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C-DEBI Newsletter – December 1, 2017
This newsletter is also accessible via our website.



Message from the Director:

Proposals for C-DEBI Research Grants and Fellowships are due today! If you miss these annual calls, don't forget we also support C-DEBI Community Workshops and Research Exchanges in a year-round call.

NSF Geoscience is again seeking input (also included below) on exciting research to call out for support in their next report. Please comment on your perspective of deep biosphere research as an area to continue to fund by 2/1/18.  

At last month's C-DEBI Annual Meeting, our presently-funded research and education community met to discuss our current activities. The meeting was preceded by a graduate student and postdoctoral professional development workshop "Key steps to landing a job and what to do once you've been offered the position." See the agenda.

Another season of our Networked Speaker Series is over and we thank the presenters for their great talks connecting all of us interested "deeply" or broadly in the deep biosphere (watch the archived talks online). Nominate an early career investigator doing exciting research with effective communication for next season's series!

Going to the 2017 AGU Fall meeting this month? Join DCO and C-DEBI for a poster swarm of Session B11G "Unearthing the Metabolic Potential of Microorganisms in the Deep Subsurface Biosphere II Posters" on Monday December 11. Gather at poster B11G-1729 at 10AM to hear short presentations of posters in the session followed by questions and discussion. See additional sessions of interest below. While you are at the meeting, share your photos, scientific ponderings, and new found knowledge with us on Twitter! Please tag any NSF-funded C-DEBI research with #NSFfunded, @NSF_GEO and @deepbiosphere. Both C-DEBI and NSF are prepared to share your Tweets!"


Cheers,

Jan Amend
C-DEBI Director

 

Publications


npj Biofilms and Microbiomes
Carbonate-rich dendrolitic cones: insights into a modern analog for incipient microbialite formation, Little Hot Creek, Long Valley Caldera,California NEW!
James Bradley*, Leslie. K. Daille, Christopher. B. Trivedi, Caitlin. L. Bojanowski, Blake. W. Stamps, Bradley. S. Stevenson, Heather. S. Nunn, Hope. A. Johnson, Sean. J. Loyd, William. M. Berelson, Frank. A. Corsetti, John R. Spear
*C-DEBI Contribution 392


Ancient putative microbial structures that appear in the rock record commonly serve as evidence of early life on Earth, but the details of their formation remain unclear. The study of modern microbial mat structures can help inform the properties of their ancient counterparts, but modern mineralizing mat systems with morphological similarity to ancient structures are rare. Here, we characterize partially lithified microbial mats containing cm-scale dendrolitic coniform structures from a geothermal pool (“Cone Pool”) at Little Hot Creek, California, that if fully lithified, would resemble ancient dendrolitic structures known from the rock record. Light and electron microscopy revealed that the cm-scale ‘dendrolitic cones’ were comprised of intertwined microbial filaments and grains of calcium carbonate. The degree of mineralization (carbonate content) increased with depth in the dendrolitic cones. Sequencing of 16S rRNA gene libraries revealed that the dendrolitic cone tips were enriched in OTUs most closely related to the genera PhormidiumLeptolyngbya, and Leptospira, whereas mats at the base and adjacent to the dendrolitic cones were enriched in Synechococcus. We hypothesize that the consumption of nutrients during autotrophic and heterotrophic growth may promote movement of microbes along diffusive nutrient gradients, and thus microbialite growth. Hour-glass shaped filamentous structures present in the dendrolitic cones may have formed around photosynthetically-produced oxygen bubbles—suggesting that mineralization occurs rapidly and on timescales of the lifetime of a bubble. The dendrolitic-conical structures in Cone Pool constitute a modern analog of incipient microbialite formation by filamentous microbiota that are morphologically distinct from any structure described previously. Thus, we provide a new model system to address how microbial mats may be preserved over geological timescales.


Scientific Drilling
Contamination tracer testing with seabed drills: IODP Expedition 357 NEW!
Beth N. Orcutt*, Markus Bergenthal, Tim Freudenthal, David C. Smith, Marvin D. Lilley, Luzie Schnieders, Sophie Green, Gretchen. L. Früh-Green
*C-DEBI Contribution 398


IODP Expedition 357 utilized seabed drills for the first time in the history of the ocean drilling program, with the aim of collecting intact sequences of shallow mantle core from the Atlantis Massif to examine serpentinization processes and the deep biosphere. This novel drilling approach required the development of a new remote seafloor system for delivering synthetic tracers during drilling to assess for possible sample contamination. Here, we describe this new tracer delivery system, assess the performance of the system during the expedition, provide an overview of the quality of the core samples collected for deep biosphere investigations based on tracer concentrations, and make recommendations for future applications of the system.


