|C-DEBI Newsletter – December 3, 2018
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Publications & Press
Environmental Microbiology Reports
Take to the high seas: microbiology labs below the ocean surface - NEW!
Julie A. Huber*, Christina Preston
*C-DEBI Contribution 445
Looking into the Crystal Ball, near term we see an expanding toolkit for microbial oceanographers and environmental microbiologists more broadly, allowing for improved spatial and temporal sampling, as well as in situ experimentation and analysis. Given many of the pieces exist in different instruments, we are confident that focused efforts to bring them together in one instrument to take us from sample collection to experiment to data is possible. Importantly, there will always be a need for expeditionary‐ and laboratory‐based work. The power of being at sea to take in a new study site and carefully collect those first few samples, thus building the hypotheses and experiments needed to answer the scientific questions, cannot be replaced. The oceans remain woefully under‐studied and under‐sampled, and the powerful microbial engines of the marine biosphere merit our attention and innovation. The next decade will provide important opportunities to observe, study and query marine microorganisms from afar, watching experiments unfold in real time as our instruments help carry out our mission to explore Earth's inner space below the ocean's surface.
Applied and Environmental Microbiology
Microbial organic matter degradation potential in Baltic Sea sediments influenced by depositional conditions and in situ geochemistry - NEW!
Laura A. Zinke*, Clemens Glombitza, Jordan T. Bird, Hans Røy, Bo Barker Jørgensen, Karen G. Lloyd, Jan P. Amend*, Brandi Kiel Reese
*C-DEBI Contribution 448
Globally, marine sediments are a vast repository of organic matter which is degraded through various microbial pathways, including polymer hydrolysis and monomer fermentation. The sources, abundances, and quality (i.e. labile or recalcitrant) of the organic matter and the composition of the microbial assemblages vary between sediments. Here, we examine new and previously published sediment metagenomes from the Baltic Sea and the nearby Kattegat to determine connections between geochemistry and the community potential to degrade organic carbon. Diverse organic matter hydrolysis encoding genes were present in sediments between 0.25 to 67 meters below seafloor, and were in higher relative abundances in those sediments that contained more organic matter. New analysis of previously published metatranscriptomes demonstrated that many of these genes were transcribed in two organic-rich Holocene sediments. Some of the variation in deduced pathways in the metagenomes correlated to carbon content and depositional conditions. Fermentation-related genes were found in all samples, and encoded for multiple fermentation strategies. Notably, genes conferring alcohol metabolism were amongst the most abundant of these genes, indicating this is an important but underappreciated aspect of sediment carbon cycling. This study is a step towards a more complete understanding of microbial food webs and the impacts of depositional facies on present sedimentary microbial communities.
Frontiers in Microbiology
Comparative Genomics and Proteomic Analysis of Assimilatory Sulfate Reduction Pathways in Anaerobic Methanotrophic Archaea - NEW!
Hang Yu, Dwi Susanti, Shawn E. McGlynn, Connor. T. Skennerton, Karuna Chourey, Ramsunder Iyer, Silvan Scheller, Patricia L. Tavormina, Robert L. Hettich, Biswarup Mukhopadhyay, Victoria J. Orphan*
*C-DEBI Contribution 449
Sulfate is the predominant electron acceptor for anaerobic oxidation of methane (AOM) in marine sediments. This process is carried out by a syntrophic consortium of anaerobic methanotrophic archaea (ANME) and sulfate reducing bacteria (SRB) through an energy conservation mechanism that is still poorly understood. It was previously hypothesized that ANME alone could couple methane oxidation to dissimilatory sulfate reduction, but a genetic and biochemical basis for this proposal has not been identified. Using comparative genomic and phylogenetic analyses, we found the genetic capacity in ANME and related methanogenic archaea for sulfate reduction, including sulfate adenylyltransferase, APS kinase, APS/PAPS reductase and two different sulfite reductases. Based on characterized homologs and the lack of associated energy conserving complexes, the sulfate reduction pathways in ANME are likely used for assimilation but not dissimilation of sulfate. Environmental metaproteomic analysis confirmed the expression of 6 proteins in the sulfate assimilation pathway of ANME. The highest expressed proteins related to sulfate assimilation were two sulfite reductases, namely assimilatory-type low-molecular-weight sulfite reductase (alSir) and a divergent group of coenzyme F420-dependent sulfite reductase (Group II Fsr). In methane seep sediment microcosm experiments, however, sulfite and zero-valent sulfur amendments were inhibitory to ANME-2a/2c while growth in their syntrophic SRB partner was not observed. Combined with our genomic and metaproteomic results, the passage of sulfur species by ANME as metabolic intermediates for their SRB partners is unlikely. Instead, our findings point to a possible niche for ANME to assimilate inorganic sulfur compounds more oxidized than sulfide in anoxic marine environments.
