2009 Course Syllabus

Week 1 Theme: The Ocean as a Microbial Habitat

• Visiting Faculty: Ken Johnson, Craig Carlson, Debbie Bronk, Dan Repeta, Ed DeLong
  UH Faculty: Matt Church, Dave Karl, Mike Rappé, Grieg Steward

Monday 08 June

0830-0900

Welcome

MSB 100

0900-1200

Lab / Chemical Safety Training

1200-1300

Lunch

1300-1400

Radiation safety

1400-1600

Student Master’s Thesis Defense
Donn Viviani

MSB 114

1700-

Informal Mixer

Tuesday 09 June

An introduction to microbial oceanography

MSB 100

0900-1015

Microbial Oceanography: Its scope, challenges, and opportunities (Dave Karl)

Readings (PDFs):

1. “Microbial Oceanography” Introduction
2. Microbial oceanography in a sea of opportunity
3. The life of diatoms in the world’s oceans (4.23 MB)
4. Microbial community structure and its functional implications
5. The microbial ocean from genomes to biomes
6. Viruses manipulate the marine environment
7. Marine Habitats
8. Microbial oceanography: paradigms, processes and promise

1015-1030

Break

1030-1230

Research Seminars: Matthew Church, Grieg Steward, Mike Rappé

1230-1400

Brownbag lunch: D. Karl, G. Steward, M. Church, M. Rappé (Campus Center 203E)

1430-1530

Research seminar: Karin Björkman

MSB 315

1530-1700

Research cruise planning meeting and discussions

MSB 315

Wednesday 10 June

Microbial Control of Nutrient Cycling in the Sea

MSB 100

0900-1015

Nitrogen cycling in the ocean (D. Bronk)

Readings (PDFs):

1. Nutrient dynamics in the deep blue sea
2. The Marine Nitrogen Cycle: Overview and Challenges

Lecture (as PDF):

1. Bronk Lecture 1 (7.9 MB)

1015-1045

Break

1045-1130

Phosphorus cycling in the sea (D. Karl)

1200-1330

Brownbag lunch: D. Bronk, K. Johnson (Campus Center 203E)

1400-1515

Ocean C-cycling: History, inventories, and dynamics (C. Carlson)

Readings (PDFs):

1. Efficient export of carbon to the deep ocean through dissolved organic matter
2. Dissolved organic matter in the ocean: Comments on a controversy
3. Uptake and Storage of Carbon Dioxide in the Ocean… (6.95 MB)
4. Marine Disolved Organic Matter and the Carbon Cycle (4.23 MB)
5. Element Stoichiometry, New Production and Nitrogen Fixation (4.15 MB)

Lecture (as PDF):

1. Carlson Lecture 1 (4 MB)

1530-1700

What would we learn with a global biogeochemical sensor array? (K. Johnson)

Readings (PDFs):

1. Net production of oxygen in the subtropical ocean
2. Simultaneous measurements of nitrate, oxygen and dissolved inorganic carbon on oceanographic moorings…
3. Chemical Sensor Networks for the Aquatic Environment
4. Observations of pigment and particle distributions in the western North Atlantic from an autonomous float and ocean color satellite

Thursday 11 June

Dissolved Organics Matter

MSB 110

0900-1015

Structure and composition of DOM (D. Repeta)

Readings (PDFs):

1. Marine Organic Geochemistry
2. Radiocarbon in dissolved organic matter in the central North Pacific Ocean

1015-1045

Break

1045-1130

Reactivity and turnover of DOM (C. Carlson)

Lecture (as PDF):

1. Carlson Lecture 2 (4 MB)

1200-1330

Brownbag lunch: C. Carlson, D. Repeta (MSB lanai)

1400-1515

DON sources: methods and processes (D. Bronk)

Lecture (as PDF):

1. Bronk Lecture 2 (7.6 MB)

1530-1645

Iron and the HNLC condition (K. Johnson)

1700-1800

Microbial iron cycling (D. Repeta)

Readings (PDFs):

1. Marine siderophores and microbial iron mobilization
2. Manipulating Iron Availability in Nearshore Waters

Friday 12 June

Student Research Talks

MSB 100

Saturday 13 June

Symposium 1: “Sea Change: New perspectives on microbially-driven elemental cycles”

Matt Church, moderator.

