OCN750: Microbial Biogeography

Z. Johnson (ph: 956-0844 / email: zij@hawaii.edu )

Monday 9:00-10:00am, MSB 306

Course Syllabus

Course Description

The goal of this course is to read and discuss current and seminar papers in microbial biogeography. This course is open to graduate students in biological, chemical and physical oceanography as well as those in microbiology. Students are encouraged to suggest papers for discussion or to solicit ideas from their major professors, but there is a list below to help get us started.

Grading, which will be credit/no-credit for 1 unit, will be based on attendance and participation.

Readings:

August 21

• Organization

August 27 (ZJ)

• Longhurst A. Ecological geography of the sea. 1-24. Academic Press. 1998
• Hughes-Martiny et al. Microbial biogeography: putting microorganisms on the map. Nature Reviews Microbiology 4, 102-112. 2006
• Ramette A. and Tiedje J. Biogeography: An Emerging Cornerstone for Understanding Prokaryotic Diversity, Ecology, and Evolution. Microbial Ecology 53, 197-207.

September 3: No Class (Labor Day)

September 10: Some observations (AA)

• Bell, T. and others 2005. Larger islands house more bacterial taxa. Science 308: 1884-1884.

• Bowman, J.P., S.A. McCammon, J.A.E. Gibson, L. Robertson, and P.D. Nichols. 2003. Prokaryotic Metabolic Activity and Community Structure in Antarctic Continental Shelf Sediments. Applied and Environmental Microbiology 69: 2448-2462.
• Cho, J.C. and J.M. Tiedje. 2000. Biogeography and degree of endemicity of fluorescent Pseudomonas strains in soil. Applied and Environmental Microbiology 66: 5448-5456.
• Staley, J.T. and J.J. Gosink. 1999. Poles apart: Biodiversity and biogeography of sea ice bacteria. Annual Review of Microbiology 53: 189-215.

September 17: No Class

September 24: No Class

October 1: Fine scale patterns (IH)

• Long, R.A. and F. Azam. 2001. Microscale patchiness of bacterioplankton assemblage richness in seawater. Aquatic Microbial Ecology 26: 103-113.
• Seymour, J.R., L. Seuront, and J.G. Mitchell. 2005. Microscale and small-scale temporal dynamics of a coastal planktonic microbial community. Marine Ecology-Progress Series 300: 21-37.
• Blackburn, N., T. Fenchel, and J. Mitchell. 1998. Microscale nutrient patches in planktonic habitats shown by chemotactic bacteria. Science 282: 2254-2256.

October 8: Basin Scale Patterns (YL)

• Baldwin, A. J., J. A. Moss, J. D. Pakulski, P. Catala, F. Joux, and W. H. Jeffrey. 2005. Microbial diversity in a Pacific Ocean transect from the Arctic to Antarctic circles. Aquat. Microb. Ecol. 41: 91-102.
• Johnson, Z.I., E.R. Zinser, A. Coe, N.P. McNulty, M. Woodward, and S.W. Chisholm. 2006. Niche partitioning among Prochlorococcus ecotypes along ocean-scale environmental gradients. Science 311: 1737-1740.
• Zwirglmaier, K., J.L. Heywood, K. Chamberlain, E.M.S. Woodward, M.V. Zubkov, and D.J. Scanlan. 2007. Basin-scale distribution patterns of picocyanobacterial lineages in the Atlantic Ocean. Environmental Microbiology 9: 1278-1290.
• Bonus Article: de Wit, R. & Bouvier, T. 2006. 'Everything is everywhere, but, the environment selects'; what did Baas Becking and Beijerinck really say? Environmental Microbiology 8:755-58.

October 17 (Wednesday): Virus Biogeography (JB)

• Breitbart, M. and F. Rohwer. 2005. Here a virus, there a virus, everywhere the same virus? Trends in Microbiology 13: 278-284.
• Silander, O.K., D.M. Weinreich, K.M. Wright, K.J. O'Keefe, C.U. Rang, P.E. Turner, and L. Chao. 2005. Widespread genetic exchange among terrestrial bacteriophages. PNAS 102: 19009-19014.
• Short, C. M. & Suttle, C. A. 2005. Nearly identical bacteriophage structural gene sequences are widely distributed in both marine and freshwater environments. Applied and Environmental Microbiology 71:480-86.

