C-DEBI Newsletter – February 1, 2019
This newsletter is also accessible via our website.

Message from the Director:

Dear C-DEBI,

Congrats to the Dorado octopus team including Geoff Wheat and Anne Hartwell for capturing the photo of octopus moms above and making NSF’s "Most popular stories of 2018”! 

I also encourage you to apply to the "NEXT: Scientific Ocean Drilling Beyond 2023" workshop for the future of scientific ocean drilling to be held in Denver, Colorado, USA on May 6-7, 2019. The NEXT workshop will convene approximately 120 IODP community members to develop the US plan for continued scientific ocean drilling without a hiatus at the end of the current program ending in 2023 and continue planning to replace the aging JOIDES Resolution with a modernized, more capable non-riser drilling vessel to help accommodate the transition to a long-term future in scientific ocean drilling. The deadline to apply is 2/15/19.


Jan Amend
C-DEBI Director


Publications & Press

Nature Geoscience
Persistent organic matter in oxic subseafloor sediment - NEW!
Emily R. Estes*, Robert Pockalny*, Steven D’Hondt*, Fumio Inagaki, Yuki Morono, Richard W. Murray, Dennis Nordlund, Arthur J. Spivack, Scott D. Wankel, Nan Xiao, Colleen M. Hansel*
*C-DEBI Contribution 450


Nearly half of the global seafloor is overlain by sediment oxygenated to the basement. Yet, despite the availability of oxygen to fuel aerobic respiration, organic carbon persists over million-year timescales. Identifying the controls on organic carbon preservation requires an improved understanding of the composition and distribution of organic carbon within deep oligotrophic marine sediments. Here we show that organic carbon in sediment from the oligotrophic North Atlantic and South Pacific is low (<0.1%), yet stable to depths of 25 m and ages of 24 million years. This organic carbon is not bound in biomass and has a low carbon/nitrogen ratio. X-ray imaging and spectroscopic analyses reveal that the chemical composition of this old, deep organic carbon is dominated (40–60%) by amide and carboxylic carbon with a proteinaceous nature. We posit that organic carbon persists in oxic oligotrophic sediment through a combination of protective processes that involve adsorption to mineral surfaces and physical inaccessibility to the heterotrophic community. We estimate that up to 1.6 × 1022 g of organic carbon are sequestered on million-year timescales in oxic pelagic sediment, which exceeds current estimates of the total global sediment organic carbon and constitutes an important, previously overlooked carbon reservoir.

Nature Communications
Metabolic diversity within the globally abundant Marine Group II Euryarchaea offers insight into ecological patterns - NEW!
Benjamin J. Tully*
*C-DEBI Contribution 452

Despite their discovery over 25 years ago, the Marine Group II Euryarchaea (MGII) remain a difficult group of organisms to study, lacking cultured isolates and genome references. The MGII have been identified in marine samples from around the world, and evidence supports a photoheterotrophic lifestyle combining phototrophy via proteorhodopsins with the remineralization of high molecular weight organic matter. Divided between two clades, the MGII have distinct ecological patterns that are not understood based on the limited number of available genomes. Here, I present a comparative genomic analysis of 250 MGII genomes, providing a comprehensive investigation of these mesophilic archaea. This analysis identifies 17 distinct subclades including nine subclades that previously lacked reference genomes. The metabolic potential and distribution of the MGII genera reveals distinct roles in the environment, identifying algal-saccharide-degrading coastal subclades, protein-degrading oligotrophic surface ocean subclades, and mesopelagic subclades lacking proteorhodopsins, common in all other subclades.

