C-DEBI Newsletter – December 1, 2014
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Proposal Calls

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. Proposals will be considered for research on subseafloor samples, participation on upcoming expeditions (including C-DEBI field programs, IODP expeditions and other field opportunities relevant to C-DEBI objectives), and shore-based investigations. Proposed research can also focus on theoretical and experimental deep biosphere studies in a broader sense, which might include, for example, testing novel techniques for deep biosphere research, lab-based experiments with deep biosphere organisms, model development, and metabolic studies of growth under deep subsurface conditions. Fundamental studies of microbial metabolism that can be applied to subsurface conditions will also be considered. In this call, we especially encourage proposals with one of the following foci:

  1. Synthesis and integration of datasets that link microbiological processes to environmental conditions. A primary goal should be to provide insight into microbial activity, connectivity, limits, evolution, or survival in deep subseafloor ecosystems.
  2. Analysis of or experimentation with samples from a recent or upcoming field program with clear C-DEBI research objectives (e.g., North Pond cruise April 2014, Juan de Fuca Ridge flank cruise in August 2014, Guaymas Basin cruise in October 2014, Dorado Outcrop cruise in November 2014, North Atlantic long-coring expedition in October-December 2014, new site surveys in preparation of subsequent drilling).
The deadline for this call is January 15, 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.

Gulf of Mexico Research Initiative (GoMRI): Request for Proposals V
The Gulf of Mexico Research Initiative (GoMRI) is pleased to release the GoMRI Request for Proposals for Individual Investigators or Small Collaborative Teams for 2016-2018. The purpose of the RFP is to select the research activities for GoMRI Years 6–8 (1 January 2016 – 31 December 2018) involving individual investigators or collaborative efforts comprising a principal investigator and up to three co-principal investigators. The total funds available for distribution through the 2016-2018 GoMRI Individual Investigators RFP will be approximately $9 million per year. Letter of Intent deadline: December 15, 2014; Full proposal deadline: March 13, 2015.

NSF: Genealogy of Life (GoLife) program solicitation
Comprehensive understanding of life and how and why it changes over time depends on knowledge of the phylogeny (evolutionary relationships) of living and extinct organisms. The goals of the Genealogy of Life (GoLife) program are to resolve the phylogenetic history of all life’s diverse forms and to integrate this genealogical architecture with underlying organismal and environmental data. The ultimate vision of this program is an open access, comprehensive Genealogy of Life that will provide the comparative framework necessary for testing questions in systematics, evolutionary biology, ecology, and other fields. Strategic integration of this genealogy of life with data layers from genomic, phenotypic, spatial, ecological and temporal data will produce an extensive synthesis of biodiversity and evolutionary sciences. The resulting knowledge infrastructure will enable synthetic research on biological dynamics throughout the history of life on Earth, within current ecosystems, and for predictive modeling of the future evolution of life. Projects submitted to this program should emphasize increased efficiency in contributing to a complete Genealogy of Life and strategic integration of various types of organismal and environmental data with phylogenies. This program also seeks to broadly train next generation, integrative phylogenetic biologists, creating the human resource infrastructure and workforce needed to tackle emerging research questions in comparative biology. Projects should train students for diverse careers by exposing them to the multidisciplinary areas of research within the proposal. Full proposal deadline: March 25, 2015.

NSF: Dear Colleague Letter: Removal of deadlines for program solicitations within the Surface Earth Processes Section of the Division of Earth Sciences in the Directorate for Geosciences
A primary objective of research support provided by the National Science Foundation (NSF) is to transform the boundaries of scientific understanding. To meet this objective, after the upcoming January 2015 deadlines, new solicitations will be released for programs in the Surface Earth Processes Section within the Division of Earth Sciences. These new solicitations will no longer require that proposals be submitted by a specific deadline. Beginning on April 16th, 2015 investigators will be allowed to submit proposals at any time. Despite this change, programs in the Surface Earth Processes Section will continue to maintain high-quality merit review through the use of panel and ad hoc reviews, as has been the practice in the Division of Earth Sciences for many years. Only solicitations for the Geobiology & Low-temperature Geochemistry, Hydrologic Sciences, Geomorphology & Land-use Dynamics, and Sedimentary Geology & Paleobiology Programs will be affected by this change. All other submissions will continue to follow deadlines outlined in their respective solicitations.

NSF: Ocean Sciences Postdoctoral Research Fellowships (OCE-PRF)
Full proposal target date: December 08, 2014.

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.

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).


