C-DEBI Newsletter – February 1, 2017
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Proceedings of the IODP
Data report: quantification of potential drilling contamination using perfluorocarbon tracer at IODP Expedition 329 sites NEW!
Justine Sauvage, Leah Lewis, Dennis Graham, Arthur J. Spivack, and Steven D’Hondt*
*C-DEBI Contribution 335

To quantify the potential for biological contamination associated with the coring process, we conducted perfluorocarbon tracer (PFT) analysis on 556 sediment samples from Integrated Ocean Drilling Program (IODP) Expedition 329. The expedition cored deep-sea sediment at seven sites in the South Pacific Gyre (Sites U1365–U1371). We analyzed two types of sediment samples: (1) samples taken in the central part of the core (i.e., interior samples) and (2) samples taken near the core edge (i.e., exterior samples). We calculated the amount of potential drilling fluid intrusion from the mass of PFT that we measured in each sample. For the seven Expedition 329 sites (15 holes analyzed), PFT content ranges from below detection to levels where contamination is extremely apparent. The centers of the sediment cores (interior samples) contained generally less PFT than the core margins (exterior samples) and thus have lower potential drilling fluid (DF) contamination. The majority of sediment samples (interior) at Sites U1370 and U1371 have a contamination potential close to or below detection levels (i.e., 1.19 × 10–4 ngPFT/gsediment or 1.78 × 10–3 µLDF/gsediment on average). We observed higher contamination values (i.e., 7.28 × 10–3 ngPFT/gsediment or 6.98 × 10–2 µLDF/gsediment on average) at Sites U1365, U1366, and U1367. Finally, we measured much higher PFT concentrations throughout the sediment of Sites U1368 and U1369 (i.e., 5.48 × 10–2 ngPFT/gsediment or 6.60 × 10–1 µLDF/gsediment on average). We observe no apparent correlation of sample PFT content to sediment lithology, degree of sediment disturbance, core section number, or porosity.

FEMS Microbiology Ecology
Inter-laboratory quantification of Bacteria and Archaea in deeply buried sediments of the Baltic Sea (IODP Expedition 347) NEW!
Joy Buongiorno, Stephanie Turner, Gordon Webster, Masanori Asai, Alexander K. Shumaker, Taylor Roy, Andrew Weightman, Axel Schippers, Karen G. Lloyd*
*C-DEBI Contribution 341

Two common quantification methods for subseafloor microorganisms are catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) and quantitative PCR (qPCR). Using these methods, we quantified Bacteria and Archaea in Baltic Sea basin sediments (IODP Exp. 347) down to 90 mbsf, testing the following hypotheses in an inter-laboratory comparison: 1) proteinase K permeabilization of Archaeal cell walls increases CARD-FISH accuracy, and 2) qPCR varies by more than an order of magnitude between laboratories using similar protocols. CARD-FISH counts did not differ between permeabilization treatments, demonstrating that proteinase K did not increase accuracy of CARD-FISH counts. However, 91% of these counts were below the quantification limit of 1.3 × 107 cells cm−3. For qPCR, data varied between laboratories, but were largely within the same order of magnitude if the same primers were used, with 88% of samples being above the quantification limit. Copy number values were elevated by preparing a sediment slurry before DNA extraction: 3.88 ×106 to 2.34 ×109 16S rRNA gene copies cm−3 vs. 1.39 × 107 to 1.87 × 109 total cells cm−3. By qPCR, Bacteria were more abundant than Archaea, although they usually were within the same order of magnitude. Overall, qPCR is more sensitive than CARD-FISH, but both require optimization to consistently achieve both precision and accuracy.

Proposal Calls

L'Oréal USA For Women in Science Fellowships
The 2017 L’Oréal USA for Women in Science will close on February 3, 2017.

