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

Message from the Director:
In tribute to the late Dr. Katrina J. Edwards, who pioneered C-DEBI and the study of microbes that “rust the crust”, a special issue of twenty-two papers, Recent Advances in Geomicrobiology of the Ocean Crust, has been published in Frontiers in Microbiology. Editors Beth Orcutt, Jason Sylvan and Cara Santelli are just a few of the many in our community inspired by her achievements in the exploration of the deep biosphere.
And a round of hearty congratulations to our C-DEBI-ers at (or formerly at) the University of Delaware: Dr. Jen Biddle, Dr. Rosa Leon Zayas and Christopher Petrone. Jen Biddle and her co-investigators have been awarded a prestigious $1 million grant from the W.M. Keck Foundation to explore how environmental factors may affect the genetics of microbes. Rosa Leon Zayas, a former C-DEBI postdoctoral fellow, begins her tenure track position at Willamette University in the Department of Biology this fall. And Chris Petrone’s C-DEBI education grant Project VIDEO, developed with Lisa Tossey, Jen Biddle and Rosa Leon Zayas, has won two national awards for audiovisual communications and electronic media. Congratulations to all of you and the C-DEBIers who contributed to the guest 15 Second Science spots!

Jan Amend
C-DEBI Director



Scientific Reports
Climate oscillations reflected within the microbiome of Arabian Sea sediments NEW!
William D. Orsi*, Marco J. L. Coolen, Cornelia Wuchter, Lijun He, Kuldeep. D. More, Xabier Irigoien, Guillem Chust, Carl Johnson, Jordon. D. Hemingway, Mitchell Lee, Valier Galy, Liviu Giosan
*C-DEBI Contribution 358

Selection of microorganisms in marine sediment is shaped by energy-yielding electron acceptors for respiration that are depleted in vertical succession. However, some taxa have been reported to reflect past depositional conditions suggesting they have experienced weak selection after burial. In sediments underlying the Arabian Sea oxygen minimum zone (OMZ), we performed the first metagenomic profiling of sedimentary DNA at centennial-scale resolution in the context of a multi-proxy paleoclimate reconstruction. While vertical distributions of sulfate reducing bacteria and methanogens indicate energy-based selection typical of anoxic marine sediments, 5–15% of taxa per sample exhibit depth-independent stratigraphies indicative of paleoenvironmental selection over relatively short geological timescales. Despite being vertically separated, indicator taxa deposited under OMZ conditions were more similar to one another than those deposited in bioturbated intervals under intervening higher oxygen. The genomic potential for denitrification also correlated with palaeo-OMZ proxies, independent of sediment depth and available nitrate and nitrite. However, metagenomes revealed mixed acid and Entner-Dourdoroff fermentation pathways encoded by many of the same denitrifier groups. Fermentation thus may explain the subsistence of these facultatively anaerobic microbes whose stratigraphy follows changing paleoceanographic conditions. At least for certain taxa, our analysis provides evidence of their paleoenvironmental selection over the last glacial-interglacial cycle.

Nature Geoscience
Microbial oxidation as a methane sink beneath the West Antarctic Ice Sheet NEW!
Alexander B. Michaud*, John E. Dore, Amanda M. Achberger, Brent C. Christner, Andrew C. Mitchell, Mark L. Skidmore, Trista J. Vick-Majors & John C. Priscu
*C-DEBI Contribution 371

Aquatic habitats beneath ice masses contain active microbial ecosystems capable of cycling important greenhouse gases, such as methane (CH4). A large methane reservoir is thought to exist beneath the West Antarctic Ice Sheet, but its quantity, source and ultimate fate are poorly understood. For instance, O2 supplied by basal melting should result in conditions favourable for aerobic methane oxidation. Here we use measurements of methane concentrations and stable isotope compositions along with genomic analyses to assess the sources and cycling of methane in Subglacial Lake Whillans (SLW) in West Antarctica. We show that sub-ice-sheet methane is produced through the biological reduction of CO2 using H2. This methane pool is subsequently consumed by aerobic, bacterial methane oxidation at the SLW sediment–water interface. Bacterial oxidation consumes >99% of the methane and represents a significant methane sink, and source of biomass carbon and metabolic energy to the surficial SLW sediments. We conclude that aerobic methanotrophy may mitigate the release of methane to the atmosphere upon subglacial water drainage to ice sheet margins and during periods of deglaciation.

Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea NEW!
Connor T. Skennerton, Karuna Chourey, Ramsunder Iyer, Robert L. Hettich, Gene W. Tyson, Victoria J. Orphan*
*C-DEBI Contribution 374

The anaerobic oxidation of methane by anaerobic methanotrophic (ANME) archaea in syntrophic partnership with deltaproteobacterial sulfate-reducing bacteria (SRB) is the primary mechanism for methane removal in ocean sediments. The mechanism of their syntrophy has been the subject of much research as traditional intermediate compounds, such as hydrogen and formate, failed to decouple the partners. Recent findings have indicated the potential for extracellular electron transfer from ANME archaea to SRB, though it is unclear how extracellular electrons are integrated into the metabolism of the SRB partner. We used metagenomics to reconstruct eight genomes from the globally distributed SEEP-SRB1 clade of ANME partner bacteria to determine what genomic features are required for syntrophy. The SEEP-SRB1 genomes contain large multiheme cytochromes that were not found in previously described free-living SRB and also lack periplasmic hydrogenases that may prevent an independent lifestyle without an extracellular source of electrons from ANME archaea. Metaproteomics revealed the expression of these cytochromes at in situ methane seep sediments from three sites along the Pacific coast of the United States. Phylogenetic analysis showed that these cytochromes appear to have been horizontally transferred from metal-respiring members of the Deltaproteobacteria such as Geobacter and may allow these syntrophic SRB to accept extracellular electrons in place of other chemical/organic electron donors.

Frontiers in Microbiology
Editorial: Recent Advances in Geomicrobiology of the Ocean Crust NEW!
Beth N. Orcutt*, Jason B. Sylvan, Cara. M. Santelli
*C-DEBI Contribution 375

Editorial on the Research Topic Recent Advances in Geomicrobiology of the Ocean Crust: Igneous oceanic crust is one of the largest potential habitats for life on earth (Orcutt et al., 2011), and microbial activity supported by rock-water-microbe reactions in this environment can impact global biogeochemical cycles (Bach and Edwards, 2003). However, our understanding of the microbiology of this system, especially the subsurface “deep biosphere” component of it, has traditionally been limited by sample availability and quality. Over the past decade, several major international programs (such as the Center for Dark Energy Biosphere Investigations, the current International Ocean Discovery Program, and its predecessor Integrated Ocean Drilling Program, and the Deep Carbon Observatory) have focused on advancing our understanding of life in this cryptic, yet globally relevant, biosphere. Additionally, many field and laboratory research programs are examining hydrothermal vent systems—a seafloor expression of seawater that has been thermally and chemically altered in subseafloor crust—and the microbial communities supported by these mineral-rich fluids. The papers in this special issue bring together recent discoveries of microbial presence, diversity, and activity in these dynamic ocean environments.

Scientific Drilling
IODP workshop: developing scientific drilling proposals for the Argentina Passive Volcanic Continental Margin (APVCM) – basin evolution, deep biosphere, hydrates, sediment dynamics and ocean evolution NEW!
Roger D. Flood , Roberto A. Violante , Thomas Gorgas , Ernesto Schwarz , Jens Grützner , Gabriele Uenzelmann-Neben , F. Javier Hernández-Molina , Jennifer Biddle, Guillaume St-Onge, and APVCM workshop participants

