|C-DEBI Newsletter – January 16, 2018
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The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans – NEW!
Benjamin J. Tully*, Elaina D. Graham, John F. Heidelberg*
*C-DEBI Contribution 407
Microorganisms play a crucial role in mediating global biogeochemical cycles in the marine environment. By reconstructing the genomes of environmental organisms through metagenomics, researchers are able to study the metabolic potential of Bacteria and Archaea that are resistant to isolation in the laboratory. Utilizing the large metagenomic dataset generated from 234 samples collected during the Tara Oceans circumnavigation expedition, we were able to assemble 102 billion paired-end reads into 562 million contigs, which in turn were co-assembled and consolidated in to 7.2 million contigs ≥2 kb in length. Approximately 1 million of these contigs were binned to reconstruct draft genomes. In total, 2,631 draft genomes with an estimated completion of ≥50% were generated (1,491 draft genomes >70% complete; 603 genomes >90% complete). A majority of the draft genomes were manually assigned phylogeny based on sets of concatenated phylogenetic marker genes and/or 16S rRNA gene sequences. The draft genomes are now publically available for the research community at-large.
Meetings & Activities
NSF: Call for Comments on Update to AC GEO Report on Dynamic Earth
Input can be sent to firstname.lastname@example.org no later than Thursday, February 1, 2018.
NSF: Town Hall at Ocean Sciences Meeting: Ocean Observatories Initiative Research Facility Board – NEW!
There will be an important Town Hall at the upcoming Ocean Sciences meeting in Portland, OR, February 13, 2018, hosted by the Ocean Observatories Initiative Facility Board (OOIFB) of the National Science Foundation (NSF). The OOIFB invites the community to hear the latest information about the OOI facility, meet the OOIFB members, and learn about research using OOI data. The Town Hall will include a series of lightning presentations where scientists will present one slide in one minute explaining how s/he has used the OOI data in their respective research. The OOIFB was created in 2017 to provide independent input and guidance regarding the management and operation of the NSF-funded Ocean Observatories Initiative (OOI). The OOIFB would like to engage the research community to learn about their thoughts and recommendations regarding the OOI. The Town Hall is aimed at researchers who are now using or are considering using OOI data, researchers interested in adding instrumentation to the OOI infrastructure, and educators at all levels interested in the OOI.
Goldschmidt 2018: Session 10a: Geomicrobiology and Microbial Persistence in the Deep Biosphere – NEW!
Attending the Goldschmidt 2018 meeting in Boston, August 12-17? Please consider submitting your abstracts, due March 30, 2018, to Session 10a: Geomicrobiology and Microbial Persistence in the Deep Biosphere (conveners Jiasong Fang, Lars Wörmer, Kasper Kjeldsen, Beth Orcutt, Yohey Suzuki): The continental and marine subsurface hosts microbial life that is involved in globally-significant geochemical transformations while existing under energy limitation and other extreme conditions. Recent advances in developing new and improved detection techniques, lowering detection limits, and increasing single cell and molecular-level resolution have uncovered new information about the size and forms of microbial life in this biosphere, physiologies of microbial groups, and possible evolutionary and adaptation mechanisms at play. However, much is still to be learned about the limits, diversity, extent and function of deep biosphere life. This session invites multidisciplinary contributions that present new findings from continental and/or marine subsurface environments, including “windows” into these systems such as deep-sea hydrothermal vents and cold seeps as well as hot springs and mud volcanoes on land and in the ocean. In particular, we welcome contributions that highlight strategies of microbial persistence in the deep biosphere, such as the formation and dispersal of endospores and other persistence forms.
Find more deep biosphere-related sessions at Goldschmidt under Theme 10: Geobiology, Organic Tracers, and Biogeochemistry.
Each newsletter, we’ll be featuring two, early-career, deep biosphere all-stars from our summer undergraduate programs. Meet the rest of our 2017 Global Enviromental Microbiology students and Community College Cultivation Cohort (C4) REU participants, or learn more about our undergraduate programs!
Education & Outreach
C-DEBI: USC students: apply now for the spring 2018 Genomics and Geobiology Undergraduate Research Experience
We will begin reviewing applications on Tuesday, January 2, 2018 but will continue to review applications until all positions are filled.
