Idaho National Laboratory Biological Systems

Publications

INL scientists contribute to numerous publications related to research in Biological Systems.

  • Zhang, C., Slater, L., Redden, G., Fujita, Y., Johnson, T. and D. Fox. 2012. Spectral induced polarization of hydroxide adsorption and mineral precipitation in porous media. Environ. Sci. Technol. 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., Zhank, 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., Dahnolkova, A.C., Fujita, Y., Beyton, 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., Weather, T., De Jong, J., Ginn, T., Sycher, N., Smith, R. and Y. Fujita. 2011. Forward and inverse bio-geochemical modeling of microbially induced calcite precipitation in half-meter column experiments.  Tranport in Porous Media, 90(1),23-29.
  • Roberto, F.F., and H.G. Silverman. 2011. Adhesive proteins from mussels. In: Innovations in Materials Manufacturing, Fabrication, and Environmental Safety, M. Schwartz (Editor), CRC Press, New York. Taylor and Francis Group LLC, Boca Raton\Chapter 3. pp 53-86.
  • Ray A.E., Connon, S.A., Sheridan P.P., Gilbreath, J., Sheilds, 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 and Ecology. 72(3):343-353.
  • Lacey, J.A. Ovule Development and Apospory in Sorghum Bicolor: Identification of Molecular Mechanisms Controlling Female Gamete Formation. 2010. Dissertation and Thesis. University of Idaho Plant, Soil, and Entomological Sciences. Moscow, Idaho.
  • Langsdorf, E.F., Malikzay, A. Lamarr W.A., Daubaras D., Kraved, C., Zhang R. Hart, R. Mansma, R., Black T. Ozbal C.C., Miesel L. Lunn, C.A. 2010. Screening for Antibacterial Inhibitors of the UDP-3-O-(R-3-Hydroxymyristoyl)-N-Acetylglucosamine Deacetylase (LpxC) Using a High-Throughput Mass Spectrometry Assay. Journal of Biomolecular Screening. 15(52):52-61.
  • Aston, J.E., W.A. Apel, B.D. Lee, and B.M. Peyton. 2010. Effects of Cell Condition, pH, and Temperature on Lead, Zinc, and Copper Sorption to Acidithiobacillus caldus BC13. Journal of Hazardous Material. 184:34-41.
  • Aston, J.E., W.A. Apel, B.D. Lee, and B.M. Peyton. Effects of Ferrous Sulfate, Inoculum History and Anionic Form of Lead, Zinc, and Copper Toxicity to Acidithiobacilus caldus BC13. Environmental Toxicology and Chemistry. 2010. 12(20), 2669-2675.
  • Aston. J.E., W.A. Apel, B.D. Lee, and B.M. Peyton. Growth Effects and Assimilation of Organic Acids in Chemostat and Batch Cultures of Acidothiobacillus caldus. World Journal of Microbiology and Biotechnology, 2010. 27:153-161.
  • Fujita, Y., J.L. Taylor, L.M. Wendt, D.W. Reed and R.W. Smith. 2010. Evaluting the Potential of Native Ureolytic Microbes to Remediate a 90Sr Contaminated Environment. Environmental Science and Technology. 44(19), 7652-7658.
  • VanEngelen, M.R., E.K. Field, R. Gerlach, B.D. Lee, W.A. Apel, and B.M. Peyton. 2010. UO22+ speciation Determines Uranium Toxicity and Bioaccumulation in an Environmental Pseudomonas sp. isolate. Environmental Toxicology and Chemistry. 29(4):763-769
  • Silverman, H.G., and F.F. Roberto. "Byssus Formation in Mytilus". 2010. In: Biological Adhesive Systems: From Nature to Technical and Medical Application, von. Bayern, J.I. Grunwald, editors, Springer-Verlag\Wien, Austria.\Chapter 18, pp 273-283.
  • Rope, A.M., Reed D.W., and Y. Fujita. Development of an Improved Standard for Quantification of the amoA Gene in Environmental Samples, DOE Office of Science Journal of Undergraduate Research. In press
  • Reed, D.W., Smith, J. M., Francis, C.S. 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
  • Inskeep, W.P., D.B. Rusch, Z.J. Jay, M.J. Herrgard, M.A. Kozubal, T.H. Richardson, R.E. Macur, N. Hamamura, R. deM. Jennings, B.W. Fouke, A.-L. Reysenbach, F. Roberto, M. Young, A. Schwartz, E.S. Boyd, J.H. Badger, E.J. Mathur, A.C. Ortmann, M. Bateson, G. Geesey, and M. Frazier, 2010. Metagenomes from high-temperature chemotrophic systems reveal geochemical controls on microbial community structure and function. PLoS One 5(3):e9773.
  • 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., Tanyu, B., 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.
  • Field, E.K., S. D'Imperio, A.R. Miller, M.R. VanEngelen, R. Gerlach, B.D. Lee, W.A. Apel, B.M. Peyton. 2010. Application of Molecular Techniques to Elucidate the Influence of Cellulosic Waste on the Bacterial Community Structure at a Simulated Low Level Waste Site. Applied and Environmental Microbiology. Online March 19, 2010.
  • Smith, W.A., D.N. Thompson, V.S. Thompson, C.W.Radtke, and B. Carter, 2009. Assessment of xylanase activity in dry storage as a potential method of reucing feedstock cost. Appl. Biochem. Biotech., 154(1-3),287-301.
