C-DEBI Newsletter – September 2, 2020
C-DEBI Newsletter – September 2, 2020
This newsletter is also accessible via our website (https://www.darkenergybiosphere.org) .
Publications
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PLOS One
Woeseiales transcriptional response to shallow burial in Arctic fjord surface sediment (http://dx.doi.org/10.1371/journal.pone.0234839) (http://dx.doi.org/10.1016/j.epsl.2020.116386) – NEW!
Joy Buongiorno*, Katie Sipes, Kenneth Wasmund, Alexander Loy, Karen G. Lloyd*
*C-DEBI Contribution 539
Distinct lineages of Gammaproteobacteria clade Woeseiales are globally distributed in marine sediments, based on metagenomic and 16S rRNA gene analysis. Yet little is known about why they are dominant or their ecological role in Arctic fjord sediments, where glacial retreat is rapidly imposing change. This study combined 16S rRNA gene analysis, metagenome-assembled genomes (MAGs), and genome-resolved metatranscriptomics uncovered the in situ abundance and transcriptional activity of Woeseiales with burial in four shallow sediment sites of Kongsfjorden and Van Keulenfjorden of Svalbard (79°N). We present five novel Woeseiales MAGs and show transcriptional evidence for metabolic plasticity during burial, including sulfur oxidation with reverse dissimilatory sulfite reductase (dsrAB) down to 4 cm depth and nitrite reduction down to 6 cm depth. A single stress protein, spore protein SP21 (hspA), had a tenfold higher mRNA abundance than any other transcript, and was a hundredfold higher on
average than other transcripts. At three out of the four sites, SP21 transcript abundance increased with depth, while total mRNA abundance and richness decreased, indicating a shift in investment from metabolism and other cellular processes to build-up of spore protein SP21. The SP21 gene in MAGs was often flanked by genes involved in membrane-associated stress response. The ability of Woeseiales to shift from sulfur oxidation to nitrite reduction with burial into marine sediments with decreasing access to overlying oxic bottom waters, as well as enter into a dormant state dominated by SP21, may account for its ubiquity and high abundance in marine sediments worldwide, including those of the rapidly shifting Arctic.
iScience
The Guaymas Basin Subseafloor Sedimentary Archaeome Reflects Complex Environmental Histories (http://dx.doi.org/10.1016/j.isci.2020.101459) (http://dx.doi.org/10.1016/j.epsl.2020.116386) – NEW!
Gustavo A. Ramírez*, Luke J. McKay, Matthew W. Fields, Andrew Buckley, Carlos Mortera, Christian Hensen, Ana Christina Ravelo, Andreas P. Teske
*C-DEBI Contribution 542
We explore archaeal distributions in sedimentary subseafloor habitats of Guaymas Basin and the adjacent Sonora Margin, located in the Gulf of California, México. Sampling locations include (1) control sediments without hydrothermal or seep influence, (2) Sonora Margin sediments underlying oxygen minimum zone water, (3) compacted, highly reduced sediments from a pressure ridge with numerous seeps at the base of the Sonora Margin, and (4) sediments impacted by hydrothermal circulation at the off-axis Ringvent site. Generally, archaeal communities largely comprise Bathyarchaeal lineages, members of the Hadesarchaea, MBG-D, TMEG, and ANME-1 groups. Variations in archaeal community composition reflect locally specific environmental challenges. Background sediments are divided into surface and subsurface niches. Overall, the environmental setting and history of a particular site, not isolated biogeochemical properties out of context, control the subseafloor archaeal communities in Guaymas Basin
and Sonora Margin sediments.
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)
Meetings & Activities
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-C-DEBI: Networked Speaker Series Seminar, Thursday, September 10, 2020,12:30pm PST (https://www.darkenergybiosphere.org/outputs-resources/networked-speaker-series/nss-rose-jones/) –
With Dr. Rose Jones, University of Minnesota on “Menu for a deep microbe; attempts in understanding microbe-mineral interactions in the deep marine seafloor.” Abstract: For microbes in the deep marine subsurface, inorganic chemical energy often is the sole energy source, catalyzing redox reactions of chemical species dissolved in fluid or from solid substrate. This influences the environment by altering subsurface minerals and geochemistry. I’m currently looking for evidence of how microbes influence mineralogy at East Pacific Rise 9.5°N, using Synchrotron microprobe X-ray fluorescence mapping (XRF), X-ray diffraction (XRD), and X-ray absorption spectroscopies (XAS) to map element distributions and phase identification for crystalline and poorly-crystalline minerals. With this information we can describe how minerals change in space and time during the transition from active to inactive venting, providing context for understanding microbial community patterns. Using bioelectrochemistry, I
also found evidence of microbes capable of influencing cool, oxic basalt at North Pond, Mid-Atlantic ridge through directly transferring electrons from the minerals. Overall, our results are attempting to understand how microbes and minerals influence each other and local geochemistry in the deep marine seafloor.
