C-DEBI Newsletter – February 1, 2018
This newsletter is also accessible via our website.


Message from the Director:

At the end of January, we had our annual site review by NSF and the external panel, and thank all involved including our strong group of undergraduates, graduate students and postdocs who continue to be one of the great successes of C-DEBI.

Congratulations to C-DEBIers who have started new positions this spring semester: Olivia Nigro (Assistant Professor of Biology at Hawaii Pacific University) and Annie Rowe (Assistant Professor of Biological Sciences at University of Cincinnati).

And don't forget to mark your calendars for this month's Professional Development Webinar "Surviving (and Maybe Even Thriving!) in a Soft Money Position" by Julie Huber, C-DEBI Associate Director, Associate Scientist, WHOI - February 28th, 12-1pm PST.


Jan Amend
C-DEBI Director



Abrupt burial imparts persistent changes to the bacterial diversity of turbidite-associated sediment profiles - NEW!
Benjamin Kimball Harrison*, A. Myrbo, B. E. Flood, Jake V. Bailey
*C-DEBI Contribution 408

The emplacement of subaqueous gravity-driven sediment flows imposes a significant physical and geochemical impact on underlying sediment and microbial communities. Although previous studies have established lasting mineralogical and biological signatures of turbidite deposition, the response of bacteria and archaea within and beneath debris flows remains poorly constrained. Both bacterial cells associated with the underlying sediment and those attached to allochthonous material must respond to substantially altered environmental conditions and selective pressures. As a consequence, turbidites and underlying sediments provide an exceptional opportunity to examine (i) the microbial community response to rapid sedimentation and (ii) the preservation and identification of displaced micro-organisms. We collected Illumina MiSeq sequence libraries across turbidite boundaries at ~26 cm sediment depth in La Jolla Canyon off the coast of California, and at ~50 cm depth in meromictic Twin Lake, Hennepin County, MN. 16S rRNA gene signatures of relict and active bacterial populations exhibit persistent differences attributable to turbidite deposition. In particular, both the marine and lacustrine turbidite boundaries are sharply demarcated by the abundance and diversity of Chloroflexi, suggesting a characteristic sensitivity to sediment disturbance history or to differences in organic substrates across turbidite profiles. Variations in the abundance of putative dissimilatory sulfate-reducing Deltaproteobacteria across the buried La Jolla Canyon sediment–water interface reflect turbidite-induced changes to the geochemical environment. Species-level distinctions within the Deltaproteobacteria clearly conform to the sedimentological boundary, suggesting a continuing impact of genetic inheritance distinguishable from broader trends attributable to selective pressure. Abrupt, <1-cm scale changes in bacterial diversity across the Twin Lake turbidite contact are consistent with previous studies showing that relict DNA signatures attributable to sediment transport may be more easily preserved in low-energy, anoxic environments. This work raises the possibility that deep subsurface microbial communities may inherit variations in microbial diversity from sediment flow and deformation events.

Metagenomic investigation of vestimentiferan tubeworm endosymbionts from Mid-Cayman Rise reveals new insights into metabolism and diversity - NEW!
Julie Reveillaud, Rika. E. Anderson, Sintra Reves-Sohn, Colleen M. Cavanaugh, Julie A. Huber*
*C-DEBI Contribution 412

The microbial endosymbionts of two species of vestimentiferan tubeworms (Escarpia sp. and Lamellibrachia sp.2) collected from an area of low-temperature hydrothermal diffuse vent flow at the Mid-Cayman Rise (MCR) in the Caribbean Sea were characterized using microscopy, phylogenetic analyses, and a metagenomic approach. The present study adds new evidence that tubeworm endosymbionts can potentially switch from autotrophic to heterotrophic metabolism, or may be mixotrophic, presumably while free-living, and also suggests their versatile metabolic potential may enable both the host and symbionts to exploit a wide range of environmental conditions. Together, the marked gene content and sequence dissimilarity at the rRNA operon and whole genome level between vent and seep symbionts suggest these newly described endosymbionts from the MCR belong to a novel tubeworm endosymbiont genera, introduced as Candidatus Vondammii.

