C-DEBI Newsletter – December 1, 2020
C-DEBI Newsletter – December 1, 2020
This newsletter is also accessible via our website (https://www.darkenergybiosphere.org) .
Publications
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Scientific Drilling
A new high-temperature borehole fluid sampler: the Multi-Temperature Fluid Sampler (http://dx.doi.org/10.5194/sd-28-43-2020) (http://dx.doi.org/10.1016/j.epsl.2020.116386) – NEW!
Charles Geoffrey Wheat*, Christopher Kitts, Camden Webb, Rachel Stolzman, Ann McGuire, Trevor Fournier, Thomas L. Pettigrew, Hans W. Jannasch
*C-DEBI Contribution 530
Deep (>1 km depth) scientific boreholes are unique assets that can be used to address a variety of microbiological, hydrologic, and biogeochemical hypotheses. Few of these deep boreholes exist in oceanic crust. One of them, Deep Sea Drilling Project Hole 504B, reaches ∼190 ^∘C at its base. We designed, fabricated, and laboratory-tested the Multi-Temperature Fluid Sampler (MTFS), a non-gas-tight, titanium syringe-style fluid sampler for borehole applications that is tolerant of such high temperatures. Each of the 12 MTFS units collects a single 1 L sample at a predetermined temperature, which is defined by the trigger design and a shape memory alloy (SMA). SMAs have the innate ability to be deformed and only return to their initial shapes when their activation temperatures are reached, thereby triggering a sampler at a predetermined temperature. Three SMA-based trigger mechanisms, which do not rely on electronics, were tested. Triggers were released at temperatures spanning from 80 to
181 ^∘C. The MTFS was set for deployment on International Ocean Discovery Program Expedition 385T, but hole conditions precluded its use. The sampler is ready for use in deep oceanic or continental scientific boreholes with minimal training for operational success.
FEMS Microbiology Ecology
Exploring the abundance, metabolic potential and gene expression of subseafloor Chloroflexi in million-year-old oxic and anoxic abyssal clay (http://dx.doi.org/10.1093/femsec/fiaa223) (http://dx.doi.org/10.1016/j.epsl.2020.116386) – NEW!
Aurèle Vuillemin, Zak Kerrigan, Steven L. D’Hondt*, William D. Orsi
*C-DEBI Contribution 551
Chloroflexi are widespread in subsurface environments, and recent studies indicate that they represent a major fraction of the communities in subseafloor sediment. Here, we compare the abundance, diversity, metabolic potential and gene expression of Chloroflexi from three abyssal sediment cores from the western North Atlantic Gyre (water depth >5400 m) covering up to 15 million years of sediment deposition, where Chloroflexi were found to represent major components of the community at all sites. Chloroflexi communities die off in oxic red clay over 10–15 million years, and gene expression was below detection. In contrast, Chloroflexi abundance and gene expression at the anoxic abyssal clay site increase below the seafloor and peak in 2–3 million-year-old sediment, indicating a comparably higher activity. Metatranscriptomes from the anoxic site reveal increased expression of Chloroflexi genes involved in cell wall biogenesis, protein turnover, inorganic ion transport, defense mechanisms and
prophages. Phylogenetic analysis shows that these Chloroflexi are closely related to homoacetogenic subseafloor clades and actively transcribe genes involved in sugar fermentations, gluconeogenesis and Wood–Ljungdahl pathway in the subseafloor. Concomitant expression of cell division genes indicates that these putative homoacetogenic Chloroflexi are actively growing in these million-year-old anoxic abyssal sediments.
The ISME Journal
Marine Dadabacteria exhibit genome streamlining and phototrophy-driven niche partitioning (http://dx.doi.org/10.1038/s41396-020-00834-5) (http://dx.doi.org/10.1016/j.epsl.2020.116386) – NEW!
Elaina D. Graham, Benjamin J. Tully*
*C-DEBI Contribution 554
The remineralization of organic material via heterotrophy in the marine environment is performed by a diverse and varied group of microorganisms that can specialize in the type of organic material degraded and the niche they occupy. The marine Dadabacteria are cosmopolitan in the marine environment and belong to a candidate phylum for which there has not been a comprehensive assessment of the available genomic data to date. Here in, we assess the functional potential of the marine pelagic Dadabacteria in comparison to members of the phylum that originate from terrestrial, hydrothermal, and subsurface environments. Our analysis reveals that the marine pelagic Dadabacteria have streamlined genomes, corresponding to smaller genome sizes and lower nitrogen content of their DNA and predicted proteome, relative to their phylogenetic counterparts. Collectively, the Dadabacteria have the potential to degrade microbial dissolved organic matter, specifically peptidoglycan and phospholipids. The
marine Dadabacteria belong to two clades with apparent distinct ecological niches in global metagenomic data: a clade with the potential for photoheterotrophy through the use of proteorhodopsin, present predominantly in surface waters up to 100 m depth; and a clade lacking the potential for photoheterotrophy that is more abundant in the deep photic zone.
