CENTER for DARK ENERGY BIOSPHERE INVESTIGATIONS

C-DEBI Newsletter – February 3, 2020

C-DEBI Newsletter – February 3, 2020
This newsletter is also accessible via our website.

 

Publications & Press

Geochimica et Cosmochimica Acta
Lower hydrogen flux leads to larger carbon isotopic fractionation of methane and biomarkers during hydrogenotrophic methanogenesis – NEW!
Tran B. Nguyen, Begüm D. Topçuoğlu, James F. Holden, Douglas E. LaRowe, Susan Q. Lang*
*C-DEBI Contribution 499

The isotopic composition of lipid biomarkers and biomass in sedimentary environments are widely used to infer microbial metabolisms and constrain carbon cycling processes. It has been observed that metabolic energy availability in the form of H2 impacts the stable carbon isotopes of CH4 during hydrogenotrophic methanogenesis, but it is unknown whether this relationship extends to lipids and amino acids. Since lipids and amino acids are long-lived, they can be used to reconstruct past conditions over geologic timescales. Therefore, the controls on their isotopic signatures are important to constrain to better interpret past environments. In this study, the isotopic distributions of carbon metabolized and reduced by the hyperthermophile Methanocaldococcus jannaschii were quantified following growth at 82 °C in a chemostat with high (80–83 µM) and low (15–27 µM) H2 concentrations. As has been shown previously, the stable carbon isotope fractionation factors for CH4 were >15‰ larger in low H2 experiments than in high H2 experiments. Lipid biomarkers and amino acids were similarly impacted with approximately 10‰ larger fractionation factors under low H2 conditions. The increase in fractionation factors can be related to the lower availability of thermodynamic energy, suggesting that even larger fractionation factors would be observed in methanogens living close to their threshold energy needs, as they do in most environments. The resulting isotopic signatures of long-lived lipid biomarkers synthesized by hydrogenotrophic methanogens may become as ‘superlight’ as those synthesized by archaea carrying out the anaerobic oxidation of methane. These results help to describe the underlying mechanisms that determine the isotopic composition of long-lived biomarkers and provide constraints for interpreting these signatures in the environment.

The ISME Journal
Evidence for auxiliary anaerobic metabolism in obligately aerobic Zetaproteobacteria – NEW!
Abhiney Jain*, Jeffrey A. Gralnick
*C-DEBI Contribution 519

Zetaproteobacteria are obligate chemolithoautotrophs that oxidize Fe(II) as an electron and energy source, and play significant roles in nutrient cycling and primary production in the marine biosphere. Zetaproteobacteria thrive under microoxic conditions near oxic–anoxic interfaces, where they catalyze Fe(II) oxidation faster than the abiotic reaction with oxygen. Neutrophilic Fe(II) oxidizing bacteria produce copious amounts of insoluble iron oxyhydroxides as a by-product of their metabolism. Oxygen consumption by aerobic respiration and formation of iron oxyhydroxides at oxic–anoxic interfaces can result in periods of oxygen limitation for bacterial cells. Under laboratory conditions, all Zetaproteobacteria isolates have been shown to strictly require oxygen as an electron acceptor for growth, and anaerobic metabolism has not been observed. However, genomic analyses indicate a range of potential anaerobic pathways present in Zetaproteobacteria. Heterologous expression of proteins from Mariprofundus ferrooxydans PV-1, including pyruvate formate lyase and acetate kinase, further support a capacity for anaerobic metabolism. Here we define auxiliary anaerobic metabolism as a mechanism to provide maintenance energy to cells and suggest that it provides a survival advantage to Zetaproteobacteria in environments with fluctuating oxygen availability.

