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Researcher

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David Reed, Ph.D.

Staff Scientist

Research Areas:
Critical Materials; Biological Processing

Biography:
A research scientist in the Biological and Chemical Processing Department at the Idaho National Laboratory, Dr. David Reed specializes in molecular microbiological approaches for extremophilic enzyme expression, characterization, and detection. In the DOE’s Critical Materials Institute, he is a principal investigator for recovery of critical metals such as rare earth elements by microbially mediated leaching and sorption. Other research includes obtaining value-added products from biomass at high-temperature and acidic conditions, metabolic engineering of microorganisms for improved production of commodity chemicals and fuels, and development of biomarkers for improved geothermometry predictions and determining rate estimates of methanogenic, methanotrophic, and ammonia oxidizing microbial activities. Reed holds a doctorate in Microbiology, Molecular Biology and Biochemistry from the University of Idaho where he studied electron transport proteins in the Archaean, Archaeoglobus fulgidus. He is an affiliate faculty member at the University of Idaho and Idaho State University and has mentored many students at the INL.

Education:

​Ph.D., Microbiology, Molecular Biology, and Biochemistry - University of Idaho

M.S., Zoology - Brigham Young University

B.S., Microbiology - Brigham Young University

A.A., Arts and Science - Ricks College

Affiliations:

​American Chemical Society

American Society for Microbiology

Publications:

Reed, D. W., J. A. Lacey, V. S. Thompson. 2018. Separations and processing of plastic films. Report for U.S. Environmental Protection Agency Office of Research and Development. INL/EXT-18-45484. doi: 10.2172/1468644.

 

Wendt, L., A. Murphy, W. Smith, Q. Nguyen, T. Robb, D. Reed, A. Ray, N. Sun, L. Liang, K. Schaller, E. Fillerup, and A. Hoover. 2018. Compatibility of high-moisture storage for biochemical conversion of corn stover: storage performance at laboratory and field scales. Front. Bioeng. Biotechnol. 30:1-13. doi: 10.3389/fbioe.2018.00030

 

Thompson, V.S., M. Gupta, H. Jin, E. Vahidi, M. Yim, M.A. Jindra, V. Nguyen, Y. Fujita, J. W. Sutherland, Y. Jiao, and D.W. Reed. 2018. Techno-economic and life cycle analysis for bioleaching rare earth elements from waste materials. ACS Sustain. Chem. Engineer. 6:1602-1609. doi: 10.1021/acssuschemeng.7b02771

 

Jin, H., D.M. Park, M. Gupta, A.W. Brewer, L. Ho, S.L. Singer, W.L. Bourcier, S. Woods, D.W. Reed, L.N. Lammers, J. W. Sutherland, Y. Jiao. 2017. Techno-economic assessment for integrating biosorption into rare earth recovery process.  ACS Sustain. Chem. Engineer. 5:10148-10155. doi: 10.1021/acssuschemeng.7b02147

 

Park, D.M., A. Brewer, D.W. Reed, P.L. Hageman, L.N. Lammers, Y. Jiao. 2017. Biomining of rare earth elements from low-grade feedstocks using engineered bacteria. Environ. Sci. Technol. 51:13471-13480. doi: 10.1021/acs.est.7b02414

 

Reed, D.W., Y. Fujita, D.L. Daubaras, D.F. Bruhn, J.H. Reiss, V.S. Thompson and Y. Jiao. 2016. Microbially mediated leaching of rare earth elements from recyclable materials. Proc. XXVIII Intern. Miner. Process. Congr. (IMPC 2016), ISBN: 978-1-926872-29-2

 

Reed, D.W., Y. Fujita, D.L. Daubaras, Y. Jiao and V.S. Thompson. 2016. Bioleaching of rare earth elements from waste phosphors and cracking catalysts. Hydrometallurgy, 166:34-40. doi:10.1016/j.hydromet.2016.08.006

 