  • Duguid, K.B., Montross, M.D., Radtke, C.W., Crofcheck, C.L., Wendt, L.M., and S.A. Shearer. 2009. Effect of Anatomical Fractionation on the Enzymatic Hydrolysis of Acid and Alkaline Pretreated Corn Stover. Bioresource Technology, 100:5189-5195
  • Bruhn, D.F., S.M. Frank, F.F. Roberto, P.J. Pinhero, S.G. Johnson. 2009. Microbial Biofilm Growth on Irradiated, Spent Nuclear Fuel Cladding. Journal of Nuclear Materials. 384:140-145.
  • 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.
  • Lehman, R.M., J.G. Lundgren, L.M. Petzke. 2009. Bacterial Communities Associated with the Digestive Tract of the Predatory Ground Beetle, Poecilus chalcites, and Their Modification by Laboratory Rearing and Antibiotic Treatment. Microbial Ecology. 57:349-358.
  • Roberto, F.F. and D.J. Rodi, 2009. Transport and dispersion of biological agents/toxins for the BioEMG. SCAPA/BWG Action Item 06-06. Report prepared for DOE NA-41.
  • Aston, J.E., W.A. Apel, B.D. Lee, B.M. Peyton. 2009. Toxicity of Select Organic Acids to the Slightly Thermophilic Acidophile Acidothiobacillus Caldus. Environmental Toxicology and Chemistry. 28:279-286
  • Foster, J.T., S.M. Beckstrom-Sternberg, T. Pearson, J.S. Beckstrom-Sternberg, P.S.G. Chain, J. Hnath, F.F. Roberto, T. Brettin, and P. Keim, 2009. Whole genome-based phylogeny and divergence of the genus Brucella. J. Bacteriol. 191, 2864-2870.
  • DeJong, J.T., Martinez, B.C., Mortensen, B.M., Nelson, D.C., Waller, J.T., Weil, M.H., Ginn, T.R., Weathers, Tl, Barlouki, 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. Mamza, M., Shahien, M. and Y. El-Mossallamy, eds. Amsterdam, Netherlands: IOS Press.
  • Viamajala, S., B.M. Peyton, R. Gerlach, V. Sivaswamy, W.A. Apel, J.N. Petersen. 2008. Permeable Reactive Biobarriers for In Situ Cr(VI) Reduction: Bench Scale Tests Using Cellulomonas sp. Strain ES6. Biotechnology and Bioengineering. 101: 1150-1162.
  • Mockos, G.R., W.A. Smith, F.J. Loge, D.N. Thompson. 2008. Selective Enrichment of a Methanol-Utilizing Consortium Using Pulp and Paper Mill Waste Streams. Applied Biochemistry and Biotechnology. 148:211-226.
  • 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. Micobiol. 74: 3444-3452.
  • Fujita, Y., J.L. Taylor, Gresham, M.E. Delwiche, F.S. Colwell, T.L. McLing, L.M. Petzke, R.W. Smith. 2008. Stimulation of Microbial Urea Hydrolysis in Groundwater to Enhance Calcite Precipitation. ES&T ASAP. DOI: 10.1021/es 702643g.
  • Duguid, K.B., Montross, M.D., Radtke, C.W., Crofcheck, C.L., Shearer, S.A., and Hoskinson, R.L. 2007. Screening for sugar and ethanol processing characteristics from anatomical fractions of wheat stover. Biomass and Bioenergy 31: 585-592.
  • Hoskinson, R.L., Karlen, D.L., Birrell, S.J. Radtke, C.W., and W.W. Wilhelm. 2007. Engineering, nutrient removal, and feedstock conversion evaluations of four corn stover harvest scenarios. Biomass and Bioenergy 31:126-136.
  • Canan, B., G.R. Olhoeft, and W.A. Smith. 2007. Experimental monitoring of Cr(VI) bio-reduction using electrochemical geophysics. Journal of Environmental and Engineering Geophysics, 12:255-266.
  • Coats, E.R., F.J. Loge, W.A. Smith, D.N. Thompson, and M.P. Wolcott. 2007. Functional stability of a mixed microbial consortium producing PHA from waste carbon sources. Applied Biochemistry and Biotechnology. 136-140: 909-925.
  • Silverman, H.G., and F.F. Roberto. 2007. Understanding Marine Mussel Adhesion. Marine Biotechnology. 9 (6): 661-681
  • Viamajala, S., W.A. Smith, R.K. Sam, W.A. Apel, J.N. Peterson, A.L. Neal, F.F. Roberto, D.T. Newby and B.M. Peyton. 2007. Isolation and characterization of Cr(VI) reducing Cellulomonas spp. from subsurface soils: implications for long term chromate reduction. Bioresource Technology. 98:612-622.
  • Tyler, T.L., P.P. Sheridan, M.E. Watwood, Y. Fujita, 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.
  • Redden, G. D., D. Fox, Y. Fujita, Y. Fang, T.D. Scheibe, 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.
  • Freeman, S.A., D.W. Reed, and Y. Fujita. 2007. 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.
  • Johnson, J.J., K. E. Eisert, M. Salehi, J. T. Liang, G. A. Bala, and S. L. Fox. 2007. Biosurfactants Produced from Agricultural Process Waste Streams to Improve Oil Recovery in Fractured Carbonate Reservoirs. SPE 106078
  • Delwiche, M. E., A. Olson, and K. Adler-Flitton. 2007. Detection of microbial sulfate-reduction associated with buried stainless steel coupons. Proceedings of the NACE International Corrosion 2007 Conference and Expo, Nashville, TN., February 2007
  • Salehi, M., S. Johnson, G. Bala, S. Fox, and J.T. Laing. 2007. Wettability alteration of carbonated rock mediated by biosurfactant produced from high starch agricultural effluents. Proceedings: Ninth Annual Wettability Symposium. Bergen, Norway.
