SBI Newsletter Header

December 2008

Research Features:

Ellen Swogger in a Shizuoka tea house with other ISSM researchers. A grad student's perspective on 7th International Symposium for Subsurface Microbiology - Ellen Swogger, a PhD student in environmental engineering, just returned from Shizuoka, Japan. Read a short Web interview where Ellen describes her experience.
A New Grant to Study Carbon Dynamics in Forest Soils - In September, Kate Lajtha, professor in the Department of Botany and Plant Pathology, received a 5-year grant to continue studies of carbon storage and accumulation in forest soils at the Andrews Experimental ForestRead a Web interview where Kate discusses the project and what the new grant will enable. David Diaz sweeping one of the DIRT plots.


Upcoming Events

Wednesday, 10 December 2008, 10:00 a.m., Burt 193. Oceanography Ph.D. defense presentation by Mark Nielsen: Utilization of Natural and Supplemental Biofuels for Harvesting Energy from Marine Sediments.


A benthic microbial fuel cell (BMFC) is an electrochemical device that generates current from the redox gradient at the sediment-water interface.Early prototypes had anodes buried in anoxic sediments and cathodes in overlying water. The BMFCs described in this dissertation are based on a chamber design that enables the use of high surface- area fiber electrodes and facilitates enhanced mass transport to the anode.

Results from Yaquina Bay, OR, show that mass transport resistance accounted for at least 93% of the total internal resistance for a particular BMFC configuration. Power output was increased 18-fold by mechanically induced fluid transport through the anode chamber. At a cold seep in Monterey Canyon, CA, naturally driven advection resulted in a five-fold increase in power from a BMFC with low-pressure check  valves relative to an identical BMFC with high-pressure check valves.  

Enhanced transport coincided with a change in the microbial community on the anode from one dominated by epsilonproteobacteria to one with relatively even representation from deltaproteobacteria, epsilonproteobacteria, firmicutes and flavobacteria/cytophaga/ bacterioides. Laboratory experiments investigated the effect of adding supplemental carbon sources to anode chambers. Repeated lactate injections appeared to stimulate sulfate reduction resulting in short term power gains but did not apparently shift the process responsible for baseline current. When a specific inhibitor of sulfate reduction was added, lactate-supplemented and unsupplemented BMFCs performed similarly.

BMFCs have been proposed as power sources for monitoring systems in remote locations. Practical implementation of this technology is governed by three conditions: 1) low-voltage current must be stepped up to meet the requirements of off-the-shelf electronic devices, 2) modest power production and variable power demands require integrated energy storage, and 3) BMFCs should be operated at the most efficient potential for energy production.  A combination power converter/ potentiostat/rechargeable battery system was designed based on these considerations and tested with a chambered BMFC in Yaquina Bay, OR.  

The BMFC provided intermittent power to an acoustic receiver, and results highlight the need to increase power, make design improvements to better seal the chamber to the sediment and increase the capacity for energy storage.

Thursday, 11 December 2008, 9:00 a.m., Owen 106. Environmental engineering Ph.D. defense presentation by Andy Sabalowsky: Electron Donor and Chlorinated Ethene Effects on Activity and Community Composition in Anaerobic Reductively Dechlorinating Consortia.


This research focused on anaerobic transformation of trichloroethene (TCE), a groundwater contaminant. The mixed anaerobic Evanite culture (EV) was studied to determine community behavior and composition in response to different electron donors and chloroethene electron acceptors. The potential toxicity of high concentrations of TCE and its daughter product cis-1,2-dichloroethene (cDCE) was also evaluated.

The electron donor and acceptor study was performed in three continuous flow stirred tank reactors (CFSTRs) operated with 12.5 day cell retention times. Each reactor received either TCE or vinyl chloride (VC) and a soluble electron donor at twice the stoichiometric hydrogen formation potential to dechlorinate the influent TCE or VC completely to ethylene (ETH). The EV inoculum for the CFSTRs contained the critical dehalogenating organisms, Dehalococcoides spp., as well as four reductive dehalogenase genes found only in Dehalococcoides and commonly referred to as the pceA, tceA, vcrA and bvcA genes. CFSTR assessments consisted of: continual chloroethene and organic acid monitoring; periodic batch rate measurements under non-limiting conditions for TCE, cDCE and VC dechlorination; and quantitative polymerase chain reaction (qPCR) analyses of the aforementioned reductase genes plus the Dehalococcoides 16S rRNA and universal Bacteria 16S rRNA genes.  

