C-DEBI Newsletter – June 1, 2020

C-DEBI Newsletter – June 1, 2020
This newsletter is also accessible via our website (https://www.darkenergybiosphere.org) .

Publications & Press
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Bioinformatics
MetaSanity: An integrated microbial genome evaluation and annotation pipeline (http://dx.doi.org/10.1093/bioinformatics/btaa512) – NEW!
Christopher Neely*, Elaina D. Graham, Benjamin J. Tully*
*C-DEBI Contribution 533

As the importance of microbiome research continues to become more prevalent and essential to understanding a wide variety of ecosystems (e.g., marine, built, host-associated, etc.), there is a need for researchers to be able to perform highly reproducible and quality analysis of microbial genomes. MetaSanity incorporates analyses from eleven existing and widely used genome evaluation and annotation suites into a single, distributable workflow, thereby decreasing the workload of microbiologists by allowing for a flexible, expansive data analysis pipeline. MetaSanity has been designed to provide separate, reproducible workflows, that (1) can determine the overall quality of a microbial genome, while providing a putative phylogenetic assignment, and (2) can assign structural and functional gene annotations with varying degrees of specificity to suit the needs of the researcher. The software suite combines the results from several tools to provide broad insights into overall metabolic function.
Importantly, this software provides built-in optimization for “big data” analysis by storing all relevant outputs in an SQL database, allowing users to query all the results for the elements that will most impact their research.

Frontiers for Young Minds
Microbial Life Deep Under the Seafloor—A Story of Not Giving Up (https://kids.frontiersin.org/article/10.3389/frym.2020.00070) – NEW!
-Man-Yin Tsang, Fumio Inagaki-

Below the seafloor are trillions of single-celled microbial life. Marine sediments bury these microorganisms deeper and deeper. Meanwhile, the microorganisms face increasing pressures and temperatures and reduced amounts of food and water. Although they are living in difficult conditions, these microorganisms stay alive and maintain their communities. To date, we know that these microbial communities can survive for millions of years, at 2.5 km below the seafloor, and at temperatures over 100°C. Scientists use multiple approaches to study these fascinating microorganisms.

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! (mailto:janicak@usc.edu)

-Quanta Magazine: Inside Deep Undersea Rocks, Life Thrives Without the Sun (https://www.quantamagazine.org/inside-deep-undersea-rocks-life-thrives-without-the-sun-20200513/) — (https://kids.frontiersin.org/article/10.3389/frym.2020.00070) — NEW!
Newly discovered worlds of microbes far beneath the ocean floor, inside old basaltic rocks, could point to a greater likelihood of life elsewhere in the universe. Featuring deep biosphere researchers Karen Lloyd, Barbara Sherwood Lollar, Virginia Edgcomb, Martin Fisk, Steve D’Hondt, William Orsi, Yohey Suzuki, Jason Sylvan, Tullis Onstott and Jennifer Biddle. Reprinted in The Atlantic (https://www.theatlantic.com/science/archive/2020/05/life-microbes-ocean-floor/611755/) .

Meetings & Activities
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-C-DEBI: Nominations open for the 2020 Networked Speaker Series (http://www.darkenergybiosphere.org/outputs-resources/networked-speaker-series/) –
C-DEBI seeks nominations for three speakers for the 2020 program. C-DEBI is continuing the Networked Speaker Series (begun in Fall 2011) as a means to enhance communication and the exchange of ideas among our spatially distributed community. Potential speakers can be nominated by colleagues, mentors, or those mentored by C-DEBI participants; they can also self nominate. Selected C-DEBI Networked Speakers will make a presentation online, using video conferencing tools, with assistance from the C-DEBI main office at USC. Nominated C-DEBI Networked Speakers should be capable of combining compelling visual materials with the ability to communicate effectively to a broad audience. We are particularly enthusiastic about giving young researchers a chance to present work to the C-DEBI community. Being selected to be a C-DEBI Networked Speaker is an honor.

