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The Subsurface Biosphere and Sustainable Natural Resources

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Related OSU Publications 2005-2008

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.

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-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.

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.

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

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

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

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.

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.

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.

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.

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.

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

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

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. 2006. Product repression of alkane monooxygenase expression in Pseudomonas butanovora. Journal of Bacteriology 188:2586-2592.

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

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

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

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.

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.

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

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.

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

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

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.

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.

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.

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

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

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

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 and 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.

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.

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.

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.

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.

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.

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.

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 and Environmental Microbiology 72:6965-6971.

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.

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

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

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.

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.

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.

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

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.

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

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.

Treseder, K. K., and A. Cross. 2006. Global Distributions of Arbuscular Mycorrhizal Fungi. Ecosystems 9:305-316.

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.

Wei, X., N. Vajrala, L. Hauser, L. A. Sayavedra-Soto, and D. J. Arp. 2006. Iron nutrition and physiological responses to iron stress in Nitrosomonas europaea. Archives of Microbiology 186:107-118.

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.

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.

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 and 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, 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.

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.

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