Formate was a better electron donor for TCE dechlorination in terms of completeness and longevity of dechlorination, and in maintaining Dehalococcoides populations. In the VC fed reactor, formate could not sustain dechlorination, but supported an unknown TCE to cDCE dechlorinating population. The lactate fed CFSTR produced a Dehalococcoides community dominated by the tceA gene, while the two formate-fed systems were generally dominated by the vcrA gene. Dehalococcoides 16S gene quantities correlated well with cDCE and VC batch-measured dechlorination rates.  cDCE and VC maximum dechlorination rates could be predicted by qPCR Dehalococcoides 16S gene measurements.

High chloroethene concentration toxicity effects were studied using batch-fed reactors, a CFSTR and a recirculating packed column. In all reactor types TCE dechlorination activity was lost as cDCE concentrations reached 9 to 12 mM. A toxicity model based on cDCE and TCE concentrations directly increasing the endogenous decay coefficients of the cultures fit the temporal concentration responses observed in all reactors, with slightly different toxicity constants.

15-19 December 2008. CBEE is offering a HAZWOPER training course at the cost of one credit for OSU students. The training is required of employees engaged in hazardous waste operations, such as removal or handling of underground tanks and/or piping, contaminated soil and/or groundwater, and many subsurface investigations. E-mail Ann Kimerling, if you are interested in participating. An 8 hour HAZWOPER refresher will also be offered at the same time.


Conference Information

6 January 2009. Deadline to propose a topic for the Geological Society of America Annual Meeting. The meeting will be held at Portland, Oregon, from October 18-21, 2009. The meeting theme is: From Volcanoes to Vineyards: Living with Dynamic Landscapes.

5-8 January 2009. Abstracts due for the 109th General Meeting of the American Society for Microbiology. The meeting will be held May 17-21, 2009, in Philadelphia, Pa. There are many session topics related to the subsurface biosphere including: Microbes from Diverse Environments, Molecular and General Biology of Archaea, Biogeography of Microorganisms, Subsurface Microbiology, and Environmental Biofilms. There will also be workshops on many topics including "DNA Sequence-Based Identification of Bacteria: Generation, Analysis of Data, and Interpretation of Results" and "DNA Microarrays: Experimental Design and Data Analysis".

14 January 2009. Deadline to submit abstracts for the 10th International Symposium on Bacterial Genetics and Ecology. It will be held in the historic academic town of Uppsala, Sweden, from 15-19 June 2009. The 10th BAGECO conference will focus on bacteria in the world around us, and the implications of a changing climate and other anthropogenic influences on bacterial genetics and ecology. Climate change is now accepted as a serious challenge to global ecosystems, but the extent of its impact on bacterial communities has only begun to be explored. Importantly, microbial community activity and function may change as a result of changing climatic and other human-induced conditions and these changes may further impact ecosystems.

Link to a calendar of other related events...


Opportunities for Students

Student Travel Grants for the 109th General Meeting of the American Society for Microbiology - Awards of $500 will be given to approximately 160 students who will be presenting a poster at the meeting. See the note above about the abstract submission deadline. Letters of recommendation for student travel grants are due January 15, 2009. There is also a travel grant program for underrepresented minority (URM) post-doctoral scholars and faculty which are due January 30, 2009.

Association for Women in Science Undergraduate and Predoctoral Fellowships. Awards of $1,000 are to female students enrolled in a behavioral, life, physical, or social science or engineering programs. The award may be used for any aspect of education, including tuition, books, housing, research, travel and meeting registration, or publication costs, for example. Applications due: January 23, 2009, for undergraduates; January 30, 2009 for predocs.

American Philosophical Society, Lewis and Clark Fund in Exploration and Field Research in Astrobiology - The program provides funding for field studies in any area of interest to astrobiology. Its scope includes research of contemporary locations on Earth that might be similar to early earth and to environments elsewhere in our Solar System. Its scope also includes investigations into extreme natural environments on Earth. Grants will be available to graduate students and postdoctoral and junior scientists who wish to participate in field studies for their theses or for other purposes. Awards are for up to $5,000. Grants are payable to the individual applicant. Applications due February 1, 2009.

ASM's Microbiology Undergraduate Research Fellowship - The goal of this program is to increase the number of underrepresented undergraduate students who wish to, and have demonstrated the ability to pursue graduate careers (Ph.D. or MD/Ph.D.) in microbiology. Students will have the opportunity to conduct full time summer research with an ASM member at their home institution or at a host institution, and present research results at the Annual Biomedical Research Conference for Minority Students and the ASM General Meeting. The program provides up to $5,850. Applications due February 1, 2009.


