C-DEBI Newsletter – October 15, 2018

Publications & Press

Nature Biotechnology
High-quality genome sequences of uncultured microbes by assembly of read clouds – NEW!
Alex Bishara, Eli L. Moss, Mikhail Kolmogorov, Alma E. Parada*, Ziming Weng, Arend Sidow, Anne E. Dekas*, Serafim Batzoglou, Ami S. Bhatt
*C-DEBI Contribution 440

Although shotgun metagenomic sequencing of microbiome samples enables partial reconstruction of strain-level community structure, obtaining high-quality microbial genome drafts without isolation and culture remains difficult. Here, we present an application of read clouds, short-read sequences tagged with long-range information, to microbiome samples. We present Athena, a de novo assembler that uses read clouds to improve metagenomic assemblies. We applied this approach to sequence stool samples from two healthy individuals and compared it with existing short-read and synthetic long-read metagenomic sequencing techniques. Read-cloud metagenomic sequencing and Athena assembly produced the most comprehensive individual genome drafts with high contiguity (>200-kb N50, fewer than ten contigs), even for bacteria with relatively low (20×) raw short-read-sequence coverage. We also sequenced a complex marine-sediment sample and generated 24 intermediate-quality genome drafts (>70% complete, <10% contaminated), nine of which were complete (>90% complete, <5% contaminated). Our approach allows for culture-free generation of high-quality microbial genome drafts by using a single shotgun experiment.
 

The Scientist: Life Thrives Within the Earth’s Crust – NEW!
From journeys into mines to explorations of volcanoes on the ocean floor, deep voyages reveal the richness of the planet’s deep biosphere. Featuring C-DEBI researchers Jason Sylvan and Julie Huber.

Motherboard: Methane-Eating Ocean Microbes Could Play a Major Role in Climate Change – NEW!
Caltech geobiologist and MacArthur Fellow Victoria Orphan sheds light on the tiny single-celled organisms that help keep Earth’s climate in check.

Proposal Calls

Apply to sail now as an Onboard Outreach Officer on Expedition 385: Guaymas Basin Tectonics and Biosphere
Application period ends on October 19, 2018.

NSF: Graduate Research Fellowship Program (GRFP)
Application deadlines: October 22-26, 2018.

NSF: Postdoctoral Research Fellowships in Biology (PRFB) – NEW!
The Directorate for Biological Sciences (BIO) awards Postdoctoral Research Fellowships in Biology to recent recipients of the doctoral degree for research and training in selected areas supported by BIO and with special goals for human resource development in biology.  The fellowships encourage independence at an early stage of the research career to permit Fellows to pursue their research and training goals in the most appropriate research locations regardless of the availability of funding for the Fellows at that site. For FY 2015 and beyond, these BIO programs are (1) Broadening Participation of Groups Under-represented in Biology, (2) Research Using Biological Collections, and (3) National Plant Genome Initiative (NPGI) Postdoctoral Research Fellowships. These areas change periodically as new scientific and infrastructure opportunities present themselves. For this reason, this solicitation will be changed as necessary to reflect the areas being funded. Full proposal deadline date: November 6, 2018.

IODP: Apply to Sail on IODP Expedition 389
The deadline to apply is November 23, 2018.

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 – NEW!
The U.S. Science Support Program is currently accepting applications for the 2019-2020 Schlanger Ocean Drilling Fellowship Program. The Schlanger Fellowship Program offers merit-based awards for outstanding graduate students to conduct research related to the International Ocean Discovery Program. Research may be related to the objectives of past expeditions or it may address broader science themes. Selected fellows will receive an award of $30,000 for a 12-month period that can be used for research, stipend, tuition, or other approved costs. Schlanger Fellowships are open to all graduate students enrolled at U.S. institutions in full-time M.S. or Ph.D. programs. Applications require reference material from two referees, one of which must be the student’s faculty advisor. 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 – NEW!
Successful projects of the URoL:Epigenetics Program are anticipated to use complementary, interdisciplinary approaches to investigate how epigenetic phenomena lead to emergent properties that explain the fundamental behavior of living systems. Ultimately, successful projects should identify general principles (“rules”) that underlie a wide spectrum of biological phenomena across size, complexity (e.g., molecular, cellular, organismal, population) and temporal scales (from sub-second to geologic) in taxa from anywhere within the tree of life. URoL:Epigenetics projects must integrate perspectives and research approaches from more than one research discipline (e.g., biology, chemistry, computer science, engineering, geology, mathematics, physics, social and behavioral sciences). The interdisciplinary scope of URoL:Epigenetics projects also provides unique training and outreach possibilities to train the next generation of scientists in a diversity of approaches and to engage society more generally. Full proposal deadline: February 1, 2019.

