|C-DEBI Newsletter – April 2, 2018
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Message from the Director:
In celebration of the 30th anniversary of the NSF Science and Technology Center Program, Discover magazine featured C-DEBI in their image gallery of some of the STCs’ groundbreaking work!
Please mark your calendars for this month’s Professional Development Webinar “Sharing Data: The Joys of Open Science” with Ben Tully (C-DEBI Bioinformatic Specialist, USC), April 25th, 12-1pm PST.
And congratulations to the proponents of proposals selected for funding in our 2017 December call for research grants and fellowships. Stay tuned on our funded projects webpage for their exciting work!
- Graduate Fellowship: Taylor Royalty (Advisor: Drew Steen, University of Tennessee Knoxville)
Characterization of subsurface extracellular enzymes and the organisms that produce them using metatranscriptomics and bottom-up metaproteomics
- Graduate Fellowship: Clarisse Sullivan (Advisor: Mike Rappe, University of Hawaii)
Population genomics of Nitrospirae bacteria inhabiting deep subseafloor fluids of the Juan de Fuca Ridge flank
- Postdoctoral Fellowship: Sarah Hu (Advisor: Julie Huber, Woods Hole Oceanographic Institution)
Probing subseafloor microbial interactions via hydrothermal vent fluids: A focus on protists
- Postdoctoral Fellowship: Claire McKinley (Advisor: Evan Solomon, University of Washington)
Evaluating the extent of microbial Fe-reduction and its role in the global methane cycle
- Research Grant: Annie Rowe, University of Cincinnati
Uncovering novel mechanisms of extracellular electron uptake in subsurface-relevant marine bacterial isolates
Publications & Press
Deep Sea Research Part I: Oceanographic Research Papers
Clusters of deep-sea egg-brooding octopods associated with warm fluid discharge: an ill-fated fragment of a larger, discrete population? - NEW!
Anne. M. Hartwell, Janet. R. Voight, Charles Geoffrey Wheat*
*C-DEBI Contribution 419
Benthic octopods cluster on bare rock on Dorado Outcrop, a ~3000 m deep basalt exposure. The outcrop hosts intermittent discharge of relatively cool (up to 12.3 °C) hydrothermal fluid that carries about half as much oxygen as bottom seawater (~54 μM vs. 108 μM). We analyzed 231 hours of video footage and still images taken by sub-sea vehicles in 2013 and 2014 that documented the clustered octopods, members of the poorly-known genus Muusoctopus. The largest cluster (102 octopods) occurred in a 19 m2 area of fluid discharge, where the basalt was sediment-free; individual octopods were also seen across the outcrop. The clustered octopods appeared to be brooding eggs and a total of 11 egg clutches were confirmed. None of the 186 eggs closely examined showed embryonic development. The intermittent fluid discharge may clear the basalt of sediment and attract gravid octopods which then spawn. However, the increased temperature and limited oxygen of the discharging fluids may threaten the octopods’ survival. Octopods in/near areas of discharging fluid had significantly higher estimated respiration rates (3.1–9.8 contractions/minute) than did octopods away from discharging fluid (0.8–6.0 contractions/minute). Warm fluids likely increase the octopods’ metabolic rate and thus their oxygen demand but provide only limited oxygen. The resultant physiological stress is hypothesized to eventually kill eggs near fluid discharge. We hypothesize, because these eggs do not survive, the population is sustained by a larger pool of undetectable females that brood their eggs inside cool conduits of this and perhaps other, unstudied basalt outcrops.
International Journal of Systematic and Evolutionary Microbiology
Thioclava electrotropha sp. nov., a versatile electrode and sulfur-oxidizing bacterium from marine sediments - NEW!
