2015 Course Syllabus

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Week 1: The Ocean as a Habitat

• Faculty: Dan Repeta, Mick Follows, Angelicque White, David Karl, Matthew Church, Daniela Böttjer, Grieg Steward, Kyle Edwards
• All Lectures in the Moore Conference Center, C-MORE Hale.

Tuesday, May 26

Welcome and laboratory safety training

0830–0915

Welcome 4MB .pptx (Church)

0915–1030

Lecture: An Introduction to Microbial Oceanography 55MB .pptx (Karl)

Readings (PDFs):

• Aylward, et al., 2015. “Microbial community transcriptional networks are conserved in three domains at ocean basin scales”
• DeLong and Béjà, 2010. “The Light-Driven Proton Pump Proteorhodopsin Enhances Bacterial Survival during Tough Times”
• Fuhrman, et al., 2015. “Marine microbial community dynamics and their ecological interpretation”
• Karl, 2002. “Nutrient dynamics in the deep blue sea”
• Karl, 2007. “Microbial oceanography: paradigms, processes and promise”
• Karl, 2015. “Solar energy capture and transformation in the sea”
• Karl and Church, 2014. “Microbial oceanography and the Hawaii Ocean Time-series programme”
• 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”
• Ottesen, et al., 2014. “Multispecies diel transcriptional oscillations in open ocean heterotrophic bacterial assemblages”
• Pace, et al., 2012. “Phylogeny and beyond: Scientific, historical, and conceptual significance of the first tree of life”
• Pedrós-Alió, 2012. “The Rare Bacterial Biosphere”
• Woese and Fox, 1977. “Phylogenetic structure of the prokaryotic domain: The primary kingdoms”

1030–1045

Coffee break

1045–1145

Lab safety (Hans Nielsen)

1145–1315

Lunch (Campus Center 203A)

1315–1415

Biosafety (Steve Case)

1415–1430

Break

1430–1630

Radiation safety (Irene Sakimoto)

1630–

Welcome Mixer

Wednesday, May 27

Processes and patterns in microbial carbon and nutrient cycles

0900–1015

Lecture: The marine carbon cycle: pools, inventories, fluxes 37MB .pptx (Repeta)

Readings (PDFs):

• Berner, 1999. “A New Look at the Long-term Carbon Cycle”
• Berner, 2013. “The long-term carbon cycle, fossil fuels and atmospheric composition”
• Falkowski, et al., 2000. “The Global Carbon Cycle: A Test of Our Knowledge of Earth as a System”

1015-1045

Coffee break

1045–1200

Lecture: Mediation of elemental cycles by ocean circulation and biological processes: from eddies to global scales 275MB .pptx (Follows)

Readings (PDFs):

• Williams and Follows, 2011. “Chap. 2: An introductory view of the ocean”
• Williams and Follows, 2011. “Chap. 4: Physics fundamentals”
• Williams and Follows, 2011. “Chap. 11: Cycling and transport of nutrients and carbon”

1215-1330

Lunchtime introductions — Karl, Follows (Campus Center 203A)

1330–1445

Lecture: The ocean P cycle 36MB .pptx (Karl)

Readings (PDFs):

• Arrigo, 2005. “Marine microorganisms and global nutrient cycles”
• Bjorkman, 2014. “Polyphosphate goes from pedestrian to prominent in the marine P-cycle”
• del Valle and Karl, 2014. “Aerobic production of methane from dissolved water-column methylphosphonate and sinking particles in the North Pacific Subtropical Gyre”
• Dyhrman, et al., 2007. “Microbes and the Marine Phosphorus Cycle”
• Elser, et al., 2011. “Stoichiogenomics: the evolutionary ecology of macromolecular elemental composition”
• Falkowski, 1997. “Evolution of the nitrogen cycle and its influence on the biological sequestration of CO2 in the ocean”
• Karl, 2014. “Microbially Mediated Transformations of Phosphorus in the Sea: New Views of an Old Cycle”
• Karl and Bjorkman, 2015. “Dynamics of Dissolved Organic Phosphorus”
• Martin, et al., 2014. “Accumulation and enhanced cycling of polyphosphate by Sargasso Sea plankton in response to low phosphorus”
• Martínez, et al., 2011. “Phosphite utilization by the marine picocyanobacterium Prochlorococcus MIT9301emi_2612”
• VanBogelen, et al., 1996. “Global Analysis of Proteins Synthesized during Phosphorus Restriction in Escherichia coli”
• VanMooy, et al., 2015. “Major role of planktonic phosphate reduction in the marine phosphorus redox cycle”

