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C-DEBI Newsletter – August 2, 2021
A biweekly digest of deep biosphere news and opportunities
from the Center for Dark Energy Biosphere Investigations

 

Crustal Ocean Biosphere Research Accelerator (COBRA) Announcement

Building from the foundation of C-DEBI, a new NSF-funded network-of-networks called COBRA - the Crustal Ocean Biosphere Research Accelerator - is spinning up this fall to bring together diverse stakeholders to accelerate research on the structure, function, resilience, and ecosystem services of the crustal ocean biosphere to inform decision making. The goal is to generate new knowledge and inform decision-making relating to emergent industrial uses of the deep ocean, such as deep-sea mining and subseafloor carbon sequestration, and decrease the likelihood of serious harm to the environment while maintaining the broad benefits that society currently enjoys. COBRA will help to close knowledge gaps by facilitating coordination of expedition and observatory efforts and dissemination of white papers generated through virtual workshops. In collaboration with international partners and leveraged expeditions of COBRA participants, COBRA will support an international early career researcher virtual expedition leadership training program, helping to build the community of experts engaged in deep-sea exploration, science, and policy. COBRA will also support international research exchanges for early career researchers wanting to engage in crustal ocean biosphere research to inform policy. All training efforts will be designed to promote team science collaboration, diversity, equity, and inclusivity.

COBRA will be led by C-DEBI Senior Scientists Beth Orcutt, Julie Huber, Andy Fisher, and Geoff Wheat along with Jim McManus and Randi Rotjan and managed by C-DEBI Managing Director Rosalynn Sylvan. As a global community of experts in deep sea and subseafloor deep biosphere science, the C-DEBI community is uniquely poised to make great contributions to COBRA efforts. COBRA officially launches October 1. Stay tuned for more details about how to get involved and find out more here!

 

Publications & Press


Environmental Microbiology - Online First
Microbial metabolism and adaptations in Atribacteria-dominated methane hydrate sediments - NEW!

Jennifer B. Glass*, Piyush Ranjan, Cecilia B. Kretz*, Brook L. Nunn, Abigail M. Johnson, Manlin Xu, James McManus, Frank J. Stewart
*C-DEBI Contribution 571

Gas hydrates harbour gigatons of natural gas, yet their microbiomes remain understudied. We bioprospected 16S rRNA amplicons, metagenomes, and metaproteomes from methane hydrate-bearing sediments under Hydrate Ridge (offshore Oregon, USA, ODP Site 1244, 2–69 mbsf) for novel microbial metabolic and biosynthetic potential. Atribacteria sequences generally increased in relative sequence abundance with increasing sediment depth. Most Atribacteria ASVs belonged to JS-1-Genus 1 and clustered with other sequences from gas hydrate-bearing sediments. We recovered 21 metagenome-assembled genomic bins spanning three geochemical zones in the sediment core: the sulfate–methane transition zone, the metal (iron/manganese) reduction zone, and the gas hydrate stability zone. We found evidence for bacterial fermentation as a source of acetate for aceticlastic methanogenesis and as a driver of iron reduction in the metal reduction zone. In multiple zones, we identified a Ni-Fe hydrogenase-Na+/H+ antiporter supercomplex (Hun) in Atribacteria and Firmicutes bins and in other deep subsurface bacteria and cultured hyperthermophiles from the Thermotogae phylum. Atribacteria expressed tripartite ATP-independent transporters downstream from a novel regulator (AtiR). Atribacteria also possessed adaptations to survive extreme conditions (e.g. high salt brines, high pressure and cold temperatures) including the ability to synthesize the osmolyte di-myo-inositol-phosphate as well as expression of K+-stimulated pyrophosphatase and capsule proteins.
 

NSF Research News
Study examines role of deep-sea microbial predators at hydrothermal vents - NEW!
(Sarah K. Hu et al., PNAS, C-DEBI Contribution 568)

Hydrothermal vent fluids from the Gorda Ridge spreading center in the Pacific Ocean create a biological hub of activity in the deep sea. There in the dark ocean, a unique food web thrives not on photosynthesis but on chemical energy from the venting fluids. Among the creatures having a field day is a diverse assortment of microbial eukaryotes, or protists, that graze on chemosynthetic bacteria and archaea.
 