Rachel Chang, Lina. J. Bird, Casey Barr, Magdalena R. Osburn, Elizabeth Wilbanks, Kenneth H. Nealson, Annette R. Rowe*
*C-DEBI Contribution 420
A taxonomic and physiologic characterization was carried out on Thioclava strain ElOx9T, which was isolated from a bacterial consortium enriched on electrodes poised at electron donating potentials. The isolate is Gram-negative, catalase-positive and oxidase-positive; the cells are motile short rods. The bacterium is facultatively anaerobic with the ability to utilize nitrate as an electron acceptor. Autotrophic growth with H2 and S0 (oxidized to sulfate) was observed. The isolate also grows heterotrophically with organic acids and sugars. Growth was observed at salinities from 0 to 10% NaCl and at temperatures from 15 to 41 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain belongs in the genus Thioclava ; it had the highest sequence similarity of 98.8 % to Thioclava atlantica 13D2W-2T, followed by Thioclava dalianensis DLFJ1-1T with 98.5 % similarity, Thioclava pacifica TL 2T with 97.7 % similarity, and then Thioclava indica DT23-4T with 96.9 %. All other sequence similarities were below 97 % to characterized strains. The digital DNA–DNA hybridization estimated when compared to T. atlantica 13D2W-2T, T. dalianensis DLFJ1-1T, T. pacifica TL 2T and T. indica DT23-4T were 15.8±2.1, 16.7+2.1, 14.3±1.9 and 18.3±2.1 %. The corresponding average nucleotide identity values between these strains were determined to be 65.1, 67.8, 68.4 and 64.4 %, respectively. The G+C content of the chromosomal DNA is 63.4 mol%. Based on these results, a novel species Thioclava electrotropha sp. nov. is proposed, with the type strain ElOx9T (=DSM 103712T=ATCC TSD-100T).
Marine Technology Society Journal
Effective Strategies for Engaging Community College Students in Research via Cutting-Edge Technology - NEW!
Stephanie Schroeder*, Jan P. Amend*
*C-DEBI Contribution 421
As we train the next generation of Science, Technology, Engineering, and Math (STEM) researchers, it is imperative that we expand our recruitment to community college students. Many of these students are highly motivated and extremely talented, but they often lack exposure to cutting edge technology found at R1 institutions, much less have the opportunities to participate in original research. The Center for Dark Energy Biosphere Investigations (C-DEBI) at the University of Southern California (USC) started a community college research internship summer program in 2013. The non-residential and residential programs combined so far have trained 60 students in the biogeosciences, with 46 of them having transferred to four-year institutions and 95% remaining in STEM fields. Their introduction to and acquired competence in several advanced technologies have further prepared these students to pursue graduate degrees and rewarding careers in research-based STEM fields.
The Marine Technology Society is a not-for-profit, international, professional association. Founded in 1963, the Society believes that the advancement of marine technology and the productive, sustainable use of the oceans depend upon the active exchange of ideas between government, industry and academia. See www.mtsociety.org. Ⓒ 2018 Marine Technology Society. This article is for personal use only, and is not to be distributed in any format.
Scientific rationale and international obligations for protection of active hydrothermal vent ecosystems from deep-sea mining - NEW!
Cindy Lee Van Dover, S. Arnaud-Haond, M. Gianni, S. Helmreich, Julie A. Huber*, A. L. Jaeckel, A. Metaxas, L. H. Pendleton, S. Petersen, E. Ramirez-Llodra, P. E. Steinberg, V. Tunnicliffe, H. Yamamoto
*C-DEBI Contribution 425
There is increasing interest in mining minerals on the seabed, including seafloor massive sulfide deposits that form at hydrothermal vents. The International Seabed Authority is currently drafting a Mining Code, including environmental regulations, for polymetallic sulfides and other mineral exploitation on the seabed in the area beyond national jurisdictions. This paper summarizes 1) the ecological vulnerability of active vent ecosystems and aspects of this vulnerability that remain subject to conjecture, 2) evidence for limited mineral resource opportunity at active vents, 3) non-extractive values of active vent ecosystems, 4) precedents and international obligations for protection of hydrothermal vents, and 5) obligations of the International Seabed Authority under the UN Convention on the Law of the Sea for protection of the marine environment from the impacts of mining. Heterogeneity of active vent ecosystems makes it extremely challenging to identify “representative” systems for any regional, area-based management approach to conservation. Protection of active vent ecosystems from mining impacts (direct and indirect) would set aside only a small fraction of the international seabed and its mineral resources, would contribute to international obligations for marine conservation, would have non-extractive benefits, and would be a precautionary approach.