Hot Off the Press: Chemolithotrophy in the continental deep subsurface: Sanford Underground Research Facility (SURF), USA (C-DEBI Contribution 235) in Frontiers in Microbiology
The deep subsurface is an enormous repository of microbial life. However, the metabolic capabilities of these microorganisms and the degree to which they are dependent on surface processes are largely unknown. Due to the logistical difficulty of sampling and inherent heterogeneity, the microbial populations of the terrestrial subsurface are poorly characterized. In an effort to better understand the biogeochemistry of deep terrestrial habitats, the authors, including C-DEBI researcher LaRowe and director Amend, evaluate the energetic yield of chemolithotrophic metabolisms and microbial diversity in the Sanford Underground Research Facility (SURF) in the former Homestake Gold Mine, SD, USA. Geochemical data, energetic modeling, and DNA sequencing were combined with principle component analysis to describe this deep (down to 8100 ft below surface), terrestrial environment. SURF provides access into an iron-rich Paleoproterozoic metasedimentary deposit that contains deeply circulating groundwater. Geochemical analyses of subsurface fluids reveal enormous geochemical diversity ranging widely in salinity, oxidation state (ORP 330 to −328 mV), and concentrations of redox sensitive species (e.g., Fe2+ from near 0 to 6.2 mg/L and Σ S2- from 7 to 2778μg/L). As a direct result of this compositional buffet, Gibbs energy calculations reveal an abundance of energy for microorganisms from the oxidation of sulfur, iron, nitrogen, methane, and manganese. Pyrotag DNA sequencing reveals diverse communities of chemolithoautotrophs, thermophiles, aerobic and anaerobic heterotrophs, and numerous uncultivated clades. Extrapolated across the mine footprint, these data suggest a complex spatial mosaic of subsurface primary productivity that is in good agreement with predicted energy yields. Notably, they report Gibbs energy normalized both per mole of reaction and per kg fluid (energy density) and find the later to be more consistent with observed physiologies and environmental conditions. Further application of this approach will significantly expand our understanding of the deep terrestrial biosphere.

Hot Off the Press: Further insights into how sediment redox status controls the preservation and composition of sedimentary biomarkers (C-DEBI Contribution 237) in Organic Geochemistry
Sedimentary biomarker distributions can record ocean productivity and community structure, but their interpretation must consider alteration during organic matter (OM) export and burial. Large changes in the water column redox state are known to impact on the preservation of biomarkers, but more subtle variation in sediment redox conditions, characteristic of major modern ocean basins, have been less thoroughly investigated. Here the authors, including C-DEBI researcher LaRowe, evaluate changes in biomarker distributions during sinking and burial across a nearshore to offshore transect in the southwestern Cape Basin (South East Atlantic), which includes a range of sedimentary environments. Biomarker concentrations and distributions in suspended particulate matter from the upper water column were determined and compared with underlying sedimentary biomarker accumulation rates and distributions. Biomarker distributions were similar in surface and subsurface waters, indicating that the OM signature is exported from the ocean mixed layer with minimal alteration. They show that, while export production (100 m) is similar along this transect, 230Thxs-corrected biomarker accumulation rate varies by over an order of magnitude in sediments and is directly associated with sedimentary redox conditions, ranging from oxic to nitrogenous–ferruginous. Biomarker distributions were dominated by sterols in surface water, and by alkenones in underlying sediments, which we propose to be primarily the result of selective preservation. Notably, the difference in sediment O2 penetration depth was associated with relative biomarker preservation. Subtle variation in sedimentary redox conditions has a dramatic impact on the distribution of preserved biomarkers. They discuss mechanisms for preferential degradation of specific biomarkers within this setting.

Hot Off the Press: Sulfate reduction and methane oxidation activity below the sulfate-methane transition zone in Alaskan Beaufort Sea continental margin sediments: Implications for deep sulfur cycling (C-DEBI Contribution 239) in Geochimica et Cosmochimica Acta
Two ∼6 m long sediment cores were collected along the ∼300 m isobath on the Alaskan Beaufort Sea continental margin. Both cores showed distinct sulfate-methane transition zones (SMTZ) at 105 and 120 cm below seafloor (cmbsf). Sulfate was not completely depleted below the SMTZ but remained between 30 and 500 μM. Sulfate reduction and anaerobic oxidation of methane (AOM) determined by radiotracer incubations were active throughout the methanogenic zone. Although a mass balance could not explain the source of sulfate below the SMTZ, geochemical profiles and correlation network analyses of biotic and abiotic data suggest a cryptic sulfur cycle involving iron, manganese and barite. Inhibition experiments with molybdate and 2-bromoethanesulfonate (BES) indicated decoupling of sulfate reduction and AOM and competition between sulfate reducers and methanogens for substrates. While correlation network analyses predicted coupling of AOM to iron reduction, the addition of manganese or iron did not stimulate AOM. Since none of the classical archaeal anaerobic methanotrophs (ANME) were abundant, the involvement of unknown or unconventional phylotypes in AOM is conceivable. The resistance of AOM activity to inhibitors implies deviation from conventional enzymatic pathways. This work, authors including C-DEBI researcher Hamdan, suggests that the classical redox cascade of electron acceptor utilization based on Gibbs energy yields does not always hold in diffusion-dominated systems, and instead biotic processes may be more strongly coupled to mineralogy.