Ocean Exploration Trust: Science & Engineering Internship Program
Application Deadline: January 26, 2018.
NOAA: Ernest F. Hollings Undergraduate Scholarship
Application deadline: January 31, 2018.
C-DEBI: Summer Undergraduate Global Environmental Microbiology (GEM) Course
Applications due: February 1, 2018.
IODP-USSSP: A Survey of Outreach and Education Activities in IODP – NEW!
This is an exciting time for IODP outreach and education. Several high-profile drilling expeditions have greatly increased public awareness of the program, international collaboration on IODP outreach activities is at an all-time high, and the U.S. is poised to launch a major outreach effort focused on scientific ocean drilling and the JOIDES Resolution. At the same time, resources for these activities are limited, so the U.S. Science Support Program and U.S. Advisory Committee for Scientific Ocean Drilling would like to solicit feedback from members of the U.S. IODP community regarding your hopes and priorities for the outreach and education programs. Please take a few moments to complete an online education and outreach survey at https://www.surveymonkey.com/r/EO-Community-Survey, and let us know your thoughts. The survey is open through February 2, 2018. Community input is critical to the implementation of a successful outreach program, so we are grateful for your opinions and guidance. You can find a concise annual review of 2017 U.S. outreach and education activity at http://bit.ly/2CJDPd2.
Geobiology 2018: An International Training Course in a Rapidly Evolving Field
Application deadline: February 9, 2018.
ASM: Undergraduate Research Fellowship: Receive Summer Research Stipend
Application Deadline: February 15, 2018.
Bigelow: Research Experience For Undergraduates – NEW!
Undergraduates in Bigelow Laboratory’s summer REU Program spend ten weeks at the Laboratory conducting independent research with guidance from a scientist mentor. Directed by Senior Research Scientist Dr. David Fields, and funded by the National Science Foundation, the REU Program is designed to give students pursuing degrees in the sciences, mathematics and engineering a laboratory-based research experience with an emphasis on hands-on, state-of-the-art methods and technologies. REU students are immersed in the Bigelow community and participate in seminars, field trips, Laboratory outreach programs, social events, and more. Research areas vary year to year, but include marine microbiology, ocean biogeochemistry, optical oceanography, remote sensing, bioinformatics, sensory biology and phytoplankton ecology. The 2018 program dates are May 29 through August 3 and will be held at the Laboratory’s East Boothbay campus. Successful applicants receive a stipend, free housing, and funds for travel to and from Bigelow Laboratory. Applications are due February 15, 2018.
C-DEBI: NSF REU: Community College Cultivation Cohort (C4)
Applications due February 23, 2018.
ASM: Research Capstone Fellowship: Funding For Professional Development and Career Networking
Application Deadline: March 1, 2018.
IODP-USSSP: New IODP Outreach: In Search of Earth’s Secrets – NEW!
In Search of Earth’s Secrets is a special project that aims to bring the JOIDES Resolution and IODP science to communities around the country. It is a 5-year project funded by the NSF’s Education and Human Resources (EHR) division, designed to create “pop-up” science events in the style of pop-up restaurants, stores and art fairs [the microbiology component was supported by a C-DEBI Education & Outreach grant to Sharon Cooper (LDEO)]. The aim is to bring high quality Earth and ocean science content to rural communities and those with a high percentage of traditionally underserved populations, and to create interest in the discoveries of IODP. The project involves working with libraries, youth organizations, program scientists, educators, and museums across the country. The exhibit includes interactive kiosks, a large interactive floor map, and an inflatable walk-through JR showing an immersive ScienceMedia-produced film inside, narrated by actress Michelle Hurd. For more information, to get involved, and to apply to bring Earth’s Secrets to your community, please visit: http://www.insearchofearthssecrets.com.
DCO: Call for Postdoctoral Fellowship Proposals in Deep Life Modeling and Visualization
Proposal submission deadline: January 20, 2018.
DOE: Early Career Research Program – NEW!
