C-DEBI Newsletter – January 15, 2016
This newsletter is also accessible via our website.

Happy New Year! To start 2016, let me briefly remind you of some highlights of 2015: C-DEBI consisted of 93 participating institutions and 47 active grants and fellowships, with over 250 active participants out of nearly 1000 networked individuals who produced 70 contributed publications and developed technologies (detailed in our annual report). We look forward to your participation and activity in 2016, and please consider applying to our call for research and education proposals, which are due at the end of this month (details below).

We also welcome into the USC administration our Diversity Director, Dr. Leticia Sanchez, who will create, coordinate, and lead our diversity efforts to serve our students, postdocs, faculty, and other participants at USC and across the nation. Dr. Sanchez received her PhD in Ecology & Evolutionary Biology from CU Boulder and comes with extensive expertise in STEM program leadership and management with a focus on diversity initiatives.


Jan Amend
C-DEBI Director


Proposal Calls

C-DEBI: Proposal Calls for Deep Biosphere Research, Fellowship and Education Grants
The NSF Science and Technology Center for Dark Energy Biosphere Investigations (C-DEBI) invites proposals for 1-year research projects (in the anticipated range of $50,000-$80,000) and 1-2 year graduate student and postdoctoral fellowships that will significantly advance C-DEBI's central research agenda: to investigate the subseafloor biosphere deep in sediments and the volcanic crust, and to conduct multi-disciplinary studies to develop an integrated understanding of subseafloor microbial life at the molecular, cellular, and ecosystem scales. Phase 2 of C-DEBI comprises a transition from dominantly exploration-based investigations to projects that balance discovery with hypothesis testing, data integration and synthesis, and ecosystem modeling. C-DEBI also invites proposals to support education and outreach projects, with a budget of up to $50,000 and a project duration of 1 year. The C-DEBI Education & Outreach Grants Program will fund the development of educational opportunities and materials that are pertinent to deep biosphere research in the subseafloor environment in support of our education and outreach goal to create distinctive, targeted education programs and promote increased public awareness about life below the seafloor. Funding is only available to individuals sponsored in US institutions. The next deadline for these annual calls is January 31, 2016.

NAS: Gulf Research Program Exploratory Grants
These grants will support projects that seek to break new ground to address an old or a new problem through innovation. By innovation, we mean the development of new approaches, technologies, or methods and/or the application of new expertise through the engagement of novel, non-traditional disciplinary or cross-sectoral perspectives. Responsive grants could include research, methods development, or approaches for translating or applying scientific evidence to decision making. These grants are modeled on the National Science Foundation’s EArly concept Grants for Exploratory Research (EAGER). They are not intended for incremental research in well-studied areas. Letter of Intent due February 17, 2016

IODP-USSSP: Apply to Sail:Expeditions 367 and 368, South China Sea Rifted Margin
The deadline to apply is January, 15 2016.

DCO: Call for Proposals - Census of Deep Life Sequencing Opportunities
Deadline: January 31, 2016.

DCO: Call for Proposals in Deep Life Modeling and Visualization
Proposal submission deadline: January 31, 2016.

National Academies: Research Associateships for Graduate, Postdoctoral and Senior Researchers
There are four annual review cycles and the next closes February 01, 2016.

National Academies of Science: Gulf Research Program Early-Career Research Fellowships
Application deadline: February 17, 2016.

Shell: Ocean Discovery XPRIZE
Regular registration deadline: June 30, 2016.

NSF: Geobiology and Low-Temperature Geochemistry Program Solicitation
Proposals accepted anytime.

IODP-USSSP: Proposals for Pre-Drilling Activities and Workshops
The U.S. Science Support Program (USSSP) accepts proposals on a rolling basis for pre-drilling activities and semi-annually for workshops, related to the International Ocean Discovery Program (IODP).



