C-DEBI Newsletter – January 16, 2017
This newsletter is also accessible via our website.

Happy New Year! We started this year off strong with our Annual Site Review by the NSF and the external review panel, and are continually proud of our graduate students and postdocs who demonstrate one of the greatest successes of C-DEBI.  We look forward to another great year!



Microbe Magazine
Ocean Sediments an Enormous but Underappreciated Microbial Habitat
Jan P. Amend* and Douglas E. LaRowe*
*C-DEBI Contribution 346


  • The oceans that cover 70% of the Earth's surface lie above 3×10 8 km3 of sediment containing an estimated 3×10 29 microbial cells.
  • The role played by spores in low-energy sedimentary ecosystems remains an enigma.
  • Despite conflicting results from earlier analyses, archaea and bacteria apparently exist in similar abundances within deep-sea sediments.
  • Within these sediments, anaerobic metabolisms dominate, especially those in which sulfate reduction and oxidation of organic matter are coupled.
  • Modeling proves crucial when trying to connect sedimentary microorganisms to their appropriate geochemical environments.

Temperature and volume of global marine sediments
Douglas E. LaRowe*, Ewa Burwicz, Sandra Arndt, Andrew W. Dale, Jan P. Amend*
*C-DEBI Contribution 350

Marine sediments contribute significantly to global element cycles on multiple time scales. This is due in large part to microbial activity in the shallower layers and abiotic reactions resulting from increasing temperatures and pressures at greater depths. Quantifying the rates of these diagenetic changes requires a three-dimensional description of the physiochemical properties of marine sediments. In a step toward reaching this goal, we have combined global data sets describing bathymetry, heat conduction, bottom-water temperatures, and sediment thickness to quantify the three-dimensional distribution of temperature in marine sediments. This model has revealed that ∼35% of sediments are above 60 °C, conditions that are suitable for petroleum generation. Furthermore, significant microbial activity could be inhibited in ∼25% of marine sediments, if 80 °C is taken as a major thermal barrier for subsurface life. In addition to a temperature model, we have calculated new values for the total volume (3.01 × 108 km3) and average thickness (721 m) of marine sediments, and provide the only known determination of the volume of marine-sediment pore water (8.46 × 107 km3), equivalent to ∼6.3% of the volume of the ocean. The results presented here can be used to help quantify the rates of mineral transformations, lithification, catagenesis, and the extent of life in the subsurface on a global scale.

Environmental Microbiology
In-situ incubation of iron-sulfur mineral reveals a diverse chemolithoautotrophic community and a new biogeochemical role for Thiomicrospira
Roman A. Barco*, Colleen L. Hoffman, Gustavo A. Ramírez, Brandy M. Toner, Katrina J. Edwards*, Jason B. Sylvan
*C-DEBI Contribution 351

Sulfide mineral precipitation occurs at mid‐ocean ridge (MOR) spreading centers, both in the form of plume particles and seafloor massive sulfide structures. A common constituent of MOR is the iron‐bearing sulfide mineral pyrrhotite, which was chosen as a substrate for in‐situincubation studies in shallow waters of Catalina Island, CA to investigate the colonization of iron‐oxidizing bacteria. Microbial community datasets were obtained from in‐situ incubated pyrrhotite, allowing for direct comparison to microbial communities of iron‐sulfides from active and inactive chimneys in deep‐sea environments. Unclassified Gammaproteobacteria and Alphaproteobacteria (Magnetovibrio) largely dominated the bacterial community on pyrrhotite samples incubated in the water column while samples incubated at the surface sediment showed more even dominance by Deltaproteobacteria (Desulfobulbus), Gammaproteobacteria (Piscirickettsiaceae), Alphaproteobacteria (Rhodobacteraceae), and Bacteroidetes (Flavobacteriia). Cultivations that originated from pyrrhotite samples resulted in the enrichment of both, sheath‐forming and stalk‐forming Zetaproteobacteria. Additionally, a putative novel species of Thiomicrospira was isolated and shown to grow autotrophically with iron, indicating a new biogeochemical role for this ubiquitous microorganism.