-WHOI: Oceans Encounters Webinar Series Season Finale, June 10, 7:30 – 8:30 pm EDT (https://www.whoi.edu/ocean-encounters/#oceanworlds) — -NEW!
Save the date for our season finale on “Oceans Beyond Earth: From Earth’s deep ocean to the search for extraterrestrial life.” With NASA Jet Propulsion Laboratory astrobiologist Kevin Hand, WHOI oceanographer Julie Huber, and WHOI deep-sea explorer Chris German and special guest, comedian Eugene Mirman.

-UNOLS: Science of the Abyss Virtual Workshops (https://ndsf.whoi.edu/alvin/workshop-alvin-in-the-abyss/) –
Please pre-register to participate in the the workshops to be held on June 16, June 30, and July 7, 2020.

-IODP-USSSP: Volunteer for a Board, Committee or Panel (https://usoceandiscovery.org/committees/) –
Scientists interested in volunteering for these opportunities should apply by July 1, 2020.

-ISSM 2020: Meeting postponed to November 1-6, call for poster abstracts extended (https://www.issm2020.com/) –
Submitting poster abstracts (oral presentation abstract submissions are now closed) has an extended deadline of July 30, 2020.

-AGI: Geoscience COVID-19 Survey (https://www.americangeosciences.org/workforce/covid19) —- NEW!
The American Geosciences Institute is conducting a year-long study to understand how geoscience employers and educational institutions are changing their workplace and instructional environments in response to the COVID-19 pandemic, and to discover which of these changes will become permanent. This study is open to all geoscientists, including geoscience students, retired, and not currently employed, who reside in the United States, and are at least 18 years old. Over the next 52 weeks, we will email a brief online status survey twice a month to each participant. The information you provide will be valuable in helping geoscience academic institutions, geoscience employers and decision makers to understand the short-term and long-term structural impacts on the geoscience enterprise from the COVID-19 pandemic. Results from the study will be reported only in aggregate and in a manner that ensures the confidentiality of the responses. Participation is voluntary, and you may discontinue your
participation at any time.

Ongoing Activities:
* C-DEBI: Rolling call for Community Workshop support (http://www.darkenergybiosphere.org/research-activities/research-support/workshops/)
* C-DEBI: Protocols.io Group Page (https://www.protocols.io/groups/center-for-dark-energy-biosphere-investigations)
* C-DEBI: Subseafloor Cultures Database (http://www.darkenergybiosphere.org/outputs-resources/subseafloor-cultures-database/)
* C-DEBI: Join us on LinkedIn (https://www.linkedin.com/company/c-debi-center-for-dark-energy-biosphere-investigations/)

Undergraduate Student Spotlight
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Learn more about our summer undergraduate course (https://www.darkenergybiosphere.org/education-diversity/for-undergraduates/gem-course/) and meet the rest of the 2019 Global Enviromental Microbiology students (https://www.darkenergybiosphere.org/spotlight/2019-gem-course-all-stars/) .

Proposal Calls
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-NOAA: Ocean Exploration Fiscal Year 2021 Funding Opportunity (https://oceanexplorer.noaa.gov/about/funding-opps/welcome.html) –
The deadline for the pre-proposal submission is June 18, 2020.

-IODP-USSSP: Apply to Sail on Expedition 377 Arctic Ocean Paleoceanography (https://usoceandiscovery.org/iodp-expedition-377/) –
The deadline to apply is June 19, 2020.

-NSF: Faculty Early Career Development Program (CAREER) (https://www.nsf.gov/pubs/2020/nsf20525/nsf20525.htm?WT.mc_id=USNSF_25&WT.mc_ev=click) –
Full proposal deadline: July 27, 2020.

-UNOLS: 2020 Ocean Observatories Initiative (OOI) Cruise Opportunities (https://www.unols.org/unols-cruise-opportunity-program) –
The application deadline for the Fall 2020 Deployment Operations cruises is is August 3, 2020.

