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C-DEBI Newsletter – January 1, 2016
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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 - Census of Deep Life Sequencing Opportunities
Since 2011, the Deep Carbon Observatory’s (DCO) Deep Life Community has sponsored the Census of Deep Life (CoDL) that has supported surveys of the diversity of microbes present in several deep continental and subseafloor environments. The first surveys (2011-2012) were conducted using 454 pyrosequencing and subsequently (2013) Illumina sequencing strategies were adopted. Through this initiative, the Deep Life Community has allowed the characterization of diversity of subsurface microbial communities at numerous sites worldwide including the subseafloor and deep continental locations from a range of geologic settings (e.g., large igneous provinces, subglacial lakes, methane hydrate-rich sediments, cratons). The Illumina platform provides increased numbers of reads for more samples at reduced cost. For DNA samples submitted to the CoDL for sequencing, proponents have the option of obtaining 400-450 nt bacterial sequences that span the V4V5 region of Bacterial and Archaeal rRNA coding regions or a greater number of reads for V6 regions that through complete overlap of forward and reverse reads allows detection of lower abundance taxa with reduced stochastic error rates. Shotgun metagenomic DNA sequencing for key samples can also be performed. Deadline: January 31, 2016.

Shell: Ocean Discovery XPRIZE
Historically, access to the deep ocean has been limited by the extraordinary physical challenges of exploring this extreme environment, high cost, limited technological advancements, and lack of investment. The $7 Million Shell Ocean Discovery XPRIZE is a global competition challenging teams to advance deep-sea technologies for autonomous, fast and high-resolution ocean exploration. The success of this prize will allow us to fully explore and map the ocean floor, and uncover our planet’s greatest wonder and resource for the benefit of humanity. The National Oceanographic and Atmospheric Administration’s (NOAA) $1 million bonus prize will incentivize teams to develop technologies to detect the source of chemical and biological signals underwater. Regular registration deadline: June 30, 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.

DCO: Call for Proposals in Deep Life Modeling and Visualization
Proposal submission deadline: January 31, 2016.

National Academies: Research Associateships for Graduate, Postdoctoral and Senior Researchers
There are four annual review cycles and the next closes February 01, 2016.

National Academies of Science: Gulf Research Program Early-Career Research Fellowships
Application deadline: February 17, 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).

 

Publications


Biogeosciences
Nitrogen cycling in the deep sedimentary biosphere: nitrate isotopes in porewaters underlying the oligotrophic North Atlantic

S.D. Wankel*, C. Buchwald*, W. Ziebis, C.B. Wenk, and M.F. Lehmann
*C-DEBI Contribution 295

