C-DEBI Newsletter – April 1, 2014
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Dear C-DEBI,

We are pleased to welcome Benjamin Tully to our team as a postdoctoral scientist at USC. Together with John Heidelberg (USC) and Julie Huber (MBL), Ben will be taking stock of past, current, and future bioinformatic needs for the C-DEBI community, including centralizing sequencing analysis tools, archiving data, and helping C-DEBI grantees with their bioinformatic needs. Requests for bioinformatic support should be made directly (in triplicate via e-mail) to Ben, John, and Julie and include a brief scope of work and current status of the project. Together with ExCom, projects will be prioritized and scope of support determined.

We are also grateful that ASLO has bestowed the Citation of Scientific Excellence on Victoria Bertics, a C-DEBI postdoctoral fellow who passed away after a courageous battle with breast cancer last year. Vicky was a Ph.D. student in Geobiology at USC from 2004-2009, after which she was awarded an Alexander von Humbolt Fellowship to study at the GEOMAR-Helmholtz Centre for Ocean Research in Kiel, Germany. In 2012, she received a C-DEBI Postdoctoral Fellowship to study deep ocean nutrient cycling at Harvard University. The ASLO award will be given to Sandra Bertics (Victoria's mother) at the Joint Aquatic Sciences meeting in Portland, Oregon, this May. The Wrigley Institute for Environmental Studies, where Vicky spent most of her time as a graduate student, currently seeks support to establish a summer fellowship in her honor.

Above: Harvard University scientist and Victoria's postdoctoral advisor Peter Girguis used Alvin’s manipulator arm to place a memorial plaque on the seafloor. From the Alvin Science Verification Cruise blog.

Activities, Workshops and Courses

ECORD/ICDP MagellanPlus Workshop: Advancing Sub-surface Biosphere and Paleoclimate Research
Convenors: Heath Mills (IODP), Jens Kallmeyer (ICDP), Fumio Inagaki (DCO, IODP), Jan Berend Stuut (IMPRESS) and Jan de Leeuw (IODP, Organiser)

Sub-surface biosphere and paleoclimatology are major research themes of the International Ocean Discovery Program (IODP), International Continental Scientific Drilling Program (ICDP), the Deep Carbon Observatory (DCO) and IMPRESS. To ensure significant progress in these scientific and societal important areas, the quality, handling and storage of samples is crucial. The goal of this MagellanPlus Workshop is to significantly advance deep-biosphere and paleoclimate research by major improvements in scientific drilling, sample collection, initial analysis and long-term storage of sub-surface samples to:
  1. Avoid biological and other contamination during drilling, sampling, storage and shipboard/shore-based experiments;
  2. Build a repository and database of high-quality sub-surface samples for microbiological and paleoclimate research over the next decade available for the scientific community world-wide;
  3. Standardize as much as possible microbiological and paleoclimate drilling, sampling and storage workflows to be able to compare results and data, both space-and time wise. 
The expected impact of this workshop is the development and implementation of new advanced methods and technologies to collect high-quality samples and data for the deep biosphere and paleoclimate scientific communities to optimise expected substantial progress in these fields over the next decade. The workshop is scheduled on 21st-23rd August 2014 in Seoul, South Korea, prior to the ISME conference (24th-29th August 2014 in Seoul). Scientists who wish to participate in this workshop are requested to contact Jan W. de Leeuw before May 5th 2014.

C-MORE: Ecological Dissertations in the Aquatic Sciences (Eco-DAS) XI, October 19-25, 2014, Honolulu, HI
The Ecological Dissertations in the Aquatic Sciences symposium series is designed to:
  1. Foster sustained, cross-disciplinary interactions among the top new researchers in ecological oceanography and limnology, to the benefit of both the science and the researchers
  2. Increase the success rate of new researchers seeking funding to build their research programs, by familiarizing them with the diversity of available research opportunities, and introducing them to representatives of funding agencies with whom they will interact in future
  3. Increase the likelihood of professional success for these new researchers by highlighting their initial work through a high-visibility, open-access publication of formal symposium proceedings focusing on the interdisciplinary and collaborative aspects of their work and establishing mentoring relationships between participants and established scientists
Applications are due by April 21, 2014.