UH William Richardson School
of Law

0830-1600

Presentations include:

• Ken Johnson (MBARI) “Insights into the variability of the microbial habitat in the subtropical Pacific from in situ biogeochemical sensors”
• Debbie Bronk (VIMS) “New approaches to study DON bioavailability”
  ¤ Lecture (as PDF): Bronk Lecture 3 (8.9 MB)
• Craig Carlson (UCSB) “Connecting heterotrophic microorganisms to the ocean C cycle at the Sargasso Sea Microbial Observatory”
• Dan Repeta (WHOI)“Moving beyond model compounds- how do we link dissolved organic matter cycling with microbial metabolism in the ocean?”
• Edward DeLong (MIT) TBD

For more information, download the flyer PDF.

Reception to follow at Stan Sheriff Center

Sunday 14 June

Hanauma Bay day trip with Ken and Brett (optional)

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Week 2 Theme: The Microbial Ocean Viewed Through the Lens of Genes & Genomes

• Visiting Faculty: Edward DeLong, Rob Edwards, Matthew Sullivan, Mike Sieracki
  UH Faculty: Matt Church, Mike Rappé, Grieg Steward

Monday 15 June

Introduction to marine microbial genomics and metagenomics

MSB 100

0900-1015

Marine microbes and genomics (E. DeLong)

Readings (PDFs):

1. RAST and MG-RAST Workshop II (Manual, 15 MB)
2. Comparative genomics of two ecotypes of the marine planktonic copiotroph Alteromonas macleodii...
3. Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum
4. Evolutionary Origins of Genomic Repertoires in Bacteria
5. Ecological Genomics of Marine Roseobacters
6. Genome Streamlining in a Cosmopolitan Oceanic Bacterium
7. Trends between gene content and genome size in prokaryotic species with larger genomes
8. Resource Partitioning and Sympatric Differentiation Among Closely Related Bacterioplankton

Lecture (as PDF):

1. DeLong Lecture 1 (13 MB)

1015-1045

Break

1045-1200

Marine cyanobacteria ecology (M. Sullivan)

1200-1330

Brownbag lunch: E. DeLong, M. Sullivan (Campus Center 203E)

1330-1700

Computational biology and informatics — Intro to MG_RAST, CAMERA, & genomics/metagenomics resources (E. DeLong / R.Edwards)

Readings (PDFs except as noted):

1. Lecture Notes (.rtf file)
2. The RAST Server: Rapid Annotations using Subsystems Technology
3. CAMERA: A Community Resource for Metagenomics (5 MB)
4. IMG/M: a data management and analysis system for metagenomes
5. MEGAN analysis of metagenomic data
6. The metagenomics RAST server — a public resource for the automatic phylogenetic and functional analysis of metagenomes

Lecture (as PDF):

1. DeLong Lecture 2

Tuesday 16 June

Phages, cells, and computer lab

MSB 100

0900-1015

Marine microbial metagenomics (E. DeLong)

1015-1045

Break

1045-1230

Statistics and comparative metagenomic analysis (R. Edwards)

Lecture (as PDFs):

1. Table of Contents and References
2. Go Genomics!!
3. Genomics and metagenomics
4. Viral oceanography
5. ARISA \96 more community profiles
6. Why you should be a marine biologist
7. How many genes are there in the world?
8. Which gene won?
9. Seeing is believing
10. Lies, damn lies, and…
11. Tell me the truth!!

1230-1330

Brownbag lunch: R. Edwards, M. Sieracki (Campus Center 203E)

1330-1700

Computer Lab I — Genomic and metagenomic analysis using MG-RAST
(R. Edwards / E. DeLong / M. Sullivan)

Readings (PDFs):

1. Proteorhodopsin phototrophy in the ocean
2. Bacterial Rhodopsin: Evidence for a New Type of Phototrophyin the Sea
3. Community Genomics Among Stratified Microbial Assemblages…
4. Microbial community gene expression in ocean surface waters
5. Proteorhodopsin lateral gene transfer between marine planktonic Bacteria and Archaea
6. The microbial ocean from genomes to biomes
7. Proteorhodopsin photosystem gene expression enables photophosphorylation in a heterologous host
8. Proteorhodopsin photosystem gene clusters exhibit co-evolutionary trends and shared ancestry…
9. Metatranscriptomics reveals unique microbial small RNAs in the ocean’s water column

Lecture (as PDF):

1. DeLong Lecture 3 (26.6 MB)

MSB 315

Wednesday 17 June

MSB 100

0900-1015

Marine cyanobacteria/phage genomics & metagenomics (M. Sullivan)

1015-1045

Break

1045-1200

Computer Lab IIa — Genomic and metagenomic analysis using MG-RAST (R. Edwards/E. DeLong/M. Sullivan)

