OSU Publications from 2005-2006 Related to the Subsurface Biosphere

The following publications were identified through searches of the Web of Science, Toxline, Environmental Sciences and Pollution Mgmt, 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, please email sbi@oregonstate.edu .

Azizian, M., Istok, J., & Semprini, L. (2005) In Lewandowski Z., Beyenal H.(Eds.), Push-pull test evaluation of the in situ aerobic cometabolism of chlorinated ethenes by toluene-utilizing microorganisms. Alliance House 12 Caxton Street London SW1H 0QS UK: IWA Publishing.

Bernhard, A. E., Colbert, D., McManus, J., & Field, K. G. (2005) Microbial community dynamics based on 16S rRNA gene profiles in a pacific northwest estuary and its tributaries. FEMS microbiology ecology, 52(1), 115-128.

Belnap, J, Phillips, SL, Sherrod, SK, Moldenke, A. (2005) Soil biota can change after exotic plant invasion: does this affect ecosystem processes?. Ecology, 86 (11), 3007-3017.

Brodhagen, M., Paulsen, I. T., and Loper, J. E. (2005) Reciprocal regulation of pyoluteorin production with membrane transporter gene expression in Pseudomonas fluorescens Pf-5. Appl. Environ. Microbiol. 71:6900-6909.

Brzostowicz, P.C., Walters, D.M., Jackson, R.E., Halsey, K.H., Ni, H. and Rouvière, P.E. (2005) Proposed involvement of a soluble methane monooxygenase homologue in the cyclohexane-dependent growth of a new Brachymonas species, Environmental Microbiology, 7(2), 179-290.

Burrows, EH, Bubier, JL, Mosedale, A, Cobb, GW, Crill, PM. (2005) Net ecosystem exchange of carbon dioxide in a temperate poor fen: a comparison of automated and manual chamber techniques. Biogeochemistry, 76 (1), 21-45.

Connon, S. A., Tovanabootr, A., Dolan, M., Vergin, K., Giovannoni, S. J., & Semprini, L. (2005) Bacterial community composition determined by culture-independent and -dependent methods during propane-stimulated bioremediation in trichloroethene-contaminated groundwater. Environmental Microbiology, 7(2), 165-178.

Crow, S. E., & Wieder, R. K. (2005) Sources of CO2 emission from a northern peatland: Root respiration, exudation, and decomposition. Ecology, 86(7), 1825-1834.

Doughty, D. M., Sayavedra-Soto, L. A., Arp, D. J., & 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.

Feil, H., Feil, W. S., Chain, P., Larimer, F., DiBartolo, G., Copeland, A., Lykidis, A., Trong, S., Nolan, M., Goltsman, E., Thiel, J., Malfatti, S., Loper, J. E., Lapidus, A., Detter, J. C., Land, M., Richardson, P. M., Kyrpides, N.C., Ivanova, N., and Lindow, S. E. (2005) Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000. Proc. Natl. Acad. Sci. (USA) 102: 11064–11069.

Ennis, E., Reed, R., Dolan, M., Semprini, L., Istok, J., & Field, J. (2005) Reductive dechlorination of the vinyl chloride surrogate chlorofluoroethene in TCE-contaminated groundwater. Environmental science & technology, 2005 Sep 1,

Field, J.A., Reed, R.A., Istok, J.D., Semprini, L., Bennett, P. (2005) Trichlorofluoroethene: A reactive tracer for evaluating reductive dechlorination in large-diameter permeable columns. Ground Water Monitoring & Remediation, 25(2), 68–77.

Fisk,M.R., Popa, R., Mason, O.U., Storrie-Lombardi, M.C., Vicenzi, E.P. (2006) Iron-Magnesium Silicate Bioweathering on Earth (and Mars?), Astrobiology, 6(1), 48-68.

Giovannoni, S. (2005) The shape of microbial diversity. Environmental Microbiology, 7 (4), 476-476.

Griffiths, R., Madritch, M., & Swanson, A. (2005) Conifer invasion of forest meadows transforms soil characteristics in the pacific northwest. Forest Ecology and Management, 208(1-3), 347-358.

Gu, BH, Yan, H, Zhou, P, Watson, DB, Park, M, Istok, J. (2005) Natural humics impact uranium bioreduction and oxidation. Environmental science & technology, 39 (14), 5268-5275.

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, 2005 Oct,

Holland, E. A., Braswell, B. H., Sulzman, J., & Lamarque, J. -. (2005) Nitrogen deposition onto the united states and western europe: Synthesis of observations and models. Ecological Applications, 15(1), 38-57.

Holub, SM, Lajtha, K, Spears, JDH, Toth, JA, Crow, SE, Caldwell, BA, Papp, M, Nagy, MT. (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 (1-3), 320-330.

Hommes, N. G., Kurth, E. G., Sayavedra-Soto, L. A., & Arp, D. J. (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(1), 343-347.

Jones, BD, Ingle, JD. (2005) Evaluation of redox indicators for determining sulfate-reducing and dechlorinating conditions. Water Research, 39 (18), 4343-4354.

Kassim, T. A., & Simoneit, B. R. T. (2005) Forensic analysis modeling and chemometric investigation of molecular markers from natural and engineered environmental systems. Environmental Engineering Science, 22(6), 725-744.

