C-DEBI Newsletter – March 16, 2015
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Published TODAY in Nature Geoscience is C-DEBI contribution 254!  The South Pacific Gyre IODP Expedition scientists, headed by Steve D'Hondt, have found oxygen and oxygen-breathing microbes all the way through the sediment from the seafloor to the igneous basement at seven sites in the South Pacific gyre, considered the “deadest” location in the ocean. Their findings contrast with previous discoveries that oxygen was absent from all but the top few millimeters to decimeters of sediment in biologically productive regions of the ocean. See the Publications section below for more information about this and other papers.

Congratulations also to the researchers heading the 6 proposals selected for funding in our latest special research call encouraging proposals with foci on synthesis and integration of datasets and samples from recent or upcoming field programs:  Eric Boyd (Montana State), Rick Colwell (Oregon State), Colleen Hansel (WHOI), Susan Lang (U So. Carolina)/Matt Schrenk (Michigan State), Grieg Steward (Hawaii), Andreas Teske (UNC Chapel Hill)/Ivano Aiello (Moss Landing)/Christina Ravelo (UCSC).  Stay tuned on our funded proposal webpage for more information as the awards become official.


Hot Off the Press: Presence of oxygen and aerobic communities from sea floor to basement in deep-sea sediments (C-DEBI Contribution 254) in Nature Geoscience
The depth of oxygen penetration into marine sediments differs considerably from one region to another. In areas with high rates of microbial respiration, O2 penetrates only millimetres to centimetres into the sediments, but active anaerobic microbial communities are present in sediments hundreds of metres or more below the sea floor. In areas with low sedimentary respiration, O2 penetrates much deeper but the depth to which microbial communities persist was previously unknown. The sediments underlying the South Pacific Gyre exhibit extremely low areal rates of respiration. Here we show that, in this region, microbial cells and aerobic respiration persist through the entire sediment sequence to depths of at least 75 metres below sea floor. Based on the Redfield stoichiometry of dissolved O2 and nitrate, we suggest that net aerobic respiration in these sediments is coupled to oxidation of marine organic matter. We identify a relationship of O2 penetration depth to sedimentation rate and sediment thickness. Extrapolating this relationship, we suggest that oxygen and aerobic communities may occur throughout the entire sediment sequence in 15–44% of the Pacific and 9–37% of the global sea floor. Subduction of the sediment and basalt from these regions is a source of oxidized material to the mantle. Authors: C-DEBI Co-I Steve D'Hondt et al. See also the NSF press release.

Hot Off the Press: The transcriptional response of microbial communities in thawing Alaskan permafrost soils (C-DEBI Contribution 258) in Frontiers in Microbiology
Thawing of permafrost soils is expected to stimulate microbial decomposition and respiration of sequestered carbon. This could, in turn, increase atmospheric concentrations of greenhouse gasses, such as carbon dioxide and methane, and create a positive feedback to climate warming. Recent metagenomic studies suggest that permafrost has a large metabolic potential for carbon processing, including pathways for fermentation and methanogenesis. Here, we performed a pilot study using ultrahigh throughput Illumina HiSeq sequencing of reverse transcribed messenger RNA to obtain a detailed overview of active metabolic pathways and responsible organisms in up to 70 cm deep permafrost soils at a moist acidic tundra location in Arctic Alaska. The transcriptional response of the permafrost microbial community was compared before and after 11 days of thaw. In general, the transcriptional profile under frozen conditions suggests a dominance of stress responses, survival strategies, and maintenance processes, whereas upon thaw a rapid enzymatic response to decomposing soil organic matter (SOM) was observed. Bacteroidetes, Firmicutes, ascomycete fungi, and methanogens were responsible for largest transcriptional response upon thaw. Transcripts indicative of heterotrophic methanogenic pathways utilizing acetate, methanol, and methylamine were found predominantly in the permafrost table after thaw. Furthermore, transcripts involved in acetogenesis were expressed exclusively after thaw suggesting that acetogenic bacteria are a potential source of acetate for acetoclastic methanogenesis in freshly thawed permafrost. Metatranscriptomics is shown here to be a useful approach for inferring the activity of permafrost microbes that has potential to improve our understanding of permafrost SOM bioavailability and biogeochemical mechanisms contributing to greenhouse gas emissions as a result of permafrost thaw. Authors: Coolen and C-DEBI research and fellowship grantee Orsi.