Park, D.M., D.W. Reed, M.C. Yung, A. Eslamimanesh, M.M. Lencka, A. Anderko, Y. Fujita, R.E. Riman, A. Navrotsky, Y. Jiao. 2016. Bioadsorption of rare earth elements through cell surface display of lanthanide binding tags. Environ. Sci. Technol. 50:2735-2742. doi: 10.1021/acs.est.5b06129

 

Aston, J.E., W.A. Apel, B.D. Lee, D.N. Thompson, J.A. Lacey, D.T. Newby, D.W. Reed and V.S. Thompson. 2016. Degradation of phenolic compounds by the lignocellulose deconstructing Thermoacidophilic Bacterium Alicyclobacillus acidocaldarius. J. Ind. Microbiol. Biotech. 43:13-23. doi: 10.1007/s10295-015-1700-z

 

Mattson, E.D., R.W. Smith, G. Neupane, C.D. Palmer, Y. Fujita, T.L. McLing, D.W. Reed, D.C. Cooper, V.S. Thompson. 2015. Improved geothermometry through multivariate reaction-path modeling and evaluation of geomicrobiological influences on geochemical temperature indicators: INL/EXT-14-33959. doi: 10.13140/RG.2.2.29198.97605

 

Reardon, C.L., T.S. Magnuson, E.S. Boyd, W.D. Leavitt, D.W. Reed, and G.G. Geesey. 2014 Hydrogenase activity of mineral-associated and suspended populations of Desulfovibrio desulfuricans Essex 6. Microbiol. Ecol. 67:318-326, 488. doi: 10.1007/s00248-013-0308-y

 

Fujita, Y., D.W. Reed, K. R. Nowak, V. S. Thompson, T. L. McLing, R.W. Smith and D. C. Cooper. 2013. Microbial impacts on geothermometry temperature predictions. Proc. Geotherm. Reserv. Eng., 38, SGP-TR-198 (p1-11).

 

Fujita, Y., J.L. Taylor, L.M. Wendt, D.W. Reed, and R.W. Smith. 2010. Evaluating the potential of native ureolytic microbes to remediate a 90Sr contaminated environment. Environ. Sci. Technol. 44:7652-7658. doi: 10.1021/es101752p

 

Reed, D.W., J.M. Smith, C.A. Francis, and Y. Fujita. 2010. Responses of ammonia-oxidizing bacterial and archaeal populations to organic nitrogen amendments in low-nutrient groundwater.  Appl. Environ. Microbiol. 76:2517-2523. doi: 10.1128/AEM.02436-09

 

Colwell, F.S., S. Boyd, M.E. Delwiche, D.W. Reed, T.J. Phelps, and D.T. Newby. 2008. Estimates of biogenic methane production rates in deep marine sediments at Hydrate Ridge, Cascadia Margin.  Appl. Environ. Microbiol. 74:3444-3452. doi: 10.1128/AEM.02114-07

 

Freeman, S., D. Reed, and Y. Fujita. 2006. Testing the Specificity of Primers to Environmental Ammonia Monooxygenase (Amoa) Genes in Groundwater Treated with Urea to Promote Calcite Precipitation.  U.S. DOE J. Undergrad. Res. Vol. 6. 114-118.

 

Colwell, F.S., T. Nunoura, M.E. Delwiche, S. Boyd, R. Bolton, D. Reed, K. Takai, R.M. Lehman, K. Horikoshi, D.A. Elias, and T.J. Phelps.  2005.  Evidence of Minimal Methanogenic Numbers and Activity in Sediments Collected from the JAPEX/JNOC/GSC et al. Mallik 5L-38 Gas Hydrate Research Well. In Scientific Results from the Mallik 2002 Gas Hydrate production Research Well Program, Mackenzie Delta, Northwest Territories, Canada. (ed.) S.R. Dallimore and T.S. Collett, Geolog. Surv. Canad. Bull., Bulletin 585:1-11

 

