|C-DEBI Newsletter – May 15, 2018
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Publications & Press
Assessment of apolar lipids in subseafloor rocks and potential contaminants from the Atlantis Massif (IODP Expedition 357) - NEW!
Katherine A. Hickok, Tran B. Nguyen, Susan Q. Lang*
*C-DEBI Contribution 428
International Ocean Discovery Program Expedition 357 drilled 17 boreholes across the Atlantis Massif with the goals of investigating carbon cycling and the presence of life in a zone of active serpentinization. The expedition recovered multiple lithologies including gabbros, basalts, carbonate sands, and serpentinites. A subset of contrasting lithologies were analyzed for apolar lipid content to determine if non-volatile organic molecules can be detected in the oceanic subsurface. The definitive detection and identification of abiotic and biological lipids in the subsurface of an actively serpentinizing system would be a significant step towards understanding a variety of scientific processes, including the evolution of pre-biotic chemistry, microbial habitability, and the global carbon cycle. Given the high potential for contamination during drilling, a suite of materials used in sample collection and processing were also analyzed to characterize their signatures. An n-alkane series ranging from C18 to C30with δ13C isotopic values of –30.9‰ to –28.8‰ was present in lithologically diverse samples. Multiple lines of evidence point to the rock saw used to remove core exteriors during sample processing as the source of these compounds. Many of the other sample-handling procedures designed to reduce surface contamination were determined to be effective and could be implemented in future projects. This result highlights the value of careful prevention and characterization of contamination to allow for more accurate interpretations of complex and dynamic subsurface processes, and the importance that future reports of these compounds occurs in conjunction with thorough contamination assessments.
USC News: USC program creates research pathways for undergrads in science, tech and engineering - NEW!
The Geobiology and Genomics Undergraduate Research Experiences (GGURE) program boosts diversity, helping students learn they can have stimulating experiences in research labs. The program is jointly funded by the Center for Dark Energy Biosphere Investigations (C-DEBI), along with the USC Office of the Provost.
Cape Cod Regional Stem Network: WHOI Summer Internship Combines Sun, Sea, and Science - NEW!
The seaside community of Woods Hole in Falmouth offers iconic Cape Cod summers with a scientific bend. From sunny beaches to the mysterious deep blue sea, CCCC STEM students interested in exploring the ocean’s frontiers are among those chosen for a summer of cutting-edge research. The eight week Community College Research Internship for Scientific Engagement (CC-RISE), is a paid summer internship that benefits CCCC STEM-focused scholars. Through a National Science Foundation grant, CC-RISE partners with WHOI to provide community college students the chance to join leading scientists in their exploration of the deepsea biosphere.
Meetings & Activities
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: Networked Speaker Series #18: Dr. Alma Parada, Stanford University, May 31, online, 9:30 AM HT / 12:30 PM PT / 3:30 PM ET - NEW!
Evaluating the diversity and distribution of novel microbes across physical and geochemical gradients in deep-sea sediments. Marine sediments harbor an estimated 50% of all microbes on earth. Despite this numerical importance, the factors controlling the diversity, metabolism, and distribution of these benthic microbes, especially in representative deep-sea sediments, are poorly understood. In this study, we collected sediment cores at 8 sites across a 300km transect off the coast of San Francisco spanning 100-4500m water depths and 0-30cm sediment depths. Using Illumina sequencing of the 16S rRNA gene and transcripts, we characterized the microbial community to compare changes in the physical and chemical parameters of the sediment to changes in the microbial community and metabolic potential. Canonical correspondence analysis indicated site, pressure, temperature and oxygen concentrations of the overlying water was correlated to stratification of the microbial community water depth, while pore water ammonium and nitrate concentrations correlated to differences in the communities across sediment depths. Interestingly, an average of 34% of the operational taxonomic units (OTUs) present in each sample were <90% similar to the 16S rRNA gene of any representative genome in the GenBank database. To investigate the metabolic capabilities of these uncharacterized lineages, we sequenced a metagenome from surface sediment at 3500m water depth and used a novel assembly method that combines 10X genomics technology and barcoded reads. We obtained 24 metagenome assembled genomes (MAGs) with >70% completion, <10% contamination, and a 16S rRNA gene. Of these, 13 (~55%) MAGs had 16S rRNA genes <90% similar to representative genomes in GenBank. OTUs with a percent identity of 99-100% to the 16S of these MAGs were widely distributed and active across the transect. The widespread presence of potentially novel organisms in sediments at depths representative of the majority of ocean indicates the importance of previously uncharacterized microbes in global carbon and biogeochemical cycles.
IODP: Workshop Announcement: Scientific Exploration of the Arctic and North Pacific, September 25-27, 2018, Mt. Hood, OR
The workshop is open to U.S. and international participants, and the deadline for U.S.-affilitated scientists to apply is June 17, 2018.
NAI: Astrobiology Webinar with Rika Anderson (Carleton College) now online - NEW!
C-DEBI: Rolling call for Community Workshop support
C-DEBI: Protocols.io Group Page
C-DEBI: Subseafloor Cultures Database
Education & Outreach
C-DEBI: Next Professional Development Webinar: June 20, 12pm PT - NEW!
Brandi Reese (Assistant Professor, TAMU-CC) leads the next C-DEBI Professional Development Webinar on “What I wish I knew before I knew it: Surviving the early years of tenure-track faculty.” The access URL for the webinar is http://usccollege.adobeconnect.com/cdebiremote/. Missed the most recent C-DEBI Professional Development Webinar on “Sharing Data: The Joys of Open Science” with Ben Tully (C-DEBI Bioinformatic Specialist)? Watch it on YouTube.