Frontiers in Microbiology
Radiolytic hydrogen production in the subseafloor basaltic aquifer
Mary E. Dzaugis*, Arthur J. Spivack,  Ann G. Dunlea,  Richard W. Murray and Steven D'Hondt*
*C-DEBI Contribution 287

Hydrogen (H2) is produced in geological settings by dissociation of water due to radiation from radioactive decay of naturally occurring uranium (238U, 235U), thorium (232Th) and potassium (40K). To quantify the potential significance of radiolytic H2 as an electron donor for microbes within the South Pacific subseafloor basaltic aquifer, we use radionuclide concentrations of 43 basalt samples from IODP Expedition 329 to calculate radiolytic H2 production rates in basement fractures. The samples are from three sites with very different basement ages and a wide range of alteration types. U, Th and K concentrations vary by up to an order of magnitude from sample to sample at each site. Comparison of our samples to each other and to the results of previous studies of unaltered East Pacific Rise basalt suggests that significant variations in radionuclide concentrations are due to differences in initial (unaltered basalt) concentrations (which can vary between eruptive events) and post-emplacement alteration. In our samples, there is no clear relationship between alteration type and calculated radiolytic yields. Local maxima in U, Th, and K produce hotspots of H2 production, causing calculated radiolytic rates to differ by up to a factor of 80 from sample to sample. Fracture width also greatly influences H2 production, where microfractures are hotspots for radiolytic H2 production. For example, H2 production rates normalized to water volume are 190 times higher in 1 μm wide fractures than in fractures that are 10 cm wide. To assess the importance of water radiolysis for microbial communities in subseafloor basaltic aquifers, we compare electron transfer rates from radiolysis to rates from iron oxidation in subseafloor basalt. Radiolysis appears likely to be a more important electron donor source than iron oxidation in old (>10 Ma) basement basalt. Radiolytic H2 production in the volume of water adjacent to a square cm of the most radioactive SPG basalt may support as many as 1500 cells.

Frontiers in Microbiology
Structural iron (II) of basaltic glass as an energy source for Zetaproteobacteria in an abyssal plain environment, off the Mid Atlantic Ridge
Pauline A. Henri,  Céline Rommevaux-Jestin, Françoise Lesongeur, Adam Mumford,  David Emerson*, Anne Godfroy and Benedicte Menez

* C-DEBI Contribution 290

To explore the capability of basaltic glass to support the growth of chemosynthetic microorganisms, complementary in situ and in vitro colonization experiments were performed. Microbial colonizers containing synthetic tholeitic basaltic glasses, either enriched in reduced or oxidized iron, were deployed off-axis from the Mid Atlantic Ridge on surface sediments of the abyssal plain (35°N; 29°W). In situ microbial colonization was assessed by sequencing of the 16S rRNA gene and basaltic glass alteration was characterized using Scanning Electron Microscopy, micro-X-ray Absorption Near Edge Structure at the Fe-K-edge and Raman microspectroscopy. The colonized surface of the reduced basaltic glass was covered by a rind of alteration made of iron-oxides trapped in a palagonite-like structure with thicknesses up to 150 µm. The relative abundance of the associated microbial community was dominated (39% of all reads) by a single operational taxonomic unit (OTU) that shared 92% identity with the iron-oxidizer Mariprofundus ferrooxydans PV-1. Conversely, the oxidized basaltic glass showed the absence of iron-oxides enriched surface deposits and correspondingly there was a lack of known iron-oxidizing bacteria in the inventoried diversity. In vitro, a similar reduced basaltic glass was incubated in artificial seawater with a pure culture of the iron-oxidizing M. ferrooxydans DIS-1 for 2 weeks, without any additional nutrients or minerals. Confocal Laser Scanning Microscopy revealed that the glass surface was covered by twisted stalks characteristic of this iron-oxidizing Zetaproteobacteria. This result supported findings of the in situ experiments indicating that the Fe(II) present in the basalt was the energy source for the growth of representatives of Zetaproteobacteria in both the abyssal plain and the in vitro experiment. In accordance, the surface alteration rind observed on the reduced basaltic glass incubated in situ could at least partly result from their activity.