Newby, D.T., *D.W. Reed, L.M. Petzke, A.L. Igoe, M.E. Delwiche, J.P. McKinley, F.F. Roberto, M.J. Whiticar, and F.S. Colwell. 2004. Diversity of methanotrophic communities from pristine groundwater in a basaltic aquifer. FEMS Microbiol. Ecol. 48:333-344.*Equal author contribution. doi: 10.1016/j.femsec.2004.02.001

 

Colwell, F.S., R. Matsumoto, and D.W. Reed. 2004. A Review of the Gas Hydrates and the Geology, and Biology of the Nankai Trough. Chem. Geol. 205:391-404. doi.org/10.1016/j.chemgeo.2003.12.023

 

Kauffman, M.E., W.K. Keener, S.R. Clingenpeel, M.E. Watwood, D.W. Reed, Y. Fujita, and R.M. Lehman. 2003. Use of 3-hydroxyphenylacetylene for activity-dependent, fluorescent labeling of bacteria that degrade toluene via 3-methylcatechol. J. Microbiol. Methods. 55:801-805. doi: 10.1016/j.mimet.2003.07.001

 

Hartzell, P. and D. Reed. Published online May 12, 2003. The Genus Archaeoglobus, p. 82-100.  In  M. Dworkin et al., eds, The Prokaryotes, Archaea. Bacteria: Firmicutes, Actinomycetes. 3 ed, vol. 3. Springer-Verlag, New York. The Prokaryotes: An Evolving Electronic Resource for the Microbiological Community, 3rd edition, release 3.13. doi: 10.1007/0-387-30743-5_6

 

Reed, D.W., Y. Fujita, M.E. Delwiche, D.B. Blackwelder, P.P. Sheridan, T. Uchida, and F.S. Colwell. 2002. Microbial communities from methane hydrate-bearing deep marine sediments in a forearc basin. Appl. Environ. Microbiol. 68:3759-3770. doi: 10.1128/AEM.68.8.3759-3770.2002

 

Pagala, V.R., J. Park, D.W. Reed, and P.L. Hartzell. 2002. Cellular Localization of D-Lactate Dehydrogenase (Dld) and NADH Oxidase (NoxA2) from Archaeoglobus fulgidus. Archaea. 1:95-104. doi: 10.1128/JB.183.24.7007-7016.2001

 

Reed, D.W., J.H. Millstein, and P.L. Hartzell. 2001. H2O2-Forming NADH Oxidase with Diaphorase (Cytochrome) Activity from Archaeoglobus fulgidus. J. Bacteriol. 183: 7007-7016. doi: 10.1128/JB.183.24.7007-7016.2001

 

Reed, D.W. December 1999. Electron Transport Proteins in Archaeoglobus fulgidus. Dept. Microbiol. Mol. Biol. Biochem. University of Idaho. Dissertation, Doctor of Philosophy.

 

Reed, D.W., and P.L. Hartzell. 1999. The Archaeoglobus fulgidus D-lactate Dehydrogenase is a Zn+2 flavoprotein. J. Bacteriol. 181:7580-7587.

 

Dai, Y-R, D.W. Reed, J.H. Millstein, P.L. Hartzell, D.A. Grahame, and E. DeMoll. 1998. Acetyl-CoA Decarbonylase/Synthase Complex from Archaeoglobus fulgidus. Arch. Microbiol. 169:525-529.

 

Reed, D.W., W.S. Bradshaw, W. Xie, and D.L. Simmons. 1996. In Vivo and In Vitro Expression of a Non-Mammalian Cyclooxygenase-1. Prostagland. 52:269-284.

 

Lu, X., W. Xie, D. Reed, W.S. Bradshaw, and D.L. Simmons. 1995. Nonsteroidal Anti-Inflammatory Drugs Cause Apoptosis and Induce Cyclooxygenases I in Chicken Embryo Fibroblasts. Proc. Natl. Acad. Sci. 92:7961-7965.

