C-DEBI Newsletter – June 17, 2019
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Publications & Press

Frontiers in Microbiology
Cytosine Methylation Within Marine Sediment Microbial Communities: Potential Epigenetic Adaptation to the Environment 
- NEW!
Ian M. Rambo, Adam Marsh*, Jennifer F. Biddle*

*C-DEBI Contribution 472

Marine sediments harbor a vast amount of Earth’s microbial biomass, yet little is understood regarding how cells subsist in this low-energy, presumably slow-growth environment. Cells in marine sediments may require additional methods for genetic regulation, such as epigenetic modification via DNA methylation. We investigated this potential phenomenon within a shallow estuary sediment core spanning 100 years of age. Here, we provide evidence of dynamic community m5-cytosine methylation within estuarine sediment metagenomes. The methylation states of individual CpG sites were reconstructed and quantified across three depths within the sediment core. A total of 6,254 CpG sites were aligned for direct comparison of methylation states between samples, and 4,235 of these sites mapped to taxa and genes. Our results demonstrate the presence of differential methylation within environmental CpG sites across an age gradient of sediment. We show that epigenetic modification can be detected via Illumina sequencing within complex environmental communities. The change in methylation state of environmentally relevant genes across depths may indicate a dynamic role of DNA methylation in regulation of biogeochemical processes.

The effect of O2 and pressure on thiosulfate oxidation by Thiomicrospira thermophila - NEW!
Jennifer L. Houghton, Dionysis I. Foustoukos*, David A. Fike
*C-DEBI Contribution 477

Microbial sulfur cycling in marine sediments often occurs in environments characterized by transient chemical gradients that affect both the availability of nutrients and the activity of microbes. High turnover rates of intermediate valence sulfur compounds and the intermittent availability of oxygen in these systems greatly impact the activity of sulfur‐oxidizing micro‐organisms in particular. In this study, the thiosulfate‐oxidizing hydrothermal vent bacterium Thiomicrospira thermophila strain EPR85 was grown in continuous culture at a range of dissolved oxygen concentrations (0.04–1.9 mM) and high pressure (5–10 MPa) in medium buffered at pH 8. Thiosulfate oxidation under these conditions produced tetrathionate, sulfate, and elemental sulfur, in contrast to previous closed‐system experiments at ambient pressure during which thiosulfate was quantitatively oxidized to sulfate. The maximum observed specific growth rate at 5 MPa pressure under unlimited O2 was 0.25 hr−1. This is comparable to the μmax (0.28 hr−1) observed at low pH (<6) at ambient pressure when T. thermophila produces the same mix of sulfur species. The half‐saturation constant for O2 (KO2) estimated from this study was 0.2 mM (at a cell density of 105 cells/ml) and was robust at all pressures tested (0.4–10 MPa), consistent with piezotolerant behavior of this strain. The cell‐specific KO2 was determined to be 1.5 pmol O2/cell. The concentrations of products formed were correlated with oxygen availability, with tetrathionate production in excess of sulfate production at all pressure conditions tested. This study provides evidence for transient sulfur storage during times when substrate concentration exceeds cell‐specific KO2 and subsequent consumption when oxygen dropped below that threshold. These results may be common among sulfur oxidizers in a variety of environments (e.g., deep marine sediments to photosynthetic microbial mats).

Geochemistry, Geophysics, Geosystems
Evidence for Low‐Temperature Diffuse Venting at North Pond, Western Flank of the Mid‐Atlantic Ridge - NEW!
Heinrich W. Villinger, P. Müller, Wolfgang Bach, Keir Becker, Beth N. Orcutt*, N. Kaul, Charles Geoffrey Wheat*
*C-DEBI Contribution 479

During expedition MSM37 on the German RV Maria S. Merian, bottom water temperature and sediment temperature profiles were measured in the vicinity of North Pond (western flank of Mid‐Atlantic Ridge) during exploratory dives with Remotely Operated Vehicle Jason II. In addition, push cores were taken at locations with high sediment temperature gradients. We could identify two locations where sediment temperature gradients exceed 1 K/m and bottom water temperatures showed an anomaly of up to 0.04 °C above background. We interpret these observations as clear indication of low‐temperature diffuse venting of fluids that have traveled through the uppermost crust. We can safely assume that the observed phenomena are widespread at ridge flank settings where sediment cover is thin or absent, and hence, we can explain the efficient heat mining on ridge flanks. Due to the difficulties of locating diffuse low‐temperature discharge sites and due to the fact that discharge can occur through thin sediment cover as well as through sediment‐free basement outcrops, it will be very difficult to quantify fluxes of energy and mass from low‐temperature diffuse venting in ridge flank settings; however, thermal anomalies may be used to locate sites of discharge for geochemical, microbial, and hydrologic characterization.

