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OSU Publications from 2005-2011 Related to the Subsurface Biosphere
The following publications were identified through searches of the Web of Science, Toxline, Environmental Sciences and Pollution Management, PubMed, 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 email@example.com .
This list was last updated May 2012.
Publications from 2012
Chong, Lauren S.; Prokopenko, Maria G.; Berelson, William M.; Townsend-Small, Amy; McManus, James. 2012. Nitrogen cycling within suboxic and anoxic sediments from the continental margin of Western North America. Marine Chemistry 128 p. 13-25 OSU author: McManus
Grace, Peter R.; Antle, John A.; Aggarwal, P. K.; Ogle, Stephen; Paustian, Keith; Basso, Bruno. 2012. Soil carbon sequestration and associated economic costs for farming systems of the Indo-Gangetic Plain: A meta-analysis Agricultural Ecosystems and Environment, 146 (1) 137-146. OSU author: Antle
Jennings, Tara N.; Smith, Jane E.; Cromack, Kermit, Jr.; Sulzman, Elizabeth W.; McKay, Donaraye, Caldwell, Bruce A., Beldin, Sarah I. 2012. Impact of postfire logging on soil bacterial and fungal communities and soil biogeochemistry in a mixed-conifer forest in central Oregon. Plant and Soil 350 (1-2) 393-411. OSU authors: Jennings, Cromack, Sulzman, Caldwell
Yan, Guiping; Smiley, Richard W.; Okubara, Patricia A. 2012. Detection and Quantification of Pratylenchus thornei in DNA Extracted from Soil Using Real-Time PCR. Phytopathology 102 (1 ) 14-22. OSU authors: Yan, Smiley
Vajrala, Neeraja; Sayavedra-Soto, Luis A.; Bottomley, Peter J.; Arp, Daniel J. 2012. Global analysis of the Nitrosomonas europaea iron starvation stimulon. Archives of Microbiology 194 (4) 305-313 OSU authors: all
Publications from 2011
Sierra, Carlos A.; Harmon, Mark E.; Perakis, Steven S. 2011. Decomposition of heterogeneous organic matter and its long-term stabilization in soils Ecological Monographs 81 (4) 619-634 OSU authors: Sierra, Harmon
Richter Daniel deB; Bacon Allan R.; Mobley Megan L.; et al. 2011. Human-Soil Relations are Changing Rapidly: Proposals from SSSA's Cross-Divisional Soil Change Working Group. Soil Science Society of America Journal 75 (6) 2079-2084 OSU author: Lajtha
Paszczynski Andrzej J.; Paidisetti Ravindra; Johnson Andrew K.; et al. 2011. Proteomic and targeted qPCR analyses of subsurface microbial communities for presence of methane monooxygenase Biodegradation 22 (6) 1045-1059. OSU author: Colwell
Schmidt Michael W. I.; Torn Margaret S.; Abiven Samuel; et al. 2011. Persistence of soil organic matter as an ecosystem property Nature 478 (7367) 49-56. OSU author: Kleber
Porter Mark L.; Valdes-Parada Francisco J.; Wood Brian D. 2011. Multiscale modeling of chemotaxis in homogeneous porous media Water Resources Research 47 . OSU authors: Porter, Wood
Kluber Laurel A.; Smith Jane E.; Myrold David D. 2011. Distinctive fungal and bacterial communities are associated with mats formed by ectomycorrhizal fungi Soil Biology & Biochemistry 43 (5) 1042-1050. OSU authors: Kluber, Myrold
Davit Y.; Iltis G.; Debenest G.; et al. 2011. Imaging biofilm in porous media using X-ray computed microtomography Journal of Microscopy 242 (1) 15-25 OSU author: Iltis, Wildenschild
Nachshon Uri; Weisbrod Noam; Dragila Maria I.; et al. 2011. Combined evaporation and salt precipitation in homogeneous and heterogeneous porous media Water Resources Research 47 (Article W03513) OSU author: Dragila
