OSU Publications from 2005-2007 Related to the Subsurface Biosphere

The following publications were identified through searches of the Web of Science, Toxline, Environmental Sciences and Pollution Management, Aquatic Sciences and Fisheries Abstracts, and Google Scholar; or were submitted by the author. At least one author on each publication is affiliated with Oregon State University. If you have publications to add to this list or see an error, please email sbi@oregonstate.edu .

This list was last updated October 1, 2007.

Publications from 2007

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.

Cliff, J. B., P. J. Bottomley, D. J. Gaspar, and D. D. Myrold. 2007. Nitrogen mineralization and assimilation at millimeter scales. Soil Biology & Biochemistry 39:823-826.

Crow, S. E., C. W. Swanston, K. Lajtha, J. R. Brooks, and H. Keirstead. 2007. Density fractionation of forest soils: methodological questions and interpretation of incubation results and turnover time in an ecosystem context. Biogeochemistry 85:69-90.

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.

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.

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. http://aem.asm.org/cgi/content/abstract/73/10/3440

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.

Hobbie, E. A., P. T. Rygiewicz, M. G. Johnscin, and A. R. Moldenke. 2007. C-13 and N-15 in microarthropods reveal little response of Douglas-fir ecosystems to climate change. Global Change Biology 13:1386-1397.

Hogberg, M. N., P. Hogberg, and D. D. Myrold. 2007. Is microbial community composition in boreal forest soils determined by pH, C-to-N ratio, the trees, or all three? Oecologia 150:590-601.

Istok, J. D., M. M. Park, A. D. Peacock, M. Oostrom, and T. Wietsma. 2007. An experimental investigation of nitrogen gas produced during denitrification. Ground Water 45:461-467.

Kleber, M., P. Sollins, and R. Sutton. 2007. A conceptual model of organo-mineral interactions in soils: self-assembly of organic molecular fragments into zonal structures on mineral surfaces. Biogeochemistry 85:9-24.

Medeiros, P. M., and B. R. Simoneit. 2007. Gas chromatography coupled to mass spectrometry for analyses of organic compounds and biomarkers as tracers for geological, environmental, and forensic research. Journal of Separation Science 30:1516.

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.

Myrold, D. D., and N. R. Posavatz. 2007. Potential importance of bacteria and fungi in nitrate assimilation in soil. Soil Biology & Biochemistry 39:1737-1743.

Redden, G., and F. S. Colwell. 2007. ISSM-ISEB 2005: Progress in understanding and predicting subsurface microbiology and biogeochemical processes. Geomicrobiology Journal 24:135-138.

Rillig, M. C., B. A. Caldwell, H. A. B. Wosten, and P. Sollins. 2007. Role of proteins in soil carbon and nitrogen storage: controls on persistence. Biogeochemistry 85:25-44.

Rockhold, M. L., R. R. Yarwood, M. R. Niemet, P. J. Bottomley, F. J. Brockman, and J. S. Selker. 2007. Visualization and modeling of the colonization dynamics of a bioluminescent bacterium in variably saturated, translucent quartz sand. Advances in Water Resources 30:1593-1607.

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.

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.

Sollins, P., C. Swanston, and M. Kramer. 2007. Stabilization and destabilization of soil organic matter—a new focus. Biogeochemistry 85:1-7.

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., Dolan, M.E., Bottomley, P.J., Semprini, L. 2007. Utilization of Fluoroethene as a Surrogate for Aerobic Vinyl Chloride Transformation. Environmental Science and Technology 41:6378-6383.

Williams, M. A., D. D. Myrold, and P. J. Bottomley. 2007. Carbon flow from C-13-labeled clover and ryegrass residues into a residue-associated microbial community under field conditions. Soil Biology & Biochemistry 39:819-822.

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.

Publications from 2005-2007

(alphabetized list including 2007 publications listed above plus additional publications from 2005-2006)

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.

Belnap, J., S. L. Phillips, S. K. Sherrod, and A. Moldenke. 2005. Soil biota can change after exotic plant invasion: does this affect ecosystem processes? Ecology 86:3007-3017.

