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C-DEBI Newsletter – December 15, 2015
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IODP Expedition 357 Update


The offshore phase of IODP Expedition 357 focused on sampling the actively serpentinizing subsurface of Atlantis Massif concluded on December 11, 2015, after 47 days at sea. The total core recovered by two seabed drills during Expedition 357 was 57 m after 109 m of total penetration, and with an overall recovery of 53% at nine different sites. Two of these holes north of the Lost City hydrothermal vent field were drilled to nearly 16.5 mbsf, with an average core recovery of 71-75%. Such high recovery in shallow mantle sequences is nearly unprecedented in the history of ocean drilling. The cored sections were highly heterogeneous, ranging from moderately to highly altered and deformed serpentinized periodotites, with varying compositions and occurrences of talc-amphibole schist zones. Less abundant lithologies included lithified basalt breccias, rodingites, and metagabbros with cataclastic to (ultra)mylonitic deformation fabrics. 

In addition to recovering lower crustal and upper mantle sequences of the detachment fault zone of the Atlantis Massif, advancements in seafloor drill rig technology were achieved during Expedition 357. For the first time, two borehole plug systems were successfully installed by the RD2 drill. These borehole packers will enable future sampling of formation fluid from the boreholes to understand geochemical and microbiological processes in an actively serpentinizing system. New sensor packages designed for the expedition were highly successful and consistently delivered real-time chemical information while drilling, allowing in situ confirmation of ephemeral events such as gas release during penetration. Finally, a new pump system was proven to deliver a geochemical tracer during drilling for contamination tracer testing. 

Now that the offshore phase of the expedition has ended, the science party will be meeting in Bremen, Germany, beginning on January 20, 2016 for a two-week on-shore sampling party. More information about the expedition is available on the web: http://www.eso.ecord.org/expeditions/357/357.php

 

Proposal Calls


C-DEBI: Proposal Calls for Deep Biosphere Research, Fellowship and Education Grants
The NSF Science and Technology Center for Dark Energy Biosphere Investigations (C-DEBI) invites proposals for 1-year research projects (in the anticipated range of $50,000-$80,000) and 1-2 year graduate student and postdoctoral fellowships that will significantly advance C-DEBI's central research agenda: to investigate the subseafloor biosphere deep in sediments and the volcanic crust, and to conduct multi-disciplinary studies to develop an integrated understanding of subseafloor microbial life at the molecular, cellular, and ecosystem scales. Phase 2 of C-DEBI comprises a transition from dominantly exploration-based investigations to projects that balance discovery with hypothesis testing, data integration and synthesis, and ecosystem modeling. C-DEBI also invites proposals to support education and outreach projects, with a budget of up to $50,000 and a project duration of 1 year. The C-DEBI Education & Outreach Grants Program will fund the development of educational opportunities and materials that are pertinent to deep biosphere research in the subseafloor environment in support of our education and outreach goal to create distinctive, targeted education programs and promote increased public awareness about life below the seafloor. Funding is only available to individuals sponsored in US institutions. The next deadline for these annual calls is January 31, 2016.

DCO: Call for Proposals in Deep Life Modeling and Visualization
The Deep Life Modeling and Visualization (DLMV) group of the Deep Carbon Observatory’s (DCO) Deep Life initiative invites applications for 3-12-month PhD student fellowships. Fellowship Goals: We aim to support innovative Deep Life research ideas and groundbreaking new projects involving (1) thermodynamic modeling, (2) modeling of microbial activity and population size, and/or (3) modeling of microbial biogeography. Applicants are strongly encouraged to include a visualization component in their modeling projects that will help illustrate potential changes in microbial energetics, activity, population size, and community composition through space and/or time. Preference will be given to research descriptions that focus on life and carbon cycling in deep subsurface environments on Earth and complement or integrate well within the greater framework of the DCO modeling initiativesFunding: The maximum funding will be $27,000 per proposal. Funds can be used for salary, research travel, research training, sample analyses, or the purchase of essential software, consumables, and scientific equipment. Proposal submission deadline: January 31, 2016.