The Argentine margin contains important sedimentological, paleontological and chemical records of regional and local tectonic evolution, sea level, climate evolution and ocean circulation since the opening of the South Atlantic in the Late Jurassic–Early Cretaceous as well as the present-day results of post-depositional chemical and biological alteration. Despite its important location, which underlies the exchange of southern- and northern-sourced water masses, the Argentine margin has not been investigated in detail using scientific drilling techniques, perhaps because the margin has the reputation of being erosional. However, a number of papers published since 2009 have reported new high-resolution and/or multichannel seismic surveys, often combined with multi-beam bathymetric data, which show the common occurrence of layered sediments and prominent sediment drifts on the Argentine and adjacent Uruguayan margins. There has also been significant progress in studying the climatic records in surficial and near-surface sediments recovered in sediment cores from the Argentine margin. Encouraged by these recent results, our 3.5-day IODP (International Ocean Discovery Program) workshop in Buenos Aires (8–11 September 2015) focused on opportunities for scientific drilling on the Atlantic margin of Argentina, which lies beneath a key portion of the global ocean conveyor belt of thermohaline circulation. Significant opportunities exist to study the tectonic evolution, paleoceanography and stratigraphy, sedimentology, and biosphere and geochemistry of this margin.

Delaware SeaGrant Reporter
Multimedia resources explore microbes, deep biosphere NEW!

The average human adult contains 10 trillion human cells but has 100 trillion microbes on their skin, hair, and mouth and in their intestines. Microbes protect us from harmful bacteria, help us digest food, even help change our mood. Microbes are also found in the sediments up to 1.5 miles below the seafloor, invisible to the naked eye and most ordinary microscopes, where they play an important role in the underwater ecosystem. Delaware Sea Grant (DESG), in partnership with the National Science Foundation-funded Center for Dark Energy Biosphere Investigations (C-DEBI), has expanded its collection of 15 Second Science videos to include longer Dive Deeper videos and virtual reality tours that explore the deep biosphere and sub-seafloor life. The full collection of 15 Second Science episodes focused on the deep biosphere and sub-surface life is available at


Meetings & Activities

AGU: 2017 Fall Meeting Deep Biosphere Sessions of Interest
Abstract submissions for the 2017 AGU Fall Meeting are due TOMORROW, August 2, 2017. Please consider submitting your abstracts to these deep-biosphere related sessions. See also the AGU 2017 Fall Meeting Sessions of Interest to the DCO Community.

ICDP: Training Course on Continental Scientific Drilling
Deadline for application is August 18, 2017.

AGU: 2018 Ocean Sciences Meeting Deep Biosphere-related Sessions NEW!
Planning on attending the 2018 Ocean Sciences Meeting in Portland, OR? Consider submitting your abstracts to these deep biosphere-related sessions. Abstracts due: September 6, 2017.


C-DEBI: Group Page NEW!
To help preserve deep biosphere methods for use in future projects, the Center encourages you to describe your lab and software-based methods using, and to link them to our group page. The website provides an easy-to-use platform to share reproducible, step-by-step scientific methods. So far, our group has 11 protocols up and we hope to preserve as many methods as possible from the community, including both successful and failed protocols. Please contact Matt Janicak if you have any questions about using the site and we hope to see your contributions up soon!

C-DEBI: Rolling call for Community Workshop support


Education & Outreach

USC / C-DEBI / Wrigley: Undergraduate Research Poster Symposium, Friday August 11, USC Irani Hall (RRI) Lobby, 1 to 4 PM

C-DEBI: Next Professional Development Webinar: August 24, 11am PT
Karen G. Lloyd (University of Tennessee) leads the next C-DEBI Professional Development Webinar on “How to Negotiate in Academia,” covering why negotiation is essential, tips for how to do so successfully and what to expect from post-doc and assistant professorship job negotiations. Missed the last webinar on “Proposal Writing, Management, and Budget Planning”? Watch it on YouTube.

Risk Innovation Lab: 2017 Science Showcase Video Contest!
Submissions close August 31, 2017.