IODP: JOIDES Resolution Assessment Report and accompanying Community Survey Data Report - NEW!
We are pleased to announce the release of the JOIDES Resolution Assessment Report, and the accompanying JOIDES Resolution Community Survey Data Report, in support of the National Science Foundation’s request to the National Science Board for the renewal of funding for the JR facility for the next five years. The community overwhelmingly supports the JR and its ability to address high priority objectives of the IODP Science Plan. The Community Survey Data Report documents the responses of 876 of our colleagues, both national and international, and provides significant insights into the IODP community. The Workshop Report reflects the outstanding effort of the 81 attendees of the September 2017 workshop, “Assessment of the JOIDES Resolution in Meeting the Challenges of the IODP Science Plan”. Their tasks included developing expedition results reports in preparation for the workshop, reviewing comments from the Community Survey, and synthesizing the two datasets. The report includes the results of plenary sessions from the workshop that focused on future scientific opportunities that can be addressed in the next five years, as well as discussion surrounding the relationship of the JR to the National Science Foundation’s Sea Change report from 2015, in addition to a list of recommendations and updates for the next five years of JR operations.
Meetings & Activities
AGU: 2018 Fall Meeting Session Proposals
The deadline for submissions is April 18, 2018.
IODP-USSSP: Host an Ocean Discovery Lecturer
The application period will close on May 18, 2018.
GRC: Apply to attend the 2018 Conference on Deep Carbon Science, June 17-22, Smithfield, RI
Applications for this meeting must be submitted by May 20, 2018. Please apply early, as some meetings become oversubscribed (full) before this deadline.
C-DEBI: Rolling call for Community Workshop support
C-DEBI: Protocols.io Group Page
C-DEBI: Subseafloor Cultures Database
Education & Outreach
IODP: Apply for Te Kura Kōhatu School of Rock 2018, July 5-13, Auckland, New Zealand - NEW!
Our School of Rock program is a professional development opportunity for formal and informal educators on board or involving the JOIDES Resolution. Teachers will work with scientists and technicians to learn about many aspects of earth science, geology, paleo-oceanography and more done aboard this amazing ship, what we learn from scientific drilling, and how to do the kinds of scientific analyses and lab exercises program-scientists do. This new-found knowledge will help teachers in creating or modifying existing resources for their students in many areas of the science curriculum. This year’s School of Rock is being jointly organized by the United States Science Support Program (USSSP) and the Australia and New Zealand International Ocean Discovery Program Consortium (ANZIC). It will focus on Pacific Rim geology and the science research of the JOIDES Resolution. In our continuing goal to broaden participation in the geosciences, we are especially interested in applicants from diverse backgrounds and/or who serve diverse communities. Apply by April 20, 2018.
MBL: Advanced Research Training Course: Strategies and Techniques for Analyzing Microbial Population Structures (STAMPS) - NEW!
Deep DNA sequencing using massively-parallel, next-generation technology has enabled nearly comprehensive environmental surveys that can describe the different kinds of microbes in a community and their relative abundance. These descriptions of richness and evenness make possible estimates of microbial diversity, but the size of the required data sets pose enormous computational challenges. The rapidly expanding flow of information from next generation DNA sequencing platforms has fueled healthy debate about best practices for data analysis while at the same time building a user demand for tools that can address important ecological questions. The STAMPS course will promote dialogue and the exchange of ideas between experts in analysis of metagenomic data and offer interdisciplinary bioinformatic and statistical training to practitioners of molecular microbial ecology and genomics. Application Deadline: April 20, 2018.
C-DEBI: Next Professional Development Webinar: April 25, 12pm PT - NEW!
Ben Tully (C-DEBI Bioinformatic Specialist) leads the next C-DEBI Professional Development Webinar on “Sharing Data: The Joys of Open Science.” The access URL for the webinar is http://usccollege.adobeconnect.com/cdebiremote/. Missed the last webinar on “Surviving (and Maybe Even Thriving!) in a Soft Money Position”? Watch it on YouTube.
MARUM: ECORD 2018 Summer School on Sub-seafloor fluid transport and gas hydrate dynamics - NEW!