NSF: Ocean Technology and Interdisciplinary Coordination Program Solicitation NEW!
The Oceanographic Technology and Interdisciplinary Coordination (OTIC) Program supports a broad range of research and technology development activities. Unsolicited proposals are accepted for instrumentation development that has broad applicability to ocean science research projects and that enhance observational, experimental or analytical capabilities of the ocean science research community. Specific announcements for funding opportunities are made for additional projects involving Improvements in Facilities, Communications, and Equipment at Biological Field Stations and Marine Laboratories (FSML) and the National Ocean Partnership Program. Full Proposal Target Date: February 15, 2017.

NSF: Chemical Oceanography Program Solicitation NEW!
The Chemical Oceanography Program supports research into the chemical components, reaction mechanisms, and geochemical pathways within the ocean and at its interfaces with the solid earth and the atmosphere. Major emphases include:  studies of material inputs to and outputs from marine waters; orthochemical and biological production and transformation of chemical compounds and phases within the marine system; and the determination of reaction rates and study of equilibria. The Program encourages research into the chemistry, distribution, and fate of inorganic and organic substances introduced into or produced within marine environments including those from estuarine waters to the deep sea. Full Proposal Target Date: February 15, 2017.

NSF: Biological Oceanography Program Solicitation NEW!
The Biological Oceanography Program supports research in marine ecology broadly defined: relationships among aquatic organisms and their interactions with the environments of the oceans or Great Lakes. Projects submitted to the program for consideration are often interdisciplinary efforts that may include participation by other OCE Programs.  (See information provided under Related URLs below). Full Proposal Target Date: February 15, 2017.

NSF: Dimensions of Biodiversity Program Solicitation NEW!
Despite centuries of discovery, most of our planet’s biodiversity remains unknown. The scale of the unknown diversity on Earth is especially troubling given the rapid and permanent loss of biodiversity across the globe. The goal of the Dimensions of Biodiversity campaign is to transform, by 2020, how we describe and understand the scope and role of life on Earth. This campaign promotes novel integrative approaches to fill the most substantial gaps in our understanding of the diversity of life on Earth. It takes a broad view of biodiversity, and focuses on the intersection of genetic, phylogenetic, and functional dimensions of biodiversity. Successful proposals must integrate these three dimensions to understand interactions and feedbacks between and among them. While this focus complements several core programs in BIO, it differs by requiring that multiple dimensions of biodiversity be addressed simultaneously, in novel ways, to understand their synergistic roles in critical ecological and evolutionary processes, especially pertaining to the mechanisms driving the origin, maintenance, and functional roles of biodiversity. Full proposal deadline date: February 21, 2017.

The National Academies: Gulf Research Program Early-Career Research Fellowships
Applications due February 22, 2017.

IODP: Apply to Sail: Expedition 381 Corinth Active Rift Development NEW!
The International Ocean Discovery Program (IODP) is currently accepting applications for Expedition 381 Corinth Active Rift Development aboard a Mission Specific Platform provided by the ECORD Science Operator. To learn more about the scientific objectives of this expedition and the technical plans, please join a web-based seminar on Tuesday, 14 February 2017 at 8:00 am EST (1:00 pm GMT). To participate in the webinar, you need access to the Internet and a computer with a speaker and microphone (optional). To register, click the following link: Exp 381 webinar. The expedition is provisionally scheduled for a maximum of 60 days during October and November, 2017, with only a subset of the science party members participating. Subsequently, an Onshore Science Party will be held at the MARUM – Center for Marine Environmental Sciences, University of Bremen, Germany, in February 2018 (exact dates to be confirmed). All science party members must attend the entire duration of the onshore science party. Opportunities exist for researchers (including graduate students) in all specialties. While other expertise may be considered, specialists in the following fields are required: paleontology, sedimentology, organic geochemistry, inorganic geochemistry, structural geology, paleomagnetics, physical properties, geophysics and petrophysics/downhole logging. For the offshore phase of the expedition, we are particularly looking for the following fields: paleontology, sedimentology, organic geochemistry, inorganic geochemistry, physical properties, and petrophysics/downhole logging. U.S.-affiliated scientists interested in participating on this expedition should apply to sail through the U.S. Science Support Program (USSSP); please visit The U.S. deadline to apply is March 3, 2017.

