C-DEBI Newsletter – October 1, 2015
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Geochimica et Cosmochimica Acta
Iron mineral structure, reactivity, and isotopic composition in a South Pacific Gyre ferromanganese nodule over 4 Ma
Matthew A. Marcus, Katrina J. Edwards*, Bleuenn Gueguen, Sirine C. Fakra, Gregory Horn, Nicolas A. Jelinski, Olivier Rouxel, Jeffry Sorensen, Brandy M. Toner
*C-DEBI Contribution 205

Deep-sea ferromanganese nodules accumulate trace elements from seawater and underlying sediment porewaters during the growth of concentric mineral layers over millions of years. These trace elements have the potential to record past ocean geochemical conditions. The goal of this study was to determine whether Fe mineral alteration occurs and how the speciation of trace elements responds to alteration over ∼3.7 Ma of marine ferromanganese nodule (MFN) formation, a timeline constrained by estimates from 9Be/10Be concentrations in the nodule material. We determined Fe-bearing phases and Fe isotope composition in a South Pacific Gyre (SPG) nodule. Specifically, the distribution patterns and speciation of trace element uptake by these Fe phases were investigated. The time interval covered by the growth of our sample of the nodule was derived from 9Be/10Be accelerator mass spectrometry (AMS). The composition and distribution of major and trace elements were mapped at various spatial scales, using micro-X-ray fluorescence (μXRF), electron microprobe analysis (EMPA), and inductively coupled plasma mass spectrometry (ICP-MS). Fe phases were characterized by micro-extended X-ray absorption fine structure (μEXAFS) spectroscopy and micro-X-ray diffraction (μXRD). Speciation of Ti and V, associated with Fe, was measured using micro-X-ray absorption near edge structure (μXANES) spectroscopy. Iron isotope composition (δ56/54Fe) in subsamples of 1–3 mm increments along the radius of the nodule was determined with multiple-collector ICP-MS (MC-ICP-MS). The SPG nodule formed through primarily hydrogeneous inputs at a rate of 4.0 ± 0.4 mm/Ma. The nodule exhibited a high diversity of Fe mineral phases: feroxyhite (δ-FeOOH), goethite (α-FeOOH), lepidocrocite (γ-FeOOH), and poorly ordered ferrihydrite-like phases. These findings provide evidence that Fe oxyhydroxides within the nodule undergo alteration to more stable phases over millions of years. Trace Ti and V were spatially correlated with Fe and found to be adsorbed to Fe-bearing minerals. Ti/Fe and V/Fe ratios, and Ti and V speciation, did not vary along the nodule radius. The δ56/54Fe values, when averaged over sample increments representing 0.25–0.75 Ma, were homogeneous within uncertainty along the nodule radius, at −0.12 ± 0.07‰ (2sd, n = 10). Our results indicate that the Fe isotope composition of the nodule remained constant during nodule growth and that mineral alteration did not affect the primary Fe isotope composition of the nodule. Furthermore, the average δ56/54Fe value of −0.12‰ we find is consistent with Fe sourced from continental eolian particles (dust). Despite mineral alteration, the trace element partitioning of Ti and V, and Fe isotope composition, do not appear to change within the sensitivity of our measurements. These findings suggest that Fe oxyhydroxides within hydrogenetic ferromanganese nodules are out of geochemical contact with seawater once they are covered by subsequent concentric mineral layers. Even though Fe-bearing minerals are altered, trace element ratios, speciation and Fe isotope composition are preserved within the nodule.

