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 sbi@oregonstate.edu .

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 BasinUS 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 weatheringGeobiology 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.

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.

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.

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.

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.

Gieg, L. M., R. E. Alumbaugh, J. A. Field, J. Jones, J. Istok, and J. M. Suflita. 2009. Assessing in situ rates of anaerobic hydrocarbon bioremediation. Microbial Biotechnology 2:222-233.

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

Golfier, F., B. D. Wood, L. Orgogozo, M. Quintard, and M. Bues. 2009. Biofilms in porous media: Development of macroscopic transport equations via volume averaging with closure for local mass equilibrium conditions. Advances in Water Resources 32:463-485.

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.

Griffiths, R. P., M. D. Madritch, and A. K. Swanson. 2009. The effects of topography on forest soil characteristics in the Oregon Cascade Mountains (USA): Implications for the effects of climate change on soil properties. Forest Ecology and Management 257:1-7.

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., P. J. Bottomley, D. J. Arp, and L. A. Sayavedra-Soto. 2009. Construction of recombinant Nitrosomonas europaea expressing green fluorescent protein in response to co-oxidation of chloroform. Applied Microbiology & Biotechnology 82:1179-1185.

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 & 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.

Haggerty, R., E. Marti, A. Argerich, D. von Schiller, and N. Grimm. 2009. Resazurin as a “smart” tracer for quantifying metabolically active transient storage in stream ecosystems. Journal of Geophysical Research: Biogeosciences 114:G03014.

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 & 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.

Hatten, J. A., D. Zabowskib, A. Ogdenb, and W. Thies. 2008. Soil organic matter in a ponderosa pine forest with varying seasons and intervals of prescribed burn. Forest Ecology and Management 255:2555-2565

Hebel, C. L., J. E. Smith, and K. Cromack. 2009. Invasive plant species and soil microbial response to wildfire burn severity in the Cascade Range of Oregon. Applied Soil Ecology 42:150-159

Heuer, V. B., J. W. Pohlman, M. E. Torres, M. Elvert, and K.-U. Hinrichs. 2009. The stable carbon isotope biogeochemistry of acetate and other dissolved carbon species in deep subseafloor sediments at the northern Cascadia Margin. Geochimica et Cosmochimica Acta 73:3323-3336

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.

Hosaka, K., M. A. Castellano, and J. W. Spatafora. 2007. Biogeography of Hysterangiales (Phallomycetidae, Basidiomycota). Mycological Research 112:448-462.

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, M. M. Michalsen, A. M. Spain, L. R. Krumholz, C. Liu, J. P. McKinley, P. Long, E. Roden, A. D. Peacock, and B. Baldwin. 2009. A thermodynamically-based model for predicting microbial growth and community composition coupled to system geochemistry: Application to uranium bioreduction . Journal of Contaminant Hydrology.

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.

Jacobs, S., J. Bechtold, H. Biggs, N. Grimm, S. Lorentz, M. McClain, R. Naiman, S. Perakis, G. Pinay, and M. Scholes. 2007. Nutrient vectors and riparian processing: A review with special reference to african semiarid savanna ecosystems. Ecosystems 10:1231-1249.

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.

Kageyama, S. A., K. G. Mandyam, and A. Jumpponen. 2008. Diversity, Function and Potential Applications of the Root-Associated Endophytes.in A. Varma, editor. Mycorrhiza: Genetics and Molecular Biology, Eco-Function, Biotechnology, Eco-Physiology, Structure and Systematics, 3rd edition. Springer.

Kageyama, S. A., N. R. Posavatz, K. E. Waterstripe, S. J. Jones, P. J. Bottomley, K. Cromack, and D. D. Myrold. 2008. Fungal and bacterial communities across meadow-forest ecotones in the western Cascades of Oregon. Canadian Journal of Forest Research 38:1053-1060.

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.

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.

Kurth, E. G., D. M. Doughty, P. J. Bottomley, D. J. Arp, and L. A. Sayavedra-Soto. 2008. Involvement of BmoR and BmoG in n-alkane metabolism in 'Pseudomonas butanovora'. Microbiology 154:139-147.

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.

Lawton, T. J., L. A. Sayavedra-Soto, D. J. Arp, and A. C. Rosenzweig. 2009. Crystal Structure of a Two-domain Multicopper Oxidase: Implications for the Evolution of Multicopper blue proteins. Journal of Biological Chemistry 284:10174-10180.

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.

Loper, J. E., M. D. Henkels, B. T. Shaffer, F. A. Valeriote, and H. Gross. 2008. Isolation and identification of rhizoxin analogs from Pseudomonas fluorescens Pf-5 by using a genomic mining strategy. Applied & Environmental Microbiology 74:3085-3093.

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.

Martin, J. G., and P. V. Bolstad. 2009. Variation of soil respiration at three spatial scales: Components within measurements, intra-site variation and patterns on the landscape. Soil Biology and Biochemistry 41:530-543.

Martin, J. G., P. V. Bolstad, S.-R. Ryu, and J. Chen. 2009. Modeling soil respiration based on carbon, nitrogen, and root mass across diverse Great Lake forests. Agricultural and Forest Meteorology 149:1722-1729.

