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Microbial Oceanography : Genomes to Biomes A summer training course

Microbial Oceanography : Genomes to Biomes A summer training course. Matt Church and Team. Training a new generation of microbial oceanographers. Studying microbes from ships to satellites…. … observations to models. Course Structure. 16 students/yr (totaling 123 since 2006)

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Microbial Oceanography : Genomes to Biomes A summer training course

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  1. Microbial Oceanography: Genomes to Biomes A summer training course Matt Church and Team

  2. Training a new generation of microbial oceanographers Studying microbes from ships to satellites… … observations to models

  3. Course Structure • 16 students/yr (totaling 123since 2006) • Student to faculty ratio ~1 • Daily lectures on contemporary topics in Microbial Oceanography. Lectures available online. • Public Symposia • 8-10 day research cruise (totaling 62 days since 2006) • Genome / Metagenomic analyses (2 genomes sequenced, 5 metagenomes) • Oceanographic, biogeochemical and molecular biology field and laboratory training

  4. THE NUMBERS (2006-2013): 123 students (40 male, 83 female) 275 days of class with 288 lectures, 96 days in the lab, 19 symposia, 72 days at sea

  5. “Typical” Course Syllabus Week 1: The Ocean as a Microbial Habitat: Variability in ocean biogeochemistry and the role of microorganisms in shaping ocean ecosystems Example guest lecturers: Mick Follows, Mary Jane Perry, Ken Johnson, Angelique White, Ken Nealson, Penny Chisholm, David Kirchman, Craig Carlson, Dan Repeta, Carlos Pedros-Alio Week 2: The Microbial Ocean Viewed Through the Lens of Genes and Genomes Example guest lecturers: Edward DeLong, Mary Ann Moran, Jonathan Zehr, Alex Worden, Nikos Krypides, Eric Allen Week 3-4: Research Cruise and Laboratory Analyses Guest faculty on cruises: Mike Sieracki, John Waterbury Week 5: Microbial Oceanography in the 21st Century Example guest lecturers: John Cullen, Oscar Schofield, Carlos Duarte, FarooqAzam, Mick Follows Week 6: Synthesis and Students’ Final Presentation

  6. Research Cruises • R/V Kilo Moana – the UH flagship • General Themes:Oceanographic field sampling; experimental design; temporal and spatial variability in plankton productivity, biomass, and diversity • Training activities: Sampling, plankton biogeochemistry, rates of microbial activity, microbial biodiversity

  7. Summary of Course Evaluations

  8. CMORE Summer Course Genome Sequencing Efforts (2010-2013) • 2010: SAR116 HIMB100 whole genome. Grote et al., Standards in Genomic Sciences (2011) • 2011: Roseobacter HIMB11 whole genome. Durham et al. Standards in Genomic Sciences (2014) • 2012: Trichodesmiummetagenome(1 MiSeq run) - sequencing completed, data in IMG. • 2013: 16S rRNA amplicon sequencing of 60 samples from 25 discrete depths (surface – 4,800 m). ~5 million reads and infinite fun!

  9. Goals for the CMORE Summer Course Sequencing Efforts • Become familiar with current sequencing technologies, tools and databases for genomic and metagenomic data and analyses • Gain hands on experience manipulating and analyzing microbial genome and metagenomicsequence data, manually curating auto-annotationsusing IMG, CAMERA, and MG-RAST • Use genomic and metagenomic sequence data to understand diversity and distribution of metabolic and nutrient acquisition pathways, major lifestyle characteristics (e.g. motility, phototrophy, carbon fixation, nitrogen fixation, etc.). • Use metagenomic data to understand the distribution of genes in organisms and in the environment, and their relationship to ecological and oceanographic processes.

  10. Course Highlights • Near peer and student-faculty interactions • - Former students continue to work with course faculty • - Students continue to interact (conferences, social networking, papers and talks) • Rapidly attained international appeal and reputation • Training of tomorrow’s (and today’s) leaders in Microbial Oceanography • Publications and presentations • Creation of new DNA sequence information (and genomic context)

  11. Lessons Learned • Promote the immersion experience • Seek balance in demographics (M/F, US/non-US) • Allow ample time for synthesis of data and discussion of results • Ownership of data is key to student engagement • Sequencing microbial genomes provides a nice entry point for students with diverse backgrounds, and provides valuable information for the broader community. • Manage cruise expectations and dynamics – take advantage of opportunity

  12. Course Challenges • Hands on versus classroom lectures • Training versus research (& publications) • Breadth versus depth in topics • Field ops and logistics (also caps max # students) • Varied training/background of students (getting everyone on same page) • Language/Cultural barriers • Sustaining funding

  13. Facing Forward… • Support from NSF (C-MORE) and Agouron Foundation through 2015 • Year 9 course is underway and currently at sea!

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