C-DEBI Newsletter – January 3, 2015
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Hot Off the Press: Marine sediments microbes capable of electrode oxidation as a surrogate for lithotrophic insoluble substrate metabolism (C-DEBI Contribution 255) in Frontiers in Microbiology
Little is known about the importance and/or mechanisms of biological mineral oxidation in sediments, partially due to the difficulties associated with culturing mineral-oxidizing microbes. C-DEBI Postdoctoral Fellow Rowe et al. demonstrate that electrochemical enrichment is a feasible approach for isolation of microbes capable of gaining electrons from insoluble minerals. To this end we constructed sediment microcosms and incubated electrodes at various controlled redox potentials. Negative current production was observed in incubations and increased as redox potential decreased (tested -50 to -400 mV vs Ag/AgCl). Electrode-associated biomass responded to the addition of nitrate and ferric iron as terminal electron acceptors in secondary sediment-free enrichments. Elemental sulfur, elemental iron and amorphous iron sulfide enrichments derived from electrode biomass demonstrated products indicative of sulfur or iron oxidation. The microbes isolated from these enrichments belong to the genera Halomonas, Idiomarina, Marinobacter, and Pseudomonas of the Gammaproteobacteria, and Thalassospira and Thioclava from the Alphaproteobacteria. Chronoamperometry data demonstrates sustained electrode oxidation from these isolates in the absence of alternate electron sources. Cyclic voltammetry demonstrated the variability in dominant electron transfer modes or interactions with electrodes (i.e., biofilm, planktonic or mediator facilitated) and the wide range of midpoint potentials observed for each microbe (from 8 to -295 mV vs. Ag/AgCl). The diversity of extracellular electron transfer mechanisms observed in one sediment and one redox condition, illustrates the potential importance and abundance of these interactions. This approach has promise for increasing our understanding the extent and diversity of microbe mineral interactions, as well as increasing the repository of microbes available for electrochemical applications.

Hot Off the Press: Earth and Life Processes Discovered from Subseafloor Environments, 1st Edition: A Decade of Science Achieved by the Integrated Ocean Drilling Program (IODP), R. Stein, D. Blackman, F. Inagaki and H.-C. Larsen (Eds.), Series: Developments in Marine Geology, Elsevier
The Integrated Ocean Drilling Program (IODP: 2000-2013) has provided crucial records of past and present processes and interactions within and between the biosphere, cryosphere, atmosphere, hydrosphere and geosphere. Research in IODP encompasses a wide range of fundamental and applied issues that affect society, such as global climate change, biodiversity, the origin of life, natural hazards involving the study of earthquakes processes, and the internal structure and dynamics of our planet. This compilation of major findings from the 2003-2013/14 phase of IODP, focusing on scientific results rather than description of data acquisition and early inferences, provides invaluable information. Anyone wondering what scientific drilling can achieve will gain quick understanding of the range of questions that are uniquely addressed with this methodology and the ways these data dovetail with other regional information. The excitement of breakthrough findings that occasionally accompanies a drilling project will be evident. IODP obtained unique records from the global ocean basins during the 2003-2013 program phase. This book highlights findings in three theme areas: Subseafloor life and the marine biosphere; Earth's changing environments; and Dynamics of the solid Earth. Each core or borehole log provides a window revealing insights that no other data achieve.

C-DEBI Researchers worked on many chapters including:
  • 2.2(b) Genetic Evidence of Subseafloor Microbial Communities, A. TeskeJ. F. Biddle, M. A. Lever (C-DEBI Contribution 246)
  • 2.3. The Underground Economy: Energetic Constraints of Subseafloor Life, S. D'Hondt, G. Wang, A. J. Spivack (C-DEBI Contribution 230)
  • 2.4. Life at Subseafloor Extremes, K. Takai, K. Nakamura, D. LaRowe, J. P. Amend (C-DEBI Contribution 224)
  • 4.2.2. Hydrologic Properties, Processes and Alteration in the Igneous Ocean, A. Fisher, W. Bach, J. Alt (C-DEBI Contribution 228)

