C-DEBI Newsletter – September 16, 2019
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Publications & Press

Electrochimica Acta
An electrochemical investigation of interfacial electron uptake by the sulfur oxidizing bacterium Thioclava electrotropha ElOx9 - NEW!
Amruta A. Karbelkar, Annette R. Rowe*, Mohamed Y. El-Naggar
*C-DEBI Contribution 493

Extracellular electron transfer (EET) allows microbes to acquire energy from solid state electron acceptors and donors, such as environmental minerals. This process can also be harnessed at electrode interfaces in bioelectrochemical technologies including microbial fuel cells, microbial electrosynthesis, bioremediation, and wastewater treatment. Improving the performance of these technologies will benefit from a better fundamental understanding of EET in diverse microbial systems. While the mechanisms of outward (i.e. microbe-to-anode) EET is relatively well characterized, specifically in a few metal-reducing bacteria, the reverse process of inward EET from redox-active minerals or cathodes to bacteria remains poorly understood. This knowledge gap stems, at least partly, from the lack of well-established model organisms and general difficulties associated with laboratory studies in existing model systems. Recently, a sulfur oxidizing marine microbe, Thioclava electrotropha ElOx9, was demonstrated to perform electron uptake from cathodes. However, a detailed analysis of the electron uptake pathways has yet to be established, and electrochemical characterization has been limited to aerobic conditions. Here, we report a detailed amperometric and voltammetric characterization of ElOx9 cells coupling cathodic electron uptake to reduction of nitrate as the sole electron acceptor, even in the absence of any added inorganic carbon source. By comparing this cellular activity to spent media controls and using medium exchange experiments, we demonstrate that one of the pathways by which ElOx9 facilitates inward EET is by a direct-contact mechanism through a redox center with a formal potential of −94 mV vs SHE, rather than soluble intermediate electron carriers. In addition to the implications for understanding microbial sulfur oxidation in marine environments, this study highlights the potential for ElOx9 to serve as a convenient and readily culturable model organism for understanding the molecular mechanisms of inward EET.

Frontiers in Microbiology
Hydrostatic Pressure Helps to Cultivate an Original Anaerobic Bacterium From the Atlantis Massif Subseafloor (IODP Expedition 357): Petrocella atlantisensis gen. nov. sp.nov. - NEW!
Marianne Quéméneur, Gaël Erauso, Eléonore Frouin, Emna Zeghal, Céline Vandecasteele, Bernard Ollivier, Christian Tamburini, Marc Garel, Bénédicte Ménez and Anne Postec


Rock-hosted subseafloor habitats are very challenging for life, and current knowledge about microorganisms inhabiting such lithic environments is still limited. This study explored the cultivable microbial diversity in anaerobic enrichment cultures from cores recovered during the International Ocean Discovery Program (IODP) Expedition 357 from the Atlantis Massif (Mid-Atlantic Ridge, 30°N). 16S rRNA gene survey of enrichment cultures grown at 10–25°C and pH 8.5 showed that Firmicutes and Proteobacteria were generally dominant. However, cultivable microbial diversity significantly differed depending on incubation at atmospheric pressure (0.1 MPa), or hydrostatic pressures (HP) mimicking the in situ pressure conditions (8.2 or 14.0 MPa). An original, strictly anaerobic bacterium designated 70B-AT was isolated from core M0070C-3R1 (1150 meter below sea level; 3.5 m below seafloor) only from cultures performed at 14.0 MPa. This strain named Petrocella atlantisensis is a novel species of a new genus within the newly described family Vallitaleaceae (order Clostridiales, phylum Firmicutes). It is a mesophilic, moderately halotolerant and piezophilic chemoorganotroph, able to grow by fermentation of carbohydrates and proteinaceous compounds. Its 3.5 Mb genome contains numerous genes for ABC transporters of sugars and amino acids, and pathways for fermentation of mono- and di-saccharides and amino acids were identified. Genes encoding multimeric [FeFe] hydrogenases and a Rnf complex form the basis to explain hydrogen and energy production in strain 70B-AT. This study outlines the importance of using hydrostatic pressure in culture experiments for isolation and characterization of autochthonous piezophilic microorganisms from subseafloor rocks.

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

Networked Speaker Series Seminar, Thursday, October 3, 2019, 12:30pm PDT - NEW!
With Dr. Jessica Labonté, Texas A&M Galveston on “You are what you eat: a geochemical and microbial study of a 3000-year old stratigraphic sediment succession.” Abstract: Microbes make up the majority of the biomass in sediment, where they play a role in cycling organic carbon and regulate the fluctuation of organic matter. In anoxic sediment, the relationships between geochemical gradients, genomic potential, and virus-host interactions remain understudied and poorly understood. I will present the results of our study of stratified sediments from anoxic sinkhole (Blackwood Sinkhole, Bahamas), where we analyzed the pore water chemistry analysis (nutrients, carbon, nitrogen), microbial community composition (16S rRNA gebe and metagenomics), and virus-host interactions. Through the characterization of the relationships of microbes between each other and with their environment, we aim to identify the role organic and inorganic matter availability plays in shaping viral and prokaryotic communities, as well as how microbial communities shape their environment.

Missed the last seminar with Taylor Royalty on “Quantitatively partitioning microbial genomic traits among taxonomic ranks: implications for subsurface microbial communities?” Watch it on YouTube.

UNOLS: Deep Submergence Science Committee (DeSSC) Call for Nominations
Applications due September 13, 2019.

