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The Subsurface Biosphere and Engineered Environmental Processes

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Related OSU Publications 2005-2008

Azizian, M. F., S. Behrens, A. Sabalowsky, M. E. Dolan, A. M. Spormann, and L. Semprini. 2008. Continuous-flow column study of reductive dehalogenation of PCE upon bioaugmentation with the Evanite enrichment culture. Journal of Contaminant Hydrology 100:11-21.

Azizian, M. F., J. D. Istok, and L. Semprini. 2005. Push-pull test evaluation of the in situ aerobic cometabolism of chlorinated ethenes by toluene-utilizing microorganisms. Water Science & Technology 52:35-40.

Azizian, M. F., J. D. Istok, and L. Semprini. 2007. Evaluation of the in-situ aerobic cometabolism of chlorinated ethenes by toluene-utilizing microorganisms using push-pull tests. Journal of Contaminant Hydrology 90:105-124.

Baldwin, B. R., A. D. Peacock, M. M. Park, D. M. Ogles, J. D. Istok, J. P. McKinley, C. T. Resch, and D. C. White. 2008. Multilevel Samplers as Microcosms to Assess Microbial Response to Biostimulation. Ground Water 46:295-304.

Behrens, S., M. F. Azizian, P. J. McMurdie, A. Sabalowsky, M. E. Dolan, L. Semprini, and A. M. Spormann. 2008. Monitoring Abundance and Expression of "Dehalococcoides" Species Chloroethene-Reductive Dehalogenases in a Tetrachloroethene-Dechlorinating Flow Column. Applied & Environmental Microbiology 74:5695-5703.

Chastanet, J., and B. D. Wood. 2008. Mass transfer process in a two-region medium. Water Resources Research 44:W05413.

Connon, S. A., A. Tovanabootr, M. E. Dolan, K. Vergin, S. J. Giovannoni, and L. Semprini. 2005. Bacterial community composition determined by culture-independent and -dependent methods during propane-stimulated bioremediation in trichloroethene-contaminated groundwater. Environmental microbiology 7:165-178.

Doughty, D. M., L. A. Sayavedra-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 71:6054-6059.

Dubbels, B. L., L. A. Sayavedra-Soto, and D. J. Arp. 2007. Butane monooxygenase of Pseudomonas butanovora: purification and biochemical characterization of a terminal-alkane hydroxylating diiron monooxygenase. Microbiology 153:1808-1816.

Eberly, J. O., and R. L. Ely. 2008. Thermotolerant hydrogenases: biological diversity, properties, and biotechnological applications. Critical Reviews in Microbiology 34:117-130.

Ennis, E., R. Reed, M. E. Dolan, L. Semprini, J. Istok, and J. Field. 2005. Reductive dechlorination of the vinyl chloride surrogate chlorofluoroethene in TCE-contaminated groundwater. Environmental science & technology 39:6777-6785.

Field, J. A., R. L. Reed, J. D. Istok, L. Semprini, P. Bennett, and T. E. Buscheck. 2005. Trichlorofluoroethene: A reactive tracer for evaluating reductive dechlorination in large-diameter permeable columns. Ground Water Monitoring and Remediation 25:68-77.

Gresham, T. L. T., P. P. Sheridan, M. E. Watwood, Y. Fujita, and F. S. Colwell. 2007. Design and validation of ureC-based primers for groundwater detection of urea-hydrolyzing bacteria. Geomicrobiology Journal 24:353-364.

Gu, B. H., H. Yan, P. Zhou, D. B. Watson, M. Park, and J. Istok. 2005. Natural humics impact uranium bioreduction and oxidation. Environmental science & technology 39:5268-5275.

Gvakharia, B. O., E. A. Permina, M. S. Gelfand, P. J. Bottomley, L. A. Sayavedra-Soto, and D. J. Arp. 2007. Global transcriptional response of Nitrosomonas europaea to chloroform and chloromethane. Applied and Environmental Microbiology 73:3440-3445.

Haggerty, R., A. Argerich, and E. Marti. 2008. Development of a "smart" tracer for the assessment of microbiological activity and sediment-water interaction in natural waters: The resazurin-resorufin system. Water Resources Research 40:W00D01.

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 alpha -subunit of butane monooxygenase. Journal of Bacteriology 189:5068-5074.

