBD) |
1400–1700 |
Students working on presentations |
Friday, June 27 |
|
0900–1030 |
Student Final Presentation
|
1030–1100 |
Break |
1100–1200 |
Student evaluations |
1200–1400 |
Lunchtime introductions (Campus Center, TBD) |
1400–1700 |
Student evaluations, lab check out |
1800–2100 |
Farewell Gala at Willows Restaurant |
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