Scientific Drilling: Workshop Report
Advancing subsurface biosphere and paleoclimate research: ECORD–ICDP–DCO–J-DESC–MagellanPlus Workshop Series Program Report
H. J. Mills, J. de Leeuw, K.-U. Hinrichs, F. Inagaki, and J. Kallmeyer

The proper pre-drilling preparation, on-site acquisition and post-drilling preservation of high-quality subsurface samples are crucial to ensure significant progress in the scientifically and societally important areas of subsurface biosphere and paleoclimate research. Two of the four research themes of IODP and ICDP and one of the four research areas of the Deep Carbon Observatory (DCO) focus on the subsurface biosphere. Increasing understanding of paleoclimate is a central goal of IODP and incorporated within the scope of the IMPRESS program, the successor of the IMAGES program. Therefore, the goal of our IODP–ICDP–DCO–J-DESC–MagellanPlus-sponsored workshop was to help advance deep biosphere and paleoclimate research by identifying needed improvements in scientific drilling planning and available technology, sample collection and initial analysis, and long-term storage of subsurface samples and data. Success in these areas will (a) avoid biological and other contamination during drilling, sampling, storage and shipboard/shore-based experiments; (b) build a repository and database of high-quality subsurface samples for microbiological and paleoclimate research available for the scientific community world-wide over the next decades; and (c) standardize, as much as possible, microbiological and paleoclimate drilling, sampling and storage workflows to allow results and data to be comparable across both space and time. A result of this workshop is the development and suggested implementation of new advanced methods and technologies to collect high-quality samples and data for the deep biosphere and paleoclimate scientific communities to optimize expected substantial progress in these fields. The members of this workshop will enhance communication within the scientific drilling community by crafting a handbook focused on pre-drilling, drilling and post-drilling operations.


Education & Outreach

C-DEBI: Applications Now Open for the 2016 Summer Undergraduate GEM Course
The GEM Course is an all-expenses paid, four-week intensive introductory course in Global Environmental Microbiology (GEM) geared for early career undergraduates from 2 and 4 year institutions. The course focuses on microbes found in aquatic environments investigated through authentic research experiences (students collect, process & interpret data).  This residential course includes lectures, labs and fieldwork at USC, the Eastern Sierra Mountains, and on Santa Catalina Island. The application deadline is February 02, 2016.

C-DEBI NSF REU: Community College Cultivation Cohort (C4)
C-DEBI’s NSF REU, C4, is a 9-week research internship targeting community college students nationwide. Students will spend their summer doing cutting edge research as they help grow, isolate, and describe previously unknown microorganisms. C4 students will work in teams in laboratories at USC, learning state-of-the-art techniques ranging from DNA sequencing to microscopy and sterile techniques to analytical chemistry. Applications due February 15, 2016.

C-DEBI: The Community College Research Internship for Scientific Engagement, June 13 - August 5, 2016
CC-RISE is an eight-week, paid, summer research internship program for community college students run by the Center for Dark Energy Biosphere Investigations. Students will gain firsthand exposure to the scientific process by working in a faculty-led research lab at the University of California Santa Cruz. In addition to research, students will participate in activities focusing on how to transition from a two-year college to a university and information on graduate school. At the end of the program, students will present their results to an audience of peers and mentors. Applications due March 18, 2016.

The Data Incubator: Data Science Fellowship, Hiring and Training
Deadline: January, 18, 2016.

NSF: Advanced Training Program in Antarctica for Early Career Scientists: Biological Adaptations to Environmental Change – July 2016
Deadline for receipt of completed applications is January 25, 2016.

DCO: Applications Now Open for 2nd Summer School
Application deadline: March 01, 2016.

Meetings & Activities
Ocean Observatories Initiative (OOI) Update
See the latest from the Ocean Observatories Initiative, including the opening of the OOI Data Portal with live streams of a hydrothermal vent site on the Axial Seamount, an Introductory Webinar on the Cabled Array infrastructure Tuesday, January,19,2015. Register by January 15, 2015.

