C-DEBI Newsletter – September 15, 2015
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Applied and Environmental Microbiology
A continuous culture system for assessing microbial activities in the piezosphere
Dionysis I. Foustoukos and Ileana Pérez-Rodríguez*
*C-DEBI Contribution 233

Continuous culture under elevated pressures is an important technique for expanding the exploration of microbial growth and survival in extreme environments associated with the deep biosphere. Here, we present a benchtop, stirred, continuous culture bioreactor capable of withstanding temperatures ranging from 25 to 120 °C and pressures up to 69 MPa. The system is configured to allow the employment of medium enriched in dissolved gases, under aerobic or anaerobic conditions, while permitting periodic sampling of the incubated organisms with minimal physical/chemical disturbance inside the reactor. In a pilot experiment, the fermentative growth of thermo-piezophilic bacterium Marinitoga piezophila was investigated unremittingly for 382 hours at 65 °C and at pressures ranging from 0.1 to 40 MPa, while varying medium flow rate from 2 to 0.025 ml/min. Enhanced growth observed at 30 and 40 MPa and 0.025 ml/min supports the pressure preferences in M. piezophila when also grown fermentatively. This assay successfully demonstrates the capabilities of the bioreactor for continuous culturing under a variety of dilution rates, pressures and temperatures. We anticipate that this technology will accelerate our understanding of the physiological and metabolic status of microorganisms under temperature, pressure and energy regimes resembling those of the Earth's piezosphere.

Proceedings of the Integrated Ocean Drilling Program, Volume 336
Data report: characteristics of sedimentary phosphorus at North Pond, IODP Expedition 336
Delphine Defforey* and Adina Paytan*
*C-DEBI Contribution 256

Phosphorus (P) plays an important role in fueling life, including microbial life in the deep subseafloor environment, which is estimated to contain up to 1% of Earth’s total biomass. These microorganisms play a significant role in controlling the chemical composition of the deep ocean and atmosphere on geological timescales by selectively degrading organic matter through metabolic respiration. Consequently, understanding P geochemistry in subseafloor sediments is important, as P bioavailability can impact microbial activity. This study focuses on characterizing and quantifying the main reservoirs of solid-phase P in open-ocean sediments. The sediment samples used in this study were collected during Integrated Ocean Drilling Program (IODP) Expedition 336 to North Pond, a sediment pond located on the western flank of the Mid-Atlantic Ridge. We characterized solid-phase P reservoirs in sediments from four holes (U1384A, U1382B, U1383D, and U1383E) using the sedimentary extraction (SEDEX) sequential extraction scheme. This method quantitatively separates five distinct sedimentary P reservoirs: (1) loosely sorbed P, (2) ferric iron-bound P, (3) authigenic carbonate fluorapatite + biogenic apatite + CaCO3-associated P, (4) detrital apatite, and (5) refractory organic P. The separation of these P-bearing phases is based on the reactivity of each targeted phase to a particular extractant solution.

The ISME Journal
A metagenomic window into carbon metabolism at 3 km depth in Precambrian continental crust
*Cara Magnabosco, Kathleen Ryan, Maggie C.Y. Lau, Olukayode Kuloyo, Barbara Sherwood Lollar, Thomas L. Kieft, Esta van Heerden and Tullis C. Onstott
*C-DEBI Contribution 276

Subsurface microbial communities comprise a significant fraction of the global prokaryotic biomass; however, the carbon metabolisms that support the deep biosphere have been relatively unexplored. In order to determine the predominant carbon metabolisms within a 3-km deep fracture fluid system accessed via the Tau Tona gold mine (Witwatersrand Basin, South Africa), metagenomic and thermodynamic analyses were combined. Within our system of study, the energy-conserving reductive acetyl-CoA (Wood-Ljungdahl) pathway was found to be the most abundant carbon fixation pathway identified in the metagenome. Carbon monoxide dehydrogenase genes that have the potential to participate in (1) both autotrophic and heterotrophic metabolisms through the reversible oxidization of CO and subsequent transfer of electrons for sulfate reduction, (2) direct utilization of H2 and (3) methanogenesis were identified. The most abundant members of the metagenome belonged to Euryarchaeota (22%) and Firmicutes (57%)—by far, the highest relative abundance of Euryarchaeota yet reported from deep fracture fluids in South Africa and one of only five Firmicutes-dominated deep fracture fluids identified in the region. Importantly, by combining the metagenomics data and thermodynamic modeling of this study with previously published isotopic and community composition data from the South African subsurface, we are able to demonstrate that Firmicutes-dominated communities are associated with a particular hydrogeologic environment, specifically the older, more saline and more reducing waters.

