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Yoshiko Fujita, Ph.D.

Staff Scientist

Research Areas:
Critical Materials; Biological Processing


Dr. Yoshiko Fujita is a senior scientist in the Biological and Chemical Processing Department at the Idaho National Laboratory.  She has served as a principal investigator on multiple projects sponsored by the U.S. Department of Energy’s Office of Science and Office of Energy Efficiency & Renewable Energy, in the areas of subsurface contaminant fate and transport, critical materials, and geothermal energy. She is the lead for the “Environmental Sustainability” thrust area within DOE’s Critical Materials Institute.

Her research interests are in the area of biogeochemistry as related to water quality, with an emphasis on fundamental studies supporting the development of practical applications and approaches for implementation. A unique feature of her career has been her extensive experience in field-based research, complemented with studies at the molecular and bench-scale. During her dissertation and postdoctoral work at Stanford University, she studied changes in organic water quality during aquifer recharge by treated wastewater.  At the INL, she continued her interest in field-based research but transitioned to a focus on mineral precipitation/dissolution and associated effects on inorganic contaminant fate and transport in the subsurface. More recently, she has investigated the potential for biomarkers to inform geothermal resource evaluation and studied interactions between rare earth elements and microorganisms, considering both impacts to ecological function and the prospect for microbiological approaches to enhance strategic metal recovery.


​Ph.D., Civil Engineering - Stanford University

M.S., Civil Engineering - Stanford University

B.A., Chemistry - Williams College

American Geophysical Union
American Chemical Society
American Society for Microbiology
Geochemical Society
Interpore Society

Reed, D. W., Fujita, Y., Daubaras, D. L., Jiao, Y. and V. S. Thompson.  Bioleaching of Rare Earth Elements from Waste Phosphors and Cracking Catalysts.  Hydrometallurgy, 166, 34-40,


Fujita, Y., Barnes, J. and S. Fox. In press.  Rare Earth Element Impacts on Biological Wastewater Treatment.  Proceedings of the International Mineral Processing Congress 2016, September 2016, Quebec City, Quebec, Canada.


Reed, D. W., Fujita, Y., Daubaras, D. L., Bruhn, D. F., Reiss, J. H., V. S. Thompson and Y. Jiao.  Microbially Mediated Leaching of Rare Earth Elements from Recyclable Materials. Proceedings of the International Mineral Processing Congress 2016, September 2016, Quebec City, Quebec, Canada.


Park, D., Reed, D.W., Yung, M., Eslamimanesh, A., Lencka, M.M., Anderko, A., Fujita, Y., Riman, R.E., Navrotsky, A.and Y. Jiao. (2016). Bioadsorption of Rare Earth Elements through Cell Surface Display of Lanthanide Binding Tags. Environmental Science & Technology, 50(5): 2735–2742, doi:  10.1021/acs.est.5b06129.


Direito, S.O., Clark, S., Cousins, C., Fujita, Y., Gluyas, J., Harley, S., Holmes, R.J., Hutchinson, I.B., Kudryavtsev, V.A., Lloyd, J., Main, I.G., Naylor, M., Payler, S., Smith, N., Spooner, N.J.C., Telfer, S., Thompson, L.G., Wouters, K., Wragg, J. and C. Cockell. (2015). Geological repositories: scientific priorities and potential high-technology transfer from the space and physics sectors. Mineralogical Magazine 79(6):1651-1664.


Fox, D. T., L. Guo, Y. Fujita, H. Huang and G. Redden. (2015). Experimental and Numerical Analysis of Parallel Reactant Flow and Transverse Mixing with Mineral Precipitation in Homogeneous and Heterogeneous Porous Media. Transport in Porous Media, 110(3), doi: 10.1007/s11242-015-0614-6.


Fujita, Y., Barnes, J., Eslamimanesh, A., Lencka, M., Anderko, A., Riman, R. and A. Navrotsky. (2015). Effects of simulated rare earth recycling wastewaters on biological nitrification. Environmental Science & Technology, 49(16): 9460-9468,  doi: 10.1021/acs.est.5b01753.


Zhang, C., A. Revil, Y. Fujita, J. Munakata-Marr and G. Redden. (2014). Quadrature conductivity: A quantitative indicator of bacterial abundance in porous media. Geophysics 79(6): D363-D375.


Gebrehiwet, T.,  Guo, L., Fox, D., Huang, H., Fujita, Y., Smith, R., Henriksen, J. and G. Redden.  (2014).  Precipitation of calcium carbonate and calcium phosphate under diffusion controlled mixing.  Applied Geochemistry, 46(0): 43-56.


