C-DEBI Newsletter – September 1, 2017
This newsletter is also accessible via our website.

Message from the Director:

Hope you are having a good start to your semester - we especially wish the same to C-DEBIers who we know have started new positions: Rika Anderson (Assistant Professor at Carleton College), Stephanie Carr (Assistant Professor at Hartwick College), Kat Dawson (Assistant Professor at Rutgers University), Caroline Fortunato (Assistant Professor at Wilkes University), Anna Kaster (Professor at Karlsruhe Institute of Technology), Ileana Perez-Rodriguez (Assistant Professor at the University of Pennsylvania), Mark Torres (Assistant Professor at Rice University), and Senior Scientist Steve Finkel (College Dean of Graduate and Professional Education at the University of Southern California).


Jan Amend
C-DEBI Director



The ISME Journal
Physiological and ecological implications of an iron- or hydrogen-oxidizing member of the Zetaproteobacteria, Ghiorsea bivora, gen. nov., sp. nov. NEW!
Jiro. F. Mori, Jarrod. J. Scott, Kevin W. Hager, Craig L. Moyer, Kirsten Küsel, David Emerson*
*C-DEBI Contribution 379

Chemosynthetic Fe-oxidizing communities are common at diffuse-flow hydrothermal vents throughout the world’s oceans. The foundational members of these communities are the Zetaproteobacteria, a class of Proteobacteria that is primarily associated with ecosystems fueled by ferrous iron, Fe(II). We report here the discovery of two new isolates of Zetaproteobacteria isolated from the Mid-Atlantic Ridge (TAG-1), and the Mariana back-arc (SV-108), that are unique in that they can utilize either Fe(II) or molecular hydrogen (H2) as sole electron donor and oxygen as terminal electron acceptor for growth. Both strains precipitated Fe-oxyhydroxides as amorphous particulates. The cell doubling time on H2 vs Fe(II) for TAG-1 was 14.1 vs 21.8 h, and for SV-108 it was 16.3 vs 20 h, and it appeared both strains could use either H2 or Fe(II) simultaneously. The strains were close relatives, based on genomic analysis, and both possessed genes for the uptake NiFe-hydrogenase required for growth on H2. These two strains belong to Zetaproteobacteria operational taxonomic unit 9 (ZetaOTU9). A meta-analysis of public databases found ZetaOTU9 was only associated with Fe(II)-rich habitats, and not in other environments where known H2-oxidizers exist. These results expand the metabolic repertoire of the Zetaproteobacteria, yet confirm that Fe(II) metabolism is the primary driver of their physiology and ecology.

Environmental Microbiology Reports
Thriving or Surviving? Evaluating active microbial guilds in Baltic Sea sediment NEW!
Laura A. Zinke*, Megan M. Mullis, Jordan T. Bird, Ian P.G. Marshall, Bo Barker Jørgensen, Karen G. Lloyd, Jan P. Amend*, Brandi Kiel Reese
*C-DEBI Contribution 380

Microbial life in the deep subsurface biosphere is taxonomically and metabolically diverse, but it is vigorously debated whether the resident organisms are thriving (metabolizing, maintaining cellular integrity, and expressing division genes) or just surviving. As part of Integrated Ocean Drilling Program (IODP) Expedition 347: Baltic Sea Paleoenvironment, we extracted and sequenced RNA from organic carbon-rich, nutrient-replete, and permanently anoxic sediment. In stark contrast to the oligotrophic subsurface biosphere, Baltic Sea Basin samples provided a unique opportunity to understand the balance between metabolism and other cellular processes. Targeted sequencing of 16S rRNA transcripts showed Atribacteria (an uncultured phylum) and Chloroflexi to be among the dominant and the active members of the community. Metatranscriptomic analysis identified methane cycling, sulfur cycling, and halogenated compound utilization as active in situ respiratory metabolisms. Genes for cellular maintenance, cellular division, motility, and antimicrobial production were also transcribed. This indicates that microbial life in deep subsurface Baltic Sea Basin sediments was not only alive, but thriving.


Meetings & Activities

AGU: 2018 Ocean Sciences Meeting Deep Biosphere-related Sessions
Abstracts due: September 6, 2017.

