C-DEBI Newsletter – May 15, 2017

Publications

eLife
Insight into the evolution of microbial metabolism from the deep-branching bacterium, Thermovibrio ammonificans – NEW!
Donato Giovannelli*, Stefan M. Sievert, Michael Hügler, Stephanie Markert, Dörte Becher, Thomas Schweder, Costantino Vetriani*
*C-DEBI Contribution 368

Anaerobic thermophiles inhabit relic environments that resemble the early Earth. However, the lineage of these modern organisms co-evolved with our planet. Hence, these organisms carry both ancestral and acquired genes and serve as models to reconstruct early metabolism. Based on comparative genomic and proteomic analyses, we identified two distinct groups of genes in Thermovibrio ammonificans: the first codes for enzymes that do not require oxygen and use substrates of geothermal origin; the second appears to be a more recent acquisition, and may reflect adaptations to cope with the rise of oxygen on Earth. We propose that the ancestor of the Aquificae was originally a hydrogen oxidizing, sulfur reducing bacterium that used a hybrid carbon fixation pathway for CO₂fixation. With the gradual rise of oxygen in the atmosphere, more efficient terminal electron acceptors became available and this lineage acquired genes that increased its metabolic flexibility while retaining ancestral metabolic traits.

Proceedings of the IODP
Data report: cultivation of prokaryotes from subsurface marine sediments of the Baltic Sea (IODP Expedition 347) – NEW!
Martin Krüger and Axel Schippers

Integrated Ocean Drilling Program (IODP) Expedition 347 to the Baltic Sea in 2013 was in line with the IODP Science Plan main research theme “Deep biosphere responses to glacial–interglacial cycles,” addressing questions such as deep biosphere evolution, its biogeochemical processes, and how the postglacial diffusive penetration of conservative seawater ions may alter the chemical composition and microbial physiology in the subseafloor biosphere. Consequently, we tried to enrich indigenous microorganisms at in situ conditions using a broad range of electron acceptors (for fermenters; Fe, Mn, and sulfate reducers; and methanogens), simple and complex carbon substrates (in mixtures or as single compounds), and a wide range of culture conditions (temperature and salinity) to cover varying environmental conditions and metabolic requirements. The most successful were enrichment cultures with a mix of polymeric substrates, which proved to be successful for all samples investigated. Also, iron- and manganese-reducing organisms could be enriched from all sites, whereas nitrate as an electron acceptor did not work well. Methanogenic enrichments were only successful for a few of the samples investigated. In these cases, different monomeric as well as complex substrates were converted to methane, indicating a metabolically versatile indigenous microbial community in the sediments.

Frontiers Research Topic on Environmental Bioenergetics: Call for Manuscripts
Abstract submission deadline: June 30, 2017.

Proposal Calls

NSF: Inclusion across the Nation of Communities of Learners of Underrepresented Discoverers in Engineering and Science (INCLUDES) Program Solicitation
Full proposal deadline: May 16, 2017.

DOE Office of Science Graduate Student Research (SCGSR) Program
Applications are due May 16, 2017.

NSF: Antarctic Research Program Solicitation
Full proposal deadline: May 23, 2017.

NAS: Building Capacity for Science Communication Partnership Awards
To apply for these awards, researchers and practitioners who have agreed to work in partnership should submit a proposal by June 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: June 1, 2017.

Simons Foundation: 2017 Postdoctoral Fellowships in Marine Microbial Ecology
Application deadline: June 15, 2017.