Proposal Calls

IODP: Submit an IODP Drilling Proposal
The Proposal Database System (PDB) is the web-based interface for completing and submitting IODP proposals. PDB offers specific guidance and many proposal components are now created interactively; proponents are advised to begin working with PDB as soon as a proposal is planned. Complete proposal preparation guidance, format requirements, and review policies are explained in the IODP Proposal Submission Guidelines. A Call for Scientific Ocean Drilling Proposals is usually published at least two months in advance of the deadline with specifics about what types proposals are being sought. Proponents are strongly encouraged to contact the Science Operators to discuss platform-specific operational and fiscal constraints before developing proposals. The IODP Proposal Manager has sole authority to accept proposals or grant exceptions to deadlines and policies. Next Proposal Submission Deadline: April 3, 2017.

NSF: Division of Environmental Biology (core programs) (DEB) Program Solicitation
Preliminary proposal due date: January 23, 2017.

NSF: Long Term Research in Environmental Biology (LTREB) Program Solicitation
Preliminary proposal due date: January 23, 2017.

L'Oréal USA For Women in Science Fellowships
The 2017 L’Oréal USA for Women in Science will close on February 3, 2017.

The National Academies: Gulf Research Program Early-Career Research Fellowships
Applications due February 22, 2017.

NSF: Arctic Sciences Program Solicitation
Proposals accepted anytime.

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

C-DEBI: Rolling call for Research Exchange proposals

Education & Outreach

C-DEBI: Applications Now Open for the 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 1, 2017.

C-DEBI: Applications Now Open for the 2017 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. Note: First generation college, women, and under-represented students encouraged to apply. 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. Applications due February 1, 2017.

IODP: Expedition 366 Outreach Video Diary
Follow along with IODP Expedition 366: Mariana Convergent Margin & South Chamorro Seamount (co-chief Geoff Wheat, Dec 8, 2016 to Feb 7, 2017) with onboard videos from Education and Outreach Officer Kristen Weiss on Vimeo!

GEOBIOLOGY 2017: An International Training Course in a Rapidly Evolving Field
The International Geobiology Course is an intense, multidisciplinary summer course that explores the co-evolution of the Earth and it’s biosphere, with an emphasis on how microbial processes affect the environment and leave imprints in the rock record. Participants get a hands-on learning experience in cutting-edge geobiological techniques including molecular biology, microbiology, geochemistry, and sedimentology and work in research groups to solve real research questions. Themes for this years’ course include: 1) Molecular biology and biogeochemistry of Mono Lake, with an emphasis on sulfur cycle processes in this unusual alkaline lake; 2) Microbiology and molecular biology of organisms living in sulfidic and/or hydrocarbon-rich environments; 3) Mineral, sedimentologic, and geochemical evidence for life in ancient rocks of the Monterey Formation. This year the course will be directed by Alex Sessions, Woody Fischer, Victoria Orphan, and Hope Johnson, but remains in a format similar to previous years. The 2017 course is open to graduate students and postdocs at any level. The cost of the course is US$4000. This year, two fellowships are available to help support postdocs trained in other fields who wish to enter geobiology as a new field of study. Applications due February 10, 2017.

Bigelow: Undergraduate Research Experience
Undergraduates in Bigelow Laboratory’s summer REU Program spend ten weeks at the Laboratory conducting independent research with guidance from a scientist mentor. Directed by Senior Research Scientist Dr. David Fields, and funded by the National Science Foundation, the REU Program is designed to give students pursuing degrees in the sciences, mathematics and engineering a laboratory-based research experience with an emphasis on hands-on, state-of-the-art methods and technologies. REU students are immersed in the Bigelow community and participate in seminars, field trips, Laboratory outreach programs, social events, and more. Each student in the program is paired with a Bigelow Laboratory scientist based on mutual research interests. During the ten weeks, students work with their mentors to identify a research question, develop a proposal, conduct their research, and prepare an abstract and poster. At the end of the program, students present their poster and give a talk at a student symposium. Research areas include the deep biosphere (check out C-DEBI researcher Orcutt’s lab page), as well as marine microbiology, ocean biogeochemistry, optical oceanography, remote sensing, bioinformatics, sensory biology and phytoplankton ecology. The 2017 program dates are May 30 through August 4 and will be held at the Laboratory’s East Boothbay campus. Successful applicants receive a stipend, free housing, and funds for travel to and from Bigelow Laboratory. Applications due February 15, 2017.