Dorado Outcrop: AT26-24 with the Submersible Alvin, November 30 - December 12, 2014, Expedition Report
AT26-24 was the second of two cruises that focused on Dorado Seamount. The first expedition occurred in December 2013 and utilized the remotely operated vehicle (ROV) Jason and the autonomous underwater vehicle (AUV) Sentry. These two assets allowed us to collect bathymetric, backscatter, side-scan, images, magnetometer, and thermal anomaly data. They also provided targets for closer inspection of the seafloor that led to the discovery of warm springs on the seafloor. In 2013 we sampled these springs with the ROV Jason, collected rock and sediment push cores, and made measurements of heat flow. We also deployed temperature loggers, OsmoSamplers, which are continuous fluid sampling devices, and enrichment experiments in several springs to asses the temporal variability in thermal and chemical signatures and to asses the rate of enrichment on particular substrates in this environment. These springs were the focus of the dive program (AT26-24) in December 2014 that utilized the submersible Alvin. We completed ten Alvin dives, collected thirteen gravity cores, conducted one CTD hydrocast, and completed four surveys using the hull-mounted bathymetric mapping system. Through these activities we collected hundreds of samples for hydrologic, biogeochemical, and microbial studies, all of which will continue ashore with a spectrum of analytical techniques and modeling efforts.

Education & Outreach

Stanford: Hopkins Microbiology Course, June 19 - July 18
The Hopkins Microbiology Course offers:

  • Four weeks of intense learning activity focused on microbes and microbial life. Our approach is integrative, holistic and concept based. The study of microbes is placed firmly within the physiological, ecological (biogeochemical), genetic and evolutionary framework.
  • Exposure to a wealth of new ideas and concepts. Dedicated faculty and experienced teaching assistants are continuously on hand to offer guidance and expertise
  • Seminars ranging from the factual to the philosophical.  Practical work forms a large part of the course and provides students with hands-on experience in isolation of a wide range of microbes, experimental evolution, population genetics, clone library construction, and bioinformatic analysis. The course experiments are not “canned” and you will make new discoveries.

By the end of the course you will have a broad, fundamental understanding of the key concepts of microbial life and how they interconnect to each other. In addition you will have a solid set of experimental tools that enables you to address contemporary questions in microbial biology. Is this the course for you? The HMC is more than an introduction to microbiology: the course provides a factual background in key aspects of microbial biology, but, in keeping in the tradition of van Niel’s teaching, there is a strong emphasis on concepts, ideas, questions and the placement of microbiological knowledge within a broader and more mainstream context.  A background in microbiology is not essential, but it is an advantage. Important is a mature approach to learning and a desire to go beyond the undergraduate lecture theatre environment. Application deadline: March 1, 2015.

C-DEBI: Now receiving applications for C-DEBI Global Environmental Microbiology (GEM) Summer Course!  
The GEM Course is an all-expenses paid, four-week intensive introductory course in Global Environmental Microbiology (GEM) geared for early career undergraduates from 2 and 4 year colleges/universities that focuses on microbes found in aquatic environments investigated through authentic research experiences (students collect, process & interpret data). Application deadline: February 03, 2015

C-DEBI: Application for Teacher Small Grants to open January 5, 2014!
The K-12 Teacher Small Grants program supports K-12 teachers who have attended a C-DEBI teacher-training program and have incorporated C-DEBI content into their classrooms.  These awards up to $2500 support items including but not limited to the following: funds for student field trips, classroom supplies, travel for presenting C-DEBI curriculum at educator meetings, or additional professional development directly related to C-DEBI research. Deadline for proposals: February 16, 2015.

Wrigley Institute: Geobiology 2015: An International Training Course in a Rapidly Evolving Field, June 19-July 21, 2015
GeoBiology 2015 is open to students and researchers at any level, although we give preference to graduate students in their early to mid years of study. Applications are due February 13, 2015.

Wrigley Institute: 2015 Summer Research Experiences for Undergraduates (REU): Coastal Ocean Processes, Jun 15 – Aug 7, 2015
This NSF-funded program will support ten highly motivated and talented undergraduate students to conduct independent but guided research that focuses on Coastal Ocean Processes at the Wrigley Marine Science Center (WMSC) on Catalina Island, CA. Applications due February 16, 2015.