Vajrala Neeraja; Sayavedra-Soto Luis A.; Bottomley Peter J.; et al. 2011. Role of a Fur homolog in iron metabolism in Nitrosomonas europaea BMC Microbiologhy 11 (37). OSU authors: all
Myrold David D.; Pett-Ridge Jennifer; Bottomley Peter J. 2011. Nitrogen Mineralization and Assimilation at Millimeter Scales. Editor(s): Klotz MG; Stein LY PT B Book Series: Methods in Enzymology 496 p. 91-114 OSU authors:all
Radniecki Tyler S.; Lauchnor Ellen G. 2011. Investigating Nitrosomonas europaea Stress Biomarkers in Batch, Continuous Culture, and Biofilm Reactors PT B Book Series: Methods in Enzymology 496 p.217-246 OSU authors: all
Sierra C. A.; Harmon M. E.; Thomann E.; et al. 2011. Amplification and dampening of soil respiration by changes in temperature variability Biogeosciences 8 (4) 951-961 OSU authors: Sierra, Harmon
Sayavedra-Soto Luis A.; Vajrala Neeraja; Arp Daniel J. 2011. Dissecting Iron Uptake and Homeostasis in Nitrosomonas europaea Book Series: Methods in Enzymology 486 p. 403-428 OSU authors: all
Sayavedra-Soto Luis A.; Stein Lisa Y. 2011. Genetic Transformation of Ammonia-Oxidizing Bacteria Book Series: Methods in Enzymology 486 p. 389-402 OSU authors: all
Skantar A. M.; Handoo Z. A.; Zasada I. A.; Ingham, R. E.; Carta, L. K.; Chitwood, D. J. 2011. Morphological and Molecular Characterization of Globodera Populations from Oregon and Idaho Phytopathology 101 (4) 480-491. OSU author: Ingham
Yin Jun; Haggerty Roy; Stoliker Deborah L.; Kent, Douglas B.; Istok, Jonathan; Greskowiak, Janek; Zachara, John M. 2011. Transient groundwater chemistry near a river: Effects on U(VI) transport in laboratory column experiments Water Resources Research 47. OSU authors: Haggerty, Istok
Thorpe Andrea S.; Callaway, Ragan M. 2011. Biogeographic differences in the effects of Centaurea stoebe on the soil nitrogen cycle: novel weapons and soil microbes Biological Invasions 13 (6) 1435-1445. OSU author: Thorpe
Bertagnolli, A. D.; Treusch, A. H.; Mason, O. U.; Stingl, U.; Vergin, K. L.; Chan, F.; Beszteri, B.; Giovannoni, S. J. 2011. Bacterial diversity in the bottom boundary layer of the inner continental shelf of Oregon, USA. Aquatic Microbial Ecology 64 (1): 15-25. OSU authors: Mason, Giovannoni
Argerich, Alba; Marti, Eugenia; Sabater, Francesc; Haggerty, Roy; Ribot, Miquel. 2011. Influence of transient storage on stream nutrient uptake based on substrata manipulation. Aquatic Sciences 73 (3): 365-376. OSU author: Haggerty
Warren, Jeffrey M.; Brooks, J. Renee; Dragila, Maria I.; Meinzer, Frederick C. 2011. In situ separation of root hydraulic redistribution of soil water from liquid and vapor transport. Oecologia 166 (4): 899-911. OSU author: Dragila
Bidartondo, Martin I.; Read, David J.; Trappe, James M.; Merckx, Vincent; Ligrone, Roberto; Duckett, Jeffrey G. 2011. The dawn of symbiosis between plants and fungi.. Biology Letters 7 (4): 574-577. OSU author: Trappe
Rau, Benjamin M.; Johnson, Dale W.; Blank, Robert R.; Tausch, Robin J.; Roundy, Bruce A.; Miller, Richard F.; Caldwell, Todd G.; Lucchesi, Annmarie. 2011. Woodland expansion's influence on belowground carbon and nitrogen in the Great Basin. US Journal of Arid Environments 75 (9): 827-835l. OSU author: Miller
