C-DEBI Newsletter – June 1, 2017
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Message from the Director:

Our Associate Director, Dr. Julie Huber begins her new position in Marine Chemistry & Geochemistry at the Woods Hole Oceanographic Institution this month, so please update your address books to use! A round of congratulations also to Dr. Jen Biddle awarded tenure in the College of Earth, Ocean, and Environment at the University of Delaware and Dr. Laura Lapham awarded tenure at the Chesapeake Biological Laboratory at the University of Maryland Center for Environmental Science. And if you are at this week’s ASM Microbe meeting, please congratulate C-DEBI Senior Scientist Dr. Steve Finkel who will receive the William A. Hinton Research Training Award on June 4 for outstanding contributions toward fostering the research training of underrepresented minorities in microbiology. Steve’s GGURE undergraduate research internship program is one of C-DEBI’s flagship STEM-retention programs.

We are also pleased to share that the International Ocean Discovery Program has just put Guaymas Basin deep drilling led by Dr. Andreas Teske on the agenda for late 2019, so keep your eye out for opportunities to sail on Expedition 385: Guaymas Basic Tectonics and Biosphere!


Jan Amend
C-DEBI Director



Geochimica et Cosmochimica Acta
Biogeochemical N signatures from rate-yield trade-offs during in vitro chemosynthetic NO3- reduction by deep-sea vent ε-Proteobacteria and Aquificae growing at different temperatures NEW!
Ileana Pérez-Rodríguez*, Stefan M. Sievert, Marilyn L. Fogel, Dionysis I. Foustoukos
*C-DEBI Contribution 238

NO3- reduction is a metabolism that is widespread among ε-Proteobacteria and Aquificae, two abundant classes of microorganisms found at deep-sea vents. In this study, we used Sulfurovum lithotrophicumCaminibacter mediatlanticus and Thermovibrio ammonificans as representatives of these groups to study ecophysiological, metabolic and biogeochemical parameters associated with chemolithoautotrophic NO3- reduction under different temperature regimes. We observed that while S. lithotrophicum and C. mediatlanticus achieved higher cell densities than T. ammonificans, the overall NO3- consumption by the latter was on average ∼ 9 and ∼ 5 times faster on a per cell basis, respectively. Comparison with previously published data from other cultured vent ε-Proteobacteria and Aquificae suggests that the rate-yield trade-offs observed in our experiments are generally conserved between these two groups in line with their ecophysiologies. Kinetic isotope effects of N from NO3- reduction were 9.6 ± 2.7 ‰ for S. lithotrophicum, 6.4 ± 0.7 ‰ for C. mediatlanticus and 8.8 ± 0.6 ‰ for T. ammonificans. Our results help evaluate how metabolic partitioning between growth efficiency and reaction kinetics during chemolithoautotrophic NO3- reduction affect the concentration and isotope composition of N compounds at deep-sea hydrothermal vents.

Environmental Microbiology
The metabolic potential of the single cell genomes obtained from the Challenger Deep, Mariana Trench within the Candidate Superphylum Parcubacteria (OD1) NEW!
Rosa León-Zayas*, Logan Peoples, Jennifer F. Biddle, Sheila Podell, Mark Novotny, James Cameron, Roger S. Lasken, Douglas H. Bartlett
*C-DEBI Contribution 369

Candidate phyla (CP) are broad phylogenetic clusters of organisms that lack cultured representatives. Included in this fraction is the candidate Parcubacteria superphylum. Specific characteristics that have been ascribed to the Parcubacteria include reduced genome size, limited metabolic potential, and exclusive reliance on fermentation for energy acquisition. The study of new environmental niches, such as the marine versus terrestrial subsurface, often expands the understanding of the genetic potential of taxonomic groups. For this reason we analyzed twelve Parcubacteria single amplified genomes (SAGs) from sediment samples collected within the Challenger Deep of the Mariana Trench, obtained during the Deepsea Challenge (DSC) Expedition. Many of these SAGs are closely related to environmental sequences obtained from deep-sea environments based on 16S rRNA gene similarity and BLAST matches to predicted proteins. DSC SAGs encode features not previously identified in Parcubacteria obtained from other habitats. These include adaptation to oxidative stress, polysaccharide modification, and genes associated with respiratory nitrate reduction. The DSC SAGs are also distinguished by relative greater abundance of genes for nucleotide and amino acid biosynthesis, repair of alkylated DNA and the synthesis of mechanosensitive ion channels. These results present an expanded view of the Parcubacteria, among members residing in an ultra-deep hadal environment.