1230-1330

Brownbag lunch: R. Edwards, M. Sieracki (Campus Center 203E)

1330-1500

Single cell genomic analysis of marine bacterioplankton (M.Sieracki)

Readings (PDFs):

1. Genomic sequencing of single microbial cells from environmental samples
2. Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time
3. Assembling the Marine Metagenome, One Cell at a Time

1500-1700

Computer Lab IIb — Genomic and metagenomic analysis using MG-RAST
(E. DeLong / M. Sullivan)

MSB 315

Thursday 18 June

MSB 307

0900-1200

ARB workshop (Amy Apprill)

1230-1400

Lunch

1430-

ARB workshop (Amy Apprill)

Friday 19 June

MSB 100

0900-1300

Loading R/V Kilo Moana
Students take cabs to Snug Harbor

1500-1700

Student Dissertation Defense (Jennifer Brum)

MSB 114

Saturday 20 June

Continued loading R/V Kilo Moana

Sunday 21 June

Free Day for students to explore O‘ahu

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Week 3 AT SEA

• Faculty and Staff for Research cruise include: M. Church, M. Rappé, G. Steward, M. Sieracki, K. Doggett, K. Björkman, T. Clemente, B. Updyke

Monday 22 –
Tuesday 30 June

Students to check out of dorm rooms by 07:15 on June 22 and take taxis to UH marine center.

Activities while at sea will include tutorials and hands-on labs to measure: primary & secondary production; microscopy/flow cytometry for enumerating/sorting picoplankton and viruses; DNA/RNA extraction; PCR & RT-PCR; cloning; various measures of microbial biomass (Chl, ATP, direct counts). Samples will also be collected for subsequent analyses of inorganic and organic nutrients; particulates; C/N/P/Si export fluxes.

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Week 4 Theme: Laboratory Sample Analyses

• No visiting faculty this week
  UH Faculty: Matt Church, Mike Rappé, Grieg Steward

Tuesday 30 June

0800-1200

Offload Research vessel

1230-1400

Students take cabs back to campus; lunch on your own

1430-

Check into campus housing

Wednesday 01 July

Sample Analyses

MSB 315

0900-1800

Cruise sample analyses
(Lunch on your own)

Thursday 02 July

Sample Analyses

MSB 315

0900-1800

Cruise sample analyses
(Lunch on your own)

Friday 03 July

Sample Analyses

MSB 315

0900-1800

Cruise sample analyses
(Lunch on your own)

Saturday 04 July

Free Day for students to explore O‘ahu

Sunday 05 July

Sample Analyses

MSB 315

0900-1800

Cruise sample analyses
(Lunch on your own)

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Week 5 Theme: Biodiversity and Sub-Euphotic Zone Life

• Visiting faculty: Gerhard Herndl, Debbie Steinberg, Mitch Sogin, Carlos Pedrós-Alió
  UH Faculty: Matt Church, Mike Rappé, Grieg Steward

Monday 06 July

Sample Analyses

MSB 315

0900-1800

Cruise sample analyses
(Lunch on your own)

Tuesday 07 July

Sample Analyses

MSB 114

0900-1800

Sample Analyses (PC/PN, TOC, PSi)
(Lunch on your own)

Wednesday 08 July

MSB 114

0900-1015

A manual to survive in the surface of the oceans: the genome of Polaribacter MED152 (C. Pedrós-Alió)

1015-1045

Break

1045-1130

Introduction to the dark ocean (D. Steinberg)

Readings (PDFs):

1. Bacterial vs. zooplankton control of sinking particle flux in the ocean’s twilight zone
2. Upper Ocean Carbon Export and the Biological Pump

Lecture (as PDF):

1. Steinberg Lecture 1

1200-1330

Brownbag lunch: D. Steinberg, C. Pedrós-Alió (Campus Center 203E)

1400-1530

Colloquium: Getting the job you want (D. Steinberg)

Thursday 09 July

MSB 100

0900-1015

Waking up from the Arctic winter: the microbial food web in the twilight zone (C. Pedrós-Alió)

1015-1045

Break

1045-1130

The new era of microbial biodiversity and phylogenetics (M. Sogin)

1200-1330

Brownbag lunch: M. Sogin (Campus Center 203E)

1400-1515

Colloquium: Art and science: Picasso and the structure of DNA (C. Pedrós-Alió)