ISSM: ISSM2020 postponed (https://www.issm2021.com/) – (http://dx.doi.org/10.1016/j.epsl.2020.116386) — NEW!
We have decided to further postpone ISSM2020. It will be held in 2021. The date is not yet set, likely in spring/summer. The accepted presentations and poster remain accepted. Possibly we will reopen abstract submission later this year. If you are a selected presenter (including key note speakers), and you are declining (hopefully not), please, let us know. We do apologize for this inconvenience in these crazy times and thank you for your understanding.
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/)
Proposal Calls
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NSF: EAR Postdoctoral Fellowships (EAR-PF) (https://www.nsf.gov/funding/pgm_summ.jsp?pims_id=503144&WT.mc_id=USNSF_46&WT.mc_ev=click) – (http://dx.doi.org/10.1016/j.epsl.2020.116386) — NEW!
The Division of Earth Sciences (EAR) awards Postdoctoral Fellowships to recent recipients of doctoral degrees to conduct an integrated program of independent research and professional development. Fellowship proposals must address scientific questions within the scope of EAR disciplinary programs and must align with the overall theme for the postdoctoral program. The program supports researchers for a period of up to two years with fellowships that can be taken to the institution of their choice (including institutions abroad). The program is intended to recognize beginning investigators of significant potential, and provide them with research experience, mentorship, and training that will establish them in leadership positions in the Earth Sciences community. Because the fellowships are offered only to postdoctoral scientists early in their career, doctoral advisors are encouraged to discuss the availability of EAR postdoctoral fellowships with their graduate students early in their
doctoral programs. Fellowships are awards to individuals, not institutions, and are administered by the Fellows. Full proposal deadline date: September 9, 2020.
JGI: CSP New Investigator (https://jgi.doe.gov/user-programs/program-info/csp-overview/csp-new-investigator/) – (http://dx.doi.org/10.1016/j.epsl.2020.116386) — -NEW!
The CSP New Investigator call seeks to target investigators and research initiatives new to the JGI, with an emphasis on providing pilot data to assess feasibility of a novel approach or form the foundation for a large-scale CSP proposal submission. Projects must be independent of ongoing JGI proposals, and lead PIs cannot have been lead PI on any previously accepted JGI CSP or FICUS proposal. Sequence requests should not exceed 500 Gbp in total. Current call topics include: Bacterial and archaeal isolates and single cell draft genomes; Genome resequencing; Plant/algal genome size estimation; RNA sequencing; Bacterial and archaeal epigenomes and high-quality draft genomes; Metagenomes and metatranscriptomes; DNA synthesis for functional assays; Metabolomics based functional analyses. Proposals are accepted on a continuous basis and will be reviewed twice a year. Letters of intent are not required. Deadline for submission is 60 days prior to the review date. Next deadline: September 19,
2020.
-NSF: Graduate Research Fellowship Program (GRFP) (https://www.nsf.gov/pubs/2020/nsf20587/nsf20587.htm?WT.mc_id=USNSF_25&WT.mc_ev=click) –
Application deadlines: October 19-22, 2020.
IODP: Call for Drilling Proposals (http://iodp.org/proposals/call-for-proposals) – (http://dx.doi.org/10.1016/j.epsl.2020.116386) — -NEW!
The International Ocean Discovery Program (IODP) explores Earth’s climate history, structure, mantle/crust dynamics, natural hazards, and deep biosphere as described in the IODP Science Plan Illuminating Earth’s Past, Present, and Future. (http://iodp.org/about-iodp/iodp-science-plan-2013-2023) IODP facilitates international and interdisciplinary research on transformative and societally relevant topics using the ocean drilling, coring, and downhole measurement facilities JOIDES Resolution (JR), Chikyu, and Mission Specific Platforms (MSP). Proposals are being actively sought for all three facilities. We also invite proposals that involve drilling on land and at sea through coordination with the International Continental Drilling Program (ICDP) and a new submission and joint review process. Investigators are reminded that the interval from the first proposal submission to expedition scheduling is on the order of 4-5 years due to the science and safety review process and required lead time
for scheduling, and that adequate site characterization / site survey data are critical for success. Proponents are strongly encouraged to contact the facility Science Operators to discuss platform-specific operational and fiscal constraints before developing proposals. The next submission deadline (following October 21, 2020) will be in early April, 2021.
NSF: International Research Experiences for Students (IRES) (https://www.nsf.gov/pubs/2020/nsf20598/nsf20598.htm?WT.mc_id=USNSF_25&WT.mc_ev=click) – (http://dx.doi.org/10.1016/j.epsl.2020.116386) — -NEW!