  • Snyder, J.C., B.Wiedenheft, M. Lavin, F. F. Roberto, J. Spuhler, A.C. Ortmann, T. Douglas, and M. Young, 2007. Virus movement maintains local virus population diversity. Proc. Natl. Acad. Sci. USA, 104, 19102-19107.
  • Roberto, F., M. Watkins, D. Grogan, and M. Young, 2007. Initial characterization of a 32-kb plasmid from a Yellowstone strain of Sulfolobus islandicus. Plasmid 57, 226-227
  • Viamajala, S., W.A. Smith, R.K. Sani, W.A. Apel, J.N. Petersen, A.L. Neal, F.F. Roberto, D.T. Newby, and B.M. Peyton. 2006. Isolation and characterization of Cr(VI) reducing Cellulomonas spp. from subsurface soils: Implication for long-term chromate reduction. Bioresource Technology. 98:621-622.
  • Lee, B. D., W. A. Apel, and M. R. Walton. 2006. Calcium Carbonate Formation by Synechococcus sp. Strain PCC 8806 and Synechococcus sp. Strain PCC 8807. Bioresource Technology 97:2427-2434.
  • Horton R.N., W.A. Apel, V.S.,Thompson, and P.P. Sheridan. 2006. Low temperature reduction of hexavalent chromium by a microbial enrichment consortium and a novel strain of Arthrobacter aurescens, BMC Microbiology, 6, Art. 5.
  • Viamajala, S., Y. Bereded-Samuel, W.A. Apel and J.N.Petersen. 2006. Selenite Reduction by a Denitrifying Culture: Batch and Packed-Bed Reactor Studies. Appl. Microbiol. Biotechnol. 71:953-962
  • Appia-Ayme, C., R. Quatrini, Y. Denis, F. Denizot, S. Silver, F. Roberto, F. Veloso, J. Valdes, J. P. Cárdenas, M. Esparza, O. Orellana, E. Jedlicki, V. Bonnefoy and D.Holmes, 2006. Insights into the central carbon metabolism of Acidithiobacillus ferrooxidans revealed by bioinformatics and microarray analysis. Hydrometallurgy 83, 273-280.
  • Quatrini, R., C. Appia-Ayme, Y. Denis, J. Ratouchniak, F. Veloso, J. Valdes, C. Lefimil, S. Silver, F. Roberto, O. Orellana, F. Denizot, E. Jedlicki, D. Holmes and V. Bonnefoy, 2006. Global analysis of the ferrous iron and sulphur energetic metabolism of Acidithiobacillus ferrooxidans by microarray transcriptome profiling. Hydrometallurgy 83, 263-272.
  • Schirp, A, F.J. Loge, K.R. Englund, M.P Wolcott, J.R. Hess, T.P. Houghton, J.A. Lacey, and D.N. Thompson. 2006. Pilot-scale production and material properties of extruded straw-plastic composites based on untreated and fungal-treated wheat straw. Forest Products Journal 56(10):90-96.
  • Robb, F.T., and D.T. Newby. 2006. Functional Genomics in Thermophilic Microorganisms. In Extremophiles, Eds. Gerday, C. and N. Glandsdorff. ASM Press. pp. 30-38.
  • Thompson, D.N., J.M. Barnes, and T.P. Houghton. 2005. Effect of additions on the ensiling and microbial community of senesced wheat straw. Appl. Biochem. Biotechnol. 121:21-46
  • Young, M., B. Wiedenheft, J. Snyder, J. Spuhler, F. Roberto, and T. Douglas. 2005. Archaeal viruses from Yellowstone’s high temperature environments. In:Geothermal biology and geochemistry in Yellowstone National Park, W.P. Inskeep and T.R. McDermott (Editors), Montana State University Publications, Bozeman, MT, pp. 289-304.
  • 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, 11 p.
  • Kauffman, M.E., W.K. Keener, S.R. Clingenpeel, M.E. Watwood, D.W. Reed, Y. Fujita, and R.M. Lehman. 2004. Use of 3-hydroxyphenylacetylene for Activity-Dependent, Fluorescent Labeling of Bacteria. J. Microbiological Methods. 55(3):801-805.
  • Reardon, C.L., D.E. Cummings, L.M. Petzke, B.L. Kinsall, D.B. Watson, B.M. Peyton, and G.G. Geesey. 2004. Composition and Diversity of Microbial Communities Recovered from Surrogate Minerals Incubated in an Acidic Uranium-Contaminated Aquifer. Appl Environ Microbiology. 70(10):6037-6046.
  • Fujita, Y., G.D. Redden, J.C. Ingram, M.M. Cortez, G. Ferris, and R.W. Smith. 2004. Strontium Incorporation into Calcite Generated by Bacterial Ureolysis. Geochemica et Cosmochimica Acta. 68(15):3261-3270.
  • Ferris, F.G., V. Phoenix, Y. Fujita, and R.W. Smith. 2004. Kinetics of Calcite Precipitation Induced by Ureolytic Bacteria at 10 to 20C in Artificial Groundwater. Geochemica et Cosmochimica Acta. 68(8):1701-1722.
  • Lehman, R.M., S.P. O’Connell, A. Banta, J.K. Fredrickson, A.L. Reysenbach, T.L. Kieft, and F.S. Colwell. Microbiological Comparison of Core and Groundwater Samples Collected from a Fractured Basalt Aquifer with that of Dialysis Chambers Incubated in-situ. Geomicrobiology J. 21(3):169-182.
