C-DEBI Newsletter – February 15, 2018

Publications & Press

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Genome Announcements
Genome Sequence of Hydrogenovibrio sp. Strain SC-1, a Chemolithoautotrophic Sulfur and Iron Oxidizer – NEW!
Christopher Neely*, Charbel Bou Khalil*, Alex Cervantes*, Raquel Diaz*, Angelica Escobar*, Karen Ho*, Stephen Hoefler*, Hillary H. Smith*, Karla Abuyen*, Pratixaben Savalia*, Kenneth H. Nealson, David Emerson, Benjamin J. Tully*, Roman A. Barco*, Jan P. Amend*
*C-DEBI Contribution 409

Hydrogenovibrio sp. strain SC-1 was isolated from pyrrhotite incubated in situ in the marine surface sediment of Catalina Island, CA. Strain SC-1 has demonstrated autotrophic growth through the oxidation of thiosulfate and iron. Here, we present the 2.45-Mb genome sequence of SC-1, which contains 2,262 protein-coding genes.

[This research was funded as part of C-DEBI's 2017 NSF Community College Cultivation Cohort (C4) Research Experience for Undergraduates! Applications for the 2018 program are due February 23, 2018.]

Frontiers in Microbiology
Changes in Microbial Energy Metabolism Measured by Nanocalorimetry during Growth Phase Transitions – NEW!
Alberto Robador*, Douglas E. LaRowe*, Steven E. Finkel*, Jan P. Amend*, Kenneth H. Nealson
*C-DEBI Contribution 414

Calorimetric measurements of the change in heat due to microbial metabolic activity convey information about the kinetics, as well as the thermodynamics, of all chemical reactions taking place in a cell. Calorimetric measurements of heat production made on bacterial cultures have recorded the energy yields of all co-occurring microbial metabolic reactions, but this is a complex, composite signal that is difficult to interpret. Here we show that nanocalorimetry can be used in combination with enumeration of viable cell counts, oxygen consumption rates, cellular protein content, and thermodynamic calculations to assess catabolic rates of an isolate of Shewanella oneidensis MR-1 and infer what fraction of the chemical energy is assimilated by the culture into biomass and what fraction is dissipated in the form of heat under different limiting conditions. In particular, our results demonstrate that catabolic rates are not necessarily coupled to rates of cell division, but rather, to physiological rearrangements of S. oneidensis MR-1 upon growth phase transitions. In addition, we conclude that the heat released by growing microorganisms can be measured in order to understand the physiochemical nature of the energy transformation and dissipation associated with microbial metabolic activity in conditions approaching those found in natural systems.

Frontiers in Microbiology
Bioenergetic Controls on Microbial Ecophysiology in Marine Sediments – NEW!
James A. Bradley*, Jan P. Amend*, Douglas E. LaRowe*
*C-DEBI Contribution 415

Marine sediments constitute one of the most energy-limited habitats on Earth, in which microorganisms persist over extraordinarily long timescales with very slow metabolisms. This habitat provides an ideal environment in which to study the energetic limits of life. However, the bioenergetic factors that can determine whether microorganisms will grow, lie dormant, or die, as well as the selective environmental pressures that determine energetic trade-offs between growth and maintenance activities, are not well understood. Numerical models will be pivotal in addressing these knowledge gaps. However, models rarely account for the variable physiological states of microorganisms and their demand for energy. Here, we review established modeling constructs for microbial growth rate, yield, maintenance, and physiological state, and then provide a new model that incorporates all of these factors. We discuss this new model in context with its future application to the marine subsurface. Understanding the factors that regulate cell death, physiological state changes, and the provenance of maintenance energy (i.e., endogenous versus exogenous metabolism), is crucial to the design of this model. Further, measurements of growth rate, growth yield, and basal metabolic activity will enable bioenergetic parameters to be better constrained. Last, biomass and biogeochemical rate measurements will enable model simulations to be validated. The insight provided from the development and application of new microbial modeling tools for marine sediments will undoubtedly advance the understanding of the minimum power required to support life, and the ecophysiological strategies that organisms utilize to cope under extreme energy limitation for extended periods of time.