Frontiers in Microbiology
Meta-omic signatures of microbial metal and nitrogen cycling in marine oxygen minimum zones
Jennifer B. Glass*, Cecilia B. Kretz*, Sangita Ganesh, Piyush Ranjan, Sherry L. Seston, Kristen N. Buck, William M. Landing, Peter L. Morton, James W. Moffett, Stephen J. Giovannoni, Kevin L. Vergin and Frank J. Stewart
*C-DEBI Contribution 281

Iron (Fe) and copper (Cu) are essential cofactors for microbial metalloenzymes, but little is known about the metalloenyzme inventory of anaerobic marine microbial communities despite their importance to the nitrogen cycle. We compared dissolved O2, NO3, NO2, Fe and Cu concentrations with nucleic acid sequences encoding Fe and Cu-binding proteins in 21 metagenomes and 9 metatranscriptomes from Eastern Tropical North and South Pacific oxygen minimum zones and 7 metagenomes from the Bermuda Atlantic Time-series Station. Dissolved Fe concentrations increased sharply at upper oxic-anoxic transition zones, with the highest Fe:Cu molar ratio (1.8) occurring at the anoxic core of the Eastern Tropical North Pacific oxygen minimum zone and matching the predicted maximum ratio based on data from diverse ocean sites. The relative abundance of genes encoding Fe-binding proteins was negatively correlated with O2, driven by significant increases in genes encoding Fe-proteins involved in dissimilatory nitrogen metabolisms under anoxia. Transcripts encoding cytochrome c oxidase, the Fe- and Cu-containing terminal reductase in aerobic respiration, were positively correlated with O2 content. A comparison of the taxonomy of genes encoding Fe- and Cu-binding vs. bulk proteins in OMZs revealed that Planctomycetes represented a higher percentage of Fe genes while Thaumarchaeota represented a higher percentage of Cu genes, particularly at oxyclines. These results are broadly consistent with higher relative abundance of genes encoding Fe-proteins in the genome of a marine planctomycete vs. higher relative abundance of genes encoding Cu-proteins in the genome of a marine thaumarchaeote. These findings highlight the importance of metalloenzymes for microbial processes in oxygen minimum zones and suggest preferential Cu use in oxic habitats with Cu > Fe vs. preferential Fe use in anoxic niches with Fe > Cu.

Proceedings of the IODP
Data report: carbon content and isotopic composition of basalts and sediments in North Pond, Expedition 336
Kasumi Sakata, Hikaru Yabuta, Minoru Ikehara, and Tadashi Kondo

The uppermost about 500 m of basaltic ocean crust is permeable, and fluid flow is focused in specific areas at the contacts of lava flows or in brecciated zones. In these areas, seawater oxidizes young basaltic crust (younger than 10 Ma), and this interaction affects the microbial ecosystems. Iron cycling, both oxidation and reduction of iron, supports metabolic activity in basalts; however, the microorganisms responsible for Fe oxidation of basalts are not clear. In this study, carbon isotopic analyses of basalts and sediments at North Pond, the western flank of the mid-Atlantic Ridge, were conducted to understand the origin and formation of carbon compounds in relation to possible microbial activity in basaltic crust. Total carbon (TC) contents range approximately from 6 to 11 wt% for whole-sediment samples. Depth profiles of the carbon isotopic compositions (δ13C-TC) for sediments (approximately –0.04‰ to +1.93‰) are similar to those of TC. TC (approximately 0.01–0.37 wt%) and total organic carbon (TOC) (approximately 0.01–0.03 wt%) contents for basalts are almost constant with depth, whereas sediment breccias and carbonates contain more carbon than basalts (approximately 3.56–11.9 wt%). The value of δ13C-TC for basalts ranges approximately from –21.8‰ to +2.69‰. Sediment breccias and carbonates have larger δ13C-TC values, approximately from –18.6‰ to +2.82‰. The value of δ13C-TOC for hard rocks is lower at greater depths. The value of δ13C-kerogen is slightly smaller than that of δ13C-TOC.