IODP: Apply to Sail: Expedition 377 Arctic Ocean Paleoceanography – NEW!
Platform (MSP) provided by the ECORD Science Operator. To learn more about the scientific objectives of this expedition, life at sea, and how to apply to sail, please join in a web-based seminar on Monday, May 22, 2017 at 1pm GMT (9am EDT). To register for the webinar, click here. The offshore phase of Expedition 377 is provisionally scheduled for a maximum of 60 days during Autumn 2018, with only a subset of the Science Party participating. Offshore activities will focus on core recovery, curation, sampling for ephemeral properties, biostratigraphy, physical properties, preliminary lithostratigraphy (whole core observed at core ends and through plastic liners), and downhole logging. The cores will not be split at sea. Subsequently, an Onshore Science Party (OSP) will be held at the MARUM – Center for Marine Environmental Sciences, University of Bremen, Germany, in early  2019 (exact dates to be confirmed), where the cores will be split. The OSP will be a maximum of 4 weeks long, the exact length dependent on core recovery. All members of the Science Party must attend the Onshore Science Party. Successful applicants will be invited either as an offshore-onshore participant, or as an onshore-only participant. Please note that there are no opportunities for offshore-only participation. Opportunities exist for researchers (including graduate students) in all specialties. While other expertise may be considered, specialists in the following fields are required: sedimentology, paleontology, palynology, organic geochemistry, inorganic geochemistry, structural geology, paleomagnetics, microbiology, physical properties, geophysics, stratigraphic correlation and downhole logging. For the offshore phase of the expedition, we are particularly looking for the following fields: sedimentology, paleontology, organic geochemistry, inorganic geochemistry, microbiology, physical properties, and petrophysics/downhole logging. U.S.-affiliated scientists interested in participating in this expedition should apply to sail through the U.S. Science Support Program. The deadline to apply is June 23, 2017.

WGBH: Rita Allen Fellowship for Science Communication
Applications due June 30, 2017.

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

NSF: Management and Operation of a National Ocean Bottom Seismometer Instrument Pool – NEW!
The Division of Ocean Sciences in the Geosciences Directorate of the National Science Foundation (NSF/OCE) intends to issue a solicitation to establish, manage and operate a National Ocean Bottom Seismometer Instrument Pool (NOBSIP) through a competitive, merit-based external peer-review process. This initiative is expected to result in the award of a five to ten-year Cooperative Agreement (CA) for this activity. It is anticipated that the competition for management and operation of the National Ocean Bottom Seismometer Instrument Pool (NOBSIP) will be open to U.S. universities, colleges, and other non-profit, non-academic organizations. NSF will require that a single academic or non-profit U.S. organization serve as the lead organization, with any other collaborators being identified as subawardees. NSF anticipates that a program solicitation will be issued in calendar year 2017. The due date for full proposals in response to the program solicitation is expected to be approximately 3 months following its publication. Eligible organizations are invited to review the listed documentation and identify additional information that could inform preparation of a responsive proposal.

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

Education & Outreach

C-DEBI: Next Professional Development Webinar June 15 – NEW!
Do you have questions like: How do I put together (or understand) a budget? How do I improve my work-life balance? How can I use social media to help my science career? If so, then this webinar series is for you! Presenting the next C-DEBI professional development webinar: Making a Proposal Budget: Where to Start. Who do you need to know to help you at your institution? What are the parts of a proposal budget and what is the “budget justification”? Learn the fundamentals to make budgeting an “easy” part of your proposal preparation! Led by Rosalynn Sylvan, C-DEBI Managing Director, University of Southern California Thursday, June 15, 2017, 12pm PT.

In case you missed them, check out the latest Professional Development Seminar on Leveraging Social Media (w/ Dr. Jen Biddle) and Networked Speaker Series (NSS) Seminar, What Heterotrophs Want: Using extracellular enzyme assays to probe the lifestyle of heterotrophic microorganisms in subsurface sediments (w/ Dr. Drew Steen). And stay tuned for the next NSS Seminar, Sept. 7 with Dr. Gus Ramirez!

DCO Webinar Wednesdays Launching 17 May 2017 – NEW!
A new series of DCO webinars focusing on big data modeling and visualization will launch Wednesday, 17 May 2017 at 2 pm EDT. Called “DCO Webinar Wednesdays,” this webinar series builds on the successful workshop program at the Third DCO International Science Meeting and will take place monthly over the summer.  We hope you join in to learn from DCO experts in data science, modeling, and data visualization, who will guide you through a series of available modeling tools and software packages that you can integrate into your research now. Synthesis Group 2019 and the DCO Engagement Team are hosting this series. You can join the webinars live, and follow along on Twitter on the hashtag #DCOWebWed. All webinars will begin with a 30-minute presentation, followed by 15 minutes for open discussion and Q&A. We will archive the webinars as they happen, so don’t worry if you miss one! The final webinar of this series on 12 October 2017 will bring together the presenters for a live Q&A, giving you plenty of opportunity to view the archive and have your questions answered by our panel of experts. Contact Katie Pratt (katie_pratt@uri.edu) or Darlene Trew Crist (dtcristdco@gmail.com) with any questions about the webinar series, or if you would like to propose a future series.

