|C-DEBI Newsletter – April 16, 2018
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Publications & Press
Frontiers in Microbiology
Energy Gradients Structure Microbial Communities Across Sediment Horizons in Deep Marine Sediments of the South China Sea - NEW!
Michael F. Graw, Grace D’Angelo, Matthew Borchers, Andrew R. Thurber*, Joel. E. Johnson, Chuanlun Zhang, Haodong Liu, Frederick S. Colwell*
*C-DEBI Contribution 423
The deep marine subsurface is a heterogeneous environment in which the assembly of microbial communities is thought to be controlled by a combination of organic matter deposition, electron acceptor availability, and sedimentology. However, the relative importance of these factors in structuring microbial communities in marine sediments remains unclear. The South China Sea (SCS) experiences significant variability in sedimentation across the basin and features discrete changes in sedimentology as a result of episodic deposition of turbidites and volcanic ashes within lithogenic clays and siliceous or calcareous ooze deposits throughout the basin's history. Deep subsurface microbial communities were recently sampled by the International Ocean Discovery Program (IODP) at three locations in the SCS with sedimentation rates of 5, 12, and 20 cm per thousand years. Here, we used Illumina sequencing of the 16S ribosomal RNA gene to characterize deep subsurface microbial communities from distinct sediment types at these sites. Communities across all sites were dominated by several poorly characterized taxa implicated in organic matter degradation, including Atribacteria, Dehalococcoidia, and Aerophobetes. Sulfate-reducing bacteria comprised only 4% of the community across sulfate-bearing sediments from multiple cores and did not change in abundance in sediments from the methanogenic zone at the site with the lowest sedimentation rate. Microbial communities were significantly structured by sediment age and the availability of sulfate as an electron acceptor in pore waters. However, microbial communities demonstrated no partitioning based on the sediment type they inhabited. These results indicate that microbial communities in the SCS are structured by the availability of electron donors and acceptors rather than sedimentological characteristics.
Nature Ecology & Evolution
Function and functional redundancy in microbial systems - NEW!
Stilianos Louca, Martin. F. Polz, Florent Mazel, Michaeline. B. N. Albright, Julie A. Huber*, Mary. I. O’Connor, Martin Ackermann, Aria. S. Hahn, Diane. S. Srivastava, Sean A. Crowe, Michael Doebeli, Laura Wegener Parfrey
*C-DEBI Contribution 427
Microbial communities often exhibit incredible taxonomic diversity, raising questions regarding the mechanisms enabling species coexistence and the role of this diversity in community functioning. On the one hand, many coexisting but taxonomically distinct microorganisms can encode the same energy-yielding metabolic functions, and this functional redundancy contrasts with the expectation that species should occupy distinct metabolic niches. On the other hand, the identity of taxa encoding each function can vary substantially across space or time with little effect on the function, and this taxonomic variability is frequently thought to result from ecological drift between equivalent organisms. Here, we synthesize the powerful paradigm emerging from these two patterns, connecting the roles of function, functional redundancy and taxonomy in microbial systems. We conclude that both patterns are unlikely to be the result of ecological drift, but are inevitable emergent properties of open microbial systems resulting mainly from biotic interactions and environmental and spatial processes.
Rice U: Ocean-going Rice postdoc featured in NSF video - NEW!
Jeanine Ash, a new Rice postdoctoral researcher and recipient of a Center for Dark Energy Biosphere Investigations (C-DEBI) fellowship, is the focus of a video about her duties as a member of the science party on the JOIDES Resolution, a research ship and part of the National Science Foundation-supported International Ocean Discovery Program. Ash was part of Expedition 374, which spent 46 days at sea this year to study the evolution of the Ross Sea ice sheet off West Antarctica and the relationship between climatic and oceanic change through the Neogene and Quaternary periods, from 23 million years ago to the present day. In the video, Ash describes her work to understand the balance between the massive amount of methane, a greenhouse gas, under the Antarctic seafloor and the microbes that consume it and keep it from escaping to the atmosphere, as well as the microbes’ susceptibility to climate change.
Meetings & Activities
AGU: 2018 Fall Meeting Session Proposals
The deadline for submissions is April 18, 2018.