Mason, O. U., C. A. Di Meo-Savoie, J. D. Van Nostrand, J. Zhou, M. R. Fisk, and S. J. Giovannoni. 2008. Prokaryotic diversity, distribution, and insights into their role in biogeochemical cycling in marine basalts. The ISME Journal.

Mason, O. U., U. Stingl, L. J. Wilhelm, M. M. Moeseneder, C. A. Di Meo-Savoie, M. R. Fisk, and S. J. Giovannoni. 2007. The phylogeny of endolithic microbes associated with marine basalts. Environmental microbiology 9:2539-2550.

McCune, B., and B. A. Caldwell. 2009. A single phosphorus treatment doubles growth of cyanobacterial lichen transplants. Ecology 90:567-570.

McDonald, V., E. Pond, M. Crowley, B. McKee, and J. Menge. 2007. Selection for and evaluation of an avocado orchard soil microbially suppressive to Phytophthora cinnamomi. Plant & Soil 299:17-28.

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. N. Smithgal, D. C. White, A. M. Spain, Y. Sanchez-Rosario, L. R. Krumholz, S. D. Kelly, K. M. Kemner, J. P. McKinley, S. M. Heald, M. A. Bogle, D. B. Watson, and J. D. Istok. 2009. Treatment of Nitric Acid-, U(VI)-, and Tc(VII)-Contaminated Groundwater in Intermediate-Scale Physical Models of an In Situ Biobarrier. Environmental science & technology 43:1952–1961.

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 & Environmental Microbiology 73:5885-5896.

Moore-Kucera, J., and R. P. Dick. 2008. PLFA profiling of microbial community structure and seasonal shifts in soils of a Douglas-fir chronosequence. Microbial Ecology 55:500-511.

Moore-Kucera, J., and R. P. Dick. 2008. A pulse-chase method to 13-carbon-label douglas-fir seedlings for decomposition studies. Soil Science 173:46-53.

Moore-Kucera, J., A. Nina Azarenko, L. Brutcher, A. Chozinski, D. D. Myrold, and R. Ingham. 2008. In search of key soil functions to assess soil community management for sustainable sweet cherry orchards. HortScience 43:38-44.

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.

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.

Norton, J. M., M. G. Klotz, L. Y. Stein, D. J. Arp, P. J. Bottomley, P. S. Chain, L. J. Hauser, M. L. Land, F. W. Larimer, M. W. Shin, and S. R. Starkenburg. 2008. Complete genome sequence of Nitrosospira multiformis, an ammonia-oxidizing bacterium from the soil environment. Applied & Environmental Microbiology 74:3559-3572.

Nunoura, T., F. Inagaki, M. E. Delwiche, F. S. Colwell, and K. Takai. 2008. Subseafloor microbial communities in methane hydrate-bearing sediment at two distinct locations (ODP Leg204) in the Cascadia Margin. Microbes and Environments 23:317-325.

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

Ochiai, N., M. L. Powelson, F. J. Crowe, and R. P. Dick. 2008. Green manure effects on soil quality in relation to suppression of Verticillium wilt of potatoes. Biology & Fertility of Soils 44:1013-1023.

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

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

Park, S., and R. L. Ely. 2008. Thermotolerant hydrogenases: Biological diversity, properties, and biotechnological applications. Archives of Microbiology 189:541-548.

Park, S., and R. L. Ely. 2009. Whole-genome transcriptional and physiological responses of Nitrosomonas europaea to cyanide: Identification of cyanide stress response genes. Biotechnology and Bioengineering 102:1645-1653.

Péchy-Tarr, M., D. J. Bruck, M. Maurhofer, E. Fischer, C. Vogne, M. D. Henkels, K. M. Donahue, J. Grunder, J. E. Loper, and C. Keel. 2008. Molecular analysis of a novel gene cluster encoding an insect toxin in plant-associated strains of Pseudomonas fluorescens. Environmental microbiology 10:2368 - 2386.

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.

Poulson, R., C. Siebert, M. J., and W. Berelson. 2006. Authigenic Molybdenum Isotope Signatures in Marine Sediments. Geology 34:56-59.

Puente, M. E., C. Y. Li, and Y. Bashan. 2009. Rock-degrading endophytic bacteria in cacti . Environmental and Experimental Botany 66:389-401.

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.

Radniecki, T. S., L. Semprini, and M. E. Dolan. 2009. Expression of merA, trxA, amoA, and hao in continuously cultured Nitrosomonas europaea cells exposed to cadmium sulfate additions. Biotechnology and Bioengineering 104:1004-1011.

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.

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., 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.

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.

Rontani, J.-F., R. Harji, S. Guasco, F. G. Prahl, J. K. Volkman, N. B. Bhosle, and P. Bonin. 2008. Degradation of alkenones by aerobic heterotrophic bacteria: Selective or not?. Organic Geochemistry 39:34-51.

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. Ingle. 2009. Monitoring of redox state in a dechlorinating culture with immobilized redox indicators. Journal of Environmental Monitoring 11:1028-1036.

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., 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.

Ryan, M. G., and B. E. Law. 2005. Interpreting, measuring, and modeling soil respiration. Biogeochemistry 73:3-27.

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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.

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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.

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