Kovacs, Gabor M.; Trappe, James M.; Alsheikh, Abdulmagid M.; Hansen, Karen; Healy, Rosanne A.; Vagi, Pal. 2011. Terfezia disappears from the American truffle mycota as two new genera and Mattirolomyces species emerge. Mycologia 103 (4): 831-840. OSU authors: Trappe
Creed, Irena F.; Sass, Gabor Z.; Buttle, Jim M.; Jones, Julia A. 2011. Hydrological principles for sustainable management of forest ecosystems. Hydrological Processes 25 (13): 2152-2160. OSU authors: Jones
Brantley SL, Megonigal, JP, Scatena, FN, Balogh-Brunstad Z, Barnes RT, Bruns, MA, van Cappelen, P, Dontsova, K, Hartnett H, Hartshorn T, Heimsath A, Herndon E, Jin L, Keller CK, Leake JR, McDowell WH, Meinzer FC, Mozder T, Petsch S, Pett-Ridge J, Raymond P, Riebe CS, Shumaker K, Sutton-Grier A, Walter R, and Yoo K. 2011. Twelve testable hypotheses on the geobiology of weathering. Geobiology 9(2):140-165. OSU authors: Pett-Ridge
Colwell, F, Schwartz, A, Briggs, B. 2011. Microbial community distribution in sediments from the Mount Elbert Gas Hydrate Stratigraphic Test Well, Alaska North Slope. Marine and Petroleum Geology 28(2) 404:410. OSU authors: all
Cross, A.; Perakis, S.S. 2011. Tree species and soil nutrient profiles in old-growth forests of the Oregon Coast Range. Canadian Journal of Forest Research 41(1):195-210. OSU authors: Cross, Perakis (courtesy)
Hogberg, P, Johannisson, C, Yarwood S, Callesen I, Nasholm T, Myrold DD, Hogberg MN. 2011. Recovery of ectomycorrhiza after 'nitrogen saturation' of a conifer forest. New Phytologist 189(2):515-525. OSU authors: Yarwood, Myrold
Kleber M, Nico PS, Plante A, Filley T, Kramer M, Swanston C, Sollins P. 2011. Old and stable soil organic matter is not necessarily chemically recalcitrant: implications for modeling concepts and temperature sensitivity. Global Change Biology 17(2):1097-1107. OSU authors: Kleber, Sollins
Lauchnor EG, Radniecki TS, and Semprini L. 2011. Inhibition and gene expression of Nitrosomonas europaea biofilms exposed to phenol and toluene. Biotechnology and Bioengineering 108 (4): 750-757. OSU authors: all
Radniecki TS, Gilroy C, and Semprini L. 2011. Linking NE1545 expression with cell volume changes in Nitrosomonas europaea cells exposed to aromatic hydrocarbons. Chemosphere, 82:514-520. OSU authors: all
Publications from 2010
Appuhamillage, TA, Bokil VA, Thomann E, Waymire E, Wood BD. 2010. Solute transport across an interface: A Fickian theory for skewness in breakthrough curves. Water Resources Research. 46(7).
Azizian, MF, Marshall IPG, Behrens S, Spormann AM, Semprini L. 2010. Comparison of lactate, formate, and propionate as hydrogen donors for the reductive dehalogenation of trichloroethene in a continuous-flow column. Journal of Contaminant Hydrology. 113(1-4):77-92.
Chaia, EE, Myrold, DD, 2010. Variation of N-15 natural abundance in leaves and nodules of actinorhizal shrubs in Northwest Patagonia. Symbiosis 50 (1-2): 97-105.
Conrad, ME, Brodie EL, Radtke CW, Bill M, Delwiche ME, Lee HM, Swift DL, Colwell FS. 2010. Field Evidence for Co-Metabolism of Trichloroethene Stimulated by Addition of Electron Donor to Groundwater. Environmental Science & Technology. 44(12):4697-4704.
Currie, W. S., M. E. Harmon, I. C. Burke, S. C. Hart, W. J. Parton, and W. Silver. 2010. Cross-biome transplants of plant litter show decomposition models extend to a broader climatic range but lose predictability at the decadal time scale. Global Change Biology 16 (6):1744-1761.