The ISME Journal
Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi - NEW!
Joel A. Boyd, Sean P. Jungbluth, Andy O. Leu, Paul N. Evans, Ben J. Woodcroft, Grayson L. Chadwick, Victoria J. Orphan*, Jan P. Amend*, Michael S. Rappé, Gene W. Tyson

*C-DEBI Contribution 457

The methyl-coenzyme M reductase (MCR) complex is a key enzyme in archaeal methane generation and has recently been proposed to also be involved in the oxidation of short-chain hydrocarbons including methane, butane, and potentially propane. The number of archaeal clades encoding the MCR continues to grow, suggesting that this complex was inherited from an ancient ancestor, or has undergone extensive horizontal gene transfer. Expanding the representation of MCR-encoding lineages through metagenomic approaches will help resolve the evolutionary history of this complex. Here, a near-complete Archaeoglobi metagenome-assembled genome (MAG; Ca. Polytropus marinifundus gen. nov. sp. nov.) was recovered from the deep subseafloor along the Juan de Fuca Ridge flank that encodes two divergent McrABG operons similar to those found in Ca. Bathyarchaeota and Ca. Syntrophoarchaeum MAGs. Ca. P. marinifundus is basal to members of the class Archaeoglobi, and encodes the genes for β-oxidation, potentially allowing an alkanotrophic metabolism similar to that proposed for Ca. Syntrophoarchaeum. Ca. P. marinifundus also encodes a respiratory electron transport chain that can potentially utilize nitrate, iron, and sulfur compounds as electron acceptors. Phylogenetic analysis suggests that the Ca. P. marinifundus MCR operons were horizontally transferred, changing our understanding of the evolution and distribution of this complex in the Archaea.

Have an upcoming manuscript about the deep subseafloor biosphere and want to increase your press coverage? NSF's Office of Legislative and Public Affairs is looking to coordinate press releases between your home institution and the NSF to coincide with the date of publication. Please contact us as soon as your publication is accepted!


Meetings & Activities

16th SoCal Geobiology Symposium @ CalTech, April 6, 2019
Registration is now open! The deadline to be considered for an oral presentation is February 8, 2019, so don’t wait too long! We will continue to accept general registration and poster abstracts after that date, but please sign up as soon as possible to aid us in logistical planning.

UofSC: 6th Annual Southeastern Biogeochemistry Symposium, March 30, 2019 - NEW!
Registration is now open for the Southeastern Biogeochemistry / Geobiology Symposium. The submission deadline for presenters is February 15, 2019. General registration will remain open through March 16, 2019. For planning purposes early registration is appreciated.

IODP-USSSP: NEXT Workshop: Instituting U.S. Scientific Ocean Drilling Beyond 2023
Application window closes February 15, 2019.

UC Boulder: Third Annual Rocky Mountain Geobiology Symposium, April 6, 2019
Registration is now open! The abstract submission deadline is February 15, 2019, and registration deadline (without abstract submission) is March 20, 2019.

AbSciCon 2019: Session on "Lessons from Earth Analogs to Inform the Search for Life in the Universe"
Abstracts are due March 6, 2019.

Goldschmidt: Session 09c: Biogeochemical Cycling in Changing Glacial Habitats and Downstream Ecosystems
Abstract submission opens January 15, 2019, and closes March 29, 2019.

2nd Geobiology Society Conference, June 9-13, 2019, Banff, Canada - NEW!
Following a very successful “Geobiology 2017” with 200 registrants, the Geobiology Society will again host a 3-day meeting at the Banff Conference Center. The dates for the conference are June 9-13, 2019. As before, this meeting will be an ideal venue for us to discuss the latest developments in Geobiology and build international collaborations in a relaxed but stimulating environment. Please register to confirm your attendance by April 19, 2019.

IODP Workshop: IBM Arc System & Analogs
Workshop participation is open to U.S. and international researchers and the deadline to apply is May 1, 2019.

Ongoing Activities:


Education & Outreach

CalTech: Geobiology 2019: An International Training Course in a Rapidly Evolving Field
Applications are due by February 8, 2019.

