C-DEBI Newsletter – February 16, 2016
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We are having a busy February - we received a bountiful 43 proposals in response to our latest call for C-DEBI research and education grants (7 graduate fellowship, 18 postdoc fellowship, 13 research, 5 education) which are currently being reviewed by C-DEBI Leadership and our E&O Steering Committee.  We've also had our annual site review by NSF and the external panel, and we continue to be proud of all of our strong group of graduate students and postdocs for being one of the great successes of C-DEBI.  Good luck to all with your NSF proposals due today!  Stay tuned for a detailed introduction and call for social networking action from our new Diversity Director, Dr. Leticia Sanchez.


Jan Amend
C-DEBI Director



ISME Journal
Coupled RNA-SIP and metatranscriptomics of active chemolithoautotrophic communities at a deep-sea hydrothermal vent
Caroline S. Fortunato and Julie A. Huber*
*C-DEBI Contribution 267

The chemolithoautotrophic microbial community of the rocky subseafloor potentially provides a large amount of organic carbon to the deep ocean, yet our understanding of the activity and metabolic complexity of subseafloor organisms remains poorly described. A combination of metagenomic, metatranscriptomic, and RNA stable isotope probing (RNA-SIP) analyses were used to identify the metabolic potential, expression patterns, and active autotrophic bacteria and archaea and their pathways present in low-temperature hydrothermal fluids from Axial Seamount, an active submarine volcano. Metagenomic and metatranscriptomic results showed the presence of genes and transcripts for sulfur, hydrogen, and ammonium oxidation, oxygen respiration, denitrification, and methanogenesis, as well as multiple carbon fixation pathways. In RNA-SIP experiments across a range of temperatures under reducing conditions, the enriched 13C fractions showed differences in taxonomic and functional diversity. At 30 °C and 55 °C, Epsilonproteobacteria were dominant, oxidizing hydrogen and primarily reducing nitrate. Methanogenic archaea were also present at 55 °C, and were the only autotrophs present at 80 °C. Correspondingly, the predominant CO2 fixation pathways changed from the reductive tricarboxylic acid (rTCA) cycle to the reductive acetyl-CoA pathway with increasing temperature. By coupling RNA-SIP with meta-omics, this study demonstrates the presence and activity of distinct chemolithoautotrophic communities across a thermal gradient of a deep-sea hydrothermal vent.

ISME Journal
The energetics of anabolism in natural settings
Douglas E. LaRowe* and Jan P. Amend*
*C-DEBI Contribution 284

The environmental conditions that describe an ecosystem define the amount of energy available to the resident organisms and the amount of energy required to build biomass. Here, we quantify the amount of energy required to make biomass as a function of temperature, pressure, redox state, the sources of C, N and S, cell mass and the time that an organism requires to double or replace its biomass. Specifically, these energetics are calculated from 0 to 125 °C, 0.1 to 500 MPa and −0.38 to +0.86 V using CO2, acetate or CH4 for C, NO3 or NH4+ for N and SO42− or HS for S. The amounts of energy associated with synthesizing the biomolecules that make up a cell, which varies over 39 kJ (g cell)−1, are then used to compute energy-based yield coefficients for a vast range of environmental conditions. Taken together, environmental variables and the range of cell sizes leads to a ~4 orders of magnitude difference between the number of microbial cells that can be made from a Joule of Gibbs energy under the most (5.06 × 1011 cells J−1) and least (5.21 × 107 cells J−1) ideal conditions. When doubling/replacement time is taken into account, the range of anabolism energies can expand even further.

ISME Journal
Novel microbial assemblages inhabiting crustal fluids within mid-ocean ridge flank subsurface basalt
Sean P. Jungbluth*, Robert M. Bowers, Huei-Ting Lin, James P. Cowen*, and Michael S. Rappé*
*C-DEBI Contribution 289

Although little is known regarding microbial life within our planet’s rock-hosted deep subseafloor biosphere, boreholes drilled through deep ocean sediment and into the underlying basaltic crust provide invaluable windows of access that have been used previously to document the presence of microorganisms within fluids percolating through the deep ocean crust. In this study, the analysis of 1.7 million small subunit ribosomal RNA genes amplified and sequenced from marine sediment, bottom seawater and basalt-hosted deep subseafloor fluids that span multiple years and locations on the Juan de Fuca Ridge flank was used to quantitatively delineate a subseafloor microbiome comprised of distinct bacteria and archaea. Hot, anoxic crustal fluids tapped by newly installed seafloor sampling observatories at boreholes U1362A and U1362B contained abundant bacterial lineages of phylogenetically unique Nitrospirae, Aminicenantes, Calescamantes and Chloroflexi. Although less abundant, the domain Archaea was dominated by unique, uncultivated lineages of marine benthic group E, the Terrestrial Hot Spring Crenarchaeotic Group, the Bathyarchaeota and relatives of cultivated, sulfate-reducing Archaeoglobi. Consistent with recent geochemical measurements and bioenergetic predictions, the potential importance of methane cycling and sulfate reduction were imprinted within the basalt-hosted deep subseafloor crustal fluid microbial community. This unique window of access to the deep ocean subsurface basement reveals a microbial landscape that exhibits previously undetected spatial heterogeneity.

