WRHSRC Final Report for the period 2001-2007

List of Publications: Journal Articles and Book Chapters

Achong, G. R., A. Rodriguez, A. M. Spormann (2001). Role of benzylsuccinate synthase in anaerobic toluene and m-xylene mineralization in Azoarcus sp. strain T: Transcriptional organization of the structural genes and analysis of a bssA mutant.” J. Bacteriol. 183 (23), 6763-6770.

Arp, D. J., C.M. Yeager and M. R. Hyman (2001). Molecular and Cellular Fundamentals of Aerobic Cometabolism of Trichloroethylene. Biodegradation 12: 81-103.

Azizian, M., S. Behrens, A. Sabalowsky, M. Dolan, A. Spormann, L. Semprini. Continuous-Flow Column Study of Reductive Dehalogenation of PCE upon Bioaugmenation with the Evanite Enrichment Culture. (under review 2007).

Benekos, I. D., O.A. Cirpka, and P.K. Kitanidis (2006). Experimental Determination of Transverse Dispersivity in a Helix and a Cochlea. Water Resources Research 42, W07406, doi:10.1029/2005WR004712.

Cantrell, K. and J. D. Ingle, Jr. (2003). The SLIM Spectrometer. Anal. Chem., 75, 27-35.

Cheng, H. and M. Reinhard (2006). Quantifying the Volume of Hydrophobic Micropores from Trichloroethylene Desorption. Environmental Science and Technology, 40 (11), 3595-3602.

Cheng, H. and M. Reinhard (2006). Sorption of Trichloroethylene in Hydrophobic Micropores of Dealuminated Y Zeolites and Natural Minerals, Environmental Science and Technology, 40 (24), 7694-7701.

Cheng, H. and M. Reinhard (2007). Sorption and Inhibited Dehydrohalogenation of 2,2-Dichloropropane in Micropores of Dealuminated Y Zeolites. Environmental Science and Technology, 41 (6), 1934-1941.

Chu, M., Kitanidis, P. K. and McCarty, P. L. Effects of biomass accumulation on microbially enhanced dissolution of a PCE pool: a numerical simulation. Journal of Contaminant Hydrology, 65, (1-2), August 2003, 79-100.

Cunningham, J.A., J.J. Deitsch, J.A. Smith, J and M. Reinhard (2005). Quantification of Contaminant Sorption-Desorption Time-Scales from Batch Experiments. Environmental Toxicology and Chemistry, 24 (9), 2160-2166. 

Cupples, A. M., Spormann, A. M., and McCarty, P. L. (2004). Comparative Evaluation of Chloroethene Dechlorination to Ethene by Dehalococcoides-like Microorganisms. Environmental Science & Technology, 38, 4768-4774.

Cupples, A. M., Spormann, A. M., and McCarty, P. L. (2003). Growth of a Dehalococcoides-like Microorganism on Vinyl Chloride and cis-Dichloroethene as Electron Acceptors as Determined by Competitive PCR. Applied and Environmental Microbiology, 69: 953-959.

Davie, Matthew G., Cheng, Hefa, Hopkins, Gary D., LeBron, Carmen A., and Reinhard, Martin (2008). Implementing Heterogeneous Catalytic Dechlorination Technology for Remediating TCE-Contaminated Groundwater. Environ. Sci. Technol., 2008, 42 (23), 8908-8915.

Doughty D.M., Sayavedra-Soto L.A., Arp D.J., and Bottomley P.J. (2005).  Effects of dichloroethene isomers on the induction and activity of butane monooxygenase in the alkane-oxidizing bacterium, Pseudomonas butanovora. Applied and Environmental Microbiology, 71(10): 6054-6059.

Doughty, D.M., L.A., Sayavedra-Soto, D.J. Arp and P.J. Bottomley (2006). Product repression of butane monooxygenase expression in Pseudomonas butanova. J. Bacteriol. 188: 2586-2592

Doughty, D.M., L., Sayavedro-Soto, D.J. Arp, and P.J. Bottomley (2005). Effects of dichloroethene isomers on the induction and activity of butane monooxygenase in the alkane-oxidizing bacterium Pseudomonas butanovora. Applied and Environmental Microbiology, Oct; 71 (10):6054-9 .

Doughty, D. M., K. H. Halsey, L. A. Sayavedra-Soto, D. J. Arp, and P. J. Bottomley (2007). Alkane monooxygenase inactivation by propionate in Pseudomonas butanovora; physiological and biochemical implications. Microbiology, 153: 3722-3729.