NSF: Community College Innovation Challenge
Are you a community college student who has a novel idea that uses science, technology, engineering or mathematics (STEM)? The National Science Foundation (NSF) and the American Association of Community Colleges (AACC) present the third annual Community College Innovation Challenge (CCIC) that asks student teams to innovate a STEM-based solution to a real-world problem. Teams will submit projects in one of three themesMaker to ManufacturerEnergy and Environment, and Security Technologies. Form your team with a faculty mentor and community and/or industry partner to enter. An entry consists of a written portion and a 90-second video. Visit the Promotional Toolkit, where you can download posters, postcards and more.  Entry period closes February 15, 2017.

Sigma Xi: 2017 Student Research Showcase
Sigma Xi, The Scientific Research Honor Society invites high school, undergraduate and graduate students to participate in the 2017 Student Research Showcase, an innovative opportunity to develop their science communication skills using a virtual platform. Effective communication to a broad audience is becoming increasingly important in our digital-driven world. Participants in the Student Research Showcase create a website that contains three components; a short video to introduce their project, an abstract, and a technical slideshow. They receive feedback from judges, who are qualified Sigma Xi members and the public. Monetary awards of up to $500 are given to the top Graduate, Undergraduate and High School winners. The winner of the People’s Choice Award is selected based on a public vote and receives a $250 monetary award. All student presenters will receive a certificate of participation.Project approval and registration deadline: February 22, 2017.


Meetings & Activities

Deep biosphere topics at the 2017 Astrobiology Science Conference (AbSciCon)
Abstracts are due shortly (THIS WEDNESDAY, January 18) for the upcoming Astrobiology Science Conference (AbSciCon) 2017 meeting in Mesa, Arizona (April 24-28, 2017). Among others, deep biosphere-related topics include “Seeking Evidence of Habitable Conditions and Life Activity in Serpentinizing Systems” (organizers: Beth Orcutt and Alexis Templeton) and “Earth’s Deep Biosphere and the Astrobiosphere: New Connections Made Through Advanced Instrumentation and Field Approaches” (organizers: D’Arcy Meyer-Dombard and Dawn Cardace). The topic organizers encourage you to consider submitting an abstract about your research!

Onshore-Offshore Drilling and Sampling to Understand Freshwater Resources along the New England Continental Shelf: An IODP-ICDP Workshop
To understand the dynamics of onshore-offshore shore hydrologic systems, this IODP- and ICDP-sponsored workshop will focus on the coupling between glacial dynamics, sea-level variations, and groundwater flow for Martha’s Vineyard, Massachusetts, USA and the U.S. Atlantic continental shelf offshore Martha’s Vineyard. The overall goals of the workshop (May 22-23, 2017; Woods Hole, Massachusetts), are to develop a new operational plan for IODP Proposal 637 and establish an amphibious component of the project to accomplish its science objectives. These goals will be accomplished by (1) developing ideal sampling and measurement plans for geology, geophysics, geochemistry, and microbiology across the shoreline and the shelf; (2) prioritizing onshore and offshore scientific operations including site order and target depths; and (3) formulating specific plans for pursuing external funds for the drilling project. Travel support is available for a limited number of participants through USSSP (for U.S.) and ICDP (for international). For more information, visit the workshop website. The workshop is open to U.S. and international participants and the deadline to apply is February 17, 2017.