Lajtha, K, Crow, S.E., Yano, Y., Kaushal, S.S., Sulzman, E., Sollins, P. and Spears, J.D.H. (2005) Detrital Controls on Soil Solution N and Dissolved Organic Matter in Soils: A Field Experiment. Biogeochemistry, 76(2), 261 - 281.

Medeiros, P. M., Bicego, M. C., Castelao, R. M., Del Rosso, C., Fillmann, G., & Zamboni, A. J. (2005) Natural and anthropogenic hydrocarbon inputs to sediments of patos lagoon estuary, brazil. Environment international, 31(1), 77-87.

Paulsen, I. T., Press, C. M., Ravel, J., Kobayashi, D. Y., Myers, G. S. A., Mavrodi, D. V., DeBoy, R. T., Seshadri, R., Ren, Q., Madupu, R., Dodson, R. J., Durkin, A. S., Brinkac, L. M., Daugherty, S. C., Sullivan, S. A., Rosovitz, M. J., Gwinn, M. L., Zhou, L., Schneider, D. J., Cartinhour, S. W., Nelson, W. C., Weidman, J., Watkins, K., Tran, K., Khouri, H., Pierson, E. A., Pierson, L. S., III, Thomashow, L. S. and Loper, J. E. (2005) Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5. Nature Biotechnology 23: 873-878.

Perakis, S, Maguire, D, Bullen, T, Cromack, K, Waring, R, Boyle, J. (2006) Coupled nitrogen and calcium cycles in forests of the Oregon Coast Range. Ecosystems, 9 (1), 63-74.

Rooklidge, S. J., Burns, E. R., & Bolte, J. P. (2005) Modeling antimicrobial contaminant removal in slow sand filtration. Water research, 39(2-3), 331-339.

Rushdi, A. I., Al-Mutlaq, K., & Simoneit, B. R. T. (2005) Sources of organic compounds in fine soil and sand particles during winter in the metropolitan area of riyadh, saudi arabia. Arch Environ Contam Toxicol.

Rushdi, AI, Simoneit, BRT. (2005) Abiotic synthesis of organic compounds from carbon disulfide under hydrothermal conditions. Astrobiology, 5 (6), 749-769.

Ryckelynck, N, Stecher, HA, Reimers, CE. (2005) Understanding the anodic mechanism of a seafloor fuel cell: Interactions between geochemistry and microbial activity. Biogeochemistry, 76 (1), 113-139.

Sayavedra-Soto, L. A., Doughty, D. M., Kurth, E. G., Bottomley, P. J., & Arp, D. J. (2005) Product and product-independent induction of butane oxidation in pseudomonas butanovora. FEMS microbiology letters, 250(1), 111-116.

Sayavedra-Soto, L. A., Doughty, D. M., Kurth, E. G., Bottomley, P. J., & Arp, D. J. (2005) Product and product-independent induction of butane oxidation in pseudomonas butanovora. FEMS microbiology letters, 2005 Sep 1,

Scheuerell, S. J., & Mahaffee, W. F. (2005) Microbial recolonization of compost after peak heating needed for the rapid development of damping-off suppression. Compost Science & Utilization, 13(1), 65-71.

Starkenburg, S.R., Chain, P.S.G., Sayavedra-Soto, L.A., Hauser, L., Land, M.L., Larimer, F.L., Malfatti, S.A., Klotz, M.G., Bottomley, P.J., Arp, D.J. and Hickey, W.J. (2006) Genome Sequence of the Chemolithoautotrophic Nitrite-Oxidizing Bacterium Nitrobacter winogradskyi Nb-255. Applied Environmental Microbiology, 72, 2050-2063.

Stockwell, V. O., and Loper, J. E. (2005) The sigma factor RpoS is required for stress tolerance and environmental fitness of Pseudomonas fluorescens Pf-5. Microbiology 151: 3001-3009.

Stockwell, V., Temple, T., Johnson, K., & Loper, J. (2005) Effect of the iron chelate FeEDDHA on control of fire blight by pseudomonas fluorescens A506. Phytopathology, 95(6).

Sulzman, E.W., Brant, J.B., Bowden, R.D., and Lajtha, K., (2005) Contribution of aboveground litter, belowground litter, and rhizosphere respiration to total soil CO2 efflux in an old growth coniferous forest. Biogeochemistry, 73, 231–256.

Usenko, S., Hageman, K. J., Schmedding, D. W., Wilson, G. R., & Simonich, S. L. (2005) Trace analysis of semivolatile organic compounds in large volume samples of snow, lake water, and groundwater. Environmental science & technology, 2005 Aug 15,

Wright, K. K., Baxter, C. V., & Li, J. L. (2005) Restricted hyporheic exchange in an alluvial river system: Implications for theory and management. Journal of the North American Benthological Society, 24(3), 447-460.

Yamazaki, Y, Danelishvili, L, Wu, M, MacNab, M, Bermudez, LE, (2006) Mycobacterium avium genes associated with the ability to form a biofilm. Applied and Environmental Microbiology, 72 (1), 819-825.

Yano, Y., Lajtha, K., Sollins, P., & Caldwell, B. A. (2005) Chemistry and dynamics of dissolved organic matter in a temperate coniferous forest on andic soils: Effects of litter quality. Ecosystems, 8(3), 286-300.

Yu, SH, Dolan, ME, Semprini, L. (2005) Kinetics and inhibition of reductive dechlorination of chlorinated ethylenes by two different mixed cultures. Environmental Science & Technology, 39 (1), 195-205.