The Office of Science of the Department of Energy is pleased to announce the request for applications for the fiscal year 2018 Early Career Research Program. The funding opportunity for researchers in universities and DOE national laboratories, now in its ninth year, supports the development of individual research programs of outstanding scientists early in their careers and stimulates research careers in the disciplines supported by the DOE Office of Science. Opportunities exist in the following program areas: Advanced Scientific Computing Research (ASCR); Biological and Environmental Research (BER); Basic Energy Sciences (BES), Fusion Energy Sciences (FES); High Energy Physics (HEP), and Nuclear Physics (NP). Pre-Application Due Date: January 25, 2018.
Duke: Mary Derrickson McCurdy Visiting Scholar
Application open until January 30, 2018.
NSF: International Research Experiences for Students (IRES)
Track I deadline: January 30, 2018; Track II deadline deadline: February 6, 2018; Track III deadline: February 13, 2018.
NSF: Major Research Instrumentation (MRI)
Submissions due February 5, 2018.
NSF: Research Traineeship (NRT) Program – NEW!
The NSF Research Traineeship (NRT) program is designed to encourage the development and implementation of bold, new, and potentially transformative models for STEM graduate education training. The NRT program seeks proposals that explore ways for graduate students in research-based master’s and doctoral degree programs to develop the skills, knowledge, and competencies needed to pursue a range of STEM careers. The program is dedicated to effective training of STEM graduate students in high priority interdisciplinary research areas, through the use of a comprehensive traineeship model that is innovative, evidence-based, and aligned with changing workforce and research needs. For FY2018, proposals are requested in any interdisciplinary research theme of national priority, with special emphasis on two high priority areas: (1) Harnessing the Data Revolution (HDR) and (2) Innovations at the Nexus of Food, Energy, and Water Systems (INFEWS). Proposal deadline: February 6, 2018.
American Philosophical Society / NAI: Lewis and Clark Fund for Exploration and Field Research in Astrobiology
Deadline: February 15, 2018.
IODP: Apply to Sail on IODP Expedition 383
The deadline to apply is March 1, 2018.
IODP: Apply to Sail on IODP Expedition 385 – NEW!
The International Ocean Discovery Program (IODP) is now accepting applications for scientific participants on Expedition 385 Guaymas Basin Tectonics and Biosphere aboard the JOIDES Resolution. IODP Expedition 385 will core and log a series of sites in the Guaymas Basin to investigate the relationship of tectonics, magmatism, sedimentation, carbon cycling, and microbial activity. The primary objectives are to: (1) explore the physical and chemical gradients along active and extinct fluid pathways associated with sill emplacement; (2) investigate subsurface microbial communities that are sustained by alteration products, in order to determine how efficiently they capture carbon-bearing alteration products; and (3) advance our understanding of the conditions that limit life in the deep biosphere. The expedition will occur from 19 September to 19 November 2019. Additional information about this expedition can be found on the Expedition 385 webpage. 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 participating in this expedition should apply to sail through the U.S. Science Support Program, by visiting http://usoceandiscovery.org/expeditions. The deadline to apply is April 15, 2018.
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.
UCSD / SIO: Assistant Professor – Low-Temperature Geochemistry
Applications due January 31, 2018.
Bermuda Institute of Ocean Sciences (BIOS): Postdoctoral Scholarship in Oceanography – NEW!
A Postdoctoral Scholar award will be offered to a new or recent doctorate in the fields of oceanography and closely related subject. Our ideal candidate will propose to study a multidisciplinary research topic that takes advantage of the research opportunities and facilities offered at BIOS (including frequent access to the deep ocean, repeat measurements and long term monitoring of ocean properties, integration of glider observations with traditional ship-based measurements). 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. The award is designed to further the education and training of the applicant with primary emphasis on supporting the individual’s research promise in his/her chosen area of research. Review of applications will begin February 1, 2018.
U Southern Mississippi: Two tenure-track positions in ocean engineering
Applicant review will begin February 1, 2018 and continue until the position is filled.
U Southern Mississippi: Endowed Chair, Division of Marine Science
Applicant review will begin February, 2018 and continue until the position is filled.
U Alaska Fairbanks: CFOS Assistant or Associate Professor
Applications due February 28, 2018.
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