Frontiers Research Topic on Environmental Bioenergetics: Call for Manuscripts
Abstract submission deadline: June 30, 2017.


Meetings & Activities

IODP-USSSP: JOIDES Resolution Assessment Workshop, September 26-27, Denver UPDATED!

Dear C-DEBI Colleagues,

Last month we urged you to fill out the JR Renewal Online Survey. You all reacted in great numbers; with a total of 876 survey takers (for all of IODP participants, including 410 from the U.S.) we are showcasing the great, wide and enthusiastic interest in IODP utilizing the JR. Thank you so much!

However, the survey was only the first step in the two-step JR Renewal process. Now we need your PARTICPATION in the Denver 2 Meeting that is officially called the JOIDES Resolution Assessment Workshop! This workshop will bring together close to 80 scientists with strong interests and/or experience in IODP, from all career stages and from all U.S. institutions. We are hoping for a strong showing from deep biosphere colleagues to represent our interests in future IODP Expeditions. SEE THE WEBSITE FOR DETAILS AND PLEASE APPLY SOON (Deadline for application is TOMORROW, June 2nd)!!!

From the perspective of the JOIDES Resolution Facility Board (JRFB) this workshop is critically important for renewal:

  1. It will provide key evidence that the U.S. community is completely satisfied with the operation and management of the JR during the period of 2014-2017;
  2. It will express powerfully the continued need for and unique use of the JR as part of the larger IODP program;
  3. It will give a strong voice to the U.S. community in proposing novel plans for the JR for operations in the last five years of the 2013-2023 IODP Program.

The results of the Denver 1 Workshop in 2012 allowed NSF to successfully secure approval by the National Science Board (NSB) for starting the 2013-2019 portion of the current IODP program. However, it also provided the ingredients for a new business and operational model that now has been implemented (to great success) by the JRFB. As always, your PARTICIPATION, ENERGY AND IDEAS are key to making Denver 2 the greatest possible success!!!

Thank you, and all the best,
Jason Sylvan & Jennifer Biddle.

IODP-USSSP: Volunteer for an IODP Board, Committee, or Panel NEW!
The U.S. Science Support Program is seeking one U.S.-based senior scientist to serve on the JOIDES Resolution Facility Board (JRFB), as well as new members for the U.S. Advisory Committee for Scientific Ocean Drilling (USAC) and the Science Evaluation Panel (SEP). All new members will serve three-year terms, beginning in October 2017. The deadline to apply is July 21, 2017.

IODP-USSSP: Drilling into Young Oceanic Crust for Subseafloor Observations at Axial Seamount, October 11-13, Palisades, NY
Deadline to apply: June 30, 2017.

Indian Ocean community workshop, September 11-13, 2017, La Jolla, CA
Abstract submission deadline: July 14, 2017

C-DEBI: Rolling call for Community Workshop support


Education & Outreach

MGLS and C-DEBI: Webinar on Proposal Writing, Management, and Budget Planning, June 15, 12pm PT / 3pm ET UPDATED!
Speakers: Donna Blackman (Scripps Institution of Oceanography) and Beth Orcutt (Bigelow Laboratory for Ocean Sciences). For our upcoming C-DEBI Professional Development Webinar, we have teamed up with the Consortium for Ocean Leadership’s Marine Geoscience Leadership Symposium (MGLS) to bring you a comprehensive webinar on proposal preparation. The webinar will focus on topics related to preparing research proposals by providing advice on writing, constructing planning timelines, managing a team through the process, and preparing a budget. Please register to access the webinar link and receive last-minute email reminders!