C-DEBI: Networked Speaker Series: Next Thursday, September 7, 12:30pm PT
Dr. Gustavo Ramírez (University of Rhode Island) will give the next Networked Speaker Series Seminar on "Microbial Neter-Khertet: Life and death post-entombment."

C-DEBI: Group Page
To help preserve deep biosphere methods for use in future projects, the Center strongly encourages you to describe your lab and software-based methods using, and to link them to our group page at The website provides an easy-to-use platform to share reproducible, step-by-step scientific methods. 

C-DEBI: Rolling call for Community Workshop support
The NSF Science and Technology Center for Dark Energy Biosphere Investigations (C-DEBI) invites proposals for $15,000 on average (and up to $20,000) in direct funds for community workshops that will help to advance C-DEBI’s central research agenda: to investigate the subseafloor biosphere deep in marine sediment and oceanic crust, and to conduct multi-disciplinary studies to develop an integrated understanding of subseafloor microbial life at the molecular, cellular, and ecosystem scales.


Education & Outreach

C-DEBI: Professional Development Webinar Now Online NEW!
Missed the last webinar on “How to Negotiate in Academia” with Karen G. Lloyd (University of Tennessee), covering why negotiation is essential, tips for how to do so successfully and what to expect from post-doc and assistant professorship job negotiations? Watch it on YouTube.

Proposal Calls

IODP: Apply to Sail on IODP Expedition 378
The deadline to apply is September 15, 2017.

IODP: Apply to Sail: Expedition 379: Amundsen Sea West Antarctic Ice Sheet History NEW!
The West Antarctic Ice Sheet (WAIS) is largely marine-based, highly sensitive to climatic and oceanographic changes, has had a dynamic history over the last several million years, and if completely melted, could result in a global sea-level rise of 3.3-4.3 m. Expedition 379 will obtain records from the continental shelf and rise of the Amundsen Sea to document WAIS dynamics in an area unaffected by other ice sheets as well and that currently experiences the largest ice loss in Antarctica. The primary objectives include (a) reconstructing the Paleogene to Holocene glacial history of West Antarctica, (b) correlating the Amundsen Sea WAIS-proximal records with global records of ice volume changes and air/seawater temperature proxy records, (c) constraining the relationship between incursions of warm water masses onto the continental shelf and the stability of marine-based ice sheet margins, and (d) reconstructing major WAIS advances onto the middle and outer shelf, including the first ice sheet expansion onto the continental shelf of the Amundsen Sea Embayment and its possible control by the uplift of Marie Byrd Land. U.S.-affiliated scientists interested in participating in these expeditions should apply to sail through the U.S. Science Support Program – visit. The deadline to apply is October 15, 2017.

IODP: Apply to Sail: Expedition 382: Iceberg Alley Paleoceanography and South Falkland Slope Drift NEW!
Expedition 382 aims to recover 600 m long Late Neogene sedimentary sequences from the Scotia Sea to reconstruct past variability in Antarctic Ice Sheet (AIS) mass loss, oceanic and atmospheric circulation and to provide the first spatially integrated record of variability in iceberg flux from Iceberg Alley, where a substantial number of Antarctic icebergs exit into the warmer Antarctic Circumpolar Current (ACC). This will (a) constrain iceberg flux during key times of AIS evolution since the Middle Miocene glacial intensification of the East Antarctic Ice Sheet, (b) provide material to determine regional sources of AIS mass loss, address interhemispheric phasing of ice-sheet and climate events, and the relation of AIS variability to sea level, (c) provide information on Drake Passage throughflow, meridional overturning in the Southern Ocean, water-mass changes, CO2 transfer via wind-induced upwelling, sea-ice variability, bottom water outflow from the Weddell Sea, Antarctic weathering inputs, and changes in oceanic and atmospheric fronts in the vicinity of the ACC, and (d) provide dust proxy records to reconstruct changes in the Southern Hemisphere westerlies to evaluate climate-dust coupling since the Pliocene, its potential role in iron fertilization and atmospheric CO2 drawdown during glacials. Expedition 382 will also core a sediment drift on the Falkland slope to obtain subantarctic multi-proxy intermediate water depth records of millennial to orbital scale variability in the ocean, atmosphere, nutrients, productivity and ice-sheet dynamics in the SW Atlantic through at least the last 1 Ma. The deadline to apply is October 15, 2017.