Doughty, D.M., Sayavedra-Soto, L.A., D.J. Arp, and P.J. Bottomley (2007). Evidence for copper ions and redox involvement in regulation of butane monooxygenase in Pseudomonas butanovora. J. Bacteriol. (In review).

Dupin, H. J., Kitanidis, P., and McCarty, P. (2001). Simulations of Two Dimensional Modeling of Biomass Aggregate Growth in Network Models. Water Resources Research 37(12): 2981-2994.

Dupin, H. J., Kitanidis, P. and McCarty, P. L. (2001). Pore-Scale Modeling of Biological Clogging Due to Aggregate Expansion: A Material Mechanics Approach. Water Resources Research 37(12): 2965-2979.

Field, J. A., J. D. Istok, L. Semprini, P. Bennett, and T. E. Buscheck. (2005). Trichlorofluoroethene: A Reactive Tracer for Evaluating the Effectiveness of In SituTrichloroethene Remediation. Ground Water Monitoring Remediation Vol 25(2):68-77.

Fienen, M.N., J. Luo, and P.K. Kitanidis, (2005). Semi-Analytical Homogeneous Anisotropic Capture Zone Delineation. Journal of Hydrology, 312(1-4): 39-50. doi:10.1016/j.jhydrol.2005.02.008.

Fienen, M.N., J. Luo, P. K. Kitanidis (2006). A Bayesian Geostatistical Transfer Function Approach to Tracer Test Analysis. Water Resources Research, 42, doi:10.1029/2005WR004576.

Frascari, D., Y. Kim, et al. (2003). A Kinetic Study of Aerobic Propane Uptake and Cometabolic Degradation of Chloroform, cis-Dichloroethylene and Trichloroethylene in Microcosms with Groundwater and Aquifer Solids. Water, Air, & Soil Pollution: Focus Vol. 3 (3) 285-298.

Gandhi, R. K., Hopkins, G. D., Goltz, M. N., Gorelick, S. M., and McCarty, P. L. (2002). Full-Scale Demonstration of In Situ Cometabolic Biodegradation of Trichloroethylene in Groundwater, 1: Dynamics of a Recirculating Well System. Water Resources Research, 38(4), 10.1-10.16

Gandhi, R. K., Hopkins, G. D., Goltz, M. N., Gorelick, S. M., and McCarty, P. L. (2002). Full-Scale Demonstration of In Situ Cometabolic Biodegradation of Trichloroethylene in Groundwater, 2: Comprehensive Analysis of Field Data Using Reactive Transport Modeling. Water Resources Research, 38(4), 11.1 - 11.19.

Goltz, M.N. and K.J. Williamson (2002). Transfer and Commercialisation of Contaminated Groundwater Remediation Technologies. International Journal of Technology Transfer and Commercialisation, 1(4):329-346.

Halsey K.H., Sayavedra-Soto L.A., Bottomley P.J., Arp D.J. (2005). Trichloroethylene degradation by butane-oxidizing bacteria causes a spectrum of toxic effects. Applied Microbiology and Biotechnology, 68(6): 794-801.  

Halsey, K.H., L.A., Sayavedra-Soto, Bottomley, P.J., and D.J. Arp (2006). Site-directed amino acid substitutions in the hydroxylase α subunit of butane monooxygenase from Pseudomonas butanovora: implications for substrates knocking at the gate. J. Bacteriol. 188: 4962-4969.

Halsey, K.H., D.M. Doughty, L.A. Sayavedra-Soto, P.J. Bottomley, and D.J. Arp (2007). Evidence for modified mechanisms of chloroethene oxidation in Pseudomonas butanovora mutants containing single amino acid substitutions in the hydroxylase α-subunit of butane monooxygenase. J. Bacteriol. 189: 5068-5074.

Johnson H. A., D. A. Pelletier, and A. M. Spormann (2001). Isolation and Purification of Anaerobic Ethylbenzene Dehydrogenase, a Novel Mo-Fe-S Enzyme. J. Bacteriol 183: 4536-4542.

Jones, B. D. and J.D. Ingle, Jr. Evaluation of Immobilized Redox Indicators as Reversible, In Situ Redox Sensors for Determining Fe(III)-Reducing Conditions in Environmental Samples. Talanta 55(4): 699-714 (2001).

Jones, B.D., and J.D. Ingle, Jr. (2005). Evaluation of redox indicators for determining sulfate-reducing and dechlorinating conditions, Water Research, 39, 4343-4350.