Proposal Calls

The Mindlin Foundation: One Tweet, One Percent
The 1% Microgrant is intended to support 1% of a single investigator’s salary for a single year, approximately 20-30 hours, or an equivalent dollar amount to cover materials and other expenses for a project of roughly that duration. Reply to this tweet TODAY, August 1, 2017.

IODP: Special Call: Expedition 376 Brothers Arc Flux NEW!
The International Ocean Discovery Program (IODP) is issuing a special call for petrophysics/downhole measurements and fluid geochemistry specialists to apply for Expedition 376 Brothers Arc Flux aboard the JOIDES Resolution. The deadline to apply is August 4, 2017.

Beckman Young Investigator Program
Application deadline: August 14, 2017

NSF: Chemical Oceanography Program Solicitation NEW!
Full Proposal Target Date: August 15, 2017.

NSF: Biological Oceanography Program Solicitation NEW!
Full Proposal Target Date: August 15, 2017.

NSF: Physical Oceanography Program Solicitation NEW!
Full Proposal Target Date: August 15, 2017.

NSF: Improving Undergraduate STEM Education: Pathways into Geoscience (IUSE: GEOPATHS)
Letter of intent due date: August 18, 2017.

NSF: Provision of Marine Seismic Capabilities to the U. S. Research Community
Full proposal deadline: August 21, 2017.

NSF: Research Experiences for Undergraduates (REU) Program Solicitation 
Full proposal deadline: August 23, 2017.

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

NSF: National Oceanographic Partnership Program announcement regarding Ocean Sensors, Cubesats, and GHRSST Data NEW!
The Division of Ocean Sciences, NSF, is pleased to announce that they are partnering with the Office of Naval Research (ONR), NASA, and NSF’s Office of Polar Programs (OPP), via the National Oceanographic Partnership Program (NOPP), in a “Broad Agency Announcement” (ONR BAA # N000014-17-S-B016) regarding three ocean research and technology topics of mutual and emerging interest. Up to $18.5 million over five years may be available for this solicitation, subject to appropriation, availability of funds, and final approval by the participating NOPP agencies. The BAA provides research opportunities for the following three topics, and please note that Topic 3 is further subdivided:

  • Topic 1. CubeSat Sensors for Investigating Littoral Ocean & Atmospheric Dynamics
  • Topic 2. Improved & Routine Production, Stewardship and Application of the Group for High Resolution Sea Surface Temperature (GHRSST) Data;
  • Topic 3. In-situ Ocean Sensor Research & Technology Development
    • 3A. Power Reduction and/or Miniaturization of In-situ Ocean Sensors and Improved On Board Processing (Arctic/ Antarctic to Tropical and full water column)
    • 3B. Sensor Research & Advanced Technology
      • 3B1. Soft Matter Electronics and Ocean Sensors
      • 3B2. In-situ Ocean Sensors for “’omics”
      • 3B3. Next Generation Autonomous In-situ Ocean Sensors
    • 3C. Improving Technology Readiness Levels of Existing & Emerging Autonomous In-situ Ocean Sensors.

For Topic 3, Letters of Intent are required by October, 16 2017 and full proposals are due January 29, 2018. Additional information may be found at and

NSF: Earth Sciences Postdoctoral Fellowships (EAR-PF) NEW!
The Division of Earth Sciences (EAR) awards Postdoctoral Fellowships to recent recipients of doctoral degrees to carry out an integrated program of independent research and professional development. Fellowship proposals must address scientific questions within the scope of EAR disciplines and must align with the overall theme for the postdoctoral program. The program supports researchers for a period of up to two years with fellowships that can be taken to the institution of their choice (including institutions abroad). The program is intended to recognize beginning investigators of significant potential, and provide them with research experience, mentorship, and training that will establish them in leadership positions in the Earth Sciences community. Because the fellowships are offered only to postdoctoral scientists early in their career, doctoral advisors are encouraged to discuss the availability of EAR postdoctoral fellowships with their graduate students early in their doctoral programs. Fellowships are awards to individuals, not institutions, and are administered by the Fellows. Full Proposal Deadline: October 25, 2017.