 

Meetings & Activities


AGU: Abstract Submission Open for the AGU 2021 Fall Meeting, December 13-17, 2021
Consider submitting your deep biosphere abstract to Session B037 - Geomicrobiology of the Deep Biosphere or to Session P034 - Tapping the Rhythms of Potential Life on Extraterrestrial Planets and Moons. Abstracts due August 4, 2021.

C-DEBI Virtual Meeting Series: Techniques for Isolating Persnickety Microbes, August 6, 2021
Our next virtual meeting features plenary speakers Roman Barco (University of Southern California) presenting "Lessons learned from studying marine chemolithoautotrophic communities on minerals" and Ileana Pérez-Rodríguez (University of Pennsylvania) presenting "From microbes in nature to nature in microbes" on Friday August 6 (10:30AM - 12:00PM Pacific). The virtual meeting series is held monthly during the first week of each month, with a regular rotation of science workshops and professional development workshops. Each workshop will contain about 90 minutes of programming, including invited speakers to give plenary tutorials and presentations, breakout icebreaker and discussion sessions, and plenary Q&A sessions. Register in advance for the meeting on August 6, 2021.

NSF GEO: Quarterly Webinar, August 12, 2021 - NEW!
NSF's Directorate for Geosciences is hosting a series of webinars for the research community. This webinar will cover general GEO updates, and presentations on the GEO Innovation Hub and the NSF Graduate Research Fellowship Program (GRFP). Register in advance for this webinar on: August 12, 2021.

UNOLS: Council Positions Call for Nominations
Nominations are due by August 12, 2021.

Joint Genome Institute: Genomics of Energy and Environment Meeting, August 30 - September 1, 2021 - NEW!
The DOE Joint Genome Institute (JGI) is convening the 2021 Annual Genomics of Energy & Environment Meeting virtually for three days of engaging talks and poster sessions. The lineup of speakers represent the full diversity of project types, disciplines, and technologies that the JGI supports. New to the Meeting this year are the “virtual lounges” where you can interact in real-time, one-on-one with JGI staff across all departments. Registration is free and open now for the meeting August 30 - September 1, 2021.

C-DEBI Virtual Meeting Series: The Future of MBIO in IODP, September 3, 2021 - NEW!
Do you have questions about how deep biosphere/microbiology sampling is part of the international scientific ocean drilling program (the International Ocean Discovery Program, IODP), and how subseafloor samples are collected? Have you wondered how you can get more involved with IODP, or how proposals for drilling are handled? Are you curious about the future of IODP beyond the current program, and how deep biosphere/microbiology science can be part of that future? This C-DEBI Virtual Meeting Series event on Friday September 3 (10:30AM - 12:00PM Pacific) will feature a panel of deep biosphere scientists highlighting these topics and answering your questions. Everyone is welcome to join – from experienced IODP users to those who have never been involved with IODP. Panelists will include Jennifer Biddle (University of Delaware), Stephanie Carr (Hartwick College), Steven D’Hondt (University of Rhode Island Graduate School of Oceanography), Jessica Labonté (Texas A&M University Galveston), Beth Orcutt (Bigelow Laboratory for Ocean Sciences), and Jason Sylvan (Texas A&M University). Register in advance for the meeting on September 3, 2021.

Joint Genome Institute: 2021 New Lineages of Life (NeLLi) Symposium, September 16 - October 21, 2021 - NEW!
The DOE Joint Genome Institute (JGI) will be hosting the 2021 New Lineages of Life (NeLLi) Symposium, held over six weeks in two-hour sessions on Thursdays, from September 16 through October 21, 2021. NeLLi2021 will highlight experimental innovations, computational advances, and other developments enabling researchers to progress from identifying microbial novelty to assigning metabolic and functional capabilities. Registration is free and open now for the symposium September 16 - October 21, 2021.
 
