James Holden

Professor & Department Head

Photo of James Holden

Phone:

413-577-1742

Fax:

413-545-1578

Email:

[email protected]

Office:

106B Morrill Science Center IVN

Ph.D.:

Oceanography, University of Washington, 1996

Lab Group Home Page

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

My laboratory conducts laboratory and field research to model microbial activity in hot environments. We study the physiology of (hyper)thermophiles and employ modern biological tools to link genotypes, phenotypes, and functional responses to integrate cellular behavior within and among organisms. We employ experimental and mathematical methods to investigate the underlying principles of metabolic pathways that then lead to emerging behaviors. Ultimately, we study how individual species and microbial communities respond and adapt to environmental shifts to predict biological diversity and ecosystem dynamics.

Rates and constraints:
We model how nutrients and energy sources define the limits of growth for various thermophiles and the impact of subseafloor life on marine biogeochemistry.

Interspecies interactions:
We model how interspecies cooperation and competition affects cell growth down to the gene expression level.

Microbe-mineral interactions:
We examine microbial respiration of iron oxides and use spectroscopic techniques to identify biosignatures in nature and correlate those with host rock and fluid chemistry compositions.

Waste-to-hydrogen conversion:
We are exploring the feasibility of using hyperthermophilic heterotrophs to treat agricultural waste and produce hydrogen as a bioenergy product.

Publications

Selected Publications

Hensley SA, Moreira E, Holden JF. 2016. Hydrogen Production and Enzyme Activities in the Hyperthermophile Thermococcus paralvinellae Grown on Maltose, Tryptone, and Agricultural Waste.. Front Microbiol. 7:167.

Stewart LC, Llewellyn JG, Butterfield DA, Lilley MD, Holden JF. 2016. Hydrogen and thiosulfate limits for growth of a thermophilic, autotrophic Desulfurobacterium species from a deep-sea hydrothermal vent.. Environ Microbiol Rep. 8(2):196-200.

Kim Y-T, Jung J-H, Stewart LC, Kwon S-W, Holden JF, Park C-S. 2015. Complete genome sequence of the hyperthermophilic methanogen Methanocaldococcus bathoardescens JH146(T) isolated from the basalt subseafloor.. Mar Genomics. 24 Pt 3:229-30.

Wang DT, Gruen DS, Lollar BSherwood, Hinrichs K-U, Stewart LC, Holden JF, Hristov AN, Pohlman JW, Morrill PL, Könneke M et al.. 2015. Methane cycling. Nonequilibrium clumped isotope signals in microbial methane.. Science. 348(6233):428-31.

Stewart LC, Jung J-H, Kim Y-T, Kwon S-W, Park C-S, Holden JF. 2015. Methanocaldococcus bathoardescens sp. nov., a hyperthermophilic methanogen isolated from a volcanically active deep-sea hydrothermal vent.. Int J Syst Evol Microbiol. 65(Pt 4):1280-3.

T Lin J, Breves EA, Dyar MD, Eecke HCVer, Jamieson JW, Holden JF. 2014. Magnetite formation from ferrihydrite by hyperthermophilic archaea from Endeavour Segment, Juan de Fuca Ridge hydrothermal vent chimneys.. Geobiology. 12(3):200-11.

Jung J-H, Seo D-H, Holden JF, Park C-S. 2014. Maltose-forming α-amylase from the hyperthermophilic archaeon Pyrococcus sp. ST04.. Appl Microbiol Biotechnol. 98(5):2121-31.

Hensley SA, Jung J-H, Park C-S, Holden JF. 2014. Thermococcus paralvinellae sp. nov. and Thermococcus cleftensis sp. nov. of hyperthermophilic heterotrophs from deep-sea hydrothermal vents.. Int J Syst Evol Microbiol. 64(Pt 11):3655-9.

Park K-H, Jung J-H, Park S-G, Lee M-E, Holden JF, Park C-S, Woo E-J. 2014. Structural features underlying the selective cleavage of a novel exo-type maltose-forming amylase from Pyrococcus sp. ST04.. Acta Crystallogr D Biol Crystallogr. 70(Pt 6):1659-68.

Jeon E-J, Jung J-H, Seo D-H, Jung D-H, Holden JF, Park C-S. 2014. Bioinformatic and biochemical analysis of a novel maltose-forming α-amylase of the GH57 family in the hyperthermophilic archaeon Thermococcus sp. CL1.. Enzyme Microb Technol. 60:9-15.

Jung J-H, Kim Y-T, Jeon E-J, Seo D-H, Hensley SA, Holden JF, Lee J-H, Park C-S. 2014. Complete genome sequence of hyperthermophilic archaeon Thermococcus sp. ES1.. J Biotechnol. 174C:14-15.

Jung J-H, Seo D-H, Holden JF, Park C-S. 2014. Identification and Characterization of an Archaeal Kojibiose Catabolic Pathway in the Hyperthermophilic Pyrococcus sp. Strain ST04.. J Bacteriol. 196(5):1122-31.

Lee J-E, Kim I-H, Jung J-H, Seo D-H, Kang S-G, Holden JF, Cha J, Park C-S. 2013. Molecular cloning and enzymatic characterization of cyclomaltodextrinase from hyperthermophilic archaeon Thermococcus sp. CL1.. J Microbiol Biotechnol. 23(8):1060-9.

