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October 2, 2009
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Recent Publications

Check out some of the papers produced by your OSU colleagues in the last several months. Know of some papers that are missing from this list? Help us keep up to date by sending us the citation:

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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

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.

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.

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., 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.

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.

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.

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.

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.

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.

White, H. K., C. E. Reimers, E. E. Cordes, G. F. Dilly, and P. Girguis. 2009. Quantitative population dynamics of microbial communities in plankton-fed microbial fuel cells. The ISME Journal 3:635–646.

Wood, B. D. 2009. The role of scaling laws in upscaling . Advances in Water Resources 32:723-736

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.

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.


Upcoming Events

Monday, October 5, ALS 4000, 4 p.m. Detrital Inputs Influence the Stabilization of Soil Organic Matter. Presenter - Kate Lajtha.

Wednesday, October 14 2 p.m., Richardson 313. Investigating the terrestrial carbon cycle at regional, continental, and global scales. Speaker: Dave Turner, Associate Professor, Dept. of Forest Ecosystems and Society.

Monday, October 19 4 p.m., ALS 4000. Organic Nitrogen Cycling in Ectomycorrhizal Mat and Non-Man Soils of An Old-Growth Douglas-Fir Forest. Presenter - Lydia Zeglin.

Thursday, October 22 4 p.m., Wilkinson 108. Environmental Tracers in Modern Hydrogeology: Reducing Uncertainty in Ground Water Flow Estimation (2009 Darcy Lecture). Speaker: Peter Cook, CSIRO Land and Water.

Wednesday, October 28, 2 p.m., Richardson 313. Arguing from the specific to the general: Lessons learned in the trenches of research. Lisa Ganio, Associate Professor, Dept. of Forest Ecosystems and Society, OSU.

Sunday, October 18 - Wednesday, October 21, Portland, Oregon. 2009 Geological Society of America Annual Meeting. The theme is From Volcanoes to Vineyards: Living with Dynamic Landscapes. Some examples of sessions relevant to SBI researchers: Characterizing, Predicting, and Managing Long-Term Contaminant Flux for Complex Subsurface Environments; Coupled Surface-Subsurface Modeling across a Range of Temporal and Spatial Scales; Fate, Transport, and Effects of Pesticides in the Environment; Diurnal Biogeochemical Processes in Rivers, Lakes, and Shallow Groundwater; Science of Geologic Carbon Sequestration.

Link to a calendar of other related events...


Congratulations to two SBI summer interns who recently received prestigious awards!

  • Paul Dornath, a senior in environmental engineering, has been awarded the Joe Hendricks Scholarship for Academic Excellence by the Oregon Statue University Honors College. Paul worked with Skip Rochefort (CBEE) and studied the leaching potential of new plastics.
  • Michelle Adlong, a senior in environmental engineering, is the winner of the 2009 AIChE Othmer National Scholarship. Michelle is one of only 15 students in the country to be selected for this award. For her summer internship, Michelle worked with Jeff Nason (CBEE) and studied the environmental effects of carbon nanoparticles.


Opportunities for Students

Sigma Xi, Research Grants for Undergraduate and Graduate Students. Sigma Xi, a scientific organization, offers grants-in-aid to fund research in science and engineering disciplines. Grant amounts range from $100 to $1,000 (with an average award of $600). Deadlines are October 15 and March 15.

NSF Graduate Research Fellowships. Consider applying for one of these prestigious fellowships! They provide three years of support for graduate study leading to research-based master’s or doctoral degrees and are intended for students who are in the early stages of their graduate study. Applications are due November 2-12, depending on discipline.

Fall 2009 EPA Science To Achieve Results (STAR) Fellowships For Graduate Environmental Study - These prestigious awards provide two to four years of full graduate support. For this year's solicitation, fellowship categories are aligned with general environmental research and development areas rather than specific disciplines - several research topics relate to the subsurface biosphere including global change, water quality: hydrogeology and surface water, science and technology for sustainability: energy among others. Applications due October 22, 2009.

National Physical Science Consortium Graduate Fellowships - The NPSC has one primary objective: increase the number of qualified U.S.- citizen PhDs in the physical sciences and related engineering fields, emphasizing recruitment of a diverse applicant pool of women and historically underrepresented minorities. Fellowship fields include: physical sciences, biochemistry, computer science, and related fields of science and engineering. There is both a traditional, multiyear fellowship program and a dissertation support program. Applications due November 5, 2009.

OSU Undergraduate Research, Innovation, Scholarship and Creativity (URISC) Program - The OSU Research Office is accepting applications for the academic year 2009-10 (Winter and/or Spring terms). Applications due November 2, 2009.

Environmental Engineers of the Future Masters Fellowship - Preference is given to qualified students that are currently enrolled in a qualified undergraduate program and planning to attend one of the participating universities to obtain a masters degree in environmental engineering. Upon graduation, the student must work for one of the sponsoring firms/agencies for a 2-year period. Funding of up to $10,000. Applications due December 1, 2009.


Opportunities for Faculty

(listed by due date)

16 October 2009. OSU General Research Fund (GRF).

Description: The intent of the GRF is to enable OSU faculty to carry out scholarly, creative work that should lead to the pursuit of other funding sources, or promote the development of scholarly activities. Projects funded through the GRF could include pilot research, emergency funding, emerging research opportunities, new research field or new research field for investigator, developing research laboratories, or centrally shared research resources.
Funding Details: Maximum award is $10,000.

26 October 2009. OSU Research Equipment Reserve Funds (RERF).

Description: Research Equipment Reserve Funds (RERF) may be used to acquire, repair, renovate, or improve EQUIPMENT directly used for research. The equipment may be inventoried capital equipment =>$5,000 per unit, fabricated capitalized equipment, or minor equipment costing less than $5,000 per unit which lasts at least two years.
Funding Details: Award amounts vary and require a 20% match from department, college or other funds. The Research Office budgets a total of approximately $800K per year for these competitive distributions.

17 November 2009. NSF Dynamics of Coupled Natural and Human Systems (CNH).

Description: This competition promotes quantitative, interdisciplinary analyses of relevant human and natural system processes and complex interactions among human and natural systems at diverse scales. Projects usually have three components: an integrated, quantitative systems-level method of inquiry, an education component, and a global perspective.
Funding Details: Grants are for up to $1.5M.

5 December 2009. NSF Hydrologic Science.

Description: Hydrologic Science focuses on the flow of water and transport processes within streams, soils, and aquifers. Particular attention is given to spatial and temporal heterogeneity of fluxes and storages of water and chemicals over a wide range of scales, to geolimnology and to interfaces with the landscape, microbial communities, and coastal areas. Studies may also deal with processes in aqueous geochemistry and with the physical, chemical, and biological processes within water bodies. Study of these processes requires expertise from many basic sciences and mathematics, and proposals often require joint review with related programs.

The SBI has funding available for proposal development and maintains a list of external grant opportunities related to the subsurface biosphere.

This newsletter is distributed by OSU's Subsurface Biosphere Initiative - an interdisciplinary consortium of faculty and students who share interests in underground ecosystems. The newsletter is distributed through the SBI email lists. To subscribe or unsubscribe, go to Questions, comments and newsletter topics may be sent to the Newsletters are also available on the Web at