Scientific Reports
Deeply-sourced formate fuels sulfate reducers but not methanogens at Lost City hydrothermal field - NEW!
Susan Q. Lang, Gretchen L. Früh-Green, Stefano M. Bernasconi, William J. Brazelton, Matthew O. Schrenk & Julia M. McGonigle

Hydrogen produced during water-rock serpentinization reactions can drive the synthesis of organic compounds both biotically and abiotically. We investigated abiotic carbon production and microbial metabolic pathways at the high energy but low diversity serpentinite-hosted Lost City hydrothermal field. Compound-specific 14C data demonstrates that formate is mantle-derived and abiotic in some locations and has an additional, seawater-derived component in others. Lipids produced by the dominant member of the archaeal community, the Lost City Methanosarcinales, largely lack 14C, but metagenomic evidence suggests they cannot use formate for methanogenesis. Instead, sulfate-reducing bacteria may be the primary consumers of formate in Lost City chimneys. Paradoxically, the archaeal phylotype that numerically dominates the chimney microbial communities appears ill suited to live in pure hydrothermal fluids without the co-occurrence of organisms that can liberate CO2. Considering the lack of dissolved inorganic carbon in such systems, the ability to utilize formate may be a key trait for survival in pristine serpentinite-hosted environments.


Meetings & Activities

NSF: Town Hall at Ocean Sciences Meeting: Ocean Observatories Initiative Research Facility Board
There will be an important Town Hall at the upcoming Ocean Sciences meeting in Portland, OR, February 13, 2018, hosted by the Ocean Observatories Initiative Facility Board (OOIFB) of the National Science Foundation (NSF).

NSF: Spring 2018 NSF Grants Conference – Save the Date - NEW!
Save the Date! The Spring 2018 National Science Foundation (NSF) Grants Conference will take place on June 4-5, 2018 in Detroit, Michigan. Registration will open on Thursday, March 15, 2018, at 12:00 PM EST. We anticipate the conference will reach capacity very quickly, so we encourage you to register as soon as it opens. In the meantime, please feel free to check for the most up-to-date information. (You may also contact us via email at:

Goldschmidt 2018: Call for Abstracts
Abstracts due March 30, 2018.

15th Annual Southern California Geobiology Symposium: Save the Date! Saturday, April 21, 2018 @ UCR - NEW!
Come join us at UC Riverside on Saturday, April 21, 2018 for the Fifteenth Annual Southern California Geobiology Symposium! Calls for posters and talks will be going out soon so stay tuned. We strongly encourage faculty members to attend, however only presentations from students and postdocs will be accepted. We would greatly appreciate it if this message could be sent forward to interested students, postdoctoral fellows, and faculty within your departments. Hope to see you here!

C-DEBI: Nominations now open for the C-DEBI 2018 Networked Speaker Series

C-DEBI: Rolling call for Community Workshop support

C-DEBI: Group Page

C-DEBI: Subseafloor Cultures Database


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

IODP-USSSP: A Survey of Outreach and Education Activities in IODP
The survey is open through February 2, 2018.

Geobiology 2018: An International Training Course in a Rapidly Evolving Field
Application deadline: February 9, 2018.

ASM: Undergraduate Research Fellowship: Receive Summer Research Stipend
Application Deadline: February 15, 2018.

Bigelow: Research Experience For Undergraduates
Applications are due February 15, 2018.

C-DEBI: NSF REU: Community College Cultivation Cohort (C4)
Applications due February 23, 2018.

C-DEBI: Next Professional Development Webinar: February 28, 12pm PT - NEW!
Julie Huber (C-DEBI Associate Director, Associate Scientist, WHOI) leads the next C-DEBI Professional Development Webinar on “Surviving (and Maybe Even Thriving!) in a Soft Money Position.” The access URL for the webinar is Missed the last webinar on “Speaking as a Scientist with Press, Politicians, and the Public”? Watch it on YouTube.

ASM: Research Capstone Fellowship: Funding For Professional Development and Career Networking
Application Deadline: March 1, 2018.

C-DEBI: Community College Research Internship for Scientific Engagement (CC-RISE) - NEW!
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 or at the Woods Hole Oceanographic Institution in Woods Hole, MA. 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 are due March 31, 2018 for UCSC and March 23, 2018 for WHOI.

NSF: Research Experiences for Undergraduates (REU), Ocean Sciences - NEW!
NSF supports Research Experiences for Undergraduates (REU) Sites at hundreds of research institutions across the country and in international locations. Most of these REU Sites host groups of 10-20 students for summer internships, although some operate during the academic year. Interns receive a stipend, housing and travel expenses. The students are paired with a scientist as a mentor, conduct an independent research project and participate in various professional development workshops. Many interns receive support to present their work at a scientific conference after the internship is complete. The Division of Ocean Sciences supports about thirty REU Sites each year. Application websites for most of these OCE REU’s are open now or will open soon and most application deadlines are in mid-February or March. The deadline for the fall semester program in Bermuda is in May. Please encourage undergraduates to apply to an OCE REU Site. Applications at each site are accepted from undergraduates enrolled in a degree program (part-time or full-time) leading to a baccalaureate or associate degree. Students must be US citizens or permanent residents of the US or its territories. Applications from veterans, students with disabilities, minorities, first-generation college students and community college students are encouraged.

