C-DEBI Newsletter – August 3, 2020

Publications
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Nature Communications
Aerobic microbial life persists in oxic marine sediment as old as 101.5 million years (http://dx.doi.org/10.1038/s41467-020-17330-1) (http://dx.doi.org/10.1016/j.epsl.2020.116386) – NEW!
Yuki Morono, Motoo Ito, Tatsuhiko Hoshino, Takeshi Terada, Tomoyuki Hori, Minoru Ikehara, Steven L. D’Hondt*, Fumio Inagaki
*C-DEBI Contribution 532

Sparse microbial populations persist from seafloor to basement in the slowly accumulating oxic sediment of the oligotrophic South Pacific Gyre (SPG). The physiological status of these communities, including their substrate metabolism, is previously unconstrained. Here we show that diverse aerobic members of communities in SPG sediments (4.3‒101.5 Ma) are capable of readily incorporating carbon and nitrogen substrates and dividing. Most of the 6986 individual cells analyzed with nanometer-scale secondary ion mass spectrometry (NanoSIMS) actively incorporated isotope-labeled substrates. Many cells responded rapidly to incubation conditions, increasing total numbers by 4 orders of magnitude and taking up labeled carbon and nitrogen within 68 days after incubation. The response was generally faster (on average, 3.09 times) for nitrogen incorporation than for carbon incorporation. In contrast, anaerobic microbes were only minimally revived from this oxic sediment. Our results suggest that
microbial communities widely distributed in organic-poor abyssal sediment consist mainly of aerobes that retain their metabolic potential under extremely low-energy conditions for up to 101.5 Ma.

See also general audience articles about the Nature Communications paper from Gizmodo (https://gizmodo.com/ancient-microbes-spring-to-life-after-100-million-years-1844529743) , Wired (https://www.wired.com/story/scientists-revive-100-million-year-old-microbes/) , BBC (https://www.bbc.com/news/science-environment-53575103) and others (https://news.google.com/stories/CAAqcQgKImtDQklTU2pvSmMzUnZjbmt0TXpZd1NqMEtFUWljbmU2eWtJQU1FV1lfaWkzc2t2VFpFaWd4TURBdGJXbHNiR2x2YmkxNVpXRnlMVzlzWkNCdGFXTnliMkpsY3lCa2FYTmpiM1psY21Wa0tBQVAB?oc=3&ceid=US:en) .

Gemochimica et Cosmochimica Acta
Organic carbon and microbial activity in marine sediments on a global scale throughout the Quaternary (http://dx.doi.org/10.1016/j.gca.2020.07.017) (http://dx.doi.org/10.1016/j.epsl.2020.116386) – NEW!
Douglas E. LaRowe*, Sandra Arndt, James A. Bradley*, Ewa Burwicz, Andrew W. Dale, Jan P. Amend*
*C-DEBI Contribution 538

Microbial degradation of organic carbon in marine sediments is a key driver of global element cycles on multiple time scales. However, it is not known to what depth microorganisms alter organic carbon in marine sediments or how microbial rates of organic carbon processing change with depth, and thus time since burial, on a global scale. To better understand the connection between the dynamic carbon cycle and life’s limits in the deep subsurface, we have combined a number of global data sets with a reaction transport model (RTM) describing first, organic carbon degradation in marine sediments deposited throughout the Quaternary Period and second, a bioenergetic model for microbial activity. The RTM is applied globally, recognizing three distinct depositional environments – continental shelf, margin and abyssal zones. The results include the masses of particulate organic carbon, POC, stored in three sediment-depth layers: bioturbated Holocene (1.7 × 10^17 g C), non-bioturbated Holocene (2.5 ×
10^18 g C) and Pleistocene (1.4 × 10^20 g C) sediments. The global depth-integrated rates of POC degradation have been determined to be 1.3 × 10^15, 1.3 × 10^14 and 3.0 × 10^14 g C yr^-1 for the same three layers, respectively. A number of maps depicting the distribution of POC, as well as the fraction that has been degraded have also been generated. Using POC degradation as a proxy for microbial catabolic activity, total heterotrophic processing of POC throughout the Quaternary is estimated to be between 10^-11 – 10^-6 g C cm^-3 yr^-1, depending on the time since deposition and location. Bioenergetic modeling reveals that laboratory-determined microbial maintenance powers are poor predictors of sediment biomass concentration, but that cell concentrations in marine sediments can be accurately predicted by combining bioenergetic models with the rates of POC degradation determined in this study. Our model can be used to quantitatively describe both the carbon cycle and microbial activity on a
global scale for marine sediments less than 2.59 million years old.