2014 SACNAS National Conference for undergraduate, graduate and post-doctoral researchers: October 15-19, 2014, Los Angeles, CA
Submit your posters by April 14, 2014. Registration fees for a limited number of presenters are available through C-DEBI and travel support can be requested through SACNAS and C-DEBI matching travel funds. If you are interested in proposing a science session or have any other questions, please contact C-DEBI Diversity Director Cynthia Joseph.
  Submit your abstracts to sessions such as "Astrobiology/Microbiology of Extreme Subsurface Environments" chaired by Tori Hoehler and Karsten Pedersen at the forthcoming International Symposium on Subsurface Microbiology meeting, which will be held at Asilomar this October, right after and near the C-DEBI Annual Meeting! Abstracts due April 21. See submission instructions at

MARUM: ECORD Summer School, "Subseafloor Biosphere: Current Advances and Future Challenges," September 22 - October 2, Bremen, Germany
Applications due May 9, 2014.

Ocean Leadership: Apply to Host Deep Biosphere IODP Distinguished Lecturer Beth Orcutt
Applications due June 1, 2014.

Proposal Calls

IODP: Apply to Sail for Expeditions 355 and 356
The International Ocean Discovery Program (IODP) has begun accepting applications for two expeditions aboard the JOIDES Resolution: Expedition 355 (Arabian Sea Monsoon, informational webinar April 7) and Expedition 356 (Indonesian Throughflow, webinar April 14). The deadline to apply is May 1, 2014.

National Academies Research Associateships for Graduate, Postdoctoral and Senior Researchers
There are four annual review cycles and the next closes May 1.

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, next submission deadline May 15, 2014, related to the International Ocean Discovery Program (IODP).

NSF: Critical Techniques and Technologies for Advancing Big Data Science & Engineering (BIGDATA) Program Solicitation
Full Proposal Deadline: June 9, 2014.

Hot Off the Press: Metagenomic analysis of organic matter degradation in methane-rich Arctic Ocean sediments (C-DEBI Contribution 195) in Limnology and Oceanography
Organic material is degraded anaerobically by a complex community of microbes making up the anaerobic food chain. This community was examined in methane-rich sediments of the Beaufort Sea, Alaska, using metagenomic sequencing, along with tag pyrosequencing and quantitative polymerase chain reaction analyses of 16S ribosomal ribonucleic acid genes. The goal of the study was to examine the relative abundance and taxonomic composition of organisms making up different parts of the anaerobic food chain. The metagenomic data suggested that genes for producing acetate via fermentation (“acetate fermentation”) were more common than genes producing other fermentation by-products, but acetate fermentation genes made up only 32% of all genes for fermentation pathways while genes for fermentation to ethanol accounted for 27%. The genes for the production of other compounds, including propionate (15%), butyrate (11%), lactate (4%), and hydrogen gas (11%), were also often abundant. Similar results were observed when the same approach was used to analyze metagenomic data previously collected from two low-latitude systems with methane-rich sediments. In all of these sediments, genes for pathways producing organic acids, ethanol, and hydrogen gas were about 30-fold more abundant than the genes for sulfate reduction and methanogenesis, processes which consume those compounds. The authors' (including C-DEBI Research Grantee L. Hamdan) results suggest that the type and abundance of fermentative microbes potentially affect the taxonomic composition of sulfate-reducing bacteria and methanogenic archaea and rates of organic carbon mineralization by the anaerobic food chain.


National Oceanography Centre (NOC): Research Scientists, Southampton and Liverpool, UK
We are seeking five excellent Research Scientists with high potential to work within, and across, five discipline-based research groups within our Directorate of Science and Technology. The National Oceanography Centre is the UK’s national research organisation delivering integrated marine science and technology from the coast to the deep ocean, and is one of the top five institutions of its kind in the world. NOC is at the vanguard of international marine research, tackling the major global environmental research issues and translational impacts to benefit society ( We provide an exciting, dynamic and outstanding research environment supported by research scientists, technologists and engineers. The facilities include super-computing facilities, world-class analytical laboratories and access to our global marine observation infrastructure including robotic underwater vehicles and oceangoing research vessels. We are seeking candidates with expertise in such areas as: particle flux oceanography, geoscience on seafloor fluid flow, geoscience on human impacts on the deep seafloor, autonomous carbon sensor engineering and nutrient micro-sensor engineering. Applications due April 6, 2014.

University of Brest / IFREMER: 3-Year Position in Stable Isotope Biogeochemistry and/or Paleoceanography
Call open until April 15 (or until a suitable candidate is found).

UNC-CH: Tenure-Track Assistant/Associate Professor in Marine Environmental Genomics or Particle Dynamics
To apply for the position, please follow this link: Applications will be reviewed starting January 15, 2014

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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