Environmental Microbiology Reports
Thermal and geochemical influences on microbial biogeography in the hydrothermal sediments of Guaymas Basin, Gulf of California
Luke McKay*, Vincent W. Klokman, Howard P. Mendlovitz, Douglas E. LaRowe*, Daniel R. Hoer, Daniel Albert, Jan P. Amend*, Andreas Teske*
*C-DEBI Contribution 293

Extreme thermal gradients and compressed metabolic zones limit the depth range of microbial colonization in hydrothermally active sediments at Guaymas Basin. We investigated the physicochemical characteristics of this ecosystem and their influence on microbial community structure. Temperature-related trends of δ13C values of methane and dissolved inorganic carbon from 36 sediment cores suggest in situ thermal limits for microbial anaerobic methane oxidation and organic carbon re-mineralization near 80°C and 100°C respectively. Temperature logging probes deposited in hydrothermal sediments for 8 days demonstrate substantial thermal fluctuations of up to 25°C. Putative anaerobic methanotroph (ANME) populations dominate the archaeal community, transitioning from ANME-1 archaea in warm surficial sediments towards ANME-1 Guaymas archaea as temperatures increase downcore. Since ANME archaea performing anaerobic oxidation of methane double on longer time scales (months) compared with relatively rapid in situ temperature fluctuations (hours to days), we conclude that ANME archaea possess a high tolerance for short-term shifts in the thermal regime.


Proposal Calls

DCO: Deep Life Cultivation Internship Program
The Deep Life Community (DLC) within the Sloan Foundation supported Deep Carbon Observatory realizes that the majority of deep microbial life has been resistant to cultivation in the laboratory, which complicates the characterization of physiological characteristics of deep community members. However, recent studies using bioreactor-cultivation techniques, under high pressure and/or temperature, have resulted in successful enrichment of previously uncultivable archaeal and bacterial components that mediate biogeochemical carbon cycling in deep subsurface (1-7). In order to maintain and strengthen cultivation strategies in future deep life missions, the DLC will support early-carrier researchers to visit some key laboratories (Inagaki - Kochi, Japan, Bartlett - La Jolla, USA, and others) to learn and practice newly developed cultivation and cultivation-dependent molecular/biogeochemical techniques using samples from the DLC’s field missions. Financial support includes $5,400 per person for travel and lodging costs and host lab research supply reimbursement. Interested applicants should send their cv, a brief one page statement of their cultivation plans, and a letter of support from their intended host to Fumio Inagaki ( and Douglas Bartlett (

NAS: Gulf Research Program Exploratory Grants
Letter of Intent due February 17, 2016

NAS: Gulf Research Program Early-Career Research Fellowships
Application deadline: February 17, 2016.

IODP: Call for Scientific Drilling Proposals
Next proposal submission deadline: April 01, 2016.

Shell: Ocean Discovery XPRIZE
Regular registration deadline: June 30, 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).


Education & Outreach

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 or at the Marine Biological Laboratory 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 due March 18, 2016.

Deadline to apply is February 19, 2016

DCO: Applications Now Open for 2nd Summer School
Application deadline: March 01, 2016.

Meetings & Activities
2016 Ocean Sciences Meeting
The 2016 Ocean Sciences Meeting will be held 21-26 February 2016 at the Ernest N. Morial Convention Center in New Orleans. Cosponsored by AGU, ASLO, and TOS, the Ocean Sciences Meeting will consist of a diverse program covering topics in all areas of the ocean sciences discipline. Registration deadline: February 20, 2016.

IODP-USSSP Workshop Announcement: Antarctic Ice & Climate
Antarctic marine sediments hold records of ice sheet dynamics and warm climates of the past that
form analogs for high-CO2 greenhouse scenarios of the next centuries. Several proposals to collect these records are in the IODP review system, and the workshop will bring together proponents, other experts, and early stage scientists to: produce an integrated overview of what IODP drilling can bring to understanding Antarctic ice sheet retreat (and hence sea level rise) under warm climates; examine existing sediment cores which have revealed Antarctica’s past marine glaciological history; and establish best practices for assessing ice and weather to conduct safe drilling operations in Antarctic waters. Deadline to apply: March 7, 2016.

Nominate a 2016 AGU Fellow for their exceptional contribution in Earth and space science
The American Geophysical Union (AGU) Fellows program is an honor given to individual AGU members who have made exceptional scientific contributions and attained acknowledged eminence in the fields of Earth and space sciences as valued by their peers and vetted by a committee of Fellows. The Fellows program serves to meet the need of identifying authorities who could advise, upon request, the various government agencies and other organizations outside the Earth and space sciences.  We know you know someone in C-DEBI, like our early-career stars, that fits the bill and deserves a shiny AGU Fellows medallion! Deadline: March 15, 2016.

