|James F. Holden
Ph.D.: Oceanography, University of Washington, 1996
Physiology and ecology of hyperthermophilic archaea; Geomicrobiology of geothermal environments
Primary producers are organisms that convert CO 2 into the organic matter that forms the base of the foodweb. While most primary production occurs by photosynthesis, there is increasing evidence that a significant portion of global primary production occurs by chemosynthesis in the absence of light within geothermal regions of the earth's crust. Geothermal fluids are predicted to circulate through vast portions of the earth's crust and it was estimated that 20% of the earth's total biomass may be found within this environment in the form of microorganisms. Some of these organisms, called hyperthermophiles, grow optimally at temperatures between 80 and 105°C without sunlight or O 2 and can grow on volcanically-derived H 2 and CO 2 as well as on iron and sulfur compounds from the surrounding minerals. The current need is to better understand the growth and physiology of these subsurface hyperthermophiles and to further develop biogeochemical models that predict the significance of their activity in subsurface environments based on predicted levels of energy sources (especially H 2 , CO 2 , Fe, and S) and fluid chemistry (pH, redox).
My research focuses on the physiology and genomics of hyperthermophilic archaea that grow near 100°C and the geomicrobiology of the geothermal environments where these organisms are found. The physiology studies within my laboratory can be separated into two sets of projects: characterization of dissimilatory Fe(III) reduction and characterization of CO 2 fixation. My genome analysis projects involve the genome sequencing of one hyperthermophile and the bioinformatic analysis of it and another hyperthermophile genome. My geomicrobiology projects include the study of hyperthermophiles from deep-sea hydrothermal vents collected from the northeastern Pacific Ocean using the deep-sea submarine Alvin. These projects will have a broader societal impact by providing tools to better understand the nature of the geothermally-heated regions of the subsurface, which represents a vast and largely unknown ecosystem and natural resource. Likewise, many of our physiology findings are likely to be new to biology and will significantly enhance our understanding of Archaea.
Yennaco, L.Y., Y. Hu, and J.F. Holden (2007) Characterization of malate dehydrogenase from the hyperthermophilic archaeon Pyrobaculum islandicum. Extremophiles, available prior to publication (DOI10.1007/s00792-007-0081-2).
Hu, Y. and J.F. Holden (2006) Citric acid cycle in the hyperthermophilic archaeon Pyrobaculum islandicum grown autotrophically, heterotrophically, and mixotrophically with acetate. J. Bacteriol. 188:4350-4355.
Feinberg, L.F., and J.F. Holden (2006) Characterization of dissimilatory Fe(III) versus NO 3 - reduction in the hyperthermophilic archaeon Pyrobaculum aerophilum . J. Bacteriol. 188:525-531.
Holden, J.F., and L.F. Feinberg (2005) Microbial iron respiration near 100°C, pp. 57-66. In R.B. Hoover, G.V. Levin, A.Y. Rozanov and G.R. Gladstone (ed.), Astrobiology and Planetary Missions, Proceedings from SPIE vol. 5906, The International Society for Optical Engineering, Bellingham, Washington.
Holden, J.F., and R.M. Daniel (2004) Upper temperature limit of life based on hyperthermophile culture experiments and field observations, pp. 13-24. In W.S.D. Wilcock, E.F. DeLong, D.S. Kelley, J.A. Baross and S.C. Cary (ed.), The Subsurface Biosphere at Mid-Ocean Ridges, Geophysical Monograph vol. 144, American Geophysical Union, Washington , D.C.
Daniel, R.M., R. van Eckert, J.F. Holden, J. Truter and D.A. Cowan (2004) The stability of biomolecules and the implications for life at high temperatures, pp. 25-39. In W.S.D. Wilcock, E.F. DeLong, D.S. Kelley, J.A. Baross and S.C. Cary (ed.), The Subsurface Biosphere at Mid-Ocean Ridges, Geophysical Monograph vol. 144, American Geophysical Union, Washington, D.C.
Holland , M.E. , J.A. Baross and J.F. Holden (2004) Illuminating subseafloor ecosystems using microbial tracers, pp. 291-303. In W.S.D. Wilcock, E.F. DeLong, D.S. Kelley, J.A. Baross and S.C. Cary (ed.), The Subsurface Biosphere at Mid-Ocean Ridges, Geophysical Monograph vol. 144, American Geophysical Union, Washington, D.C.
Holden, J.F., and M.W.W. Adams (2003) Microbe-metal interactions in marine hydrothermal environments. Curr. Opin. Chem. Biol. 7:160-165.
Lim, H., J. Eng, J.R. Yates III, S.L. Tollaksen, C.S. Giometti, J.F. Holden, M.W.W. Adams, C.I. Reich, G.J. Olsen, and L.G. Hays (2003) Identification of 2D-gel proteins: a comparison of MALDI/TOF peptide mass mapping to µ LC-ESI tandem mass spectrometry. J. Am. Soc Mass Spectrom. 14: 957-970.
Holden, J.F., and M.W.W. Adams (2002) Unique aspects of the hyperthermophile proteome. In C. Gerday and N. Glansdorff (ed.), Extremophiles, Encyclopedia of Life Support Systems (EOLSS), developed under the auspices of the UNESCO, Eolss Publishers, Oxford, UK.
Holden, J.F., F.L. Poole, II, S.L. Tollaksen, C.S. Giometti, H. Lim, J.R. Yates, III, and M.W.W. Adams (2001) Identification and prediction of membrane proteins in the hyperthermophilic archaeon Pyrococcus furiosus using proteomics and prediction programs. Comp. Funct. Genom. 2:275-288.
Holden, J.F., K. Takai, M. Summit, S. Bolton, J. Zyskowski, and J.A. Baross (2001) Diversity among three novel groups of hyperthermophilic deep-sea Thermococcus species from three sites in the northeastern Pacific Ocean. FEMS Microbiol. Ecol. 36:51-60.
Adams, M.W.W., J.F. Holden, A. Lal Menon, G.J. Schut, A.M. Grunden, C. Hou, A.M. Hutchins, F.E. Jenney, Jr., C. Kim, K. Ma, G. Pan, R. Roy, R. Sapra, S.V. Story, and M.F.J.M. Verhagen (2001) A key role for sulfur in peptide metabolism and in the regulation of three hydrogenases in the hyperthermophilic archaeon Pyrococcus furiosus. J. Bacteriol. 183:716-724.
Hutchins, A. M., J. F. Holden, and M. W. W. Adams (2001) Phosphoenolpyruvate synthetase from the hyperthermophilic archaeon Pyrococcus furiosus. J. Bacteriol. 183:709-715.