Applied and Environmental Microbiology
Evidence for a growth zone for deep subsurface microbial clades in near-surface anoxic sediments (http://dx.doi.org/10.1128/aem.00877-20) (http://dx.doi.org/10.1016/j.epsl.2020.116386) – NEW!
Karen G. Lloyd*, Jordan T. Bird, Joy Buongiorno, Emily Deas, Richard T. Kevorkian, Talor Noordhoek, Jacob Rosalsky, Taylor Roy
*C-DEBI Contribution 540

Global marine sediments harbor a large and highly diverse microbial biosphere, but the mechanism by which this biosphere is established during sediment burial is largely unknown. During burial in marine sediments, concentrations of easily-metabolized organic compounds and total microbial cell abundance decrease. However, it is unknown whether some microbial clades increase with depth. We show total population increases in 38 microbial families over 3 cm of sediment depth in the upper 7.5 cm of White Oak River (WOR) estuary sediments. Clades that increased with depth were more often associated with one or more of the following: anaerobes, uncultured, or common in deep marine sediments relative to those that decreased. Maximum doubling times (in situ steady state growth rates could be faster to balance cell decay) were estimated as 2-25 years by combining sedimentation rate with either quantitative PCR (qPCR) or the product of the Fraction Read Abundance of 16S rRNA genes and total Cell
counts (FRAxC). Doubling times were within an order of magnitude of each other in two adjacent cores, as well as in two laboratory enrichments of Cape Lookout Bight (CLB), NC, sediments (average difference of 28 ± 19%). qPCR and FRAxC in sediment cores and laboratory enrichments produced similar doubling times for key deep subsurface uncultured clades Bathyarchaeota (8.7 ± 1.9 years) and Thermoprofundales/MBG-D (4.1 ± 0.7 years). We conclude that common deep subsurface microbial clades experience a narrow zone of growth in shallow sediments, offering an opportunity for selection of long-term subsistence traits after resuspension events.

Crystal Growth & Design
Mainly on the Plane: Deep Subsurface Bacterial Proteins Bind and Alter Clathrate Structure (http://dx.doi.org/10.1021/acs.cgd.0c00855) (http://dx.doi.org/10.1016/j.epsl.2020.116386) – NEW!
Abigail M. Johnson, Dustin J.E. Huard, Jongchan Kim, Priyam Raut, Sheng Dai, Raquel L. Lieberman, Jennifer B. Glass*
*C-DEBI Contribution 541

Gas clathrates are both a resource and a hindrance. They store massive quantities of natural gas but also can clog natural gas pipelines, with disastrous consequences. Eco-friendly technologies for controlling and modulating gas clathrate growth are needed. Type I Antifreeze Proteins (AFPs) from cold-water fish have been shown to bind to gas clathrates via repeating motifs of threonine and alanine. We tested whether proteins encoded in the genomes of bacteria native to natural gas clathrates bind to and alter clathrate morphology. We identified putative clathrate-binding proteins (CBPs) with multiple threonine/alanine motifs in a putative operon (cbp) in metagenomes from natural clathrate deposits. We recombinantly expressed and purified five CbpA proteins, four of which were stable, and experimentally confirmed that CbpAs bound to tetrahydrofuran (THF) clathrate, a low-pressure analogue for structure II gas clathrate. When grown in the presence of CbpAs, the THF clathrate was
polycrystalline and platelike instead of forming single, octahedral crystals. Two CbpAs yielded branching clathrate crystals, similar to the effect of Type I AFP, while the other two produced hexagonal crystals parallel to the [1 1 1] plane, suggesting two distinct binding modes. Bacterial CBPs may find future utility in industry, such as maintaining a platelike structure during gas clathrate transportation.

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)

Gizmodo: ‘It Really Is Otherworldly’: What It’s Like to Visit the Hot Springs of the Deep Sea (https://earther.gizmodo.com/it-really-is-otherworldly-what-it-s-like-to-visit-th-1844305760) (http://dx.doi.org/10.1016/j.epsl.2020.116386) – NEW!
Thousands of feet below the ocean’s surface, boiling hot plumes of seawater shoot like geysers into the abyss. There, some of the strangest life on Earth thrives. Thousands of white crabs with spindly legs creep along the seafloor. Eight-foot-long worms with bright red, mouthless heads poke out of white PVC-looking tubes. Massive golden octopuses float silently through the dark water. This may sound like the last place on Earth you’d want to go, but what happens in this bizarre ecosystem can have huge implications for the biological makeup of the rest of the ocean. So a team of scientists with the Sylvan Geomicrobiology Lab traveled to the ocean’s bottom last year to check them out.