Bernhard, A. E., D. Colbert, J. McManus, and K. G. Field. 2005. Microbial community dynamics based on 16 S rRNA gene profiles in a Pacific Northwest estuary and its tributaries. FEMS Microbiology Ecology 52:115-128.

Bottomley, P. J., R. R. Yarwood, S. A. Kageyama, K. E. Waterstripe, M. A. Williams, K. Cromack, and D. D. Myrold. 2006. Responses of soil bacterial and fungal communities to reciprocal transfers of soil between adjacent coniferous forest and meadow vegetation in the Cascade Mountains of Oregon. Plant and Soil 289:35-45.

Boyle, S. A., J. J. Rich, P. J. Bottomley, K. Cromack, and D. D. Myrold. 2006. Reciprocal transfer effects on denitrifying community composition and activity at forest and meadow sites in the Cascade Mountains of Oregon. Soil Biology & Biochemistry 38:870-878.

Brant, J. B., D. D. Myrold, and E. W. Sulzman. 2006. Root controls on soil microbial community structure in forest soils. Oecologia 148:650-659.

Brant, J. B., E. W. Sulzman, and D. D. Myrold. 2006. Microbial community utilization of added carbon substrates in response to long-term carbon input manipulation. Soil Biology & Biochemistry 38:2219-2232.

Brenner, R. E., R. D. Boone, J. B. Jones, K. Lajtha, and R. W. Ruess. 2006. Successional and physical controls on the retention of nitrogen in an undisturbed boreal forest ecosystem. Oecologia 148:602-611.

Brodhagen, M., I. Paulsen, and J. E. Loper. 2005. Reciprocal Regulation of Pyoluteorin Production with Membrane Transporter Gene Expression in Pseudomonas fluorescens Pf-5. Applied and Environmental Microbiology 71:6900-6909.

Bruck, D. J., J. E. Snelling, A. J. Dreves, and S. T. Jaronski. 2005. Laboratory bioassays of entomopathogenic fungi for control of Delia radicum (L.) larvae. Journal of Invertebrate Pathology 89:179-183.

Brzostowicz, P. C., D. M. Walters, R. E. Jackson, K. H. Halsey, H. Ni, and P. E. Rouviere. 2005. Proposed involvement of a soluble methane monooxygenase homologue in the cyclohexane-dependent growth of a new Brachymonas species. Environmental Microbiology 7:179-190.

Burrows, E. H., J. L. Bubier, A. Mosedale, G. W. Cobb, and P. M. Crill. 2005. Net Ecosystem Exchange of Carbon dioxide in a Temperate Poor Fen: a Comparison of Automated and Manual Chamber Techniques. Biogeochemistry 76:21-45.

Caldwell, B. A. 2005. Enzyme activities as a component of soil biodiversity: A review. Pedobiologia 49:637-644.

Caldwell, B. A. 2006. Effects of invasive scotch broom on soil properties in a Pacific coastal prairie soil. Applied Soil Ecology 32:149-152.

Cazares, E., J. M. Trappe, and A. Jumpponen. 2005. Mycorrhiza-plant colonization patterns on a subalpine glacier forefront as a model system of primary succession. Mycorrhiza 15:405-416.

Cheng, S., H. Liu, and B. E. Logan. 2006. Increased performance of single-chamber microbial fuel cells using an improved cathode structure. Electrochemistry Communications 8:489-494.

Cliff, J. B., P. J. Bottomley, D. J. Gaspar, and D. D. Myrold. 2007. Nitrogen mineralization and assimilation at millimeter scales. Soil Biology & Biochemistry 39:823-826.

Cliff, J. B., D. J. Gaspar, P. J. Bottomley, and D. D. Myrold. 2005. Microbial C and N assimilation in soils and model systems as revealed by ToF-SIMS. Geochimica Et Cosmochimica Acta 69:A527-A527.

Collins, H. P., A. Alva, R. A. Boydston, R. L. Cochran, P. B. Hamm, A. McGuire, and E. Riga. 2006. Soil microbial, fungal, and nematode responses to soil fumigation and cover crops under potato production. Biology and Fertility of Soils 42:247-257.

