BIOS Summer Courses: Immerse Yourself in Marine Science
Microbial Oceanography: The Biogeochemistry, Ecology and Genomics of Oceanic Microbial Ecosystems
June 22 - July 12, 2008
Open to All Students
Instructors: Dr. Craig Carlson, University of California, Santa Barbara / Dr. Stephen Giovannoni, Oregon State University / Dr. John Heidelberg, The Institute for Genomics Research (TIGR) / Dr. Robert M. Morris, University of Washington
The course is offered with two major components, Microbial Molecular Ecology and Microbial Genomics. The instructors and lectures overlap.
Marine Microbial Molecular Ecology
Interactions among microbes and with their environment greatly affect the cycling of elements and energy in the marine system. The course will cover traditional microbiological topics such as physiology, microbial diversity and growth within the context of biogeochemical processes. The lectures will focus on how biological processes and the ecological structure within the water column control the cycling of important elements in the ocean such as carbon, nitrogen and phosphorus. A series of field trips and laboratory experiments will be conducted to investigate microbial processes in the open ocean and in the coral reef dominated waters of Bermuda. We will introduce modern methodology used in microbial ecological studies. We well also focus on modern molecular techniques and how they are used to break apart the "black" boxes often associated with biogeochemical processes.
The types of lectures/laboratories associated with course include:
1) What are marine bacterioplankton?
- The size of the smallest bacteria
- The number of prokaryotic cells in the ocean: marine microbial abundance and biomass
2) The role of bacteria in marine food webs and the global carbon cycle
- The "Microbial Loop"
- Bacterial production and DOM production mechanisms
- The "Biological Pump"
3) The Origin of Life in the Oceans
- The Earliest Cells
- The Origins of Cyanobacteria
- Proterozoic Seas
- Heterotrophs: Cells that Use Organic Carbon
- The Modern Ocean
4) The Physiology of Life in an Extremely Dilute Environment
- Cells, sinking and motility
- The Importance of Surface to Volume Ratios
- Oligotrophs and Copiotrophs
- Microbial energetics and growth yields
- Modeling Bacterioplankton Activities in the Laboratory
- Photochemistry and microbes
5) Ribosomes: Deciphering the Evolution of Life on Earth
- How Proteins are Made
- Ribosomal RNA: Using Gene Sequences to Understand Evolution
- The Tree of Life
6) Molecular Sleuths: Solving the Riddle of Marine Bacterioplankton
- The "Great Plate Count Anomaly"
- Systematics and the Classical Culturable Bacterioplankton
- Molecular Biology and DNA from Natural Environments
- Bacterial Diversity as Revealed by Gene Sequences
7) The Major Bacterioplankton Groups
- Oxygenic Phototrophs - The Prochlorophytes and Cyanobacteria
- Gene Clusters and Bacterioplankton Population Genetics
- The Marine Archaea
- The Ubiquitous SAR11 and other Alpha Proteobacteria
- The Culturable and Non-Culturable Gamma Proteobacteria
- SAR202 and the Mesopelagic GNS Species
- Coastal vs. Open Ocean Bacterioplankton Species
- Particle-Associated Bacterioplankton
- Controversies and Biogeography
8) Molecular Ecology
- The Polymerase Chain Reaction
- Gene Cloning and Sequencing
- Hybridization Probes
- Fluorescence In Situ Hybridization
- Cloning large DNA fragments from plankton
9) Predation
- Bacteriovory and mixotrophy
- Bacterial viruses
10) Bacterioplankton Population Dynamics
- The Stratification of Bacterioplankton Populations
- Seasonal Patterns of Change
- Ecological Theory and Bacterioplankton Diversity
- Links between Community Structure and Biogeochemical Cycles
- Bacteria-particle interactions
11) Nitrification in the Nitrogen Cycle
12) Research Horizons
- Linking Species to Processes
- Environmental Genomics
- Useful Products from Bacterioplankton Diversity
Marine Microbial Genomics
High throughput sequencing data is at the foundation of several new culture-independent methods for studying environmental microorganisms. As sequencing cost continue to decrease and total capacities increase, there will continue to be an increase in the number of researchers using sequence data in their studies. Therefore, there is a need to understand the capabilities and limitations of this technology such that one can better develop how to use this technology to address specific hypotheses.
Currently, genomic tools being utilized by microbial ecologists include whole genome sequence analysis, comparative genomics of different strains, survey sequencing, and "meta-" or community genomics of entire ecosystems. A brief introduction to the types of data that can be obtained from such methods and the computational tools useful in the analysis of sequence data will be given.
COURSE FEE: $4,250 (tuition, room and board)
SCHOLARSHIPS and FINANCIAL AID: Scholarships and financial aid are based on academic background/performance and demonstrated need. Full scholarships are rare and only available in exceptional circumstances. We encourage students to apply for other sources of funding that BIOS can supplement or match. Travel and SCUBA equipment are NOT included under any circumstance. Some scholarships and financial aid are open to all nationalities. We particularly encourage students from Canada, the UK and developing countries to apply, as there are specific funding sources for these students.