Frontiers in Microbiology
Biogeography and evolution of Thermococcus isolates from hydrothermal vent systems of the Pacific
Mark T. Price,  Heather Fullerton and Craig L. Moyer*
*C-DEBI Contribution 279

Thermococcus is a genus of hyperthermophilic archaea that is ubiquitous in marine hydrothermal environments growing in anaerobic subsurface habitats but able to survive in cold oxygenated seawater. DNA analyses of Thermococcus isolates were applied to determine the relationship between geographic distribution and relatedness focusing primarily on isolates from the Juan de Fuca Ridge and South East Pacific Rise. Amplified fragment length polymorphism (AFLP) analysis and multilocus sequence typing (MLST) were used to resolve genomic differences in 90 isolates of Thermococcus, making biogeographic patterns and evolutionary relationships apparent. Isolates were differentiated into regionally endemic populations however there was also evidence in some lineages of cosmopolitan distribution. The biodiversity identified in Thermococcus isolates and presence of distinct lineages within the same vent site suggests the utilization of varying ecological niches in this genus. In addition to resolving biogeographic patterns in Thermococcus, this study has raised new questions about the closely related Pyrococcus genus. The phylogenetic placement of Pyrococcus type strains shows the close relationship between Thermococcus and Pyrococcus and the unresolved divergence of these two genera.

Workshops & Activities
2015 C-DEBI Sediment Workshop Report
This year, the C-DEBI theme workshops were replaced by biome (basement and sediment) workshops integrated across the research themes to review the state of knowledge at the end of Phase 1. Summary: The 2015 C-DEBI Sediment Workshop was held at the University of Southern California, June 25-26. There were 16 in-person attendees and 2 people participating remotely. During the first part of the first day, each participant gave a short presentation on a research project or interest relevant to the subseafloor sedimentary biosphere. For the remainder of the first day and the second day, the participants engaged in group discussion of the following three questions about the deep subseafloor sedimentary biosphere: 1.What is known? 2.What are the major questions? 3.How can we go about answering these questions?

National Deep Submergence Facility (NDSF): Applications Open for the Deep Submergence Science Committee (DeSSC) New-Users Program
  • Opportunity: Participate in a workshop tailored to engage new users of deep submergence science facilities, including students, early-career scientists, engineers and scientists with little or no previous experience in deep-sea research. The workshop is scheduled for Saturday and Sunday, December 12-13, 2015 in San Francisco, CA (before the AGU Fall meeting).
  • Background: The National Deep Submergence Facility (or NDSF) manages and operates the U.S. submersible Alvin, the remotely operated vehicle Jason/Medea, and the autonomous underwater vehicle Sentry. These deep submergence vehicles are renowned for facilitating and advancing deep-sea research, e.g. the discovery of hydrothermal vents, studying the Deepwater Horizon oil spill, etc. The UNOLS Deep Submergence Science Committee (DeSSC) is a committee of scientists who provide recommendations and advice to the operator and supporting funding agencies of the NDSF. The organizing committee for the DeSSC New-Users Program includes Peter Girguis (DeSSC Chair/Harvard University), Vicki Ferrini (Lamont-Doherty Earth Observatory), and Karyn Rogers (Rensselaer Polytechnic Institute).
  • DeSSC New-Users Program:  DeSSC is committed to increasing the involvement of students and postdoctoral/early-career scientists. To that end, we have developed the new-users program to: 1) expose students, early-career scientists and other new-users to DeSSC and the NDSF, 2) engage participants in DeSSC advisory activities, 3) offer participants training and mentoring in the process of developing research programs that use NDSF vehicles, and 4) enable participants to network with scientists actively involved in NDSF-supported research. These goals will be achieved through a workshop (prior to the DeSSC meeting) in which more experienced deep-sea scientists and NDSF operators provide instruction on deep-sea research, grant-writing, technology, and data management, and by directly involving participants in the DeSSC fall meeting. Applications for travel and lodging support are being accepted through Wednesday, September 30, 2015.
25th International Geological Congress, Cape Town, South Africa, August 27-September 4, 2016: IODP Symposium call for abstracts
Dear IODP supporters: This is to invite you to contribute to the IODP symposium entitled "Achievements and Perspectives in  Scientific Ocean Drilling" that will be organized at the 25th International Geological Congress in Cape Town, South Africa from August 27th to September 4th, 2016. This symposium appears under the Marine Geosciences and Oceanography theme. The abstract submission is now open until January 2016. Please feel free to circulate this information widely to interested colleagues. We look forward to hearing from you soon on that matter and to meeting you in Cape Town next year.

