C-DEBI Newsletter – May 15, 2019
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The ISME Journal
Active subseafloor microbial communities from Mariana back-arc venting fluids share metabolic strategies across different thermal niches and taxa - NEW!
Elizabeth Trembath-Reichert, David A. Butterfield, Julie A. Huber*
*C-DEBI Contribution 470

There are many unknowns regarding the distribution, activity, community composition, and metabolic repertoire of microbial communities in the subseafloor of deep-sea hydrothermal vents. Here we provide the first characterization of subseafloor microbial communities from venting fluids along the central Mariana back-arc basin (15.5–18°N), where the slow-spreading rate, depth, and variable geochemistry along the back-arc distinguish it from other spreading centers. Results indicated that diverse Epsilonbacteraeota were abundant across all sites, with a population of high temperature Aquificae restricted to the northern segment. This suggests that differences in subseafloor populations along the back-arc are associated with local geologic setting and resultant geochemistry. Metatranscriptomics coupled to stable isotope probing revealed bacterial carbon fixation linked to hydrogen oxidation, denitrification, and sulfide or thiosulfate oxidation at all sites, regardless of community composition. NanoSIMS (nanoscale secondary ion mass spectrometry) incubations at 80 °C show only a small portion of the microbial community took up bicarbonate, but those autotrophs had the highest overall rates of activity detected across all experiments. By comparison, acetate was more universally utilized to sustain growth, but within a smaller range of activity. Together, results indicate that microbial communities in venting fluids from the Mariana back-arc contain active subseafloor communities reflective of their local conditions with metabolisms commonly shared across geologically disparate spreading centers throughout the ocean.

Microbial Diversity in Sub-Seafloor Sediments from the Costa Rica Margin - NEW!

Amanda J. Martino*, Matthew E. Rhodes, Rosa León-Zayas, Isabella E. Valente, Jennifer F. Biddle*, Christopher H. House
*C-DEBI Contribution 473

The exploration of the deep biosphere continues to reveal a great diversity of microorganisms, many of which remain poorly understood. This study provides a first look at the microbial community composition of the Costa Rica Margin sub-seafloor from two sites on the upper plate of the subduction zone, between the Cocos and Caribbean plates. Despite being in close geographical proximity, with similar lithologies, both sites show distinctions in the relative abundance of the archaeal domain and major microbial phyla, assessed using a pair of universal primers and supported by the sequencing of six metagenomes. Elusimicrobia, Chloroflexi, Aerophobetes, Actinobacteria, Lokiarchaeota, and Atribacteria were dominant phyla at Site 1378, and Bathyarchaeota, Chloroflexi, Hadesarchaeota, Aerophobetes, Elusimicrobia, and Lokiarchaeota were dominant at Site 1379. Correlations of microbial taxa with geochemistry were examined and notable relationships were seen with ammonia, sulfate, and depth. With deep sediments, there is always a concern that drilling technologies impact analyses due to contamination of the sediments via drilling fluid. Here, we use analysis of the drilling fluid in conjunction with the sediment analysis, to assess the level of contamination and remove any problematic sequences. In the majority of samples, we find the level of drilling fluid contamination, negligible.

Frontiers in Microbiology
Microbial Selection and Survival in Subseafloor Sediment - NEW!
John B. Kirkpatrick*, Emily A. Walsh, Steven D’Hondt*
*C-DEBI Contribution 474

Many studies have examined relationships of microorganisms to geochemical zones in subseafloor sediment. However, responses to selective pressure and patterns of community succession with sediment depth have rarely been examined. Here we use 16S rDNA sequencing to examine the succession of microbial communities at sites in the Indian Ocean and the Bering Sea. The sediment ranges in depth from 0.16 to 332 m below seafloor and in age from 660 to 1,300,000 years. The majority of subseafloor taxonomic diversity is present in the shallowest depth sampled. The best predictor of sequence presence or absence in the oldest sediment is relative abundance in the near-seafloor sediment. This relationship suggests that perseverance of specific taxa into deep, old sediment is primarily controlled by the taxonomic abundance that existed when the sediment was near the seafloor. The operational taxonomic units that dominate at depth comprise a subset of the local seafloor community at each site, rather than a grown-in group of geographically widespread subseafloor specialists. At both sites, most taxa classified as abundant decrease in relative frequency with increasing sediment depth and age. Comparison of community composition to cell counts at the Bering Sea site indicates that the rise of the few dominant taxa in the deep subseafloor community does not require net replication, but might simply result from lower mortality relative to competing taxa on the long timescale of community burial.