Dossa, E. L., S. Diedhiou, J. E. Compton, K. B. Assigbetse, and R. P. Dick. 2010. Spatial patterns of P fractions and chemical properties in soils of two native shrub communities in Senegal. Plant and Soil 327 (1-2):185-198.
Feaga, J. B., J. S. Selker, R. P. Dick, and D. D. Hemphill. 2010. Long-Term Nitrate Leaching Under Vegetable Production with Cover Crops in the Pacific Northwest. Soil Science Society of America Journal 74 (1):186-195.
Griffiths, R. P., A. N. Gray, and T. A. Spies. 2010. Soil Properties in Old-growth Douglas-fir Forest Gaps in the Western Cascade Mountains of Oregon. Northwest Science 84 (1):33-45.
Hassan, K. A., A. Johnson, B. T. Shaffer, Q. H. Ren, T. A. Kidarsa, L. D. H. Elbourne, S. Hartney, R. Duboy, N. C. Goebel, T. M. Zabriskie, I. T. Paulsen, and J. E. Loper. 2010. Inactivation of the GacA response regulator in Pseudomonas fluorescens Pf-5 has far-reaching transcriptomic consequences. Environmental Microbiology 12 (4):899-915.
Istok, J. D., M. Park, M. Michalsen, A. M. Spain, L. R. Krumholz, C. Liu, J. McKinley, P. Long, E. Roden, A. D. Peacock, and B. Baldwin. 2010. A thermodynamically-based model for predicting microbial growth and community composition coupled to system geochemistry: Application to uranium bioreduction. Journal of Contaminant Hydrology 112 (1-4):1-14.
Janssens, I. A., W. Dieleman, S. Luyssaert, J. A. Subke, M. Reichstein, R. Ceulemans, P. Ciais, A. J. Dolman, J. Grace, G. Matteucci, D. Papale, S. L. Piao, E. D. Schulze, J. Tang, and B. E. Law. 2010. Reduction of forest soil respiration in response to nitrogen deposition. Nature Geoscience 3 (5):315-322.
Kayler, Z. E., E. W. Sulzman, W. D. Rugh, A. C. Mix, and B. J. Bond. 2010. Characterizing the impact of diffusive and advective soil gas transport on the measurement and interpretation of the isotopic signal of soil respiration. Soil Biology & Biochemistry 42 (3):435-444.
Kleber, M., and M. G. Johnson. 2010. Advances in Understanding the Molecular Structure of Soil Organic Matter: Implications for Interactions in the Environment Advances in Agronomy, Vol 106 106:77-142.
Lajtha, K, Jones J. 2010. Comment on ‘Kane et al. 2008. Precipitation control over inorganic nitrogen import-export budgets across watersheds: a synthesis of long-term ecological research. Ecohydrology 1(2): 105-117’. Ecohydrology.
Lee, J. H., M. Dolan, J. Field, and J. Istok. 2010. Monitoring Bioaugmenation with Single-Well Push-Pull Tests in Sediment Systems Contaminated with Trichloroethene. Environmental Science & Technology 44 (3):1085-1092.
Li, J. W., X. Shang, Z. X. Zhao, R. L. Tanguay, Q. X. Dong, and C. J. Huang. 2010. Polycyclic aromatic hydrocarbons in water, sediment, soil, and plants of the Aojiang River waterway in Wenzhou, China. Journal of Hazardous Materials 173 (1-3):75-81.
McFarlane, K. J., S. H. Schoenholtz, R. F. Powers, and S. S. Perakis. 2010. Soil Organic Matter Stability in Intensively Managed Ponderosa Pine Stands in California. Soil Science Society of America Journal 74 (3):979-992.
Phillips, C. L., N. Nickerson, D. Risk, Z. E. Kayler, C. Andersen, A. Mix, and B. J. Bond. 2010. Soil moisture effects on the carbon isotope composition of soil respiration. Rapid Communications in Mass Spectrometry 24 (9):1271-1280.
Porter, ML, Wildenschild D. 2010. Image analysis algorithms for estimating porous media multiphase flow variables from computed microtomography data: a validation study. Computational Geosciences. 14(1):15-30.
