C-DEBI Newsletter – January 16, 2014
This newsletter is also accessible via our website.

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

Proposal Calls

Moore Foundation: Data-Driven Discovery Initiative
Our Data-Driven Discovery Initiative seeks to advance the people and practices of data-intensive science, to take advantage of the increasing volume, velocity, and variety of scientific data to make new discoveries. Within this initiative, we’re supporting data-driven discovery investigators – individuals who exemplify multidisciplinary, data-driven science, coalescing natural sciences with methods from statistics and computer science. These innovators are striking out in new directions and are willing to take risks with the potential of huge payoffs in some aspect of data-intensive science. Successful applicants must make a strong case for developments in the natural sciences (biology, physics, astronomy, etc.) or science enabling methodologies (statistics, machine learning, scalable algorithms, etc.), and applicants that credibly combine the two are especially encouraged. Note that the Science Program does not fund disease targeted research. It is anticipated that the DDD initiative will make about 15 awards at ~$1,500,000 each, at $200K-$300K/year for five years. Pre-applications are due Monday, February 24, 2014 by 5 pm Pacific Time. We expect to extend invitations for full applications in April 2014.  Full applications will be due five weeks after the invitation is sent, currently anticipated for mid-May 2014.

DCO: Deep Life Community Call for Proposals
The Deep Life Community (DLC) of the Deep Carbon Observatory invites proposals for short-term funding of exploratory projects and/or activities aimed at addressing the DLC’s decadal goals and/or strengthening the international DLC community and its abilities to generate funding for new and ongoing initiatives. The DLC will accept 3 to 4 page, electronic submissions prior to 31 March 2014, 30 June 2014, 30 September 2014, and 31 December 2014.


Cruise Report from AT26-09: Discovery, sampling, and quantification of flows from cool yet massive ridge flank hydrothermal springs on Dorado Outcrop, eastern Pacific Ocean
There were many successes in the expedition to Dorado Outcrop and to the CORKs at ODP Holes 1253A and 1255A despite losing a week of scheduled ship, Jason, and Sentry time to accommodate HOV Alvin certification. Major accomplishments at Dorado Outcrop include: (1) proving correct the hypothesis that Dorado outcrop is a regional focus of massive, low-temperature, hydrothermal discharge, (2) locating, sampling, and deploying experiments in numerous springs of low-temperature hydrothermal fluid emanating from the outcrop; (3) completion of 72 measurements of heat flow on and around Dorado outcrop, most co-located on chirp or seismic lines; and (4) conducting extensive surveys from which we produced bathymetric, sediment thickness, and water column temperature anomaly maps. Major accomplishment at the ODP Hole 1253A and 1255A CORKs include: (1) downloading long-term pressure data from both holes; and (2) recovering the downhole instrument string from ODP Hole 1253A. The weather and crews of the Atlantis, Jason and Sentry made it possible for us to utilize all assets to collect the most complete data set possible in the given time frame. NSF OCE 1130146 “Collaborative Research: Discovery, sampling, and quantification of flows from cool yet massive ridge flank hydrothermal springs on Dorado Outcrop, eastern Pacific Ocean” was awarded to C-DEBI Co-I Wheat, Co-I Fisher and Hulme. Additional support was provided by C-DEBI through Research Grants (Orcutt, McManus, Vidoudez) and Postdoctoral Fellowships (Bertics, Briggs, and Inderbitzen).

Hot Off the Press: Carbon adsorption onto Fe oxyhydroxide stalks produced by a lithotrophic iron-oxidizing bacteria (C-DEBI Contribution 201) in Geobiology
Iron (Fe)-oxidizing bacteria have the potential to produce morphologically unique structures that may be used as biosignatures in geological deposits. One particular example is Mariprofundus ferrooxydans, which produces extracellular twisted ribbon-like stalks consisting of ferrihydrite, co-located with organic and inorganic elements. It is currently thought that M. ferrooxydans excrete and co-precipitate polysaccharides and Fe simultaneously; however, the cellular production of these polysaccharides has yet to be confirmed. Here, Bennett et al. report on a time-series study that used scanning transmission X-ray microscopy and C 1s and Ca 2p near-edge X-ray adsorption fine structure spectroscopy to investigate production of polysaccharides over the growth cycle of M. ferrooxydans. The production and morphology of twisted iron stalks were consistent with previous observations, but unexpectedly, in the log phase, the carbon content of the stalks was extremely low. It was not until stationary growth phase that a significant component of carbon was detected on the stalks. During the log phase, low levels of carbon, only detectable when the stalks were thin, suggested that M. ferrooxydans produce an extracellular polysaccharide template onto which the Fe precipitates. By stationary phase, the increased carbon association with the stalks was a result of adsorption of organic compounds that were released during osmotic shock post-stalk production. In the environment, elevated concentrations of DOC could adsorb onto the Fe stalks as well as a number of other elements, for example, Si, P, Ca, which, by preventing chemical interactions between the Fe nanoparticles, will prevent structural deformation during recrystallization and preserve the structure of these filaments in the rock record.