Nitrogen (N) is a key component of fundamental biomolecules. Hence, its cycling and availability are central factors governing the extent of ecosystems across the Earth. In the organic-lean sediment porewaters underlying the oligotrophic ocean, where low levels of microbial activity persist despite limited organic matter delivery from overlying water, the extent and modes of nitrogen transformations have not been widely investigated. Here we use the N and oxygen (O) isotopic composition of porewater nitrate (NO3) from a site in the oligotrophic North Atlantic (Integrated Ocean Drilling Program – IODP) to determine the extent and magnitude of microbial nitrate production (via nitrification) and consumption (via denitrification). We find that NO3 accumulates far above bottom seawater concentrations (~ 21 μM) throughout the sediment column (up to ~ 50 μM) down to the oceanic basement as deep as 90 m b.s.f. (below sea floor), reflecting the predominance of aerobic nitrification/remineralization within the deep marine sediments. Large changes in the δ15N and δ18O of nitrate, however, reveal variable influence of nitrate respiration across the three sites. We use an inverse porewater diffusion–reaction model, constrained by the N and O isotope systematics of nitrification and denitrification and the porewater NO3 isotopic composition, to estimate rates of nitrification and denitrification throughout the sediment column. Results indicate variability of reaction rates across and within the three boreholes that are generally consistent with the differential distribution of dissolved oxygen at this site, though not necessarily with the canonical view of how redox thresholds separate nitrate regeneration from dissimilative consumption spatially. That is, we provide stable isotopic evidence for expanded zones of co-occurring nitrification and denitrification. The isotope biogeochemical modeling also yielded estimates for the δ15N and δ18O of newly produced nitrate (δ15NNTR (NTR, referring to nitrification) and δ18ONTR), as well as the isotope effect for denitrification (15ϵDNF) (DNF, referring to denitrification), parameters with high relevance to global ocean models of N cycling. Estimated values of δ15NNTR were generally lower than previously reported δ15N values for sinking particulate organic nitrogen in this region. We suggest that these values may be, in part, related to sedimentary N2 fixation and remineralization of the newly fixed organic N. Values of δ18ONTR generally ranged between −2.8 and 0.0 ‰, consistent with recent estimates based on lab cultures of nitrifying bacteria. Notably, some δ18ONTR values were elevated, suggesting incorporation of 18O-enriched dissolved oxygen during nitrification, and possibly indicating a tight coupling of NH4+ and NO2 oxidation in this metabolically sluggish environment. Our findings indicate that the production of organic matter by in situ autotrophy (e.g., nitrification, nitrogen fixation) supplies a large fraction of the biomass and organic substrate for heterotrophy in these sediments, supplementing the small organic-matter pool derived from the overlying euphotic zone. This work sheds new light on an active nitrogen cycle operating, despite exceedingly low carbon inputs, in the deep sedimentary biosphere.


Frontiers in Microbiology
Microbial Communities on Seafloor Basalts at Dorado Outcrop Reflect Level of Alteration and Highlight Global Lithic Clades
Michael D. Lee*, Nathan G. Walworth, Jason B. Sylvan*, Katrina J. Edwards*, and Beth N. Orcutt*
*C-DEBI Contribution 286


Areas of exposed basalt along mid-ocean ridges and at seafloor outcrops serve as conduits of fluid flux into and out of a subsurface ocean, and microbe–mineral interactions can influence alteration reactions at the rock–water interface. Located on the eastern flank of the East Pacific Rise, Dorado Outcrop is a site of low-temperature (<20°C) hydrothermal venting and represents a new end-member in the current survey of seafloor basalt biomes. Consistent with prior studies, a survey of 16S rRNA gene sequence diversity using universal primers targeting the V4 hypervariable region revealed much greater richness and diversity on the seafloor rocks than in surrounding seawater. Overall, Gamma-, Alpha-, and Deltaproteobacteria, and Thaumarchaeota dominated the sequenced communities, together making up over half of the observed diversity, though bacterial sequences were more abundant than archaeal in all samples. The most abundant bacterial reads were closely related to the obligate chemolithoautotrophic, sulfur-oxidizing Thioprofundum lithotrophicum, suggesting carbon and sulfur cycling as dominant metabolic pathways in this system. Representatives of Thaumarchaeota were detected in relatively high abundance on the basalts in comparison to bottom water, possibly indicating ammonia oxidation. In comparison to other sequence datasets from globally distributed seafloor basalts, this study reveals many overlapping and cosmopolitan phylogenetic groups and also suggests that substrate age correlates with community structure.


Geology and Geophysics: Project Update
Scientific Ocean Drilling Charts a New Course
Susan Humphris and Anthony A.P. Koppers


The International Ocean Discovery Program (IODP) continues the 45-year history of accomplishments set by its predecessor programs: the Integrated Ocean Drilling Program (2003–2013), the Ocean Drilling Program (1983–2003), and the Deep Sea Drilling Project (1968–1983). Guided by a new science plan, IODP provides opportunities for international interdisciplinary research teams to conduct transformative and societally relevant research through scientific ocean drilling. The United States has participated in scientific ocean drilling since the program’s inception and continues to do so today through operation of the drilling vessel JOIDES Resolution. Highlights from recent JOIDES Resolution expeditions include investigating subduction and the formation of continental crust, the Asian monsoon systems, and the initiation of rifting and ocean basin formation.