ICDP: Training Course on Downhole Measurements, June 24-28, 2019, Kuopio / Outokumpu, Finland - NEW!
This training course will encompass the different technical and scientific aspects of downhole measurements and their analysis in scientific drilling, including borehole logging under various conditions and scientific demands, seismic borehole measurements, downhole hydraulic tests, fluid logging & sampling, and fibre optical methods. The training course is recommended for graduate students, PhD students, Early-Careers and Senior Scientists involved in running or upcoming scientific drilling projects. Preference will be given to applicants involved in ICDP drilling projects, applicants from ICDP member countries, developing countries, and those from countries considering ICDP membership. For the successful candidates, expenses including those for travelling, visa, meals and accommodation will be covered by ICDP. The deadline for applications is February 15, 2019.

Bigelow: Undergraduate Research Experience
Application period closes February 15, 2019.

C-DEBI: Next Professional Development Webinar: February 27, 12pm PST - NEW!
Jason Sylvan, (Assistant Professor, Texas A&M) leads the next C-DEBI Professional Development Webinar on “Lessons Learned: Adventures in Online Teaching and Trying to Balance Research & Teaching.” Missed the most recent C-DEBI Professional Development Webinar on “Scientific Editing as a Career” with Delphine Defforey (Nature Communications)? Watch it on YouTube.


Proposal Calls

NSF: Enabling Discovery through GEnomic Tools (EDGE) - NEW!
The Division of Integrative Organismal Systems (IOS) recognizes that a lack of methods for analysis of gene function represents an obstacle to progress in a range of diverse non-model organisms. These organisms are important for understanding numerous basic science questions in organismal biology as funded through the Division’s core programs. Enabling Discovery through Genomic Tools (EDGE) is designed to provide support for development of tools, approaches and infrastructure necessary for direct tests of cause and effect hypotheses between gene function and phenotypes in diverse plants, animals, microbes, viruses and fungi for which these methods are presently unavailable. Such approaches are essential to advance understanding of the genomes-to-phenomes relationship, an area relevant to Understanding the Rules of Life: Predicting Phenotype, one of the 10 Big Ideas for future NSF investment. To meet the goal of catalyzing communities to enable direct tests of cause-and-effect hypotheses about genes and phenotypes in organisms for which such tools and infrastructure are presently lacking, EDGE proposals must include training and rapid dissemination plans enabling larger communities of investigators to utilize the newly-developed tools quickly, thereby catalyzing an increase in the capacity of research communities to test cause-and-effect hypotheses about genes and phenotypes in organisms for which such tools and infrastructure are presently lacking. Full Proposal Deadline Date: February 12, 2019.

Earth Sciences: Laboratory Technician Support (EAR/LTS) - NEW!
The Instrumentation and Facilities Program in the Division of Earth Sciences (EAR/IF) supports meritorious requests for infrastructure that promotes research and education in areas supported by the Division. Under this solicitation EAR/IF will consider proposals for Laboratory Technician Support to provide for optimal and efficient operation of advanced instrumentation, analytical protocol development, and user training for Earth science research instrumentation. Support is available through grants in response to investigator-initiated proposals. Technician support duties that promote human resource development and education are expected to be an integral part of proposals. Efforts to support participation of underrepresented groups in laboratory and/or field instrument use and training are encouraged as part of any described technician’s duties. Proposals from early career (tenure track but untenured) lead investigators are also encouraged. Such proposals will be given due consideration as part of the Broader Impacts merit review criterion. Full proposal deadline date: February 14, 2019.

NSF: Biological Oceanography - NEW!
The Biological Oceanography Program supports fundamental research in biological oceanography and marine ecology (populations to the ecosystems) broadly defined: relationships among aquatic organisms and their interactions with the environments of the oceans or Great Lakes. Projects submitted to the program are often interdisciplinary efforts that may include participation by other OCE Programs. Full proposal deadline dates: February 14, 2019  and August 15, 2019.

NSF: Chemical Oceanography - NEW!
The Chemical Oceanography Program supports research into the chemistry of the oceans and the role of the oceans in global geochemical cycles. Areas of interest include chemical composition, speciation, and transformation; chemical exchanges between the oceans and other components of the Earth system; internal cycling in oceans, seas, and estuaries; and the use of measured chemical distributions as indicators of physical, biological, and geological processes. Full proposal deadline dates: February 15, 2019  and August 15, 2019.