AGU: Nominate an individual for the Asahiko Taira International Scientific Ocean Drilling Research Prize NEW!
The Asahiko Taira International Scientific Ocean Drilling Research Prize (The Taira Prize) is given annually to one honoree in recognition of  “outstanding transdisciplinary research accomplishment in ocean drilling.” Established in 2014, the Taira Prize is a partnership between the American Geophysical Union (AGU) and the Japan Geoscience Union (JpGU), and is made possible through the generous donation from the Integrated Ocean Drilling Program Management International (IODP-MI). The prize is given in honor of Dr. Asahiko Taira of the Japan Agency for Marine-Earth Science and Technology. Nominations due March 15, 2017.

IODP: Apply to Sail on IODP Expedition 376 NEW!
The International Ocean Discovery Program (IODP) is now accepting applications for scientific participants on Expedition 376 Brothers Arc Flux aboard the JOIDES Resolution. Expedition 376 will investigate the fundamental, interrelated processes governing subseafloor hydrothermal activity at Brothers volcano, southern Kermadec arc (IODP proposal 818-Full2). The primary objectives are to (1) Characterize the subsurface, magma-derived volatile phase for testing models predicting the existence of either a single-phase gas or a two-phase brine-vapor; (2) Explore the distribution of base and precious metals and metalloids at depth as well as the reactions that have taken place during their precipitation along fluid migration pathways to the seafloor; (3) Quantify the mechanisms and extent of fluid-rock interaction, and what this implies for the mass flux of metals and metalloids to the ocean as well as the role of magma-derived carbon and sulfur species in acting as agents for those fluxes; and (4) Assess the diversity, extent, and metabolic pathways of microbial life in an extreme, acidic, and metal-toxic (sub)volcanic environment. The expedition will occur from 5 May through 5 July 2018. Opportunities exist for researchers (including graduate students) in specialties including (but not limited to) sedimentologists, petrologists (igneous/metamorphic/sulfide), structural geologists, paleomagnetists, petrophysicists, borehole geophysicists, microbiologists, and inorganic/organic geochemists. U.S.-affiliated scientists interested in participating in this expedition should apply to sail through the U.S. Science Support Program, by visiting The deadline to apply is April 1, 2017.

IODP: Submit an IODP Drilling Proposal
Next Proposal Submission Deadline: April 3, 2017.

NSF: Arctic Sciences Program Solicitation
Proposals accepted anytime.

NSF: Tribal Colleges and Universities Program (TCUP) Program Solicitation
Preparing for TCUP Implementation 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).

C-DEBI: Rolling call for Research Exchange proposals

Education & Outreach

C-DEBI: Applications Now Open for the NSF REU: Community College Cultivation Cohort (C4)
Applications due TODAY, February 1, 2017.

C-DEBI: Applications Now Open for the 2017 Summer Undergraduate GEM Course
Applications due TODAY, February 1, 2017.

GEOBIOLOGY 2017: An International Training Course in a Rapidly Evolving Field
Applications due February 10, 2017.

IRES: Undergraduate Research Opportunities in Microbiology and Biogeosciences of Siberian Deep Subsurface Permafrost NEW!
The Center for Environmental Biotechnology at the University of Tennessee is now recruiting undergraduate students for the International Research Experience for Students (IRES) program IRES program, funded by the NSF, which take place June 8-July 22, 2017 in Russia. The research projects will focus on the microbiology and biogeoscience of Siberian deep subsurface permafrost. Stipends and travel expenses will be covered by the program. The newly extended deadline is February 14, 2017. More information about the IRES program and application process could be found here: Please contact Karen Lloyd,, with any questions.

Bigelow: Undergraduate Research Experience
Applications due February 15, 2017.

NSF: Community College Innovation Challenge
Entry period closes February 15, 2017.

Sigma Xi: 2017 Student Research Showcase
Project approval and registration deadline: February 22, 2017.