1500–1530

Break

1530–1645

Lecture: An introduction to Station ALOHA 35MB .pptx (Church)

Readings (PDFs):

• Church, et.al., 2013. “Sea change: Charting the course for biogeochemical ocean time-series research in a new millennium”
• Riser and Johnson, 2008. “Net production of oxygen in the subtropical ocean”

1645–1845

Student Research Talks

Thursday, May 28

Measures and models of plankton productivity

0830–0945

Lecture: A primer on marine productivity: Definitions, measurements, and models 288MB .pptx (White)

Readings (PDFs):

• Juranek and Quay, 2013. “Using Triple Isotopes of Dissolved Oxygen to Evaluate Global Marine Productivity”
• Quay, et al., 2010 “Measuring primary production rates in the ocean: Enigmatic results between incubation and non-incubation methods at Station ALOHA”
• Bender, et al., 1987. “A comparison of four methods for determining planktonic community production”

0945–1015

Coffee break

1015–1130

Lecture: Trait-based phytoplankton models 10MB .pptx (Edwards)

1130–1300

Lunchtime introductions – Repeta, White (Campus Center 203A)

1315–1430

Lecture: Modeling size-structure and trophic strategies of plankton populations at the global scale 135MB .pptx (Follows)

Readings (PDFs):

• Hartmann, et al., 2012. “Mixotrophic basis of Atlantic oligotrophic ecosystems”
• Teng, et al., 2014. “Global-scale variations of the ratios of carbon to phosphorus in exported marine organic matter”
• Ward, et al., 2012. “A size-structured food-web model for the global ocean”
• Ward, et al., 2013. “Modelling spatial and temporal patterns in size-structured marine plankton communities: top–down and bottom–up controls”
• Zimmerman, et al., 2014. “Phosphate supply explains variation in nucleic acid allocation but not C: P stoichiometry in the western North Atlantic”

1430–1500

Break

1500–1730

Student Research Talks (con’t.)

Friday, May 29

Organic matter cycling in the sea

0900–1015

Lecture: The microbial loop 38MB .key (Steward)

Worksheet and Readings (PDFs):

• Worksheet. “Visualization Exercise: Life at the Microscale”
• Azam, et al., 1983. “The Ecological Role of Water-Column Microbes in the Sea”
• Pomeroy, 1974. “The Ocean’s Food Web: A Changing Paradigm”
• Purcell, 1977. “Life at low Reynolds number”
• Mitchell, et al., 1995. “Natural Assemblages of Marine Bacteria Exhibiting High-Speed Motility and Large Accelerations”

1015–1045

Coffee break

1045–1200

Lecture: Dissolved organic matter: Pools and fluxes 8MB .pptx (Repeta)

Readings (PDFs):

• Hansell, et al., 2009. “Dissolved Organic Matter in the Ocean”
• Kujawinski, 2011. “The Impact of Microbial Metabolism on Marine Dissolved Organic Matter”
• Repeta, 2015. “Chemical Characterization and Cycling of Dissolved Organic Matter”

1215–1330

Lunchtime introductions — Church, Steward (Campus Center 203A)

1345–1500

Lecture: Remote sensing of primary productivity 16MB .pptx (White)

1530–1700

Lecture: Stupid questions only (All)

1830–

Group Dinner

Saturday, May 30

Plankton ecology and biogeochemistry

0900–1015

Lecture: Distributions and forms of metal-binding ligands 13MB .pptx (Repeta)

Readings (PDFs):