Porter, ML, Valdes-Parada FJ, Wood BD. 2010. Comparison of theory and experiments for dispersion in homogeneous porous media. Advances in Water Resources. 33(9):1043-1052.
Sabalowsky, AR, Semprini, L. 2010. Trichloroethene and cis-1,2-dichloroethene Concentration-Dependent Toxicity Model Simulates Anaerobic Dechlorination at High Concentrations: I. Batch-Fed Reactors. Biotechnology and Bioengineering 107 (3): 529-539.
Sabalowsky, AR, Semprini, L. 2010. Trichloroethene and cis-1,2-Dichloroethene Concentration-Dependent Toxicity Model Simulates Anaerobic Dechlorination at High Concentrations. II: Continuous Flow and Attached Growth Reactors. Biotechnology and Bioengineering 107 (3): 540-549.
Sayavedra-Soto, L. A., B. Gvakharia, P. J. Bottomley, D. J. Arp, and M. E. Dolan. 2010. Nitrification and degradation of halogenated hydrocarbons-a tenuous balance for ammonia-oxidizing bacteria. Applied Microbiology and Biotechnology 86 (2):435-444.
Slesak, R. A., S. H. Schoenholtz, and T. B. Harrington. 2010. Soil Respiration and Carbon Responses to Logging Debris and Competing Vegetation. Soil Science Society of America Journal 74 (3):936-946.
Wood, BD. 2010. Reply to comment by Philippe Baveye on“The role of scaling laws in upscaling”. Advances in Water Resources. 33(1):125-127.
Publications from 2005 through 2009
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.
Barker, J. S. 2007. Decomposition of Douglas-fir coarse woody debris in response to differing moisture content and initial heterotrophic colonization. Forest Ecology and Management 255:598-604.
Becerra, A. G., E. R. Nouhra, M. P. Silva, and D. McKay. 2009. Ectomycorrhizae, arbuscular mycorrhizae, and dark-septate fungi on Salix humboldtiana in two riparian populations from central Argentina. Mycoscience 50:343-352.
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.
Beldin, S., B. Caldwell, P. Sollins, E. W. Sulzman, K. Lajtha, and S. Crow. 2007. Cation exchange capacity of density fractions from paired conifer/grassland soils. Biology & Fertility of Soils 43:837-841.
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.
Boyle, S. A., R. R. Yarwood, P. J. Bottomley, and D. D. Myrold. 2008. Bacterial and fungal contributions to soil nitrogen cycling under Douglas fir and red alder at two sites in Oregon. Soil Biology & Biochemistry 40:443-451.
Boyle-Yarwood, S. A., P. J. Bottomley, and D. D. Myrold. 2008. Community composition of ammonia-oxidizing bacteria and archaea in soils under stands of red alder and Douglas fir in Oregon. Environmental microbiology 10:2956-2965.
Brandt, A. J., E. W. Seabloom, and P. R. Hosseini. 2009. Phylogeny and provenance affect plant–soil feedbacks in invaded California grasslands. Ecology 90:1063-1072.
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 & 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.
Burke, D. J., S. M. Dunham, and A. M. Kretzer. 2008. Molecular analysis of bacterial communities associated with the roots of Douglas fir (Pseudotsuga menziesii) colonized by different ectomycorrhizal fungi. FEMS Microbiology Ecology 65:299-309.
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.
Caldwell, S., J. R. Laidler, E. A. Brewer, J. O. Eberly, S. C. Sandborgh, and F. S. Colwell. 2008. Anaerobic oxidation of methane: mechanisms, bioenergetics, and the ecology of associated microorganisms. Environmental Science and Technology 42:6791–6799.
Capalbo, S., C. Wu, D. Goldberg, J. Matter, and A. Slagle. 2009. Economic dimensions of geological CO2 storage: Key factors in an assessment of sub-seafloor and continental sequestration options . Energy Procedia 1:2745-2752.
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.
Chaer, G. M., M. F. Fernandes, D. D. Myrold, and P. J. Bottomley. 2009. Comparative resistance and resilience of soil microbial communities and enzyme activities in adjacent native forest and agricultural soils. Microbial Ecology.