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

IODP-USSSP: Workshop on Demystifying the IODP Proposal Process for Early Career Scientists, February 17-20, 2020 - NEW!
Scientific ocean drilling is central to the study of Earth’s climate history, tectonic evolution, geohazards, and deep biosphere. In an effort to foster a larger, more dynamic, and more diverse ocean drilling community, we encourage early career researchers to apply to this workshop, Demystifying the IODP Proposal Process for Early Career Scientists: Pacific Ocean. The workshop will begin with a series of speakers explaining the structure of IODP and how early career scientists can become involved in IODP activities, from sailing to expedition proposals. Then, workshop participants will work on the initial stages of developing real drilling proposals in the Pacific Ocean, where the JOIDES Resolution is expected to be operating beginning in 2023-2024. We aim to attract a diverse array of specialists (in geophysics, paleoceanography, deep biosphere, tectonics, etc.) to facilitate interdisciplinary collaborations. Workshop participation support is available from the U.S. Science Support Program for IODP, for a limited number of graduate students and early career researchers (i.e., those who have completed their PhD within the past 10 years) from U.S. institutions and organizations. The deadline to submit an application is October 18, 2019.

Ongoing Activities:


Proposal Calls

International Research Experiences for Students (IRES)
Full Proposal Deadlines: September 10, 2019 (Track I), September 17, 2019 (Track II) and September 24, 2019 (Track III).

Moore Foundation / Simons Foundation: Origin of the Eukaryotic Cell
The deadline for submitting a proposal is September 30, 2019.

IODP: Submit an IODP drilling proposal - NEW!
The International Ocean Discovery Program (IODP) explores Earth’s climate history, structure, mantle/crust dynamics, natural hazards, and deep biosphere as described in the IODP Science Plan Illuminating Earth’s Past, Present, and Future. IODP facilitates international and interdisciplinary research on transformative and societally relevant topics using the ocean drilling, coring, and downhole measurement facilities JOIDES Resolution (JR), Chikyu, and Mission Specific Platforms (MSP). Proposals are being actively sought for all three facilities. The JR is currently scheduled into the beginning 2022. Due to the recent facility renewal, we plan to schedule JR expeditions through the end of 2024. The JR is expected to operate in the Equatorial and North Atlantic, Gulf of Mexico, Mediterranean, Caribbean, and the Arctic in 2021 and 2022, and to complete its circumnavigation with a return to the east Pacific region by 2023, the western Pacific by 2023-2024, and potentially the Indian Ocean by the end of 2024. Proposals for these future operational areas are now needed. MSP expeditions are planned to operate once every other year to recover core from targets that are inaccessible by the other facilities (e.g., shallow water, enclosed seas, inland seas). MSP proposals for any ocean are welcomed. Completely new Chikyu riser proposals (other than CPPs) will not be accepted until after publication of a new post-2023 science plan. We also invite proposals that involve drilling on land and at sea through coordination with the International Continental Drilling Program (ICDP). Investigators are reminded that the interval from the first proposal submission to expedition scheduling is on the order of 4-5 years due to the science and safety review process and required lead time for scheduling, and that adequate site characterization / site survey data are critical for success. Next submission deadline: October 1, 2019.

IODP: Apply to Sail on IODP Expedition 391: Walvis Ridge Hotspot
The deadline to apply to sail is October 1, 2019.

WHOI: Postdoctoral Scholarships for 2020-2021postposts
Completed applications must be received by October 15, 2019.

NSF: Graduate Research Fellowship Program (GRFP)
Application deadlines October 21-25, 2019 and October 19-23, 2020.

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

NASA: Postdoctoral Program Opportunities
Please contact C-DEBI Senior Scientist Beth Orcutt ( and Associate Director Julie Huber ( to discuss your interest studying the marine deep biosphere as an analog for life on ocean worlds. Fellowship applications due Nov 1, 2019.

NSF: Postdoctoral Research Fellowships in Biology (PRFB)
Proposal deadline November 19, 2019.

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

NSF: Dear Colleague Letter: An Update to the Approach for the Provision of Marine Seismic Capabilities for the U.S. Research Community - NEW!
This Dear Colleague Letter provides updated information regarding the National Science Foundation’s (NSF) Division of Ocean Sciences (OCE) support of the marine seismic community need for long-term sustainable access to seismic data collection capability.

Rolling Calls:



WWU: Assistant Professor in Marine Molecular Biology - NEW!
The Biology Department and the Marine and Coastal Science (MACS) program at Western Washington University (WWU) invite applications for a tenure-track, assistant professor position in MARINE MOLECULAR BIOLOGY, beginning FALL 2020. As one of the initial faculty hires into the MACS program, the successful applicant will foster an interdisciplinary approach to teaching and research in marine and coastal science. We seek an individual who is enthusiastic about teaching and who will establish a vigorous research program, focused on testing biological questions in marine biological systems using molecular approaches, that involves undergraduate and Masters-level students. A primary teaching responsibility in Biology will be introductory molecular and cellular biology for majors. Additional teaching responsibilities in Biology could include advanced courses in molecular biology, genetics, cellular biology, and/or bioinformatics/computational biology/’omics. Application review begins October 8, 2019; position is open until filled.

MSU: Postdoctoral Positions in the Department of Microbiology & Immunology

MBL: Computational Postdoctoral Scientist

DRI: Postdoctoral Fellow, Microbial Ecology: Genomes to Phenomes

UH Manoa: Assistant Researcher (Theoretical Ecologist)

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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