  • Colwell, F.S., R. Matsumoto, and D.W. Reed. 2004. A Review of Gas Hydrates, Geology, and Biology of the Nankai Trough. Chemical Geology. 205(3,4):391-404.
  • Houghton, T.P., D.N. Thompson, J.R. Hess, J.A. Lacey, M.P. Wolcott, A. Schirp, K. Englund, D. Dostal, and F. Loge. 2004. Fungal upgrading of wheat straw for straw-thermoplastics production. Appl. Biochem. Biotechnol. 113-116:71-93.
  • Wright, C.T., P.A. Pryfogle, N. Stevens, E.D. Steffler, J.R. Hess, T.H. Ulrich, and J.A. Lacey. 2004. Biomechanics of Wheat/Barley Straw and Corn Stover. Proceedings of the 26th Symposium on Biotechnology For Fuels and Chemicals,” May 9-12, 2004, Chattanooga, TN.
  • Schaller, K.D. and G.A. Bala. 2004. Characterization of Surfactin from Bacillus subtilis for Application as an Agent for Enhanced Oil Recovery. Applied Biochemistry and Biotechnology. 115(4):827-836.
  • Xie, X., and G.A. Bala. 2004. Spontaneous Imbibition in Porous Basalt Mediated by Microbial Perturbations. Proceedings of the 8th Annual Wettability Symposium, Houston, TX
  • Fidler, B.R., K.L. Sublette, G.E. Jenneman, and G.A. Bala. 2004. Bioregenerable Selective Sorbents for Hydrogen Sulfide Removal From Natural Gas. Gas Technology Institute Natural Gas Technologies II Conference and Exhibition.
  • Lee, B. D., W. A. Apel, M. R. Walton. 2004. Determining the effect of cyanobacterial species variation on calcification. Biotechnol. Prog. 20:1345-1351.
  • Viamajala, S., B. M. Peyton, R. K. Sani, W. A. Apel, and J. N. Petersen. 2004. Toxic effects of Cr(VI) on anaerobic and aerobic growth of Shewanella oneidensis MR-1. Biotechnol. Prog. 20:87-95.
  • Wiedenheft, B., K. Stedman, F. Roberto, D. Willits, A.-K. Gleske, L. Zoeller, J. Snyder, T. Douglas, and M. Young, 2004. Comparative genomic analysis of hyperthermophilic archaeal fuselloviridae viruses. J. Virol. 78, 1954-1961.
  • Rice, G., L.Tang, K. Stedman, F. Roberto, J. Spuhler, E. Gillitzer, J. E. Johnson, T. Douglas and M. Young, 2004. The structure of a thermophilic archaeal virus shows a dsDNA viral capsid type that spans all domains of life. Proc. Nat’l Acad. Sci. USA 101, 7716-7720.
  • Snyder, J .C., J. Spuhler, B. Wiedenheft, F. F. Roberto, and M. J. Young. 2004. Effects of culturing on the population structure of a hyperthermophilic virus from Yellowstone National Park. Microbial Ecol. 48,561-566.
  • Newby, D.T., D.W. Reed, L.M. Petzke, A.L. Igoe, M.E. Delwiche, F.F. Roberto, J.P. McKinley, M.J. Whiticar, and F.S. Colwell. 2004. Diversity of methanotroph communities in a basalt aquifer proximal to a TCE plume. FEMS Microbiol. Ecol. 48, 333-344.
  • Macbeth, T.W., D.E. Cummings, S. Spring, L.M. Petzke, and K.S. Sorenson Jr. 2004. Molecular Characterization of a Dechlorinating Community Resulting from in-situ Biostimulation in a Trichloroethene-Contaminated Deep, Fractured Basalt Aquifer and Comparison to a Derivative Laboratory Culture. Appl. Environ. Microbiology. 70(12):7329-7341.
  • Hartzell, P., and D. Reed. The Genus Archaeoglobus. In M. Dworkin et al., eds., The Prokaryotes: An Evolving Electronic Resource for the Microbiological Community, 3rd edition, release 3.13, May 12, 2003, Springer-Verlag, New York.
  • 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.
  • Johnson, D.B., D.F. Bruhn, and F. F. Roberto, 2003. Survival of acidophilic bacteria under conditions of substrate depletion. International Biohydrometallurgy Symposium, Athens, Greece, Sep. 2003.
  • Johnson, D.B., N. Okibe, and F.F. Roberto, 2003. Physiological and phylogenetic characteristics of moderately thermophilic and acidophilic bacteria isolated from Yellowstone National Park. Arch. Microbiol. 180, 60-68.
  • Newby, D.T., T. L. Hadfield, and F.F. Roberto, 2003. Real-time PCR Detection of Brucella abortus: a Comparative Study of SYBR Green I, 5’-exonuclease, and Hybridization Probe Assays. Appl. Environ. Microbiol 69(8), 4753-4759.
  • Roberto, F.F., 2003. Nucleotide sequence of a small cryptic plasmid from Acidithiobacillus ferrooxidans strain A-6.” Hydrometallurgy 71(1-2), 133-137.
  • Marchbank, A.R., E. Kirby, and F.F. Roberto, 2003. The application of biologically mediated leaching methods – A comprehensive review. CIM Bulletin 96, 143-147.
  • Ho, N.W.Y. and F.F. Roberto, 2003. Microbial catalysis and metabolic engineering. Appl. Biochem. Biotechnol. 105, 245-246.