Rolling Calls:

• 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)

Employment

Bigelow: Two Postdoctoral Researchers in Single Cell Genome-to-Phenome Studies of Environmental Microorganisms
Applications due November 1, 2018.

Harvard: Tenure-Track Professor in Earth History
Application Deadline: November 1, 2018.

Rice: Wiess and Pan Post-Doctoral Research Fellowships
The applications are due on November 1, 2018.

Nature Research: Associate/Senior Editors – Nature Reviews Earth & Environment – NEW!
Nature Research, the publisher of Nature, is looking to recruit two Associate or Senior Editors for Nature Reviews Earth and Environment, a new journal that will launch in 2020. Nature Reviews Earth and Environment will join our highly influential family of Nature Reviews journals, renowned for their editorial quality and supported by best-in-class artwork. Our aim in launching Nature Reviews Earth and Environment is to provide the broad scientific community with high-quality, critical reviews of the latest, most important findings in all areas of earth and environmental sciences. As part of this exciting new publishing venture, we are now recruiting two Associate or Senior Editors for Nature Reviews Earth and Environment. Broad scientific knowledge and training, excellent literary skills, the ability to absorb new areas of research, and a keen interest in the practice and communication of science are all required. Candidates with expertise in geology or biogeochemistry are particularly encouraged to apply. Working closely with the Chief Editor, the editors will commission articles, edit manuscripts, organise peer review, write for the journal, and develop the journal’s website. The ideal candidates will have a PhD in a core aspect of earth or environmental science and ideally relevant postdoctoral research experience. Previous editorial experience would be an advantage, but is not essential. The position will be based in the London office of Springer Nature, and the terms and conditions are competitive, reflecting the importance and responsibilities of the role. Closing Date: November 8, 2018

Bigelow: Senior Research Scientist
For full consideration, the application should be received by November 30, 2018.

ASU: 2019 Exploration Fellowship in Earth and Space Science – NEW!
The School of Earth and Space Exploration (SESE) at Arizona State University invites applications for the postdoctoral research scholar position of Exploration Fellow. The mission of the postdoctoral fellowship is to foster SESE’s interdisciplinary research program by attracting and supporting outstanding early-career scientists and engineers to pursue independent research in collaboration with SESE faculty. Research areas within SESE encompass theoretical and observational astrophysics, astrobiology, cosmology, earth and planetary science, instrumentation and systems engineering, and science education. Anticipated start date for the position is July 2019. Incoming Fellows will receive an annual stipend of $65,000 with health benefits, plus $12,000 per year in discretionary research funds. A relocation allowance will be provided. The initial appointment is for one year with subsequent annual renewal for up to a total of three years, contingent upon satisfactory performance, the needs of the university, and availability of resources. Initial review of complete applications will begin on December 1, 2018.

WHOI: Tenure Track Staff Scientist- Marine Chemistry & Geochemistry – NEW!
The Marine Chemistry & Geochemistry at the Woods Hole Oceanographic Institution (WHOI) invites exceptional candidates to apply to one or more of our full-time exempt tenure track positions on our scientific staff. We seek to hire at the Assistant Scientist level; however, extraordinary candidates may be considered at Associate Scientist without Tenure, Associate Scientist with Tenure, or Senior Scientist levels. The successful candidate(s) will conduct research in any area of marine chemistry and geochemistry that complements existing programs on the chemistry of the ocean and its interactions with the Earth as a whole. Core departmental strengths include: biogeochemistry and organic geochemistry; microbial ecology and molecular biology; carbon, nutrient, and trace element cycling; environmental change including climate change, air sea exchange; photochemistry; coastal, estuarine, wetland and river geochemistry & biogeochemistry; sediment geochemistry; fluid-rock interactions; igneous geochemistry; noble gas geochemistry; and isotope systematics, including radiochemistry. Applicants should have a doctoral degree, postdoctoral experience, and a record of scientific research publications in scholarly journals. Scientific staff members are expected to develop independent, externally-funded, and internationally-recognized research programs. They also have the option of advising graduate students and teaching courses through the MIT/WHOI Joint Program in Oceanography and Oceanographic Engineering. WHOI’s Scientific Staff is expected to provide for their salaries from grants and contracts. The Institution provides salary support when no other funding is available, as well as significant internal funding opportunities for developing innovative research projects. Candidates hired at the junior level will receive an initial appointment for four years with salary guaranteed. Review of applications will begin on December 17, 2018.

BMSIS: Postdoctoral Scholar Position Available in Evolutionary and Isotopic Enzymology

U Delaware: Postdoctoral positions in genetic markers and biochemistry of microbial Fe oxidation

BIOS: Postdoctoral Scholarship in Oceanography

U South Florida: Two Tenure-Track Faculty Positions in Chemical and Geological Oceanography

U Southern Mississippi: Three Positions (Postdoctoral Researcher, Graduate Student, Research Technician) in Marine Microbial Ecology