C-DEBI Newsletter – May 1, 2019
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Message from the Director:

Seafloor borehole observatories (CORKs) at Juan de Fuca Ridge flank to be revisited this month to make further discoveries about the activity of life in the deep crustal biosphere. Photo courtesy of 2013 Juan de Fuca Ridge flank cruise AT26-03 with ROV Jason (WHOI, chief scientist Andrew Fisher of University of California, Santa Cruz, NSF).

Dear C-DEBI,

The month of May finds several C-DEBI scientists returning to the Juan de Fuca Ridge flank to examine microbes in the crustal subsurface. Led by C-DEBI Senior Scientist Beth Orcutt, the NSF-funded “Slow Life in the Fast Lane” cruise has a primary objective to measure microbial activity in this environment. Orcutt’s group will be conducting stable isotope incubations in situ and shipboard to measure various microbial metabolisms in this ecosystem, and comparing these to shore-based potential rate measurements. Leveraging these experiments, Orcutt and colleagues will also be applying new cell sorting techniques developed by collaborator Ramunas Stepanauskas to identify active microbial groups in this ecosystem as well as in the overlying water column, with leveraged funding from NASA and NSF. C-DEBI community members Stephanie Carr, Olivia Nigro, and Michael Rappé will also be on the cruise with support from NSF to lead parallel guided cultivation, ecogenomic and viral studies on the crustal fluids in collaboration with an international team of cultivation and thermophilic spore experts. The cruise will take place May 15-28 aboard the RV Atlantis with ROV Jason. Follow along on Twitter at #SlowLifeFastLane.  

We also congratulate C-DEBIers who have recently been awarded, promoted or are starting new positions: James Bradley (Assistant Professor at Queen Mary University of London); Jen Glass (Associate Professor at Georgia Institute of Technology); and Everett Shock (Arizona State University), honored with the 2019 Geochemistry Division Medal by the American Chemical Society.


Jan Amend
C-DEBI Director



Uncultured Microbial Phyla Suggest Mechanisms for Multi-Thousand-Year Subsistence in Baltic Sea Sediments - NEW!
Jordan T. Bird, Eric D. Tague, Laura A. Zinke*, Jenna M. Schmidt, Andrew D. Steen*, Brandi Kiel Reese*, Ian P.G. Marshall, Gordon Webster, Andrew Weightman, Hector F. Castro, Shawn R. Campagna, Karen G. Lloyd*
*C-DEBI Contribution 471

Energy-starved microbes in deep marine sediments subsist at near-zero growth for thousands of years, yet the mechanisms for their subsistence are unknown because no model strains have been cultivated from most of these groups. We investigated Baltic Sea sediments with single-cell genomics, metabolomics, metatranscriptomics, and enzyme assays to identify possible subsistence mechanisms employed by uncultured Atribacteria, Aminicenantes, Actinobacteria group OPB41, Aerophobetes, Chloroflexi, Deltaproteobacteria, Desulfatiglans, Bathyarchaeota, and Euryarchaeota marine group II lineages. Some functions appeared to be shared by multiple lineages, such as trehalose production and NAD+-consuming deacetylation, both of which have been shown to increase cellular life spans in other organisms by stabilizing proteins and nucleic acids, respectively. Other possible subsistence mechanisms differed between lineages, possibly providing them different physiological niches. Enzyme assays and transcripts suggested that Atribacteria and Actinobacteria group OPB41 catabolized sugars, whereas Aminicenantes and Atribacteria catabolized peptides. Metabolite and transcript data suggested that Atribacteria utilized allantoin, possibly as an energetic substrate or chemical protectant, and also possessed energy-efficient sodium pumps. Atribacteria single-cell amplified genomes (SAGs) recruited transcripts for full pathways for the production of all 20 canonical amino acids, and the gene for amino acid exporter YddG was one of their most highly transcribed genes, suggesting that they may benefit from metabolic interdependence with other cells. Subsistence of uncultured phyla in deep subsurface sediments may occur through shared strategies of using chemical protectants for biomolecular stabilization, but also by differentiating into physiological niches and metabolic interdependencies.

Forearc carbon sink reduces long-term volatile recycling into the mantle - NEW!
P. H. Barry, J. M. de Moor, D. Giovannelli, M. Schrenk, D. R. Hummer, T. Lopez, C. A. Pratt, Y. Alpízar Segura, A. Battaglia, P. Beaudry, G. Bini, M. Cascante, G. d’Errico, M. di Carlo, D. Fattorini, K. Fullerton, E. Gazel, G. González, S. A. Halldórsson, K. Iacovino, J. T. Kulongoski, E. Manini, M. Martínez, H. Miller, M. Nakagawa, S. Ono, S. Patwardhan, C. J. Ramírez, F. Regoli, F. Smedile, S. Turner, C. Vetriani, M. Yücel, C. J. Ballentine, T. P. Fischer, D. R. Hilton & K. G. Lloyd

Carbon and other volatiles in the form of gases, fluids or mineral phases are transported from Earth’s surface into the mantle at convergent margins, where the oceanic crust subducts beneath the continental crust. The efficiency of this transfer has profound implications for the nature and scale of geochemical heterogeneities in Earth’s deep mantle and shallow crustal reservoirs, as well as Earth’s oxidation state. However, the proportions of volatiles released from the forearc and backarc are not well constrained compared to fluxes from the volcanic arc front. Here we use helium and carbon isotope data from deeply sourced springs along two cross-arc transects to show that about 91 per cent of carbon released from the slab and mantle beneath the Costa Rican forearc is sequestered within the crust by calcite deposition. Around an additional three per cent is incorporated into the biomass through microbial chemolithoautotrophy, whereby microbes assimilate inorganic carbon into biomass. We estimate that between 1.2 × 108 and 1.3 × 1010 moles of carbon dioxide per year are released from the slab beneath the forearc, and thus up to about 19 per cent less carbon is being transferred into Earth’s deep mantle than previously estimated.