  • Cummings, D.E., O.L. Snoeyenbos-West, D.T. Newby, A.M. Niggemyer, D.R. Lovley, L.A. Achenbach, and R.F. Rosenzweig. 2003. Diversity of Geobacteraceae Species Inhabiting Metal-Polluted Freshwater Lake Sediments Ascertained by 16S rDNA Analyses. Microbial Ecol. 46:257-269.
  • Mikucki, J. A., Yitai Liu, Mark Delwiche, Frederick S. Colwell, and David R. Boone. 2003. Isolation of a Methanogen from Deep Marine Sediments that Contain Methane Hydrates, and Description of Methanoculleus submarinus sp. nov. App. and Env. Micro. 69(6):3311-3316.
  • Thompson, D.N., T.P. Houghton, J.A. Lacey, P.G. Shaw, and J.R. Hess. 2003. Preliminary investigation of fungal bioprocessing of wheat straw for straw-thermoplastic composites production. Appl. Biochem. Biotechnol. 105-108:423-436.
  • Thompson, D.N., J.A. Lacey, and P.G. Shaw. 2003. Post-harvest processing methods for reduction of silica and alkali metals in wheat straw. Appl. Biochem. Biotechnol. 105-108:205-218.
  • Hess, J.R., D.N. Thompson, R.L. Hoskinson, P.G. Shaw, and D.R. Grant. 2003. Physical separation of straw stem components to reduce silica. Appl. Biochem. Biotechnol. 105-108:43-51.
  • Sublette, K.L., G.E. Jenneman, and G.A. Bala. 2003. A Novel Approach to Hydrogen Sulfide Removal From Natural Gas. SPE/EPA/DOE Exploration and Production Environmental Conference. SPE Manuscript 81203
  • Aiken, A. M., B. M. Peyton, W. A. Apel, and J.N. Petersen. 2003. Heavy metal induced inhibition of Aspergillus niger nitrate reductase: applications for rapid contaminant detection in aqueous samples. Analytica Chimica Acta 480:131-142.
  • Lee, B. D., W. A. Apel, and M. R. Walton. 2003. Primary evidence for the use of gas phase bioreactors containing cyanobacteria for the conversion of carbon dioxide in flue gas. Paper #69602. In the Proceedings of the Air and Waste Management Association's 96th Annual Conference and Exhibition.
  • Peyton, B. M., M. R. Mormile, V. Alva, C. Oie, F. Roberto, W. A. Apel, and A. Oren. 2003. "Biotransformation of toxic organic and inorganic contaminants by halophilic bacteria", (In) Halophilic Microorganisms, Ventosa, A. (Ed.), Springer-Verlag, Berlin, Germany.
  • Thompson, V.S., K.D. Schaller, and W.A. Apel. 2003. Purification and characterization of a novel thermo-alkali-stable catalase from Thermus brockianus. Biotechnol. Prog. 19:1292-1299.
  • 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.
  • P. A. Pryfogle, G. L. Mines, T. L. Sperry, and R. G. Allred. 2002. Investigation of an Electrochemical Monitor for Tracking Biofilm Development at the Bonnett Geothermal Plant, Cove Fort, Utah. Transactions of the Geothermal Resources Council. v. 26. pp. 745-748.
  • Stanescue, M.A., D.M. Ginosar, G.A. Bala and R.P. Anderson. 2002. Biocatalytic Treatment of Organosulfur Compounds in Emulsions in Supercritical Fluids. Fuel Chemistry Preprints, ACS, 47(2), 524-526.
  • Bala, G.A., S.L. Fox, D.N. Thompson. 2002. Microbiological Production of Surfactant From Agricultural Process Residuals for IOR Application. Proceedings of the 13th Annual DOE/SPE Symposium on Improved Oil Recovery. SPE 75239.
  • Noah, K.S., , S.L. Fox, D.F. Bruhn, D.N. Thompson, and G.A. Bala. 2002. Development of Continuous Surfactin Production from Potato Process Effluent by Bacillus subtilis in an Airlift Reactor. Applied Biochemistry and Biotechnology. Vols. 98-100, pp. 803-813.
  • Watwood, M.E., Keener, W.K., and Smith, W.A. 2002. Characterization of microbial isolates from the Idaho National Engineering and Environmental Laboratory Test Area North aquifer: Identifying potential enzymatic pathways for toluene oxidation. In Link, P.K., and Mink, L.L., eds., Geology, Hydrogeology, and Environmental Remediation: Idaho National Engineering and Environmental Laboratory, Eastern Snake River Plain, Idaho: Boulder, Colorado, Geological Society of America Special Paper 353, p. 279-285.
  • Lee, B. D., Walton, M. R. and Meigio, J. L. 2002. Interaction of Microbes and Uranium during Enrichment for TCE Reductive Dechlorination. In Anaerobic Degradation of Chlorinated Solvents. Mager, V. S., Fennell, D. E., Morse, J. J., Alleman, B. C. and Leeson A. (Eds.). Battelle Press, Columbus, OH. pp. 77-85.
  • Sani, R.K., B. M. Peyton, W. A. Smith, W. A. Apel, and J. N. Petersen. 2002. Dissimilatory reduction of Cr(VI), Fe(III), and U(VI) by Cellulomonas isolates. Appl. Microbiol. Biotechnol. 60:192-199.
  • Smith, W. A., W. A. Apel, J. N. Petersen, and B. M. Peyton. 2002. Effect of carbon and energy source on bacterial chromate reduction. Bioremediation Journal. 6(1):1-11.