Connon, S. A., A. Tovanabootr, M. 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.

Crow, S. E., E. W. Sulzman, W. D. Rugh, R. D. Bowden, and K. Lajtha. 2006. Isotopic analysis of respired CO2 during decomposition of separated soil organic matter pools. Soil Biology & Biochemistry 38:3279-3291.

Crow, S. E., C. W. Swanston, K. Lajtha, J. R. Brooks, and H. Keirstead. 2007. Density fractionation of forest soils: methodological questions and interpretation of incubation results and turnover time in an ecosystem context. Biogeochemistry 85:69-90.

Crow, S. E., and R. K. Wieder. 2005. Sources of Co-2 emission from a northern peatland: Root respiration, exudation, and decomposition. Ecology 86:1825-1834.

Darby, H. M., A. G. Stone, and R. P. Dick. 2006. Compost and manure mediated impacts on soilborne pathogens and soil quality. Soil Science Society of America Journal 70:347-358.

Devereux, R., P. Rublee, J. H. Paul, K. G. Field, and J. W. Santo Domingo. 2006. Development and applications of microbial ecogenomic indicators for monitoring water quality: Report of a workshop assessing the state of the science, research needs and future directions. Environmental Monitoring and Assessment 116:459-479.

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.

Doughty, D. M., L. A. Sayavedra-Soto, D. J. Arp, and P. J. Bottomley. 2006. Product Repression of Alkane Monooxygenase Expression in Pseudomonas butanovora. Journal of Bacteriology 188:2586-2592.

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.

Ennis, E., R. Reed, M. 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.

Fahey, T. J., T. G. Siccama, C. T. Driscoll, G. E. Likens, J. Campbell, C. E. Johnson, J. J. Battles, J. D. Aber, J. J. Cole, M. C. Fisk, P. M. Groffman, S. P. Hamburg, R. T. Holmes, P. A. Schwarz, and R. D. Yanai. 2005. The biogeochemistry of carbon at Hubbard Brook. Biogeochemistry 75:109-176.

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.

Fisk, M. R., R. Popa, O. U. Mason, M. C. Storrie-Lombardi, and E. P. Vicenzi. 2006. Iron-magnesium silicate bioweathering on Earth (and Mars?). Astrobiology 6:48-68.

Giovannoni, S. 2005. The shape of microbial diversity. Environmental Microbiology 7:476-476.

Grant, S. R., E. J. Fisher, J. H. Chang, B. M. Mole, and J. L. Dangl. 2006. Subterfuge and manipulation: Type III effector proteins of phytopathogenic bacteria. Annual Review of Microbiology 60:425-449.

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.

Griffiths, R., M. Madritch, and A. Swanson. 2005. Conifer invasion of forest meadows transforms soil characteristics in the Pacific Northwest. Forest Ecology and Management 208:347-358.

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.

Hallett, S. L., S. D. Atkinson, and J. L. Bartholomew. 2005. Countering morphological ambiguities: development of a PCR assay to assist the identification of Tubifex tubifex oligochaetes. Hydrobiologia 543:305-309.

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 and 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.

Hibbard, K. A., B. E. Law, M. Reichstein, and J. Sulzman. 2005. An analysis of soil respiration across northern hemisphere temperate ecosystems. Biogeochemistry 73:29-70.

Hobbie, E. A., P. T. Rygiewicz, M. G. Johnscin, and A. R. Moldenke. 2007. C-13 and N-15 in microarthropods reveal little response of Douglas-fir ecosystems to climate change. Global Change Biology 13:1386-1397.

Hogberg, M. N., P. Hogberg, and D. D. Myrold. 2007. Is microbial community composition in boreal forest soils determined by pH, C-to-N ratio, the trees, or all three? Oecologia 150:590-601.

Högberg, M. N., D. D. Myrold, R. Giesler, and P. Högberg. 2006. Contrasting patterns of soil N-cycling in model ecosystems of Fennoscandian boreal forests. Oecologia 147:96-107.