NSF: 2017 STC Professional Development Workshop
Applications are due by June 9, 2017.

DCO Webinar Wednesdays UPDATED!
Next up: Visual Tools for Big Data Network Analysis, June 14, 2017.

Risk Innovation Lab: 2017 Science Showcase Video Contest! NEW!
The 2017 Science Showcase Video Contest celebrates the best in researcher-created science videos. A staggering number of people use YouTube — over 200 million in the U.S. alone – many of whom are passionate about science. Yet there are remarkably few researchers making videos that people want to watch. This is a huge missed opportunity, and one we’re on a mission to address. Wouldn’t it be awesome if scientists were as fluent in “YouTube” as they are in “Blog” and “Twitter”? The Science Showcase Video Contest is all about getting researchers excited about communicating their science to curious-minded people on YouTube. So if you are doing cool research, and have a passion for telling others about it, get creating! Qualifying videos will be showcased on the Science Showcase YouTube channel, and the best reviewed by our panel of distinguished guest judges, including BrainCraft’s Vanessa Hill, NPR’s Richard Harris, ACS Reaction’s Adam Dylewski, and Google’s Cat Allman. Submissions close August 31, 2017.

Proposal Calls

NAS: Building Capacity for Science Communication Partnership Awards
To apply for these awards, researchers and practitioners who have agreed to work in partnership should submit a proposal by TODAY, June 1, 2017.

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). Next workshop submission deadline: TODAY, June 1, 2017.

IODP-USSSP: Special Call: Exp. 381 Corinth Active Rift Development NEW!
The International Ocean Discovery Program (IODP) is issuing a special call for experienced scientists to apply for IODP Expedition 381 Corinth Rift Development aboard a Mission Specific Platform provided by the ECORD Science Operator in the following specialties: inorganic geochemistry, foraminifer micropaleontology, and nannofossil micropaleontology. The call is only for scientists able to sail during the offshore phase (56 days starting between October  2nd and 16th, 2017 from Corinth, Greece). The new deadline to apply is June 9, 2017.

Simons Foundation: 2017 Postdoctoral Fellowships in Marine Microbial Ecology
Application deadline: June 15, 2017.

IODP: Apply to Sail: Expedition 377 Arctic Ocean Paleoceanography
The deadline to apply is June 23, 2017.

WGBH: Rita Allen Fellowship for Science Communication
Applications due June 30, 2017.

NSF: Provision of Marine Seismic Capabilities to the U. S. Research Community NEW!
Proposals are solicited to support needs of the marine seismic research community that are currently provided by the specialized seismic research vessel R/V Marcus G. Langseth. The vessel is owned by the National Science Foundation and operated by the Lamont Doherty Earth Observatory of Columbia University (LDEO). NSF has determined that the current operational model is unsustainable and, with this solicitation, seeks proposals that provide comparable access to marine seismic capability through innovative approaches to R/V Marcus G. Langseth use or by other means.The successful proposal will be administered as a Cooperative Agreement over the five-year period of performance. Full proposal deadline: August 21, 2017.

NSF: Research Experiences for Undergraduates (REU) Program Solicitation 
Full proposal deadline: August 23, 2017.

NSF: Management and Operation of a National Ocean Bottom Seismometer Instrument Pool

NSF: Using JOIDES Resolution to Collect Cores with Advanced Piston Coring (APC) System

DCO: Deep Life Cultivation Internship Program

NSF: Arctic Sciences Program Solicitation
Proposals accepted anytime.