IODP-USSSP: Host an Ocean Discovery Lecturer
The application period will close on May 18, 2018.
GRC: Apply to attend the 2018 Conference on Deep Carbon Science, June 17-22, Smithfield, RI
Applications for this meeting must be submitted by May 20, 2018. Please apply early, as some meetings become oversubscribed (full) before this deadline.
C-DEBI: Rolling call for Community Workshop support
C-DEBI: Protocols.io Group Page
C-DEBI: Subseafloor Cultures Database
Education & Outreach
IODP: Apply for Te Kura Kōhatu School of Rock 2018, July 5-13, Auckland, New Zealand
Apply by April 20, 2018.
MBL: Advanced Research Training Course: Strategies and Techniques for Analyzing Microbial Population Structures (STAMPS)
Application Deadline: April 20, 2018.
C-DEBI: Next Professional Development Webinar: April 25, 12pm PT
Ben Tully (C-DEBI Bioinformatic Specialist) leads the next C-DEBI Professional Development Webinar on “Sharing Data: The Joys of Open Science.” The access URL for the webinar is http://usccollege.adobeconnect.com/cdebiremote/. Missed the last webinar on “Surviving (and Maybe Even Thriving!) in a Soft Money Position”? Watch it on YouTube.
MARUM: ECORD 2018 Summer School on Sub-seafloor fluid transport and gas hydrate dynamics
The application deadline is May 4, 2018.
NSF-UNOLS: Early Career Training Cruise to the East Pacific Rise 9° 50’N , December 2018 - NEW!
UNOLS is seeking applications from early career scientists at U.S. universities who are interested in participating in an oceanographic research cruise that will continue an investigation of a chain of seamounts west of the East Pacific Rise at 8° 20’ N followed by a detailed survey the East Pacific Rise ~ 9° 50’ N that last erupted in 2005-2006. The NSF-funded cruise will take place aboard RV Atlantis Dec. 3-21, 2018, departing Manzanillo, MX and returning to San Diego, CA. The primary ECS objective will involve hands-on instruction on conducting deep-submergence vehicle-based field research. New faculty and post-docs are welcome to apply. It may be possible to accommodate graduate students; however, this will depend on the applicant pool and disciplinary breadth. A maximum of 10 applicants will be selected to participate on the cruise and others may be selected for shore-based collaboration as there will be daily ship/shore and reverse communications capabilities via increased satellite bandwidth on the ship for the cruise duration. Applicants should submit their application materials by May 15, 2018.
C-DEBI: Bioinformatics Workshop for Metagenomic and Microbiome Analysis - NEW!
Detailed insight into the microbiome of a system can shape our understanding of it, but the learning curve for incorporating computationally intensive tools can be very high! Join instructor Dr. Benjamin Tully, C-DEBI Bioinformatic Specialist, for an upcoming bioinformatics workshop at the University of Southern California, June 21-22, 2018. All expenses are covered courtesy of the NSF STCs C-DEBI, EBICS, and BEACON. Topics include: Unix command line; Illumina sequence quality control; Metagenomic experimental design; Sequence Assembly; Metageomic binning; Functional Annotation; and Phylogenetic analysis. Note: participation requires a laptop with 40 GB of hard drive space. To apply: email firstname.lastname@example.org by May 28, 2018 – be sure to include your home institution, your home STC, and what you hope to get out of the workshop. All levels are welcome. There is a 15 participant maximum, so apply soon!
NSF: Cyberinfrastructure for Sustained Scientific Innovation (CSSI) - Data and Software
Full proposal deadline: April 18, 2018.
NSF: Dear Colleague Letter: Research Opportunities in Europe for NSF Postdoctoral Research Fellows and CAREER Awardees
The application deadline is April 20, 2018.
NSF: Dear Colleague Letter: Stimulating Research Related to Navigating the New Arctic (NNA), One of NSF's 10 Big Ideas
Organizations submitting proposals to programs and funding vehicles without deadlines are encouraged to submit proposals by May 1, 2018, to be considered for FY 2018 funding.
Improving Undergraduate STEM Education: Education and Human Resources (IUSE: EHR) Program Flyer
Beginning in FY 2018, there will be no single date deadlines for Exploration and Design proposals. Please note however that proposals received after May 1, 2018 will be held over to the subsequent financial year for possible award.