• Blain, et al., 1999. “Effect of natural iron fertilization on carbon sequestration in the Southern Ocean”
• Boyd, 2007. “Iron findings”
• Coale, et al., 2004. “Southern Ocean Iron Enrichment Experiment: Carbon Cycling in High- and Low-Si Waters”
• Gledhill and Buck, 2012. “The organic complex ation of iron in the marine environment: a review”
• Vraspir and Butler, 2009. “Chemistry of Marine Ligands and Siderophores”

1015–1045

Break

1045–1200

Lecture: Plankton blooms and nitrogen fixation 36MB .pptx (White)

1200–1330

Lunch (provided)

1330–1445

Lecture: Some models of nitrogen fixation: cellular to global scales 17MB .pptx (Follows)

Readings (PDFs):

• Moore, et al., 2009. “Large-scale distribution of Atlantic nitrogen fixation controlled by iron availability”
• Tilman, 1977. “Resource Competition between Plankton Algae: An Experimental and Theoretical Approach”
• Ward, et al., 2013. “Iron, phosphorus, and nitrogen supply ratios define the biogeography ofnitrogen fixation”

1445–1500

Break

1500–1615

Lecture: Ocean acidification and microbes 54MB .pptx (Böttjer)

Readings (PDFs):

• Boyd, 2011. “Beyond ocean acidification”
• Dore, et al., 2009. “Physical and biogeochemical modulation of ocean acidification in the central North Pacific”
• Joint, et al., 2011. “Will ocean acidification affect marine microbes?”
• Pörtner, et al, 2014. “Ocean Systems”

1630–1800

Reception

Sunday, May 31

 Free day to snorkel and explore with Ken

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Week 2: Microbial oceanography through the lens of genomics

• Faculty: Eric Allen, Bethany Jenkins, Alison Murray, Penny Chisholm (virtually), Grieg Steward, Craig Nelson, Ed DeLong
• All Lectures in the Moore Conference Center, C-MORE Hale

Monday, June 01

Introduction to microbial genomics

0900–1015

Lecture: Microbial Genomics 101 37MB .pptx (DeLong)

Readings (PDFs):

• Berger, et al., 2013. “Computational solutions for omics data”
• Blainey, 2013. “The future is now: single-cell genomics of bacteria and archaea”
• Giovannoni, et al., 2005. “Genome Streamlining in a Cosmopolitan Oceanic Bacterium”
• Hehemann, et al., 2010. “Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota”
• Lauro, et al., 2009. “The genomic basis of trophic strategy in marine bacteria”

1015–1045

Coffee break

1045–1200

Lecture: Env Genome assembly: genomics & metagenomics 37MB .pptx (Allen)

1200–1330

Lunchtime introductions — Allen, DeLong (Campus Center 203B)

1345–1500

Lecture: Culture independent approaches to studying marine microorganisms 116MB .pptx (Nelson)

1500–1515

Break

1515–1630

Lecture: Marine viral ecology (Steward)

1630–1730

Cruise planning meeting (Church)

Tuesday, June 02

Microbial ecology and diversity

0900–1015

Lecture: Phytoplankton genomics and transcriptomics 56MB .pptx (Jenkins)

1015–1045

Coffee Break

1045–1200

Lecture: Microbial life in permanently cold environments 40MB .ppt (Murray)

Readings (PDFs):

• Ghiglione, et al., 2012. “Pole-to-pole biogeography of surface and deep marine bacterial communities”
• Grzymski, et al., 2012. “A metagenomic assessment of winter and summer bacterioplankton from Antarctica Peninsula coastal surface waters”
• Margasin & Miteva, 2011. “Diversity and ecology of psychrophilic microorganisms”
• Murray, et al., 2012. “Microbial life at -13 °C in the brine of an ice-sealed Antarctic lake”
• Nunorura, et al., 2015. “Hadal biosphere: Insight into the microbial ecosystem in the deepest ocean on Earth”

1200–1345

Lunchtime introductions — Jenkins, Murray (Campus Center 203B)

