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March 3, 2009
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Two Funding Opportunities from the SBI Available

Graduate Fellowships for Incoming Students - These graduate fellowships are for $5,000 and are intended to help faculty attract highly qualified graduate students interested in subsurface biosphere research. The awards can be used to supplement financial offers such as TA's and GRA's. Nominations for fellowships received prior to March 15, 2009, will be given first priority. Note that the Graduate School offers a similar $5000 scholarship through the Graduate Diversity Recruitment Bonus Program which also has a March 15 deadline.

Summer 2009 Undergraduate Internships - The program provides up to $4,000 to help faculty support a summer intern. It focuses on, but is not limited to, under-represented minority and women students. The SBI Web site has examples of past internship projects. Applications for internships are now being accepted and will be reviewed on receipt. Application by April 30, 2009, is encouraged.

For more information about these programs follow the links or contact


In the News

Dig It - Oregon's Agricultural Progress magazine features OSU soil scientists in its Winter 2009 issue.


2008 OSU Publications Related to the Subsurface Biosphere

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

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.

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.

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.

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.

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, 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.

Chastanet, J., and B. D. Wood. 2008. Mass transfer process in a two-region medium. Water Resources Research 44:W05413.

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.

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.

Eberly, J. O., and R. L. Ely. 2008. Thermotolerant hydrogenases: biological diversity, properties, and biotechnological applications. Critical Reviews in Microbiology 34:117-130.

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.

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

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.

Kageyama, S. A., K. G. Mandyam, and A. Jumpponen. 2008. Diversity, Function and Potential Applications of the Root-Associated 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.

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.

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.

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.

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.

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.

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

Park, S., and R. L. Ely. 2008. Genome-wide transcriptional responses of Nitrosomonas europaea to zinc. Archives of Microbiology 189:541-548.

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.

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.

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.

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.

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.

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.

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.

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., 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.

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.

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.


Upcoming Events

Wednesday, March 4, 3:30-4:30 p.m., ALS 4001. Venture Capital and Company Formation in the University, CGRB Seminar. Speaker: John Hamer, Burrill & Company. Host: Scott Givan.

Thursday, March 19, 4:00 p.m., Burt 193. Are There Predictable Soil Microbial Community Responses to Climate Change? (SBI Seminar) Speaker: Eoin Brodie, Ph.D., research scientist in the Earth Sciences Division, Lawrence Berkeley National Lab. Abstract: A critical first step towards predicting the impacts of climate change on terrestrial ecosystems involves determining the fundamental controllers of soil microbial community composition and structure, and subsequently evaluating climate change scenarios that alter these controllers. In this presentation I will discuss how despite this enormous phylogenetic and physiological complexity, soil bacteria and archaea community structure could be predicted from a limited number of environmental factors. I will also present data from greenhouse experiments where we test predictions about the impact of changing precipitation patterns on soil microbial community structure. FMI: Rick Colwell,

Sunday, March 22 - Saturday, March 28. FE538 Field Hydrology. An intense, hands-on field course held at the HJ Andrews Experimental Forest. You will learn how to program data loggers, develop a snow course, work with snow pillow data, conduct steady-state stream tracer experiments, measure groundwater-streamflow interactions, measure soil hydraulic properties, set-up a met station and compute a surface energy balance (among other things). The course is limited to an enrollment of 15. There will be an organizational meeting on March 6 (4-5pm, Peavy 004) for those planning to take the course. Led by Jeff McDonnell, Department of Forest Engineering, Resources and Management.

Wednesday, April 8, 3:30-4:30 p.m., ALS 4001. Exploring the Energy Landscape: Disorder, Dynamics, and Protein Function, CGRB Seminar. Speaker: Peter Wright, Department of Molecular Biology, The Scripps Research Institute. Host: Andy Karplus.


Conference Information

May 5-8, 2009 in Baltimore, Md. Batelle 10th International In Situ and On-Site Bioremediation Symposium - The symposium integrates recent developments in risk assessment, fundamental research, and innovative engineering applications for both traditional and emerging contaminants. The Bioremediation Symposium offers a broad perspective on environmental biotechnology worldwide.

Sunday, July 12 - Friday, July 17, Mount Holyoke College, Ma. Gordon Research Conference on Applied and Environmental Microbiology (From Single Cells to the Environment). The Conference will feature a wide range of topics such as single cell techniques (including genomics, imaging, and NanoSIMS), microbial diversity at scales ranging from clonal to global, environmental "meta-omics," biodegradation and bioremediation, horizontal gene transfer from viruses to bacteria and archaea, animal microbiomes and symbioses. The Conference will bring together investigators who are at the forefront of their field, and will provide opportunities for junior scientists and graduate students to present their work in poster format and exchange ideas with leaders in the field. Some poster presenters will be selected for short talks. Applications must be submitted by June 21, 2009, but early application is recommended.