C-DEBI: Community College Research Internship for Scientific Engagement (CC-RISE) NEW!
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 or at the Woods Hole Oceanographic Institution in Woods Hole, MA. 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 are due March 20, 2017 for UCSC and March 24, 2017 for WHOI.

NSF Advanced Training Program in Antarctica for Early-Career Scientists: Biological Adaptations to Environmental Change NEW!
This US National Science Foundation sponsored Antarctic Biology Course will be held during January 2018 in Antarctica, at the United States Antarctic Program’s McMurdo Station. The training program is designed to provide early-career scientists with opportunities to work in Antarctica and to study polar biology. Applications are invited from graduate students currently enrolled in a Ph.D. program and researchers who have completed a Ph.D. within the past five years. This is an international training program, open to all nationalities. Partial support is available to cover the cost of travel from each participant’s home institution. While in Antarctica, full support is provided for room & board and science activities. The emphasis of the Antarctic Biology Course is on integrative biology, with laboratory- and field-based projects focused on adaptations to extreme polar environments. This program will also provide opportunities to understand and appreciate the complexities and logistical challenges of undertaking successful science in Antarctica. A diverse instructional faculty will offer participants the opportunity to study a wide range of Antarctic organisms (bacteria, algae, invertebrates, fish), using different levels of biological analysis (spanning molecular biology, physiological ecology, species diversity, and evolution). Deadline for receipt of completed applications is April 17, 2017. More information and the on-line application form are at and

Microbiology Society Podcast: Microbes in the Deep Dark Ocean NEW!
What’s it like to travel right down to the bottom of the ocean? Deep sea microbiologist Julie Huber should know. Her group, at the Marine Biological Laboratory in Massachusetts, USA, is trying to uncover more about the microbes living in the deepest darkest depths of the ocean. But that’s not all – there are even microbes living thousands of metres beneath the ocean floor itself, within the rocks and sediment. This is an environment that couldn’t be more different to our world on land – no light, huge pressures, underwater volcanoes and hardly any nutrients. So what kind of microbes do we see living there, and how do they manage to make a living?

IODP: Expedition 366 Outreach Video Diary
Follow along with IODP Expedition 366: Mariana Convergent Margin & South Chamorro Seamount (co-chief Geoff Wheat, December 8, 2016 to February 7, 2017) with onboard videos from Education and Outreach Officer Kristen Weiss on Vimeo!


Meetings & Activities

Onshore-Offshore Drilling and Sampling to Understand Freshwater Resources along the New England Continental Shelf: An IODP-ICDP Workshop
The workshop is open to U.S. and international participants and the deadline to apply is February 17, 2017.

Register and submit abstracts for the 2017 SoCal Geobiology Symposium
Abstract submission is due March 3, 2017.

6th International Symposium on Chemosynthesis-Based Ecosystems (CBE6), Woods Hole, Massachusetts, USA, August 27 – September 1, 2017 NEW!
Please join us in Woods Hole on beautiful Cape Cod as we celebrate the 40th anniversary of the discovery of deep-sea hydrothermal vents at the Galapagos Spreading Center in 1977. This has forever changed our perception of life on Earth and has sparked a new line of research to investigate the role of chemosynthesis in various ecosystems, from cold seeps and organic falls to the extensive oxygen deficient zones of the oceanic water column. The discovery of deep-sea hydrothermal vents 40 years ago has thrust the process of chemosynthesis into the limelight. However, it is only more recently that chemosynthesis has been identified to be an important driver for many environmentally relevant processes on a global scale. CBE6 represents the 6th iteration of a successful symposium series that started back in Funchal, Madeira, Portugal in 1997 and has since been held in Brest, France (2001), San Diego, USA (2005), Okinawa, Japan (2009), and most recently in Victoria, BC, Canada (2013), ever broadening in scope from an initial focus on the biology of deep-sea hydrothermal vents. We look forward to hosting an exciting meeting that will highlight the newest discoveries and developments in studying chemosynthesis-based ecosystems and their societal relevance, while at the same time also evoking the early days of deep-sea vent discovery – in a way connecting the past with the present, with a glimpse into the future! The program will be as diverse as the ecosystems being studied, and will include topics such as biogeography, biogeochemistry, chemosynthetic habitats and society, community structure and dynamics, evolution and evolutionary history, metapopulation and metacommunity (including connectivity and resilience), microbiology, physiology and adaptation, symbiosis, and trophic interactions, including chemosynthetic energy transfer. We look forward to seeing you in Woods Hole! Abstract submission deadline March 17, 2017.