Tunnel Formation in Basalt Glass - NEW!
Martin R. Fisk, Radu Popa, and David Wacey
We propose a model whereby microscopic tunnels form in basalt glass in response to a natural proton flux from seawater into the glass. This flux is generated by the alteration of the glass as protons from water replace cations in the glass. In our proton gradient model, cells are gateways through which protons enter and alter the glass and through which cations leave the glass. In the process, tunnels are formed, and cells derive energy from the proton and ion fluxes. Proton flux from seawater into basalt glass would have occurred on Earth as soon as water accumulated on the surface and would have preceded biological redox catalysis. Tunnels in modern basalts are similar to tunnels in Archean basalts, which may be our earliest physical evidence of life. Proton gradients like those described in this paper certainly exist on other planetary bodies where silicate rocks are exposed to acidic to slightly alkaline water.
||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!|
NSF: Deep biosphere beneath the seafloor explored at American Geophysical Union fall meeting - NEW!
Scientists present recent findings on ‘dark energy’ in the subsurface biosphere.
Meetings & Activities
AGU: 2018 Fall Meeting Deep Biosphere-related Sessions of Interest - UPDATED!
Attending the 2018 AGU Fall Meeting in Washington D.C., December 10-14, 2018? Be sure to check out these C-DEBI-related sessions of interest! See also the Deep Carbon Observatory’s AGU Fall Meeting Guide. Missing a session of interest? Let us know!
DCO Webinar: Breaking the mold of the traditional field expedition: Biology Meets Subduction - NEW!
The sampling expedition Biology Meets Subduction: A Collaborative and Multidisciplinary Deep Carbon Field Initiative was designed to develop novel connections between microbiology, volcanic systems, and the cycling of living and dead (biotic and abiotic) carbon as Earth’s plates move and subduct past each other. With the fieldwork complete, the team, led by DCO early career scientists has started to publish their findings. Join Peter Barry (University of Oxford, UK), Karen Lloyd (University of Tennessee Knoxville, USA), and Donato Giovannelli(CNR-IRBIM, Italy and Rutgers University, USA) as they discuss their fieldwork in Costa Rica and Panama and share the value added and problems created by conducting a multidisciplinary scientific investigation in the field. The live webinar will be held January 23, 2019 at 11am PT / 2pm ET.
Education & Outreach
C-DEBI: Latest Professional Development Webinar Now Online! - NEW!
Missed the last Professional Development Webinar on “Scientific editing as a career” with Delphine Defforey (Nature Communications)? Watch it on YouTube.
CalTech: Geobiology 2019: An International Training Course in a Rapidly Evolving Field
Applications are due by February 8, 2019.
2018 Guaymas Basin Cruise Blog
NSF: Graduate Research Fellowship Program (GRFP) - Graduate Research Internship Program (GRIP)
GRIP applications are due December 4, 2018.
IODP-USSSP: Apply for a Schlanger Ocean Drilling Fellowship
The submission deadline is December 7, 2018.
NOPP: FY2019 Broad Agency Announcement
Proposal deadlines of December 21, 2018 and January 18. 2019.