National Academies of Science: Gulf Research Program Early-Career Research Fellowships
Early-Career Research Fellowships will recognize professionals at the critical pretenure phase of their careers for exceptional leadership, past performance, and potential for future contributions to improving oil system safety, human health and well being, or environmental protection. These two-year fellowships will be awarded to tenure-track faculty (or equivalent) at colleges, universities, and research institutions. Up to ten Fellows will be selected in 2016. Application deadline: February 17, 2016.

NOAA: Ocean Exploration 2016 Funding Opportunity
Closing date for applications: January 8, 2016.

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

IODP-USSSP: Apply to Sail:Expeditions 367 and 368, South China Sea Rifted Margin
The deadline to apply is January, 15 2016.

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


C-DEBI NSF REU: Community College Cultivation Cohort (C4)
C-DEBI’s NSF REU, C4, is a 9-week research internship targeting community college students nationwide. Students will spend their summer doing cutting edge research as they help grow, isolate, and describe previously unknown microorganisms. C4 students will work in teams in laboratories at USC, learning state-of-the-art techniques ranging from DNA sequencing to microscopy and sterile techniques to analytical chemistry. Applications due February 15, 2016.

C-DEBI: Applications Now Open for the 2016 Summer Undergraduate GEM 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 institutions. The course 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. The application deadline is February 02, 2016.

MATE/UNOLS: 2016 Six-Month Internship
This spring/summer (approximately mid-March to mid-September 2016), the MATE Center and the University National Oceanographic Laboratory System (UNOLS) fleet will sponsor one marine technical internship onboard the research vessels: R/V Kilo Moanaand R/V Sikuliaq. The intern will work with marine technicians on shore and at sea, learning how to operate and maintain a variety of scientific and navigational equipment in support of shipboard scientific research. The internship will begin in Honolulu,HI and end in Seward, Alaska. The exact schedule through September will be determined before the acceptance date, but will involve work on the R/V Kilo Moanaand R/V Sikuliaq and at their on-shore facilities. Internship projects will be dependent on the funded science but previous interns have worked on cruises to support science ranging from chemical oceanography, marine biology, GIS/bathymetric surveys (seafloor mapping), geological studies, work with ROVs and much more! The position will last 6 months, and students will receive a stipend of $500 per week, reimbursement for travel expenses, and on-station housing while ashore. Applications due January 06, 2016.

The Rolex Scholarships
Application deadline: December 31, 2015.

MARUM: ECORD Training Course, March 7-11, 2016
The application deadline is January 06, 2016.

NSF: Advanced Training Program in Antarctica for Early Career Scientists: Biological Adaptations to Environmental Change – July 2016
Deadline for receipt of completed applications is January 25, 2016.

 

Publications


Environmental Microbiology
Subseafloor microbial communities in hydrogen-rich vent fluids from hydrothermal systems along the Mid-Cayman Rise
Julie Reveillaud, Emily Reddington, Jill McDermott, Christopher Algar, Julie L. Meyer, Sean Sylva, Jeffrey Seewald, Christopher R. German, Julie A. Huber*
*C-DEBI Contribution 282


Warm fluids emanating from hydrothermal vents can be used as windows into the rocky subseafloor habitat and its resident microbial community. Two new vent systems on the Mid-Cayman Rise each exhibit novel geologic settings and distinctively hydrogen-rich vent fluid compositions. We have determined and compared the chemistry, potential energy yielding reactions, abundance, community composition, diversity, and function of microbes in venting fluids from both sites: Piccard, the world's deepest vent site, hosted in mafic rocks, and Von Damm, an adjacent, ultramafic-influenced system. Von Damm hosted a wider diversity of lineages and metabolisms in comparison to Piccard, consistent with thermodynamic models that predict more numerous energy sources at ultramafic systems. There was little overlap in the phylotypes found at each site, although similar and dominant hydrogen-utilizing genera were present at both. Despite the differences in community structure, depth, geology, and fluid chemistry, energetic modeling and metagenomic analysis indicate near functional equivalence between Von Damm and Piccard, likely driven by the high hydrogen concentrations and elevated temperatures at both sites. Results are compared to hydrothermal sites worldwide to provide a global perspective on the distinctiveness of these newly discovered sites and the interplay between rocks, fluid composition, and life in the subseafloor.