Geobiology 2017 NEW!
Following three very successful International Geobiology Conferences held in Wuhan (2010, 2012, 2014) and the recent Geobiology Gordon Research Conference in Galveston (2016), the newly created Geobiology Society will host a 3-day meeting in June 2017 at the Banff Conference Center. With 400 anticipated attendees from across the globe, this meeting will be an ideal venue for us to discuss the latest developments in Geobiology and build international collaborations in a relaxed but stimulating environment. “Geobiology 2017” will take a page out of the 1-day regional Geobiology meetings held across the United States and Western Canada, emphasizing the work of early career scientists – graduate students, post-doctoral fellows and assistant professors. The three days are designed to cover various topics pertaining to how microbial processes affect the modern environment and leave imprints on the rock record. Days 1 and 2 will explore the modern tools of organic and inorganic geochemistry, molecular biology and microbial ecology, sedimentary geology and paleontology. Day 3 will focus on the interpretation of the rock record, and how the modern can be used to infer the past. To investigate these topics, the mornings will be devoted to oral sessions while the afternoons will be devoted to extended poster sessions. Each evening will also offer either a talk by an awardee or a point-counterpoint discussion on a topic of timely importance. Abstract deadline: April 1, 2017.

Call for Abstracts: Goldschmidt 2017, Paris, August 13-18 NEW!
Goldschmidt is the foremost annual, international conference on geochemistry and related subjects, organized by the European Association of Geochemistry and the Geochemical Society. Deep biosphere-related themes include: Geobiology of the ModernGeo-omics Meets Organic GeochemistryInnovation in Geochemical Methods and Models and Data in Geochemistry. Abstract submissions are due April 1, 2017.

Aarhus University: International Workshop on "Marine Geomicrobiology" in Denmark NEW!
We invite applications to the International Workshop on “Marine Geomicrobiology – a Matter of Energy” which will take place at the beautiful Sandbjerg Manor in southern Denmark during August 28 to September 1, 2017. An outstanding program of 35 international speakers will explore how microorganisms harvest energy from sunlight, from chemical reactions and even from electric currents to drive key processes of element cycling in the ocean and seabed. We will focus on recent discoveries and on open questions that provoke curiosity and require new research. The workshop marks the ten years of the Center for Geomicrobiology, Aarhus University, and the retirement of Bo Barker Jørgensen. We invite researchers and students to participate in the workshop and to present a poster on their research. Application takes place through the workshop webpage where the program and other relevant information are provided (see link below).  Deadline for applications is April 1, 2017.

IODP-USSSP: Call for IODP-ICDP Session Conveners at AGU 2017 Fall Meeting NEW!
To the IODP and ICDP Communities: Following discussions with the AGU Fall Meeting Program Chair, Denis-Didier Rousseau, a three-year plan (2017-2019) for IODP-ICDP sessions at the AGU has been defined, culminating with the celebration of the AGU Centennial in 2019. We have highlighted three overarching, societally relevant themes that are well aligned with both IODP and ICDP science plan themes. These themes (and examples of topics; identified priorities are underlined) are the following: 1) Georesources, Storage, and Sustainability: Unconventional Energy (Supercritical and magma geothermics, EGS, methane and gas hydrates, hydrogen resources and storage), Deep Carbon fluxes and storage and Water resources (Groundwater vs. Seawater). 2) Climate, Environment and Ecosystem: Life in extreme environments: the hidden biosphereLinks between geological and biological systems at depth, Analogs and models of recent climate changes in geological archives, Impact of climate and ocean changes on ecosystems, Impact of Earth processes on Earth’s environment. 3) Geological Hazards: Monitoring and mitigating man-made geohazards? (e.g., induced seismicity, landslides), Hazards in the geological record: from improving risk assessment and prediction of catastrophic events towards mitigation, Underlying mechanisms of geological hazards: faulting, earthquakes, volcanoes, impacts. We seek potential conveners (who must be AGU members) to submit AGU session proposals on these three overarching themes. Please keep us informed so that actions and proposal submissions can be coordinated. The provisional dates of the call for session proposal are February 15th – April 19th, 2017.