Best regards,
Gilbert CAMOIN, CEREGE, Aix-en-Provence, France (
James AUSTIN, UTIG, Austin, USA (
Keir BECKER, RSMAS, Miami, USA (
Yoshi TATSUMI, Kobe Unversity, Japan (

Proposal Calls
IODP: Call for Scientific Ocean Drilling Proposals
The International Ocean Discovery Program (IODP) explores Earth’s history, structure, dynamics, and deep biosphere through seafloor drilling, coring, and downhole measurements. Themes of highest priority are described in the program’s science plan. Three types of drilling platforms permit operations in a variety of environments: (a) The D/V JOIDES Resolution (JR); (b) the riser-equipped (with riserless option) D/V Chikyu; and (c) Mission Specific Platforms (MSP), which provide a wide range of technologies for drilling and long-coring in various types of environments not accessible or suitable to JR and Chikyu. JR is planned to operate for 8 months or more per year, depending on available support, under a long-term, global circumnavigation plan based on proposal pressure. MSP expeditions are planned to operate once per year on average. Operations of Chikyu will be project-based. JR is expected to operate in the Indian and western Pacific Oceans through 2017, and then follow a path from the southwestern Pacific Ocean, through the Southern Ocean, and into the Atlantic Ocean for opportunities for drilling there starting in 2019. JR is then expected to operate in the Atlantic, Mediterranean, Caribbean, and Gulf of Mexico over the next few years. Although JR proposals for any region are welcomed, proposals for these areas are encouraged. MSP proposals for any ocean are welcomed. New proposals to use Chikyu in riser mode must be Complementary Project Proposals (with cost-sharing). See for more proposal guidance and contact with questions. Proposal submission deadline: October 1, 2015.

IODP-USSSP: Special Call for Applications for Expedition 364
The International Ocean Discovery Program (IODP) is seeking micropaleontologists with expertise in nannofossil biostratigraphy and knowledge of the Cenozoic, and ideally Paleogene, to sail on Expedition 364 Chicxulub Impact Crater aboard a Mission Specific Platform provided by the ECORD Science Operator. The deadline to apply to this special call is September 25, 2015.

NSF: Small Business Technology Transfer Program Phase I (STTR) Proposal Solicitation
NSF's STTR program provides non-dilutive funds for early-stage research and development (R&D) at small businesses. This R&D should be based on innovative, transformational technology with potential for substantial commercial and/or societal benefits. The program invites proposals from small businesses across a broad range of science and engineering disciplines in collaboration with researchers at universities, Federally-Funded Research and Development Centers, and other non-profit institutions. If you are successful, you will receive a grant of up to $225,000 for a 6-12 month development/feasibility project. You can then compete for a second grant of up to $750,000 over a 2 year period, with the aim of advancing the technology toward commercial deployment. Full proposal deadline: December 11, 2015.

