C-DEBI Newsletter – February 15, 2019
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Publications & Press

The ISME Journal
Carboxydotrophy potential of uncultivated Hydrothermarchaeota from the subseafloor crustal biosphere - NEW!
Stephanie A. Carr*, Sean P. Jungbluth, Emiley A. Eloe-Fadrosh, Ramunas Stepanauskas, Tanja Woyke, Michael S. Rappé, Beth N. Orcutt*
*C-DEBI Contribution 451

The exploration of Earth’s terrestrial subsurface biosphere has led to the discovery of several new archaeal lineages of evolutionary significance. Similarly, the deep subseafloor crustal biosphere also harbors many unique, uncultured archaeal taxa, including those belonging to Candidatus Hydrothermarchaeota, formerly known as Marine Benthic Group-E. Recently, Hydrothermarchaeota was identified as an abundant lineage of Juan de Fuca Ridge flank crustal fluids, suggesting its adaptation to this extreme environment. Through the investigation of single-cell and metagenome-assembled genomes, we provide insight into the lineage’s evolutionary history and metabolic potential. Phylogenomic analysis reveals the Hydrothermarchaeota to be an early-branching archaeal phylum, branching between the superphylum DPANN, Euryarchaeota, and Asgard lineages. Hydrothermarchaeota genomes suggest a potential for dissimilative and assimilative carbon monoxide oxidation (carboxydotrophy), as well as sulfate and nitrate reduction. There is also a prevalence of chemotaxis and motility genes, indicating adaptive strategies for this nutrient-limited fluid-rock environment. These findings provide the first genomic interpretations of the Hydrothermarchaeota phylum and highlight the anoxic, hot, deep marine crustal biosphere as an important habitat for understanding the evolution of early life.

Microbiology Resource Announcements
Draft Genome Sequences of Penicillium spp. from Deeply Buried Oligotrophic Marine Sediments - NEW!
Morgan S. Sobol, Tatsuhiko Hoshino, Taiki Futagami, Fumio Inagaki, Brandi Kiel Reese*
*C-DEBI Contribution 458

Here, we report genome sequences of two Penicillium isolates from below the seafloor of the oligotrophic South Pacific Gyre. These genomes are the first reported for fungi from deeply buried marine sediment. Both genomes will provide valuable information regarding the role of fungi and carbon cycling in the energy-limited subsurface biosphere.

The kinetics of siderophore-mediated olivine dissolution - NEW!
Mark A. Torres*, Sijia Dong, Kenneth H. Nealson, A. Joshua West
*C-DEBI Contribution 460

Silicate minerals represent an important reservoir of nutrients at Earth's surface and a source of alkalinity that modulates long‐term geochemical cycles. Due to the slow kinetics of primary silicate mineral dissolution and the potential for nutrient immobilization by secondary mineral precipitation, the bioavailability of many silicate‐bound nutrients may be limited by the ability of micro‐organisms to actively scavenge these nutrients via redox alteration and/or organic ligand production. In this study, we use targeted laboratory experiments with olivine and the siderophore deferoxamine B to explore how microbial ligands affect nutrient (Fe) release and the overall rate of mineral dissolution. Our results show that olivine dissolution rates are accelerated in the presence of micromolar concentrations of deferoxamine B. Based on the non‐linear decrease in rates with time and formation of a Fe3+‐ligand complex, we attribute this acceleration in dissolution rates to the removal of an oxidized surface coating that forms during the dissolution of olivine at circum‐neutral pH in the presence of O2 and the absence of organic ligands. While increases in dissolution rates are observed with micromolar concentrations of siderophores, it remains unclear whether such conditions could be realized in natural environments due to the strong physiological control on microbial siderophore production. So, to contextualize our experimental results, we also developed a feedback model, which considers how microbial physiology and ligand‐promoted mineral dissolution kinetics interact to control the extent of biotic enhancement of dissolution rates expected for different environments. The model predicts that physiological feedbacks severely limit the extent to which dissolution rates may be enhanced by microbial activity, though the rate of physical transport modulates this limitation.

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!

Scientific American's "The Artful Amoeba" Blog: Inside Earth, Microbes Approach Immortality - NEW!
Earth’s crust appears to be simply lousy with idling, ancient bacteria parked in power-save mode, ready at nearly a moment’s notice to throw the gearshift into drive. But what a life! Eons spent entombed in a dark, airless, silent matrix, barely eating, barely breathing, barely moving, barely living. But not dead. Not dead. Featuring the modeling study from C-DEBI Contribution 438 (Bradley et al., 2018 in Geobiology).