Proceedings of the IODP
Expedition 370: Temperature Limit of the Deep Biosphere off Muroto NEW!
Heuer, V.B., Inagaki, F., Morono, Y., Kubo, Y., Maeda, L., and the Expedition 370 Scientists


International Ocean Discovery Program (IODP) Expedition 370 explored the limits of the biosphere in the deep subseafloor where temperature exceeds the known temperature maximum of microbial life (~120°C) at the sediment/basement interface ~1.2 km below the seafloor. Site C0023 is located in the protothrust zone in the Nankai Trough off Cape Muroto at a water depth of 4776 m, in the vicinity of Ocean Drilling Program (ODP) Sites 808 and 1174. In 2000, ODP Leg 190 revealed the presence of microbial cells at Site 1174 to a depth of ~600 meters below seafloor (mbsf), which corresponds to an estimated temperature of ~70°C, and reliably identified a single zone of elevated cell concentrations just above the décollement at around 800 mbsf, where temperature presumably reached 90°C; no cell count data was reported for other sediment layers in the 70°–120°C range because the detection limit of manual cell counting for low-biomass samples was not low enough. With the establishment of Site C0023, we aimed to detect and investigate the presence or absence of life and biological processes at the biotic–abiotic transition utilizing unprecedented analytical sensitivity and precision. Expedition 370 was the first expedition dedicated to subseafloor microbiology that achieved time-critical processing and analyses of deep biosphere samples, conducting simultaneous shipboard and shore-based investigations.


IODP-USSSP: Letter from the USSSP Director: Thoughts and Advice on Applying to Sail NEW!
When Lamont-Doherty assumed management of the U.S. Science Support Program (USSSP) in early 2015, one of our main goals was to make the IODP expedition staffing process as transparent as possible. As we approach our fourth year of management, we would like to provide some statistics on U.S. shipboard participation in IODP over the past three years, as well as advice for those aspiring to sail.


 

Meetings & Activities


C-DEBI: Nominations now open for the C-DEBI 2018 Networked Speaker Series! NEW!
C-DEBI seeks nominations for three speakers for the 2018 program. C-DEBI is continuing the Networked Speaker Series (begun in Fall 2011) as a means to enhance communication and the exchange of ideas among our spatially distributed community. Potential speakers can be nominated by colleagues, mentors, or those mentored by C-DEBI participants; they can also self nominate. Selected C-DEBI Networked Speakers will make a presentation online, using video conferencing tools, with assistance from the C-DEBI main office at USC. Nominated C-DEBI Networked Speakers should be capable of combining compelling visual materials with the ability to communicate effectively to a broad audience. We are particularly enthusiastic about giving young researchers a chance to present work to the C-DEBI community. Being selected to be a C-DEBI Networked Speaker is an honor.

2017 AGU Fall Meeting Deep Biosphere Sessions of Interest

Missing a session of interest? Let us know! See also the DCO’s AGU 2017 Fall Meeting Guide.

EGU: Deep biosphere session - call for abstracts
Please consider submitting an abstract to our session, due January 10, 2018.

NSF: Call for Comments on Update to AC GEO Report on Dynamic Earth NEW!
The National Science Foundation’s Advisory Committee for Geosciences (AC GEO) is updating its 2014 report, Dynamic Earth: GEO Imperatives & Frontiers 2015-2020 to incorporate recent developments and to explore future directions for the many disciplines supported by NSF’s Directorate for Geosciences (GEO). With your input, AC GEO will develop a report that provides a clear picture of the exciting areas on the leading edge of the geosciences, captures the importance of curiosity-driven research to better understand our planet and its many interconnected systems, and explains the importance of the geosciences to our society and economy. We welcome your perspective and suggestions on the content and organizational structure for our upcoming report. Input can be sent to geovision@nsf.gov no later than Thursday, February 1, 2018. Thank you for your thoughtful consideration of this request.

C-DEBI: Subseafloor Cultures Database
Interested in looking up which microbial groups have been isolated or enriched from the deep biosphere? Having information about new isolates or enrichments that you would like to add to this list? C-DEBI maintains an unofficial list on the C-DEBI website as a Resource that the community is welcome to access and contribute to.