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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-AGU: 2020 Fall Meeting Deep Biosphere-related Sessions of Interest (https://www.darkenergybiosphere.org/meetings-and-activities/deep-biosphere-related-sessions-of-interest/) –
Attending the 2020 AGU Fall Meeting, December 1-17, online? Check out these deep biosphere-related sessions.
-UNOLS: Deep Submergence Science Committee (DeSSC) 2020 Annual Community Meeting (https://www.unols.org/event/meeting/2020-dessc-annual-community-meeting) –
The UNOLS Deep Submergence Science Committee (DeSSC) invites you to attend their fall meeting, Friday, December 4, 2020 at 1pm EST. Ocean scientists and students interested in deep submergence science are encouraged to attend the DeSSC meeting. Registration via the website is required.
-C-DEBI: Last Networked Speaker Series Seminar Now Online (https://www.darkenergybiosphere.org/outputs-resources/networked-speaker-series/nss-julia-mcgonigle/) –
Missed the last NSS seminar with Dr. Julia McGonigle, Bigelow Laboratory for Ocean Sciences on “Formate metabolism by Chloroflexi is key in unlocking deep carbon for the Lost City chimney ecosystem”? Watch it on YouTube (https://youtu.be/0P6mEongeHE) .
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: Dear Colleague Letter: Career-Life Balance (CLB) Supplemental Funding Requests (https://www.nsf.gov/pubs/2021/nsf21021/nsf21021.jsp?WT.mc_id=USNSF_25&WT.mc_ev=click) – (http://dx.doi.org/10.1016/j.epsl.2020.116386) — NEW!
Instituted in 2012, NSF’s Career-Life Balance (CLB) initiative is an agency-wide approach to help attract, retain, and advance graduate students, postdoctoral researchers, and other researchers in STEM fields. This effort aims to help reduce the rate at which early-career researchers depart from the STEM workforce. With this Dear Colleague Letter (DCL), NSF draws attention to the opportunity for supplemental funding to help researchers, who are confronted with a short-term increase in dependent care responsibilities, ensure that the research activities supported by an NSF award can continue. NSF recognizes that primary dependent care responsibilities and other family considerations pose unique challenges to the STEM workforce. The purpose of this DCL is to announce NSF’s continued interest in CLB supplemental funding requests, with two key changes from CLB DCLs issued in FY 2013: 1) an increase in the amount and duration of salary support that may be requested; and 2) an extension of the
opportunity to Principal Investigators (PIs) and co-PIs of all active NSF grant or cooperative agreements. Career Life Balance supplements may be requested to support additional personnel (e.g., a technician or research assistant) for existing research awards, graduate research fellowships and postdoctoral fellowship programs when award personnel are on family leave for primary dependent care responsibilities and other direct family considerations. The supplemental request may include funding for up to six months of salary support or stipend for a maximum of $30,000 in direct costs of salary compensation or stipend, but the duration of the salary or stipend support may not exceed the duration of the family leave. Fringe benefits and associated indirect costs, but not tuition, may be included in addition to the salary costs, and therefore, the total supplemental funding request may exceed $30,000.
-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) –
Small Grants for Research (SGR) deadline: December 10, 2020.
-IODP-USSSP: Apply for a Schlanger Ocean Drilling Fellowship (https://usoceandiscovery.org/fellowships/) –
All application materials, including reference material, must be submitted by December 11, 2020.
-USGS: Mendenhall Research Fellowship: Geology, geochemistry and global context of deep-ocean marine minerals (https://www.usgs.gov/centers/mendenhall/19-8-geology-geochemistry-and-global-context-deep-ocean-marine-minerals) –
The deadline for submission of applications, which include research proposals, will be January 4, 2021.
-MBARI: 2021 Postdoctoral Fellowship (https://www.mbari.org/2021-postdoctoral-fellowship/) –
Application deadline: January 20, 2021.
-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: Understanding the Rules of Life: Microbiome Interactions and Mechanisms (URoL:MIM) (https://www.nsf.gov/pubs/2021/nsf21534/nsf21534.htm?WT.mc_id=USNSF_25&WT.mc_ev=click) – (http://dx.doi.org/10.1016/j.epsl.2020.116386) — NEW!