NSF: Alan T. Waterman Award Call for Nominations
Nominations due September 20, 2021.

Bigelow Laboratory for Ocean Sciences: Course in Bioinformatics of Microbial Single Cells, April 3-9, 2022 - NEW!
With the hope that the worst of the pandemic is behind us, we are planning to host an on-site Course in Bioinformatics of Microbial Single Cells at Bigelow Laboratory for Ocean Sciences on April 3-9, 2022. The course will provide hands-on training in computational techniques for the integration of single amplified genome (SAG) data in studies of microbial ecology and evolution. The intended audience is faculty, postdocs, graduate students and other professionals planning to work with SAG data. The course will be limited to ~20 attendees. Further details will be available and the registration will begin in October 2021.

Ongoing Activities:

 

Proposal Calls


NSF: Organizational Change for Gender Equity in STEM Academic Professions (ADVANCE)
Various deadlines.

NSF OCE: Chemical Oceanography
Full proposal target dates: August 16, 2021 and February 15, 2022.

NSF OCE: Physical Oceanography
Full proposal target dates: August 16, 2021 and February 15, 2022.

NSF: Research Experiences for Undergraduates (REU)
Full proposal deadline date: August 25, 2021.

NSF: Research Traineeship (NRT) Program
Full proposal deadline date: September 6, 2021.

NSF OISE: International Research Experiences for Students (IRES)
Track I: IRES Sites (IS) due date: September 21, 2021. Track II: Advanced Studies Institutes (ASI) due date: September 28, 2021.

NSF: Inclusion across the Nation of Communities of Learners of Underrepresented Discoverers in Engineering and Science (NSF INCLUDES)
Letter of intent deadline date: October 4, 2021.

NSF: Accelerating Research through International Network-to-Network Collaborations (AccelNet)
Full proposal deadline: October 11, 2021.

NSF: Graduate Research Fellowship Program (GRFP) - 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 over a five-year fellowship period for the graduate education of individuals who have demonstrated their potential for significant research achievements in STEM or STEM education. NSF101 has five tips from a program officer to help you with your application. Full proposal deadlines vary by discipline: October 18-22, 2021.

NASA: Postdoctoral Program
Current cycle deadline: November 1, 2021.

NSF GEO: Ocean Sciences Postdoctoral Research Fellowships (OCE-PRF)
Full proposal deadlines: November 12, 2021.

NSF HRD: Tribal Colleges and Universities Program (TCUP)
See the program solicitation for proposal windows and deadlines through 2021.

NSF BIO: Integrative Research in Biology (IntBIO)
Full proposal deadline date: January 25, 2022.

NSF: Mid-Career Advancement (MCA)
Full proposal target date: February 7, 2022.

NSF BIO / NIH: Enabling Discovery through GEnomics (EDGE)
Full proposal deadlines: February 17, 2022.

Rolling Calls:



Employment


NSF OCE: Marine Geology and Geophysics Program Director (Rotator)
Formal consideration of interested applicants will begin August 2, 2021 and will continue until a selection is made.

University of St. Andrews: Postdoctoral Research Fellow in Hydrothermal Vent Geochemistry - NEW!
We are seeking a postdoctoral researcher who will be responsible for driving the development and application of a hydrothermal reactor experiment that can be used to test the mobility of nutrient elements in fluids under elevated pressure and temperature. The post will also involve the setup of a new analytical method for reduced phosphorus species by ion chromatography-mass spectrometry. The project is fully funded by the Natural Environment Research Council (NERC) in the UK. The deadline for applications is August 16, 2021.

