Yaquina Head LighthouseSBI/ESB-IGERT 2008 Summer Workshop

June 15-17, 2008 -- Hallmark Resort, Newport, Oregon

Workshop Booklet

Download the Workshop Booklet (PDF) which includes the workshop agenda and abstracts from presentations and posters.

About 50 scientists gathered in Newport to present and discuss their research at the fourth annual subsurface biosphere workshop. The meeting interspersed talks by invited speakers from across the country with presentations by local faculty and students. It also included a discussion about ways to advance subsurface biosphere research nationally and a poster session highlighting research projects by students. This was the last year that the Earth's Subsurface Biosphere Interdisciplinary Graduate Education and Research Traineeship Program (ESB-IGERT) co-sponsored the workshop.

Photo from poster session.

Mark Nielsen describes some of his data to Dan Arp.

Eric Triplett, Chair of the Department of Microbiology and Cell Science at the University of Florida, gave the keynote presentation on Sunday night. His talk described efforts to quantify the diversity of soil microbes using high throughput 16S rRNA analysis. His team's work suggests that there are about 20,000 bacterial “species” in a gram of soil and that the four soils they sampled each had unique communities. He highlighted specific genuses that are little studied but were abundant in their samples and gave advice to graduate students about specific analytical skills that will facilitate their ability to work with the large datasets generated by modern genomic techniques.

Jennifer Pett-Ridge a post-doctoral fellow at Lawrence Livermore National Laboratory, began Monday's talks with an explanation of a new analysis technique, Nano-Secondary Ion Mass Spectrometry (NanoSIMS). The technique can produce a "map" of isotope distribution at a subcellular level and can be used to link microbial genetic information with structure and function. Jennifer described her isotope-labeling experiments to study nutrient uptake and movement in bacteria.

Laurel Kluber, an OSU ESB-IGERT student in soil science, spoke about her dissertation research involving a suite of studies comparing the microbial communities found in forest soils with and without symbiotic fungal communities on tree roots called ectomycorrhizal mats. Radu Popa, associate professor of biology at Portland State University spoke about nitrogen and its unique characteristics that make it a potential signature for life on other planets. He also spoke about new techniques that can be used to analyze qPCR data to determine phylotype abundance.

Dave Myrold, professor of soil science, led off the afternoon presentations with some comments about the ESB-IGERT program. The joint OSU-PSU program is in its sixth and final year of funding from the National Science Foundation. The program funded two years of study for 34 students and brought the students together for interdisciplinary courses and seminars. Each cohort of students also participated in a "Group Process Training" exercise where they collaborated on an interdisciplinary research project. In his update, Dave Myrold described efforts by faculty to submit a renewal proposal to NSF to support the program for another six years. The renewal proposal expanded the program to include Oregon Health Science University and the University of Oregon in the consortium. The proposal was not funded during 2008 but was highly rated and the team has resubmitted a preproposal for the next IGERT funding cycle. Dave also reported on the annual gathering of IGERT programs, held in May in Arlington, Va.

Also on Monday afternoon Maria Dragila, OSU professor of soil science and Anna Louise Reysenbach, PSU professor of biology, gave presentations on their research. Maria spoke about her work to model and visualize how colloids, particles the size of clays and bacteria, move through porous media such as soil or sediment. She and her team have carried out a number of experiments with an “ideal pore” they constructed out of glass spheres. Anna Louise filled in for Hollie Oakes-Miller, a PSU graduate student who was called away from the workshop unexpectedly. Anna Louise spoke about temporal and spatial patterns of microbial diversity at deep sea vents.

During the last part of the afternoon, the ESB-IGERT "Group Process Training" students led a discussion about advancing subsurface biosphere research. They had compiled a poster with examples of how interdisciplinary research makes strides forward. They asked the group to split up and discuss three questions:

  • What societal or basic research “drivers” push our science?
  • What tools or facilities are available or required in order to address these drivers?
  • What research networks will permit scientists from multiple disciplines to make substantive progress in addressing the drivers that already exist or can be conceived?

They hope to assemble the results of their research and comments from the discussion into a short article for Eos, the news magazine of the American Geophysical Union. The students also thanked their GPT faculty advisor, Rick Colwell and presented gifts to him and to Julie Cope, the IGERT assistant director, who has encouraged and supported students throughout the six years of the program.

Erika Kraft and Gaurav Saini.

Erika Kraft and Gaurav Saini discuss his poster.

In the evening, participants gathered for a poster session. Presenters gave one-minute introductions to their research and then invited participants to visit their posters individually.

On Tuesday morning, Harry Beller, a geological staff scientist at Lawrence Berkeley National Laboratory, spoke about bacteria that can remobilize solid-phase uranium. This process is of concern because it can potentially reverse a favored groundwater clean up technique that stops the spread of uranium contamination by converting soluable uranium into a solid-phase in situ. His presentation generated discussion both about the specifics of the bacterium and about his experiments to identify specific genes that enable the bacteria to metabolize solid-phase electron donors.

Sean Sandborg, an OSU ESB-IGERT student and Tyler Radniecki, a faculty research associate in environmental engineering at OSU gave presentations about their studies of ammonia oxidizing bacteria important for waste water treatment. They discussed their research to identify "sentinal genes" -- genes that would indicate when a contaminant was present in a waste water stream and inhibiting the ability of bacteria to efficiently remove nitrogen from the effluent. Jim Laidler, a PSU ESB-IGERT student, gave the final talk of the workshop. He spoke about his efforts to determine whether viruses can become encased and preserved in silica deposits in environments such as hot springs. He is hoping to identify a signature that can be used to identify viruses in the fossil record.

Lew Semprini, Chair of the SBI Executive Committee, concluded the meeting with remarks about the connections that have been made over the six years of the ESB-IGERT and SBI workshops. The meetings have strengthed the interdisciplinary connections across the OSU campus and benefited both faculty and students by bringing national experts to share their knowledge. The SBI plans to hold another workshop next summer.