Idaho National Laboratory Biological Systems

James Henriksen


Dept. of Biological Systems,
Idaho National Laboratory,
Department of Energy

James.Henriksen@inl.gov
(208) 526-8190

Current Projects

SEM of bacteria embedded in calcite precipitantI am currently leading research in microbial community impacts on algal biofuel growth (involving culture-dependent detection and metagenome-directed culturing of environmental organisms) and biosensors for the detection of the environmental releases of nanoparticles.  With Dr. Yoshiko Fujita, I investigate methods for the bioremediation of subsurface groundwater contaminants by microbial precipitation of minerals.  In one project, we are investigating the response of the microbial population to amendments of urea and detecting the in situ prevalence and expression of genes involved in calcite precipitation and strontium immobilization.  My other research has included community metagenomics and modeling of biogeochemical subsurface reactions.

Research Interests

Microorganisms are at the center of most of the biogeochemical cycles of the planet.I am an environmental microbiologist interested in using novel culturing, molecular, and bioinformatic techniques to understand the metabolic capabilities of environmental microorganisms and applying these capabilities to solve problems.  The vast physiological diversity of microorganisms provides us with a powerful toolbox of useful chemical and environmental functions that we are only beginning to learn how to apply.  I use isolated cultures, chemostats, enrichment, and in situ sampling as well as proteomics, genetic manipulation, and other molecular technigues to understand biological problems.
UPGMA trees and heatmap of environments and ribotypesWith the increasing amount of biological and sequence data available, bioinformatic techniques are becoming increasingly important for microbiologists. I use a variety of tools to investigate biological questions, including Linux shell scripts, programming languages (Perl and Python), and specialized programs and code libraries.  I enjoy investigating biological questions on many scales, from small experiments on desktop workstations to huge community metagenomics datasets requiring high performance computing (HPC) distributed clusters.  

Education

Summer 2010:  Microbial Diversity course at The Marine Biological Laboratory, Woods Hole.

2001-2008: Ph.D. graduate, University of Georgia, Department of Microbiology

For my graduate work under the direction of Dr. William B. Whitman, I investigated genes involved in DMSP degradation in Silicibacter pomeroyi , a marine heterotroph, and the physiology of this marine bacteria. DMSP is a ubiquitous marine compound whose degradation is important in carbon and sulfur cycles and influences global climate due to its degradation product DMS. I developed a suite of genetic techniques for this environmental isolate, and knocked out genes identified in a differential display proteomic screen.

1995-2000: Undergraduate Degrees, University of Oklahoma
B.S. in Microbiology, with cum laude honors.
B.S. in Chemistry with a specialization in Biochemistry.

Selected Publications

E. C. Howard, J. R. Henriksen, A. Buchan, C. R. Reisch, H. Burgmann, R. Welsh, W. Ye, J. M. Gonzalez, K. Mace, S. B. Joye, R. P. Kiene, W. B. Whitman, and M. A. Moran. 2006. Bacterial Taxa That Limit Sulfur Flux from the Ocean. Science. 314(5799):649-652.

M. A. Moran, A. Buchan, J. M. Gonzalez, J. F. Heidelberg, W. B. Whitman, R. P. Kiene, J. R. Henriksen, G. M. King, R. Belas, C. Fuqua, L. Brinkac, M. Lewis, S. Johri, B. Weaver, G. Pai, J. A. Eisen, E. Rahe, W. M. Sheldon, W. Ye, T. R. Miller, J. Carlton, D. A. Rasko, I. T. Paulsen, Q. Ren, S. C. Daugherty, R. T. Deboy, R. J. Dodson, A. S. Durkin, R. Madupu, W. C. Nelson, S. A. Sullivan, M. J. Rosovitz, D. H. Haft, J. Selengut, N. Ward. 2004. Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment. Nature. 432(7019):910-3.

J. M. Gonzalez, J. S. Covert, W. B. Whitman, J. R. Henriksen, F. Mayer, B. Scharf, R. Schmitt, A. Buchan, J. A. Fuhrman, R. P. Kiene, M. A. Moran. 2003. Silicibacter pomeroyi sp. nov. and Roseovarius nuhibens sp. nov., dimethylsulfoniopropionate-demethylating bacteria from marine environments. International Journal of Systematic and Evolutionary Microbiology. 53(5):1261-1269.

J. M. Senko, B. S. Campbell, J. R. Henriksen, M. S. Elshahed, T. A. Dewers, L. R. Krumholz. 2004. Barite deposition resulting from phototrophic sulfide oxidizing bacterial activity. Geochimica et Cosmochimica Acta. 68(4):773-780.

Additional Material

Professional Memberships: 2001-Present American Society for Microbiology

Department of energy

DOE Office of Nuclear Energy
DOE-Idaho Office
Battelle