Li, Z., Haynes, R., Sato, E., Shields, M., Fujita, Y. and C. Sato.  (2014).  Microbial Community Analysis of a Single Chamber Microbial Fuel Cell Using Potato WastewaterWater Environment Research, 86(4), 324-330, doi: 10.2175/106143013X13751480308641.


Redden, G., D. Fox, C. Zhang, Y. Fujita, L. Guo, and H. Huang.  (2013).  CaCO3 Precipitation, Transport and Sensing in Porous Media with In Situ Generation of Reactants, Environmental Science & Technology, 48(1), 542-549, doi:10.1021/es4029777. 


Guo, L., Huang, H., Gaston, D.R., Permann, C.J., Andrs, D., Redden, G.D., Lu, C., Fox, D.T. and Y. Fujita. (2013).  A Parallel Fully-coupled Fully-implicit Solution to Reactive Transport in Porous Media Using Preconditioned Jacobian-Free Newton-Krylov Method, Advances in Water Resources, 53, 101–108, doi: 10.1016/j.advwatres.2012.10.010.


Fujita, Y., Reed, D. W., Nowack, K.R., Thompson, V.S., McLing, T.L., Smith, R.W., and D.C. Cooper. (2013). Microbial Impacts on Geothermometry Temperature Predictions.  Proceedings of the 2013 Stanford Geothermal Workshop, Feb., 2013, Stanford, CA.


Zhang, C., Slater, L., Redden, G., Fujita, Y., Johnson, T. and D. Fox.  (2012).  Spectral induced polarization signatures of hydroxide adsorption and mineral precipitation in porous media. Environmental Science & Technology, 46, 4357-4364, doi: 10.1021/es204404e.


Gebrehiwet, T., Redden, G.D., Fujita, Y., Beig, M.S. and R.W. Smith. (2012).  The effect of ion activity ratios on the precipitation of calcium carbonate and Sr2+ partitioning.  Geochemical Transactions, 13(1), doi:10.1186/1467-4866-13-1.


Wright, K. E., Hartmann, T. and Y. Fujita.  (2011).  Inducing mineral precipitation in groundwater by addition of phosphate.  Geochemical Transactions, 12(8), doi:10.1186/1467-4866-12-8.


Wu, Y., Ajo-Franklin, J.B., Spycher, N., Hubbard, S.S., Zhang, G., Williams, K.H., Taylor, J., Fujita, Y. and R. Smith.  (2011).  Geophysical monitoring and reactive transport modeling of ureolytically-driven calcium carbonate precipitation.  Geochemical Transactions, 12(7), doi:10.1186/1467-4866-12-7.


Ray, A.E., Bargar, J.R., Sivaswamy, V., Dohnalkova, A.C., Fujita, Y., Peyton, B.M. and T.S. Magnuson. (2011).  Evidence for multiple modes of uranium immobilization by an anaerobic bacterium.  Geochimica Cosmochimica Acta, 75(10), 2684-2695.


Barkouki, T., Martinez, B., Mortensen, B., Weathers, T., De Jong, J., Ginn, T., Spycher, N., Smith, R. and Y. Fujita. (2011).  Forward and inverse bio-geochemical modeling of microbially induced calcite precipitation in half-meter column experiments.  Transport in Porous Media, 90(1), 23-39.


Fujita, Y., Taylor, J.L., Wendt, L.M., Reed, D.W. and R.W. Smith. (2010).  Evaluating the potential of native ureolytic microbes to remediate a 90Sr contaminated environment.  Environmental Science & Technology, 44(19), 7652-7658.


Ray, A.E., Connon, S.A., Sheridan, P.P., Gilbreath, J., Shields, M., Newby, D.T., Fujita, Y. and T.S. Magnuson. (2010).  Intragenomic heterogeneity of the 16s rRNA gene in strain ufo1 caused by a 100-bp insertion in helix 6.  FEMS Microbiology Ecology, 72(3), 343-353.


Reed, D.W., Smith, J.M., Francis, C.A. and Y. Fujita. (2010).  Response of ammonia-oxidizing bacterial and archaeal populations to organic nitrogen amendments in low-nutrient groundwater.  Applied and Environmental Microbiology, 76(8), 2517-2523.


Fujita, Y., Smith, R.W. and J.L.Taylor. (2009).  In situ calcite precipitation for contaminant immobilization.  In Proceedings of the 10th International In Situ and On-Site Bioremediation Symposium, May 5-9, 2009, Baltimore, MD. Columbus, OH:  Battelle.