NSF: Understanding the Rules of Life (URoL): Epigenetics
Full proposal deadline: February 1, 2019.
IODP-USSSP: Apply to Sail on Expedition 387: Amazon Margin - NEW!
The International Ocean Discovery Program (IODP) is now accepting applications for scientific participants on Expedition 387 Amazon Margin, aboard the JOIDES Resolution. IODP Expedition 387 will drill the upper portion of the Foz do Amazonas basin of the equatorial margin of Brazil to recover a complete, high-resolution sedimentary sequence spanning nearly the entire Cenozoic. This expedition is the marine complement to the Trans-Amazon Drilling Project transect of continental drill sites, and will address fundamental questions about the Cenozoic climatic evolution of the Amazon region, the origins and evolution of the neotropical rain forest and its incomparable biodiversity, the paleoceanographic history of the western equatorial Atlantic, and the origins of the transcontinental Amazon River. Core and log data from sites on the uppermost continental slope will be used to: (1) generate a continuous record of climate and biodiversity in Cenozoic South America at unprecedented resolution; (2) reconstruct the oceanographic conditions of the western tropical Atlantic; (3) provide critical marine biostratigraphic control for correlation with the Trans-Amazon Drilling Project; (4) determine the onset and history of trans-continental drainage of the proto-Amazon River into the Atlantic; and (5) test major hypotheses about the originations and extinctions of tropical South American biota. The expedition will take place from 26 April to 26 June 2020. Opportunities exist for researchers (including graduate students) in all shipboard specialties, including but not limited to sedimentologists, micropaleontologists, paleomagnetists, inorganic/organic geochemists, petrologists, petrophysicists, microbiologists, and borehole geophysicists. U.S.-affiliated scientists interested in responding to the special call should apply to sail through the U.S. Science Support Program. The deadline to apply is March 1, 2019.
IODP-USSSP: Apply to Sail on Expedition 388: Equatorial Atlantic Gateway - NEW!
The International Ocean Discovery Program (IODP) is now accepting applications for scientific participants on Expedition 388 Equatorial Atlantic Gateway, aboard the JOIDES Resolution. IODP Expedition 388 will study the tectonic, climatic, and biotic evolution of the Equatorial Atlantic Gateway (EAG) at three sites on and near the Pernambuco Plateau (northeastern Brazilian continental shelf). These will target Late Cretaceous-Recent sediments and oceanic crust and are strategically located both near the continental margin and at paleo-water depths that are shallow enough (< 2000 m) to provide well-preserved organic biomarkers and calcareous microfossils for proxy reconstructions of greenhouse climates. Core and log data will address four key themes: (1) the early rift history of the Equatorial Atlantic; (2) the biogeochemistry of the restricted Equatorial Atlantic; (3) the long-term paleoceanography of the EAG; and, (4) the limits of tropical climates and ecosystems under conditions of extreme warmth. This expedition will constrain the long-term interactions between tectonics, oceanography, ocean biogeochemistry and climate, and the functioning of tropical ecosystems and climate during intervals of extreme warmth. The expedition will take place from 26 June to 26 August 2020. Opportunities exist for researchers (including graduate students) in all shipboard specialties, including but not limited to sedimentologists, micropaleontologists, paleomagnetists, inorganic/organic geochemists, microbiologists, petrologists, petrophysicists, and borehole geophysicists. U.S.-affiliated scientists interested in responding to the special call should apply to sail through the U.S. Science Support Program. The deadline to apply is April 1, 2019.
NSF: Opportunities for Promoting Understanding through Synthesis (OPUS)
Full proposal deadline: August 5, 2019.