  • Viamajala, S., B. M. Peyton, W. A. Apel, and J. N. Petersen. 2002. Chromate reduction in Shewanella oneidensis MR-1 is an inducible process associated with anaerobic growth. Biotechnol. Prog. 18:290-295.
  • Viamajala, S., B. M. Peyton, W. A. Apel, and J. N. Petersen. 2002. Chromate/nitrite interactions in Shewanella oneidensis MR-1: Evidence for multiple Cr(VI) reduction mechanisms dependent on physiological growth conditions. Biotechnol. Bioeng. 78:770-778.
  • Apel, W. A., J. N. Petersen, and B. M. Peyton and W. A. Smith. 2002. Remediation of environmental hexavalent chromium contamination using chromate-reducing bacterial consortia. Paper #41646. In the Proceedings of the Air and Waste Management Association's 95th Annual Conference and Exhibition.
  • Lacey, J. A., B. D. Lee, and W. A. Apel. 2002. PCR-DGGE as a method to monitor microbial populations in nitric oxide biofilters. Paper #43271. In the Proceedings of the Air and Waste Management Association's 95th Annual Conference and Exhibition.
  • Flanagan, W. P., W. A. Apel, J. M. Barnes, and B. D. Lee. 2002. Development of gas phase bioreactors for the removal of nitrogen oxides from synthetic flue gas streams. FUEL 81:1953-1961.
  • Noah, K.S., S.L. Fox, D.F. Bruhn, D.N. Thompson, and G.A. Bala. 2002. Continuous production and separation of surfactin from potato process effluent by Bacillus subtilis 21332. Appl. Biochem. Biotechnol. 98-100:803-813.
  • 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. App. and Env. Micro. 68(8):3759-3770.
  • Roberto, F.F., J.M. Barnes and D.F. Bruhn. 2002. Evaluation of a GFP reporter gene construct for environmental arsenic detection. Talanta 58(1), 181-188.
  • Radtke, C.W. D.M. Smith, G. S. Owen, and F.F. Roberto. 2002. Field demonstration of acetone pretreatment and composting of particulate-TNT-contaminated soil. Bioremediation J. 6(2), 191-204.
  • Radtke, C.W., D. Gianotto and F.F. Roberto. 2002. Estimating contamination at a former explosives testing area. Chemosphere 46(1), 3-9.
  • Roberto, F.F. 2002. Bioleaching of Minerals. In:The Encyclopedia of Environmental Microbiology, G. Bitton and R.S. Burlage (Editors), J. Wiley and Sons, Inc. , New York, pp 641-650.
  • Knight, J., C. Cheeseman, and R. Rogers. 2002. Microbial influenced degradation of solidified waste binder. Waste Manage. 22:187-193.
  • 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.
  • Idachaba, M., N. Egiebor, K. Nyavor, and R.D. Rogers. 2001. A refinement of the biofilm formation method for waste forms stability evaluation. J. Hazard. Mater. 84: 95-106.
  • Idachaba, MA, K. Nyavor, N.O. Egiebor, and R.D.Rogers. 2001. Microbial stability evaluation of waste containment materials using a biofilm formation approach. Environ. Eng. Sci. 18 (1): 25-41.
  • Miller, A.R., W.K. Keener, M.E. Watwood and F.F. Roberto. 2001. A rapid fluorescence-based assay for detecting soluble methane monooxygenase. Appl. Microbiol. Biotechnol. 58, 183-188.
  • Lehman, R.M, F.F. Roberto, D. Earley, D.F. Bruhn, S.E. Brink, S. P. O'Connell, M.E. Delwiche and F.S. Colwell. 2001. Attached and unattached microbial communities in closely-paired groundwater and core samples from an acidic, crystalline rock aquifer. Appl. Environ. Microbiol. 67(5):2095-2106.
  • Johnson, D.B., D.A. Body, T.A.M. Bridge, D.F. Bruhn, and F.F. Roberto. 2001. Biodiversity of acidophilic moderate thermophiles isolated from two sites in Yellowstone National Park and their roles in the dissimilatory oxido-reduction of iron. In: Thermophiles: Biodiversity, Ecology and Evolution. A.L. Reysenbach, M. Voytek, and R. Mancinelli, (Editors), Plenum Publishing Co., New York, pp. 23-39.
  • Keener W.K., M.E. Watwood, K.D. Schaller, M.R. Walton, J.K. Partin, W.A. Smith, and S.R. Clingenpeel. 2001. Use of Selective Inhibitors and Chromogenic Substrates to Differentiate Bacteria Based on Toluene Oxygenase Activity. Journal of Microbiological Methods. 46:171-185.
  • Lehman RM, Roberto FF, Earley D, Bruhn DF, Brink SF, O’Connell SP, Delwiche ME and Colwell FS. 2001. Attached and unattached microbial communities in closely-paired groundwater and core samples from an acidic, crystalline rock aquifer. Appl. Environ. Microbiol. 67(5): 2095-2106.
  • Thompson, D.N. and M.A. Hamilton. 2001. Production of bacterial cellulose from alternate feedstocks. Appl. Biochem. Biotechnol. 91-93:503-513.
  • Lehman, R.M., F.S. Colwell, and G.A. Bala. 2001. Attached and Unattached Microbial Communities in a Simulated Basalt Aquifer Under Fracture- and Porous –Flow Conditions. Applied and Environmental Microbiology. 67(6):2799 – 2809.