Philosophical Transactions of the Royal Society A
Subglacial Lake Whillans microbial biogeochemistry: a synthesis of current knowledge
J.A. Mikucki, P.A. Lee, D. Ghosh, A.M. Purcell, A.C. Mitchell, K.D. Mankoff, A.T. Fisher*, S. Tulaczyk, S. Carter, M.R. Siegfried, H.A. Fricker, T. Hodson, J. Coenen, R. Powell, R. Scherer, T. Vick-Majors, A.A. Achberger, B.C. Christner, M. Tranter, the WISSARD Science Team
*C-DEBI Contribution 283


Liquid water occurs below glaciers and ice sheets globally, enabling the existence of an array of aquatic microbial ecosystems. In Antarctica, large subglacial lakes are present beneath hundreds to thousands of metres of ice, and scientific interest in exploring these environments has escalated over the past decade. After years of planning, the first team of scientists and engineers cleanly accessed and retrieved pristine samples from a West Antarctic subglacial lake ecosystem in January 2013. This paper reviews the findings to date on Subglacial Lake Whillans and presents new supporting data on the carbon and energy metabolism of resident microbes. The analysis of water and sediments from the lake revealed a diverse microbial community composed of bacteria and archaea that are close relatives of species known to use reduced N, S or Fe and CH4 as energy sources. The water chemistry of Subglacial Lake Whillans was dominated by weathering products from silicate minerals with a minor influence from seawater. Contributions to water chemistry from microbial sulfide oxidation and carbonation reactions were supported by genomic data. Collectively, these results provide unequivocal evidence that subglacial environments in this region of West Antarctica host active microbial ecosystems that participate in subglacial biogeochemical cycling.


International Journal of Systematic and Evolutionary Microbiology
Deferrisoma paleochoriense sp. nov., a thermophilic, iron(III)-reducing bacterium from a shallow-water hydrothermal vent in the Mediterranean Sea
Ileana Perez-Rodriguez*,  Matthew Rawls,  D. Katharine Coykendall, Dionysis I. Foustoukos
*C-DEBI Contribution 292


A novel thermophilic, anaerobic, mixotrophic bacterium, designated strain MAG-PB1T, was isolated from a shallow-water hydrothermal vent system in Paleochori Bay off the coast of Milos Island, Greece. The cells were Gram-negative, rugose short rods approximately 1.0 μm in length and 0.5 μm in width. Strain MAG-PB1T grew between 30 and 70 °C (optimum 60 °C), 0 and 50 g NaCl l-1 (optimum 15-20 g l-1) and pH 5.5 and 8.0 (optimum pH 6.0). Generation time under optimal conditions was 2.5 hours. Optimal growth occurred under chemolithoautotrophic conditions with H2 as the energy source and CO2 as the carbon source. Fe(III), Mn(IV), arsenate and selenate were used as electron acceptors. Peptone, tryptone, Casamino acids, dextrose, sucrose, yeast extract, D-fructose, α-D-glucose and D-(-)-arabinose also served as electron donors. No growth occurred in the presence of lactate or formate. G + C content of the genomic DNA was 66.7 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that this organism is closely related to Deferrisoma camini, a recently described genus in the Deltaproteobacteria. Based on the 16S rDNA phylogenetic analysis and on physiological, biochemical and structural characteristics, the strain was found to represent a novel species for which the name Deferrisoma paleochoriense sp. nov. is proposed. The type strain of Deferrisoma paleochoriense is MAG-PB1T (=JCM 30394 T; = DSM 29363T).


Frontiers in Microbiology
In situ Detection of Microbial Life in the Deep Biosphere in Igneous Ocean Crust
Everett C. Salas, Rohit Bhartia, Louise Anderson, William F. Hug, Ray D. Reid, Gerardo Iturrino and Katrina J. Edwards*
*C-DEBI Contribution 312


The deep biosphere is a major frontier to science. Recent studies have shown the presence and activity of cells in deep marine sediments and in the continental deep biosphere. Volcanic lavas in the deep ocean subsurface, through which substantial fluid flow occurs, present another potentially massive deep biosphere. We present results from the deployment of a novel in situ logging tool designed to detect microbial life harbored in a deep, native, borehole environment within igneous oceanic crust, using deep ultraviolet native fluorescence spectroscopy. Results demonstrate the predominance of microbial-like signatures within the borehole environment, with densities in the range of 105 cells/mL. Based on transport and flux models, we estimate that such a concentration of microbial cells could not be supported by transport through the crust, suggesting in situ growth of these communities.