Education & Outreach

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).  This residential course includes lectures, labs and fieldwork at USC, the Eastern Sierra Mountains, and on Santa Catalina Island.

Where:  University of Southern California
When:  June 7 – July 2, 2015
Who:  Undergraduates from 2 or 4-year colleges
Cost:  FREE, including travel, room and board plus modest stipend
Application Deadline: February 03, 2015

First generation college, women, and under-represented students are encouraged to apply. For further information, please email Cynthia Joseph, C-DEBI Diversity Director, at

Cruise News
  • Submarine Ring of Fire: C-DEBI scientists will be aboard the "Submarine Ring of Fire" expedition 11/29-12/21 to the Mariana Arc investigating the ecology of microbial mats at seamount associated Fe-rich hydrothermal vent systems. Find "hot" resources at the expedition website!
  • North Atlantic Sediment Coring: Follow along with the North Atlantic Sediment Coring expedition scientists on their blog.
  • Guaymas Basin: Check out this update from last month's Guaymas Basin cruise with C-DEBI scientists Andreas Teske and Luke McKay!
Institute for Broadening Partcipation, Pathways to Science: Resources for students considering an undergraduate summer research program and/or applying to graduate school
IBP’s mission is to increase diversity in the Science, Technology, Engineering and Mathematics (STEM) workforce. We design and implement strategies to increase access to STEM education, funding, and careers, with special emphasis on reaching underserved communities and diverse underrepresented groups. makes it easy for faculty and administrators to access resources that can assist them in their efforts to reduce barriers to participation, create environments rich in the positive factors that support student success on the STEM pathway, and conduct outreach to underserved communities and underrepresented groups by implementing recruitment and retention strategies that broaden participation and increase diversity. Please announce these opportunities in any classes or at presentations you may be making, and forward or post the links below in this email -- as you deem appropriate. We’d be happy to answer any questions you have and to provide your students with assistance in applying to these programs.
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.

Meetings, Workshops and Activities

AGU: Register to judge posters and oral presentations
Are you attending AGU and looking for a way to meet new people or even prospective graduate students or post-docs? Here is a suggestion. 
AGU needs judges to review posters and oral presentations. This year, AGU sponsored a pre-conference “Student & Early Career Scientist Conference” focused on preparing students for next steps in science careers and on Hydrology. Register to be a judge by December 06, 2014.

IODP Primer: An Introduction to Ocean Drilling Programs
The course will be held the afternoon before the AGU Fall Meeting in San Francisco (December 14, 1-5pm). Registration is free, but space is limited. To register, please visit: Also be sure to stop by the IODP, ICDP, and ANDRILL Town Hall, Tuesday, December 16; Posters and Reception: 6:00 – 8:00 pm; Plaza Room A, Hilton Union Square (333 O'Farrell Street).

AGU: Deep biosphere-related sessions
We invite you to join the EarthCube Oceanography and Geobiology Environmental 'Omics (ECOGEO) Research Coordination Network (RCN)! ECOGEO is a recently NSF-funded RCN led by Dr. Ed DeLong (MIT/UH Manoa). ECOGEO's mission is to identify community needs and develop necessary plans to create a federated cyberinfrastructure to enable ocean and geobiology environmental ‘omics. The website has links on how to join EarthCube and our RCN and get signed up for our listserv. In addition to the RCN site, we are also conducting a BRIEF research survey aimed at identifying community needs with respect to 'omics research. Please take 5-15 minutes to participate in the survey, as this will help create the foundation of our RCN's mission. Thanks for your time! We look forward to working with you to create a new, community-supported way to do 'omics research. If you have any questions, please contact Elisha Wood-Charlson, our communications project manager (

Consortium for Ocean Leadership: Apply for the Marine Geoscience Leadership Symposium
The deadline to apply is December 22, 2014.