Origins of Life and Evolution of Biospheres
Reactivity of Metabolic Intermediates and Cofactor Stability under Model Early Earth Conditions – NEW!
Thora R. Maltais, David VanderVelde, Douglas E. LaRowe*, Aaron D. Goldman, Laura M. Barge
*C-DEBI Contribution 521

Understanding the emergence of metabolic pathways is key to unraveling the factors that promoted the origin of life. One popular view is that protein cofactors acted as catalysts prior to the evolution of the protein enzymes with which they are now associated. We investigated the stability of acetyl coenzyme A (Acetyl Co-A, the group transfer cofactor in citric acid synthesis in the TCA cycle) under early Earth conditions, as well as whether Acetyl Co-A or its small molecule analogs thioacetate or acetate can catalyze the transfer of an acetyl group onto oxaloacetate in the absence of the citrate synthase enzyme. Several different temperatures, pH ranges, and compositions of aqueous environments were tested to simulate the Earth’s early ocean and its possible components; the effect of these variables on oxaloacetate and cofactor chemistry were assessed under ambient and anoxic conditions. The cofactors tested are chemically stable under early Earth conditions, but none of the three compounds (Acetyl Co-A, thioacetate, or acetate) promoted synthesis of citric acid from oxaloacetate under the conditions tested. Oxaloacetate reacted with itself and/or decomposed to form a sequence of other products under ambient conditions, and under anoxic conditions was more stable; under ambient conditions the specific chemical pathways observed depended on the environmental conditions such as pH and presence/absence of bicarbonate or salt ions in early Earth ocean simulants. This work demonstrates the stability of these metabolic intermediates under anoxic conditions. However, even though free cofactors may be stable in a geological environmental setting, an enzyme or other mechanism to promote reaction specificity would likely be necessary for at least this particular reaction to proceed.

Philosophical Transactions of the Royal Society A
Serpentinite in the Earth system – NEW!
Editors: Andrew McCaig, Peter Kelemen, Gretchen Früh-Green and Damon Teagle

This theme issue brings together international scientists working on all aspects of serpentinisation, a process that may have been important for the origin of life on Earth and perhaps other planets. Serpentine is also a key carrier of water to depth in subduction zones, leading to intermediate depth earthquakes and the formation of island arc volcanoes. This issue is based on a Royal Society discussion meeting held in November 2018.

 

 
 
 
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Meetings & Activities

Goldschmidt: Hawai'i 2020, June 21-26
Planning on attending? Consider submitting your abstracts to: Session 11e: Recognizing Preserved Microbial Signatures in Modern and Ancient Environments, and Session 6i: Harnessing Multidimensionality in Complex, Co-evolving Earth Systems–Network Analysis, Cluster Analysis, and Other Machine Learning and Advanced Visualization Applications. Abstract submission deadline: February 14, 2020.

AGU: 2020 Ocean Sciences Town Hall: Developing a coordinated vision for transdisciplinary deep ocean research – NEW!
Drs. Samantha Joye, Anna-Louise Reysenbach and Adam Soule will host a Town Hall at the 2020 Ocean Sciences Meeting. The Town Hall is scheduled for Monday, February 17 from 12:25 to 1:45 pm at the San Diego Convention Center, 9, UL. The Town Hall is aimed at researchers who are interested in contributing to development of a grassroots community vision that will promote a new phase of deep sea discovery through coordinated transdisciplinary research efforts made possible through development of a Research Coordination Network proposal. This effort will advance the field and create new directions in deep sea science, promote new collaborations, and foster coordination and training across disciplinary, organizational, geographic, and international boundaries all while broadening participation in deep ocean science.

AGU: 2020 Ocean Sciences Town Hall: Expanding the Reach of the Research Fleet: Autonomous (and Piloted) Airborne Systems in Support of Ocean Sciences
If you will/have used airborne resources in your oceanographic work and wish to present a lightning talk please sign up here by February 14, 2020.