  • Thompson, D.N., S.L. Fox, and G.A. Bala. 2001. The Effect of Pretreatment on Surfactin Production from Potato Process Effluent by Bacillus subtilis. Applied Biochemistry and Biotechnology. Vol. 91-93, pp. 487-501.
  • McComas, C., K. Sublette, G. Jenneman, and G. Bala. 2001. Characterization of a Novel Biocatalyst System for Sulfide Oxidation. Biotechnology Progress. Vol. 17 No. 3, pp. 139-446 (Web Release Date: March 29, 2001) .
  • Lacey, J. A., Lee, B. D. and Apel, W. A., 2001. Comparison of NOx removal efficiencies in compost based biofilters using four different compost sources. In the Proceedings of the Air and Waste Management Association's 94th Annual Conference and Exhibition. June 24-28, 2001.
  • Lee, B.D., W. A. Apel, and W. A. Smith. 2001. Oxygen effects on thermophilic microbial populations in biofilters treating nitric oxide containing off-gas streams. Environ. Prog. 20(3):157-166.
  • P. A. Pryfogle. 2000. Evaluation of Biological Measurement Methods Used at the Geysers. Transactions of the Geothermal Resources Council. v. 24, pp. 311-315.
  • Fox, S.L., and G.A. Bala. 2000. Production of Surfactant from Bacillus subtilis ATCC 21332 using Potato Starch. Bioresource Technology. 75:235-240.
  • Thompson, D.N., S.L. Fox, and G.A. Bala. 2000. Biosurfactants from Potato Process Effluents. Applied Biochemistry and Biotechnology. Vol. 84-86, pp. 917-930.
  • Schmieman, E. A., D. R. Yonge, J. N. Petersen, M. A. Rege, and W. A. Apel. 2000. Kinetics of chromium reduction by mixed cultures during growth phase. Water Environ. Research 72(5):523-530.
  • Lee, B. D., K. D. Schaller, M. E. Watwood and W. A. Apel. 2000. Transition metal catalyst-assisted reductive dechlorination of perchloroethylene by anaerobic aquifer enrichment. Bioremed. J. 4(2):97-110.
  • Lee, B.D., W. P. Flanagan, J.M. Barnes, K.B. Barrett, L.B. Zaccardi, and W. A. Apel. 2000. Comparison of three bed packings for biological removal of nitric oxide from gas streams. Proc. USC-TRG Conference on Biofiltration. Univ. S. California. pp. 211-219.
  • Cook, L. L., Hubler, T. B., Apel, W. A., Noah, K. S., and Gostomski, P. A. 2000. Biofiltration of Asphalt Emissions: Full-scale Operation Treating Odorous Gases from Asphalt Product Storage and Loading Facilities. Paper #816, Proceedings of the 93rd Annual Meeting of the Air and Waste Management Association. Salt Lake City, UT
  • Thompson, D.N., R.L. Sayer, and K.S. Noah. 2000. Sawdust-supported passive bioremediation of western United States acid rock drainage in engineered wetland systems. Miner. Metall. Process. J. 17(2):96-104.
  • Radtke, C.W., R.M. Lehman, and F.F. Roberto, 2000. Increased biotransformation efficiency of chunk-TNT-contaminated soil using acetone pretreatments. Bioremediation J. 4(1), 57-69.
  • Idachaba MA, Nyavor K, Egiebor NO, Rogers, RD. 2000. Development of a biofilm formation method for waste forms stability evaluation. J. Hazard. Mater. 77 (1-3): 133-147.
  • Bar-Yosef, B., R.D. Rogers, J.H. Wolfram, E. Richman. 1999. Pseudomonas cepacia mediated rock phosphate solubilization in kaolinite and montmorillonite suspensions. Soil Sci. Soc. Am J. 63:1703-1708.
  • Rogers, R.D., M.E. McIlwain, J.H. Wolfram, L.O. Nelson. 1999. Industrialization of phosphate bioprocessing. IN Beneficiation Of Phosphates: Advances In Research And Practice. P. Zhang, H. El-Shall, R. Wiegel (eds). Soc. Mining, Metallurgy, and Exploration, Inc. Littleton CO.
  • Hamilton, MA, Rogers RD, Nelson LO. 1999. Biodecontamination: cost-benefit analysis of a novel approach for decontamination of massive concrete structures. Nucl Energ-J Br Nucl 38 (6): 351-355.
  • Rogers, RD. 1999. Effects of microbially influenced degradation on massive geothermal field concrete structures. Corros. Rev. 17 (3-4): 155-166 1999
  • Bruhn, D.F., C.R. Breckenridge, M.N. Tsang, C.S. Watkins, W.E. Windes, F.F. Roberto, R.N. Wright, P.J. Pinhero, and R.F. Brey. 1999. Gamma and UV irradiation of microbes from spent nuclear fuel storage pool environments. In:Global '99, American Nuclear Society.
  • Yahya, A., Roberto, F.F., and D.B. Johnson. 1999. Novel mineral-oxidizing bacteria from Montserrat (W.I.): physiological and phylogenetic characteristics. In:Biohydrometallurgy and the environment toward the mining of the 21st century, Part A, R.Amils and A. Ballester (Editors), Elsevier Science B.V., pp. 729-739.