Holt, E. A., and P. M. Severns. 2005. The Effects of Prescribed Burning on Wet Prairie Lichen Communities. Natural Areas Journal 25:130-136.

Holub, S. M., K. Lajtha, J. D. H. Spears, J. A. Toth, S. E. Crow, B. A. Caldwell, M. Papp, and P. T. Nagy. 2005. Organic matter manipulations have little effect on gross and net nitrogen transformations in two temperate forest mineral soils in the USA and central Europe. Forest Ecology and Management 214:320-330.

Hommes, N. G., E. G. Kurth, L. A. Sayavedra-Soto, and D. J. Arp. 2006. Disruption of sucA, Which Encodes the E1 Subunit of alpha -Ketoglutarate Dehydrogenase, Affects the Survival of Nitrosomonas europaea in Stationary Phase. Journal of Bacteriology 188:343-347.

Hood, R. R., E. A. Laws, R. A. Armstrong, N. R. Bates, C. W. Brown, C. A. Carlson, F. Chai, S. C. Doney, P. G. Falkowski, R. A. Feely, M. A. M. Friedrichs, M. R. Landry, J. K. Moore, D. M. Nelson, T. L. Richardson, B. Salihoglu, M. Schartau, D. A. Toole, and J. D. Wiggert. 2006. Pelagic functional group modeling: Progress, challenges and prospects. Deep-Sea Research Part II -Topical Studies in Oceanography 53:459-512.

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.

Istok, J. D., M. M. Park, A. D. Peacock, M. Oostrom, and T. Wietsma. 2007. An experimental investigation of nitrogen gas produced during denitrification. Ground Water 45:461-467.

Izzo, A. D., M. Meyer, J. M. Trappe, M. North, and T. D. Bruns. 2005. Hypogeous Ectomycorrhizal Fungal Species on Roots and in Small Mammal Diet in a Mixed-Conifer Forest. Forest Science 51:243.

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. 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.

Kleber, M., P. Sollins, and R. Sutton. 2007. A conceptual model of organo-mineral interactions in soils: self-assembly of organic molecular fragments into zonal structures on mineral surfaces. Biogeochemistry 85:9-24.

Lajtha, K., S. E. Crow, Y. Yano, S. S. Kaushal, E. Sulzman, P. Sollins, and J. D. H. Spears. 2005. Detrital controls on soil solution N and dissolved organic matter in soils: a field experiment. Biogeochemistry 76:261-281.

Larney, F. J., D. M. Sullivan, K. E. Buckley, and B. Eghball. 2006. The role of composting in recycling manure nutrients. Canadian Journal of Soil Science 86:597-611.

Leon, M. C. C., A. Stone, and R. R. Dickc. 2006. Organic soil amendments: Impacts on snap bean common root rot (Aphanomyes euteiches) and soil quality. Applied Soil Ecology 31:199-210.

Longnecker, K., D. S. Homen, E. B. Sherr, and B. F. Sherr. 2006. Similar community structure of biosynthetically active prokaryotes across a range of ecosystem trophic states. Aquatic Microbial Ecology 42:265-276.

Luoma, D. L., C. A. Stockdale, R. Molina, and J. L. Eberhart. 2006. The spatial influence of Pseudotsuga menziesii retention trees on ectomycorrhiza diversity. Canadian Journal of Forest Research 36:2561–2573.

Machado, S., K. Rhinhart, and S. Petrie. 2006. Long-Term Cropping System Effects on Carbon Sequestration in Eastern Oregon. Journal of Environmental Quality 35:1548-1553.

McMahon, S. K., M. A. Williams, P. J. Bottomley, and D. D. Myrold. 2005. Dynamics of microbial communities during decomposition of carbon-13 labeled ryegrass fractions in soil. Soil Science Society of America Journal 69:1238-1247.

McManus, J., W. M. Berelson, S. Severmann, R. L. Poulson, D. E. Hammond, G. P. Klinkhammer, and C. Holm. 2006. Molybdenum and uranium geochemistry in continental margin sediments: Paleoproxy potential. Geochimica et Cosmochimica Acta 70:4643-4662.