1530-1800

Students completing lab analyses

Friday 10 July

MSB 100

0900-1015

The biological pump and fueling the deep sea (D.Steinberg)

Lecture (as PDF):

1. Steinberg Lecture 2 (17 MB)

1015-1045

Break

1045-1130

Flux of particles to the deep sea (D. Karl)

1200-1330

Brownbag lunch: (Campus Center 203E)

1400-1515

Protist diversity and evolution (M. Sogin)

Lecture for Thursday 09 and Friday 10 July (as PPT):

1. Sogin Lecture (18 MB)

1530-

Students completing lab analyses

Saturday 11 July

Symposium 2: “To the twilight zone and beyond: life from sea surface to sea floor ”

East-West Center Asia Room, UH

0830-1600

Presentations include:

• Debbie Steinberg (VIMS) “Planktonic food web controls on carbon cycling in the ocean’s twilight zone”
• Craig R. Smith (UHM) “Abyssal ecosystem structure and function, organic carbon limitation and climate change”
• Doug Bartlett (Scripps) “Life under pressure”
  Readings (PDFs):
  ¤ Life at Depth: Photobacterium profundum Genome…
  ¤ Deep-Sea Bacterium Photobacterium profundum SS9 Utilizes…
  ¤ Large-Scale Transposon Mutagenesis of Photobacterium…
• Mitch Sogin (MBL) “The Rare Biosphere is everywhere”
• Carlos Pedrós-Alió (ICMB) “Dipping into the rare biosphere”

For more information, download the flyer PDF.

Reception to follow.

Sunday 12 July

Shark’s Cove day trip with Ken and Brett (optional)

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Week 6 Theme: The Changing Sea: Models, Challenges, and Opportunities

• Visiting faculty: Mick Follows, Ed Laws, Chris Bowler, Tony Michaels, Ken Buesseler, John Dore
  UH Faculty: Matt Church, Mike Rappé, Grieg Steward

Monday 13 July

MSB 114

0900-1200

Student presentation preparations — All Day

Tueday 14 July

MSB 114

0900-1015

Modeling marine microbial communities (M. Follows)

Readings (PDFs):

1. Physical Transport of Nutrients and the Maintenance of Biological Production
2. A chronology of plankton dynamics in silico: how computer models have been used to study marine ecosystems

1015-1045

Break

1045-1200

The role of stability in structuring marine microbial communities (E. Laws)

1230-1400

Brownbag lunch: M. Follows (Campus Center 203E)

1430-

Student presentation preparations

Wednesday 15 July

MSB 114

0900-1015

Ocean transport of nutrients and the maintenance of biological productivity in the oceans (M. Follows)

1015-1045

Break

1045-1130

Understanding the ocean’s biological pump (Buesseler)

Readings (PDFs):

1. An assessment of the use of sediment traps for estimating upper ocean particle fluxes
2. Shedding light on processes that control particle export and flux attenuation in the twilight zone of the open ocean
3. Ocean Iron Fertilization — Moving Forward in a Sea of Uncertainty
4. Mesoscale Iron Enrichment Experiments 1993–2005: Synthesis and Future Directions

1230-1400

Brownbag lunch: K. Buesseler (MSB Lanai)

1430-1545

Ocean fertilization: ironing out uncertainties in climate engineering (K. Buesseler)

Thursday 16 July

MSB 114

0900-1200

Student Symposium

1230-1400

Brownbag lunch: A. Michaels (MSB Lanai)

1430-

Career directions discussion (A. Michaels)

Friday 17 July

Symposium 3: “Microbial Oceanography in a Changing SeaScape”

East-West Center Asia Room, UH

0830-1600

Presentations include:

• Ken Buesseler (WHOI) “Shedding light on the ocean’s biological pump and twilight zone processes”
  ¤ Watch the video presentation
• Mick Follows (MIT) “Patterns of phytoplankton diversity in a model ocean”
  ¤ Watch the video presentation
• Chris Bowler (CNRS) “Systems Biology in the Ocean: Linking Community Structure with Community Function”
  ¤ Watch the video presentation
• John Dore (MSU) “Ocean biogeochemical cycles in the Anthropocene: Challenges and opportunities presented by complex interactions and multiple feedback loops”
  ¤ Watch the video presentation
• Anthony Michaels (PI) “Ocean Microbiologists and Global Sustainability
  ¤ Watch the video presentation

For more information, download the flyer PDF.

Farewell Banquet to follow at The Willows Restaurant

Saturday 18 July

Free Day for students

Sunday 19 July

Students check out of dorms

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