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

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

Harris, S. H., J. D. Istok, and J. M. Suflita. 2006. Changes in organic matter biodegradability influencing sulfate reduction in an aquifer contaminated by landfill leachate. Microbial Ecology 51:535-542.

Isaacson, C., T. K. G. Mohr, and J. A. Field. 2006. Quantitative determination of 1,4-dioxane and tetrahydrofuran in groundwater by solid phase extraction GC/MS/MS. Environmental science & technology 40:7305-7311.

Jin, S., P. H. Fallgren, J. M. Morris, and E. S. Edgar. 2008. Degradation of trichloroethene in water by electron supplementation. Chemical Engineering Journal 140:642-645.

Jones, B. D., and J. D. Ingle. 2005. Evaluation of redox indicators for determining sulfate-reducing and dechlorinating conditions. Water Research 39:4343-4354.

Kim, Y., J. Istok, and L. Semprini. 2008. Single-well, gas-sparging tests for evaluating the in situ aerobic cometabolism of cis-1,2-dichloroethene and trichloroethene. Chemosphere 71:1654-1664.

Kim, Y., J. D. Istok, and L. Semprini. 2006. Push-pull tests evaluating in situ aerobic cometabolism of ethylene, propylene, and cis-1,2-dichloroethylene. Journal of Contaminant Hydrology 82:165-181.

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 52:125-131.

Michalsen, M. M., B. A. Goodman, S. D. Kelly, K. M. Kemner, J. P. McKinley, J. W. Stucki, and J. D. Istok. 2006. Uranium and technetium bio-immobilization in intermediate-scale physical models of an in situ bio-barrier. Environmental science & technology 40:7048-7053.

Michalsen, M. M., A. D. Peacock, A. M. Spain, A. N. Smithgal, D. C. White, Y. Sanchez-Rosario, L. R. Krumholz, and J. D. Istok. 2007. Changes in microbial community composition and geochemistry during uranium and technetium bioimmobilization. Applied and Environmental Microbiology 73:5885-5896.

Nielsen, M. E., G. E. Reimers, and H. A. Stecher. 2007. Enhanced Power from Chambered Benthic Microbial Fuel Cells. Environmental science & technology 41:7895-7900.

Niemet, M. R., and L. Semprini. 2005. Column studies of anaerobic carbon tetrachloride biotransformation with Hanford Aquifer material. Ground Water Monitoring and Remediation 25:82-92.

Ochiai, N., E. L. Kraft, and J. S. Selker. 2006. Methods for colloid transport visualization in pore networks. Water Resources Research 42.

Park, S., and R. L. Ely. 2008. Candidate Stress Genes of Nitrosomonas europaea for Monitoring Inhibition of Nitrification by Heavy Metals. Applied and Environmental Microbiology 74:5475-5482.

Radniecki, T. S., M. E. Dolan, and L. Semprini. 2008. Physiological and transcriptional responses of Nitrosomonas europaea to toluene and benzene inhibition. Environmental Science and Technology 42:4093-4098.

Radniecki, T. S., and R. L. Ely. 2008. Zinc chloride inhibition of Nitrosococcus mobilis. Biotechnology and Bioengineering 99:1085-1095.

Radniecki, T. S., L. Semprini, and M. E. Dolan. 2009. Expression of merA, amoA and hao in continuously cultured Nitrosomonas europaea cells exposed to zinc chloride additions. Biotechnology and Bioengineering 102:546-553.

Ramirez, J. M., E. A. Thomann, E. C. Waymire, J. Chastanet, and B. D. Wood. 2008. A note on the theoretical foundations of particle tracking methods in heterogeneous porous media. Water Resources Research 44:W01501.

Reimers, C. E., P. Girguis, H. A. Stecher, L. M. Tender, N. Ryckelynck, and P. Whaling. 2006. Microbial fuel cell energy from an ocean cold seep. Geobiology 4:123-136.

Reimers, C. E., H. A. Stecher Iii, J. C. Westall, Y. Alleau, K. A. Howell, L. Soule, H. K. White, and P. R. Girguis. 2007. Substrate Degradation Kinetics, Microbial Diversity, and Current Efficiency of Microbial Fuel Cells Supplied with Marine Plankton. Applied & Environmental Microbiology 73:7029-7040.