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!

IODP Workshop Report
Scientific Exploration of the Arctic and North Pacific: Community-driven Priorities for Ocean Drilling - NEW!

The Northern Pacific, Bering Sea and Western Arctic regions contain important records of linked tectonic and paleoceanographic histories. The primary goal of this workshop was to develop new proposals and reinvigorate existing proposals for scientific ocean drilling in the region. By focusing on regional coordination across scientific themes, our breakout groups and working sessions encouraged new collaborations to develop coordinated drilling strategies.


Meetings & Activities

24th ISEB Symposium, Potsam, Germany, September 22-27, 2019 - NEW!
The International Society for Environmental Biogeochemistry (ISEB) Symposium - to be held at the Helmholtz Centre Potsdam German Research Centre for Geosciences (GFZ) - will bring together scientists from all over the world to discuss recent developments and discoveries from all aspects of Environmental Biogeochemistry, including but not limited to microbiology, chemistry, soil science, geoscience, limnology, ecology, marine and atmospheric sciences both from fundamental and applied perspectives. The meeting will be in a single session format, so all participants have the chance to attend all oral presentations. Daily poster sessions provide sufficient time for discussions among the participants. Abstract submission deadline: May 31, 2019.

ISSM: Submit your abstracts to the 11th ISSM conference, June 14-19, 2020, Utrecht, The Netherlands
Abstracts due in September 2019.

Ongoing Activities:


Education & Outreach

C-DEBI: Latest Professional Development Webinar Now Online! - NEW!
Missed the last Professional Development Webinar on “Broadening your thinking and your impact: Tips on how to develop effective outreach programs” with Pete Girguis (Harvard)? Watch it on YouTube.

C-DEBI: Call for Nominations: Professional Development Webinar Series
Know someone who can share their knowledge of essential skills not learned in graduate school, like developing a syllabus, how to choose what professional service committees to serve on or how to transition to a career in industry? C-DEBI seeks nominations for its Professional Development Webinar series.ecord

IODP-USSSP: Apply to host an Ocean Discovery Lecturer
For the 2018-19 academic year, an exciting lineup of distinguished lecturers is available to speak at your institution, including C-DEBI researchers Ginny Edgcomb and Brandi Kiel Reese. Application deadline to host an Ocean Discovery Lecturer: May 17, 2019.

ECORD Summer School 2019 on Sub­duc­tion Zone Pro­cesses, Bremen,Germany
Application deadline: June 19, 2019.


Proposal Calls

NOAA: Ocean Exploration and Research FFO Announcement
The deadline for the pre-proposal submission is May 24, 2019.

NSF: Research Experiences for Undergraduates (REU) - NEW!
The Research Experiences for Undergraduates (REU) program supports active research participation by undergraduate students in any of the areas of research funded by the National Science Foundation. REU projects involve students in meaningful ways in ongoing research programs or in research projects specifically designed for the REU program. This solicitation features two mechanisms for support of student research: (1) REU Sites are based on independent proposals to initiate and conduct projects that engage a number of students in research. REU Sites may be based in a single discipline or academic department or may offer interdisciplinary or multi-department research opportunities with a coherent intellectual theme. Proposals with an international dimension are welcome. (2) REU Supplements may be included as a component of proposals for new or renewal NSF grants or cooperative agreements or may be requested for ongoing NSF-funded research projects. Full Proposal Deadlines: May 24, 2019 and August 28, 2019.

Simons Foundation: Postdoctoral Fellowships in Marine Microbial Ecology
Application deadline: June 14, 2019.

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

NSF: Biological Oceanography
Full proposal deadline date: August 15, 2019.

NSF: Chemical Oceanography
Full proposal deadline date: August 15, 2019.

NSF: Physical Oceanography
Full proposal deadline date: August 15, 2019.

NSF: Accelerating Research through International Network-to-Network Collaborations (AccelNet)
Letter of intent due date: October 30, 2019.

NSF: Research Traineeship (NRT) Program
Next letter of intent window: November 25, 2019 – December 6, 2019.

Rolling Calls:



TAMU: Instructional Assistant Professor
Application deadline: June 1, 2019.

MBL: Computational Postdoctoral Scientist - NEW!
A computational postdoctoral position in Ocean Biogeochemical Modeling is available at the Marine Biological Laboratory, Woods Hole. This NSF-funded, collaborative project with the Massachusetts Institute of Technology will focus on combining thermodynamics and trait-based biogeochemical models to augment an existing marine ecosystem modeling framework (“Darwin model”) developed at MIT. We are seeking an individual with a PhD in oceanography, engineering, applied math or related field who has interest or experience in marine biogeochemical modeling. While not required, knowledge in thermodynamics, numerical analysis and/or optimal control theory will be considered advantageous. The successful candidate will be expected to work collaboratively with teams at both MBL and MIT, but will be employed at MBL. Review of applications will begin July 1, 2019 and continue until the position is filled.

LMU: Professorship of Geological Earth Surface Processes

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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