-NSF: Biological Oceanography (https://www.nsf.gov/funding/pgm_summ.jsp?pims_id=11696&WT.mc_id=USNSF_46&WT.mc_ev=click) –
Full proposal target dates: August 17, 2020 and February 15, 2021.

-NSF: Chemical Oceanography (https://www.nsf.gov/funding/pgm_summ.jsp?pims_id=11698&WT.mc_id=USNSF_46&WT.mc_ev=click) –
Full proposal target date: August 17, 2020 and February 15, 2021.

-NSF: Physical Oceanography (https://www.nsf.gov/funding/pgm_summ.jsp?pims_id=12729&WT.mc_id=USNSF_46&WT.mc_ev=click) –
Full proposal target date: August 17, 2020 and February 15, 2021.

-NSF: Improving Undergraduate STEM Education: Pathways into the Earth, Ocean, Polar and Atmospheric & Geospace Sciences (IUSE:GEOPAths) (https://www.nsf.gov/pubs/2020/nsf20516/nsf20516.htm?WT.mc_id=USNSF_25&WT.mc_ev=click) –
Letter of Intent Due Date: November 17, 2020.

-NSF: Research Traineeship (NRT) Program (https://www.nsf.gov/funding/pgm_summ.jsp?pims_id=505015&WT.mc_id=USNSF_46&WT.mc_ev=click) –
Full Proposal Deadline Date: February 6, 2021.

-NSF: COVID-19 Impacts (https://www.nsf.gov/news/special_reports/coronavirus/) –
Links: NSF Coronavirus webpage (https://www.nsf.gov/news/special_reports/coronavirus/) , NSF Implementation of OMB Memorandum M-20-17 (https://www.nsf.gov/bfa/dias/policy/covid19/covid19_nsfombimplementation.pdf) , COVID-19 Information for the Geosciences Research Community (https://www.nsf.gov/news/news_summ.jsp?cntn_id=300299&org=GEO) .

-NSF OCE: Upcoming proposals to OCE, shiptime and data proposals (https://www.darkenergybiosphere.org/proposal-call/upcoming-proposals-to-oce-shiptime-and-data-proposals/) –

Rolling Calls:
* C-DEBI: Rolling call for Research Exchange proposals (http://www.darkenergybiosphere.org/research-activities/research-support/exchange/)
* IODP-USSSP: Proposals for Pre-Drilling Activities (http://usoceandiscovery.org/pre-drilling-activities/)
* NSF: Antarctic Research Program Solicitation (https://www.nsf.gov/pubs/2020/nsf20568/nsf20568.htm?WT.mc_id=USNSF_25&WT.mc_ev=click)
* NSF: Arctic Sciences Program Solicitation (http://www.nsf.gov/pubs/2016/nsf16595/nsf16595.htm?WT.mc_id=USNSF_25&WT.mc_ev=click)
* NSF: Dear Colleague Letter: Poorly Sampled and Unknown Taxa (PurSUiT) (https://www.nsf.gov/pubs/2020/nsf20059/nsf20059.jsp?WT.mc_id=USNSF_25&WT.mc_ev=click)
* NSF: Division of Environmental Biology (core programs) (DEB) (https://www.nsf.gov/pubs/2020/nsf20502/nsf20502.htm)
* NSF: Enabling Discovery through GEnomic Tools (EDGE) (https://www.nsf.gov/pubs/2020/nsf20532/nsf20532.htm?WT.mc_id=USNSF_25&WT.mc_ev=click)
* NSF: Infrastructure Innovation for Biological Research (IIBR) (https://www.nsf.gov/pubs/2018/nsf18595/nsf18595.htm)
* NSF: Instrument Capacity for Biological Research (ICBR) (https://www.nsf.gov/funding/pgm_summ.jsp?pims_id=505542&WT.mc_id=USNSF_25&WT.mc_ev=click)
* NSF: Non-Academic Research Internships for Graduate Students (INTERN) Supplemental Funding Opportunity (https://www.nsf.gov/pubs/2018/nsf18102/nsf18102.jsp?WT.mc_id=USNSF_179)
* NSF: Research Assistantships for High School Students (RAHSS): Funding to Broaden Participation in the Biological Sciences (https://www.nsf.gov/pubs/2018/nsf18088/nsf18088.jsp?WT.mc_id=USNSF_25&WT.mc_ev=click)
* NSF: Research Experience for Teachers (RET): Funding Opportunity in the Biological Sciences (https://www.nsf.gov/pubs/2018/nsf18089/nsf18089.jsp?WT.mc_id=USNSF_25&WT.mc_ev=click)
* NSF: Tribal Colleges and Universities Program (TCUP) (https://www.nsf.gov/funding/pgm_summ.jsp?pims_id=5483&WT.mc_id=USNSF_46&WT.mc_ev=click)
* Queen Mary U of London: PhD Project: Microbial survival in the energy-limited deep biosphere (https://www.findaphd.com/phds/project/microbial-survival-in-the-energy-limited-deep-biosphere/?p111036)
* Queen Mary U of London: PhD Project: Microbial life and activity on glaciers and in Arctic soils (https://www.findaphd.com/phds/project/microbial-life-and-activity-on-glaciers-and-in-arctic-soils/?p111037)
* UNOLS: Cruise Opportunity Program (https://www.unols.org/unols-cruise-opportunity-program)