IODP-USSSP: New IODP Outreach: In Search of Earth's Secrets

Mentoring365: Become an Earth and Space Science Mentor or Mentee

NOAA: Graduate Research & Training Scholarship Program

Proposal Calls

NSF: Major Research Instrumentation (MRI)
Submissions due February 5, 2018.

NSF: Research Traineeship (NRT) Program
Proposal deadline: February 6, 2018.

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

NSF: Chemical Oceanography Program Solicitation - NEW!
The Chemical Oceanography Program supports research into the chemical components, reaction mechanisms, and geochemical pathways within the ocean and at its interfaces with the solid earth and the atmosphere. Major emphases include:  studies of material inputs to and outputs from marine waters; orthochemical and biological production and transformation of chemical compounds and phases within the marine system; and the determination of reaction rates and study of equilibria. The Program encourages research into the chemistry, distribution, and fate of inorganic and organic substances introduced into or produced within marine environments including those from estuarine waters to the deep sea. Full Proposal Target Date: February 15, 2018.

NSF: Biological Oceanography Program Solicitation - NEW!
The Biological Oceanography Program supports research in marine ecology broadly defined: relationships among aquatic organisms and their interactions with the environments of the oceans or Great Lakes. Projects submitted to the program for consideration are often interdisciplinary efforts that may include participation by other OCE Programs. Full Proposal Target Date: February 15, 2018.

NSF: Physical Oceanography Program Solicitation - NEW!
The Physical Oceanography Program supports research on a wide range of topics associated with the structure and movement of the ocean, with the way in which it transports various quantities, with the way the ocean’s physical structure interacts with the biological and chemical processes within it, and with interactions between the ocean and the atmosphere, solid earth and ice that surround it. Full Proposal Target Date: February 15, 2018.

NSF: Ocean Technology and Interdisciplinary Coordination - NEW!
The Oceanographic Technology and Interdisciplinary Coordination (OTIC) Program supports a broad range of research and technology development activities. Unsolicited proposals are accepted for instrumentation development that has broad applicability to ocean science research projects and that enhance observational, experimental or analytical capabilities of the ocean science research community. Specific announcements for funding opportunities are made for additional projects involving Improvements in Facilities, Communications, and Equipment at Biological Field Stations and Marine Laboratories (FSML) and the National Ocean Partnership Program. Full Proposal Target Date: February 15, 2018.

American Philosophical Society / NAI: Lewis and Clark Fund for Exploration and Field Research in Astrobiology
Deadline: February 15, 2018.

IODP: Apply to Sail on IODP Expedition 383: Dynamics of the Pacific Antarctic Circumpolar Current
The deadline to apply is March 1, 2018.

IODP: Apply to Sail on IODP Expedition 385: Guaymas Basin Tectonics and Biosphere
The deadline to apply is April 15, 2018.

NSF: Cyberinfrastructure for Sustained Scientific Innovation (CSSI) - Data and Software - NEW!
The Cyberinfrastructure for Sustained Scientific Innovation (CSSI) umbrella program encompasses the long-running Data Infrastructure Building Blocks (DIBBs) and Software Infrastructure for Sustained Innovation (SI2) programs, as NSF seeks to enable funding opportunities that are flexible and responsive to the evolving and emerging needs in data and software cyberinfrastructure. Full proposal deadline: April 18, 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: 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



U Alaska Fairbanks: CFOS Assistant or Associate Professor
Applications due February 28, 2018.

University of Western Brittany (UBO): Postdoctoral researcher position - NEW!
The Laboratoire de Microbiologie des Environnements Extrêmes (LM2E) is offering a Postdoctoral researcher position in the international Horizon 2020 funded project S4CE ( Starting on April 15th, 2018, the position offers the possibility to enlarge the expertise and skills in terrestrial deep biosphere environmental Microbiology. The main task of the Postdoc project will be to study the deep biosphere microbiome (depending on samples available from several drilled sites) with a particular focus on diversity and function within the context of the environmental extreme conditions. Next generation sequencing methods including amplicon sequencing and metagenomics/metatranscriptomics will be used towards this goal. The postdoc will have the opportunity to extract genomic RNA and DNA for sequencing. The main emphasis will be on the bioinformatic processing and interpretation of NGS-generated data. Please send your application no later than April 1, 2018.

Karlsruhe Institute of Technology: Two Ph.D. Positions - NEW!
Hunters of microbial dark matter: we are looking for two highly motivated Ph.D. students in the field of molecular biology and bioinformatics. The topics will be single cell genomics and transcriptomics of unknown microbial species. The applicants should have some knowledge of molecular biology, microbiology, and genetics – bioinformatics skills are a big plus. For more info and applications please email Prof. Anne Kaster (

U Penn: Two Graduate Research Assistant Positions

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!

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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