AGU/JpGU: Taira Prize Call for Nominations
The Asahiko Taira International Scientific Ocean Drilling Research Prize (The Taira Prize) is given annually to one honoree in recognition of  “outstanding transdisciplinary research accomplishment in ocean drilling.” Established in 2014, the Taira Prize is a partnership between the American Geophysical Union (AGU) and the Japan Geoscience Union (JpGU), and is made possible through the generous donation from the Integrated Ocean Drilling Program Management International (IODP-MI). The prize includes:
  • $18,000 monetary prize
  • Engraved award (award will be presented at AGU Fall Meeting during odd presentation year, and at the JpGU Annual Meeting during even presentation year)
  • Invitation to present a lecture at the AGU Fall Meeting during odd award presentation year, and at the JpGU Annual Meeting during even award presentation year
  • Recognition in Eos
  • Recognition at the AGU Fall Meeting during award presentation year
  • Two complimentary tickets to the Honors Banquet at the AGU Fall Meeting during the award presentation year
Nominations due March 15, 2016.

SoCal Geobiology Symposium: Call for Abstract Submissions
The 13th annual Southern California Geobiology Symposium will be held on Saturday, May 7th 2016 at the California Institute of Technology (see program for details). Registration and abstract submission are now open! We are looking forward to welcoming all guests at Caltech on May 7th. If you have any questions, please do not hesitate to contact us. The Southern California Geobiology Symposium is an annual student-run event designed to bring geobiologists together to discuss current research and build local collaborations. It is an opportunity for undergraduate students, graduate students and post-docs to present geobiological research in the form of oral and poster presentations. The topics presented span various disciplines including geology, geochemistry, astrobiology, microbiology, oceanography, paleobiology/-ecology and environmental sciences. Conference registration is open to all geobiological researchers in CA and neighboring states. Abstract submission deadline: April 01, 2016.

Goldschmidt 2016: Yokohama, Japan on June 26-July 1, 2016
Planning on attending this year's Goldschmidt Conference? Please consider submitting your abstracts to Session 14g: Deep Biosphere: Biogeochemical Elemental Cycles, Serpentinization and Evolution of Life in the Earth’s Interior. Abstracts submission deadline: February 26, 2016.

Societé Francaise de Minéralogie: Serpentine Days
Deadline for pre-registration: March 01, 2016.



Cardiff University: Senior Lecturer / Reader / Chair in Geomicrobiology, School of Earth and Ocean Sciences
To maintain its international research activity in Geomicrobiology the School of Earth and Ocean Sciences, Cardiff University, intends to appoint a Senior Lecturer, Reader or Professor in Geomicrobiology. We seek exceptional candidates whose research is focused on microbial impacts on the Earth's biosphere, atmosphere, hydrosphere and geosphere, past and present. We are particularly looking for applicants with experience in one or more of the following fields: near surface to deep subsurface biosphere, microbial influences on element cycling, biosphere/geosphere interactions, anaerobic microbiology, biomineralization and microbe/mineral interactions, sedimentary and/or soil biogeochemistry, biogeochemical cycles, anaerobic microbial ecology and applied environmental microbiology. The successful candidate must develop and sustain an internationally recognized, externally funded research programme in geomicrobiology. We particularly seek candidates who complement our current geomicrobiology research programme and can integrate across other research areas in the. This position is a full-time (35 hours per week), open-ended post and is available immediately. For informal enquiries, please contact Professor Ian Hall, Head of School ( More information on the School of Earth and Ocean Sciences can be found at: Closing date: March 31, 2016.

University of Hawaii at Manoa: Post Doctoral and Graduate Student Research

The Rappé laboratory at the University of Hawaii at Manoa's Hawaii Institute of Marine Biology is seeking a postdoctoral researcher and one to two graduate students (M.S. or Ph.D.) to join a project investigating the population genomics of planktonic marine bacteria. Review of applications will begin immediately; to ensure full consideration, apply by February 25, 2016.

LMU Munich: Postdoctoral Research Fellowship Program
The Orsi lab at the University of Munich is inviting interested graduate students and postdocs to apply for the LMU Postdoctoral Research Fellowship Program, to study the activity, biochemistry, and genomics of bacteria in subseafloor sediment. Informal inquiries should be sent to Bill Orsi ( The deadline for applications is February 29, 2016.

IFREMER: Life at the extremes: microbial EcoGenomics of deep-sea extremophiles: Postdoctoral position (starting immediately) 
The Lab for Microbiology of Extreme environments in Brest (France) has an 18-month postdoctoral position available to carry out research in the ecology of bacterial and archaeal communities in deep-sea brine lakes and hydrothermal vent systems. The appointment should start no later than April 1 2016. Please send inquiries and application to Loïs Maignien ( and A.M. Eren (


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

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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