Methanotrophic archaea possessing diverging methane-oxidizing and electron-transporting pathways in ISME Journal
Anaerobic oxidation of methane (AOM) is a crucial process limiting the flux of methane from marine environments to the atmosphere. The process is thought to be mediated by three groups of uncultivated methane-oxidizing archaea (ANME-1, 2 and 3). Although the responsible microbes have been intensively studied for more than a decade, central mechanistic details remain unresolved. On the basis of an integrated analysis of both environmental metatranscriptome and single-aggregate genome of a highly active AOM enrichment dominated by ANME-2a, Wang et al. provide evidence for a complete and functioning AOM pathway in ANME-2a. All genes required for performing the seven steps of methanogenesis from CO2 were found present and actively expressed. Meanwhile, genes for energy conservation and electron transportation including those encoding F420H2 dehydrogenase (Fpo), the cytoplasmic and membrane-associated Coenzyme B–Coenzyme M heterodisulfide (CoB-S-SCoM) reductase (HdrABC, HdrDE), cytochrome C and the Rhodobacter nitrogen fixation (Rnf) complex were identified and expressed, whereas genes encoding for hydrogenases were absent. Thus, ANME-2a is likely performing AOM through a complete reversal of methanogenesis from CO2 reduction without involvement of canonical hydrogenase. ANME-2a is demonstrated to possess versatile electron transfer pathways that would provide the organism with more flexibility in substrate utilization and capacity for rapid adjustment to fluctuating environments. This work lays the foundation for understanding the environmental niche differentiation, physiology and evolution of different ANME subgroups.
Summer Courses, Internships and REUs
Wrigley Institute: 2014 Summer Research Experiences for Undergraduates (REU): Coastal Ocean Systems and Sustainability program
This NSF-funded program will support highly motivated and talented undergraduate students to conduct independent but guided research that focuses on Coastal Ocean Systems and Sustainability at the Wrigley Marine Science Center (WMSC) on Catalina Island, CA, June 16 – August 8, 2014 (8 weeks). Students will get hands-on research experience, training in laboratory and field methodologies, introductory lectures and seminars in oceanography and marine science, academic and career advisement, as well as opportunities to explore different parts of the island and ecosystems.  Other benefits include: $500/week stipend, housing at the WMSC, reimbursement for travel from host institution (up to $500), and transportation between the WMSC and the mainland. We welcome applications from students who have completed at least one year of undergraduate study and will be enrolled as an undergraduate in the Fall of 2014.  Students must be U.S. citizens, U.S. nationals or permanent residents of the U.S. to be eligible for this program. We especially encourage students from underrepresented groups in STEM fields or schools with limited research opportunities to apply. This program will be particularly useful for undergraduate students with a strong interest in pursuing graduate school or a career in marine science.  Competitive applicants will have at least a 3.0 GPA, one semester of chemistry, one semester of biology, and one semester of calculus or statistics. Application deadline: February 17, 2014.

C-DEBI - Global Environmental Microbiology (GEM) Summer Course for Undergraduates, July 7 - August 1, 2014
Applications are due February 7, 2014. Please contact Cindy Joseph at with any questions.

C-DEBI - Community College Research Internship for Scientific Engagement (CC-RISE), June 16 - August 8, 2014
See the website for more details and application instructions. Applications are due March 1, 2014.

Wrigley Institute - GeoBiology 2014: An International Training course in a Rapidly Evolving Field
Deadline for applications is February 15, 2014.

DCO - Deep Carbon Observatory (DCO) Summer School, July 13 - 18, 2014
To be eligible, applicants must be pursuing research related to one of the DCO themes as a current graduate student or postdoc within three years of completing his/her PhD. Applications due February 1, 2014.

MBARI - 2014 EARTH Workshop for educators, July 27 - August 1, 2014
Submit your application for our next EARTH workshop before the deadline of February 28, 2014. Test drive one of our published activities, or one of the many developed during previous workshops.

Activities and Workshops

Goldschmidt 2014: Deep life-related session at, June 8-14, Sacramento, CA
Session 05f: Serpentinization Processes: From Mantle to Microbe, Past and Present (Conveners: Susan Lang, Muriel Andreani, Tom McCollom). This session seeks to bring together scientists from a range of backgrounds to discuss the many different aspects of serpentinization and its geophysical, geochemical, and biological consequences. Serpentinites are widespread in both oceanic and continental lithospheres on Earth, and likely occur in a number of other planetary bodies in the solar system as well. The formation of serpentinites through hydration of ultramafic rocks plays a role in many other processes, including the geophysical and geochemical evolution of the ocean crust from ridges to subduction zones, transfer of elements and volatiles to overlying rocks and seawater, production of reduced compounds that support chemosynthetic microbial communities in surface and subsurface settings, sequestration of CO2 in carbonate minerals, and abiotic synthesis of methane and other organic compounds. Serpentinites have contributed to these processes throughout Earth’s history, and perhaps provided a setting for the evolution of the earliest forms of life. We invite contributions concerning these and other topics related to serpentinization, including field, laboratory, and theoretical studies. Contributions that explore links between the geophysical, geochemical, biological, and astrobiological aspects of serpentinization are especially encouraged. Deadline for abstracts is February 8th, and information on submitting abstracts can be found at:

C-DEBI: Nominations open for the 2013-2014 Networked Speaker Series
C-DEBI seeks nominations for the next three speakers for this program. 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. Presentations are to be about 30 minutes in length, with time allocated for questions and discussion. For more information about the Speaker Series and nomination request, please see:
The workshop takes place February 23, 2014 at the Ocean Sciences Meeting in Honolulu, HI.
Fill out our registration form to reserve your spot now. For additional information, please contact Dr. Carrie Ferraro or Janice McDonnell.

The 3rd International Conference of Geobiology, June 16-18, 2014, Wuhan, China
Registration deadline is Feb 28, 2014.

ISSM 2014: Call for Abstracts
ISSM 2014 is seeking presentations on the newest developments in subsurface microbiology and microbial ecology. We are calling on microbiologists, ecologists, geoscientists, and others in the field to submit an abstract for an oral or poster presentation. Student oral and poster presentations are also welcome. Abstract Deadline: April 1, 2014.

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
Administrative Assistant
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.
You are receiving this e-mail because you opted in at our website or requested to be added via e-mail.

Unsubscribe <<Email Address>> from this list.
Forward this email to a friend
Subscribe to this list.
Update your profile
Email Marketing Powered by Mailchimp