NSF: 2017 STC Professional Development Workshop
Applications are due by June 9, 2017.

Meetings & Activities

ISSM 2017: Call for Abstracts
Abstract submissions due May 29, 2017.

IODP-USSSP: JOIDES Resolution Assessment Workshop, September 26-27, Denver – NEW!
In preparation for the 2018 NSF presentation to the National Science Board seeking renewal of the JOIDES Resolution facility (JR), the U.S. IODP scientific community will convene a workshop to review and assess the role of the JR in meeting the challenges of the 2013-2023 IODP Science Plan, Illuminating Earth’s Past, Present and Future. This assessment will focus on the period beginning with the start of the International Ocean Discovery Program (Expedition 349 in January 2014) and include both an inventory of facility accomplishments and an identification of specific Science Plan challenges that require the continued use of the JR to meet. The workshop aim is to provide community guidance to the NSF via a white paper as it prepares its request to the National Science Board for continued support of the JR to conduct the current IODP Science Plan. Applications are encouraged from all members of the U.S. scientific ocean drilling community, from senior researcher to graduate student, who can provide necessary context to the survey results and contribute to the resulting white paper. Participants with a desire to aid future planning through discussion of research opportunities for the JR that have developed since the start of the current Science Plan are particularly welcome. The application deadline is June 2, 2017.

IODP-USSSP: Drilling into Young Oceanic Crust for Subseafloor Observations at Axial Seamount, October 11-13, Palisades, NY – NEW!
Axial Seamount is the most magmatically active submarine volcano in the northeast Pacific and has been the focus of inter-disciplinary study for over three decades. The range of scientific interests includes volcanology, geophysical characterization and monitoring, hydrothermal vent formation and geochemistry, quantification of heat and chemical fluxes, hydrogeology, and the diversity and evolution of microbiological and animal communities. Axial Seamount erupted in January 1998, April 2011, and April 2015, thus the site presents a unique opportunity to study the interaction between volcanic, hydrothermal, and biological responses to magmatic and volcanic events. For these reasons, Axial Seamount was chosen as one of the key sites on the Ocean Observatories Initiative’s (OOI) cabled observatory network, the Cabled Array (CA). Now that the CA is fully operational with data streaming live to shore for two years from a diverse suite of cabled instruments, we want to explore how ocean drilling and related studies can complement seafloor-based investigations by gaining access to the subseafloor to expand our understanding of microbiological, geophysical, hydrologic, and geochemical processes at Axial Seamount. The overall goal will be to develop a full IODP proposal for drilling and related experiments at Axial Seamount. The workshop will bring together a multidisciplinary group of scientists and engineers across a broad spectrum of ocean sciences and engineering to discuss recent engineering advances and practical issues related to drilling into zero-age oceanic crust, and to identify high priority science objectives and research opportunities that can only be achieved with ocean drilling at Axial Seamount. Contact Julie Huber (jhuber@whoi.edu) with any questions and to apply for the workshop. Deadline to apply: June 30, 2017.

Indian Ocean community workshop, September 11-13, 2017, La Jolla, CA
Abstract submission deadline: July 14, 2017

C-DEBI: Rolling call for Community Workshop support

Employment

Second Genome: Bioinformatic Scientist, Research Solutions

University of Southern Mississippi: PhD and MS Graduate Research Assistantship in Marine Microbial Ecology

University of Southern Mississippi: Postdoctoral Research Position in Marine Microbial Ecology

University of Munich: Postdoctoral scholar, microbial transcriptional activity in subseafloor sediment