Journal of Geophysical Research: Biogeosciences
Necromass as a limited source of energy for microorganisms in marine sediments – NEW!
James A. Bradley*, Jan P. Amend*, Douglas E. LaRowe*
*C-DEBI Contribution 416

The in situ production of necromass and its role as a power source in sustaining heterotrophic microorganisms in natural settings has never been quantified. Here, we quantify the power availability from necromass oxidation to living microorganisms buried in marine sediments over millions of years, first in the oligotrophic South Pacific Gyre (SPG), and second on a global scale. We calculate that power from autochthonously produced necromass in the upper meter of sediment at SPG provides only a small fraction (~0.02%) of the maintenance power demand of the living community (1.9×10^-19 W cell^-1). Power from necromass oxidation diminishes considerably with increasing sediment depth (and thus sediment age). Alternatively, the oxidation of allochthonous organic matter, and of radiolytic H₂, provides power equivalent to or in excess of the maintenance demands of living microorganisms at SPG. On a global scale, necromass may support the maintenance power demand of 2 to 13% of the microbial community in relatively young sediments (<10,000 years) when it is oxidized with SO₄^2- and O₂ respectively. However, in older sediments, the power supplied by necromass is negligible (<0.01%). Nevertheless, the oxidation of a single dead cell per year provides sufficient power to support the maintenance demands of dozens to thousands of cells in low-energy marine sediments. This raises the possibility that the production and oxidation of necromass may provide a mechanism for non-growing microorganisms to endure unfavorable, low-energy settings over geological timescales.

TED Talks: This deep-sea mystery is changing our understanding of life – NEW!
How deep into the Earth can we go and still find life? Marine microbiologist Karen Lloyd introduces us to deep-subsurface microbes: tiny organisms that live buried meters deep in ocean mud and have been on Earth since way before animals. Learn more about these mysterious microbes, which refuse to grow in the lab and seem to have a fundamentally different relationship with time and energy than we do.

 

Meetings & Activities

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C-DEBI: Workshop on deep sea mining impacts on microbial ecosystem services – NEW!
If you have an interest in using your expertise in deep sea microbial ecology and/or biogeochemistry to define possible microbial ecosystem service impacts that may result from deep sea mining activities, please consider attending a small workshop focused on this topic that will be held April 18-19, 2018, at the Bigelow Laboratory for Ocean Sciences in Maine.

USRA: 3rd Ocean Worlds meeting, May 21-24, Houston, TX – NEW!
In the next of a series of Ocean Worlds meetings, the focus will be on the potential for silicate-water interactions to occur on Ocean Worlds beyond Earth, from a multi-disciplinary and inter-disciplinary perspective. As with past Ocean Worlds meetings, a primary motivation is to engender a cross-fertilization of ideas and expertise by soliciting contributions from both the Ocean Sciences and Planetary Sciences communities. Consequently, contributions are invited that address any aspects of this broad water-rock interaction theme, across the Planetary and Ocean Science fields, including geophysics, hydrogeology, geochemistry and microbiology. Abstracts due March 7, 2018.

COL: Save the date for COL's Public Policy Forum: March 7, 2018 – NEW!
On Wednesday, March 7, 2018, Consortium for Ocean Leadership’s annual Public Policy Forum will be at the Reserve Officers Association on Capitol Hill. This year’s theme is Power of Partnerships: Advancing Ocean Science and Tech and will feature leadership roundtables and case studies with experts from across the federal government and around the country, as well as remarks by several Members of Congress. Power of Partnerships investigates partnering as a tool to advance the national ocean science and technology enterprise. A draft agenda can be found on our website. Breakfast and lunch will be provided, and a reception will be held in the evening.

NSF: Spring 2018 NSF Grants Conference – Save the Date
Registration will open on Thursday, March 15, 2018, at 12:00 PM EST.

Goldschmidt 2018: Call for Abstracts
Abstracts due March 30, 2018.

15th Annual Southern California Geobiology Symposium: Save the Date! Saturday, April 21, 2018 @ UCR
Calls for posters and talks will be going out soon so stay tuned.

C-DEBI: Nominations now open for the C-DEBI 2018 Networked Speaker Series

C-DEBI: Rolling call for Community Workshop support

C-DEBI: Protocols.io Group Page

C-DEBI: Subseafloor Cultures Database

 

C-DEBI Spotlight

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Meet the rest of our 2017 Global Enviromental Microbiology students and Community College Cultivation Cohort (C4) REU participants, or learn more about our undergraduate programs!

Education & Outreach

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C-DEBI: NSF REU: Community College Cultivation Cohort (C4)
C-DEBI’s NSF REU, C4, is a 9-week research internship targeting community college students nationwide. Students will spend their summer doing cutting edge research as they help grow, isolate, and describe previously unknown microorganisms. C4 students will work in teams in laboratories at USC, learning state-of-the-art techniques ranging from DNA sequencing to microscopy and sterile techniques to analytical chemistry. Applications due February 23, 2018.