Meetings & Activities
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SoCal GeoBio: 17th Annual Symposium rescheduled to Spring 2021 @ USC (https://earth.usc.edu/geobio/index.html) – (http://dx.doi.org/10.1016/j.epsl.2020.116386) — -NEW!
Due to the recent COVID-19 outbreak, we are rescheduling the SoCal Geobio Symposium to Spring 2021. Information about a specific date will be released in January 2021. We have made this decision in order to avoid contributing to the spread of COVID-19. Registration and abstract submission will reopen in January 2021. For the originally scheduled symposium in April, we received a record number of registrations and abstract submissions, and we hope to see many of these same entries for the rescheduled symposium in Spring 2021. We apologize for any inconvenience that this may have caused, but we hope to put on the best possible SoCal Geobiology Symposium while keeping the health and safety of all of our attendees in mind.

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: 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 extended to August 11, 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: Research Experiences for Undergraduates (REU) (https://www.nsf.gov/funding/pgm_summ.jsp?pims_id=5517&WT.mc_id=USNSF_46&WT.mc_ev=click) – (http://dx.doi.org/10.1016/j.epsl.2020.116386) — -NEW!
The Research Experiences for Undergraduates (REU) program supports active research participation by undergraduate students in any of the areas of research funded by the National Science Foundation. REU projects involve students in meaningful ways in ongoing research programs or in research projects specifically designed for the REU program. This solicitation features two mechanisms for support of student research: (1) REU Sites are based on independent proposals to initiate and conduct projects that engage a number of students in research. REU Sites may be based in a single discipline or academic department or may offer interdisciplinary or multi-department research opportunities with a coherent intellectual theme. Proposals with an international dimension are welcome. (2) REU Supplements may be included as a component of proposals for new or renewal NSF grants or cooperative agreements or may be requested for ongoing NSF-funded research projects. Undergraduate student participants in
either REU Sites or REU Supplements must be U.S. citizens, U.S. nationals, or permanent residents of the United States. Students do not apply to NSF to participate in REU activities. Students apply directly to REU Sites or to NSF-funded investigators who receive REU Supplements. To identify appropriate REU Sites, students should consult the directory of active REU Sites (https://www.nsf.gov/crssprgm/reu/reu_search.cfm) . Full proposal deadline: August 26, 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) – (http://dx.doi.org/10.1016/j.epsl.2020.116386) — -NEW!
The purpose of the NSF Graduate Research Fellowship Program (GRFP) is to help ensure the quality, vitality, and diversity of the scientific and engineering workforce of the United States. The program recognizes and supports outstanding graduate students who are pursuing full-time research-based master’s and doctoral degrees in science, technology, engineering, and mathematics (STEM) or in STEM education. The GRFP provides three years of support for the graduate education of individuals who have demonstrated their potential for significant research achievements in STEM or STEM education. NSF actively encourages women, members of underrepresented minority groups, persons with disabilities, veterans, and undergraduate seniors to apply. Application deadlines: October 19-22, 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: 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: 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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Bigelow: Senior Research Scientists (https://bigelow.freshteam.com/jobs/vWoZiZSrSzM2/senior-research-scientists-bigelow-laboratory) – (http://dx.doi.org/10.1016/j.epsl.2020.116386) — NEW!
Bigelow Laboratory for Ocean Sciences invites applications for Senior Research Scientists (SRSs). Our new strategic plan calls for hiring six new SRSs over the next five years to lead transformative, interdisciplinary research that advances Bigelow Laboratory’s mission. We seek candidates in the following, broad research areas: (1) the ocean’s genetic potential, (2) ocean-climate interactions, and (3) the foundation of ocean food webs. Particularly encouraged are applicants who increase the breadth of the Laboratory’s scientific portfolio and approaches, including those on the periphery of marine sciences. Minimum requirements include a Ph.D. degree in a relevant field. We will consider candidates at all levels of their career progression. Strong candidates will have demonstrated capability to acquire external funding and lead scientific programs appropriate to their career stage. We welcome applications from candidates who will bring to their research the perspective that comes from a
nontraditional educational background or understanding of the experiences of those underrepresented in higher education. Dual-career applicants are welcome. Bigelow Laboratory is a “soft money” institution where SRSs have the freedom to pursue their own funded research and entrepreneurial portfolio that advances the institutional mission. SRSs also have opportunities to participate in Bigelow Laboratory’s sponsored teaching and mentoring activities. SRSs receive institutional salary support to engage in governance and administrative activities associated with the Laboratory’s unique operational model. Salary and start-up packages are based upon current career level, but are negotiable. 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

—
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.