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Alison Buchan PhD: Marine Sciences, University of Georgia, 2001 620 Science & Engineering Bldg |
Keywords:
Marine Bacteria, Genomics, Community Structure and Interactions
Research Area:
Molecular microbial ecology
Description of Research:
Our research is driven by a desire to understand the roles of microbes in natural environments. Major objectives include linking microbial taxa to critical ecosystem processes, exploring functional gene diversity and its relation to community structure and biogeochemical processes, and identifying novel enzymes and/or catabolic pathways.
A current project focuses on the microbial remineralization of the aromatic biopolymer lignin and its related compounds. The catabolism of these compounds is critical to the global carbon cycle, yet little is known of the natural communities and the processes involved. The coastal salt marshes of the southeastern U.S. are heavily influenced by lignin-related compounds of local and allochthonous origins, and are ideal sites for investigations of catabolic pathways that are harbored within decomposer communities. Members of one lineage of marine bacteria, the Roseobacter clade, are particularly well-suited for such studies as they are abundant in these coastal salt marshes, are easily cultured, and are hypothesized to be responsible for a significant fraction of aromatic compound degradation in these systems. At present we are focusing on Roseobacter isolate Silicibacter pomeroyi, a bacterium cultured from a Georgia salt marsh, using genome data, physiological growth studies, and gene expression levels to better understand the catabolic processes and regulatory networks mediating the transformation of the constituents of lignin by members of this group. Molecular tools are also being developed to assess the diversity and activity of these catabolic processes in salt marsh systems.
Another objective of the lab is to elucidate the significance of genetic variation within functional genes. For these studies, we focus on a key ring-cleaving enzyme in the catabolism of naturally occurring aromatic compounds, protocatechuate 3,4 dioxygenase (PcaHG). In earlier studies, a high degree of sequence diversity for this enzyme was found in natural communities prompting the question of whether this variation plays a role in niche partitioning in the environment. We are presently addressing this issue by conducting structure-function studies with genetic variants of this enzyme. This work is facilitated by the use of a soil bacterium, Acinetobacter baylyi, which is highly competent for natural transformation. We have engineered a system for the heterologous expression of native and variant PcaHGs from several of our marine Roseobacters in A. baylyi, allowing us to identify residues that are critical to enzyme activity and substrate specificity.
Selected Publications (of 13):
- Buchan, A. and L. N. Ornston. (2005). When coupled to natural transformation, PCR-mutagenesis is made less random by mismatch repair.. Applied and Environmental Microbiology.. 71(2): 7610-7612.
- Buchan, A., J. M. Gonzáléz, and M. A. Moran. (2005). An Overview of the Marine Roseobacter Lineage. Applied and Environmental Microbiology. 71(10): 5665-5677.
- Poretsky, R. S., N. Bano, A. Buchan, G. LeCleir, J. Kleikemper, M. Pickering, M.A. Moran, and J. T. Hollibaugh. (2005). Analysis of microbial gene transcripts in environmental samples.. Applied and Environmental Microbiology.. 71(7): 4121-4126.
- Mary Ann Moran, Alison Buchan, José M. González, John F. Heidelberg, William B. Whitman, Ronald P. Kiene, James R. Henriksen, Gary M. King, Robert Belas, Clay Fuqua, Lauren Brinkac, Matt Lewis, Shivani Johri, Bruce Weaver, Grace Pai, Jonathan A. Eisen, Elisha Rahe, Wade M. Sheldon, Wenying Ye, Todd R. Miller, Jane Carlton, David A. Rasko, Ian T. Paulsen, Qinghu Ren, Sean C. Daugherty, Robert T. Deboy, Robert J. Dodson, A. Scott Durkin, Ramana Madupu, William C. Nelson, Steven A. Sullivan, M. J. Rosovitz, Daniel H. Haft, Jeremy Selengut and Naomi Ward (2004). Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment. Nature. 432: 910-913.
- LeCleir, G. R., A. Buchan, and J. T. Hollibaugh. (2004). Chitinase gene sequences retreived from diverse aquatic habitats reveal environment-specific distributions.. Applied and Environmental Microbiology. 70(12): .
- Buchan, A., E. L. Neidle, and M. A. Moran. (2004). Diverse organization of genes of the beta-ketoadipate pathway in members of the marine Roseobacter lineage.. Applied and Environmental Microbiology. 70(3): 1658-1668.
- Buchan, A., S. Y. Newell, M. Butler, E. J. Biers, J. T. Hollibaugh and M. A. Moran. (2003). Dynamics of bacterial and fungal communities on decaying salt marsh grass. Applied and Environmental Microbiology.. Applied and Environmental Microbiology. 69(11): .