NSF: Innovations in Graduate Education (IGE) Program NEW!
The Innovations in Graduate Education (IGE) program is designed to encourage the development and implementation of bold, new, and potentially transformative approaches to STEM graduate education training. The 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. IGE focuses on projects aimed at piloting, testing, and validating innovative and potentially transformative approaches to graduate education. IGE projects are intended to generate the knowledge required for their customization, implementation, and broader adoption. The program supports testing of novel models or activities with high potential to enrich and extend the knowledge base on effective graduate education approaches. The program addresses both workforce development, emphasizing broad participation, and institutional capacity building needs in graduate education. Strategic collaborations with the private sector, non-governmental organizations (NGOs), government agencies, national laboratories, field stations, teaching and learning centers, informal science centers, and academic partners are encouraged. Full Proposal Deadline: October 25, 2017.

NSF: Management and Operation of the Ocean Bottom Seismometer Instrument Center (OBSIC) NEW!
This solicitation seeks the services of a qualified organization to manage and operate an Ocean Bottom Seismometer Instrument Center established and sponsored by Marine Geology and Geophysics research programs within NSF’s Division of Ocean Sciences. Research activities requiring the use of the existing pool of instruments supported by NSF are expected to continue well beyond the period of performance for the existing Ocean Bottom Seismometer Instrument Pool Management Office award, scheduled to expire in early 2018. The award resulting from this solicitation will be administered as a Cooperative Agreement with a single Lead Institution that will perform the OBSIC activities described herein. Full Proposal Deadline: October 25, 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



TAMU: Research Scientist, Texas A&M International Ocean Discovery Program
We will begin reviewing applications on TODAY, August 1, 2017, but will continue to accept applications until candidates are selected for interviews.

TAMU: Research Specialist II, Texas A&M International Ocean Discovery Program
We will begin reviewing applications on TODAY, August 1, 2017, but will continue to accept applications until candidates are selected for interviews.

MLML: Faculty Position in Chemical Oceanography
Applications due August 23, 2017.

TAMU: Research Associate, International Ocean Discovery Program NEW!
The JOIDES Resolution Science Operator (JRSO) at Texas A&M University invites applications for a Research Associate (Clearance and Permitting Specialist) in the Science Operations Department. The position will be responsible for obtaining research clearance for R/V JOIDES Resolution International Ocean Discovery Program (IODP) expeditions, environmental studies or permitting, and ensuring clearance for seafloor cables and other seafloor hazards. A Bachelor’s degree in Earth Sciences or related field (e.g., Geology, Geophysics, Oceanography, Geography), plus two years of relevant experience is required. A Master’s degree is preferred, which is equivalent to two years of experience. We will begin reviewing applications on August 28, 2017, but will continue to accept applications until candidates are selected for interviews.

Bigelow: Postdoctoral Research Scientist – Geomicrobiology / Microbial Ecology NEW!
Bigelow Laboratory for Ocean Sciences in East Boothbay, Maine seeks a Postdoctoral Research Scientist to help carry out a project working with lithotrophic Fe-oxidizing bacteria. The primary aims of this project are to learn more about the composition of extracellular micro-structures produced by different groups of Fe-oxidizing bacteria, and what environmental factors most influence their production. The position will be in Dr. David Emerson’s laboratory at Bigelow, and is a collaborative project with Dr. Clara Chan at the University of Delaware. The goal is to learn more about the potential utility of these biogenic materials for uses as varied as developing metal-fiber reinforced materials, or organo-metallic frameworks for chemical catalysis, or selective filtering systems. This will be a laboratory-intensive project involving growth of both marine and freshwater Fe-oxidizing bacteria, some biochemical analysis of their products, as well as development of laboratory systems for controlled growth and monitoring, via imaging, of the bacteria, including the use of RNA-seq based transcriptome approaches. In addition, comparative genomics will play an important part in strategizing research approaches. The well-suited candidate will have experience in geomicrobiology, microbial ecology and/or physiology with a strong interest and inclination toward experimental laboratory work, as well as an adequate background in genomics. It’s important to have an intellectual interest in applying this knowledge to the capacity for lithotrophic bacteria to grow on iron, as well as the potential for the development of novel materials. There will be opportunities to do some local field work. For full consideration, the application should be received by August 31, 2017.