Ver Eecke HC, Akerman NH, Huber JA, Butterfield DA, Holden JF. 2013. Growth kinetics and energetics of a deep-sea hyperthermophilic methanogen under varying environmental conditions.. Environ Microbiol Rep. 5(5):665-71.

Jung J-H, Holden JF, Seo D-H, Park K-H, Shin H, Ryu S, Lee J-H, Park C-S. 2012. Complete genome sequence of the hyperthermophilic archaeon Thermococcus sp. strain CL1, isolated from a Paralvinella sp. polychaete worm collected from a hydrothermal vent.. J Bacteriol. 194(17):4769-70.

Ver Eecke HC, Butterfield DA, Huber JA, Lilley MD, Olson EJ, Roe KK, Evans LJ, Merkel AY, Cantin HV, Holden JF. 2012. Hydrogen-limited growth of hyperthermophilic methanogens at deep-sea hydrothermal vents.. Proc Natl Acad Sci U S A. 109(34):13674-9.

Jung J-H, Lee J-H, Holden JF, Seo D-H, Shin H, Kim H-Y, Kim W, Ryu S, Park C-S. 2012. Complete genome sequence of the hyperthermophilic archaeon Pyrococcus sp. strain ST04, isolated from a deep-sea hydrothermal sulfide chimney on the Juan de Fuca Ridge.. J Bacteriol. 194(16):4434-5.

Oslowski DM, Jung J-H, Seo D-H, Park C-S, Holden JF. 2011. Production of hydrogen from α-1,4- and β-1,4-linked saccharides by marine hyperthermophilic Archaea.. Appl Environ Microbiol. 77(10):3169-73.

Ver Eecke HC, Kelley DS, Holden JF. 2009. Abundances of hyperthermophilic autotrophic Fe(III) oxide reducers and heterotrophs in hydrothermal sulfide chimneys of the northeastern Pacific Ocean.. Appl Environ Microbiol. 75(1):242-5.

Feinberg LF, Srikanth R, Vachet RW, Holden JF. 2008. Constraints on anaerobic respiration in the hyperthermophilic Archaea Pyrobaculum islandicum and Pyrobaculum aerophilum.. Appl Environ Microbiol. 74(2):396-402.

Yennaco LJ, Hu Y, Holden JF. 2007. Characterization of malate dehydrogenase from the hyperthermophilic archaeon Pyrobaculum islandicum.. Extremophiles. 11(5):741-6.

Hu Y, Holden JF. 2006. Citric acid cycle in the hyperthermophilic archaeon Pyrobaculum islandicum grown autotrophically, heterotrophically, and mixotrophically with acetate.. J Bacteriol. 188(12):4350-5.

Feinberg LF, Holden JF. 2006. Characterization of dissimilatory Fe(III) versus NO3- reduction in the hyperthermophilic archaeon Pyrobaculum aerophilum.. J Bacteriol. 188(2):525-31.

Lim H, Eng J, Yates JR, Tollaksen SL, Giometti CS, Holden JF, Adams MWW, Reich CI, Olsen GJ, Hays LG. 2003. Identification of 2D-gel proteins: a comparison of MALDI/TOF peptide mass mapping to mu LC-ESI tandem mass spectrometry.. J Am Soc Mass Spectrom. 14(9):957-70.

Holden JF, Adams MWW. 2003. Microbe-metal interactions in marine hydrothermal environments.. Curr Opin Chem Biol. 7(2):160-5.

Adams MW, Holden JF, Menon AL, Schut GJ, Grunden AM, Hou C, Hutchins AM, Jenney FE, Kim C, Ma K et al.. 2001. Key role for sulfur in peptide metabolism and in regulation of three hydrogenases in the hyperthermophilic archaeon Pyrococcus furiosus.. J Bacteriol. 183(2):716-24.

Holden JF, Poole Ii FL, Tollaksen SL, Giometti CS, Lim H, Yates Iii JR, Adams MW. 2001. Identification of membrane proteins in the hyperthermophilic archaeon pyrococcus furiosus using proteomics and prediction programs.. Comp Funct Genomics. 2(5):275-88.

Hutchins AM, Holden JF, Adams MW. 2001. Phosphoenolpyruvate synthetase from the hyperthermophilic archaeon Pyrococcus furiosus.. J Bacteriol. 183(2):709-15.

Craig SA, Holden JF, Khaled MY. 2001. Determination of polydextrose in foods by ion chromatography: collaborative study.. J AOAC Int. 84(2):472-8.

Holden JF, Takai K, Summit M, Bolton S, Zyskowski J, Baross JA. 2001. Diversity among three novel groups of hyperthermophilic deep-sea Thermococcus species from three sites in the northeastern Pacific Ocean.. FEMS Microbiol Ecol. 36(1):51-60.

Craig SA, Holden JF, Khaled MY, Craig SA, Holden JF, Khaled MY. 2000. Determination of polydextrose as dietary fiber in foods.. J AOAC Int. 83(4):1006-12.

Baross JA, Holden JF. 1996. Overview of hyperthermophiles and their heat-shock proteins.. Adv Protein Chem. 48:1-34.

Holden JF, Baross JA. 1993. Enhanced thermotolerance and temperature-induced changes in protein composition in the hyperthermophilic archaeon ES4.. J Bacteriol. 175(10):2839-43.

Research interests - short:

Physiology and ecology of hyperthermophilic archaea; Geomicrobiology of geothermal environments