Medeiros, P. M., M. C. Bicego, R. M. Castelao, C. Del Rosso, G. Fillmann, and A. J. Zamboni. 2005. Natural and anthropogenic hydrocarbon inputs to sediments of Patos Lagoon Estuary, Brazil. Environment International 31:77-87.

Medeiros, P. M., M. F. Fernandes, R. P. Dick, and B. R. T. Simoneit. 2006. Seasonal variations in sugar contents and microbial community in a ryegrass soil. Chemosphere 65:832-839.

Medeiros, P. M., and B. R. Simoneit. 2007. Gas chromatography coupled to mass spectrometry for analyses of organic compounds and biomarkers as tracers for geological, environmental, and forensic research. JOURNAL OF SEPARATION SCIENCE 30:1516.

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.

Myrold, D. D., and N. R. Posavatz. 2007. Potential importance of bacteria and fungi in nitrate assimilation in soil. Soil Biology & Biochemistry 39:1737-1743.

Nielsen, M. E., M. R. Fisk, J. D. Istok, and K. Pedersen. 2006. Microbial nitrate respiration of lactate at in situ conditions in ground water from a granitic aquifer situated 450 m underground. Geobiology 4:43.

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.

Oline, D. K. 2006. Phylogenetic comparisons of bacterial communities from serpentine and nonserpentine soils. Applied and Environmental Microbiology 72:6965-6971.

Perakis, S. S., D. A. Maguire, T. D. Bullen, K. Cromack, R. H. Waring, and J. R. Boyle. 2006. Coupled Nitrogen and Calcium Cycles in Forests of the Oregon Coast Range. Ecosystems 9:63-74.

Poinar, G., Jr., and R. Poinar. 2005. Fossil evidence of insect pathogens. Journal of Invertebrate Pathology 89:243-250.

Poulson, R., C. Siebert, M. J., and W. Berelson. 2006. Authigenic Molybdenum Isotope Signatures in Marine Sediments. Geology 8:56-59.

Redden, G., and F. S. Colwell. 2007. ISSM-ISEB 2005: Progress in understanding and predicting subsurface microbiology and biogeochemical processes. Geomicrobiology Journal 24:135-138.

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., 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.

Rillig, M. C., B. A. Caldwell, H. A. B. Wosten, and P. Sollins. 2007. Role of proteins in soil carbon and nitrogen storage: controls on persistence. Biogeochemistry 85:25-44.

Rockhold, M. L., R. R. Yarwood, M. R. Niemet, P. J. Bottomley, F. J. Brockman, and J. S. Selker. 2007. Visualization and modeling of the colonization dynamics of a bioluminescent bacterium in variably saturated, translucent quartz sand. Advances in Water Resources 30:1593-1607.

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.

Rotenberg, D., L. Cooperband, and A. Stone. 2005. Dynamic relationships between soil properties and foliar disease as affected by annual additions of organic amendment to a sandy-soil vegetable production system. Soil Biology & Biochemistry 37:1343-1357.

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.

Rusch, A., M. Huettel, C. Wild, and C. E. Reimers. 2006. Benthic oxygen consumption and organic matter turnover in organic-poor, permeable shelf sands. Aquatic Geochemistry 12:1-19.

Rushdi, A. I., K. Al-Mutlaq, and B. R. T. Simoneit. 2005. Sources of organic compounds in fine soil and sand particles during winter in the metropolitan area of Riyadh, Saudi Arabia. Archives of Environmental Contamination and Toxicology 49:457-470.

Rushdi, A. I., S. Al-Zarban, and B. R. T. Simoneit. 2006. Chemical compositions and sources of organic matter in fine particles of soils and sands from the vicinity of Kuwait city. Environmental Monitoring and Assessment 120:537-557.

Rushdi, A. I., A. A. DouAbul, S. S. Mohammed, and B. R. T. Simoneit. 2006. Compositions and sources of extractable organic matter in Mesopotamian marshland surface sediments of Iraq: II. Polar compounds. Environmental Geology 50:1171-1181.

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