NSF: Dear Colleague Letter: Advancing Long-term Reuse of Scientific Data - NEW!
Through this Dear Colleague Letter (DCL), the National Science Foundation’s (NSF) Office of Advanced Cyberinfrastructure (OAC) announces its intention to support initial exploratory activities toward the creation of social and technical infrastructure solutions that further NSF’s commitment to public access. These solutions are a means to accelerate the dissemination and use of fundamental research results in the form of data that will advance the frontiers of knowledge and help sustain the Nation’s prosperity well into the future. Specifically, this DCL encourages two types of funding requests: (1) proposals for Conferences (i.e., community workshops and other events) that are designed to bring together stakeholders to explore opportunities to converge on innovative solutions to advancing public access; and (2) proposals for Early-Concept Grants for Exploratory Research (EAGER) for high-risk/high-reward innovative concepts and pilot projects that yield new fundamental research discoveries from existing NSF-funded data or that ultimately result in deployment of ambitious, sustainable socio-technical infrastructure resources and capabilities that enhance and accelerate new discoveries from existing NSF-funded data. The deadline for submission of Conference and EAGER proposals proposal submission date is May 23, 2018.
Simons Postdoctoral Fellowships in Marine Microbial Ecology
Application deadline: June 15, 2018.
NSF: Dear Colleague Letter: Towards a New Approach for the Provision of Marine Seismic Capabilities to the U.S. Research Community - NEW!
As stated in the DCL, NSF is no longer accepting new proposals that require use of R/V Langseth. NSF will also begin developing the activities required for divesting from ownership of R/V Langseth, and it is anticipated that the end of field commitments using the vessel will be no later than mid-2020. The NSF Ocean Sciences Marine Geology and Geophysics (MG&G) Program’s immediate goal is to define a path forward for providing long-offset, large-tuned source seismic capabilities for the US research community after R/V Langseth is no longer available. In the near term, NSF will work with the Marine Seismic Research Oversight Committee (MSROC) of UNOLS to engage the broad community in this effort. A community workshop, to be held in the Fall of 2018, will be the first step in evaluating future research needs and identifying creative options for providing the necessary marine seismic infrastructure. Throughout the transition to the post-Langseth environment, NSF will accept proposals that include large tuned source, long-offset data acquisition, but access to these capabilities will need to be coordinated by Principal Investigators as part of their proposals, such as through industry providers or international/institutional partners. NSF will also continue to accept proposals to use other seismic acquisition capabilities (e.g., portable multichannel seismic equipment, ocean-bottom seismometers, CHIRP systems, P-cable, etc.).
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
TAMU: IODP-JRSO Assistant Research Scientist Position - NEW!
The International Ocean Discovery Program (IODP) at Texas A&M University invites applications for anAssistant Research Scientist (Expedition Project Manager/Staff Scientist) in our Science Operations section. Applications in any field of geoscience pertinent to IODP will be considered although preference will be given to those with expertise that fits well with our current group. A Ph.D. in geosciences or related field, and demonstrated on-going research experience is required. Applicants must have a demonstrated fluency in written and spoken English. Experience as a seagoing scientist, especially in scientific ocean drilling, is preferred. This position will serve as the Expedition Project Manager to coordinate all aspects of precruise expedition planning, sea-going implementation, and postcruise activities. These duties include sailing as the IODP scientific representative on a two-month IODP expedition approximately once every 1 to 2 years. Individual scientific research, as well as collaboration with colleagues at Texas A&M University in fulfilling its educational mission, is required. This position will also provide scientific advice on laboratory developments in their area of specialization including scientific implementation of downhole logging on theJOIDES Resolution. Applicants must be able to cooperate and work harmoniously with others, have the ability to be an effective team leader, and foster collaboration among diverse scientific participants. Passing a new employee medical exam and annual seagoing medical exams are a requirement of the position. We will begin reviewing applications on June 30, 2018, but will continue to accept applications until candidates are selected for interviews.
BIOS: Postdoctoral Scholarship in Oceanography
Karlsruhe Institute of Technology: Two Ph.D. Positions
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