Intl. Assc. of Sedimentologists (ISA) 35th Meeting: Call for Abstracts, Session on "Microbial imprint on the sediment record: From organomineralization to global biogeochemical cycling" – NEW!
Conveners: Thomas C. (University of Geneva, Switzerland), Petráš D. (Czech Geological Survey, Czech Republic), Pérez A.M. (Institute of Palaeontology ZRC SAZU, Slovenia). Session description: From iron formations to stromatolitic facies, microbes have been instrumental for the formation, composition and preservation of sedimentary units since the dawn of life on Earth. As such, the chemical and isotopic signatures imparted by their activity in these rocks have been used to disentangle the long-term chemical evolution of the atmosphere and ancient oceans. Nonetheless, assessing the primary origin and biogenicity of certain minerals and textures remains challenging, despite these factors being crucial to our quest to understand key stages in evolution of life and earth systems. The diversity and complexity of life forms and metabolisms interacting from the moment of deposition and during shallow burial, along with the rare availability of exceptionally well-preserved ancient chemical rocks has also encouraged an active search for modern analogues to ancient microbially influenced sedimentary deposits. For this session, we seek contributions envisioning approaches for understanding the signatures derived from microbial activity on any type of sedimentary archive, including carbonates, silica-rich deposits, shales, modern lacustrine or marine sediments, soil crusts, etc. Studies describing how active microbes act as key agents in both mineral authigenesis and diagenetic alteration are particularly welcome. Given the complexity of studying such processes, the session is also open to the presentation of approaches allowing multiscale analyses, at the interface between biology and geology. Abstract submission is open until the February 15, 2020 and there are options for early career scientists to find support for coming to beautiful Prag in June via the IAS.

JpGU: Submit an abstract to the Japan Geoscience Union (JpGU)-AGU Joint Meeting, May 2020, Chiba, Japan – NEW!
The Japan Geoscience Union (JpGU) commemorates the coming year 2020; it is the 15th anniversary since JpGU was founded in 2005, and the 30th anniversary since its predecessor, the Japan Earth and Planetary Science Joint Meeting, was first held in 1990. On this occasion, the 2020 annual meeting will be held joint with the American Geophysical Union (AGU) as the JpGU-AGU Joint Meeting 2020, following the first cooperative effort with AGU in 2017. Furthermore, the Joint Meeting anticipates expansion and enrichment of joint sessions with the Asia Oceania Geosciences Society (AOGS) and the European Geosciences Union (EGU). The JpGU has recently grown to embrace over 51 members of academic societies and over 10,000 individual members. The attendance at the 2019 Annual Meeting exceeded 8,400 total participants (including approximately 2,400 students), with over 650 participants from abroad (covering 41 nations and areas). The meeting provides an indispensable opportunity for participants from the fields of Earth and planetary science to interact. The annual survey indicates that the participants would like to see a wider range of session programs, including some open to the public, and an expansion of English-language sessions. Hopes are high for the promotion and expansion of interdisciplinary and border-area researches and further internationalization of Earth and planetary science research. Abstract submission deadline: February 18, 2020.

UNOLS: Quality of Life at Sea Survey
Please complete the survey by February 28, 2020.

USC: 17th Annual Southern California Geobiology Symposium – UPDATED!
Abstract submission and registration will close on March 4, 2020.

AGU: Nominate Your Peers for 2020 Honors
Nominations are now open for 2020 AGU honors, including the Asahiko Taira International Scientific Ocean Drilling Research Prize. Deadline: March 15, 2020.

ISSM 2020: Call for poster abstracts – UPDATED!
The deadline for submitting poster abstracts (oral presentation abstract submissions are now closed) is March 31, 2020.

GRC: Exploring Fluxes, Forms and Origins of Deep Carbon in Earth and Other Terrestrial Planets, June 28-July 3, 2020, Lewiston, ME, USA
Applications for this meeting must be submitted by May 31, 2020.

Microenergy 2020: 4th International Workshop on Microbial life under extreme energy limitation, September 7-11, Sandbjerg Manor, Denmark – NEW!
At several hundred meters below our feet or below the sea floor, the energy flux and the theoretical growth rate of bacteria are orders of magnitude below anything we can understand from research on cultivated microorganisms. Studies of the carbon and energy turnover deep beneath the seafloor and in the terrestrial subsurface indicate that the prokaryotic cells living here subsist at an energy flux that barely allows cell growth over tens to thousands of years. It remains unexplained whether the organisms have properties beyond our current understanding of microbial life and whether these organisms in fact represent the predominant mode of microbial life on our planet – or whether energy sources may be available that have not yet been identified. The limits of microbial life and the exploration of the biological demand for energy is the focus of the International Workshop on Microbial Life under Extreme Energy Limitation (co-sponsored by C-DEBI), held 7-11 September at Sandbjerg Manor near Sønderborg, Denmark. We invite researchers and students from different relevant disciplines to participate in the workshop in order to discuss microbial energy requirements and stimulate new thinking and new approaches. The deadline for abstract submissions is April 1, 2020.