Meetings, Workshops and Activities

IODP/COL: Marine Geoscience Leadership Symposium, March 16-20, 2015, Washington, DC
The deadline to apply for the 2015 Marine Geoscience Leadership Symposium has been extended to January 8, 2015.

IODP: Workshop for Scientific Drilling in the Indian Ocean Crust and Mantle
For more information and to register, please visit:

IODP: ECORD Training Course: The Virtual Drillship Experience; March 9-13, 2015; Bremen, Germany
U.S.-affiliated students and researchers may apply for partial travel support through the U.S. Science Support Program. A limited number of travel grants are available. To apply for U.S. travel support, submit a two-page CV to and complete the online application at The deadline to apply for travel support and to register for the training course is January 5, 2015.
The workshop is open to U.S. and international participants, and the deadline to register is March 15, 2015. Travel funding is available for U.S. participants, and the deadline to apply for those funds is January 31, 2015.

Regional Graduate Network in Oceanography: Microbial and Geochemical Oceanography in Upwelling Ecosystems
Application deadline: January 15, 2015.
Proposal Calls

NSF: Dimensions of Biodiversity Program Solicitation
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 among them. While this focus complements several core programs in BIO and GEO, 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. The Dimensions of Biodiversity program again includes partnerships with the National Natural Science Foundation of China (NSFC) and São Paulo Research Foundation (FAPESP) of Brazil in fiscal year 2015. Investigators wishing to inquire about the suitability of potential projects for Dimensions of Biodiversity are encouraged to email a brief summary and contact information to Full proposal deadline: April 09, 2015.

IODP: Experienced Paleomagnetists and Nannofossil Micropaleontologists Needed for Expedition 359
The International Ocean Discovery Program is seeking experienced paleomagnetists and nannofossil micropaleontologists to sail on Expedition 359 Maldives Monsoon aboard the JOIDES Resolution. Expedition 359 will investigate Neogene Indian Ocean environmental change and the onset of the modern carbonate depositional system driven by fluctuations in sea level and ocean currents. The expedition will take place from 30 September to 30 November 2015. 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 The deadline to apply is 16 January 2015.

ECORD: Research Grants for Graduate Students and Postdocs at ECORD Country Institutions
The European Consortium for Ocean Research Drilling (ECORD) is sponsoring merit-­‐based awards for outstanding young scientists to conduct innovative research related to the  International Ocean Discovery Program. The research may be directed toward the objectives of  upcoming or past DSDP/ODP/IODP expeditions, using core material and/or data, or address  broader aspects directly related to the IODP Science Plan. The ECORD Grants will cover travel and lab expenses or other approved costs related to the study. Preference will be given to  studies conducted in a laboratory/institution other than the applicant’s home institution and  to studies that promote new collaborations and/or the acquisition of new scientific expertise. Grants will not typically exceed 2000 €. Applicants should be enrolled in either a PhD or “early­career,” post-­doctoral research programme at any institution from an ECORD country. The deadline to apply for an ECORD Research Grant is March 31, 2015.

NSF: Improving Undergraduate STEM Education: Pathways into Geoscience (IUSE: GEOPATHS)
Letter of intent due January 05, 2015.

IODP: Apply to Sail for Expedition 357 Atlantis Massif Serpentinization and Life
Information on this expedition: U.S.-affiliated scientists should apply at: Application Deadline: January 09, 2015. E-mail co-chief scientist Beth Orcutt ( with any questions. To learn more about the scientific objectives of this expedition, life at sea, and how to apply to sail, please join us for a web-based seminar on Tuesday, January 6th at 12 PM Eastern. To register, please send an email to with your name and your institution, with Expedition 357 Webinar Registration in the subject line.

C-DEBI Special Call for Deep Biosphere Research Proposals
C-DEBI invites proposals for one-year projects that will significantly advance our central research agenda—to investigate the subseafloor biosphere deep in sediments and the crust. C-DEBI intends to fund 2-3 proposals in response to this call, up to $100,000 each. The deadline for this call is January 15, 2015.