FIERY ICE 2017: Corpus Christi, Texas, USA, December 6-8 2017 NEW!
The 1st International Workshop on Methane Hydrate R&D was held in March 2001 in Honolulu, Hawaii. The primary objective of that and subsequent workshops was to provide a forum where hydrate researchers and stakeholders could freely exchange information and identify research priorities in an effort to promote collaboration. Subsequent workshops have been held, on average, every 1.5 years in different countries including the U.S., Chile, Canada, the U.K., Norway, New Zealand, Japan, and India. This effort has resulted in a broad range of field and laboratory research pertaining to gas hydrate distributions, stability and formation, and contribution to climate change and coastal ocean carbon cycling. Based on previous workshop foci and developments in this field over the last 16 years, the 11th workshop will focus on: 1) Gas Hydrate Energy: exploration, production, and economics; 2) Methane and Climate Change: Arctic, Antarctic and regions in between; 3) Natural and Anthropogenic Warming Contributions to Coastal and Industrial Platform Stability; and 4) Carbon dioxide injection for methane acquisition and sequestration. We hope that previous participants in this workshop series, as well as other interested parties, will be able to join us in Corpus Christi this winter December 6th through 8th, 2017. The Workshop website is under construction and is expected to be operational May 2017. The 2nd Announcement will be distributed electronically once the website is up, and will include information on registration, logistics, and a call for abstracts. Questions? Please email Workshop Liaison Mrs. Alessandra Garcia at

ISSM 2017: Call for Abstracts

C-DEBI: Rolling call for Community Workshop support


Shanghai Ocean University: Faculty Positions in Bioinformatics and Proteomics at HAST NEW!
The Hadal Science and Technology Research Center (HAST) of Shanghai Ocean University invites applications for two faculty positions, one in bioinformatics and one in proteomics. HAST was established to explore the largely unknown hadal zones of the world’s oceans. The center’s activities are a balanced mix of basic and translational scientific research with an emphasis on hadal technology development. We are in the final stage of developing a “movable laboratory” which includes three full ocean depth (FOD) landers, one FOD hybrid AUV/ROV unmanned vehicle (ARV), one FOD human occupied vehicle (HOV), and a dedicated mothership of 5000-ton displacement. Faculty position in Bioinformatics: Preference will be given to candidates conducting high impact research in one of the following areas: genomics, functional genomics, and computational biology algorithm development. Experience in metagenome, metatranscriptome and whole genome analysis is a plus. Faculty position in Proteomics: All areas of proteomic research will be considered, and we are particularly interested in those whose research deals with protein structure, function, and interactions. Applications from researchers with expertise in lipidomics, glycomics, or metabolomics or other biology based omics-disciplines are also encouraged. Candidates with the following qualifications are desired: in-depth understanding of both hardware and software of LC-electrospray MS; proficiency in LC-MS related software and data analysis; and experience in both top-down and bottom-up proteomics. Review and evaluation of applications will begin immediately. Applications will continue to be accepted until all available positions are filled. Contact: Dr. Jiasong Fang (

University of Rhode Island: Assistant Professor in Biological Oceanography
First consideration will be given to applications received by January 17, 2017. Second consideration may be given to applications received by February 15, 2017.

Don’t forget to email me with any items you'd like to share in future newsletters! We will also broadcast this information on our social media outlets, Twitter and Facebook. 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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