1400–1515

Lecture: Modern rRNA tag surveys and statistical analyses (Nelson)

1515–1545

Break

1545–1700

Lab Practical: Flow cytometry of marine plankton 56MB .pptx + 25MB IMG_3078.MOV & 1MB Laminar_flow_regime.mp4 (Doggett)

Wednesday, June 03

Genomics and meta-omics

0900–1015

Lecture: Prochlorococcus: The Power of Diversity — I 55MB PDF (Chisholm)

Readings (PDFs):

• Biller, et al., 2014. “Prochlorococcus: the structure and function of collective diversity”
• Biller, et al., 2014. “Bacterial Vesicles in Marine Ecosystems”
• Chisholm, 2012. “Unveiling Prochlorococcus: The Life and Times of the Ocean’s Smallest Photosynthetic Cell”
• Kashtan, et al., 2014. “Single-Cell Genomics Reveals Hundreds of Coexisting Subpopulations in Wild Prochlorococcus”

1015–1045

Coffee Break

1030–1200

Lecture: Molecular markers for phytoplankton physiology 18MB .pptx (Jenkins)

1200–1345

Lunchtime introduction — Nelson, Steward (Campus Center 203B)

1400–1515

Lecture: Metagenomics in extreme environments — Antarctica 18MB .pptx + 18MB Murray-Lecture3.pptx + 81MB thermohaline_conveyor_30fps.mp4 (Murray)

Readings (PDFs):

• Orcutt, et al., 2011. “Microbial Ecology of the Dark Ocean above, at, and below the Seafloor”
• Siddiqui, et al., 2013. “Psychrophiles”
• Wilkins, et al., 2012. “Key microbial drivers in Antarctic aquatic environments”
• Wilkins, et al., 2013. “Advection shapes Southern Ocean microbial assemblages independent of distance and environment effects”
• Williams, et al., 2012. “A metaproteomic assessment of winter and summer bacterioplankton from Antarctic Peninsula coastal surface waters”

1515–1530

Break

1530–1730

Lecture: Metagenomics in extreme environments — hypersalinity 42MB .pptx (Allen)

1830–

Group Dinner

Thursday, June 04

Comparative Genomics

0900–1015

Lecture: Prochlorococcus: The Power of Diversity — II (Chisholm)

1015–1045

Coffee Break

1045–1200

Lecture: Microbial metatranscriptomics in marine systems I 319MB DeLong_Lec2_transcriptomics_2015.pptx + 307MB JGI_DeLong_Mar2015.pptx + 226MB earth_rotate_sd_pal_photojpeg.mov (DeLong)

Readings (PDFs):

• Aylward, et al., 2015. “Microbial community transcriptional networks are conserved in three domains at ocean basin scales”
• DeLong, 2013. “Microbial Earth: the motion picture”
• Dillies, et al., 2012. “A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis”
• Frias-Lopez, et al., 2008. “Microbial community gene expression in ocean surface waters”
• Gifford, et al., 2010. “Quantitative analysis of a deeply sequenced marine microbial metatranscriptome”
• Ottesen, et al., 2011. “Metatranscriptomic analysis of autonomously collected and preserved marine bacterioplankton”
• Ottesen, et al., 2013. “Pattern and synchrony of gene expression among sympatric marine microbial populations”
• Ottesen, et al., 2014. “Multispecies diel transcriptional oscillations in open ocean heterotrophic bacterial assemblages”
• Paulson, et al., 2013. “Differential abundance analysis for microbial marker-gene surveys”
• Shi, et al., 2009. “Metatranscriptomics reveals unique microbial small RNAs in the ocean’s water column”

1200–1345

Lunchtime introductions (Campus Center 203B)

1400–1530

Lecture: Microbial cycling of dissolved organic matter 129MB .pptx (Nelson)

1530–1545

Break

1545–1700

Lecture: Marine viral genome diversity (Steward)

Friday, June 05

0900–1015

Lecture: Microbial metatranscriptomics in marine systems II 42MB .pptx (DeLong)