NSF: Scholarships in Science, Technology, Engineering, and Mathematics (S-STEM)
Full proposal deadline: September 22, 2015.

NSF: Graduate Research Fellowship Program (GRFP)
NSF also encourages undergraduate seniors to apply. Application deadline (Geosciences; Life Sciences): October 26, 2015.

National Academies: Research Associateships for Graduate, Postdoctoral and Senior Researchers
There are four annual review cycles and the next closes November 01, 2015.

Simons Foundation: Early Career Investigator in Marine Microbial Ecology and Evolution Awards
The deadline for receipt of letters of intent (LOI) is November 2, 2015.

NSF: Earth Sciences Postdoctoral Fellowships (EAR-PF)
Full proposal deadline: January 12, 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).

Education & Outreach
The Rolex Scholarships
Application deadline: December 15, 2015.

USC: Open-Rank, Tenured or Tenure-Track Faculty Position in Geobiology
The Departments of Earth Sciences and Biological Sciences of the Dana and David Dornsife College of Letters, Arts and Sciences at the University of Southern California (Los Angeles, California) invite applications for an open-rank, tenured or tenure-track faculty position in geobiology anticipated to start Fall 2016. We are looking for an interdisciplinary scientist who will apply modern, quantitative and innovative techniques to solve major problems in any area of geobiology. Our interests include but are not limited to candidates with expertise in geomicrobiology, biogeochemistry, microbial ecology, and/or organic geochemistry, who combine field-based studies with state-of-the-art analytical capabilities and laboratory experimentation. For further information, please contact the Chair of the search committee, Jan Amend ( Review of applications will begin October 15, 2015.

UCSC: C-DEBI Postdoctoral Research Opportunity in Marine Hydrogeology
Andy Fisher anticipates bringing in a new postdoctoral researcher in Spring/Summer/Fall 2016. This will be a one-year position, with potential for renewal. Project(s) will involve studies of seafloor hydrothermal circulation, emphasizing low-temperature ("ridge-flank") environments. A successful researcher will develop numerical models to gain understanding as to how these systems work, what factors control the geometries and rates of fluid (heat, solute) transport, relations between crustal structure and fluid flow, etc. There is a lot of observational data that can be used to generate domain geometries and properties, and provides strong constraints on acceptable output. Much of the modeling will be done in collaboration with colleagues who have expertise in biogeochemistry and/or microbiology. Developing and testing models that link hydrogeologic, thermal, chemical and microbiological characteristics is a research frontier and is important to C-DEBI. Experience in modeling/programming is a prerequisite, so that we can make good progress in a short time, as are strong writing and communication skills, and analytical strengths and knowledge of the literature in some combination of hydrothermal systems, hydrogeology, geophysics, engineering, geochemistry, or related disciplines. More information on Fisher's research group, projects, and specifications for preparing an application for this postdoctoral position can be found here. Please contact Fisher ( with questions and/or to submit an application. Review of applications will occur in Fall 2015.
Ecole Polytechnique Federale Lausanne (EPFL) / Environmental Microbiology Laboratory (EML): Postdoctoral researcher position to investigate the microbial community in deep sulfidic boreholes in Finland
Start date: October 01, 2015.

Rice University: Wiess Post-Doctoral Research Fellowship in Earth and Planetary Science
The application deadline is November 1, 2015.

Oregon Health & Science University, Institute of Environmental Health: Postdoctoral Position in Environmental & Biomolecular Systems
The position is available immediately. Posted July 21, 2015.

Curtin University, Perth: PhD scholarships
Several PhD scholarships are available for national and international students (including fee waivers for exceptional scholars). Priority areas: Application of biomarkers (organic geochemistry), compound-specific isotope analysis, palaeogenomics and geomicrobiology. Please send Expression of interest, CV and names of three referees to: Professor Kliti Grice, and A/Professor Marco Coolen,

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

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