DeJong, J.T., Martinez, B.C., Mortensen, B.M., Nelson, D.C., Waller, J.T., Weil, M.H., Ginn, T.R., Weathers, T., Barkouki, T., Fujita, Y., Redden, G., Hunt, C., Major, D. and B. Tanyu.  (2009).  Upscaling of bio-mediated soil improvement.  In Proceedings of the 17th International Conference on Soil Mechanics and Geotechnical Engineering, October 5-9, 2009, Alexandria, Egypt.  Hamza, M., Shahien, M. and Y. El-Mossallamy, eds.  Amsterdam, Netherlands:  IOS Press.


Fujita, Y., Taylor, J.L., Gresham, T.L.T., Delwiche, M.E., Colwell, F.S., McLing, T.L., Petzke, L.M., and R.W. Smith.  (2008).  Stimulation of microbial urea hydrolysis in groundwater to enhance calcite precipitation.  Environmental Science & Technology. 42(8), 3025-3032.  


Redden, G.D., Fox, D., Fujita, Y., Fang, Y., Scheibe, T.D., and A.M. Tartakovsky.  (2007).  Fluid flow, solute mixing and precipitation in porous media.  In Proceedings of the 2nd International Conference on Porous Media and its Applications in Science and Engineering, June 17-21, 2007, Kauai, Hawaii, USA.


Tyler, T.L., Sheridan, P.P., Watwood, M.E., Fujita, Y. and F.S. Colwell. (2007).  Design and validation of polymerase chain reaction primers based on ureC for environmental detection of urea-hydrolyzing bacteria.  Geomicrobiology Journal, 24(3), 353-364.


Freeman, S. A., Reed, D. W. and Y. Fujita.  (2006).  Testing the specificity of primers to environmental ammonia monooxygenase (amoA) genes in groundwater treated with urea to promote calcite precipitation.  Journal of Undergraduate Research, vol. VI, 114-118.


Colwell, F.S., R.W. Smith, F.G. Ferris, A.-L. Reysenbach, Y. Fujita, T.L. Tyler, J.L. Taylor, A. Banta, M.E. Delwiche, T. McLing, and M.E. Watwood. (2005).  Microbially-mediated subsurface calcite precipitation for removal of hazardous divalent cations: Microbial activity, molecular biology, and modeling.  In Subsurface Contamination Remediation: Accomplishments of the Environmental Management Science Program. American Chemical Society Symposium Series 904. E. Berkey and T. Zachry, American Chemical Society: 117-137.


Fujita, Y., Redden, G.D., Ingram, J.A., Cortez, M.M., Ferris, F.G. and R.W. Smith. (2004).  Strontium incorporation into calcite generated by bacterial ureolysis.  Geochimica et Cosmochimica Acta, 68, 3261.


Ferris, F. G., Phoenix, V., Fujita, Y. and R.W. Smith. (2004).  Kinetics of calcite precipitation induced by ureolytic bacteria at 10 to 20°C in artificial groundwater.  Geochimica et Cosmochimica Acta, 68, 1701.


Kauffman, M.E., Keener, W.K.., Clingenpeel, S.R., Watwood, M.E., Reed, D.W., Fujita, Y. and R.M. Lehman. (2003).  Use of 3-hydroxyphenylacetylene for activity-dependent, fluorescent labeling of bacteria that degrade toluene via 3-methylcatechol.  Journal of Microbiological Methods, 55(3), 801-805.


Reed, D. W., Fujita, Y., Delwiche, M.E., Blackwelder, D.B., Uchida, T. and F.S. Colwell. (2002).  Microbial communities from methane hydrate-bearing deep marine sediments in a forearc basin.  Applied and Environmental Microbiology, 68(8), 3759-3770.


Fujita ,Y., Campbell, J. A., Mong, G. M. and M. Reinhard.  (2001).  Characterization of a nitrogen-containing octylphenol ethoxylate metabolite by chemical derivatization and degradation in combination with mass spectrometry.  International Journal of Environmental Analytical Chemistry, 81, 41-54. 


Fujita, Y., Ferris, F.G., Lawson, R.D., Colwell, F.S. and R.W. Smith. (2000).  Calcium carbonate precipitation by ureolytic subsurface bacteria.  Geomicrobiology Journal, 17, 305-318.


