C-DEBI Newsletter – June 2, 2014
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Meetings, Workshops and Activities

C-DEBI: Networked Speaker Series Seminar: Jason Sylvan, June 18, 2014 from 12:00-12:45pm PT, Online!
The Center for Dark Energy Biosphere Investigations (C-DEBI) is a “networked” Science and Technology Center (STC), gathering expertise, ideas, and participation from institutions across the U.S. and around the world. C-DEBI runs the Networked Speaker Series as one means to enhance communication and the exchange of ideas via short (30 minute) presentations with time for questions and discussion. The series is presented live online for remote participants (login instructions will be distributed before the talk), and is recorded and available on the website for those unable to attend the live broadcasts. 

Missed the last Networked Speaker Series seminar with Luke McKay on "Approaching the high temperature boundary for life in the hydrothermally altered sediments of Guaymas Basin"? Watch it now online.

C-DEBI's next Networked Seminar Speaker is Dr. Jason Sylvan from the University of Southern California, Department of Biological Sciences:

Microbial life in old subseafloor basaltic crust
The aquifer in subseafloor basaltic crust is a massive, continuous microbial substrate, yet sparingly little is known about life in this habitat.  The work to date has focused largely on young crust at oceanic spreading regions and ridge flanks, where the basaltic crust is still porous and fluid flow through it is active.  Heat flow models predict that little fluid moves through subseafloor basalt >65 million years old, but recent work proves that seamounts, which are found throughout the seafloor, act as mid-plate conduits into and exits out of the subsurface aquifer for fluids and possibly microbes.  To determine if life does indeed exist in old subseafloor basaltic crust, I sampled 64-74 million year old extinct seamounts along the Louisville Seamount Chain in the southwest Pacific Ocean during Integrated Ocean Drilling Program Expedition 330. Newly developed methods for quantifying subsurface microbes were applied to these samples, providing the first quantification of microbes in cores retrieved from subseafloor basaltic crust. Analysis of community DNA indicated archaea are extremely rare in this setting.  The most abundant bacterial classes detected were Actinobacteria, Flavobacteria, Sphingobacteria, Bacilli, Clostridia, Alpha-, Beta and Gammaproteobacteria.  Genera putatively carrying out hydrocarbon oxidation and nitrogen, sulfur and metal redox processes were commonly detected in core samples as well as enrichment incubations started during the cruise.  This work shows that old subseafloor basalt is indeed home to microbial communities that may have a significant impact on marine biogeochemistry. I will discuss these results in more detail and put them in context with previous studies of microbiology in subseafloor basaltic crust. 

2015 Gulf of Mexico Oil Spill & Ecosystem Science Conference: Submit a Scientific Session
You are invited to Submit a Scientific Session for the 2015 Gulf of Mexico Oil Spill and Ecosystem Science Conference. The 2015 Conference Sessions should be designed to share the latest research findings and to allow dialog on research implications, applications, and synthesis. This year’s conference will seek to answer the questions “What have we learned, what does it mean and how can it be used?” A strong emphasis will be placed on the impact of the research and application of published research findings. The Deadline to submit a session proposal is June 15th, 2014. Please don’t hesitate to forward this email to any colleagues who may be interested. Click here to learn more about the conference and how to submit a scientific session.

Ocean Leadership/IODP: Seeking new Members for USAC, JOIDES Resolution Facility Board, Science Evaluation Panel
Scientists interested in volunteering for these opportunities should send a cover letter and a two-page CV to by June 15, 2014.

Hot Off the Press: Interactions of proteins with biogenic iron oxyhydroxides and a new culturing technique to increase biomass yields of neutrophilic, iron-oxidizing bacteria (C-DEBI Contribution 212), in Frontiers in Microbiology
Authors: C-DEBI Graduate Fellow Barco and researcher Edwards. Neutrophilic, bacterial iron-oxidation remains one of the least understood energy-generating biological reactions to date. One of the reasons it remains under-studied is because there are inherent problems with working with iron-oxidizing bacteria (FeOB), including low biomass yields and interference from the iron oxides in the samples. In an effort to circumvent the problem of low biomass, a new large batch culturing technique was developed. Protein interactions with biogenic iron oxides were investigated confirming that such interactions are strong. Therefore, a protein extraction method is described to minimize binding of proteins to biogenic iron oxides. The combination of these two methods results in protein yields that are appropriate for activity assays in gels and for proteomic profiling.

Meeting report: Ocean ‘omics science, technology and cyberinfrastructure: current challenges and future requirements (August 20-23, 2013), in Standards in Genomic Sciences
The National Science Foundation’s EarthCube End User Workshop was held at USC Wrigley Marine Science Center on Catalina Island, California in August 2013. The workshop was designed to explore and characterize the needs and tools available to the community that is focusing on microbial and physical oceanography research with a particular emphasis on ‘omic research. The assembled researchers outlined the existing concerns regarding the vast data resources that are being generated, and how we will deal with these resources as their volume and diversity increases. Particular attention was focused on the tools for handling and analyzing the existing data, on the need for the construction and curation of diverse federated databases, as well as development of shared, interoperable, “big-data capable” analytical tools. The key outputs from this workshop include (i) critical scientific challenges and cyber infrastructure constraints, (ii) the current and future ocean ‘omics science grand challenges and questions, and (iii) data management, analytical and associated and cyber-infrastructure capabilities required to meet critical current and future scientific challenges. The main thrust of the meeting and the outcome of this report is a definition of the ‘omics tools, technologies and infrastructures that facilitate continued advance in ocean science biology, marine biogeochemistry, and biological oceanography.