Rockhold, M. L., R. R. Yarwood, M. R. Niemet, P. J. Bottomley, and J. S. Selker. 2005. Experimental observations and numerical modeling of coupled microbial and transport processes in variably saturated sand. Vadose Zone Journal 4:407-417.

Ruiz-Haas, P., and J. D. Ingle. 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 24:365-378.

Ryckelynck, N., H. A. Stecher, and C. E. Reimers. 2005. Understanding the anodic mechanism of a seafloor fuel cell: interactions between geochemistry and microbial activity. Biogeochemistry 76:113-139.

Saini, G., and B. D. Wood. 2008. Metabolic uncoupling of Shewanella oneidensis MR-1, under the influence of excess-substrate and 3, 3?, 4?, 5 tetrachlorosalicylanilide (TCS). Biotechnology and Bioengineering 99:1352-1360.

Sayavedra-Soto, L. A., W. N. Chang, T. K. Lin, C. L. Ho, and H. S. Liu. 2006. Alkane utilization by Rhodococcus strain NTU-1 alone and in its natural association with Bacillus fusiformis L-1 and Ochrobactrum sp. Biotechnology Progress 22:1368-1373.

Sayavedra-Soto, L. A., D. M. Doughty, E. G. Kurth, P. J. Bottomley, and D. J. Arp. 2005. Product and product-independent induction of butane oxidation in Pseudomonas butanovora. Fems Microbiology Letters 250:111-116.

Schroth, M. H., and J. D. Istok. 2006. Models to determine first-order rate coefficients from single-well push-pull tests. Ground Water 44:275-283.

Semprini, L., M. A. Dolan, G. D. Hopkins, and P. L. McCarty. 2008. Bioaugmentation with butane-utilizing microorganisms to promote in situ cometabolic treatment of 1,1,1-trichloroethane and 1,1-dichloroethene. Journal of Contaminant Hydrology.

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.

Semprini, L., M. E. Dolan, M. A. B. 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.

Skinner, K. M., A. Martinez-Prado, M. R. Hyman, K. J. Williamson, and L. M. Ciuffetti. 2008. Pathway, inhibition and regulation of methyl tertiary butyl ether oxidation in a filamentous fungus, Graphium sp. Applied Microbiology & Biotechnology 77:1359-1365.

Spain, A. M., A. D. Peacock, J. D. Istok, M. S. Elshahed, F. Z. Najar, B. A. Roe, D. C. White, and L. R. Krumholz. 2007. Identification and isolation of a Castellaniella species important during biostimulation of an acidic nitrate- and uranium-contaminated aquifer. Applied and Environmental Microbiology 73:4892-4904.

Taylor, A. E., M. E. Dolan, P. J. Bottomley, and L. Semprini. 2007. Utilization of fluoroethene as a surrogate for aerobic vinyl chloride transformation. Environmental science & technology 41:6378-6383.

Williamson, K., L. Semprini, G. Rorrer, and J. McGuire. 2006. Integration of chemical engineering, environmental engineering, and bioengineering to facilitate research and education in nanotechnology, biotechnology, and sustainability. Water Environment Research 78:555-556.

Wood, B. D. 2007. Inertial effects in dispersion in porous media. Water Resources Research 43.

Wood, B. D., and R. M. Ford. 2007. Biological processes in porous media: from the pore scale to the field. Advances in Water Resources 30:1387-1391.

Wood, B. D., K. Radakovich, and F. Golfier. 2007. Effective reaction at a fluid-solid interface: Applications to biotransformation in porous media. Advances in Water Resources 30:1630-1647.

Wymore, R. A. 2007. Field evidence for intrinsic aerobic chlorinated ethene cometabolism by methanotrophs expressing soluble methane monooxygenase. Bioremediation Journal 11:125-139.

Yarwood, R. R., M. L. Rockhold, M. R. Niemet, J. S. Selker, and P. J. Bottomley. 2006. Impact of microbial growth on water flow and solute transport in unsaturated porous media. Water Resources Research 42.

Yu, S., M. E. Dolan, and L. Semprini. 2005. Kinetics and inhibition of reductive dechlorination of chlorinated ethylenes by two different mixed cultures. Environmental science & technology 39:195-205.

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