 

Reed, D.W. December 1994. Cloning and Characterization of Chicken COX1 cDNAs. Dept. Zool., Brigham Young University. Thesis. Masters of Science.

Patents:

Y. Jiao, D.M. Park, M. C. Yung, D.W. Reed. Engineered Microbes for Rare Earth Element Adsorption. Filed 2017 (application #15400948). Patent Cooperation Treaty application filed Feb 2018. Publication Jul 12, 2018 US 2018/0195147.

 

Lee, B.D., D.T. Newby, J. A. Lacey, D.N. Thompson, V.S. Thompson, W.A. Apel, F.F. Roberto, and D.W. Reed. May 1, 2018. Type II restriction-modification system methylation subunit of Alicyclobacillus acidocaldarius. Division. United States patent US 9,957,510.

 

Thompson, D.N., W.A. Apel, V.S. Thompson, D.W. Reed, J.A. Lacey, and E.D. Henriksen.  Feb 20, 2018. Thermophilic and thermoacidophilic biopolymer-degrading genes and enzymes from Alicyclobacillus acidocaldarius and related organisms, methods. CIP. United States patent US 9,896,707.

 

Lee, B.D., D.T. Newby, J. A. Lacey, D.N. Thompson, V.S. Thompson, W.A. Apel, F.F. Roberto, and D.W. Reed. Feb 13, 2018. Type II restriction-modification system methylation subunit of Alicyclobacillus acidocaldarius. Division. United States patent US 9,890,385.

 

Thompson, V.S., W.A. Apel, D.W. Reed, Lee, B.D., D.N. Thompson, F.F. Roberto and J.A. Lacey. Jan 30, 2018. Thermophilic and thermoacidophilic metabolism genes and enzymes from Alicyclobacillus acidocaldarius and related organisms, methods. CIP. United States patent US 9,879,247.

 

Thompson, V.S., D.N. Thompson, D.W. Reed, J.A. Lacey, and W.A. Apel.  Jan 9, 1018. Thermophilic acetylxylanase esterase from Alicyclobacillus acidocaldarius. Original. United States patent US 9,862,981.

 

Thompson, D.N., W.A. Apel, V.S. Thompson, D.W. Reed, and J.A. Lacey.  Jun 13, 1017. Thermophilic and thermoacidophilic glycosylation genes and enzymes from Alicyclobacillus acidocaldarius and related organisms, methods. Division. United States patent US 9,677,054.

 

Lee, B.D., D.T. Newby, J. A. Lacey, D.N. Thompson, V.S. Thompson, W.A. Apel, F.F. Roberto, and D.W. Reed. Feb 14, 2017. Type II restriction-modification system methylation subunit of Alicyclobacillus acidocaldarius. Division. United States patent US 9,567,595.

 

Lee, B.D., D.N. Thompson, W.A. Apel, V.S. Thompson, D.W. Reed and J.A. Lacey. Nov 22, 2016. Transcriptional control in Alicyclobacillus acidocaldarius and associated genes, proteins, and methods. Division. United States patent US 9,499,824.

 

Thompson, D.N., W.A. Apel, V.S. Thompson, D.W. Reed, J.A. Lacey, and E.D. Henriksen.  Aug 2, 2016. Thermophilic and thermoacidophilic biopolymer-degrading genes and enzymes from Alicyclobacillus acidocaldarius and related organisms, methods. CIP. United States patent US 9,404,134.

 

Thompson, D.N., D.W. Reed, V.S. Thompson, J.A. Lacey, and W.A. Apel. July 12, 2016. Alteration and modulation of protein activity by varying post-translational modification. Division. United States patent US 9,388,398.

 

Thompson, D.N., E.D. Henriksen, D.W. Reed, and J.J. Jensen. Mar 15, 2016 Methods for determining enzymatic activity comprising heating and agitation of closed volumes. Original. United States patent US 9,284,596.