Readings (PDFs):

• Béjà, et al., 2000. “Bacterial Rhodopsin: Evidence for a New Type of Phototrophy in the Sea”
• Canfield, et al., 2010. “A Cryptic Sulfur Cycle in Oxygen-Minimum-Zone Waters off the Chilean Coast”
• Chan, et al., 2008. “Emergence of Anoxia in the California Current Large Marine Ecosystem”
• Diaz, et al., 2008. “Spreading Dead Zones and Consequences for Marine Ecosystems”
• Stramma, et al., 2008. “Expanding Oxygen-Minimum Zones in the Tropical Oceans”
• Ganesh, et al., 2013. “Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone””
• Ganesh, et al., 2013 (supplement). “Supplementary Information: Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone”
• Lam, et al., 2009. “Revising the nitrogen cycle in the Peruvian oxygen minimum zone”
• Martinez, et al., 2007. “Proteorhodopsin photosystem gene expression enables photophosphorylation in a heterologous host”
• Martinez, et al., 2010. “Widespread known and novel phosphonate utilization pathways in marine bacteria revealed by functional screening and metagenomic analyses”
• McSorley, et al., 2012. “PhnY and PhnZ Comprise a New Oxidative Pathway for Enzymatic Cleavage of a Carbon-Phosphorus Bond”
• Stewart, et al., 2012. “Microbial metatranscriptomics in a permanent marine oxygen minimum”
• Ulloa, et al., 2012. “Microbial oceanography of anoxic oxygen minimum zones”
• Wright, et al., 2012. “Microbial ecology of expanding oxygen minimum zones”

1015–1045

Coffee Break

1045–1200

Lecture: Statistical analyses in microbial ecology (Nelson)

1200–1345

Lunchtime introductions (Campus Center 203B)

1400–1530

Computer Lab: Metagenomics: Galaxy analysis tools 9MB .pptx (Cardwell)

Readings (PDFs):

• DeLong (ed.), 2013. “Methods in Enzymology: Microbial Metagenomics, Metatranscriptomics, and Metaproteomics”
• Goff, et al., 2011. “The iPlant collaborative: cyberinfrastructure for plant biology”
• Kielbasa, et al., 2011. “Adaptive seeds tame genomic sequence comparison”
• Ladoukakis, et al., 2014. “Integrative workflows for metagenomic analysis”
• Markowitz, et al., 2014. “IMG 4 version of the integrated microbial genomes comparative analysis system”
• Meyer, et al., 2008. “The metagenomics RAST server — a public resource for the automatic phylogenetic and functional analysis of metagenomes”
• Zhao, et al., 2012. “RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data”

1530–1545

Break

1545–1700

Computer Lab: Metagenomics: Galaxy analysis tools (Cardwell)

Readings (PDFs):

• Goecks, et al., 2010. “Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences”

Saturday, June 06

Free Day to Explore O‘ahu

Sunday, June 07

Load R/V Kilo Moana for research cruise
Note: Closed-toed shoes required; also make sure to bring sunscreen and a hat

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Weeks 3 and 4: Research Cruise and Laboratory Analyses

• Faculty/staff: Church, Steward, Nelson, Doggett, Clemente, Soares, Björkman

Monday, June 08

Class Exercise: Microbial biomass contributions to organic carbon (Steward)

Worksheet and Readings (PDFs):

• Worksheet. “Biomass Calculations”
• Bertilisson, et al., 2003. “Elemental composition of marine Prochlorococcus and Synechococcus: Implications for the ecological stoichiometry of the sea”
• Heldal, et al., 2003. “Elemental composition of single cells of various strains of marine Prochlorococcus and Synechococcus using X-ray microanalysis”
• Menden-Deuer, et al., 2000. “Carbon to Volume Relationships for Dinoflagellates, Diatoms, and Other Protist Plankton”
• Riemann, et al., 1989. “The carbon and chlorophyll content of phytoplankton from various nutrient regimes”
• Steward, et al., 2007. “Microbial biomass and viral infections of heterotrophic prokaryotes in the sub-surface layer of the central Arctic Ocean”
• Taylor, et al., 1997. “Seasonal and latitudinal dependencies of phytoplankton carbon-to-chlorophyll a ratios: results of a modelling study”