Serpentine Days: 5th Workshop, September 21-24, Sestri Levante (Genova, Italy)
Registration will close June 30, 2020.

UNOLS: Science in the Abyss Workshops

Ongoing Activities:

Education & Outreach

IODP-USSSP: Apply to sail on the JR as an Onboard Outreach Officer for Expeditions 391 and 392
Deadline: February 10, 2020.

USC Wrigley Institute: Summer REU: Coastal Ocean Processes
Applications are due by February 14, 2020.

IODP-USSSP: U.S. Travel Support for ECORD Summer School: Downhole Logging – NEW!
Returning to the University of Leicester for the fifth year, the ECORD Summer School: Downhole Logging for IODP Science focuses on downhole logging within IODP and the applications of downhole measurements in various geoscientific fields, including paleoclimatology and sedimentology, as well as for broader geological and ecological processes. The Summer School is a 1-week long CPD-accredited course offering 36 hours of training in the core principles of petrophysics and downhole logging, from data collection to interpretation. The School will be hosted at the University of Leicester (UK) and will run from the 4th July to the 10th of July 2020. The course is open to applicants from the international community, but applications from early career researchers (including PhD students) are particularly encouraged. U.S.-affiliated students and researchers may also apply for travel support through the U.S. Science Support Program. A limited number of travel grants are available and priority may be given to applicants actively engaged or interested in research using IODP data. The deadline to apply for travel support and for the course is February 14, 2020.

RPI: School of Earth and Environmental Sciences: Graduate School Applications
Applications are welcome at any time.

Proposal Calls

NSF-OCE: Proposal Compliance Reminders – NEW!
We would like to remind our community of the importance of following the proposal preparation guidelines of the NSF Proposal & Award Policies & Procedures Guide (PAPPG). While NSF has instituted several automatic compliance checkers in the last few years, there are errors that persist. When errors are identified, all NSF Programs have the option of returning non-compliant proposals without review, however OCE has traditionally tried to be flexible, and allow PIs to correct proposals after submission. We want to share that the level of non-compliance with PAPPG guidelines for OCE proposals has reached 50%, so we need to enlist your help in reducing that number. These compliance errors delay the start of the review process and put additional pressure on our reviewer community. In addition to identified errors resulting in your proposals potentially being returned without review, uncorrected errors in proposals that have gone through the review process can also lead to delays in making awards or, infrequently, in our not being able to recommend a particular proposal for award. The following are examples of issues we currently encounter most frequently: Inclusion of URLs in the Project Description (including Results of Prior Support); Not including distinct subheadings for Intellectual Merit and Broader Impacts in the Project Summary, Project Description, and Results of Prior Support; Not including Results of Prior Support for all project PIs and Co-PIs; Incomplete budget documentation for subawards. These four items are just common examples, and do not cover all the errors that we ask PIs to correct. We also note that new releases of the PAPPG, which are issued every year, often contain new requirements. The PAPPG itself contains a checklist that you may find useful in proposal preparation. We also call your attention to the Division of Ocean Sciences Sample and Data Policy, for guidance in preparing data management plans that conform with OCE Policy. Please note that this policy asks that the disposition of project data and samples should be included in the description of Results of Prior Support, in accordance with the PAPPG.

NSF: Frontier Research in Earth Sciences (FRES)
Full proposal deadline: February 5, 2020.

NSF: Understanding the Rules of Life: Epigenetics
Full proposal deadline: February 6, 2020.

NSF: Research Traineeship (NRT) Program
Full Proposal Deadline Date: February 6, 2020; February 6, Annually Thereafter.

NSF: Ocean Technology and Interdisciplinary Coordination – NEW!
The Oceanographic Technology and Interdisciplinary Coordination (OTIC) Program supports a broad range of research and technology development activities. Unsolicited proposals are accepted for instrumentation development that has broad applicability to ocean science research projects and that enhance observational, experimental or analytical capabilities of the ocean science research community. Specific announcements for funding opportunities are made for additional projects involving Improvements in Facilities, Communications, and Equipment at Biological Field Stations and Marine Laboratories (FSML) and the National Ocean Partnership Program. Full proposal target date: February 18, 2020.