NSF: National Oceanographic Partnership Program announcement regarding Ocean Sensors, Cubesats, and GHRSST Data
Letters of Intent are required by October, 16 2017.

NSF: Earth Sciences Postdoctoral Fellowships (EAR-PF)
Full Proposal Deadline: October 25, 2017.

NSF: Innovations in Graduate Education (IGE) Program
Full Proposal Deadline: October 25, 2017.

NSF: Management and Operation of the Ocean Bottom Seismometer Instrument Center (OBSIC)
Full Proposal Deadline: October 25, 2017.

The Hertz Foundation: Graduate Fellowship Award NEW!
The Hertz Graduate Fellowship Award is based on merit (not need) and consists of a cost-of-education allowance and a personal-support stipend. The cost-of-education allowance is accepted by all of the participating schools in lieu of all fees and tuition. Hertz Fellows therefore have no liability for any ordinary educational costs, regardless of their choice among participating schools. In addition to providing the necessary funding along with the research freedom to pursue their PhD, we also provide mentorship and counsel through the lifelong community of peers to which they now belong—the Hertz Community. This Community is comprised of current in-school Fellows who are pursuing their graduate degree, as well as the entire group of alumni Fellows (now totaling over 1,200). When Hertz Fellows complete graduate school, we intend that they do so armed with more than their degree, research experience, and colleagues from that university, but also with a set of collaborators across disciplines, geography, and generations, all ready to help them succeed throughout their careers. Application deadline: October 27, 2017.

UNOLS: Cruise Opportunities on R/V Sally Ride NEW!
The primary goal of the UNOLS Cruise Opportunity Program is to provide graduate students currently completing a degree in a field of oceanographic research with the opportunity to participate in a research cruise. The participant will be a member of the scientific party and be involved in data collection and all other activities at sea. It is envisioned that the graduate student will be familiar with the science to be conducted at sea, and thus, form new collaborations and potentially develop new research directions. To be eligible to participate in this program, the graduate student must currently be studying at a U.S.-based institution and have either a U.S. Passport or a U.S. Work Visa. Please note that at this time the UNOLS Office is unable to provide travel funds; your advisor or institution may have some ideas. Fall 2017 cruise: The cruise has two legs: Sep 25 – Oct 11 and Oct 11 – Oct 26 – applications will be accepted until full. Spring 2018 cruise: Applications for a cruise April 20 – May 22, 2018 are due December 1, 2017.

IODP-USSSP: Proposals for Pre-Drilling Activities and Workshops
The U.S. Science Support Program (USSSP) accepts proposals on a rolling basis for pre-drilling activities and semi-annually for workshops, related to the International Ocean Discovery Program (IODP). Next workshop submission deadline: December 1, 2017.

NSF: Using JOIDES Resolution to Collect Cores with Advanced Piston Coring (APC) System

DCO: Deep Life Cultivation Internship Program

NSF: Arctic Sciences Program Solicitation
Proposals accepted anytime.

NSF: Tribal Colleges and Universities Program (TCUP) Program Solicitation
Preparing for TCUP Implementation proposals accepted anytime.

C-DEBI: Rolling call for Research Exchange proposals



Oklahoma State University: Assistant Professor Position in Paleontology/Sedimentary Geology
Screening of candidates will begin on September 15, 2017 and will continue until the position is filled.

University of Delaware: Postdoctoral Researcher 
The position will be open until filled and applications are being reviewed starting August 28, 2017.

Bigelow: Postdoctoral Research Scientist – Viral Control of Microbial Communities in Antarctic Lakes
Review of applicants will begin immediately and proceed until the position is filled.

WHOI: Two Postdoctoral Investigator Positions

Bigelow: Postdoctoral Scientist in Horizontal Gene Transfer in Marine Bacterioplankton

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

Exploring life beneath the seafloor and making transformative discoveries that advance science, benefit society, and inspire people of all ages and origins.

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