C-DEBI Newsletter – July 15, 2013
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Dear C-DEBI,
It's been a busy month for C-DEBI education, outreach and teacher professional development activities with several programs now midway through their duration, including the Community College Research Internship for Scientific Engagement (CC-RISE)Global Environmental Microbiology (GEM) course, both catering to undergraduates at 2-year colleges, and the the jointly held MBARI/C-MORE/C-DEBI Earth Workshop for educators in Hawaii. Outreach for the recently launched Atlantis/JASON expedition AT26-03 to the Juan de Fuca Ridge Flank includes media, blog entries and live video feeds of the ship and ROVs in action: check it out! Additionally, be sure to tune into the final Networked Speaker Series talk of our 2012-2013 season next week featuring Dr. Karen Lloyd, July 25th, 12 PM PT.

Proposal Calls

C-DEBI invites proposals for one-year biomolecular projects that will significantly advance understanding in one or more of the central research themes of C-DEBI. C-DEBI intends to fund 2-3 proposals in response to this call, at levels of $100,000-$150,000. Successful proposals will support one or more state-of-the-art biomolecular approaches, be innovative, and aim to answer one or more fundamental research questions and/or contribute to the development of new hypotheses and goals for future studies. Relevant molecular approaches include, but are not limited to: metagenomics, single cell genomics, tag pyrosequencing, functional gene surveys, transcriptomics, proteomics and metabolomics. Proposed research can address the deep biosphere from one or more perspectives, e.g., molecular interrogation of subseafloor samples, analysis of lab‐based experiments with deep biosphere organisms, or study of organisms grown under deep subsurface conditions. Please see the website or PDF for more details. Submissions are due 7/31/13.

The JOIDES Resolution Facility Board recently announced that after the Indian Ocean, the JOIDES Resolution will likely work in the southern Pacific Ocean, followed by the southern and central Atlantic Ocean. The U.S. Science Support Program associated with the Integrated Ocean Drilling Program is seeking workshop proposals to specifically develop expeditions in these regions. Proposed workshops should promote the development of new ideas to study the Earth’s processes and history via scientific ocean drilling. Broad-based scientific community involvement, co-sponsorship by related programs, and the active participation of graduate students are strongly encouraged. Funding may also be requested for small meetings (<$5,000) or to support participants at larger international workshops. Workshops should result in a drilling proposal submitted to IODP within one year of the meeting. The workshop submission deadline for this special call is August 15, 2013. (Workshops focusing on any region will still be accepted at the USSSP standing deadline of October 1, 2013.) For more information, please visit
Scientific Activities and Programs

A goal for the International Ocean Discovery Program (IODP) is to develop more efficient ship tracks that minimize transits and maximize scientific output in relation to time and cost. Carefully conceived flow line transects that serve as transits have the potential to address multiple 2013-2023 IODP Science Plan challenges, because a number of high priority science objectives such as high resolution paleoclimate records or the aging of the ocean crust and the consequent impacts on basement physical properties, hydrogeology and the deep biosphere, require transects of boreholes across ocean basins. We are convening a workshop to sketch out nascent multidisciplinary and interdisciplinary transect drilling proposals to exploit the potential transits of the JOIDES Resolution drillship between or within large basins. We will hold this 2.5-day workshop in College Station, Texas, November 11-13, 2013 at the IODP Gulf Coast Repository.  The meeting venue will facilitate collaborations among IODP science and technical personnel and members of the international scientific drilling community. If you are interested in participating, please send a brief statement of interest and relevant scientific ocean drilling experience to Debbie Thomas ( by September 23, 2013.  Partial travel support is available, and we especially encourage the participation of early career scientists.  For additional information, please visit

AGU 2013: Submit Your Abstracts to C-DEBI Related Meeting Sessions
See B020: Deep biosphere research: presence, diversity and activity of microbes (conveners M. Lever, J. Biddle, J. Fang and M. Rappe), B073: Windows Into to the Deep Subsurface Biosphere: Coupled Geochemical and Biological Investigations of Terrestrial Hot Spring Ecosystems (conveners E. Boyd and E. Shock), B028: Geobiological Perspectives on the Energetic Limits of Life (conveners J. Marlow and S. McGlynn), and B015: Carbon Transformations in Hydrothermal Systems (conveners F. Klein, E. Reeves, F. Schubotz, W. Orsi). Abstracts are due August 6, 2013.
Early registration opens in August, and more information is available at
New C-DEBI Contributed Publications

