James Holden


Photo of James Holden





102A Morrill Science Center IVN


Oceanography, University of Washington, 1996

Mailing address: 

James F. Holden, Ph.D.
Department of Microbiology
418 Morrill Science Center IVN
University of Massachusetts
639 North Pleasant Street
Amherst, MA 01003-9298

Research Interests

Primary producers are organisms that convert CO2 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 are thermophiles and hyperthermophiles that grow on volcanically-derived H2, CO2, S compounds and Fe oxide minerals rather than sunlight or O2. The current need is to better understand the growth and physiology of these subsurface (hyper)thermophiles and to further develop biogeochemical models that predict the significance of their activity in subsurface environments based on energy sources (e.g., H2, CO2, Fe, S), other fluid chemistry (pH, redox), and temperature. While very good ecological models exist that are based on molecular sequence data and the energy available for various redox reactions, there is a pressing need to better understand the growth and metabolite production rates and constraints and the life strategies of specific model microorganisms to improve these models.

My research focuses on the physiology and genomics of thermophilic and hyperthermophilic archaea and the geomicrobiology of the geothermal environments where these organisms are found. My lab is developing a reactive transport model for the growth of methanogens and production of CH4 in hydrothermal vents, determining microbe-mineral interactions and biogenic mineral transformations in hydrothermal ‘black smoker’ chimneys, and examining H2 production and syntrophy by heterotrophs. My genome analysis projects examine each of the organisms involved in these processes (Methanocaldococcus, Pyrodictium, Thermococcus). My field research occurs at deep-sea hydrothermal vents at Axial Seamount and the Endeavour Segment in the northeastern Pacific Ocean and uses the deep-sea submarine Alvin and remotely-operated submarines such as Jason II and ROPOS. Our hyperthermophilic H2 production studies are being translated into new ways of remediating agricultural wastes in bioreactors to produce bioenergy, kill pathogens, and prevent eutrophication.

Selected Publications

Research interests - short: 

Physiology and ecology of hyperthermophilic archaea; Geomicrobiology of geothermal environments