Special Issue of Frontiers in Microbiology: manuscript submission deadline extended
Deep biosphere researchers: please note that the deadline for submitting a manuscript to the special issue of Frontiers in Microbiology, Recent Advances in Geomicrobiology of the Ocean Crust (topic eds. B.N. Orcutt, J.B. Sylvan, C.M. Santelli), has been extended to January 04, 2016.

 

Meetings & Activities
Save the Date: SoCal Geobiology Symposium, April, 09 2015
We are pleased to announce that the date has been set for the Southern California Geobiology Symposium, hosted this year at Caltech in Pasadena. Now in its 12th year, the Symposium is a regional conference which provides opportunities for students and post-docs studying one of the myriad facets of geobiology to come together and share their findings. The symposium is just one day long but will include both oral and poster presentations. Breakfast, lunch, and dinner are provided to attendees and registration is free. Although only presentations from students and faculty will be accepted, faculty are more than welcome to attend. This year's symposium will be held at Caltech in the Arms building on Saturday, April 9. A registration website will be available soon, but for now, just mark the date on your calendars. In the meantime, we would appreciate it if you would kindly forward this email to any other interested students and/or post-doctoral fellows.

University of Namibia: African Fall School on Microbial and Geochemical Oceanography in Upwelling Ecosystems
From March 29 to April 29 2016 the Sam Nujoma Campus of the University of Namibia hosts the 3rd African “Research Discovery Camp” for research-based training on the “Sustainable Use and Management of marine Ecosystems.” Selected students, instructors and lecturers from countries all over the world will carry out research in the Benguela Upwelling Ecosystem (BUE). They will be working at sea on the R/V MIRABILIS and in the laboratories of the Marine Research Center in Henties Bay. The Benguela Current creates one of the world’s strongest upwelling system that is the basis for a rich biodiversity and an economically important fish stock productivity. This year’s research topics are focused on questions related to microbial and geochemical processes that assure the proper functioning of the ecosystem. Topics of interest are the cycling of nutrients and trace elements between sediments and the water column, the release of CO2 and the loss of nitrogen and associated acidification in oxygen minimum zones and the diversity of microorganisms that mediate these processes. Another line of experiments is devoted to the natural mechanisms that can lead to phosphorite deposits, to causes of toxic microbial blooms and the search for biotechnologically useful marine microbes. Deadline for application is February 01, 2016.

Geobiology Gordon Research Conference, January 31 - February 5, 2016
The deadline for submitting applications is January 3, 2016.

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

 

Employment


University of South Florida: Chemical Oceanographer, College of Marine Science
The College of Marine Science at the University of South Florida invites applications for a tenure-track, nine-month academic appointment in Chemical Oceanography at the Assistant, Associate, or Professor level. Rank is dependent on qualifications and experience. We seek a Chemical Oceanographer who will contribute to an understanding of the ocean/climate system, past, present, and future, from basic disciplinary topics to ecosystems analyses. Qualified candidates will employ modern tools of multi-disciplinary science to understand regional and global issues critical to the ocean system, including but not limited to organic and inorganic carbon cycling, trace element cycling, nutrient cycling, ocean-atmosphere and/or ocean-land interactions, and biogeochemical processes and modeling. Position is open until filled, however, priority review of applications will begin by January 15, 2016.

Harvard: Postdoctoral position available in crystal growth and geobiology
The position is open immediately and will remain open through December 31, 2015.

URI: Assistant Professor of Oceanography
Applications will be reviewed beginning January 7, 2016 and continue until the position is filled.

University of South Carolina: PhD. and M.S. positions available in subsurface biogeochemistry
The Isotope Biogeochemistry group at the University of South Carolina is recruiting Ph.D. and M.S. students to work on research focused on life and the fate of carbon in the subsurface. Interested students should contact Dr. Susan Lang at slang@geol.sc.edu to discuss the project in more detail, and in advance of submitting an application to the USC graduate program (deadline January 15, 2016).




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!
 
Best, 
 
Matt
 
-- 
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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