Funding Opportunities for Faculty

(listed by due date)

6 January 2009. USEPA STAR Integrated Design, Modeling, and Monitoring of Geologic Sequestration of Anthropogenic Carbon Dioxide to Safeguard Sources of Drinking Water.

Description: Seeking applications to conduct research to support the development of sound risk management strategies for the underground injection of anthropogenic carbon dioxide (CO2) in candidate subsurface geologic formations. To further the scientific understanding of this practice, research is needed to investigate how integrating approaches in design, siting, modeling and monitoring of CO2 in the subsurface can provide safe and effective storage, mitigate potential risks, and prevent endangerment of existing and potential sources of drinking water.
Funding Details: Four three-year awards of up to $900K each anticipated.

8 January 2009. DOD Strategic Environmental Research & Development Program - Core Solicitation.

Description: Specific Topics within the Environmental Restoration category include: ERSON-10-02 - The Impact of Contaminant Storage in Low-Permeability Zones on Chlorinated Solvent Groundwater Plumes; ERSON-10-03 - Mechanisms of Contaminant Interaction with Soil Components and Its Impact on the Bioavailability of Contaminants; ERSON-10-04 - Improved Fundamental Understanding of Contaminant Bioavailability in Aquatic Sediments.

12 January 2009. NSF Molecular and Cellular Biosciences (MCB) - Cellular Systems Cluster.

Description: The Cellular Systems Cluster focuses on the structure, function, and regulation of plant, animal and microbial cells, and their interactions with the environment and with one another. Areas supported include studies of the structure, function, and assembly of cellular elements, such as the cytoskeleton, membranes, organelles, intracellular compartments, intranuclear structures, and extracellular matrix, including eukaryotic and prokaryotic cell walls and envelopes. In addition, support is provided for the study of intracellular and transmembrane signal transduction mechanisms and cell-cell signaling processes, including those that occur in biofilms. Research on cellular recognition and self defense mechanisms is included.

12 January 2009. NSF - Division of Integrative Organismal Systems -Physiological and Structural Systems Cluster.

Description: This program supports research aimed at furthering the understanding of organisms as integrated units of biological organization. It considers proposals focused on interacting physiological and structural systems, their environmental and evolutionary contexts, and how these components are constrained by their integration into the whole organism. Projects that use systems approaches to understand why particular patterns of architecture and regulatory control have emerged as general organismal properties are particularly encouraged. Multidisciplinary approaches to the study of organismal systems including research at the interfaces of biology, physics, chemistry, mathematics, computer science and engineering are encouraged in each of the following areas: Symbiosis, Defense and Self-recognition; Processes, Structures and Integrity; Organism-Environment Interactions.

16 January 2009. NSF Division of Earth Sciences - Geobiology and Low-Temperature Geochemistry Program.

Description: This program encourages studies of 1) the interactions between biological and geological systems at all scales of space and time; 2) geomicrobiology and biomineralization processes; 3) the role of life in the evolution of the Earth's system; 4) inorganic and organic geochemical processes occurring at or near the earth's surface now and in the past, and at the broad spectrum of interfaces ranging in scale from planetary and regional to mineral-surface and supramolecular; 5) mineralogy and chemistry of soils and sediments; 6) surficial chemical and biogeochemical systems and cycles and their modification through natural and anthropogenic change; and 7) development of tools, methods, and models for low-temperature geochemistry and geobiological research. GG facilitates cross-disciplinary efforts to harness new bioanalytical tools - such as those emerging from molecular biology - in the study of the terrestrial environment.

15 February 2009 (Dissertation enhancement awards can be submitted at any time). Developing Global Scientists and Engineers (International Research Experiences for Students (IRES).

Description: The program supports groups of U.S. undergraduate or graduate students conducting research abroad in collaboration with foreign investigators. The goal is to educate a globally-engaged science and engineering workforce capable of performing in an international research environment in order to remain at the forefront of world science and technology. Proposals are submitted by a faculty member to support student work.
Funding Details: The maximum award size is $50,000 per year for up to three years and is primarily for student expenses.

15 February 2009. NSF Biological Oceanography. (Proposals to several other NSF Oceanography programs also due on this date including NSF Marine Geology and Geophysics and the NSF Ocean Drilling Program.)

Description: The Biological Oceanography Program supports research in marine ecology broadly defined - relationships among marine organisms and their interactions with the environment of the sea. Projects that fall within the purview of the Program may focus on marine environments ranging from estuarine and coastal systems to the deep sea, and also include studies in the Great Lakes. Areas of research include ecosystem and biogeochemical processes; community and population ecology; behavioral, reproductive and life-history ecology; physiological and chemical ecology; and evolutionary ecology.

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