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

C-DEBI: Rolling call for Research Exchange proposals



Bigelow: Postdoctoral Scientist in Horizontal Gene Transfer in Marine Bacterioplankton NEW!
The hired scientist will be engaged in a large-scale study of the lineage boundaries, mechanisms, rates, and consequences of horizontal gene transfer (HGT) in marine bacterioplankton. Bacterial and archaeal HGT enables fast adaptation to environmental changes, as suggested by studies of human pathogens. Therefore HGT may also play an important role in bacterioplankton responses to natural and human-induced perturbations. However, microevolutionary processes are often overlooked in microbial ecology and biogeochemistry studies. The specific mechanisms, rates and consequences of microbial HGT in nature remain largely unknown, to a large degree due to methodological limitations. Unlike earlier, cultivation-based and metagenomic approaches, single cell genomics is well suited for in situ studies of HGT, because it recovers genomes from a randomized subset of unicellular individuals and successfully captures genome regions that have divergent evolutionary histories (e.g. HGT events) or are located on separate DNA molecules (e.g. plasmids). The project is led by Dr. Stepanauskas, utilizes single cell genomics and other cutting-edge technologies, and takes advantage of significant bioinformatics support and computational resources at Bigelow Laboratory and collaborating institutions. Candidates must have a PhD degree or post-degree experience in relevant fields, such as evolution, bioinformatics and microbiology.

University of Pennsylvania: Postdoctoral Scholar Position NEW!
The Department of Earth and Environmental Science at the University of Pennsylvania seeks a postdoctoral scholar to study microbial remediation of asbestos through chemosynthesis. The position involves the cultivation of chemosynthetic microorganisms relevant to Fe- and N-based energy metabolisms. DESIRED LABORATORY SKILLS INCLUDE: (i) experience with microbial cultivation under batch and/or continuous culture conditions, (ii) experience with aqueous geochemistry techniques, (iii) experience with epifluorescent, SEM and/or TEM microscopy and (iv) basic molecular techniques. [Note: these are the required skills for the implementation of the project. Training in certain areas can be provided, as long as the intellectual motivation is well aligned with this research]. DESIRED ACADEMIC SKILLS INCLUDE: (i) team-working and interpersonal skills, (ii) excellent written and oral communication skills, (iii) commitment to developing peer-reviewed manuscripts, and (iv) desire to work at the intersection between geology, chemistry and biology. The position includes full benefits and is for two years. Candidates should submit a CV, max 2-page statement of experience/interests and the names of 3 contact references. Please send application materials and/or informal inquiries to Dr. Ileana Pérez-Rodríguez ( The position is available starting September 1st. Applications are accepted until position is filled. The successful candidate must have completed his/her Ph.D. at the time of the appointment.

NSF: Marine Geology & Geophysics Science Assistant Position NEW!
The Division of Ocean Sciences at the National Science Foundation is looking to hire a Science Assistant for the Marine Geology and Geophysics (MGG) Program. Science Assistants work closely with Program Officers and assist with running the MGG program, support the merit review process for proposals submitted to MGG, help with Program initiatives and strategic planning and interact with the community and other internal parties at NSF. Science Assistants may also participate in other career development assignments including data analysis and report preparation, assisting in site visits, and working with other parts of NSF and/or other government agencies. This is a two-year, terminal, position open for people with a recent Master’s degree in marine geology or geophysics or other related scientific fields. Candidates must have completed their Master’s degree prior to starting the position. The position allows the incumbents to develop an understanding of key aspects of the science and engineering enterprise and develop skills that can be valuable to a future professional scientific career. The start date will be no later than January 1, 2018. For additional questions regarding the positions, please contact Barbara Ransom ( at 703-292-7792 or Andrea Portier ( If interested, please submit a CV and a letter of interest to Barbara Ransom at the above email.

Second Genome: Bioinformatic Scientist, Research Solutions

University of Southern Mississippi: PhD and MS Graduate Research Assistantship in Marine Microbial Ecology

University of Southern Mississippi: Postdoctoral Research Position in Marine Microbial Ecology

University of Munich: Postdoctoral scholar, microbial transcriptional activity in subseafloor sediment

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

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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