Chaer, G. M., M. F. Fernandes, D. D. Myrold, and P. J. Bottomley. 2009. Shifts in microbial community composition and physiological profiles across a gradient of induced soil degradation. Soil Biology & Biochemistry 73:1327-1334.
Chaer, G. M., D. D. Myrold, and P. J. Bottomley. 2009. A soil quality index based on the equilibrium between soil organic matter and biochemical properties of undisturbed coniferous forest soils of the Pacific Northwest. Soil Biology and Biochemistry 41:822-830.
Chastanet, J., and B. D. Wood. 2008. Mass transfer process in a two-region medium. Water Resources Research 44:W05413.
Claridge, A. W., J. M. Trappe, and K. Hansen. 2008. Do fungi have a role as soil stabilizers and remediators after forest fire? . Forest Ecology and Management 257:1063-1069
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 & Fertility of Soils 42:247-257.
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. Applied & Environmental Microbiology published online ahead of print on 14 March 2008.
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.
Cooley, R. B., B. L. Dubbels, L. A. Sayavedra-Soto, P. J. Bottomley, and D. J. Arp. 2009. Kinetic characterization of the soluble butane monooxygenase from Thauera butanivorans, formerly 'Pseudomonas butanovora'. Microbiology 155 2086-2096.
Crow, S., K. Lajtha, R. D. Bowden, Y. Yano, J. B. Brant, B. A. Caldwell, and E. Sulzman. 2009. Increased coniferous needle inputs accelerate decomposition of soil carbon in an old-growth forest. Forest Ecology and Management.
Crow, S., K. Lajtha, T. R. Filley, C. Swanston, R. D. Bowden, and B. A. Caldwell. 2009. Sources of plant-derived carbon and stability of organic matter in soil: implications for global change. Global Change Biology 15:2003-2019
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 Co2 emission from a northern peatland: Root respiration, exudation, and decomposition. Ecology 86:1825-1834.
Cusack, D. F., W. W. Chou, W. H. Yang, M. E. Harmon, W. L. Silver, and T. L. Team. 2008. Controls on long-term root and leaf litter decomposition. Global Change Biology 15:1339 - 1355.
D'Andrea, A. F., and T. H. DeWitt. 2009. Geochemical ecosystem engineering by the mud shrimp Upogebia pugettensis (Crustacea: Thalassinidae) in Yaquina Bay, Oregon: Density-dependent effects on organic matter remineralization and nutrient cycling. Limnology and Oceanography 54:1911-1932.
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.
Davis, B. M., J. D. Istok, and L. Semprini. 2009. Numerical simulations of radon as an in situ partitioning tracer for quantifying NAPL contamination using push–pull tests. Journal of Contaminant Hydrology 78:87-103.
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.
Diedhiou, S., E. L. Dossa, A. N. Badiane, M. S. Diedhiou, and R. P. Dick. 2008. Decomposition and spatial microbial heterogeneity associated with native shrubs in soils of agroecosystems in semi-arid Senegal. Pedobiologia.
Doughty, D. M., E. G. Kurth, L. A. Sayavedra-Soto, D. J. Arp, and P. J. Bottomley. 2008. Evidence for Involvement of Copper Ions and Redox State in Regulation of Butane Monooxygenase in Pseudomonas butanovora. Journal of Bacteriology 190:2933-2938.
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 & Environmental Microbiology 71:6054-6059.
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Fujita, Y., J. L. Taylor, T. L. T. Gresham, M. E. Delwiche, F. S. Colwell, T. L. McLing, L. M. Petzke, and R. W. Smith. 2008. Stimulation Of Microbial Urea Hydrolysis In Groundwater To Enhance Calcite Precipitation. Environmental science & technology 42:3025-3032.
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Scheuerell, S. J., D. M. Sullivan, and W. F. Mahaffee. 2005. Suppression of seedling damping-off caused by Pythium ultimum, P irregulare, and Rhizoctonia solani in container media amended with a diverse range of Pacific northwest compost sources. Phytopathology 95:306-315.
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 103:157-167.
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.
Siebert, C., J. McManus, A. Bice, R. L. Poulson, and W. M. Berelson. 2006. Molybdenum isotope signatures in continental margin marine sediments. Earth and Planetary Science Letters 241:723-733.
