C-DEBI Newsletter – November 16, 2019
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Publications & Press
Frontiers in Microbiology
Diversity, Ecology, and Prevalence of Antimicrobials in Nature – NEW!
Megan M. Mullis*, Ian M. Rambo, Brett J. Baker, Brandi Kiel Reese*
*C-DEBI Contribution 496
Microorganisms possess a variety of survival mechanisms, including the production of antimicrobials that function to kill and/or inhibit the growth of competing microorganisms. Studies of antimicrobial production have largely been driven by the medical community in response to the rise in antibiotic-resistant microorganisms and have involved isolated pure cultures under artificial laboratory conditions neglecting the important ecological roles of these compounds. The search for new natural products has extended to biofilms, soil, oceans, coral reefs, and shallow coastal sediments; however, the marine deep subsurface biosphere may be an untapped repository for novel antimicrobial discovery. Uniquely, prokaryotic survival in energy-limited extreme environments force microbial populations to either adapt their metabolism to outcompete or produce novel antimicrobials that inhibit competition. For example, subsurface sediments could yield novel antimicrobial genes, while at the same time answering important ecological questions about the microbial community.
Geochimica et Cosmochimica Acta
Fluid Transport and Reaction Processes Within a Serpentinite Mud Volcano: South Chamorro Seamount – NEW!
Charles Geoffrey Wheat*, Jeffrey S. Seewald, Ken Takai
*C-DEBI Contribution 497
Natural fluids with a pH (25°C) up to 12.3 were collected from a sub-seafloor borehole observatory (Ocean Drilling Program (ODP) Hole 1200C) on South Chamorro Seamount, a serpentinite mud volcano in the Mariana forearc. We used systematic differences in the chemical compositions of pore waters from drilling operations during ODP Leg 195 and borehole fluids collected subsequently from Hole 1200C to define two endmember solutions, one of which was a sulfate-rich fluid with a methane concentration of 50 mM that ascends from the subduction channel and the other was a low-sulfate fluid. The sequence of sample collection and fluid compositions constrain subsurface hydrologic conditions. Deep-sourced, sulfate- and methane-rich, sterile fluids from the subduction channel can reach the seafloor unchanged within the central conduit, whereas other fluid pathways likely intersect the pelagic sediment that underlies the serpentinite mud volcano, providing potentially suitable conditions and inoculum for microbial anaerobic oxidation of methane (AOM). These AOM-affected, low-sulfate fluids also make it to the seafloor where they discharge. The source of the sulfate- and methane-rich fluid in the subduction channel is attributed to abiotic methane production fueled by hydrogen production from serpentinization and carbonate dissolution. This methane production includes a mechanism to raise the pH above values from serpentinization alone. Results from South Chamorro Seamount represent an end member along a transect defined by the distance from the trench. Results from this site are applied to other serpentinite mud volcanoes along this transect to speculate on likely chemical conditions within shallower and cooler portions of the subduction channel.
Expedition 385T, Panama Basin Crustal Architecture and Deep Biosphere: Revisiting Holes 504B and 896A, Preliminary Report – NEW!
Masako Tominaga, Beth N. Orcutt, Peter Blum and the Expedition 385T Scientists
International Ocean Discovery Program (IODP) Expedition 385T aimed to take advantage of a transit of the R/V JOIDES Resolution from Antofagasta, Chile, to San Diego, California (USA), to accomplish new sampling and data collection from legacy borehole observatories in Deep Sea Drilling Project (DSDP) and Ocean Drilling Program (ODP) Holes 504B and 896A on the southern flank of the Costa Rica Rift. In addition, the US Science Support Program organized the participation of 3 Outreach Officers to evaluate the performance of the JOIDES Resolution Outreach Officer program as well as 2 educators and 12 undergraduate students for a shipboard “JR Academy.” Our scientific objectives were to collect (1) new Formation MicroScanner logs from Hole 504B for improving lithologic interpretations of crustal architecture at this archetype deep oceanic crust hole and (2) fluid samples from both holes for evaluating the crustal deep biosphere in deep and warm oceanic crust. These operations in Holes 504B and 896A have direct relevance to Challenges 5, 6, 9, 10, 13, and 14 of the IODP 2013–2023 Science Plan. Accomplishing both of these scientific objectives required the removal of old wireline CORK observatories, including associated inflatable packers that were installed in the cased boreholes in 2001. The fluid sampling plan also included testing a new Multi-Temperature Fluid Sampler. Despite successfully removing the CORK wellhead platforms from both holes, we were unable to remove the packers stuck in casing at both locations after 48 h of milling operations in Hole 504B and 2 h of milling operations in Hole 896A, thus precluding accomplishing any of the scientific objectives of the expedition. We provide an assessment of the final state of the holes and recommendations for possible future operations.
||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!|
Science Rules! with Bill Nye Podcast: Underwater Clues About Aliens – NEW!