This summer school will combine lab exercises on IODP-style shipboard methodologies (“virtual ship”) as well as interactive lectures by world-leading scientists in the field of mid-ocean ridge research. Participation will prepare you for future involvement in IODP and for research work on mid-ocean ridge processes. The summer school will take advantage of the unique and integrated facilities offered by the IODP Bremen Core Repository and MARUM laboratories. To apply, please visit the course web page given below. A total of 30 participants can be accepted. The course fee is €150. Travel, accommodation and meals must be covered by the participants. The application deadline is May 4, 2018.
NSF: Inclusion across the Nation of Communities of Learners of Underrepresented Discoverers in Engineering and Science
Full Proposal Deadline Date: April 4, 2018.
IODP: Register Now: Expedition 385 (Guaymas Basin Tectonics and Biosphere) Webinar
To learn more about the scientific objectives of the expedition, life at sea, and how to apply to sail, please register and join us for a web-based seminar on Wednesday, April 4, 2018 at 12:00 PM EDT.
IODP: Apply to Sail on IODP Expedition 385: Guaymas Basin Tectonics and Biosphere
The deadline to apply is April 15, 2018.
NSF: Cyberinfrastructure for Sustained Scientific Innovation (CSSI) - Data and Software
Full proposal deadline: April 18, 2018.
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 European Community and the United States, an Implementing Arrangement was signed 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. 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. This is the final year of the program. ERCEA has provided a list of ERC-funded principal investigators and research teams interested in hosting NSF Postdoctoral Fellows. NSF Fellows should request this list via email from firstname.lastname@example.org, and then communicate directly with ERC PIs to as certain areas of mutual interest and research goals for a visit. Fellows may then submit their requests directly to their NSF Program Officers. If approved by NSF, the request is forwarded to ERCEA for review and for making arrangements with the ERC-funded project. The European hosts will provide funding to support in-country living expenses during the visits. NSF will provide travel funds to and from Europe. The application deadline is April 20, 2018.
NSF: Dear Colleague Letter: Stimulating Research Related to Navigating the New Arctic (NNA), One of NSF's 10 Big Ideas
Organizations submitting proposals to programs and funding vehicles without deadlines are encouraged to submit proposals by May 1, 2018, to be considered for FY 2018 funding.
Improving Undergraduate STEM Education: Education and Human Resources (IUSE: EHR) Program Flyer
Beginning in FY 2018, there will be no single date deadlines for Exploration and Design proposals. Please note however that proposals received after May 1, 2018 will be held over to the subsequent financial year for possible award.
Simons Postdoctoral Fellowships in Marine Microbial Ecology - NEW!
The Simons Foundation invites applications for postdoctoral fellowships to support research on fundamental problems in marine microbial ecology. The foundation is particularly interested in applicants with training in different fields who want to apply their experience to understanding the role of microorganisms in shaping ocean processes, and vice versa, as well as applicants with experience in modeling or theory development. While these cross-disciplinary applicants will receive particular attention, applicants already involved in ocean research are also encouraged to apply. The foundation anticipates awarding five fellowships in 2018. Applicants should have received their Ph.D. or equivalent degree within three years of the fellowship’s start date. Preference will be for applicants with no more than one year of postdoctoral experience. Applicants may be citizens of any country. Awards can only be issued to nonprofit research universities or research institutions in the U.S. Application deadline: June 15, 2018.
DCO: Deep Life Cultivation Internship Program
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).
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
BIOS: Postdoctoral Scholarship in Oceanography - NEW!
A Postdoctoral Scholar award will be offered to a new or recent PhD in the fields of oceanography or closely related subjects. We welcome a broad range of potential topics for study, including physical oceanography process studies at all scales, biogeochemical research with practical experimentation, and system modeling with strong integration of data. We seek a candidate who will take advantage of the opportunities and facilities offered at BIOS which include bi-weekly access to the deep ocean, repeat measurements and long-term monitoring of ocean properties, integration of glider observations with traditional ship-based measurements and laboratory access for chemical and biological measurements and experimentation. The position will remain open until filled.
Karlsruhe Institute of Technology: Two Ph.D. Positions
U Penn: Two Graduate Research Assistant Positions
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