Research Interests, Projects, and Approaches

Microorganisms have dominated the history of Earth, playing an intimate role in shaping its chemical and physical properties.  Microbes continue their role as agents of biogeochemistry today as they drive a wide range of processes, including the cycling of carbon, oxygen, nitrogen, sulfur, and metals.  My research interests are focused on this interplay between the biosphere and the geosphere, examining how microbes drive geochemistry and how geochemistry in turn shapes microbial diversity, metabolism, and evolution.  Many biogeochemical cycles are actively driven by genetically encoded molecules that are often carefully regulated to be produced only under certain environmental or physiological conditions.  Thus an understanding of biogeochemical cycles that take place on global scales demands knowledge of dynamics that take place on molecular scales.  As such, my research relies heavily on molecular-biological approaches that are closely coupled with geochemical approaches to achieve an integrated view of geomicrobiology.
 
Current and past research projects include:
•       Genetics, biochemistry, physiology, and genomics of Mn(II)-oxidizing bacteria that catalyze the formation of biogenic Mn oxides.  Work in this area has focused on a marine a-proteobacteria and Bacillus spores.
•     Diversity and function of microbial communities in deep-sea hydrothermal plumes.  This project investigates the microbially-mediated formation of Mn oxides in deep-sea hydrothermal vent plumes in Guaymas Basin (Gulf of California).  It also addresses questions of how deep-sea microbial communities respond to and transform potential energy sources emanating from deep-sea hydrothermal vents, such as methane, ammonium, sulfur, iron, and manganese.
•     Microbial community genomics of acid mine drainage (AMD).  This project, in Jill Banfield’s laboratory (http://seismo.berkeley.edu/~jill/banres.html), investigates how microbes drive the dissolution of pyrite and the formation of acid mine drainage.  Community genomics and proteomics are used to understand molecular mechanisms and evolutionary processes in this extremely acidic, chemolithoautotrophic ecosystem.  My work has focused on sulfur cycling, assembly of metagenomic DNA sequences, and bioinformatic methods to analyze low-abundance community members.

Approaches and technical interests:
•       Genomics (metagenomics) and proteomics of microbial communities in natural environments; functional approaches for identifying genes and enzymes. 
•     Bioinformatics.
•     Biochemistry: protein purification and enzyme function.
•     Microbial physiology: isolation and physiological studies of microbes in pure culture.

Dick, G.J., and B.M. Tebo (submitted). Microbial diversity and biogeochemistry of the Guaymas Basin hydrothermal plume. Environmental Microbiology.

Dick, G.J., B.G. Clement, S.M. Webb, F.J. Fordrie, J.R. Bargar, and B.M. Tebo (2009). Enzymatic microbial Mn oxidation in the Guaymas Basin deep-sea hydrothermal plume. Geochimica et Cosmochimica Acta, 73: 6517-6530.

Dick, G.J., A. Andersson, B.J. Baker, S.S. Simmons, B.C. Thomas, A.P. Yelton, and J.F. Banfield (2009). Community-wide analysis of microbial genome sequence signatures. Genome Biology, 10: R85.

Goltsman, D.S.A., V.J. Denef, S.W. Singer, N.C. VerBerkmoes, M.Lefsrud, R. Muller, G.J. Dick, C. Sun, K. Wheeler, A. Zemla, B.J. Baker, L. Hauser, M. Land, M. Shah, M.P. Thelen, R.L. Hettich, and J.F. Banfield (2009). Genomics and comparative proteogenomics of chemoautotrophic, iron-oxidizing “Leptospirillum rubarum” and Leptospirillum ferrodiazotrophum populations in biofilm communities. Applied and Environmental Microbiology, 75: 4599-4615.

Andersen, C.R.*, G.J. Dick*, M-L. Chu, J-C. Cho, R. Davis, S. Bräuer, and B.M. Tebo (2009). Aurantimonas manganoxydans, sp. nov. and Aurantimonas litoralis, sp. nov. : Manganese oxidizing representatives of a globally distributed clade of a-proteobacteria from the order Rhizobiales. Geomicrobiology Journal, 26: 189-198 (*these authors contributed equally).

Dick,G.J., Podell,S., Johnson,H.A., Rivera-Espinoza,Y., Bencheikh-Latmani,R., McCarthy,J.K., Torpey, J.W., Clement,B.G., Gaasterland,T., Tebo,B.M. Genomic insights into Mn(II) oxidation by the marine alphaproteobacterium Aurantimonas strain SI85-9A1 (2008). Applied and Environmental Microbiology, 74: 2646-2658.

Dick, G.J., J.W. Torpey, T.J. Beveridge, and B.M. Tebo (2008). Direct identification of a bacterial Mn(II) oxidase, the multicopper oxidase MnxG, from spores of several different marine Bacillus species . Applied and Environmental Microbiology, 74: 1527-1534.

Tebo, B.M., B.G. Clement, and G.J. Dick (2007). Biotransformations of manganese, p. 1223-1238. In C. J. Hurst, R. L. Crawford, J. L. Garland, D. A. Lipson, A. L. Mills, and L. D. Stetzenbach (ed.), Manual of environmental microbiology, 3rd ed. ASM Press, Washington, DC.

Dick, G.J., Y.E. Lee, and B.M. Tebo. Manganese(II)-oxidizing Bacillus spores in Guaymas Basin hydrothermal sediments and plumes (2006). Applied and Environmental Microbiology, 72: 3184-3190.

Dick, G.J., (2006), Microbial Manganese(II) oxidation: biogeochemistry of a deep-sea hydrothermal plume, enzymatic mechanism, and genomic perspectives. PhD dissertation, University of California, San Diego.

Mix, L, G.J. Dick, and F.J. Stewart (2006). Redox chemistry and metabolic diversity. In: The Astrobiology Primer, an outline of general knowledge-Version 1, 2006. Astrobiology, 6: 735-813.

Webb, S.M., G.J. Dick, J.R. Bargar, and B.M. Tebo. Evidence for the presence of Mn(III) intermediates in the bacterial oxidation of Mn(II) (2005). Proceedings of the National Academy of Sciences, 102: 5558-5563.

Tebo, B.M., J.R. Bargar, B.G. Clement, G.J. Dick, K.J. Murray, D. Parker, R. Verity, and S.M. Webb. (2004) Biogenic manganese oxides: Properties and mechanisms of formation. Annu. Rev. Earth Planet. Sci. 32, 287-328.