MARUM: ECORD 2018 Summer School on Sub-seafloor fluid transport and gas hydrate dynamics
The application deadline is May 25, 2018.
C-DEBI: Bioinformatics Workshop for Metagenomic and Microbiome Analysis
Detailed insight into the microbiome of a system can shape our understanding of it, but the learning curve for incorporating computationally intensive tools can be very high! Join instructor Dr. Benjamin Tully, C-DEBI Bioinformatic Specialist, for an upcoming bioinformatics workshop at the University of Southern California, June 21-22, 2018. All expenses are covered courtesy of the NSF STCs C-DEBI, EBICS, and BEACON. Topics include: Unix command line; Illumina sequence quality control; Metagenomic experimental design; Sequence Assembly; Metageomic binning; Functional Annotation; and Phylogenetic analysis. Note: participation requires a laptop with 40 GB of hard drive space. To apply: email email@example.com by May 28, 2018 – be sure to include your home institution, your home STC, and what you hope to get out of the workshop. All levels are welcome. There is a 15 participant maximum, so apply soon!
MEDSALT: Deep Life in Buried Salt Deposits Training School @ U Essex and and Boulby Intl. Subsurface Astrobio Lab (UK), September 9-16, 2018 - NEW!
The goal of the Deep Life in Buried Salt Deposits course is to provide training for Ph.D. students and early career researchers in the microbiology and geochemistry needed to investigate life in buried salt deposits. The course includes lectures, laboratory practicals and an underground experience at the Boulby International Subsurface Astrobiology Laboratory! The organizing committee and lecturers include Giovanni Aloisi (IPGP, France), Terry McGenity (University of Essex, UK), Tina Treude (University of California, Los Angeles, USA), Charles Cockell (University of Edinburgh, UK), Sean Paling (University of Sheffield, UK), Josefa Anton Botella (University of Alicante, Spain) and Petra Rettberg (German Aerospace Center, DLR). MEDSALT will support the participation of up to 20 trainees with a fixed grant to cover travel and subsistence costs. Applications due June 15, 2018.
NSF: Dear Colleague Letter: Advancing Long-term Reuse of Scientific Data
The deadline for submission of Conference and EAGER proposals proposal submission date is May 23, 2018.
IODP-USSSP: Proposals for Pre-Drilling Activities and Workshops - NEW!
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, 2018.
NSF: Tribal Colleges and Universities Program (TCUP) - NEW!
The Tribal Colleges and Universities Program (TCUP) provides awards to Tribal Colleges and Universities, Alaska Native-serving institutions, and Native Hawaiian-serving institutions to promote high quality science (including sociology, psychology, anthropology, economics, statistics, and other social and behavioral sciences as well as natural sciences), technology, engineering and mathematics (STEM) education, research, and outreach. Support is available:
- To TCUP-eligible institutions for transformative capacity-building projects
- For collaborations that involve multiple institutions of higher education, led by TCUP institutions. Including the Partnerships for Geoscience Education (PAGE), proposals due June 11, 2018.
- To individual faculty members for research studies at TCUP institutions. Including Small Grants for Research (SGR) projects, proposals due December 10, 2018.
Simons Postdoctoral Fellowships in Marine Microbial Ecology
Application deadline: June 15, 2018.
DCO: RFP: Census of Deep Life Sequencing Opportunities
The proposal deadline is July 15, 2018.
NSF: Graduate Research Fellowship Program (GRFP) - Graduate Research Internship Program (GRIP)
GRIP applications are due December 4, 2018.
DCO: Deep Life Cultivation Internship Program
NSF: Arctic Sciences Program Solicitation
Proposals accepted anytime.
C-DEBI: Rolling call for Research Exchange proposals
Karlsruhe Institute of Technology: Ph.D. and Postdoc position available - NEW!
Hunting the Microbial Dark Matter: Prokaryotic microorganisms are the oldest, most abundant, and particularly most diverse forms of life on earth and dominate many functions of the biosphere, including the global cycles of carbon. They also harbor an enormous potential for novel natural product discovery, bioremediation and bioenergy production. However, it is estimated that over 99% of all microbial species from environmental microcosms remain uncultured, attempts to grow them under laboratory conditions fail or they grow too slowly to obtain sufficient biomass for analysis. Genome sequencing for the vast majority of Prokaryotes has therefore been inaccessible, obscuring the knowledge of microbial diversity, metabolic potentials and evolutionary histories. We are a young dynamic group using culture-independent approaches like Single Cell Genomics and Metagenomics in combination with Bioinformatics to hunt for unknown microorganisms in various interesting habitats. Ph.D. position: We seek highly motivated and creative persons with a Masters degree in Biology/Bioinformatics/Chemistry or related fields, interests and knowledge in microbiology, bioinformatics, molecular genetics, evolution and ecology. Knowledge in command-line programming (e.g. perl, python, R) and data processing/analysis as well as in next-generation sequencing techniques and molecular biology methods is a plus but not necessary. Postdoc position: We seek highly motivated and creative persons with a Ph.D. in Biology/Bioinformatics/Chemistry or related fields, interests and knowledge in bioinformatics (command-line programming) and preferably teaching experience. For more info and applications please email Prof. Anne Kaster (firstname.lastname@example.org).
TAMU: IODP-JRSO Assistant Research Scientist Position
We will begin reviewing applications on June 30, 2018, but will continue to accept applications until candidates are selected for interviews.
Two Faculty Positions at Shanghai Ocean University
BIOS: Postdoctoral Scholarship in Oceanography
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