Skinner, K. M., L. M. Ciuffetti, and M. R. Hyman. 2009. Metabolism and Cometabolism of Cyclic Ethers by a Filamentous Fungus, a Graphium sp.. Applied & Environmental Microbiology 75:5514-5522.
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.
Smiley, R. W., R. G. Whittaker, J. A. Gourlie, and S. A. Easley. 2006. Geocenamus brevidens Associated with Reduced Yield of No-Till Annual Spring Wheat in Oregon. Plant Disease 90:885-890.
Sollins, P., M. Kramer, C. Swanston, K. Lajtha, T. R. Filley, A. K. Aufdenkampe, R. Wagai, and R. D. Bowden. 2009. Sequential density fractionation across soils of contrasting mineralogy: evidence for both microbial- and mineral-controlled soil organic matter stabilization . Biogeochemistry 96:209-231.
Sollins, P., C. Swanston, M. Kleber, T. Filley, M. Kramer, S. Crow, B. A. Caldwell, K. Lajtha, and R. Bowden. 2006. Organic C and N stabilization in a forest soil: Evidence from sequential density fractionation. Soil Biology & Biochemistry 38:3313-3324.
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 & Environmental Microbiology 73:4892-4904.
Starkenburg, S. R., D. J. Arp, and P. J. Bottomley. 2008. D-Lactate metabolism and the obligate requirement for CO2 during growth on nitrite by the facultative lithoautotroph Nitrobacter hamburgensis. Microbiology 154:2473-2481.
Starkenburg, S. R., D. J. Arp, and P. J. Bottomley. 2008. Expression of a putative nitrite reductase and the reversible inhibition of nitrite-dependent respiration by nitric oxide in Nitrobacter winogradskyi Nb-255. Environmental microbiology 10:3036-3042.
Starkenburg, S. R., P. S. G. Chain, L. A. Sayavedra-Soto, L. Hauser, M. L. Land, F. W. Larimer, S. A. Malfatti, M. G. Klotz, P. J. Bottomley, D. J. Arp, and W. J. Hickey. 2006. Genome sequence of the chemolithoautotrophic nitrite-oxidizing bacterium Nitrobacter winogradskyi Nb-255. Applied & Environmental Microbiology 72:2050-2063.
Starkenburg, S. R., F. W. Larimer, L. Y. Stein, M. G. Klotz, P. S. Chain, L. A. Sayavedra-Soto, A. T. Poret-Peterson, M. E. Gentry, D. J. Arp, B. Ward, and P. J. Bottomley. 2008. Complete Genome Sequence of Nitrobacter hamburgensis X14 and Comparative Genomic Analysis of Species within the Genus Nitrobacter. Applied & Environmental Microbiology 74:2852-2863.
Stockwell, V. O., and J. E. Loper. 2005. The sigma factor RpoS is required for stress tolerance and environmental fitness of Pseudomonas fluorescens Pf-5. Microbiology 151:3001-3009.
Stubbs, M. M., and D. A. Pyke. 2005. Available nitrogen: A time-based study of manipulated resource islands. Plant and Soil 270:123-133.
Sulzman, E. W., J. B. Brant, R. D. Bowden, and K. Lajtha. 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.
Taylor, A. E., and P. J. Bottomley. 2006. Nitrite production by Nitrosomonas europaea and Nitrosospira sp. AV in soils at different solution concentrations of ammonium. Soil Biology & Biochemistry 38:828-836.
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.
Thomas, C., J. G. Martin, M. Goeckede, M. B. Siqueira, T. Foken, B. E. Law, H. W. Loescher, and G. Katul. 2008. Estimating daytime subcanopy respiration from conditional sampling methods applied to multi-scalar high frequency turbulence time series. Agricultural and Forest Meteorology 148:1210-1229.
Thomas, W. J., C. A. Thireault, J. A. Kimbrel, and J. H. Chang. 2009. Recombineering and stable integration of the Pseudomonas syringae pv. syringae 61 hrp/hrc cluster into the genome of the soil bacterium Pseudomonas fluorescens Pf0-1. The Plant Journal.