Kim, Y., D. J. Arp, et al. (2002). A Combined Method for Determining Inhibition Type, Kinetic Parameters, and Inhibition Coefficients for Aerobic Cometabolism of 1,1,1-Trichloroethane by a Butane-grown Mixed Culture. Biotechnology and Bioengineering 77: 564-576.

Kim, Y. D. J. Arp, and L. Semprini (2002). Kinetic and Inhibition Studies for the Aerobic Cometabolism of 1,1,1-Trichloroethane, 1,1-Dichloroethylene, and 1,1-Dichloroethane by a Butane-grown Mixed Culture. Biotechnology and Bioengineering. 80:498-508.

Kim, Y. and L. Semprini. (2005). Cometabolic Transformation of cis-1,2-dichloroethylene and cis-1,2-dichloroethylene epoxide by a butane-grown mixed culture. Water Science & Technology, 52 (8), 125-131. 

Koch, Corey R., James D. Ingle, Vincent T. Remcho. Bonding Upchurch NanoPorts to PDMS. Lab on a Chip (submitted 2007).

Koch, Corey R., James D. Ingle, Vincent T. Remcho. Magnets for facile molding of via holes in PDMS. Lab on a Chip (submitted 2007). 

Lee, I., Bae, J., Yang , Y., McCarty , P. L. (2004). Simulated and Experimental Evaluation of Factors Affecting the Rate and Extent of Reductive Dehalogenation of Chloroethenes with Glucose. Journal of Contaminant Hydrology, 74, 313-331.

Luo, J., and Kitanidis, P. K. (2004). Fluid Residence Times Within a Recirculation Zone Created by and Extraction - Injection Well Pair. Journal of Hydrology, 295 (1-4), 149-162.

Luo, J., Cirpka, O.A., Kitanidis, P.K. (2006). Temporal-moment matching for truncated breakthrough curves for step or step-pulse injection. Adv. Water Resour. 29 (9), 1306-1313.

Luo, J., Wu, W-M., Fienen, M.N., Jardine, P.M., Mehlhorn, T.L., Watson, D.B., Cirpka, O.A., Criddle, C.S., Kitanidis, P.K. (2006). A nested-cell approach for in situ remediation. Ground Water, 44(2), 266-274.

McMurdie, P. J., S. F. Behrens, S. Holmes, and A. M. Spormann (2007). Unusual Codon Bias in Vinyl Chloride Reductase Genes of Dehalococcoides Species. Appl. Environ. Microbiol. 73:2744-2747.

Müller, J. A., B. M. Rosner, G. von Abendroth, G. Simon-Meshulam, P. L. McCarty, and A. M. Spormann (2004). Molecular Identification of the Catabolic Vinyl Chloride Reductase from Dehalococcoides sp. Strain VS and Its Environmental Distribution. Applied and Environmental Microbiology. 70(8):4880-4888.

Munakata, N., and M. Reinhard (2007). Palladium-catalyzed aqueous hydrodehalogenation in column reactors: Modeling of deactivation kinetics with sulfide and comparison of regenerants. Applied Catalysis B: Environmental 75, 1–10.

Niemet, M.R., and L. Semprini (2005). Column Studies of Anaerobic Carbon Tetrachloride Biotransformation with Hanford Aquifer Material. Ground Water Monitoring Remediation,25(3),82-92.

Pon, G., Hyman, M. R. and Semprini, L. (2003). Acetylene Inhibition of Trichloroethene and Vinyl Chloride Reductive Dechlorination. Environmental Science and Technology, Vol. 37(14): 3181-3188.

Pon, G. and L. Semprini. (2004). Anaerobic Reductive Dechlorination of 1-chloro-1-fluoroethene to Track the Transformation of Vinyl Chloride. Environ. Sci. Technol Vol.38 (24) 6803-6808.

Ruiz-Haas, P. and Ingle, J.D, Jr (2007) .Monitoring Redox Conditions with Flow-Based and Fiber Optic Sensors Based on Redox Indicators: Application to Reductive Dehalogenation in a Bioaugmented Soil Column. Geomicrobiology Journal, Vol. 24 (3/4) 365-378.

Ruiz-Haas, P. and Ingle, J. D, Jr. Monitoring of Redox State in a Dechlorinating Culture with Redox Indicators. Journal of Environmental Monitoring (submitted October 2007).