WHOI: Two Postdoctoral Investigator Positions NEW!
The Marine Chemistry and Geochemistry Department is searching for two Postdoctoral Investigators to join their team. These are temporary positions and the initial appointment will be for one year starting (available immediately) with the possibility of an extension for up to two years. These positions will work in Dr. Julie Huber’s laboratory at WHOI. Dr. Huber’s research focuses on the composition and function of microbes in the deep-sea, to understand microbial dynamics and the resulting biogeochemical implications. Much of her work has involved the ocean crustal aquifer (e.g., hydrothermal systems; ocean ridge and arc volcanoes; off-ridge sub-seafloor crust). More broadly, her research interests span from the deep-sea to coastal ponds and astrobiology. The Postdoctoral Investigator positions will participate in studies of subseafloor crustal microbial communities. The emphasis is on examining microbial community biomass, function, and activity in the subseafloor habitat. While the primary focus of the work will be in research, the postdoctoral investigator will have an opportunity to participate in educational and outreach activities associated with the project.

Caltech: Postdoctoral Research Position: Becoming Biotic: Recapitulating Ancient Metabolic Pathways on the Early Earth NEW!
The California Institute of Technology (Caltech), Postdoctoral Scholars Program at the Jet Propulsion Laboratory (JPL) invites applications for a postdoctoral research position in JPL’s Planetary Ices Group. Dr. Laurie Barge will serve as JPL postdoctoral advisor to the selected candidate. The appointee will carry out research in collaboration with the JPL advisor, resulting in publications in the open literature. The “Becoming Biotic” project, funded by the NSF-NASA Ideas Lab for the Origins of Life, aims to provide the first direct examination of hypotheses regarding the emergence of metabolic pathways. The goal is to attempt to recapitulate ancient metabolic pathways by replacing protein enzymes with non-protein catalysts in early Earth conditions. The two-year project will consist of tasks conducted in a multi-institution effort between JPL, University of Southern California, and Oberlin College. Frequent communication and coordination will be required with the USC/Oberlin Co-I’s and their postdocs and students. The successful candidate will: 1. Identify a set of early Earth conditions under which we will test whether the cofactors can drive metabolic reactions. This will be done jointly with Co-I’s at USC and Oberlin. 2. Test individual cofactors for their ability to catalyze metabolic reactions in the absence of protein enzymes. This Task will also involve the development of synthesis procedures for organic and inorganic cofactors. 3. Measure the kinetics of cofactor-driven reactions for a set of ancient metabolic pathways under several early Earth conditions. 4. Recapitulate an ancient metabolic pathway under several early Earth conditions using cofactors without protein enzymes. Candidates should have a recent Ph.D. in chemistry, organic chemistry, biochemistry, geochemistry or related fields. Most important is direct experience in protein cofactor chemistry outside of cellular environments, mineral synthesis, and anoxic chemical synthesis methods. Candidates should have experience working with analytical methods (particularly 1H liquid NMR) and working with hazardous chemicals (e.g. thioacetic acid, hydrogen sulfide).

Montana State University, Bozeman: Postdoctoral Research Position in Environmental Microbiology

Bigelow: Postdoctoral Scientist in Horizontal Gene Transfer in Marine Bacterioplankton

University of Pennsylvania: Postdoctoral Scholar Position

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.

C-DEBI is now on Twitter! Follow and tweet to us @deepbiosphere or tag #CDEBI.
You are receiving this e-mail because you opted in at our website or requested to be added via e-mail.

Unsubscribe <<Email Address>> from this list.
Forward this email to a friend
Subscribe to this list.
Update your profile
Email Marketing Powered by Mailchimp