  • Colwell, F.S., M.E. Delwiche, D. Blackwelder, M.S. Wilson, R.M. Lehman and T. Uchida. 1999. Microbial communities from core intervals, JAPEX/JNOC/GSC Mallik 2L-38 gas hydrate research well. In: SR Dallimore, T Uchida, and TS Collett. Scientific Results From JAPEX/JNOC/GSC Mallik 2L-38 Gas Hydrate Research Well, MacKenzie Delta, Northwest Territories, Canada. GSC Bulletin 544; 189-195
  • Bruhn, D.F., D.N. Thompson, and K.S. Noah. 1999. Microbial ecology assessment of a mixed oxide/sulfide dump leach operation. In: Process Metallurgy 9A. Biohydrometallurgy and the Environment Toward the Mining of the 21st Century, Part A: Bioleaching, Microbiology. R. Amils and A. Ballester (eds.). Elsevier, Amsterdam. pp. 799-808.
  • Kastner, J.R., D.N. Thompson, and R.S. Cherry. 1999. Water soluble polymer for increasing the biodegradation of sparingly soluble vapors. Enzym. Microb. Technol. 24(1/2):104-110.
  • Rege, M.A., D. R. Yonge, D. P. Mendoza, J. N. Petersen, Y. Bared-Samuel, D. L. Johnstone, W. A. Apel, and J. M. Barnes. 1999. Selenium Reduction by a Denitrifying Consortium. Biotechnol. Bioeng. 62(4):479-484.
  • Lee, B. D., W. A. Apel, and W. Smith. 1999. Effect of oxygen on thermophilic dentrifying populations in biofilters treating nitric oxide containing off-gas streams. Proceedings of the 91st Annual Meeting and Exhibition of the Air and Waste Management Association. Paper 99-322. St. Louis, MO . June 1999
  • Andrews, G. and W. A. Apel. 1999. Bioreactors, gas treatment. (In) Encyclopedia of Bioprocess Technology: Fermentation, Biocatalysis, and Bioseparation. Eds. M. C. Flickinger and S. W. Drew. John Wiley & Sons, Inc., New York, NY. pp. 381-394.
  • Blake, C., L. L. Cook, W. A. Apel, and P. A. Gostomski. 1999. Biofiltration controls odors from asphalt processing plant. Oil Gas J. 97(30):69-72.
  • Lee, B. D., W. A. Apel, and A. R. Miller. 1999. Removal of low concentration of carbon tetrachloride in compost-based biofilters operated under methanogenic conditions. J. Air Waste Manage. Assoc. 49:1068-1074.
  • Cook, L. L., P. A. Gostomski, and W. A. Apel. 1999. Biofiltration of asphalt emissions: full-scale operation treating off-gases from polymer-modified asphalt product. Environ. Progr. 18(3):178-187.
  • Schmieman, E. A., D. R. Yonge, M. A. Rege, J. N. Petersen, C. E. Turick, D. L. Johnstone, and W. A. Apel. 1998. Comparative kinetics of bacterial reduction of chromium. J. Environ. Eng. 124:449-455.
  • Smith, William A. and Watwood, Mary E. 1998. Poster—Impacts of polyacrylamide treatment on microbial ecology and nitrogen cycling in agricultural soils. Eighth International Symposium on Microbial Ecology Halifax, Nova Scotia.
  • Smith, William A. and Watwood, Mary E. 1998. Poster—Impacts of polyacrylamide treatment on the community level physiological profiles in agricultural soils. Annual Meeting of the Intermountain Branch of the American Society for Microbiology, Idaho Falls, Idaho.
  • Smith, William A. and Watwood, Mary E. April, 1998. Poster—Impacts of polyacrylamide (PAM) treatment on nitrogen mineralization and nitrification in agricultural soils. 40th Annual Meeting of the Idaho Academy of Science, Boise, Idaho.
  • Keener, W. K., M. E. Watwood, and W. A. Apel. 1998. Activity-dependent fluorescent labeling of bacteria that degrade toluene via toluene 2,3-dioxygenase. Appl. Microbiol. Biotechnol. 49:455-462.
  • Lee, B. D. and W. A. Apel. 1998. Evaluation of NOx removal using compost based biofilters operated under denitrifying conditions. Proc. of 1998 Conf. on Biofiltration. pp. 51-59. USC, Los Angeles, CA.
  • Turick, C. E., C. Graves, and W. A. Apel. 1998. Bioremediation potential of Cr(VI)-contaminated soil using indigenous microorganisms. Bioremed. J. 2(1):1-6.
  • Lee, B. D., Apel, W. A., Walton, M. R., Miller, A. R., and Gabrylczyk, L. 1998. Comparison of Anaerobic Biofilters and Anaerobic Biotrickling Filters for Carbon Tetrachloride Removal from Synthetic Off-Gas Streams. Proceedings of the 91st Annual Meeting and Exhibition of the Air and Waste Management Association. Paper 98-MP20A.07. San Diego, CA. June 1998
  • Lee, B. D. and Apel, W. A. 1998. Biofilter Development for Removal of Environmentally Significant Contaminants from Off-Gas Streams. Proceedings of the Chemical Engineering Exposition and Conference, Volume IV, Advances in Reactions and Separations. Houston, TX. June 3-4, 1998
  • Thompson, D.N., B.R. Hames, C.A. Reddy, and H.E. Grethlein. 1998. In vitro degradation of insoluble lignin in aqueous media by lignin peroxidase and manganese peroxidase. Appl. Biochem. Biotechnol. 70-72:967-982.
  • Thompson, D.N., B.R. Hames, C.A. Reddy, and H.E. Grethlein. 1998. In vitro degradation of natural insoluble lignin in aqueous media by the extracellular peroxidases of Phanerochaete chrysosporium. Biotechnol. Bioeng. 57(6):704-717.

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