C-DEBI: Protocols.io Group Page
To help preserve deep biosphere methods for use in future projects, the Center strongly encourages you to describe your lab and software-based methods using protocols.io, and to link them to our group page at https://www.protocols.io/groups/center-for-dark-energy-biosphere-investigations. The protocols.io website provides an easy-to-use platform to share reproducible, step-by-step scientific methods. 

C-DEBI: Rolling call for Community Workshop support
The NSF Science and Technology Center for Dark Energy Biosphere Investigations (C-DEBI) invites proposals for $15,000 on average (and up to $20,000) in direct funds for community workshops that will help to advance C-DEBI’s central research agenda: to investigate the subseafloor biosphere deep in marine sediment and oceanic crust, and to conduct multi-disciplinary studies to develop an integrated understanding of subseafloor microbial life at the molecular, cellular, and ecosystem scales.


 

C-DEBI Spotlight


Each newsletter, we’ll be featuring two, early-career, deep biosphere all-stars from our summer undergraduate programs. Meet the rest of our 2017 Global Enviromental Microbiology students and Community College Cultivation Cohort (C4) REU participants, or learn more about our undergraduate programs!
 

 

 

Education & Outreach


Cards Against Humanity: Science Ambassador Scholarship
Applications close on December 11, 2017.

NOAA: Ernest F. Hollings Undergraduate Scholarship
Application deadline: January 31, 2018.

C-DEBI: Applications Now Open for the 2018 Summer Undergraduate GEM Course
The GEM Course is an all-expenses paid, three-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 and on Santa Catalina Island.

Where: University of Southern California campus and Santa Catalina Island, CA
When: June 10 – June 29, 2018
Who: Undergraduates from 2 or 4-year colleges
Cost: FREE, including travel, plus modest stipend
How to apply: http://www.darkenergybiosphere.org/education-diversity/for-undergraduates/gem-course/
Note:  First generation college, women, and under-represented students encouraged to apply

Application Opens: November 1, 2017
Application Deadline: February 1, 2018 at 5:00pm PST

For questions and comments, contact Gwen Noda at gnoda@usc.edu.

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 23, 2018.

Mentoring365: Become an Earth and Space Science Mentor or Mentee

NOAA: Graduate Research & Training Scholarship Program




Proposal Calls


C-DEBI: Call for Research and Fellowship Proposals
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 marine sediment and oceanic crust, and to conduct multi-disciplinary studies to develop an integrated understanding of subseafloor microbial life at the molecular, cellular, and ecosystem scales. C-DEBI’s research agenda balances exploration-based discovery, hypothesis testing, data integration and synthesis, and systems-based modeling. C-DEBI welcomes proposals from applicants who would enhance diversity in C-DEBI and STEM fields. This request for proposals is open to all interested researchers at US institutions able to receive NSF funding as a subaward. The deadline for this call is TODAY, December 1, 2017.

IODP-USSSP: Apply for a Schlanger Ocean Drilling Fellowship
All application materials, including reference material, must be submitted by December 15, 2017.

DCO: Census of Deep Life Sequencing Opportunities NEW!
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 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. Application Deadline: December 31, 2017.

IODP: Apply to Sail on IODP Expedition 358
The deadline to apply is January 4, 2018.

Duke: Mary Derrickson McCurdy Visiting Scholar
Application open until January 30, 2018.

NSF: International Research Experiences for Students (IRES)
Track I deadline: January 30, 2018Track II deadline deadline: February 6, 2018Track III deadline: February 13, 2018.

NSF: Major Research Instrumentation (MRI) NEW!
The Major Research Instrumentation (MRI) Program serves to increase access to multi-user scientific and engineering instrumentation for research and research training in our Nation’s institutions of higher education and not-for-profit scientific/engineering research organizations. An MRI award supports the acquisition or development of a multi-user research instrument that is, in general, too costly and/or not appropriate for support through other NSF programs. MRI provides support to acquire critical research instrumentation without which advances in fundamental science and engineering research may not otherwise occur. MRI also provides support to develop next-generation research instruments that open new opportunities to advance the frontiers in science and engineering research. Additionally, an MRI award is expected to enhance research training of students who will become the next generation of instrument users, designers and builders. Submissions due February 5, 2018.