Applied and Environmental Microbiology
Complex microbial communities drive iron and sulfur cycling in Arctic fjord sediments - NEW!
Joy Buongiorno, L. C. Herbert, Laura M. Wehrmann, Alexander B. Michaud, K. Laufer, Hans Røy, Bo Barker Jørgensen, A. Szynkiewicz, A. Faiia, K. M. Yeager, K. Schindler, Karen G. Lloyd*
*C-DEBI Contribution 476

Glacial retreat is changing biogeochemical cycling in the Arctic, where glacial runoff contributes iron for oceanic shelf primary production. In Svalbard fjords, we hypothesize that microbes catalyze intense iron and sulfur cycling in low organic matter sediments. This is because low organic matter limits sulfide generation, allowing iron mobility to the water column instead of precipitation as iron monosulfides. Here, we tested this with high-depth-resolution 16S rRNA gene libraries in the upper 20 cm at two sites in Van Keulenfjorden, Svalbard. At the site closer to the glaciers, iron-reducing Desulfuromonadales, iron-oxidizing Gallionella and Mariprofundus, and sulfur-oxidizing Thiotrichales and Epsilonproteobacteria were abundant above 12 cm depth. Below this depth, the relative abundances of sequences for sulfate-reducing Desulfobacteraceae and Desulfobulbaceae increased. At the outer station, the switch from iron-cycling clades to sulfate reducers occurred at shallower depths (∼5 cm), corresponding to higher sulfate reduction rates. Relatively labile organic matter (shown by δ13C and C/N ratios) was more abundant at this outer site and ordination analysis suggested that this affected microbial community structure in surface sediments. Network analysis revealed more correlations between predicted iron- and sulfur-cycling taxa, and with uncultured clades proximal to the glacier. Together, these results suggest that complex microbial communities catalyze redox cycling of iron and sulfur, especially closer to the glacier, where sulfate reduction is limited due to low organic matter availability. Diminished sulfate reduction in upper sediments enables iron to flux into the overlying water, where it may be transported to the shelf.

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

C-DEBI: 2019 Networked Speaker Series, Starting Thursday, May 30, 12:30pm PT - NEW!
Don't miss the first of the 2019 online seminars with Dr. Jeanine Ash (Rice University) on "Making and Breaking Molecules." Abstract: Gases like molecular oxygen and methane are fundamentally significant to Earth’s habitability and the evolution of life.  The concentration of these gases in our atmosphere are the result of constant interplay between the biological and geological process that create and consume them. My work focuses on the enzyme-level processes that make and break these molecules, and how recent advances in isotope ratio mass spectrometry can provide new tools for tracing these process at the global level.  In this talk I’ll introduce the concept of multiply-substituted isotopologues (commonly called “clumped” isotopes), and share case studies that show how these tools can be used to illuminate deep biosphere processes.

24th ISEB Symposium, Potsdam, Germany, September 22-27, 2019
Abstract submission deadline: May 31, 2019.

IODP-USSSP: Volunteer to serve on the JOIDES Resolution Facility Board (JRFB), U.S. Advisory Committee for Scientific Ocean Drilling (USAC), or Science Evaluation Panel (SEP) - NEW!
Deadline: June 24, 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: 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.

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)
Full Proposal Deadlines: May 24, 2019 and August 28, 2019.

IODP-USSSP: Submit an IODP Workshop Proposal - NEW!
The U.S. Science Support Program, associated with the International Ocean Discovery Program, is currently accepting proposals for planning workshops. Proposed workshops should promote the development of new ideas and strategies to study the Earth’s processes and history using scientific ocean drilling. Workshops may focus on a specific scientific theme or topic, or they may focus on a geographic region, integrating multiple topics. Regionally-focused workshops offer opportunities to synthesize scientific results from past expeditions, or to develop drilling proposals for future expeditions. Prospective workshop proponents should consider long-term projected ship tracks in identifying potential geographic areas for focus. Funding may be requested for U.S.-based meetings or to support U.S. participants at larger international workshops. Broad-based scientific community involvement, co-sponsorship by related programs, and the active participation of early career researchers are strongly encouraged. The submission deadline is June 1, 2019.