NSF: Biological Oceanography – NEW!
The Biological Oceanography Program supports fundamental research in biological oceanography and marine ecology (populations to the ecosystems) broadly defined: relationships among aquatic organisms and their interactions with the environments of the oceans or Great Lakes. Projects submitted to the program are often interdisciplinary efforts that may include participation by other OCE Programs. Full proposal target dates: February 18, 2020 and August 17, 2020.

NSF: Chemical Oceanography – NEW!
The Chemical Oceanography Program supports research into the chemistry of the oceans and the role of the oceans in global geochemical cycles. Areas of interest include chemical composition, speciation, and transformation; chemical exchanges between the oceans and other components of the Earth system; internal cycling in oceans, seas, and estuaries; and the use of measured chemical distributions as indicators of physical, biological, and geological processes. Full proposal target dates: February 18, 2020 and August 17, 2020.

NSF: Physical Oceanography – NEW!
The Physical Oceanography Program supports research on a wide range of topics associated with the structure and movement of the ocean, with the way in which it transports various quantities, with the way the ocean’s physical structure interacts with the biological and chemical processes within it, and with interactions between the ocean and the atmosphere, solid earth and ice that surround it. Full proposal target dates: February 18, 2020 and August 17, 2020.

UNOLS: 2020 Ocean Observatories Initiative (OOI) Cruise Opportunities – NEW!
The primary goal of the UNOLS Cruise Opportunity Program is to provide graduate students currently completing (or who have recently completed) a degree in a field of oceanographic research with the opportunity to participate in a research cruise. The participant will be a member of the scientific party and be involved in data collection and all other activities at sea. It is envisioned that the individual will be familiar with the science to be conducted at sea, and thus, form new collaborations and potentially develop new research directions. To be eligible to participate in this program, the individual must be either currently be studying at a U.S.-based institution or a recent graduate, and must have either a U.S. Passport or a U.S. Work Visa. The application deadline for the Spring 2020 Deployment Operations cruises is February 28, 2020; for Fall 2020, the application deadline is August 3, 2020.

NSF: EarthCube
Full proposal deadline: March 12, 2020.

NSF: Dimensions of Biodiversity
The 2020 program is restricted to projects supported by international partnerships with the National Natural Science Foundation of China (NSFC), the São Paulo Research Foundation (FAPESP) of Brazil, and the National Research Foundation (NRF) of South Africa. Full Proposal Deadline: March 27, 2020.

NSF: Facilitator of Marine Seismic Capabilities for the U. S. Research Community
The proposal submission deadline is April 10, 2020.

NSF: Faculty Early Career Development Program (CAREER)
Full proposal deadline: July 27, 2020.

NSF: Improving Undergraduate STEM Education: Pathways into the Earth, Ocean, Polar and Atmospheric & Geospace Sciences (IUSE:GEOPAths)
Letter of Intent Due Date: November 17, 2020.

Rolling Calls:

Employment

UCSD: International Ocean Discovery Program Data Manager – UPDATED!
Filing deadline extended to: February 7, 2020.

BIOS: Assistant Scientist in Oceanography (Physical Oceanography/Biogeochemical System Approaches) – NEW!
The Bermuda Institute of Ocean Sciences (BIOS), an independent U.S. not-for-profit marine research institution based in Bermuda, is seeking an early career candidate for an Assistant Scientist position. We seek applications from current postdoctoral scholars/fellows or recent PhD graduates in oceanography or closely related subjects. We welcome a broad range of potential topics for study, including physical oceanography process studies at all scales, biogeochemical research with practical experimentation, and system modeling with strong integration of data. We seek a candidate who will take advantage of the opportunities and facilities offered at BIOS which include bi-weekly access to the deep ocean, repeat measurements and long-term monitoring of ocean properties, integration of glider observations with traditional ship-based measurements and laboratory access for chemical and biological measurements and experimentation. The successful candidate will oversee a fleet of autonomous underwater gliders equipped with sensors systems for biogeochemical and physical oceanographic research. The position will remain open until filled.

WHOI: Tenure Track Scientist – Marine Chemistry & Geochemistry

U of Georgia: Assistant or Associate Professor – Biological Oceanography

WWU: 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
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.

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