University of St. Andrews: Postdoctoral Research Fellow in Early Earth and Hydrothermal Vent Phylogenomics - NEW!
We are seeking a postdoctoral researcher who will be responsible for conducting phylogenomic analyses of microbial genomes with the aim of reconstructing the expansion of microbial metabolisms and functions through Earth history. The particular focus of this project will be on the characterization of microbial metabolism and function over time in deep-sea and hydrothermal vent microbial communities. The project is fully funded by the Natural Environment Research Council (NERC) in the UK. It will be carried out under joint supervision between Dr. Eva Stueeken at the University of St Andrews, UK, and Dr. Rika Anderson at Carleton College, USA. The postdoctoral researcher would be based at St Andrews and join the research group of PI Eva Stueeken but stay in regular contact with project partner Rika Anderson through virtual and in-person meetings. The deadline for applications is August 20, 2021.

University of Lausanne: Postdoctoral Researcher in Microbial Geochemistry
The deadline for applications is August 20, 2021.

NSF OCE: Science Analyst - NEW!
The National Science Foundation is seeking qualified candidate for a Science Analyst position for the Integrative Programs Section in the Division of Ocean Sciences (OCE) within the Directorate for Geosciences (GEO), Alexandria, VA. The employee in this position reports to the Head of the Integrative Programs Section (IPS) and will primarily provide support for the activities and programs within IPS as well as the related programs across the Division. The position includes a wide spectrum of research facilities, grants policy and process administration activities in support of the organization. In addition, the employee will help develop reports, analyses and presentations regarding the facilities portfolio of the Division. These activities will involve day-to-day interactions with staff throughout the Division, Directorate, other Directorates, and with other Federal Government organizations. The deadline for applications is August 23, 2021.

UCSD Scripps: Postdoctoral Researcher Microbial Oceanography/Molecular Biogeochemistry - NEW!
Scripps Institution of Oceanography at UCSD invites applications for a postdoctoral researcher to investigate coupling between the carbon and iron cycles in marine systems in the context of the heterotrophic bacteria that are the primary drivers of the turnover of organic matter in the oceans. A functional genomics approach will be employed, using model organisms that have been shown to represent a spectrum in terms of their carbon substrate utilization and lifestyle strategies. Research questions will be addressed through a combination of transcriptomic, mutagenic and experimental approaches with model strains. The successful candidate will work with Prof. Katherine Barbeau (SIO/UCSD) and Dr. Christopher Dupont (JCVI La Jolla) and will be expected to conduct independent research, publish papers and present results at scientific meetings. The deadline for applications is August 31, 2021.

Texas A&M University: Assistant Professor in Oceanography
Initial review of applications will begin on September 1, 2021 and continue until the position is filled.

University of Lausanne: PhD Position in Microbial Geochemistry (17814) - NEW!
We invite applications for a 5-year PhD position in the Environmental Microbiogeochemistry Lab in the Institute of Earth Surface Dynamics (IDYST) at the University of Lausanne. The newly launched research group headed by Prof. Berg specializes in the application of interdisciplinary approaches – borrowing methods from the fields of biology, geology, and chemistry – to solve complex environmental questions related to biogeochemical cycling. Steady-state concentrations of certain redox species may arise from the balance between continuous oxidation and reduction reactions, and although concentration changes cannot be measured, their rapid turnover can play a key role in the environment and sustain highly active and diverse microbial communities. This project will focus on hidden or “cryptic” microbial oxygen cycling and its implications for ancient earth to modern-day ecosystems. The deadline for applications is September 1, 2021.

University of Minnesota, Duluth (UMD): Term Assistant Professor in Earth & Environmental Sciences - NEW!
The Department of Earth and Environmental Sciences at the University of Minnesota Duluth anticipates hiring a Spring 2022 semester term visiting faculty appointment. We seek a broad-based earth scientist who will teach two courses that help fill our curricular needs, including Introduction to Geology and Earth Systems, and a choice of a core course in solid earth geology (Earth's Dynamic Interior), a mineral-resources related elective, or an advanced elective. We welcome candidates who seek to incorporate elements of environmental justice into their courses. The position has the potential to be extended to a second year if the successful candidate can teach structural geology with a lab in the 2022-2023 academic year.  Appointment at the Visiting Assistant Professor level is preferred and requires the completion of a PhD, however, applicants with appropriate qualifications who are still ABD may be considered. Review of applications is expected to begin on September 7, 2021, and will continue until the position is filled.