C-DEBI: Next Professional Development Webinar: February 28, 12pm PT
Julie Huber (C-DEBI Associate Director, Associate Scientist, WHOI) leads the next C-DEBI Professional Development Webinar on “Surviving (and Maybe Even Thriving!) in a Soft Money Position.”

ASM: Research Capstone Fellowship: Funding For Professional Development and Career Networking
Application Deadline: March 1, 2018.

IODP: Onboard Outreach Program – NEW!
The USSSP Onboard Outreach Program (formerly known as the Educator Officer Program) gives formal and informal educators, artists, writers, videographers and other participants the opportunity to spend an entire expedition with an IODP shipboard party and translate their experiences for students and the general public via blogs, videos, social networking sites, live ship-to-shore video events and development of educational resources. Onboard Outreach Program participants are selected through a competitive application and interview process. All expenses for Onboard Outreach Program participants, such as travel to and from the ports of call, and a $10,000 stipend, are paid by USSSP. The selected individual(s) will also be flown to a three-day training session prior to their expedition. Non-US applicants will be directed to their country’s IODP Program Member Office but are still encouraged to apply. The application period will close on March 5, 2018.

ICDP: Training Course on Planning, Management and Execution of Continental Scientific Drilling Projects – NEW!
the International Continental Scientific Drilling Program ICDP invites Principal Investigators, project managers and leading scientists of upcoming continental scientific drilling projects to apply for the ICDP Training Course on Planning, Management and Execution of Continental Scientific Drilling Projects to be held from May 15-17, 2018, at the GeoZentrum KTB (Germany). This training course will touch upon relevant aspects for managing a scientific drilling project, including: Proposal Writing & Multi-Source Fundraising; Drilling Workflow & Terminologies; Health, Safety and Environment; On-Site Management; Sample Handling and Curation; Dowhhole Logging Planning and Execution; Data Management; Outreach. Preference will be given to applicants involved in ICDP drilling projects, applicants from ICDP member countries, developing countries, and those from countries considering ICDP membership. For the successful candidates, costs including those for travel, visas, and accommodation will be covered by the ICDP. The application deadline is March 15, 2018.

IODP-USSSP: Travel Support for the Petrophysics Summer School 2018 – NEW!
Petrophysics is the study of the physical (and chemical) properties of rocks and their interactions with fluids, and integrates downhole in situ data from logs with core and seismic data. This has significant applications in the hydrocarbon industry in terms of both exploration for, and production of, oil and gas. It is also an important component of the International Ocean Discovery Program (IODP) in helping to answer the many and varied questions posed by ocean research drilling expeditions around the world. This third Petrophysics Summer School will provide a unique workshop that will bring together experts from both academia and industry to give training in the theory and practice of petrophysics and, notably its applications across both IODP and industry. There are few opportunities for training, especially for non-industry researchers, and with recent reports indicating significant skills shortages in the hydrocarbon sector, the workshop could attract a variety of participants including those who might not normally engage with the IODP community. In addition, the summer school will strengthen links between IODP and industry, increase the visibility of IODP, provide essential training to the next generation of petrophysicists and, importantly, enable future expedition participants to best utilize these data in their investigations of the ocean floor. U.S.-affiliated students and researchers may apply for partial travel support through the U.S. Science Support Program. A limited number of travel grants are available. To apply for U.S. travel support, complete an online application by March 23, 2018.

C-DEBI: Community College Research Internship for Scientific Engagement (CC-RISE)
CC-RISE is an eight-week, paid, summer research internship program for community college students run by the Center for Dark Energy Biosphere Investigations. Students will gain firsthand exposure to the scientific process by working in a faculty-led research lab at the University of California Santa Cruz or at the Woods Hole Oceanographic Institution in Woods Hole, MA. In addition to research, students will participate in activities focusing on how to transition from a two-year college to a university and information on graduate school. At the end of the program, students will present their results to an audience of peers and mentors. Applications are due March 31, 2018 for UCSC and March 23, 2018 for WHOI.

Institute for Broadening Participation: Not too late – STEM summer research programs – NEW!
It’s not too late! If you know of any students still looking for STEM summer research programs for this summer, now’s the time to apply. Deadlines are fast approaching, but we still have 100+ programs in our database that have deadlines coming up in the next 45 days. All programs in our database are funded programs — most provide a stipend of around $3,000 – $5,000 plus travel and housing. Students can use our advanced search page to find programs with upcoming deadlines: http://pathwaystoscience.org/programs.aspx?adv=adv. And this quick video tutorial on using our search engine may be helpful: https://www.youtube.com/watch?v=FxKsAGk8dAw&t=16s. Any students who need help finding a program should feel free to email the Institute for Broadening Participation’s Senior Advisor, Liv Detrick (ldetrick@ibparticipation.org).