Employment
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-MSU: Postdoctoral Researcher position on Asgard archaea ecophysiology (http://nebula.wsimg.com/cd7d3e4d7def0eed4144485bcaf634ff?AccessKeyId=48B9AC89493A56C67DF6&disposition=0&alloworigin=1) — -NEW!
The Hatzenpichler Environmental Microbiology Lab at Montana State University (Bozeman, MT) is looking for a postdoctoral researcher to join a collaborative project on the diversity, genomics, physiology, and ultrastructure of Asgard archaea and its implications for eukaryogenesis. This research project is part of an international collaboration between the Hatzenpichler lab and the groups of Brett Baker, Mark Ellisman, and Thijs Ettema. Together, we seek to obtain a comprehensive genetic catalog of Asgard archaea diversity, determine their physiology, and characterize their cellular ultrastructure. To achieve this, we will employ an array of “omics”, physiology, and microscopic approaches. Determining the identity of archaea most closely related to eukaryotes, their physiological interactions, and cellular structure will transform our understanding of eukaryogenesis. The postdoc will use a combination of cutting-edge next-generation physiology approaches targeted at Asgard archaea physiology
and cell-cell (metabolic and physical) interactions. Approaches to be employed include stable isotope probing, substrate analog probing, fluorescence activated cell sorting, Raman micro-spectroscopy, different in situ visualization techniques, as well as genome analyses and targeted cultivation. The postdoc’s main objective will be to experimentally test genomic predictions on Asgard archaea physiology and cellular interactions, and (ideal case scenario) obtain an enrichment culture of an Asgard archaeon. The position will be available starting September 1st 2020 and will remain open until filled.

-LDEO: Associate Research Scientist/Assistant Director, Education & Outreach for USSSP (https://pa334.peopleadmin.com/postings/5440) –

-U of Georgia: Assistant or Associate Professor – Biological Oceanography (https://www.ugajobsearch.com/postings/126262) –

-WWU: Assistant Professor in Marine Molecular Biology (https://employment.wwu.edu/cw/en-us/job/497146/assistant-professor-in-marine-molecular-biology) –

Don’t forget to email me with any items you’d like to share in future newsletters! We will also broadcast this information on our social media outlets, Twitter and Facebook. You are what makes our deep biosphere community!

Best,

Matt

—
Matthew Janicak
Data Manager
Center for Dark Energy Biosphere Investigations (C-DEBI)
University of Southern California
janicak@usc.edu (mailto:janicak@usc.edu)
3616 Trousdale Pkwy, AHF 209, Los Angeles, CA 90089-0371
Phone: 708-691-9563, Fax: 213-740-2437
Exploring life beneath the seafloor and making transformative discoveries that advance science, benefit society, and inspire people of all ages and origins.