Frontiers in Microbiology: Seeking Contributions for Special Topic on Ocean Crust Geomicrobiology
A special issue of Frontiers in Microbiology journal on the topic of "Recent Advances in Geomicrobiology of the Ocean Crust" is seeking contributions from the C-DEBI community. Over the last five years, several major international programs focused on understanding life in oceanic crust were initiated. In addition, there have been many field and laboratory programs focused on understanding hydrothermal vent systems, which are an expression of fluids altered in the subeafloor crust, as well as in continental exposures of seafloor crust, including ophiolites and ore bodies. This research topic brings together recent discoveries of the microbial presence, diversity and activity in these environments, with analysis of the implications for global systems. Specifically, this research topic will address genetic strategies for survival in these diverse, extreme habitats; rates of metabolic and alteration processes; the impact of crustal life on global carbon cycles; and constraints on the magnitude of biomass in subsurface oceanic crust. Articles in the research topic are in tribute to the late Katrina J. Edwards, who was a pioneer in diverse aspects of exploring life in oceanic crust. For more information, contact topic editors Beth Orcutt, Cara Santelli, or Jason Sylvan, or visit the journal webpage.

Proposal Calls

NSF: Faculty Early Career Development Program (CAREER)
The Faculty Early Career Development (CAREER) Program is a Foundation-wide activity that offers the National Science Foundation's most prestigious awards in support of junior faculty who exemplify the role of teacher-scholars through outstanding research, excellent education and the integration of education and research within the context of the mission of their organizations. Such activities should build a firm foundation for a lifetime of leadership in integrating education and research. NSF encourages submission of CAREER proposals from junior faculty members at all CAREER-eligible organizations and especially encourages women, members of underrepresented minority groups, and persons with disabilities to apply. The minimum CAREER award, including indirect costs, will total $400,000 for the 5-year duration with the following exceptions: proposers to the Directorate for Biological Sciences (BIO), the Directorate for Engineering (ENG), or the Division of Polar Programs (PLR) must submit budget requests for a minimum of $500,000 for the 5-year duration. Full proposal deadlines: July 21-23, 2015.

NSF: Small Business Technology Transfer Program Phase I Solicitation (STTR) 
NSF's STTR program provides non-dilutive funds for early-stage research and development (R&D) at small businesses. This R&D should be based on innovative, transformational technology with potential for substantial commercial and/or societal benefits. The program invites proposals from small businesses across a broad range of science and engineering disciplines in collaboration with researchers at universities, Federally-Funded Research and Development Centers, and other non-profit institutions. If you are successful, you will receive a grant of up to $225,000 for a 12-month development/feasibility project. You can then compete for a second grant of up to $750,000 over a 2 year period, with the aim of advancing the technology toward commercial deployment. NSF encourages proposals from a diversity of entrepreneurs -- new and seasoned. What is most important is that you have a transformative idea or innovation and that your team's primary goal is the commercialization of the technology. Having no commercialization track record will not count against you – for many companies, an NSF STTR award is their first attempt at commercializing an innovation. Full proposal deadline: June 18, 2015.

L'Oréal USA: For Women in Science Fellowships
Applications are due on Friday, March 20, 2015.

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

ECORD: Research Grants for Graduate Students and Postdocs at ECORD Country Institutions
The deadline to apply for an ECORD Research Grant is March 31, 2015.

IODP: Call for Scientific Ocean Drilling Proposals
Submit by April 01, 2015.

IODP: Apply to sail on Expedition 362 Sumatra Seismogenic Zone aboard the JOIDES Resolution
WebinarApril 01, 2015. The deadline to apply is April 15, 2015

NSF: Dimensions of Biodiversity Program Solicitation
Full proposal deadline: April 09, 2015.
National Academies Research Associateships for Graduate, Postdoctoral and Senior Researchers
There are four annual review cycles and the next closes May 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).