- C-DEBI: Rolling call for Research Exchange proposals
- DCO: Deep Life Cultivation Internship Program
- IODP-USSSP: Proposals for Pre-Drilling Activities
- NSF: Arctic Sciences Program Solicitation
- NSF: Division of Environmental Biology (core programs) (DEB)
- NSF: Infrastructure Innovation for Biological Research (IIBR)
- NSF: Instrument Capacity for Biological Research (ICBR)
- NSF: Non-Academic Research Internships for Graduate Students (INTERN) Supplemental Funding Opportunity
- NSF: Research Assistantships for High School Students (RAHSS): Funding to Broaden Participation in the Biological Sciences
- NSF: Research Experience for Teachers (RET): Funding Opportunity in the Biological Sciences
- NSF: Tribal Colleges and Universities Program (TCUP)
Yale: Bateman Postdoctoral Fellowship
The deadline for receipt of all application materials is December 15, 2018.
WHOI: Tenure Track Staff Scientist- Marine Chemistry & Geochemistry
Review of applications will begin on December 17, 2018.
U Oldenburg: Professorship in Benthic Microbiology - NEW!
The Institute for Chemistry and Biology of the Marine Environment (ICBM) at the School of Mathematics and Natural Sciences invites applications for the position of a Professorship (W3) in Benthic Microbiology commencing as soon as possible. The appointed professor is expected to cover the complete field of teaching microbiology in the Bachelor’s and Master’s programs of the School of Mathematics and Natural Sciences. We seek a microbiologist with distinct expertise in physiology and diversity of prokaryotes, preferentially with anaerobic organisms. The appointed professor should investigate fundamental questions in marine microbiology, combining classical-microbiological and modern OMICS-driven approaches, and bearing the potential for modern and innovative microbiome research. It is expected that the appointed professor will contribute to future interdisciplinary, process-oriented research projects of the ICBM (see collaborative research at www.icbm.de) and participate in joint research cruises. Prerequisites for employment include a dissertation of superior quality, a habilitation or an equivalent scientific achievement, and pedagogical aptitude proven by practical experience. Excellence in research is expected as well as international experience, generally attained by a research stay abroad. Successful acquisition of third-party funds is required. Applications should be submitted by no later than January 15, 2019.
USGS: Mendenhall Research Fellowship Program
The deadline for submission is Friday, January 18, 2019.
MSU: Assistant/Associate Professor of Environmental Microbiology - NEW!
The Department of Microbiology & Immunology at Montana State University invites applications for an Assistant/Associate Professor tenure-track faculty position in the field of environmental microbiology. Microorganisms drive global geochemical cycles and link critical ecosystem processes influencing plant, animal, and environmental health. We seek to attract an exceptional individual to establish a nationally recognized, externally funded research program aimed at understanding the dynamic interactions between microbial life and the environment, to teach both undergraduate and graduate students through development of innovative courses, and to participate in professional/service activities. We are particularly interested in individuals whose work complements and strengthens the research interests of MSU faculty, including those focused on microbial physiology and ecology, molecular evolution, virology, biomedical microbiology, environmental health, and host-pathogen interactions. Screening of applications will begin on February 1, 2019; however, applications will continue to be accepted until an adequate applicant pool has been established.
U Toronto: Postdoctoral Positions in Fluid-Rock Interactions and Deep Subsurface Life - NEW!
One or more postdoctoral positions are available for research projects on the origin, residence times and geochemical signatures of deep crustal fluids and the subsurface microbial communities that are sustained by water-rock reactions in the deep Earth. Field, laboratory and modeling opportunities are available to extend the existing program to explore the implications of our work on Earth analogs to the search for life on the rocky bodies and ocean worlds of our solar system. Applicants with a PhD in geochemistry, geobiology, chemistry or related disciplines are encouraged to apply. Contact: Dr. B. Sherwood Lollar, email@example.com. Position is open immediately and will remain open until the position(s) are filled.
UNC Chapel Hill: Guaymas Basin postdoc opportunity
TAMU: Instructional Assistant Professor
BMSIS: Postdoctoral Scholar Position Available in Evolutionary and Isotopic Enzymology
BIOS: Postdoctoral Scholarship in Oceanography
U South Florida: Two Tenure-Track Faculty Positions in Chemical and Geological Oceanography
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