 

Thompson, D.N., W.A. Apel, V.S. Thompson, D.W. Reed, and J.A. Lacey.  Jan 12, 1016. Thermophilic and thermoacidophilic glycosylation genes and enzymes from Alicyclobacillus acidocaldarius and related organisms, methods. Original. United States patent US 9,234,228.

 

Thompson, V.S., W.A. Apel, D.W. Reed, Lee, B.D., D.N. Thompson, F.F. Roberto and J.A. Lacey. Dec 29, 2015. Thermophilic and thermoacidophilic metabolism genes and enzymes from Alicyclobacillus acidocaldarius and related organisms, methods. Division. United States patent US 9,222,094.

 

Lee, B.D., D.N. Thompson, W.A. Apel, V.S. Thompson, D.W. Reed and J.A. Lacey. Nov 17, 2015. Transcriptional control in Alicyclobacillus acidocaldarius and associated genes, proteins, and methods. Division. United States patent US 9,187,753.

 

Thompson, D.N., W.A. Apel, V.S. Thompson, D.W. Reed, J.A. Lacey, and E.D. Henriksen.  Jun 2, 2015. Thermophilic and thermoacidophilic biopolymer-degrading genes and enzymes from Alicyclobacillus acidocaldarius and related organisms, methods. CIP. United States patent US 9,045,741.

 

Lee, B.D., D.T. Newby, J. A. Lacey, D.N. Thompson, V.S. Thompson, W.A. Apel, F.F. Roberto, and D.W. Reed. May 12, 2015. Type II restriction-modification system methylation subunit of Alicyclobacillus acidocaldarius. Division. United States patent US 9,029,114.

 

Thompson, D.N., D.W. Reed, V.S. Thompson, J.A. Lacey, and W.A. Apel. Mar. 3, 2015. Alteration and modulation of protein activity by varying post-translational modification. Original. United States patent US 8,969,033.

 

Thompson, V.S., W.A. Apel, D.W. Reed, Lee, B.D., D.N. Thompson, J.A. Lacey and F.F. Roberto. May 20, 2014. Thermophilic and thermoacidophilic metabolism genes and enzymes from Alicyclobacillus acidocaldarius and related organisms, methods. Original. United States patent US 8,728,803.

 

Lee, B.D., D.N. Thompson, W.A. Apel, V.S. Thompson, D.W. Reed and J.A. Lacey. May 6, 2014. Transcriptional control in Alicyclobacillus acidocaldarius and associated genes, proteins, and methods. Original. United States patent US 8,716,011.

 

Thompson, D.N., W.A. Apel, V.S. Thompson, D.W. Reed, and J.A. Lacey.  Nov. 5, 2013. Thermophilic and thermoacidophilic sugar transporter genes and enzymes from Alicyclobacillus acidocaldarius and related organisms, methods. Division. United States patent US 8,575,323.

 

Lee, B.D., D.T. Newby, J. A. Lacey, D.N. Thompson, V.S. Thompson, W.A. Apel, F.F. Roberto, and D.W. Reed. Oct 29, 2013. Type II restriction-modification system methylation subunit of Alicyclobacillus acidocaldarius. Division. United States patent US 8,569,030.

 

Thompson, D.N., W.A. Apel, V.S. Thompson, D.W. Reed, E.D. Henriksen, and J.A. Lacey.  Oct 15, 2013. Thermophilic and thermoacidophilic biopolymer-degrading genes and enzymes from Alicyclobacillus acidocaldarius and related organisms, methods. CIP. United States patent US 8,557,557.

 

Thompson, D.N., W.A. Apel, V.S. Thompson, D.W. Reed, E.D. Henriksen, and J.A. Lacey.  July 30, 2013. Thermophilic and thermoacidophilic biopolymer-degrading genes and enzymes from Alicyclobacillus acidocaldarius and related organisms, methods. CIP. United States patent US 8,497,110.