Register and submit abstracts for the 2017 SoCal Geobiology Symposium
It is our pleasure to host the SoCal Geobiology Symposium 2017 at the University of Southern California! We would like to welcome scientists in the area who do research broadly related to geobiology, geochemistry, paleoclimatology, and more. This year, the symposium will take place on April 8, 2017 at the beautiful Mudd Hall on USC campus. We invite attendees of all career levels, and encourage undergraduates, graduate students, and post-doctoral fellows to submit abstracts for posters and 15 minute talks. Registration and abstract submission is free. You may confirm your attendance and submit your abstracts by clicking on this link and completing the google form. We look forward to hearing from you, and please do not hesitate to contact us with any questions or concerns by emailing us at Feel free to forward this message to other researchers who would be interested in attending as well. Abstract submission is due March 3, 2017.

C-DEBI: Networked Speaker Series 2016-2017: Call for nominations

Community Webinars: Searching for Rock Hosted Life on Mars

ISSM 2017: Call for Abstracts

C-DEBI: Rolling call for Community Workshop support


University of Hawai'i: 3 Postdoctoral Research Positions in Geophysics, Microbiology/Geochemistry, and Hydrological Numerical Modeling
This RII Track-I project, named ‘Ike Wai (from the Hawaiian ‘ike, meaning knowledge, and wai, meaning water) tests the central hypothesis that hydrogeology of the Hawaiian islands depends critically on the internal structure of the volcano. ‘Ike Wai will collect new geophysical and groundwater chemistry and microbial data, integrate these data into new, detailed groundwater models, and generate a much improved understanding of subsurface water location, volume and flow paths. Data and outputs from ‘Ike Wai will provide decision making tools to address challenges to water sustainability from climate variability, increasing population demands, and water contamination. The successful applicants for these three-year postdoctoral positions will interact with scientists and students across disciplines and actively engage in professional development training in areas such as leadership, diversity, pedagogy and mentoring. Within the objectives and scope of ‘Ike Wai, applicants will have significant flexibility in defining projects that capitalize on the diverse expertise and collaborative interests of the team as they relate to water sustainability. ‘Ike Wai postdoctoral researchers will participate in a work environment that encourages knowledge of, respect for, and development of skills to engage with diverse communities in Hawai‘i and the Pacific on issues surrounding water sustainability. Applications due January 24, 2017.

University of South Carolina: Graduate Student Position in Biogeochemistry of Lost City Hydrothermal Field
Funding for a Ph.D. student is available starting Summer/Fall 2017 to work on an NSF-funded project in Isotope Biogeochemistry lab at the University of South Carolina. The goals of the project are to explore how microbes survive and thrive in a warm, high pH serpentinization system, to investigate the fate of deep sea organic matter as it passes through the rocky subsurface, and to determine whether small organic molecules are formed abiotically. This research has implications for the earliest development of life on Earth and other planets, and on Earth’s carbon cycle. Field work includes a 22-day oceanographic expedition with the remotely operated vehicle Jason to the Lost City Hydrothermal Field. Stipend and tuition support are available for the length of the project in a combination of research and teaching assistantships. We are looking for a motivated, curious, problem-solver who enjoys being in the lab and field. A background in chemistry and/or isotopes, HPLC, GC, or IC is particularly welcome. For additional information, please visit our website ( Interested students can send a letter of interest, CV, and unofficial transcripts to Dr. Susan Lang at and/or submit applications through the School of the Earth, Ocean and Environment ( Preference will be given to submission prior to January 27, 2017 but the position will remain open until filled.

University of Rhode Island: Assistant Professor in Biological Oceanography
We seek a biological oceanographer focused on understanding changing biological processes from the organismal to ecosystem levels. Areas of expertise may include, but are not limited to, food-web dynamics, benthic habitats, population ecology, and ecosystem modeling. The new hire will have access to the Marine Science Research Facilities, estuarine research on URI small boats, and the opportunity to participate in the active sea-going community of GSO on ships.  Preference will be given to scientists conducting sea-going research in coastal or open-ocean regions.  We invite applicants with a strong commitment to research, to excellence in teaching and mentorship of graduate and undergraduate students, and to outreach activities. The search will remain open until filled. First consideration will be given to applications received by 17 January 2017. Second consideration may be given to applications received by 15 February 2017.

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

Exploring life beneath the seafloor and making transformative discoveries that advance science, benefit society, and inspire people of all ages and origins.

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