Education & Outreach

Meetings, Workshops and Activities

Bigelow: Third Microbial Single Cell Genomics Workshop, June 14-18, 2015, Boothbay Harbor, ME
Workshop goals are to exchange research results, methods and ideas related to microbial single cell genomics (SCG), in this way stimulating further progress in this exciting research field. Application deadline March 29, 2015.

Gordon Research Seminar on Applied and Environmental Microbiology: Solving Important Microbiological Questions in the "Omics" Era; July 11-12, Mt. Holyoke College, South Hadley, MA
The Gordon Research Seminar on Applied & Environmental Microbiology is a unique forum for graduate students, post-docs, and other scientists with comparable levels of experience and education to present and exchange new data and cutting edge ideas. This GRS will provide an open forum for the presentation and discussion of the latest research findings on the environmental impact and industrial application of microorganisms at the single cell and ecosystem level, including presentations in metagenomics, single cell genomics, transcriptomics and proteomics. This meeting will also include a mentoring session with experts in the field of academia, industry and scientific publishing as well as 2 poster sessions. Chair: C-DEBI fellowship awardee Anne KasterOral presentation abstracts due April 11, 2015; meeting application due June 13, 2015.

Microenergy 2015: 3rd International Workshop on Microbial Life Under Extreme Energy Limitation, September 21-25, Sandbjerg, Denmark
Deadline for submission of abstracts is April 30, 2015.

DCO: Second DCO Early Career Scientist Workshop, August 31 - September 5, 2015, São Miguel, Portugal
Applications are encouraged from senior graduate students, postdoctoral researchers, fellows, and newly appointed assistant professors, due May 01, 2015.


Texas A&M, College Station: Postdoctoral research associate, Microbiology/Molecular Biology
ADDOMEx, a recently funded program seeking to define interactions between microbes, oil, dispersants and exopolymeric substances, seeks a Postdoctoral Research Associate to be based out of Texas A&M University in College Station. Duties will include maintaining microbial isolates, participating in incubation experiments ranging from small experiments on microfluidic chips up through large experiments in 100 L mesocosms, analysis of metagenomic and metatranscriptomic datasets, working up the data and assisting with writing reports, papers and presenting the data at national meetings. Experience with microbial cultivation and/or analysis of high throughput sequencing datasets is preferred. Funding is available for up to three years, contingent upon a review after the first year. To apply, please send a cover letter with a brief overview of your own research interests and background, a CV and a list of three personal references to Jason Sylvan (e:, w: The position will be filled as soon as possible, but by July 2015 at the latest.

MBARI: Principle Investigator
The Monterey Bay Aquarium Research Institute (MBARI) seeks a Principal Investigator (PI) to develop and direct a marine carbon cycle research team. A Ph.D. in the physical or biological sciences, D. Eng., or equivalent is required. Applicants who are at an early stage in their career (equivalent to assistant professor) with a demonstrated ability to work in an interdisciplinary environment are highly encouraged to respond. MBARI offers unique opportunities for advanced, technology-based marine research; cooperative projects between scientists, engineers, and marine operations personnel are strongly encouraged. The successful candidate will be expected to develop an independent research program consistent with that ethos. An interest in developing novel systems for detecting and quantifying key elements and compounds that actively influence the growth and distribution of marine organisms is also desired. In addition, the new PI will be expected to engage in one or more ongoing MBARI programs, such as the development and application of stationary and mobile ocean-observing platforms, design and use of novel chemical and biological sensors, and studies of biogeochemical cycling in the water column and benthic environments.

Bermuda Institute of Ocean Sciences: Chemical/Physical/Biological Oceanographer
Review of applications will begin April 15, 2015.

UTK: Professor and Head Department of Microbiology, The College of Arts & Sciences
Review of applications will begin on March 31, 2015 and will continue until the position is filled.

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.

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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