American Philosophical Society / NAI: Lewis and Clark Fund for Exploration and Field Research in Astrobiology NEW!
The Lewis and Clark Fund for Exploration and Field Research in Astrobiology is open to graduate students and postdoctoral and junior scientists who wish to participate in field studies for their theses or for other purposes. Applications will be reviewed by a committee that includes members of the NASA Astrobiology Institute, the APS, and the wider science community as needed. Recipients will be designated as Lewis and Clark Field Scholars in Astrobiology. Amounts will depend on travel costs, but will ordinarily be in the range of several hundred dollars up to about $5,000. Deadline: February 15, 2018.

IODP: Apply to Sail on IODP Expedition 383 NEW!
The International Ocean Discovery Program (IODP) is now accepting applications for scientific participants on Expedition 383 Dynamics of the Pacific Antarctic Circumpolar Current aboard the JOIDES Resolution.  IODP Expedition 383 will investigate the Pliocene-Pleistocene atmosphere-ocean-cryosphere dynamics of the Pacific Antarctic Circumpolar Current (ACC), and their role in regional and global climate and atmospheric CO2 based on sediment records with the highest possible stratigraphic resolution. The expedition will test two major scientific hypotheses: (1) ACC dynamics and Drake Passage throughflow conditioned the global Meridional Overturning Circulation and high-low climate linkages on orbital and submillennial time-scales since the Pliocene. (2) Variations in the Pacific ACC determine the physical and biological characteristics of the oceanic carbon pump and atmospheric CO2. The expedition will occur from ~20 May to ~20 July 2019. Additional information about this expedition can be found on the Expedition 383 webpage. Opportunities exist for researchers (including graduate students) in all shipboard specialties, including but not limited to sedimentologists, micropaleontologists, paleomagnetists, inorganic/organic geochemists, petrologists, petrophysicists, microbiologists, and borehole geophysicists. U.S.-affiliated scientists interested in participating in this expedition should apply to sail through the U.S. Science Support Program, by visiting http://usoceandiscovery.org/expeditions. The deadline to apply is March 1, 2018.

DCO: Deep Life Cultivation Internship Program

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).

NSF: Using JOIDES Resolution to Collect Cores with Advanced Piston Coring (APC) System

NSF: Arctic Sciences Program Solicitation
Proposals accepted anytime.

NSF: Tribal Colleges and Universities Program (TCUP) Program Solicitation
Preparing for TCUP Implementation proposals accepted anytime.

C-DEBI: Rolling call for Research Exchange proposals
C-DEBI facilitates scientific coordination and collaborations by supporting student, postdoctoral, and faculty exchanges to build, educate and train the deep subseafloor biosphere community. We award small research exchange grants for Center participants. These grants may be used to support research, travel for presenting C-DEBI research at meetings, or travel exchanges to other partner institutions or institutions that have new tools and techniques that can be applied to C-DEBI research. We anticipate ~10 awards of $500-5000 with additional matched funds to be granted annually.


 

Employment

Two Postdoctoral Researcher Positions: Deep-sea microbiology and biogeochemistry; Microbial ‘dark matter’ in terrestrial hot springs NEW!
The Dekas Geomicrobiology Laboratory at Stanford University seeks two highly motivated postdoctoral researchers. Each successful candidate will have a Ph.D. in a related field, a strong publication record, research experience in microbial ecology, a desire to learn/use nanoscale secondary ion mass spectrometry (nanoSIMS) and specific expertise as indicated in the announcement. Interested candidates should send a complete CV, cover letter, and a list of three professional references to Dr. Anne Dekas at dekas@stanford.edu. Review of applications will begin on December 20, 2017, after which applications will be reviewed on a rolling basis.

WHOI: Tenure Track Research Scientist (Ocean Biogeochemical Modeler) - Marine Chemistry & Geochemistry (17-09-12)
Review of applications will begin on January 5, 2018.

U Penn: Two Graduate Research Assistant Positions

Oberlin: Postdoctoral Research Fellow in Computational Biology

MBL: Postdoctoral Scientist - Molecular Microbial Ecology






Don’t forget to email me with any items you'd like to share in future newsletters! We will also broadcast this information on our social media outlets, Twitter and Facebook. 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
janicak@usc.edu
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.

C-DEBI is now on Twitter! Follow and tweet to us @deepbiosphere or tag #CDEBI.
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