25th International Geological Congress, Cape Town, South Africa, August 27-September 4, 2016: IODP Symposium call for abstracts
This symposium appears under the Marine Geosciences and Oceanography theme. The abstract submission is now open until January 31, 2016

University of Namibia: African Fall School on Microbial and Geochemical Oceanography in Upwelling Ecosystems
From March 29 to April 29 2016 the Sam Nujoma Campus of the University of Namibia hosts the 3rd African “Research Discovery Camp” for research-based training on the “Sustainable Use and Management of marine Ecosystems.” Deadline for application is February 01, 2016.



LMU Munich: Postdoctoral Research Fellowship Program
The Orsi lab at the University of Munich is inviting interested graduate students and postdocs to apply for the LMU Postdoctoral Research Fellowship Program, to study the activity, biochemistry, and genomics of bacteria in subseafloor sediment. Candidates should have a Ph.D focusing on environmental microbiology. The ideal candidate would have proficiency in bioinformatics and genomics, and molecular microbiology techniques. The position would be for two years with possibility to extend for a third year.  Salary will be competitive and commensurate with experience, and includes fringe benefits. The fellowship comes with an additional annual research budget of 10,000 Euro, and can include a start up grant of up to 25,000 Euro for equipment. Postdocs at LMU are integrated into the faculty and thus also have opportunities for teaching at the undergraduate or graduate levels. Informal inquiries should be sent to Bill Orsi ( The deadline for applications is February 29, 2016.

IFREMER: Life at the extremes: microbial EcoGenomics of deep-sea extremophiles: Postdoctoral position (starting immediately) 
The Lab for Microbiology of Extreme environments in Brest (France) has an 18-month postdoctoral position available to carry out research in the ecology of bacterial and archaeal communities in deep-sea brine lakes and hydrothermal vent systems. Samples from these extreme environments were collected collected during recent cruises in the Mediterranean Sea and Atlantic Ocean. The postdoctoral fellow will seek to understand the environmental constrains on microbial microbial community structure, with a strong emphasis on thermal, pressure, redox and and salinity gradients, as well as stochastic processes. The successful candidate will be co-advised by A. Murat Eren at MBL in Woods Hole/U Chicago to utilize state-of-the-art bioinformatics tools and analyze high-throughput sequencing datasets of 16S rRNA amplicons and shotgun metagenomes to study deep-sea microorganisms. Candidate Profile: per postdoctoral program requirements, the candidate should have worked 12 months outside France since May 5, 2011, and this appointment should start no later than April 1 2016. International applications are welcome! Please send inquiries and application to Loïs Maignien ( and A.M. Eren (  

WHOI: Scientific Staff Positions in Marine Chemistry and Geochemistry
The Department of Marine Chemistry and Geochemistry (MC&G) at the Woods Hole Oceanographic Institution invites exceptional candidates to apply for one or more tenure-track and tenured scientific-staff positions (Assistant, Associate and Senior Scientist) to complement and expand existing programs on the chemistry of the ocean and its interactions with the Earth as a whole. Core departmental strengths include: biogeochemistry and organic geochemistry; microbial ecology and molecular biology; carbon, nutrient, and trace element cycling; air-sea exchange; coastal, estuarine, wetland and river chemistry; sediment geochemistry; fluid-rock interactions; igneous geochemistry; and isotope systematics. MC&G scientific staff conducts research throughout the world’s open-ocean, deep-sea, and coastal environments, develops sensors for in-situ measurements, analyzes samples in the laboratory using state-of-the-art analytical techniques, carries out laboratory-based experimental studies, and applies computer models and remote sensing techniques. Candidates in all of the core areas described above are welcome to apply, but we are particularly interested in applicants who conduct research on ocean water column geochemistry-biogeochemistry as well as marine benthic-water column interactions. Review of applications will begin on January 15, 2016.

University of South Florida: Chemical Oceanographer, College of Marine Science
Position is open until filled, however, priority review of applications will begin by January 15, 2016.

Newcastle University: Lecturers in Geology, Geochemistry / Geomicrobiology
Closing date: January 31, 2016.

URI: Assistant Professor of Oceanography
Applications will be reviewed beginning January 7, 2016 and continue until the position is filled.

Texas A&M: Geosciences Postdoctoral Fellowship

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
Data Manager
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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