NSF: Physical Oceanography - 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 deadline dates: February 15, 2019  and August 15, 2019.

Frontier Research in Earth Sciences (FRES) - NEW!
The FRES program will support research in Earth systems from its core through the critical zone. The project may focus on all or part of the surface, continental lithospheric, and deeper Earth systems over the entire range of temporal and spatial scales. FRES projects will typically have a larger scientific scope and budget than those considered for funding by core programs in the Division of Earth Sciences (EAR). FRES projects may be interdisciplinary studies that do not fit well within the core programs or cannot be routinely managed by sharing between core programs. Innovative proposals within a single area with results that will have broad relevance to Earth Science research are also encouraged. Investigations may employ any combination of field, laboratory, and computational studies with observational, theoretical, or experimental approaches. Projects should be focused on topics that meet the guidelines for research funded by the Division of Earth Sciences. Full proposal deadline date: February 21, 2019 .

IODP-USSSP: Apply to Sail on Expedition 387: Amazon Margin
The deadline to apply is March 1, 2019.

AGU: Submit a nomination for the Taira Prize - NEW!
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 is given in honor of Dr. Asahiko Taira of the Japan Agency for Marine-Earth Science and Technology. Deadline to nominate: March 15, 2019.

IODP-USSSP: Apply to Sail on Expedition 388: Equatorial Atlantic Gateway
The deadline to apply is April 1, 2019.

NSF: Opportunities for Promoting Understanding through Synthesis (OPUS)
Full proposal deadline: August 5, 2019.

NSF: Research Traineeship (NRT) Program - NEW!
The NSF Research Traineeship (NRT) program is designed to encourage the development and implementation of bold, new, and potentially transformative models for science, technology, engineering and mathematics (STEM) graduate education training. The NRT program seeks proposals that explore ways for graduate students in research-based master’s and doctoral degree programs to develop the skills, knowledge, and competencies needed to pursue a range of STEM careers. Next letter of intent window: November 25, 2019 – December 6, 2019.

Rolling Calls:




MSU: Assistant/Associate Professor of Environmental Microbiology
Screening of applications will begin on February 1, 2019; however, applications will continue to be accepted until an adequate applicant pool has been established.

Bigelow: Postdoctoral Research Scientist - Genomics - NEW!
Bigelow Laboratory for Ocean Sciences is seeking a postdoctoral researcher to study planetary-scale interactions among the evolutionary, biogeochemical and biogeographic processes of marine bacterioplankton, taking advantage of a unique, massive dataset of single cell genomes. The hired scientist will join Dr. Stepanauskas’ research group and will be engaged in collaborations with Dr. Penny Chisholm’s group (MIT) and other partners. The postdoctoral scientists at Bigelow Laboratory have access to an active professional training program and possibilities for undergraduate student mentoring and teaching. Candidates must have either a PhD degree or a PhD ABD in a relevant field and demonstrated experience in microbial genomics, environmental microbiology and evolutionary biology. Excellent written and verbal communication skills and ability to work harmoniously in a collaborative research team are crucial. The position is offered for a period of two years. We want to fill this position as soon as possible, but the start date may be negotiated. Applicants should submit the following to our online application portal by February 11, 2019.

MBL: Faculty Position in Evolutionary Genomics and Molecular Evolution - NEW!
The Josephine Bay Paul Center at the Marine Biological Laboratory (MBL) invites applications for a faculty position at the Assistant Scientist level in the area of evolutionary and functional genomics. The successful candidate will apply experimental and computational approaches to research areas including but not limited to: microbiome interactions, functional studies of host-associated marine microbial communities, evolutionary and ecological changes in marine systems, or genomic and transcriptomic studies of marine organisms. For full consideration applications should be submitted by March 1, 2019.

Princeton University: Assistant Professor

U Toronto: Postdoctoral Positions in Fluid-Rock Interactions and Deep Subsurface Life

UNC Chapel Hill: Guaymas Basin postdoc opportunity

TAMU: Instructional Assistant Professor

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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