There are teeny-tiny organisms living at the depths of our oceans, which can tell us a lot about the possibility of life beyond Earth. Real life deep sea explorer (and C-DEBI Associate Director) Dr. Julie Huber from the Woods Hole Oceanographic Institution joins us to talk about the clues the deep water gives us about alien life. And as usual, we go to the phones to answer your questions, like one from Patrick, who asks, “how close to an alien environment are our oceans near the underwater volcanic vents?”
Meetings & Activities
ISSM 2020: Call for abstracts – UPDATED!
The International Society for Subsurface Microbiology (ISSM) is made up of microbiologists, ecologists, geoscientists, and other researchers around the world fascinated by the various aspects of subsurface microbiology, a rapidly expanding field that focuses on microbial life below the surface of the earth. ISSM has organized numerous symposiums on subsurface microbiology in locations as diverse as Germany, Japan, New Zealand, USA and the UK. These symposia are meant to showcase the latest technologies and research in subsurface microbiology, including microbial ecology. The deadline for submitting abstracts (presentations and posters) is December 1, 2019.
IODP: Submit an IODP Workshop Proposal
The submission deadline is December 1, 2019.
AGU: 2019 Fall Meeting Deep Biosphere-Related Sessions of Interest
Attending the AGU Fall Meeting in San Francisco, December 9-13, 2019? Be sure to check out these C-DEBI-related sessions of interest. See also the Deep Carbon Observatory’s AGU Fall Meeting Guide and consider attending IODP's AGU Town Hall. Missing a session of interest? Let us know.
AGU: Nominate Your Peers for 2020 Honors – NEW!
Nominations are now open for 2020 AGU honors, including the Asahiko Taira International Scientific Ocean Drilling Research Prize. The extended nomination period aims to increase selection and diversity among the nominees and to allow more time for nominators to develop multiple nomination packages. Deadline: March 15, 2020.
GRC: Exploring Fluxes, Forms and Origins of Deep Carbon in Earth and Other Terrestrial Planets, June 28-July 3, 2020, Lewiston, ME, USA – NEW!
The meeting will highlight the importance of deep carbon science for understanding the various reservoirs of carbon in our solar system – from cores to atmospheres on Earth and other planets, and from diamonds to microbial cells. We will highlight the quantities, movements, forms and origins of carbon on Earth and elsewhere. Oral sessions and discussions will focus on the origins of carbon in all of its forms in the solar system, the knowns and unknowns of Earth’s deep carbon cycle, and the forms and functions of carbon under extreme physical, chemical and biological conditions. After discussing novel means to distinguish whether organic compounds derive from biological or abiotic processes, we will discuss the interplay of key geological and biological processes associated with abiotic synthesis of organic matter and deep life in serpentinizing systems and other relevant geological settings. We will then explore the factors limiting life at depth on Earth and the implications for interactions between carbon reservoirs and life at great depths. The final phase of the conference will address the movements of carbon from planetary interiors to atmospheres and the role of carbon recycling by subduction. The presentations will be concluded with a set of late-breaking topic presentations selected by early-career scientists from solicited abstracts and GRS submissions. Our program fortifies and strengthens the ties between disparate fields of inquiry engaged in understanding the science of deep carbon. Applications for this meeting must be submitted by May 31, 2020.
- 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
Education & Outreach
DOE: Scholars Program – NEW!
The DOE Scholars Program is designed to provide opportunities and attract talented undergraduate and graduate students, as well as recent graduates to appointments that are carefully designed to help prepare participants towards the full range of entry and mid-level research, technical and professional positions within DOE and organizations that support the DOE mission. DOE Scholars Program will introduce highly qualified students and postgraduates to DOE missions, functions, and operations. You will receive a stipend for your living expenses during this educational experience. Payments rates are determined by DOE, and are based on your educational level, skills, and experience. The minimum stipend for undergraduates is $ 600/week and $650/week graduate students and recent graduates. Travel reimbursement of inbound and outbound costs up to $1,000 for participants who live more than fifty miles, one-way, from the assigned hosting site. Depending on your project assignment, duration of appointment and funding availability, you may be eligible to receive an allowance for travel and training. Application deadline: January 3, 2020.
USC Wrigley Institute: Summer REU: Coastal Ocean Processes – NEW!
This NSF-funded Research Experiences for Undergraduates (REU) program will support ten highly motivated and talented undergraduate students to conduct independent but guided research that focuses on Coastal Ocean Processes during an intensive 10-week program at the USC Wrigley Marine Science Center on Catalina Island, CA. The program will provide students with hands-on research experience, training in laboratory and field methodologies, introductory lectures and special seminars in oceanography and marine science, academic and career advisement, professional development workshops, group activities and field trips to explore Catalina Island’s unique ecosystems. Applications are due by February 14, 2020.