Applied and Environmental Microbiology
Nanocalorimetry reveals growth dynamics of Escherichia coli cells undergoing adaptive evolution during long-term stationary phase - NEW!
Alberto Robador*, Jan P. Amend*, Steven E. Finkel*
*C-DEBI Contribution 480

Bacterial populations in long-term stationary phase laboratory cultures can provide insights into physiological and genetic adaptations to low-energy conditions and population dynamics in natural environments. While overall population density remains stable, these communities are very dynamic and characterized by the rapid emergence and succession of distinct mutants expressing the Growth Advantage in Stationary Phase (GASP) phenotype, which can reflect an increased capacity to withstand energy limitations and environmental stress. Here we characterize the metabolic heat signatures and growth dynamics of GASP mutants within an evolving population using isothermal calorimetry. We aged Escherichia coli in anaerobic batch cultures over 20 days inside an isothermal nanocalorimeter and observed distinct heat events related to the emergence of three mutant populations expressing the GASP phenotype after 1.5, 3, and 7 days. Given the heat produced by each population, the maximum number of GASP mutant cells was calculated revealing abundances of ∼2.5 x 107, ∼7.5 x 106, and ∼9.9 x 106 cells in the population, respectively. These data indicate that mutants capable of expressing the GASP phenotype can be acquired during the exponential growth phase and subsequently expressed in long-term stationary phase (LTSP) culture.

Geosciences Journal: Special Issue "Tracking the Deep Biosphere through Time" - Call for Manuscripts - NEW!
This Special Issue seeks to cover all geobiological aspects of the upper crust (continental and marine) and we invite contributions with relevance to geomicrobiology, isotope geochemistry, microbial-activity-associated geochronology and related geochemical and hydrochemical proxies as well as presentations on new methods, techniques, and experimental approaches in both the modern and ancient crust. We wish to cover a broad spectrum of environments such as ultra-mafic, mafic, and felsic systems, as well as hydrothermal/geothermal areas and sedimentary successions. We encourage contributions related to scientific drilling programs as well as research from underground facilites and deep drillings related to mining activity or nuclear waste disposal, in addition to studies of exposed ancient crust. Astrobiological implications are also encouraged. Deadline for manuscript submissions: September 1, 2019.
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!

TED: Karen Lloyd: The mysterious microbes living deep inside the earth -- and how they could help humanity - NEW!
The ground beneath your feet is home to a massive, mysterious world of microbes — some of which have been in the earth’s crust for hundreds of thousands of years. What’s it like down there? Take a trip to the volcanoes and hot springs of Costa Rica as microbiologist Karen Lloyd shines a light on these subterranean organisms and shows how they could have a profound impact on life up here.


Education & Outreach

ECORD Summer School 2019 on Sub­duc­tion Zone Pro­cesses, Bremen,Germany
Application deadline: June 19, 2019.

C-DEBI: Next Professional Development Webinar: June 26, 12pm PDT
Janice McDonnell (Science Agent, Department of Youth Development, Rutgers University) leads the next C-DEBI Professional Development Webinar on “How to Use the Broader Impact Wizard: A Tool to Help Advance the Impact of Research in Society.” Missed the last Professional Development Webinar on “Broadening your thinking and your impact: Tips on how to develop effective outreach programs” with Pete Girguis (Harvard)? Watch it on YouTube.

C-DEBI: Call for Nominations: Professional Development Webinar Series
Know someone who can share their knowledge of essential skills not learned in graduate school, like developing a syllabus, how to choose what professional service committees to serve on or how to transition to a career in industry? C-DEBI seeks nominations for its Professional Development Webinar series.


Meetings & Activities

IODP-USSSP: Volunteer to serve on the JOIDES Resolution Facility Board (JRFB), U.S. Advisory Committee for Scientific Ocean Drilling (USAC), or Science Evaluation Panel (SEP)
Deadline: June 24, 2019.

CalTech: International Geobiology Course "Geobiology of Symbiosis" Symposium, June 24, 2019 - NEW!
There will be a 1-day symposium held at Caltech on Monday, June 24, sponsored by the International Geobiology Course. The topic of the symposium is “Geobiology of Symbiosis” (see PDF for the detailed schedule). The symposium will be held in the Sharp Lecture Hall on Monday, June 24 starting at 9am. It is open to the scientific public and free of charge. You are cordially invited to attend, either in part or for the entire symposium depending on interest. A continental breakfast and buffet lunch will also be served to symposium participants. If you are interested in participating, please click here to RSVP so that we can plan appropriately for food and drink. If you want to just stop by to hear a speaker or two, please feel free and there is no need to respond.

24th ISEB Symposium, Potsdam, Germany, September 22-27, 2019 - UPDATED!
The International Society for Environmental Biogeochemistry (ISEB) Symposium – to be held at the Helmholtz Centre Potsdam German Research Centre for Geosciences (GFZ) – will bring together scientists from all over the world to discuss recent developments and discoveries from all aspects of Environmental Biogeochemistry, including but not limited to microbiology, chemistry, soil science, geoscience, limnology, ecology, marine and atmospheric sciences both from fundamental and applied perspectives. Exploration of the deep terrestrial and marine biosphere will be a major topic of the conference; so far, 20% of the abstracts are deep biosphere related. The meeting will be in a single session format, so all participants have the chance to attend all oral presentations. Daily poster sessions provide sufficient time for discussions among the participants. Abstract submission deadline extended to June 30, 2019.