Meetings & Activities

UofSC: 6th Annual Southeastern Biogeochemistry Symposium, March 30, 2019
The submission deadline for presenters is February 15, 2019. General registration will remain open through March 16, 2019.

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
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
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

American Museum of Natural History (NYC): The Layers of the Ocean (Milstein Science Series), this Sunday, February 17, 11am to 4pm - NEW!
Enjoy a day under the blue whale exploring the five “zones” of the oceans, where a diverse array of marine species and ecosystems can be found at different depths. Find out how temperatures, salinity, and the amount of sunlight changes from zone to zone. Plus, learn how some species can only survive in the oceans’ sunlit uppermost layer, while others must dive deep to find food. The Milstein Science: Layers of the Ocean program includes a 45-foot inflated replica of the JOIDES Resolution from the C-DEBI-supported, travelling, pop-up outreach, In Search of Earth’s Secrets.

C-DEBI: Next Professional Development Webinar: February 27, 12pm PST
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.

RGNO 2019 in Namibia: Biogeochemical Oceanography in Upwelling Ecosystems - NEW!
We are pleased to announce the 6th course of the Regional Graduate Network in Oceanography (RGNO), a SCOR-supported cooperative Research and Capacity Building Initiative in southern Africa. The course will again be hosted by the University of Namibia’s Sam Nujoma Marine Research Center in Henties Bay and Namibia’s National Marine Information and Research Center in Swakopmund, and take place between April 28 and May 24, 2019. The RGNO is a research-driven, intense learning experience in the biogeosciences of the Benguela Current Ecosystem (BCE), a particularly interesting ocean habitat. Participation is most valuable for people who are actively involved in an ongoing research project to which the course topics can contribute and who would like to apply their skills to a better understanding of the BCE. Applications are due March 10, 2019.

C-DEBI: Community College Research Internship for Scientific Engagement (CC-RISE) - NEW!
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 Woods Hole Oceanographic Institution 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 are due March 29, 2019.

IODP-USSSP: U.S. Travel Support for Petrophysics Summer School - NEW!
The 2019 Petrophysics Summer School will provide a unique workshop that will bring together experts from both academia and industry to give training in the theory and practice of petrophysics and, notably its applications across both IODP and industry. It will include lectures, discussion groups, and practical exercises on the different elements and data types used in petrophysical analysis. In addition, basic training in an industry-standard software package, Schlumberger’s Techlog, will form a core part of the school. The European Petrophysics Consortium and its collaborators offer this unique training opportunity for a summer school through the provision of technical and scientific expertise in the fields of downhole logging and core petrophysics. The course is open to applicants from the international community, but applications from early career researchers (including PhD students) are particularly encouraged. U.S.-affiliated students and researchers may apply for partial travel support through the U.S. Science Support Program. The deadline to apply for travel support and for the course is April 22, 2019.

IODP-USSSP: Apply to host an Ocean Discovery Lecturer - NEW!
For over 20 years, the Ocean Discovery Lecture Series (formerly the Distinguished Lecturer Series) has brought the remarkable scientific results and discoveries of the International Ocean Discovery Program and its predecessor programs to academic research institutions, museums, and aquaria. Since 1991, over 1,000 presentations to diverse audiences have been made through the Lecture Series. 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. The topics of their lectures range widely, and include monsoon history, ice sheet dynamics, sediment diagenesis, and more. Open to any U.S. college, university, or nonprofit organization. Application deadline to host an Ocean Discovery Lecturer: May 17, 2019.


Proposal Calls

Frontier Research in Earth Sciences (FRES)
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
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: 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) - NEW!
This solicitation invites proposals for the creation of international networks of networks in research areas aligned either with one of the NSF Big Ideas or a community-identified scientific challenge with international dimensions. AccelNet awards are meant to support the connections among research networks, rather than supporting fundamental research as the primary activity.  Each network of networks is expected to engage in innovative collaborative activities that promote synergy of efforts across the networks and provide professional development for students, postdoctoral scholars, and early-career researchers. There are two proposal categories covered by this solicitation: Catalytic and Full-Scale Implementation. 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:




MBL: Faculty Position in Evolutionary Genomics and Molecular Evolution
For full consideration applications should be submitted by March 1, 2019.

MSU: Assistant/Associate Professor of Environmental Microbiology

Princeton University: Assistant Professor

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

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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