Trappe, M. J., K. Cromack, J. M. Trappe, J. Wilson, M. C. Rasmussen, M. A. Castellano, and S. L. Miller. 2009. Relationships of current and past anthropogenic disturbance to mycorrhizal sporocarp fruiting patterns at Crater Lake National Park, Oregon. Canadian Journal of Forest Research 39:1662-1676.
Treseder, K. K., and A. Cross. 2006. Global Distributions of Arbuscular Mycorrhizal Fungi. Ecosystems 9:305-316.
Valdes-Parada, F. J., M. L. Porter, K. Narayanaswamy, R. M. Ford, and B. D. Wood. 2009. Upscaling microbial chemotaxis in porous media. Advances in Water Resources 32:1413-1428.
Wallenstein, M. D., D. D. Myrold, M. Firestone, and M. Voytek. 2006. Environmental controls on denitrifying communities and denitrification rates: Insights from molecular methods. Ecological Applications 16:2143-2152.
Watrud, L. S., K. Martin, K. K. Donegan, J. K. Stone, and C. G. Coleman. 2006. Comparison of taxonomic, colony morphotype and PCR-RELP methods to characterize microfungal diversity. Mycologia 98:384-392.
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Williams, M. A., D. D. Myrold, and P. J. Bottomley. 2006. Carbon flow from C-13-labeled straw and root residues into the phospholipid fatty acids of a soil microbial community under field conditions. Soil Biology & Biochemistry 38:759-768.
Williams, M. A., D. D. Myrold, and P. J. Bottomley. 2006. Distribution and fate of C-13-labeled root and straw residues from ryegrass and crimson clover in soil under western Oregon field conditions. Biology & Fertility of Soils 42:523-531.
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.
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.
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Wood, B. D. 2009. The role of scaling laws in upscaling . Advances in Water Resources 32:723-736
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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.
Wu, S. M., D. X. Hu, and E. R. Ingham. 2005. Comparison of soil biota between organic and conventional agroecosystems in Oregon, USA. Pedosphere 15:395-403.
Wymore, R. A. 2007. Field evidence for intrinsic aerobic chlorinated ethene cometabolism by methanotrophs expressing soluble methane monooxygenase. Bioremediation Journal 11:125-139.
Xu, Y., B. R. T. Simoneit, and R. Jaffe. 2007. Occurrence of long-chain n-alkenols, diols, keto-ols and sec-alkanols in a sediment core from a hypereutrophic, freshwater lake. Organic Geochemistry 38:870-883.
Yamazaki, Y., L. Danelishvili, M. Wu, M. MacNab, and L. E. Bermudez. 2006. Mycobacterium avium Genes Associated with the Ability To Form a Biofilm. Applied & Environmental Microbiology 72:819-825.
Yano, Y., K. Lajtha, P. Sollins, and B. A. Caldwell. 2005. Chemistry and dynamics of dissolved organic matter in a temperate coniferous forest on Andic soils: Effects of litter quality. Ecosystems 8:286-300.
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.
Yarwood, S. A., and E. W. Sulzman. 2008. An exercise to demonstrate soil microbial diversity in introductory environmental science classrooms. Journal of Natural Resources and Life Science Education 37:53-58.
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.
Yu, S., and L. Semprini. 2009. Enhanced reductive dechlorination of PCE DNAPL with TBOS as a slow-release electron donor . Journal of Hazardous Materials 167:97-104.
Zarate-del Valle, P. F., and B. R. T. Simoneit. 2005. The generation of hydrothermal oil in sediments of the Chapala Lake and its relation with the geothermal activity in the Citala rift, Jalisco State, Mexico. Revista Mexicana De Ciencias Geologicas 22:358-370.
Zeglin, L. H., R. L. Sinsabaugh, J. E. Barrett, M. N. Gooseff, and C. D. Takacs-Vesbach. 2009. Landscape distribution of microbial activity in the McMurdo Dry Valleys: Linked biotic processes, hydrology, and geochemistry in a cold desert ecosystem. Ecosystems 12:562-573.
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