 

Thompson, D.N., V.S. Thompson, K.D. Schaller, W.A. Apel, D.W. Reed, and J.A. Lacey. April 30, 2013. Thermal and acid tolerant xylosidases, arabinofuranosidases, genes encoding, related organisms and methods. CIP. United States patent US 8,431,379.

 

Thompson, D.N., W.A. Apel, V.S. Thompson, D.W. Reed, E.D. Henriksen, and J.A. Lacey.  April 23, 2013. Thermophilic and thermoacidophilic biopolymer-degrading genes and enzymes from Alicyclobacillus acidocaldarius and related organisms, methods. CIP. United States patent US 8,426,185.


Thompson, D.N., W.A. Apel, V.S. Thompson, D.W. Reed, and J.A. Lacey.  Jan. 29, 2013. Thermophilic and thermoacidophilic sugar transporter genes and enzymes from Alicyclobacillus acidocaldarius and related organisms, methods. Division. United States patent US 8,362,226.

 

Thompson, D.N., W.A. Apel, V.S. Thompson, D.W. Reed, and J.A. Lacey.  Jan. 15, 2013. Thermophilic and thermoacidophilic sugar transporter genes and enzymes from Alicyclobacillus acidocaldarius and related organisms, methods. Division. United States patent US 8,354,517.

Thompson, D.N., W.A. Apel, V.S. Thompson, D.W. Reed, E.D. Henriksen, and J.A. Lacey.  June 19, 2012. Thermophilic and thermoacidophilic biopolymer-degrading genes and enzymes from Alicyclobacillus acidocaldarius and related organisms, methods. Division. United States patent US 8,202,716.

Thompson, D.N., W.A. Apel, V.S. Thompson, D.W. Reed, and J.A. Lacey.  Dec. 6, 2011. Thermophilic and thermoacidophilic sugar transporter genes and enzymes from Alicyclobacillus acidocaldarius and related organisms, methods. Division. United States patent US 8,071,748.

 

Thompson, D.N., V.S. Thompson, K. Schaller, W.A. Apel, J.A. Lacey, and D.W. Reed. Nov. 22, 2011. Thermal and acid tolerant beta-xylosidases, genes encoding, related organisms, and methods. Mexico 292,528.

 

Thompson, D.N., W.A. Apel, V.S. Thompson, D.W. Reed, and J.A. Lacey.  Jun. 14, 2011. Thermophilic and thermoacidophilic sugar transporter genes and enzymes from Alicyclobacillus acidocaldarius and related organisms, methods. Original. United States patent US 7,960,534.

 

Thompson, D.N., V.S. Thompson, K. Schaller, W.A. Apel, J.A. Lacey, and D.W. Reed. Apr. 12, 2011. Thermal and acid tolerant beta-xylosidases, genes encoding, related organisms, and methods. Original. United States patent US 7,923,234.

 

Thompson, D.N., W.A. Apel, V.S. Thompson, D.W. Reed, and J.A. Lacey. Dec. 28, 2010. Thermophilic and thermoacidophilic biopolymer-degrading genes and enzymes from Alicyclobacillus acidocaldarius and related organisms, methods. Original. United States patent US 7,858,353.

 

Thompson, D.N., V.S. Thompson, K. Schaller, W.A. Apel, J.A. Lacey, and D.W. Reed. Jan. 23, 2009. Thermal and acid tolerant beta-xylosidases, genes encoding, related organisms, and methods. New Zealand 585,947.

Awards:

​Inventor's Hall of Fame, Life Time Achievement, Idaho National Laboratory, 2014, 2015, 2017

American Society for Microbiology, Intermountain Branch Secretary, 2011-2013

Research Interests:

​Understanding the physiological activities of microorganisms from extreme environments important for solving energy and environmental challenges.

Version: 20.0
Created at 10/19/2015 4:02 PM by Phyllis L. King
Last modified at 11/5/2018 1:46 PM by hailey.goddard@inl.gov