Tuesday, June 09

Class Exercise: Mental metagenomics: Sources of DNA in seawater (Steward)

Worksheet and Readings (PDFs):

• Worksheet. “Metagenomics Calculations”
• “A Sense of Scale”
• “DNA Molecule Facts”
• Brum, et al., 2004. “A novel method for the measurement of dissolved deoxyribonucleic acid in seawater”
• Giovannoni, et al., 2005. “Genome Streamlining in a Cosmopolitan Oceanic Bacterium”
• Karner, et al., 2001. “Archaeal dominance in the mesopelagic zone of the Pacific Ocean”
• Misumi, et al., 2008. “Genome analysis and its significance in four unicellular algae, Cyanidioshyzon merolae, Ostreococcus tauri, Chlamydomonas reinhardtii, and Thalassiosira pseudonana”
• Steward, et al., 2000. “Genome size distributions indicate variability and similarities among marine viral assemblages from diverse environments”
• Walker, et al., 2010. “Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea”

Wednesday, June 10

Depart Snug Harbor aboard R/V Kilo Moana

Wednesday, June 17

Return to Snug Harbor, offload ship and check into dorms
Lunch on your own on campus
Begin laboratory analyses @ 1400 in CMORE Hale

Thursday, June 18

0800–1130

Biogeochemical laboratory analyses (LLN, LLP, PSi, PPO4, LLSi, PC/PN, flow cyto)

1130–1330

Lunchtime introductions (Campus Center 310)

1330–1730

Biogeochemical laboratory analyses (LLN, LLP, PSi, PPO4, LLSi, PC/PN, flow cyto)

Friday, June 19

0800–1130

Students complete biogeochemical laboratory analyses (LLN, LLP, PSi, PPO4, LLSi, PC/PN, flow cyto)

1130–1300

Lunchtime introductions — Gifford, students (Hemmingway Hall 211)

1300–1430

Lecture: Cultivation of marine microbes (Gifford)

1430–1500

Break

1500–1700

Students begin molecular laboratory analyses (sequencing tutorial)

Saturday, June 20

0800–1130

Molecular laboratory analyses (Amplicon sequencing)

0130–1330

Lunchtime introductions (Campus Center 203B)

1330–1730

Molecular laboratory analyses (Amplicon sequencing)

Sunday, June 21

Free Day to Explore O‘ahu

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Week 5: Laboratory Analyses and Synthesis

Monday, June 22

0800–0930

Lecture: Interpreting the physiological state and activity of microbes using quantitative transcriptomics (Gifford)

0930–1000

Break

1000–1130

Molecular laboratory analyses (Metagenomics)

Readings (PDFs):

• Illumina, 2012. “Nextera® XT DNA Sample Preparation Guide”

1130–1300

Lunchtime introductions (Campus Center 203B)

1330–1730

Molecular laboratory analyses (Metagenomics)

Tuesday, June 23

0800–1130

Molecular laboratory analyses (Metagenomics)

1130–1330

Lunchtime introductions (Campus Center 203B)

1330–1730

Molecular laboratory analyses (Metagenomics)

Wednesday, June 24

0900–1015

Molecular laboratory analyses (Metagenomics)

1015–1030

Break

1030–1200

Molecular laboratory analyses (Metagenomics)

1200–1400

Lunchtime introductions (Campus Center 203B)

1400–1700

Student break out groups on data analyses

Thursday, June 25

0900–1015

Student break out groups on data analyses

1015–1030

Break

1030–1200

Student break out groups on data analyses

1200–1400

Lunchtime introductions (Campus Center 203B)

1400–1700

Students working on presentations

Friday, June 26

0900–1200

Students’ final presentation

1200–1400

Lunch

1400–1600

Student evaluations and lab check out

1800–2100

Farewell Gala at Waikiki Aquarium

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