C-DEBI Newsletter – June 17, 2019

Publications & Press

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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.

Geobiology
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 μ_max (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 (K_O2) 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 K_O2 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 K_O2 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.

 

 

Meetings & Activities

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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!

• B036 Creating Data Synchronicity Across Earth Microbiome Research 
  Elisha M Wood-Charlson¹, Bonnie L Hurwitz², Emiley Eloe-Fadrosh³ and Kjiersten Fagnan³, (1)Lawrence Berkeley National Laboratory, Berkeley, CA, United States(2)University of Arizona, Agricultural and Biosystems Engineering, Tucson, AZ, United States(3)Joint Genome Institute, Walnut Creek, CA, United States
• B046 Exploring microbial ecosystems using cutting edge advances in isotope and omics analyses 
  James Moran, Pacific Northwest National Laboratory, Richland, WA, United States, Paul Dijkstra, Northern Arizona Univ, Flagstaff, AZ, United States and Steven Blazewicz, Lawrence Livermore National Laboratory, Livermore, CA, United States
• B047 Exploring the Biotic Fringe 
  Everett Shock¹, Marshall Wayne Bowles^2,3, Elizabeth Trembath-Reichert¹ and Mark Alexander Lever⁴, (1)Arizona State University, Tempe, AZ, United States(2)MARUM – University of Bremen, Bremen, Germany(3)Louisiana Universities Marine Consortium, Chauvin, LA, United States(4)ETH Zurich, Department of Environmental Systems Science, Institute of Biogeochemistry & Pollutant Dynamics, Zürich, Switzerland
• B074 Microbial contributions to methane cycling 
  Christopher Abin, University of Oklahoma Norman Campus, Microbiology and Plant BIology, Norman, OK, United States, Ellen Grace Lauchnor, Montana State University, Civil Engineering, Bozeman, MT, United States and Erika Espinosa-Ortiz, Montana State University, Chemical and Biological Engineering, Bozeman, MT, United States
• B076 Microbial Metabolisms and Biogeochemical Processes in Earth’s Subsurface 
  James Bradley, University of Southern California, Los Angeles, CA, United States, Cara Magnabosco, Simons Foundation, Flatiron Institute Center for Computational Biology, New York, NY, United States and Nagissa Mahmoudi, McGill University, Montreal, Canada
• B085 Omics-Informed Models of Microbial Dynamics and Processes from Cells to Ecosystems 
  Timothy D Scheibe, Pacific Northwest National Laboratory, Richland, WA, United States, Romy Chakraborty, Lawrence Berkeley Nat’l Lab, Berkeley, CA, United States, Pamela Weisenhorn, Argonne National Laboratory, Argonne, United States and John D Moulton, Los Alamos National Laboratory, Los Alamos, NM, United States
• ED021 Curating the creative: Science, art, and public engagement 
  Katie Pratt, University of Rhode Island, Graduate School of Oceanography, Narragansett, RI, United States, Darlene Trew Crist, Deep Carbon Observatory, Narragansett, RI, United States and Emma Liu, University of Cambridge, Earth Sciences, Cambridge, United Kingdom
• ED024 Efforts to improve and support REU Internship Programs 
  Valerie Sloan, National Center for Atmospheric Research, Education & Outreach, Boulder, CO, United States, Gabriela Noriega, Southern California Earthquake Center, University of Southern California, Los Angeles, CA, United States, Diane Y Kim, University of Southern California, Los Angeles, CA, United States and Kenneth Voglesonger, Northeastern Illinois University, Earth Science and Environmental Science Program, Chicago, IL, United States
• H034 Characterizing Spatial and Temporal Variability of Hydrological and Biogeochemical Processes across Scales 
  Bhavna Arora, Lawrence Berkeley National Laboratory, Berkeley, CA, United States and Haruko Murakami Wainwright, Lawrence Berkeley National Lab, Berkeley, CA, United States
• OS001 Advancements in Understanding Seafloor Volcanism and Life: Axial Seamount  – A Wired Submarine Volcano Observatory 
  Deborah S Kelley, University of Washington Seattle Campus, School of Oceanography, Seattle, WA, United States and William W. Chadwick Jr, Oregon State University, CIMRS, and NOAA/PMEL, Newport, WA, United States
• OS004 Beyond Hydrography: Seafloor Mapping as Critical Data for Understanding Our Oceans 
  Nicole Raineault, Ocean Exploration Trust, Narragansett, RI, United States, Vicki Lynn Ferrini, LDEO, Palisades, NY, United States, Rachel Medley, NOAA Office of Exploration and Research, Silver Spring, United States and Maria T Judge, Geological Survey of Ireland, Marine Geology, Dublin, Ireland
• OS014 General topics in biological or chemical oceanography in poster format 
  John Crusius, USGS Alaska Science Center at UW School of Oceanography, Seattle, WA, United States and Zackary I Johnson, Duke University, Beaufort, NC, United States
• V027 Izu-Bonin-Mariana arc system:  synthesis and remaining questions 
  Susan DeBari, Western Washington University, Bellingham, WA, United States, Julie Prytulak, Imperial College London, London, United Kingdom, Charles Geoffrey Wheat, NURP/ Univ Alaska, Moss Landing, CA, United States and Shuichi Kodaira, Yokohama National University, Yokohama, Japan

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

Ongoing Activities:

• C-DEBI: Rolling call for Community Workshop support
• C-DEBI: Protocols.io Group Page
• C-DEBI: Subseafloor Cultures Database
• C-DEBI: Join us on LinkedIn

 

Best, 

 

Matt

 

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Matthew Janicak

Data Manager

Center for Dark Energy Biosphere Investigations (C-DEBI)

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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