Workshops & Activities
2015 C-DEBI Basement Workshop Report
This year, the C-DEBI theme workshops were replaced by biome (basement and sediment) workshops integrated across the research themes to review the state of knowledge at the end of Phase 1. Summary: The initial invitation for the workshop summarized the desired outcomes: as the Center for Dark Energy Biosphere Investigations (C-DEBI) enters the final stage of Phase I, we are organizing a workshop to synthesize what we have learned about the microbial ecology of subseafloor basement environments, including igneous rocks and crustal fluids. Topics of discussion will include where the bleeding edge of subseafloor crustal microbiology lies, the biggest current obstacles to overcome, commonalities between sites and regimes that have come to light over the last five years (or more), and what questions will be most exciting to address in the coming decade. We are looking for input from microbial ecologists as well as geochemists and petrologists to help synthesize the current research and try to invigorate the community with interdisciplinary goals for the next phase of C-DEBI. Unlike previous C-DEBI workshops, this one will not focus on a specific theme, such as activity or diversity, but will rather look at the entirety of crustal microbiology. We hope you can join us in Boston this July for a few days of stimulating and productive discussions.
See also the 2015 C-DEBI Sediment Workshop Report

Second DCO Early Career Scientist Workshop Report
A large proportion of the scientific program was devoted to the participants themselves, with each one presenting both oral and poster presentations. Early career scientists from all four DCO Communities (Deep Energy, Reservoirs and Fluxes, Deep Life, and Extreme Physics and Chemistry) presented short talks on their work. These talks, intentionally broad, allowed cross-disciplinary interests to blossom. Evening poster sessions further facilitated these interactions.

25th International Geological Congress, Cape Town, South Africa, August 27-September 4, 2016: IODP Symposium call for abstracts
This symposium appears under the Marine Geosciences and Oceanography theme. The abstract submission is now open until January 2016

Proposal Calls
Lawrence Postdoctoral Fellowship
The Lawrence Fellowship is a highly-competitive postdoctoral position at LLNL that is open to all technical disciplines. Fellowships are awarded to candidates with exceptional talent, scientific track records, and potential for significant achievements. Typically, two to four fellowships are awarded each year, and the awards are for three years. Fellows are free to pursue their own research agenda under the guidance of a senior staff scientist who serves as a mentor. The fellows most often conduct their research in a collaborative, multidisciplinary manner with others in a team environment. Application deadline: November 1.

Exploration Postdoctoral Fellow, Arizona State University
The School of Earth and Space Exploration (SESE) at Arizona State University invites applications for the position of Exploration Postdoctoral Fellow.  The fellowship provides opportunities for outstanding early-career scientists and engineers emphasizing interdisciplinary collaboration.  Research areas within SESE encompass astrobiology, astrophysics and cosmology, earth and planetary sciences, instrumentation and systems engineering, and science education. Incoming Fellows will receive an annual stipend of $61,000 with health benefits, plus $9,000 per year in discretionary research funds.  A relocation allowance of up to $2,500 will be provided.  Appointments will be for up to three years and shall commence on or around July 1, 2016. Complete applications and separate letters of reference are due by October 31, 2015.

NSF: Graduate Research Fellowship Program (GRFP)
NSF also encourages undergraduate seniors to apply. Application deadline (Geosciences; Life Sciences): October 26, 2015.

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

Simons Foundation: Early Career Investigator in Marine Microbial Ecology and Evolution Awards
The deadline for receipt of letters of intent (LOI) is November 2, 2015.

NSF: Small Business Technology Transfer Program Phase I (STTR) Proposal Solicitation
Full proposal deadline: December 11, 2015.

NSF: Earth Sciences Postdoctoral Fellowships (EAR-PF)
Full proposal deadline: January 12, 2016

NSF: Geobiology and Low-Temperature Geochemistry Program Solicitation
Proposals accepted anytime.

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).

Education & Outreach
The Data Incubator
The Data Incubator is an intensive 7 week fellowship that prepares the best scientists and engineers with advanced degrees to work as data scientists and quants. It identifies fellows who already have the 90% difficult-to-learn skills and equips them with the last 10%: the tools and technology stack that make them self-sufficient, productive contributors. The program is free for fellows. Employers only pay a tuition fee if they successfully hire. Early Deadline: October 12, 2015. Regular Deadline: October 19, 2015.

The Rolex Scholarships
Application deadline: December 15, 2015.