Bigelow: SCGC Bioinformatics Course Informational Survey – NEW!
The Single Cell Genomics Center (SCGC) at Bigelow Laboratory for Ocean Sciences will host a week-long bioinformatics course in October 2020. The purpose will be to enable existing and potential users of microbial single cell genomics data to work with their data more efficiently and effectively. Please help us determine potential topics to cover by filling this online survey.
IODP: Expedition 385 Guaymas Basin Cruise Blog
Follow along on IODP Expedition 385 “Guaymas Basin Tectonics and Deep Biosphere” with the cruise blog of Andreas Teske, co-chief scientist and professor in the Department of Marine Sciences at the University of North Carolina-Chapel Hill.
NSF: Postdoctoral Research Fellowships in Biology (PRFB)
Proposal deadline November 19, 2019.
NSF: Research Traineeship (NRT) Program
Next letter of intent window: November 25, 2019 – December 6, 2019.
IODP: Apply to sail: Expedition 392 Agulhas Plateau Cretaceous Climate
The deadline to apply is December 2, 2019.
IODP-USSSP: Schlanger Ocean Drilling Fellowships
The deadline for submission is December 6, 2019.
NSF: Understanding the Rules of Life: Microbiome Theory and Mechanisms (URoL:MTM) – NEW!
Understanding the Rules of Life (URoL): Predicting Phenotype is one of NSF’s 10 big ideas and is focused on predicting the set of observable characteristics (phenotypes) based on the genetic makeup of the individual and the nature of its environment. The Understanding the Rules of Life: Microbiome Theory and Mechanisms (URoL:MTM) program is an integrative collaboration across Directorates and Offices within the National Science Foundation. The objective of URoL:MTM is to understand and establish the theory and mechanisms that govern the structure and function of microbiomes, a collection of microbes in a specific habitat/environment. This may include but is not limited to host-associated microbiomes, such as those with humans and other organisms, where i) the microbiome impacts host physiology, behavior, development, and fitness; ii) the host influences the metabolic activity, dynamics and evolution of the microbiome, and iii) the environment (biological, chemical, physical, and social) influences and is influenced by both the host and the microbiome. Letter of Intent due date: January 17, 2020.
NSF: Frontier Research in Earth Sciences (FRES) – NEW!
The FRES program will support research in Earth systems from the core through the critical zone. The project may focus on all or part of the surface, continental lithospheric, and deeper Earth systems over the entire range of temporal and spatial scales. FRES projects should have a larger scientific scope and budget than those considered for funding by disciplinary programs in the Division of Earth Sciences (EAR). FRES projects may be interdisciplinary studies that do not fit well within EAR’s disciplinary programs or cannot be routinely managed by sharing between disciplinary programs. Innovative proposals within a single disciplinary area with outcomes of potential broad relevance to Earth Science research are also encouraged. Investigations may employ any combination of field, laboratory, and computational studies with observational, theoretical, or experimental approaches. Projects should be focused on topics that meet the guidelines for research funded by the Division of Earth Sciences. Full proposal deadline: February 5, 2020.
- C-DEBI: Rolling call for Research Exchange proposals
- DCO: Deep Life Cultivation Internship Program
- IODP-USSSP: Proposals for Pre-Drilling Activities
- NSF: Arctic Sciences Program Solicitation
- NSF: Division of Environmental Biology (core programs) (DEB)
- NSF: Infrastructure Innovation for Biological Research (IIBR)
- NSF: Instrument Capacity for Biological Research (ICBR)
- NSF: Non-Academic Research Internships for Graduate Students (INTERN) Supplemental Funding Opportunity
- NSF: Research Assistantships for High School Students (RAHSS): Funding to Broaden Participation in the Biological Sciences
- NSF: Research Experience for Teachers (RET): Funding Opportunity in the Biological Sciences
- NSF: Tribal Colleges and Universities Program (TCUP)
- Queen Mary U of London: PhD Project: Microbial survival in the energy-limited deep biosphere
- Queen Mary U of London: PhD Project: Microbial life and activity on glaciers and in Arctic soils
- UNOLS: Cruise Opportunity Program
CIW: Carnegie Postdoctoral Fellowships
Completed applications for a Carnegie fellowship should be submitted no later than December 1, 2019.
Dalhousie U: 2020 Killam Postdoctoral Program
The application deadline is December 16, 2019.
WHOI: Tenure Track Scientist – Marine Chemistry & Geochemistry
Review of applications will begin on December 16, 2019.
SIO: Fisheries Oceanographer/Protistan Biologist/Sea-Going Benthic Ecologist – Assistant Professor
For full consideration, please apply by December 20, 2019.
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