Data report: X-ray fluorescence scanning of sediment cores from Holes U1382B, U1383D, U1384A, and 1074A from the North Pond area, in Proceeding of the IODP
We report semiquantitative geochemical data of four sediment cores from the North Pond area on the western flank of the Mid-Atlantic Ridge at 22°45′N, 46°06′W. Three of the sediment cores, from Holes U1382B, U1383D, and U1384A, were drilled during Integrated Ocean Drilling Program Expedition 336. Core from Hole 1074A (Ocean Drilling Program Leg 174B) was also included in this study. The data show highly variable fluorescence intensities for Ca, Al, Si, Fe, Mn, and K. These variations can be explained by varying proportions and frequencies of foraminiferal sand intercalating with clayey nannofossil ooze. The sand layers show high Ca counts and low counts for all other measured elements. The ooze layers show noticeable counts for K, Al, and Si, which is interpreted as illite clay fraction. In addition, the concentrations of Fe and Mn increase toward the sediment/basement interface in Holes U1382B and Hole 1074A and especially in Hole U1384A, but not in Hole U1383D. The sediment pile at all four drill sites shows slight enrichments in Fe and Mn in the uppermost few meters. Rock debris (millimeter to centimeter sized) is present in Holes U1382B and U1383D and to lesser extent in Hole 1074A, but not in Hole U1384A in the northwesternmost part of the sediment pond. These data provide a cursory assessment of the different sediment lithologies in the North Pond area, in which coupled hydrological-geochemical-microbiological subbasement experiments are currently being conducted.

Global rates of marine sulfate reduction and implications for sub–sea-floor metabolic activities, in Science
Sulfate reduction is a globally important redox process in marine sediments, yet global rates are poorly quantified. We developed an artificial neural network trained with 199 sulfate profiles, constrained with geomorphological and geochemical maps to estimate global sulfate-reduction rate distributions. Globally, 11.3 teramoles of sulfate are reduced yearly (~15% of previous estimates), accounting for the oxidation of 12 to 29% of the organic carbon flux to the sea floor. Combined with global cell distributions in marine sediments, these results indicate a strong contrast in sub–sea-floor prokaryote habitats: In continental margins, global cell numbers in sulfate-depleted sediment exceed those in the overlying sulfate-bearing sediment by one order of magnitude, whereas in the abyss, most life occurs in oxic and/or sulfate-reducing sediments.

Ocean Leadership: Apply to Host Deep Biosphere IODP Distinguished Lecturer Beth Orcutt
C-DEBI researcher and Activity Theme Team Leader Dr. Beth Orcutt (Bigelow Laboratory for Ocean Sciences) is one of the Ocean Leadership Distinguished Lecturers touring the country during the 2014-2015 academic year. Apply now to host her at your institution and learn about “Buried Alive: Life Beneath the Seafloor.”  The Consortium for Ocean Leadership’s U.S. Science Support Program offers the Distinguished Lecturer Series to bring the exciting scientific results and discoveries of the Integrated Ocean Drilling Program to academic research institutions, museums, and aquaria. Applications are due June 1, 2014. If you or someone you know is interested in becoming a Distinguished Lecturer, email their name, institution, and potential lecture topic to Charna Meth ( by the nomination deadline of June 15, 2014.

Ocean Leadership: Share Your Ocean Story with the BBC
Ocean Leadership has built a website to help BBC solicit ideas/content/contacts for their upcoming seven-part series follow-up to Blue Planet entitled Ocean: New Frontiers.

Proposal Calls & Competitons

IODP: Deadline Extended: Apply to Sail on Indonesian Throughflow
The deadline to apply to sail on International Ocean Discovery Program (IODP) Expedition 356 Indonesian Throughflow aboard the JOIDES Resolution had been extended to June 2, 2014. U.S.-affiliated scientists interested in participating in this expedition should apply to sail through the U.S. Science Support Program of the Consortium for Ocean Leadership; please visit:

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

National Academies Research Associateships for Graduate, Postdoctoral and Senior Researchers
There are four annual review cycles and the next closes August 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 November 15, 2014, related to the International Ocean Discovery Program (IODP).


University of Minnesota, Department of Earth Sciences: Assistant Professor in Geomicrobiology and Bioremediation  
The Department of Earth Sciences and The BioTechnology Institute (BTI) at the University of Minnesota seek applications for a tenure-track faculty position in the area of Geomicrobiology and Bioremediation. We are interested in a broad range of topics in geomicrobiology, microbiology, biogeochemistry, or related fields, with application in areas such as acid mine drainage bioremediation, dynamics of sulfate and nitrate removal, microbial bioremediation, biomining, and/or groundwater bioremediation. The appointment will be a 9 month (B-Term), tenure-track position at the assistant or associate professor level with responsibilities in research, teaching, and service. Review of applications will begin September 8, 2014; applications will continue to be accepted until the position is filled. Expected appointment is Fall 2015. Questions may be directed to Prof. Chris Paola at

LUBEM, University of Brest (UBO), France: 12-month Postdoctoral Position
Interested candidates are encouraged to send a curriculum vitae, a cover letter outlining previous experience and support letters from 2 colleagues with first-hand knowledge of their work experience as soon as possible by e-mail to Gaëtan Burgaud ( See the flyer for more information.

Montana State University, Bozeman: Postdoctoral Researcher in Geomicrobiology
Screening of applications will begin on April 16, 2014 and will continue to be accepted until an adequate candidate pool has been established.

Texas A&M, College of Geosciences: 4 Faculty Positions
The search committee will commence review of applications starting 1 May and will continue until the positions are filled.

ABYSS: PhD and Post-Doctoral fellowships in Geodynamics, Mineralogy, Hydrodynamics, Thermodynamics and (Bio-)Geochemistry
We are now recruiting 10 PhDs and 1 post-doctoral fellow, including PhD position ESR11 in geobiology, "The ocean crust as microbial incubator." The deadline for application is June 1, 2014.
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
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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