USC: C-DEBI Seeks a Diversity Program Specialist
The USC Dornsife College of Letters, Arts and Sciences Center for Dark Energy Biosphere Investigations (C-DEBI) is seeking a Program Specialist to join its team. C-DEBI is a multi-institutional research and education center funded by the National Science Foundation Science and Technology Center (NSF-STC) program with USC as its headquarters. In addition to the science of exploring microbial life beneath the seafloor, education and diversity are priorities to the Center’s efforts to strengthen the STEM pipeline by integrating research and educational programs for diverse future generations. The full-time Program Specialist will serve as Diversity Specialist, helping to create, coordinate, and lead our education, outreach, and diversity efforts to serve our students, postdocs, faculty, and other participants at USC and across the nation. The Program Specialist will assist the C-DEBI Education Manager with the development and management of these programs. The ideal candidate for the position of C-DEBI Diversity Specialist has: 
  • 3 years of experience developing and managing educational STEM programs with multiple institutions with a focus on diversity initiatives 
  • Strong oral and written communication skills 
  • Experience using social media for professional outreach 
  • Research experience at Ph.D. level
For more information and application instructions, please visit the USC careers website, job ID 1004620.

USC: Open-Rank, Tenured or Tenure-Track Faculty Position in Geobiology
The Departments of Earth Sciences and Biological Sciences of the Dana and David Dornsife College of Letters, Arts and Sciences at the University of Southern California (Los Angeles, California) invite applications for an open-rank, tenured or tenure-track faculty position in geobiology anticipated to start Fall 2016. We are looking for an interdisciplinary scientist who will apply modern, quantitative and innovative techniques to solve major problems in any area of geobiology. Our interests include but are not limited to candidates with expertise in geomicrobiology, biogeochemistry, microbial ecology, and/or organic geochemistry, who combine field-based studies with state-of-the-art analytical capabilities and laboratory experimentation. For further information, please contact the Chair of the search committee, Jan Amend ( Review of applications will begin October 15, 2015.

UCSC: C-DEBI Postdoctoral Research Opportunity in Marine Hydrogeology
Andy Fisher anticipates bringing in a new postdoctoral researcher in Spring/Summer/Fall 2016. This will be a one-year position, with potential for renewal. Project(s) will involve studies of seafloor hydrothermal circulation, emphasizing low-temperature ("ridge-flank") environments. A successful researcher will develop numerical models to gain understanding as to how these systems work, what factors control the geometries and rates of fluid (heat, solute) transport, relations between crustal structure and fluid flow, etc. There is a lot of observational data that can be used to generate domain geometries and properties, and provides strong constraints on acceptable output. Much of the modeling will be done in collaboration with colleagues who have expertise in biogeochemistry and/or microbiology. Developing and testing models that link hydrogeologic, thermal, chemical and microbiological characteristics is a research frontier and is important to C-DEBI. Experience in modeling/programming is a prerequisite, so that we can make good progress in a short time, as are strong writing and communication skills, and analytical strengths and knowledge of the literature in some combination of hydrothermal systems, hydrogeology, geophysics, engineering, geochemistry, or related disciplines. More information on Fisher's research group, projects, and specifications for preparing an application for this postdoctoral position can be found here. Please contact Fisher ( with questions and/or to submit an application. Review of applications will occur in Fall 2015.

Rice University: Wiess Post-Doctoral Research Fellowship in Earth and Planetary Science
The application deadline is November 1, 2015.

Oregon Health & Science University, Institute of Environmental Health: Postdoctoral Position in Environmental & Biomolecular Systems
The position is available immediately. Posted July 21, 2015.

Curtin University, Perth: PhD scholarships
Several PhD scholarships are available for national and international students (including fee waivers for exceptional scholars). Priority areas: Application of biomarkers (organic geochemistry), compound-specific isotope analysis, palaeogenomics and geomicrobiology. Please send Expression of interest, CV and names of three referees to: Professor Kliti Grice, and A/Professor Marco Coolen,

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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