Sunday, July 19 - Friday, July 24, Andover, NH. Gordon Research Conference on Microbial Population Biology. The meeting will include sessions on the evolution of infectious diseases, social evolution, the evolution of symbioses, experimental evolution, adaptive landscapes, community dynamics, and the evolution of protein structure and function. While genomic approaches continue to make inroads, broadening our knowledge and encompassing new questions, the conference will also emphasize the use of experimental approaches to test hypotheses decisively. Applications for this meeting must be submitted by June 28, 2009, but early application is recommended.

Link to a calendar of other related events...


Opportunities for Students

2009 ASM Presentation Institute - May 16 and 17 in Philadelphia, Pa. (immediately prior to the ASM General Meeting). Graduate students at the master’s or doctoral level are encouraged to apply for a two-day workshop that helps participants develop the skills needed to make successful presentations at scientific meetings and to interact professionally with colleagues. Apply by March 15, 2009.

Sigma Xi Student Research Grants - Grants of up to $1,000 to support undergraduate and graduate student research in any field of science and engineering. International students and non-U.S. citizens are encouraged to apply. Proposals due March 15, 2009.

National Ground Water Research and Educational Foundation Len Assante Undergraduate Scholarships - The scholarships are awarded to young people in ground water-related fields. Applications due April 1, 2009.

NSF Doctoral Dissertation Enhancement Projects (DDEP) - NSF's Office of International Science and Engineering supports dissertation research conducted by graduate students at a foreign site. Students are expected to work in close cooperation with a host country institution and investigator. The applicant is responsible for making all necessary arrangements with the host country institution and scientist. The doctoral faculty advisor, on behalf of the student, submits the dissertation enhancement proposal. Proposals may be submitted at any time.

Ewing Marion Kauffman Foundation Entrepreneur Postdoctoral Fellowship - The new program will train scientists to commercialize their technology innovations into start-up businesses. Participants will receive training on how to evaluate their research for marketplace potential and will learn the process of taking promising research forward for commercialization. Each fellow will be matched with a business mentor who has a science background, will receive a customized internship experience, and will be enrolled in intensive entrepreneurship workshops, where they will network with entrepreneurs and experts from the legal, business, and financial communities. Fellows will also work with an academic advisor to understand specifically how to commercialize their innovations and research findings by starting a business. Fellows receive a one-year stipend plus a travel and conference stipend to attend a business or entrepreneurship conference. The candidate must have received either a Ph.D. or M.D. and be in a postdoctoral research position by the start of the fellowship program to be eligible. Deadline:  May 1, 2009.

Funding Opportunities for Faculty

(listed by due date)

3 April 2009 OSU Promising Scholar Award.

Description: A new OSU award designed to recognize the scholarship of junior faculty.
Funding Details
: The award consists of a $1,500 honorarium.

3 April 2009 OSU Impact Award for Outstanding Scholarship.

Description: This recognizes faculty who have demonstrated outstanding scholarship in a specific project or activity resulting in substantial impact beyond the university setting. The recipient will be invited to present highlights of their work at a public presentation.
Funding Details
: The award consists of a $2,500 honorarium.

30 April 2009. Naval Research Laboratory, Applications of Molecular Biology, Biochemistry, Analytical Chemistry, BAA 61-07-05.

Description: Areas of primary interest include: (1) characterization of environmental processes and their application to remediation and restoration technologies; (3) unique analytical chemistry tools for more efficient and cost effective sampling processing; (4) genetic- and molecular biological-based tools (4a) techniques for the preservation and characterization of cells, tissue and biomaterials; (5) improved and alternative fuel sources.

30 April 2009. Naval Research Laboratory, Seafloor Sciences BAA 74-07-02.

Description: NRL invites proposals on biological, geological, geochemical, historical, and subsequent diagenetic processes that control the distribution, range, and variability of sediment physical properties including bathymetry, roughness, and subseafloor morphology. Proposals that develop state-of-the-art laboratory, in situ, and remote sensing instrumentation to measure required geophysical, geoacoustic, and geotechnical properties both under controlled laboratory conditions and the field are also encouraged.

21 May 2009. NSF Course, Curriculum, and Laboratory Improvement (CCLI).

Description: This program seeks to improve the quality of science, technology, engineering, and mathematics (STEM) education for all undergraduate students. The program supports efforts to create new learning materials and teaching strategies, develop faculty expertise, implement educational innovations, assess learning and evaluate innovations, and conduct research on STEM teaching and learning. The program supports three types of projects representing three different phases of development, ranging from small, exploratory investigations to large, comprehensive projects.

29 June 2009. NSF Directorate for Biological Sciences - Research Coordination Networks in Biological Sciences (RCN).

Description: The goal of this program is to encourage and foster interactions among scientists to create new research directions or advance a field. Innovative ideas for implementing novel networking strategies are especially encouraged. Groups of investigators will be supported to communicate and coordinate their research, training and educational activities across disciplinary, organizational, institutional, and geographical boundaries. The proposed networking activities should have a theme as a focus of its collaboration. The focus could be on a broad research question, a specific group of organisms, or particular technologies or approaches.

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