The URoL:MIM program defines a microbiome as a community of microorganisms with more than one type of organism, including bacteria, archaea, fungi, protists, and viruses that inhabit a particular habitat. The habitat can be a living host or a particular environment, broadly defined to include the biological, chemical, physical, and/or social state, settings, or conditions. The URoL:MIM Program is focused on the causal and mechanistic understanding of the structure and function of these microbiomes and the connections, interactions, and interdependencies within and among the microbiome, the host, and the environment (biological, chemical, physical, and social). The major objective of URoL:MIM is to develop an integrated understanding of how microbiome organisms communicate and interact with each other, with their hosts, and with their environments, across various spatial and temporal scales. This includes mechanisms underlying how the microbiome affects the phenotypes of organisms and their
robustness, resilience, and adaptability. How the underlying relationships among the microbiomes, hosts, and physical, social, and built environments ultimately emerge as properties that affect phenotype of the microbiome, the host, or both is of interest. Full proposal deadline: February 23, 2021.
-JGI: CSP New Investigator (https://jgi.doe.gov/user-programs/program-info/csp-overview/csp-new-investigator/) –
Next deadline: March 1, 2021.
-NSF: EarthCube: Developing a Community-Driven Data and Knowledge Environment for the Geosciences (https://www.nsf.gov/pubs/2021/nsf21515/nsf21515.htm?WT.mc_id=USNSF_25&WT.mc_ev=click) –
Full proposal deadlines: March 2, 2021.
-NSF: Navigating the New Arctic (NNA) (https://www.nsf.gov/pubs/2021/nsf21524/nsf21524.htm?WT.mc_id=USNSF_25&WT.mc_ev=click) –
Full Proposal Deadline: March 5, 2021.
-IODP: Call for Drilling Proposals (http://iodp.org/proposals/call-for-proposals) –
The next submission deadline 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) –
Track I: IRES Sites (IS) due date: September 21, 2021. Track II: Advanced Studies Institutes (ASI) due date:September 28, 2021.
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 (https://www.nsf.gov/pubs/2021/nsf21526/nsf21526.htm)
* 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: DCL: 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: DCL: Non-Academic Research Internships for Graduate Students (INTERN) Supplemental Funding Opportunity (https://www.nsf.gov/pubs/2021/nsf21013/nsf21013.jsp?WT.mc_id=USNSF_25&WT.mc_ev=click)
* NSF: DCL: UKRI/BBSRC-NSF/BIO Lead Agency Opportunity in Biological Informatics, Microbes and the Host Immune System, Quantum Biology and Synthetic Cell (https://www.nsf.gov/pubs/2020/nsf20118/nsf20118.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)
* UNOLS: Cruise Opportunity Program (https://www.unols.org/unols-cruise-opportunity-program)
Employment
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-USC: Assistant Professor of Quantitative and Computational Biology (https://usccareers.usc.edu/job/los-angeles/assistant-professor-of-quantitative-and-computational-biology/1209/17668361) –
Review of applications will begin December 15, 2020, and continue until the position is filled.
-USC: Assistant Professor of Biological Sciences (https://usccareers.usc.edu/job/los-angeles/assistant-professor-of-biological-sciences/1209/17785043) –
Review of applications will begin December 15, 2020.
-USC: Assistant Professor in Global Environmental Change (https://usccareers.usc.edu/job/los-angeles/assistant-professor-in-global-environmental-change/1209/17868768) –
Earth. Evaluation of applications will begin on December 20 2020, and continue until the position is filled.
Queen Mary U of London: Postdoctoral Research Assistant in Biogeochemical Modelling (https://webapps2.is.qmul.ac.uk/jobs/job.action?jobRef=QMUL23274) – (http://dx.doi.org/10.1016/j.epsl.2020.116386) — NEW!
We are seeking a 36-month PDRA to work on a joint NERC-NSF funded project ‘Sensors Under Snow: Seasonal Processes in the Evolution of Arctic Soils (SUN SPEARS).’ The PDRA will develop a novel microbial-biogeochemical model for Arctic soils. The overall aim is to improve the understanding of how seasonal processes contribute to the long-term development of Arctic soils, by linking soil biogeochemical, microbial, geophysical and hydrogeological processes in a mechanistic model. The model will address how soils form following glacier retreat, quantify ecosystem and biogeochemical dynamics, and simulate the future fate of Arctic soils following large-scale ice retreat and climate warming. These activities are linked to the main SUN SPEARS project, which will monitor High-Arctic glacier forefield soils year-round via geophysical sensors and measurement of soil microbial and biogeochemical processes. Model development and calibration will make use of field datasets that will be collected during
fieldwork campaigns throughout 2021 and 2022. The PDRA will therefore work within a multidisciplinary team (biogeochemistry, modelling, geomicrobiology, geophysics) and thus develop an interdisciplinary skill set. There may be opportunities for the PDRA to participate in fieldwork in Svalbard. The closing date for applications is January 15, 2021.
-WHOI: Research Assistant / Research Associate – MC&G (https://careers-whoi.icims.com/jobs/1292/research-assistant—research-associate—mc%26g/job) –
-MBARI: Principal Investigator or Principal Engineer (focus on seafloor patterns and processes) (https://www.mbari.org/principal_investigator_engineer/) –
We are currently receiving applications for this position, which will remain open until filled.