AGU: 2019 Fall Meeting Call for Abstracts - NEW!
Attending the AGU Fall Meeting, December 9-13, 2019? Consider submitting your abstracts (due July 31, 2019) to these deep biosphere-related Session Proposals. Missing a session of interest? Let us know!

ISSM: Submit your abstracts to the 11th ISSM conference, June 14-19, 2020, Utrecht, The Netherlands
Abstracts due in September 2019.

Ongoing Activities:


Proposal Calls

NSF: Dear Colleague Letter: Research Opportunities in Europe for NSF Postdoctoral Research Fellows and CAREER Awardees
Requests must be received at NSF at least 3 months prior to the proposed visit, but no later than June 21, 2019, for consideration using Fiscal Year 2019 funds.

IODP: Apply to Sail on IODP Expedition 386 - NEW!
The International Ocean Discovery Program (IODP) is now accepting applications for scientific participants on Expedition 386 Japan Trench Paleoseismology, aboard a Mission-Specific Platform (MSP) organized by the ECORD Science Operator (ESO) and jointly implemented with the Institute for Marine-Earth Exploration and Engineering (MarE3) within the Japan Agency for Marine-Earth Science and Technology (JAMSTEC). Opportunities exist for researchers (including graduate students) in all specialties. While other expertise may be considered, specialists in the following fields are required: sedimentology (with special focus on deep-water and hadal trench depositional environments, sediment fabrics, and X-ray computed tomography), event stratigraphy, micropaleontology (including expertise with siliceous microfossils and benthic foraminifera), tephra stratigraphy, paleomagnetics, stratigraphic correlation, organic geochemistry, inorganic geochemistry, physical properties, geophysics, paleoseismology, structural geology, and microbiology. For the offshore phase of the expedition, we are particularly looking for the following fields: sedimentology, micropaleontology, organic geochemistry, inorganic geochemistry, physical properties, event stratigraphy, stratigraphic correlation, geophysics and microbiology. The deadline to apply is July 5, 2019.

IODP: Apply to Sail on IODP Expeditions 390/393
The deadline to apply is August 1, 2019.

NSF: Opportunities for Promoting Understanding through Synthesis (OPUS)
Full proposal deadline: August 5, 2019.

NSF: Biological Oceanography
Full proposal deadline date: August 15, 2019.

NSF: Chemical Oceanography
Full proposal deadline date: August 15, 2019.

NSF: Physical Oceanography
Full proposal deadline date: August 15, 2019.

NSF: Research Experiences for Undergraduates (REU)
Full Proposal Deadline: August 28, 2019.

International Research Experiences for Students (IRES) - NEW!
The International Research Experiences for Students (IRES) program supports international research and research-related activities for U.S. science and engineering students. The IRES program contributes to development of a diverse, globally-engaged workforce with world-class skills. IRES focuses on active research participation by undergraduate or graduate students in high quality international research, education and professional development experiences in NSF-funded research areas. The overarching, long-term goal of the IRES program is to enhance U.S. leadership in research and education and to strengthen economic competitiveness through training the next generation of research leaders. This solicitation features three mechanisms; proposers are required to select one of the following tracks to submit their proposal. Track I focuses on the development of world-class research skills in international cohort experiences. Track II is dedicated to targeted, intensive learning and training opportunities that leverage international knowledge at the frontiers of research. Track III supports U.S. institutional collaborations to develop, implement and evaluate innovative models for high-impact, large-scale international research and professional development experiences for U.S. graduate students. Student participants supported by IRES funds must be citizens, nationals, or permanent residents of the United States. Students do not apply directly to NSF to participate in IRES activities. Students apply to NSF-funded investigators who receive IRES awards. To identify appropriate IRES projects, students should consult the directory of active IRES awards. Full Proposal Deadlines: September 10, 2019 (Track I), September 17, 2019 (Track II) and September 24, 2019 (Track III).

NSF: Accelerating Research through International Network-to-Network Collaborations (AccelNet)
Letter of intent due date: October 30, 2019.

NSF: Research Traineeship (NRT) Program
Next letter of intent window: November 25, 2019 – December 6, 2019.

Rolling Calls:



Karlsruhe Institute of Technology: PhD / PostDoc position - NEW!
We are seeking a highly motivated PhD student and Postdoc (part time) with enthusiasm for bioinformatics and molecular biology. For more info and applications please email Prof. Anne Kaster:

MBL: Computational Postdoctoral Scientist
Review of applications will begin July 1, 2019 and continue until the position is filled.

Tokyo Institute of Technology: Principal Investigator (Professor or Associate Professor), Earth-Life Science Institute
Application deadline: August 30, 2019.

DRI: Postdoctoral Fellow, Microbial Ecology: Genomes to Phenomes

UH Manoa: Assistant Researcher (Theoretical Ecologist)

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!


Matthew Janicak
Data Manager
Center for Dark Energy Biosphere Investigations (C-DEBI)
University of Southern California
3616 Trousdale Pkwy, AHF 209, Los Angeles, CA 90089-0371
Phone: 708-691-9563, Fax: 213-740-2437

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