The International Research Experiences for Students (IRES) program supports international research and research-related activities for U.S. science and engineering students. The IRES program contributes to development of a diverse, globally engaged workforce with world-class skills. IRES focuses on active research participation by undergraduate and/or graduate students in high quality international research, education and professional development experiences in NSF-funded research areas. The overarching, long-term goal of the IRES program is to enhance U.S. leadership in science and engineering research and education and to strengthen economic competitiveness through training the next generation of research leaders. This solicitation features two mechanisms; proposers are required to select one of the following tracks to submit their proposal. Track I: IRES Sites (IS) projects engage a group of undergraduate and/or graduate students in active high-quality collaborative research, in
principle at an international site with mentorship from researchers at a host lab. IRES Sites must be organized around a coherent intellectual theme that may involve a single discipline or multiple disciplines funded by NSF. Track II: Advanced Studies Institutes (ASI) are intensive short courses with related activities that engage advanced graduate students in active learning and research at the frontiers of knowledge. ASIs typically range in length from ten to twenty-one days and, in principle, must be held outside the United States. For all IRES proposals, PIs are strongly encouraged to outline virtual, hybrid or other alternative approaches to strengthen and maintain international collaboration in the event travel is not undertaken, and/or in addition to travel. Track I: IRES Sites (IS) due dates: November 12, 2020 and September 21, 2021. Track II: Advanced Studies Institutes (ASI) due dates: November 9, 2020 and September 28, 2021.
NSF: Postdoctoral Research Fellowships in Biology (PRFB) (https://www.nsf.gov/pubs/2020/nsf20602/nsf20602.htm?WT.mc_id=USNSF_25&WT.mc_ev=click) – (http://dx.doi.org/10.1016/j.epsl.2020.116386) — -NEW!
The Directorate for Biological Sciences (BIO) awards Postdoctoral Research Fellowships in Biology (PRFB) 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. For applications under this solicitation, these areas are (1) Broadening Participation of Groups Underrepresented in Biology, (2) Integrative Research Investigating the Rules of Life Governing Interactions Between Genomes, Environment and Phenotypes, and (3) Plant Genome Postdoctoral Research Fellowships. 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 in collaboration with sponsoring scientists. It is expected that the sponsoring scientists will actively mentor the Fellows and will greatly benefit from collaborating with these talented early-career scientists and incorporating them
into their research groups. The research and training plan of each fellowship must address important scientific questions within the scope of BIO and the specific guidelines in this fellowship program solicitation. Because the fellowships are offered to postdoctoral scientists only early in their careers, NSF encourages doctoral students to discuss the availability of these postdoctoral fellowships with their doctoral mentors and potential postdoctoral sponsors early in their doctoral programs to take advantage of this funding opportunity. Fellowships are awards to individuals, not institutions, and are administered by the Fellows. Full proposal deadline: November 18, 2020.
-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) –
Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science in Tribal Colleges and Universities (SEA-PHAGES in TCUs) deadline: September 4, 2020. Small Grants for Research (SGR) deadline: December 10, 2020.
-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: 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 date: 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: 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: February 15, 2021.
-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: DCL: Collaborative Proposals under NSF and US-Israel Binational Science Foundation (BSF) Collaborative Research Opportunities (https://www.nsf.gov/pubs/2020/nsf20094/nsf20094.jsp?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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MBARI: Principal Investigator or Principal Engineer (focus on seafloor patterns and processes) (https://www.mbari.org/principal_investigator_engineer/) – (http://dx.doi.org/10.1016/j.epsl.2020.116386) — NEW!
MBARI is hiring a Principal Investigator or Principal Engineer to develop an independent research program investigating seafloor patterns and processes, including but not limited to geology, chemistry, biology, or ecology. We seek to promote a programmatic vision that fosters the development of novel observational and analytical methods to advance our understanding of the interplay between abiotic and biotic systems in the deep sea. A Doctorate or equivalent in a scientific or engineering discipline and a minimum of 3 years demonstrated success in conducting research is required, along with a record of significant, original, and promising research contributions and potential to secure extramural funding. Applicants at an early- to mid-career stage (equivalent to an incoming assistant to associate professor) with a demonstrated ability to work in an interdisciplinary, team-oriented environment are encouraged to apply. We are currently receiving applications for this position, which will
remain open until filled.
-Bigelow: Senior Research Scientists (https://bigelow.freshteam.com/jobs/vWoZiZSrSzM2/senior-research-scientists-bigelow-laboratory) –
For full consideration, the application should be received by September 15, 2020.
-NC State U: Assistant Professor – Chemical Oceanography (https://jobs.ncsu.edu/postings/133726) –
Review of applications will begin on October 12, 2020 and the position will remain open until filled.
-MSU: Postdoctoral Researcher position on Asgard archaea ecophysiology (http://nebula.wsimg.com/cd7d3e4d7def0eed4144485bcaf634ff?AccessKeyId=48B9AC89493A56C67DF6&disposition=0&alloworigin=1) –
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