Moore Foundation: Symbiosis in Aquatic Systems Initiative funding opportunity for investigator awards - NEW!
The Symbiosis in Aquatic Systems Initiative of the Gordon and Betty Moore Foundation is soliciting pre-applications for investigator awards. Each award will fund research in a single investigator’s laboratory. Our goal with the awards is to provide scientists with the resources and flexibility to pursue innovative, risky research that has high potential for significant conceptual and methodological advances in aquatic symbiosis. We anticipate investigators will generate new technologies, resources, theory, natural history and hypotheses to spark discovery in understanding aquatic organisms and their symbioses. We envision a vibrant cohort of investigators that serves as a source of ideas for the initiative, collaborates among peers, and moves the community towards a more comprehensive understanding how marine and freshwater organisms interact in symbiotic associations involving microbes. We anticipate awards encompassing one or more of three central themes: origins and evolution, mechanisms of symbiotic interactions, and/or ecology and natural history. We are interested in symbioses where at least one partner is a microbe and where the symbiosis takes place in a marine or freshwater environment. We anticipate the initiative will support approximately 12 scientists for five years (2020-2025) who represent both early and established career stages and include both current and emerging leaders in their fields. Investigators will convene at an annual symposium to share research findings and build connections across symbiosis researchers. Awards will range from approximately $200K-$400K/year in direct costs. Pre-application deadline: June 3, 2019.

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

NSF: Dear Colleague Letter: Research Opportunities in Europe for NSF Postdoctoral Research Fellows and CAREER Awardees - NEW!
To further scientific and technological cooperation between the United States and the European Community, the National Science Foundation and the European Research Council signed an Implementing Arrangement on July 13, 2012 to enable U.S. scientists and engineers with NSF-funded CAREER awards and Postdoctoral Research Fellowships to pursue research collaboration with European colleagues supported through EU-funded European Research Council (ERC) grants. Connecting researchers with complementary strengths and shared interests promotes scientific progress in solving some of the world’s most vexing problems. This international research opportunity is mutually beneficial to the U.S. participants and the hosts through cooperative activities during research visits and establishing international research partnerships to enrich future research activities in the U.S. and Europe. Under the Arrangement, the ERC Executive Agency (ERCEA) identifies ERC-funded research groups who wish to host NSF Postdoctoral Research Fellows for research visits of up to one year within their ERC funding. The 2018 Dear Colleague Letter for this opportunity noted that 2018 would be the final year in its current form. NSF is extending the current opportunity for one additional year. NSF intends to announce a new, related opportunity in FY 2020. Requests must be received at NSF at least 3 months prior to the proposed visit, but no later than June 21, 2019, for consideration using Fiscal Year 2019 funds.

IODP: Apply to Sail on IODP Expeditions 390/393 - NEW!
Expeditions 390 and 393 are a multidisciplinary and joint scientific ocean drilling project that aims to recover complete sedimentary sections and ~200 m of oceanic crust along a crustal age transect at ~31°S across the South Atlantic Ocean to: (1) investigate the history of low-temperature hydrothermal interactions between the aging ocean crust and the evolving South Atlantic Ocean; (2) quantify past hydrothermal contributions to global geochemical cycles; (3) investigate sediment and basement-hosted microbial community variation with substrate composition and age in the low energy South Atlantic Gyre subseafloor biosphere; and (4) investigate the responses of Atlantic Ocean circulation patterns and the Earth’s climate system to rapid climate change, including elevated CO2 during the Cenozoic. The expeditions will occur from 5 October to 5 December 2020 (Expedition 390) and 6 April to 6 June 2021 (Expedition 393). Opportunities exist for researchers (including graduate students) in all shipboard specialties, including but not limited to sedimentologists, petrologists, micropaleontologists, paleomagnetists, petrophysicists, geophysicists, inorganic and organic geochemists, and microbiologists. The deadline to apply is August 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)
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
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

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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