NSF OCE: Division Director in the Division of Ocean Sciences - NEW!
The NSF Directorate for Geosciences (GEO) seeks candidates for the position of Division Director in the Division of Ocean Sciences (OCE). The Division Director provides leadership and management to the Division's programs and assists the GEO Assistant Director in carrying out Directorate-wide responsibilities such as the preparation of budget submission for Congress, oversight and management of Division budgets, and recruitment of scientific staff. The incumbent also supervises and provides leadership and guidance to administrative and support personnel within the Division. Externally, the Division Director represents OCE in a variety of NSF-wide and interagency activities related to research and education, and in interactions with the community. The deadline for applications is September 10, 2021.

University of Lausanne: PhD Position in Microbial Geochemistry (17822) - NEW!
We invite applications for a 5-year PhD position in the Environmental Microbiogeochemistry Lab in the Institute of Earth Surface Dynamics (IDYST) at the University of Lausanne. The newly launched research group headed by Prof. Berg specializes in the application of interdisciplinary approaches – borrowing methods from the fields of biology, geology, and chemistry – to solve complex environmental questions related to biogeochemical cycling. Steady-state concentrations of certain redox species may arise from the balance between continuous oxidation and reduction reactions, and although concentration changes cannot be measured, their rapid turnover can play a key role in the environment and sustain highly active and diverse microbial communities. This project will focus on hidden or “cryptic” microbial sulfur cycling and its implications for ancient earth to modern-day ecosystems. The deadline for applications is September 15, 2021.

NOAA: Director of the Office of Ocean Exploration and Research - NEW!
The Office of Ocean Exploration and Research (OER) provides programmatic direction for NOAA in the field of ocean exploration, research and advanced technology development. OER leads agency efforts in targeted education and outreach to translate, communicate, and disseminate the products and discoveries in order to increase public awareness and literacy in ocean science and provide public data streams from exploration and discovery missions. The Director provides programmatic direction for NOAA in the field of exploration, research and advanced technology development and provides advice to the NOAA Assistant Administrator for Research (AA) and the Under Secretary. The incumbent is responsible for the effective planning, management, and evaluation of OER activities. The deadline for applications is September 16, 2021.

LUMCON: Assistant Professors in Coastal or Marine Science - NEW!
The Louisiana Universities Marine Consortium for research and education (LUMCON) seeks to hire two new Assistant Professors in the third phase of multi-year faculty expansion. We are interested in interdisciplinary scientists whose research addresses a wide range of fundamental questions in ocean and coastal sciences. For the first position, we invite qualified coastal or marine scientists, regardless of discipline, whose research uses observation, modeling, theory, and/or laboratory experiments to address these questions, to apply. For the second faculty position, we invite qualified coastal or marine scientists who either primarily focus on engineering/technology or incorporate considerable engineering/technology into their research to apply. This faculty position specifically will both leverage and build programs at LUMCON’s new Blue Works facility. Review of applicants will begin September 20, 2021, and continue until the positions are filled.

UCSD Scripps: Assistant, Associate, or Full Researcher in Oceans and Atmosphere - NEW!
The Scripps Institution of Oceanography (SIO) at the University of California San Diego invites applications for one or more full-time Researcher positions to be funded by extramural research grants and contracts in any of the research areas listed below. We seek one or more candidates in all areas relevant to the Oceans and Atmosphere Section, broadly including physical oceanography, atmospheric science, climate science, ocean acoustics, and geochemistry, with particular interest in machine learning, coastal ocean-atmosphere interactions, hydrology, and marine robotic sensors. The deadline for applications is September 30, 2021.

MBARI: Principal Investigator (Focus on Seafloor Processes)
Initial review of applications will begin on October 1, 2021 and continue until the position is filled.

