Holden Lab: Research Projects

Geomicrobiology of deep-sea hydrothermal vents
This project examines the spatial distribution, metabolic processes, and growth constraints of hyperthermophilic archaea in deep-sea hydrothermal vent environments. We are also working with others to determine the overall diversity, distribution, and impact of microorganisms on hydrothermal fluids and black smoker chimneys and their relationship with the mineralogy and fluid chemistry of this environment. Our primary study sites have been along the Juan de Fuca Ridge, namely the Endeavour Segment, and Axial Volcano, in the northeastern Pacific Ocean where the Holden lab has been collecting samples since 2004.

Ver Eecke, H.C., D.S. Kelley, and J.F. Holden (2009) Abundances of hyperthermophilic autotrophic Fe(III) oxide reducers and heterotrophs in deep-sea hydrothermal sulfide chimneys of the northeastern Pacific Ocean. Appl. Environ. Microbiol. 75:242-245. [PDF] [supplement]

Physiology of dissimilatory iron reduction in hyperthermophilic archaea
This project examines terminal electron acceptor processes in hyperthermophilic archaea, namely Pyrobaculum aerophilum, Pyrobaculum islandicum, and Hyperthermus butylicus, with emphasis on understanding their physiological mechanisms of dissimilatory iron reduction. P. aerophilum and P. islandicum lack polyheme c-type cytochromes, which set them apart from the mesophilic bacteria Geobacter and Shewanella as model organisms for the study of dissimilatory iron reduction.

Feinberg, L.F., R. Srikanth, R.W. Vachet, and J.F. Holden (2008) Constraints on anaerobic growth in the hyperthermophilic archaea Pyrobaculum islandicum and Pyrobaculum aerophilum. Appl. Environ. Microbiol. 74:396-402. [PDF] [supplement]
Feinberg, L.F., and J.F. Holden (2006) Characterization of dissimilatory Fe(III) versus NO3- reduction in the hyperthermophilic archaeon Pyrobaculum aerophilum. J. Bacteriol. 188:525-531. [PDF] [authors’ correction]

Sugar-to-hydrogen conversion by hyperthermophilic heterotrophs
This project examines the ability of hyperthermophilic heterotrophs, such as Pyrococcus and Thermococcus species, to catabolize alpha-1,4 and beta-1,4 links polysaccharides with concomitant hydrogen production. We are interested in the ways that various suites of sugar hydrolases may be used to degrade polysaccharides and identifying which hydrolases are used.

Carbon dioxide and acetate assimilation in hyperthermophilic archaea
This project examines the role of various pathways, such as the citric acid cycle and the citramalate cycle, for carbon dioxide and acetate assimilation by hyperthermophilic archaea. Our studies have focused on Pyrobaculum islandicum, which can grow autotrophically, heterotrophically, and mixotrophically on acetate.

Yennaco, L.J., Y. Hu, and J.F. Holden (2007) Characterization of malate dehydrogenase from the hyperthermophilic archaeon Pyrobaculum islandicum. Extremophiles 11:741-746. [PDF]
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. [PDF]