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.

 

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.

C-DEBI: The Community College Research Internship for Scientific Engagement, June 13 - August 5, 2016
CC-RISE is an eight-week, paid, summer research internship program for community college students run by the Center for Dark Energy Biosphere Investigations. Students will gain firsthand exposure to the scientific process by working in a faculty-led research lab at the University of California Santa Cruz. In addition to research, students will participate in activities focusing on how to transition from a two-year college to a university and information on graduate school. At the end of the program, students will present their results to an audience of peers and mentors. Applications due March 18, 2016.

DCO: Applications Now Open for 2nd Summer School
The Deep Carbon Observatory (DCO) will hold its second Summer School in Yellowstone National Park from 23 - 28 July 2016. This Summer School will build on the success of the first DCO Summer School, held in Yellowstone National Park in 2014, and will introduce approximately 35 students and early career researchers to the interdisciplinary concepts which are the cornerstone of DCO’s approach to understanding Earth. The weeklong Summer School program will incorporate a variety of classroom- and field-based experiences, including lectures, poster sessions, field trips, and interactive problem-solving exercises. DCO will cover participants' lodging, meals, and field trips, as well as a portion of their transportation costs. To be eligible, applicants must be pursuing research related to a DCO theme as a current graduate student or early postdoc within three years of completing his/her PhD. To publicize the Second DCO Summer School in your department, download the flyer. Application deadline: March 01, 2016.

MATE/UNOLS: 2016 Six-Month Internship
Applications due January 06, 2016.

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

The Data Incubator: Data Science Fellowship, Hiring and Training
Deadline: January, 18, 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.

 

Meetings & Activities
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 31, 2016

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.” Deadline for application is February 01, 2016.

 

Employment


Newcastle University: Lecturers in Geology, Geochemistry / Geomicrobiology
The School of Civil Engineering and Geoscience at Newcastle University is seeking two motivated individuals who have the potential for being a world-leading researcher. We are especially interested in candidates with the capacity to contribute to multi-disciplinary research projects within our School as well as collaborating with our national and international academic and industrial partners. Current major geoscience research themes at Newcastle include microbial processes in the deep subsurface, carbon capture in soils, biogeochemical processes and climate feedbacks in modern and past extreme environments, and petroleum geochemistry of hydrocarbon systems, both conventional and non-conventional. Your research interests could complement these current themes, however the School also wishes to encourage the development of new, internationally leading geoscience research which reflects your expertise. You will teach on our new Earth Science undergraduate programme (including field teaching) and our leading geochemistry MSc programmes. You should hold a PhD in a relevant area, and have the potential for professional Chartered status in the UK. Closing date: January 31, 2016.

Texas A&M: Geosciences Postdoctoral Fellowship
The Geochemical Environmental Research Group (GERG) at Texas A&M, a Center of Excellence in the College of Geosciences is looking for a Postdoctoral Fellow to develop new techniques in passive samplers for environmental contaminants using various types of media. The position is to work cooperatively with four different recently funded projects where these systems will be used. Research areas include the effects of oil and chemical dispersants on corals, effects of oil and chemical dispersants on deep-sea organisms and a project on production of exopolymers by phytoplankton. The fourth project is assessing the background of contaminants in the Gulf of Mexico using ships of opportunity and autonomous vehicles. This position is initially funded for 2 years but can be extended. A PhD in chemistry, organic biogeochemistry, chemical oceanography or a related field, knowledge of general laboratory protocols, extraction techniques, gas and liquid chromatography. Familiarity with GC/MS, LC/MS, GC/MSMS and LC/MSMS would be beneficial (www.gerg.tamu.edu). Contact: tknap@tamu.edu.

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

University of South Florida: Chemical Oceanographer, College of Marine Science
Position is open until filled, however, priority review of applications will begin by January 15, 2016.

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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