Fujita, Y., Zhou, J., Orwin, E., Reinhard, M., Davisson, M. L. and G. B. Hudson.  (1998).  Tracking the Movement of Recharge Water After Infiltration.  In Artificial Recharge of Groundwater: Proceedings of the Third International Symposium - TISAR 98, Taylor & Francis, Oxford, UK, 155-160.


Fujita, Y., and M. Reinhard. (1997).  Identification of metabolites from the biological transformation of the nonionic surfactant residue octylphenoxyacetic acid and its brominated analog.  Environmental Science & Technology, 31(5), 1518-1524.


Fujita, Y., Ding, W., Zhou, J., Orwin, E., Rivlin, T. and M. Reinhard.  (1997).  Santa Ana River Water Quality & Health Study: Organic Contaminant Behavior During Groundwater Recharge With Reclaimed Wastewater and Santa Ana River Water:  A Laboratory and Field Evaluation.  Final report submitted to the Orange County Water District, October 1997.


Fujita, Y., Ding, W.H. and M. Reinhard. (1996).  Identification of wastewater dissolved organic carbon (DOC) characteristics in reclaimed wastewater and recharged groundwater.  Water Environment Research, 68, 867-876.


Ding, W. H., Fujita, Y., Aeschimann, R., and M. Reinhard.  (1996).  Identification of Organic Residues in Tertiary Effluents by GC/EI-MS, GC/CI-MS and GC/TSQ-MS.  Fresenius' Journal of Analytical Chemistry, 354, 48-55.


Fujita, Y., Aeschimann, R., Ding, W. H., and M. Reinhard.  (1995).  DOC Characterization of Reclaimed Wastewater.  In Artificial Recharge of Ground Water, II. Proceedings of the Second International Symposium on Artificial Recharge of Ground Water, American Society of Civil Engineers, New York, NY, 386-395.


Reinhard, M., Ding, W. H., Fujita, Y., Semadeni, M. and J. Wu.  (1995).  Behavior and Fate of Organic Contaminants During Groundwater Recharge with Reclaimed Wastewater and Santa Ana River Water - A Field and Laboratory Investigation.  Report to the Orange County Water District.  Department of Civil Engineering, Stanford University, Stanford, CA.  


Ding, W. H., Fujita, Y., and M. Reinhard.  (1994).  Chemical Ionization Mass Spectra of Linear Alcohol Polyethoxy Carboxylates and Polyethylene Glycol Dicarboxylates, Rapid Communications in Mass Spectrometry, 8: 1016-1020.


Reinhard, M., Ding, W. H., and Y. Fujita.  (1994).  Organic Carbon Characterization of Advanced Treated Wastewater at Water Factory 21, Orange County.  Technical Report No. 320, Department of Civil Engineering, Stanford University, Stanford, CA.


Tikkanen, W.; Fujita, Y. and J.L. Petersen.  (1986).  Functionalized Group 4 metallocene complexes as binucleating ligands: synthesis and structural characterization of tetracarbonyl [[P, P'-bis (diphenylphosphino) cyclopentadienyl)] dichlorozirconium (IV)] molybdenum (0). Organometallics, 5(5), 888-894.



COST Action TD 1407 Workshop on Environmental Concentrations, Cycling & Modeling of Technology Critical Elements, Weizmann Institute of Science, Rehovot, Israel, January 18-19, 2017


American Geophysical Union Fall Meeting, San Francisco, CA, December 2016


Advanced Lecture Series on the Development of the Backend of the Nuclear Fuel Cycle, Hokkaido University, Sapporo, Japan, July 2016


Goldschmidt 2016, Yokohama, Japan, June 2016


GeoRepNet meeting, Edinburgh, United Kingdom, September 2013


International Seminar Series on Environmental Radioactivity 2 (Scientific Basis for Remediation in Fukushima), Sapporo, Japan, November 2012


Interpore, Purdue University, Indiana, June 2012


American Chemical Society, San Diego, CA, March 2012


Japan Atomic Energy Agency, Tokaimura, Japan, March 2012


Battelle’s 10th International in situ and On-site Bioremediation Symposium, Baltimore, MD,  May 2009


State Regulators Consensus Workshop, Phoenix, AZ, February 2005

DOE Office of Science Undergraduate Research Programs Outstanding Mentor Award, 2006

Jack Edward McKee Medal, Water Environment Federation.  Award for “professional achievement in groundwater protection, restoration, or sustainable use,” 1997
Research Interests:

​Biogeochemistry in subsurface environments and water quality

Version: 10.0
Created at 10/19/2015 3:42 PM by Phyllis L. King
Last modified at 10/6/2016 11:22 AM by Phyllis L. King