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


Moore Foundation: Program Officer, Marine Microbiology Initiative
Marine Microbiology Initiative with the Science Program: the Marine Microbiology Initiative (MMI) seeks to gain a comprehensive understanding of marine microbial communities, including their genetic diversity, composition and function; their ecological role in the oceans; and their contribution to ocean health and productivity. More information about MMI can be found at position: 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. The primary responsibilities are to implement MMI’s strategies, manage a multi-million dollar portfolio of high impact grants, and enhance the Foundation’s impact in the field of marine microbial ecology.

University of Texas, Marine Science Institute: Postdoctoral fellowship in marine microbial ecology 
A postdoctoral fellowship in marine microbial ecology is available at the University of Texas, Marine Science Institute ( located in the seaside community of Port Aransas, Texas. The Baker lab ( is studying microbial biogeochemical cycling in a variety of marine and estuary habitats (namely sediments). The position will involve reconstruction of numerous (bacteria and archaea) genomes, and tracking gene activity in situ via transcriptomics, to understand how metabolic and ecological roles are partitioned in nature. Experience with metagenomic assembly of high-throughput (including transcriptomic) sequencing data, evidence of programming skills, and publication record are desirable. We are looking for a creative, independent scientist who can work and communicate effectively in an interdisciplinary, collaborative environment. A PhD and research experience in an appropriate discipline are required. The initial appointment will be for a two-year period, with the possibility of a yearly extension to up to three years based upon performance. To apply, please submit a cover letter, CV, and contact information for 3 references via email to Brett Baker at

New Zealand National Institute of Water and Atmospheric Research (NIWA): Marine Phyto/Microbial Ecologist
NIWA is a dynamic research organisation whose purpose is to enhance the economic value and sustainable management of New Zealand's aquatic resources and environments, and to provide better understanding of climate and the oceans to improve the safety and wellbeing of New Zealanders. We are seeking an enthusiastic researcher to drive research in the area of marine microbial ecological processes, focussing on phytoplankton and/or bacterial community structure and functioning in New Zealand's Exclusive Economic Zone and the Ross Sea sector of the Southern Ocean. This involves the implementation and development of research streams that will advance our knowledge of marine biological processes and the dynamic interactions with physical and chemical systems. In this position, the appointee is expected to work across NIWA to develop research streams that enhance our biological oceanography research, contribute to multi-disciplinary project teams, usually in close collaboration with others, prepare proposals for CAPEX purchases and develop and foster relationships with international and national stakeholders, including commercial interests. The position contributes proactively to NIWA's and NZ's biological oceanography research programme that spans expertise at all NIWA sites and the Wellington campus in particular, which includes marine biologists, fisheries scientists, zooplanktologists, physical oceanographers, biogeochemists, laboratory analysts, food web modellers, and ocean remote-sensing specialists. Technical support in the laboratory and at sea will be provided. Candidates should have a PhD in the area of marine ecological processes, focussing on phytoplankton and/or bacterial community structure and functioning.  It may be acceptable that the PhD will be awarded within a few months at the time of application. The candidate should have experience in the acquisition and analysis of phytoplankton and/or microbial datasets, familiarity with state-of-the-art methods and instrumentation for use at sea and in the laboratory, and a demonstrated ability to undertake quantitative biology-environment analyses. Applications close on December 12, 2014.

Exxon Mobil: Postdoctoral Fellow - Microbiology
We are seeking a candidate to join a team executing programs aimed at understanding and manipulating microbial metabolism related to the oil and gas industry. Experience with hydrocarbon metabolism, community analysis, and metatranscriptomics/metaproteomics is desirable.

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.

Aarhus University, Department of Bioscience, Center for Geomicrobiology: Postdoc position in marine microbial ecology
All applications must be made online and received by December 15, 2014.

Aarhus University, Department of Bioscience, Center for Geomicrobiology: Postdoc position in marine microbial ecology
All applications must be made online and received by: December 15, 2014.

New Mexico State University: Assistant Professor / Environmental Soil Microbiology
Application closing date: December 31, 2014.

Aarhus University, Department of Bioscience, Center for Geomicrobiology: Postdoc position in marine biogeochemistry
All applications must be made online and received by January 01, 2015.

UCSC: C-DEBI research opportunities in Marine Hydrogeology and related fields
Andy Fisher anticipates bringing in one new PhD student and a new postdoctoral researcher for Fall 2015 (postdoc might start Winter or Spring 2016). Please contact Fisher ( with questions and/or to express interest in one of these positions. Graduate student applications to UCSC must be completed by January 05, 2015.

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

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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