University of Toronto: Postdoctoral Position(s) in Fluid-Rock Interactions & Investigation of Deep Subsurface Life - NEW!
Water-rock reactions supporting the deep subsurface biosphere by producing electron donors and acceptors in the subsurface have been identified, from serpentinization (mineral hydration reactions), to radiogenic reactions. In the Stable Isotope Laboratory of Dr. Barbara Sherwood Lollar, this project focuses on the potential for a radiolytically driven H, S, and C deep cycle in the Earth’s subsurface, and the reaction mechanisms and rates sustaining deep subsurface microorganisms in the absence of interaction with the surface photosphere. The Earth-based focus on this work will have direct relevance for models of planetary habitability capable of sustaining subsurface chemolithotrophic life on planets or moons where photosynthesis may never have arisen. Field, laboratory and modelling opportunities are available to extend the existing program to explore the implications of our work on Earth analogs to the search for life on the rocky bodies and ocean worlds of our solar system.

Consortium for Ocean Leadership: Program Associate for Ocean Observing - NEW!
The Program Associate for Ocean Observing has a unique opportunity to support a range of ocean science, technology, and policy activities. The candidate will work with a small team in the Research & Education department focused on advancing regional, national, and international ocean observing strategies. The candidate will primarily support, and in some cases lead, various projects associated with the Interagency Ocean Observation Committee, a body comprised of all U.S. Federal agencies with ocean infrastructure, assets, and data. Duties also include supporting broader community engagement efforts that integrate disparate, emerging, and proven methods for collecting, assimilating, and distributing ocean data and information.

St. Mary's College of Maryland: Open Rank Faculty Position in Marine Science - NEW!
St. Mary’s College of Maryland (SMCM) at St. Mary’s City has a newly established major in Marine Science. We are interested in finding a colleague equipped to help develop the Marine Science major into a signature program. We seek an engaging teacher and scholar trained in physical oceanography who will work collaboratively with the existing SMCM faculty to develop the program. Teaching responsibilities include six undergraduate courses per year at the introductory, intermediate and advanced levels as well as academic advising. A demonstrated interest in attracting and retaining students from underrepresented and/or marginalized groups is desirable.

Carnegie Institution (Stanford): Postdoctoral in Microbial Ecological Modeling of the Marine Nitrogen Cycle - NEW!
We seek a Postdoctoral Fellow in the field of microbial ecology and biogeochemistry, focusing on how microbial metabolisms and ecological interactions drive nitrogen transformations at large scales. Research will use theory and computational modeling to understand how nitrogen-cycling microorganisms provide feedbacks to current changes in the climate system. Specific project focuses are flexible, and may include, for example, the ecology and biogeochemical impacts of aerobic and anaerobic metabolisms in anoxic marine zones or the global-scale ecology of nitrification in relation to the carbon cycle. Fellows will work primarily under the guidance of Dr. Emily Zakem in the Department of Global Ecology (DGE) at the Stanford University campus of the Carnegie Institution for Science.

Carnegie Institution (Stanford): Postdoctoral in Ecological Modeling of Marine Microheterotrophic Communities - NEW!
We seek a Postdoctoral Fellow in the field of microbial ecology and biogeochemistry, focusing on how the diverse communities of microorganisms that consume nonliving organic matter impact the carbon cycle at large scales. Research will use theory and computational modeling to understand how microheterotrophic ecological interactions give rise to observed community composition and nutrient cycling. Specific project focuses are flexible, and may include, for example, the factors maintaining the diversity of free-living microheterotrophic functional types or the controls on the spectrum of organic carbon turnover rates. Fellows will work primarily under the guidance of Dr. Emily Zakem in the Department of Global Ecology (DGE) at the Stanford University campus of the Carnegie Institution for Science.

Pennsylvania State University: Postdoctoral Researcher on Microbial Metabolic Networks


Email me with any items you'd like to share in future newsletters. You are what makes our deep biosphere community!

 
Rosalynn Sylvan
C-DEBI Managing Director
University of Southern California, Los Angeles, CA 90089-0371
rosalyyl@usc.edu

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