Becker, C-DEBI Co-Investigator Fisher and Tsuji report new drillstring packer permeability tests conducted during Integrated Ocean Drilling Program (IODP) Expedition 327 in upper oceanic basement in Hole U1362A on the eastern flank of the Juan de Fuca Ridge. Hole U1362A lies within a closely-spaced array (40-2460 m separation) of six holes in well sedimented 3.5-3.6 m.y. old crust that were drilled, tested and instrumented with borehole observatories during Ocean Drilling Program (ODP) Leg 168 and IODP Expeditions 301 and 327. The permeability tests in Hole U1362A complement similar experiments previously conducted in nearby Holes 1026B, 1027C, and U1301B. The new results suggest consistency of upper crustal permeability between Holes U1362A and U1301B, which penetrate 290 and 320 m of basement and are separated by ~825 m. We obtain similar bulk permeability values of 1-3 x 10-12 m2 for the sections deeper than ~150 m into basement in both holes. These values are significantly higher than results of packer experiments in the shallowest few tens of m of basement in nearby Holes 1026B and 1027C, suggesting that the highest basement permeabilities in this area are not found in the shallowest basement layers. Downhole logs of density and penetration rate during drilling and coring in Holes U1362A and U1301B show similar trends within the upper crust, reinforcing the inference that there may be considerable lateral continuity in hydrogeologic properties. This continuity may be associated with the fundamental lithostratigraphy of the crust and/or influenced by ridge-parallel faulting and fracturing associated with the formation of abyssal hill topography.

Share your C-DEBI-supported publications with the community and request a contribution number! Contact Matt Janicak ( for details.

Other New Publications

Total Cell Counts and qPCR Abundance of Archaea and Bacteria in Shallow Subsurface Marine Sediments of North Pond: Gravity Cores Collected During Site Survey Cruise Prior to IODP Expedition 336
The total number of prokaryotes in deeply buried marine sediments decreases with sediment depth and varies over orders of magnitude in different areas of the ocean. It is mainly controlled by the content of organic carbon in the sediment as the microbial substrate. Organic-lean, oligotrophic, and oxic sediments of the Pacific host oxygen-respiring prokaryotes. Specific archaeal communities for sediments with different trophic states could be detected. An open question is if Bacteria or Archaea dominate in oligotrophic sediments as previously discussed for eutrophic sediments based on quantitative polymerase chain reaction (qPCR) analysis. Similar to oligotrophic Pacific sediments, oligotrophic (total organic carbon = ~0.15% ± 0.07%) and oxic sediments from the North Pond area in the 7 m.y. old western flank of the Mid-Atlantic Ridge at 23°N have been shown to contain molecular oxygen downhole to >8 m sediment depth. Aerobic respiration likely dominates organic carbon oxidation. During a site survey cruise prior to Integrated Ocean Drilling Program (IODP) Expedition 336 to North Pond, sediment cores were collected to 8 meters below seafloor (mbsf). Breuker and Schippers sampled these cores to count total cells and determine the abundance of Bacteria and Archaea by qPCR using modified protocols.


Two Tenure-Track Faculty Positions: Marine Geochemistry, Department of Oceanography, University of Hawai`i at Manoa
The Department of Oceanography, University of Hawai`i at Manoa, invites applications for two full time, tenure-track faculty positions. Areas of interest include (but are not limited to) Sediment Geochemistry / Biogeochemistry, Global Geochemical / Biogeochemical Cycles, Paleoceanography, Physical-Biogeochemical Interactions, Land-Ocean Dynamics, and Marine Atmospheric Chemistry. Appointments are expected to be at the Assistant Professor level, although candidates with suitable qualifications may be considered for appointment at the Associate level, subject to position clearance and availability of funds. The anticipated start date is August 1, 2014. The successful candidates will be expected to develop and sustain outstanding research programs and contribute to the department’s educational mission (including classroom instruction) at both the graduate and undergraduate level. The latter will include teaching in the Department’s Global Environmental Science Bachelor of Science degree program.  Applicants must have a Ph.D. degree in oceanography or another relevant discipline received by 1 June 2013; excellent communication skills; demonstrated capability for creative, high quality research; and the demonstrated capability/experience and desire to contribute to teaching and mentoring of undergraduate and graduate students. At the Associate level, the minimum qualifications are as stated above, with four years of experience at the rank of Assistant (or equivalent). Applications should include a curriculum vitae, statement of research and teaching interests, three representative publications, and the names and contact information for at least three references. Questions should be directed to Dr. Kathleen Ruttenberg, chair of the search committee, at More information about the Department can be found at Review of applications will begin on August 15, 2013. The University of Hawai`i is an equal opportunity/affirmative action institution.

University of Bremen / MARUM: Marine Geomicrobiology Junior Research Group Leader
Applications are due no later than August 1, 2013. For more details, please see the online job posting.
Review of applications will commence August 1, 2013. To apply, and for more information, please see

Don’t forget to email me with any items you'd like to share in future newsletters! You are what makes our deep biosphere community!
Matthew Janicak
Administrative Assistant
Center for Dark Energy Biosphere Investigations (C-DEBI)
University of Southern California
3616 Trousdale Pkwy, AHF 209, Los Angeles, CA 90089-0371
Phone: 708-691-9563, Fax: 213-740-2437

Exploring life beneath the seafloor and making transformative discoveries that advance science, benefit society, and inspire people of all ages and origins.
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