NSF: Postdoctoral Research Fellowships in Biology (PRFB)
Fellowship Competitive Area 1: Broadening Participation in Biology. Proposal deadline: January 08, 2015.
NSF: OCE  Research Initiation Grants
The submission deadline is January 12, 2015.

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

NSF: Genealogy of Life (GoLife) program solicitation
Full proposal deadline: March 25, 2015.

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, 2015, related to the International Ocean Discovery Program (IODP).


Bigelow: Two Postdoctoral Research Scientists in Microbial Evolution and Ecology
Two postdoctoral positions are available in Dr. Stepanauskas' laboratory. One position is focused on the deep evolution of Bacteria and Archaea and the genome content of the "microbial dark matter". Another position is focused on chemolithoautotrophy in the deep ocean and hydrothermal systems. The hired scientists will be engaged in large, collaborative projects, and will employ single cell genomics and other advanced molecular biology and biogeochemistry research tools. Anticipated employment duration: 2 years, with potential extension. Bigelow Laboratory's new campus is located in scenic, coastal Maine with abundant opportunities for outdoor and cultural activities. It is about an hour drive from Portland and a 3-hour drive from Boston. Hired scientists will be responsible to lead computational analyses of large single cell genomics, community "omics" and biogeochemical data sets, prepare manuscripts, supervise undergraduate students, and assume gradually increasing responsibilities in project management. These positions also include opportunities for field expeditions and laboratory analytical work. Candidates must have a PhD degree in microbiology, evolutionary sciences, bioinformatics, computational biology, or a related field. Prior experience in computational analyses of large microbial genomic data sets will be necessary for this opportunity. For full consideration, the application should be received by February 1, 2015.

Post-doctoral position in marine microbial ecology at the University of Hawaii 
The University of Hawaii is seeking a Postdoctoral Investigator to work with Dr. Matthew Church on a multi-institutional, international program conducting baseline studies of benthic biology in the Clarion-Clipperton Fracture Zone of the North Pacific Ocean. The work is being conducted as part of a contract to the University of Hawaii from UKSRL (UK Seabed Resources, LTD) to provide baseline studies on the diversity of benthic organisms in abyssal polymetallic nodule fields. The successful post-doctoral candidate will focus on assessing microbial diversity associated with the water column, sediments, and nodules in this region of the ocean. The successful candidate must have a Ph.D. in Marine Science, Oceanography, or Microbiology, with preference given to candidates with a background in microbial oceanography and ecology. Must have excellent written and oral communication skills, with demonstrated laboratory experience with methodologies for evaluating microbial diversity, including next generation sequencing and computer-based bioinformatics tools. Must be able to work at sea as a member of a research team. Candidates must be able to participate in a ~40 day research cruise in early 2015. The position will be located at the University of Hawaii at Manoa, working in the laboratories of the Center for Microbial Oceanography: Research and Education (C-MORE). The initial appointment is for one year with re-appointment for subsequent years possible, contingent on satisfactory performance and funding availability. Applications should include a CV, statement of research interests, a one-page summary of research interests and experience, and names/addresses of three references. Postdoctoral stipends will be commensurate with experience and qualifications. Application materials should be submitted to Matthew Church ( Applications will be reviewed beginning December until position is filled, beginning on December 23, 2014. The successful applicant will be expected to start in early 2015. For additional information regarding the position, please contact Dr. Matthew Church (

Moore Foundation: Program Officer, Marine Microbiology Initiative
The Foundation is seeking an accomplished scientist with expertise in a biological, oceanographic or other field relevant to marine microbial ecology, a passion for broad scientific inquiry and advancement, and excitement about MMI’s goals.

Aarhus University: Professor in Geomicrobiology
All applications must be made online and received by January 15, 2015.

New Mexico State University:  Environmental Science/Environmental Chemistry Postdoctoral Position
Application closing date: January 30, 2015

University of Nevada, Las Vegas: Postdoctoral Fellow in microbiology (“microbial dark matter” biology)
The review of materials will begin December 01, 2014, and will continue until the position is filled.

Skidaway Institute of Oceanography: Two Tenure Track Faculty Positions in Oceanography
The committee will begin to review applications on October 24, 014 and will continue until the positions are filled.

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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