NSF: Research Experiences for Undergraduates (REU), Ocean Sciences
Application websites for most of these OCE REU’s are open now or will open soon and most application deadlines are in mid-February or March.

IODP-USSSP: New IODP Outreach: In Search of Earth's Secrets

Mentoring365: Become an Earth and Space Science Mentor or Mentee

NOAA: Graduate Research & Training Scholarship Program

Proposal Calls

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NSF: Dimensions of Biodiversity – NEW!
Despite centuries of discovery, most of our planet’s biodiversity remains unknown. The scale of the unknown diversity on Earth is especially troubling given the rapid and permanent loss of biodiversity across the globe. The goal of the Dimensions of Biodiversity campaign is to transform, by 2020, how we describe and understand the scope and role of life on Earth. This campaign promotes novel integrative approaches to fill the most substantial gaps in our understanding of the diversity of life on Earth. It takes a broad view of biodiversity, and focuses on the intersection of genetic, phylogenetic, and functional dimensions of biodiversity. Successful proposals must integrate these three dimensions to understand interactions and feedbacks among them. While this focus complements several core programs in BIO, it differs by requiring that multiple dimensions of biodiversity be addressed simultaneously, in novel ways, to understand their synergistic roles in critical ecological and evolutionary processes, especially pertaining to the mechanisms driving the origin, maintenance, and functional roles of biodiversity. Full proposal deadline: February 28, 2018.

IODP: Apply to Sail on IODP Expedition 383: Dynamics of the Pacific Antarctic Circumpolar Current
The deadline to apply is March 1, 2018.

AGU: The Asahiko Taira International Scientific Ocean Drilling Research Prize – NEW!
The Asahiko Taira International Scientific Ocean Drilling Research Prize (The Taira Prize) is given annually to one honoree in recognition of “outstanding transdisciplinary research accomplishment in ocean drilling.” Established in 2014, the Taira Prize is a partnership between the American Geophysical Union (AGU) and the Japan Geoscience Union (JpGU), and is made possible through the generous donation from the Integrated Ocean Drilling Program Management International (IODP-MI). The prize is given in honor of Dr. Asahiko Taira of the Japan Agency for Marine-Earth Science and Technology. The nominee must be an active early career/early mid-career scientist who is within 15 years of receiving their Ph.D. of any discipline, and must be making an impact in the field of ocean drilling. Deadline to nominate: March 15, 2018.

IODP: Apply to Sail on IODP Expedition 385: Guaymas Basin Tectonics and Biosphere
The deadline to apply is April 15, 2018.

NSF: Cyberinfrastructure for Sustained Scientific Innovation (CSSI) – Data and Software
Full proposal deadline: April 18, 2018.

Kochi Core Center: Deep biosphere samples from IODP Expeditions 366 and 370 now available – NEW!
We are happy to inform the C-DEBI community that deep biosphere samples from IODP Exp. 366 and Exp. 370 are now available to all scientists. Exp. 366 cored the summits and flanks of serpentinite mud volcanoes on the forearc of the Mariana system. The aim of exp. 370 was to study the relationship between the deep subseafloor biosphere and temperature. The major subject of these two expeditions was the deep biosphere, and samples are kept in good condition. Microbiologists will be interested. The information about the samples was updated on our website, http://www.kochi-core.jp/DeepBIOS/, and interested scientists can also contact sample curator Nan Xiao (nanxiao@jamstec.go.jp) directly for assistance in submitting sample requests.

DCO: Deep Life Cultivation Internship Program

IODP-USSSP: Proposals for Pre-Drilling Activities and Workshops
The U.S. Science Support Program (USSSP) accepts proposals on a rolling basis for pre-drilling activities and semi-annually for workshops, related to the International Ocean Discovery Program (IODP).

NSF: Arctic Sciences Program Solicitation
Proposals accepted anytime.

NSF: Tribal Colleges and Universities Program (TCUP) Program Solicitation
Preparing for TCUP Implementation proposals accepted anytime.

C-DEBI: Rolling call for Research Exchange proposals

 

Employment

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U Alaska Fairbanks: CFOS Assistant or Associate Professor
Applications due February 28, 2018.

University of Western Brittany (UBO): Postdoctoral researcher position
Please send your application no later than April 1, 2018.

Karlsruhe Institute of Technology: Two Ph.D. Positions

U Penn: Two Graduate Research Assistant Positions

MBL: Postdoctoral Scientist – Molecular Microbial Ecology