Sayavedra-Soto, L.A., D.M. Doughty, E. Kurth, P.J. Bottomley, and D.J. Arp (2005). Inducer and inducer –independent induction of butane oxidation in Pseudomonas butanovora. FEMS Microbiology Letters, 250:111-116. 

Schroth, M.H., J.D. Istok. (2005). Approximate solution for solute transport during spherical-flow push-pull tests, Ground Water, 43(2), 280-284.  

Semprini, L., M. E. Dolan, M. A. Mathias, G. D. Hopkins and P. L. McCarty (2007). Laboratory, field and modeling studies of bioaugmentation of butane-utilizing microorganisms for the in situ cometabolic treatment of 1,1-dichloroethene, 1,1-dichloroethane, and 1,1,1-trichloroethane. Advances in Water Resources, 30 1528-1546.

Semprini, L., M.E. Dolan, M.A. Mathias, G.D. Hopkins, and P. L. McCarty (2007). Bioaugmentation of Butane-Utilizing Microorganisms for the In-situ Cometabolic Treatment of 1,1-Dichloroethene, 1,1-Dichloroethane, and 1,1,1-Trichloroethane. European Journal of Soil Biology. 43 322-327. 

Skinner, K.M., A. Martinez-Prado, K.J. Williamson, and L.M. Ciuffetti. Pathway, Inhibition and Regulation of MTBE Oxidation by a Filamentous Fungus, a Graphium sp..Applied Microbiology and Biotechnology (in press 2007).

Skinner, K.M., L.M. Ciuffetti, and M.R. Hyman. Metabolism and Cometabolism of Cyclic Ethers by a Filamentous Fungus, a Graphium sp. Applied and Environmental Microbiology (manuscript under review 2007).

Sriwatanapongse, W., M. Reinhard, and C. A. Klug (2006). Reductive hydrodehalogenation of trichloroethylene by palladium-on-alumina catalyst: 13C-NMR study of adsorption. Langmuir, 22, 4158-4164.

Taylor, A.E., M. E. Dolan, P.J. Bottomley, and L. Semprini (2007). Utilization of Fluoroethene as a Surrogate for Aerobic Vinyl Chloride Degradation. Environ. Sci. Technol. 41: 6378-6383.

Yang, Y., and McCarty, P. L. (2002). Comparison of Donor Substrates for Biologically Enhanced Tetrachloroethene (PCE) DNAPL Dissolution. Environmental Science & Technology, 36(15), 3400-3404.

Yeager, C. M., P.J. Bottomley, and D.J. Arp (2001). Cytotoxicity associated with trichloroethylene oxidation in Burkholderia cepacia G4. Appl. Environ. Microbiol 67: 2107-2115.

Yeager, C. M., P. J. Bottomley, and D. J. Arp (2001). Requirement of DNA repair mechanisms for survival of Burkholderia cepacia G4 upon degradation of trichloroethylene. Appl. Environ. Microbiol 67: 5384-5391 

Yeager, C.M., P.J. Bottomley and D.J. Arp. Trichloroethylene degradation by toluene-oxidizing bacteria grown on non-aromatic substrates. Biodegradation 15: 19-28 (2004).

Yu, S., and L. Semprini (2002). Comparison of Trichloroethylene Reductive Dehalogenation by Microbial Communities Stimulated on Silicon-based Organic Compounds as Slow-release Anaerobic Substrates. Water Research 36(20): 4985-4996.

Yu, S; Semprini (2004) L. Kinetics and modeling of reductive dechlorination at high PCE and TCE concentrations. Biotechnol. Bioeng. 88 (4), 451-464.

Yu, S., M. E. Dolan, and L. Semprini (2005). Kinetics and Inhibition of Reductive Dechlorination of Chlorinated by Two Different Mixed Cultures. Environmental Science and Technology (1); 195-205.


Book Chapters

McCarty, P. L. and Ellis, D. E. (2002). Natural Attenuation. Innovative Approaches to the On-Site Assessment and Remediation of Contaminated Sites, eds. D. Reible and K. Demnerova, Kluwer Academic Publishers, Dordrecht, 141-181.

Munakata, N., M. Reinhard (2001). Palladium Catalysis for the Treatment of Waters Contaminated with Halogenated Hydrocarbons, Nonhalogenated Aromatics, Oxidized Carbon and Oxidized Nitrogen Species. Physicochemical Groundwater Remediation. J. A. S. a. S. E. Burns, Academic/Plenum Publisher, Dordrecht, The Netherlands: 45-71.