October 22: Metagenomic Patterns (FL)

• DeLong, E.F., C.M. Preston, T. Mincer, V. Rich, S.J. Hallam, N.-U. Frigaard, A. Martinez, M.B. Sullivan, R. Edwards, B.R. Brito et al. 2006. Community Genomics Among Stratified Microbial Assemblages in the Ocean's Interior. Science 311: 496-503.

• Rusch, D.B., A.L. Halpern, G. Sutton, K.B. Heidelberg, S. Williamson, S. Yooseph, D. Wu, J.A. Eisen, J.M. Hoffman, K. Remington et al. 2007. The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific, PLoS. e77.

October 29: Phylogeography (AA)

• Doolittle, W. F., and R. T. Papke. 2006. Genomics and the bacterial species problem. Genome Biology. 7: 116.
• Sogin, M.L., H.G. Morrison, J.A. Huber, D.M. Welch, S.M. Huse, P.R. Neal, J.M. Arrieta, and G.J. Herndl. 2006. Microbial diversity in the deep sea and the underexplored "rare biosphere". PNAS 103: 12115-12120.

• Thompson, J.R., S. Pacocha, C. Pharino, V. Klepac-Ceraj, D.E. Hunt, J. Benoit, R. Sarma-Rupavtarm, D.L. Distel, and M.F. Polz. 2004. Genotypic diversity within a natural coastal bacterioplankton population. Science 307: 1311-1313.

• Cohan, F.M. (2006) Towards a conceptual and operational union of bacterial systematics, ecology, and evolution. Philosophical Transactions of the Royal Society B: Biological Sciences 361: 1985-1996.

November 5: Mechamisms (IH)

• Green, J.L., A.J. Holmes, M. Westoby, I. Oliver, D. Briscoe, M. Dangerfield, M. Gillings, and A.J. Beattie. 2004. Spatial scaling of microbial eukaryote diversity. Nature 432: 747-750.
• Horner-Devine, M.C., M. Lage, J.B. Hughes, and B.J.M. Bohannan. 2004. A taxa-area relationship for bacteria. Nature 432: 750-753.
• Li, W.K.W. (2002) Macroecological patterns of phytoplankton in the northwestern North Atlantic Ocean. Nature 419: 154-157.
• Martin, E.S., Harris, R.P., and Irigoien, X. (2006) Latitudinal variation in plankton size spectra in the Atlantic Ocean. Deep-Sea Research Part II 53: 1560-1572.

November 12: No Class (Veteran's Day)

November 19: Ecological Theory (YL)

• Hubbell, S.P. 2001. The unified neutral theory of biodiversity and biogeography . Princeton University Press, Princeton. (Chapter 6)

• Whitaker, R.J., D.W. Grogan, and J.W. Taylor. 2003. Geographic barriers isolate endemic populations of hyperthermophilic archaea. Science 301: 976-978.
• Finlay, B.J. 2002. Global dispersal of free-living microbial eukaryote species. Science 296: 1061-1063.

November 26: Random (JB)

• Woodcock, S., van der Gast, C.J., Bell, T., Lunn, M., Curtis, T.P., Head, I.M., and Sloan, W.T. (2007) Neutral assembly of bacterial communities. Fems Microbiology Ecology 62: 171-180.
• Huber, J.A., Welch, D.B.M., Morrison, H.G., Huse, S.M., Neal, P.R., Butterfield, D.A., and Sogin, M.L. (2007) Microbial population structures in the deep marine biosphere. Science 318: 97-100.

December 3: Modeling (FL)

• Follows, M.J., S. Dutkiewicz, S. Grant, and S.W. Chisholm. 2007. Emergent Biogeography of Microbial Communities in a Model Ocean. Science 315: 1843-1846.

• Hood, R., E. Laws, M.J. Follows, and D.A. Siegel. 2007. Modeling and prediction of marine microbial populations in the genomic era. Oceanography 20: 155-165.
• Sloan, W.T., Woodcock, S., Lunn, M., Head, I.M., and Curtis, T.P. (2007) Modeling taxa-abundance distributions in microbial communities using environmental sequence data. Microbial Ecology 53: 443-455.