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May 2008

SBI Summer Workshop

Mark your calendars! The 2008 SBI and ESB IGERT Workshop will be June 15 to June 17th, 2008. It will be held at the Hallmark Resort in Newport, Oregon and have a format similar to last year with both oral presentations and poster sessions. The meeting agenda will be posted on the SBI Web site soon. Please note that the abstracts for poster and talks should be sent to Garrett Jones by June 6, (541) 737-2751,


Recent Publications

Check out what your colleagues are writing! In March and April 2008, OSU researchers published the following journal articles related to the subsurface biosphere. If you know of an article that is missing, please email

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. Published article online 03 Apr 2008.

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.

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.

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.

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.

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.

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. Published online ahead of print on 4 April 2008.

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.

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.


Upcoming Seminars

Tuesday, May 13, 2008, 3:00 p.m., ALS 4001. Genomes, Silence, and the Big Deal about Small RNA. Speaker: James C. Carrington, Professor of Botany and Plant Pathology and Director of the Center for Genome Research and Biocomputing. Dr. Carrington received the 2007 Sigma Xi Researcher of the Year Award, and in this lecture he will describe the research that led to this award.

Thursday, May 22nd, 2008, 4:00 p.m., Burt 193. Earth's Subsurface Biosphere IGERT Seminar. Dr. Steven L. Bryant, Associate Professor, Petroleum and Geosystems Engineering, Crockell School of Engineering, The University of Texas at Austin. 4:00 p.m. on the OSU campus, 193 Burt.

Thursday, May 29th, 2008, 4:00 p.m., 162 Science Building 2, Portland State University. Earth's Subsurface Biosphere IGERT Seminar. Speaker: Dr. Ron Crawford, Director - Environmental Biotechnology Institute and Distinguished Professor, University of Idaho.


Upcoming Abstract Deadlines and Workshops

June 16, 2008. Deadline to submit abstracts for the International Symposium for Subsurface Microbiology. The symposium will be held November 16-21, 2008 in Shizuoka, Japan.

June 30, 2008. Deadline to submit abstracts for the Fifth International Conference on Remediation of Contaminated Sediments, to be held in Jacksonville, Florida, February 2-5, 2009. Presentations will cover all current aspects of contaminated sediment characterization and assessment, management, and remediation and restoration.

July 21, 2008. Deadline to submit abstracts for the AGU Chapman Conference on Biogeophysics. The meeting will be held October 13-16 in Portland, Maine. “Biogeophysics” is a rapidly evolving Earth science discipline concerned with the geophysical signatures of (1) microbial cells themselves in the Earth, (2) the interaction between microorganisms and subsurface geologic media, and (3) alteration of the physical properties of geologic media as a result of microbial activity. The objective of the Chapman Conference is to define the current state of the science, identify the critical questions facing the community and to generate a roadmap for firmly establishing biogeophysics as a critical subdiscipline of earth science research.

July 28 – August 8, 2008, Bozeman, MT. Biofilms Summer School. Offered by the Center for Biofilm Engineering -Biofilm structure and function research group at Montana State University.

Link to a calendar of other related events...


Funding Opportunities for Students

Charles A. and Anne Morrow Lindbergh Grants - For projects that further the Lindberghs' vision of a balance between the advance of technology and the preservation of the natural/ human environment. Lindbergh Grants are made in the following categories: (1) agriculture; (2) aviation/aerospace; (3) conservation of natural resources, including animals, plants, water, and general conservation (land, air, energy, etc.); (4) education, including humanities/education, the arts, and intercultural communication; (5) exploration; (6) health, including biomedical research, health and population sciences, and adaptive technology; and (7) waste minimization and management. Grants are awarded for up to $10,580 each (the cost of building the Spirit of St. Louis in 1927). Applications due: June 12, 2008.

OSU Undergraduate Research, Innovation, Scholarship and Creativity Grants for 2008-2009 - The URISC Fund is intended to enable undergraduate students to initiate a scholarly relationship with faculty members early in their academic careers. Awards are made to support scholarly, creative, and research activities and can support student wages, travel and some other expenses. Proposals due June 16, 2008.


Funding Opportunities for Faculty

NSF Hydrologic Science - Hydrologic Sciences 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. Proposals due: June 1, 2008.

U.S. Environmental Protection Agency (EPA) Broad Agency Announcement for Conferences, Workshops, and/or Meetings - Grants for the planning, arranging, administering and/or conducting of conferences, workshops, and/or meetings that focus on research to protect human health and safeguard the environment. Specifically, EPA is interested in supporting scientific and technical research conferences that address the following research program areas: (1) human health; (2) ecosystems; water and security; (3) economics and sustainability; (4) air and global climate change; and (5) technology. Grants range from $15-75K. Proposals due: June 5, 2008 and December 9, 2008.

NASA ROSES Planetary Protection Research - Planetary protection involves preventing biological contamination on both outbound and sample return missions to other planetary bodies. This program solicits research in the following areas: characterizing the limits of life in laboratory simulations of planetary environments or in appropriate Earth analogs, and particularly studies of the potential and dynamics of organism survival and reproduction in conditions present on the surface or subsurface of Mars; modeling of planetary environmental conditions and transport processes that could permit mobilization of spacecraft-associated contaminants to locations in which Earth organisms might thrive; the development or adaptation of modern molecular analytical methods to rapidly detect, classify, and/or enumerate the widest possible spectrum of Earth microbes carried by spacecraft; new or improved methods, technologies, and procedures for spacecraft sterilization, that are compatible with spacecraft materials and assemblies. Total annual program budget: ~ $300-500K, 2-4 new awards expected. Notice of intent due June 26, 2008; full proposals due September 5, 2008.

NSF Directorate for Biological Sciences - Research Coordination Networks in Biological Sciences (RCN). 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. This program has recently made $500k awards to place-based (e.g. the Elwha Basin) and topic-based (e.g. denitrification) projects. Proposals are due June 30, 2008.

NSF Long Term Research in Environmental Biology. This program encourages the submission of proposals aimed at generating extended time series of biological and environmental data that address ecological and evolutionary processes aimed at resolving important issues in environmental biology. Researchers must have collected at least six years of previous data to qualify for funding. The proposal also must present a cohesive conceptual rationale or framework for ten years of research. Questions or hypotheses outlined in this conceptual framework must guide an initial 5-year proposal as well as a subsequent, abbreviated renewal. Together, these will constitute a decadal research plan appropriate to begin to address critical and novel long-term questions in environmental biology. Proposals due July 9, 2008.

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