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C-DEBI Newsletter – August 15, 2018
This newsletter is also accessible via our website.


 

Message from the Director:

Hope you are having a good start to your semester – we especially wish the same to C-DEBIers who have been promoted or are starting new positions: Karen Lloyd (Associate Professor at University of Tennessee Knoxville), Nagissa Mahmoudi (Assistant Professor at McGill University), and Alberto Robador (Research Assistant Professor at University of Southern California).

And a sincere congratulations to C-DEBIers being recognized for their scientific excellence and more this year: Victoria Orphan (Caltech) recipient of the NOMIS Distinguished Scientist and Scholar AwardBeth Orcutt (Bigelow) to receive the Geological Society of America Geobiology & Geomicrobiology Division Post-Tenure Award, and Andy Fisher (UCSC) and Adina Paytan (UCSC) to be named American Geophysical Union Fellows. Please share your personal kudos if you will also be attending the GSA Annual Meeting in Indiana in November and the AGU Fall Meeting in DC in December.

Cheers and good luck to all submitting NSF proposals due today!

Jan Amend
C-DEBI Director


 

Publications


Proceedings of the IODP
Data report: IODP Expedition 366 pore water trace element (V, Mo, Rb, Cs, U, Ba, and Li) compositions - NEW!
Charles Geoffrey Wheat*, Trevor Fournier, Claudia Paul, Catriona Menzies, Roy E. Price, Jeffrey Ryan, Oliver Sissman
*C-DEBI Contribution 429

International Ocean Discovery Program (IODP) Expedition 366 focused, in part, on the study of geochemical cycling, matrix alteration and transport, and deep biosphere processes in the Mariana subduction zone. This research was accomplished by sampling the summit and flank regions of three active serpentinite mud volcanoes in the Mariana forearc: Yinazao (Blue Moon), Fantangisña (Celestial), and Asùt Tesoro (Big Blue) Seamounts. These mud volcanoes represent a transect with increasing distance from the trench. Because these mud volcanoes discharge fluids and materials from the subduction channel, they provide a means to characterize thermal, geochemical, and pressure conditions within the seismogenic zone. Previous coring on Ocean Drilling Program (ODP) Legs 125 and 195 at two other serpentinite mud volcanoes (Conical and South Chamorro Seamounts, respectively) and piston, gravity, and push cores from several other Mariana serpentinite mud volcanoes add to this transect of deep-sourced material that is discharged at the seafloor.

Pore waters were squeezed from cored serpentinite materials to determine the composition of deep-sourced fluid from the subduction channel and to assess the character, extent, and effect of diagenetic reactions and mixing with seawater on the flanks of three serpentinite seamounts (Yinazao, Fantangisña, and Asùt Tesoro). In addition, two water-sampling temperature probe (WSTP) fluid samples were collected in two of the cased boreholes, each with at least 30 m of screened casing that allowed formation fluids to discharge into the borehole. Here we report shore-based Li, Rb, Cs, Ba, V, Mo, and U measurements of pore waters and one of the WSTP samples. The alkali metals were analyzed to constrain the temperature of reaction in the subduction channel. The other elements were analyzed to assess potential biogenic and diagenetic reactions as the serpentinite material weathers and exchanges with bottom seawater via diffusion. Results were generally consistent with earlier coring and drilling operations, resulting in systematic changes in the composition of the deep-sourced fluid with distance from the trench.


Limnology and Oceanography: Methods
Influence of commercial DNA extraction kit choice on prokaryotic community metrics in marine sediment - NEW!
Gustavo A. Ramírez*, Dennis Graham, Steven L. D’Hondt*
*C-DEBI Contribution 432

Commercial DNA extraction kits are widely used for cultivation‐free surveys of marine sediment. However, the consequences of popular extraction‐kit choices for sequence‐based biological inferences about marine sedimentary communities have not previously been exhaustively assessed. To address this issue, we extracted DNA from multiple paired subsamples of marine sediment using two popular commercial extraction kits (MO BIO Laboratories PowerSoil® DNA isolation kit and MP Biomedicals FastDNATM Spin Kit for Soil). We report comparisons of (1) total DNA yield, (2) extract purity, (3) gene‐targeted quantification, and (4) post‐sequencing ecological inferences in near‐seafloor (< 1 meter below seafloor [mbsf]) and subsurface (> 1 mbsf) marine sediment. In near‐seafloor sediment, the MP Biomedicals FastDNATM Spin Kit for Soil exhibits higher extraction yields, higher 16S rRNA gene loads, higher taxonomic diversity, and lower contaminant loads. In subseafloor sediment, both kits yield similar values for all of these parameters. The MO BIO Laboratories PowerSoil® DNA isolation kit generally co‐extracts less protein with the DNA in both near‐seafloor and subseafloor sediment. For samples from all depths, both kits exhibit similar depth‐dependent community richness patterns, taxonomic composition, and ordination‐based similarity trends. We conclude that, despite kit‐specific differences in extract yields, purity and reagent contaminant loads, ecological inferences based on next‐generation sequencing of DNA extracted using these popular commercial kits are robustly comparable, particularly for subseafloor sediment samples.


 
 
 
 
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. If your publication is accepted, but not yet online with a DOI, contact us for more information.



 

Education & Outreach


C-DEBI: USC students: apply now for the 2018-2019 Genomics and Geobiology Undergraduate Research Experience - NEW!
The Genomics and Geobiology Undergraduate Research Experience (GGURE) is a research internship program for USC sophomores, juniors, and seniors majoring in the life sciences, earth and marine sciences, computational sciences, and engineering. There is both a part-time program during the academic year and a full-time program over 10 weeks during the summer break at the University of Southern California. The GGURE program offers USC undergraduates the opportunity to participate actively in a research group, with either an experimental or computational focus, and perform original research under the direct supervision of a faculty mentor. We will begin reviewing applications on Monday, August 20, 2018 but will continue to review applications until all positions are filled.

C-DEBI: Next Professional Development Webinar: August 31, 12pm PT
Drew Steen (C-DEBI Assistant Professor of Environmental Geology, University of Tennessee) leads the next C-DEBI Professional Development Webinar on “Work-life Balance is Essential and also it can’t Possibly Exist.” The access URL for the webinar is http://usccollege.adobeconnect.com/cdebiremote/. Missed the most recent C-DEBI Professional Development Webinar on “What I wish I knew before I knew it: Surviving the early years of tenure-track faculty” with Brandi Kiel Reese (TAMU)? Watch it on YouTube.

ICDP: Training Course on Continental Scientific Drilling
The deadline for applications is September 14, 2018.

IODP: How to bring the new JOIDES Resolution Traveling Exhibit to your community


 

Meetings & Activities


NSTC: Public Comment Period Now Open for Science and Technology for America’s Oceans: A Decadal Vision
Public comment period for the document is open now until August 27, 2018.

SXSW 2019: Help NSF get to South by Southwest! - NEW!
The National Science Foundation (NSF) needs your help! We have put together a number of fascinating panels comprising an all-star cast of NSF-funded scientists, filmmakers, inventors, small business founders and partners for the 2019 South by Southwest (SXSW) festival in Austin, Texas. Now we need your support  — and your vote  — to get our panels picked! Over 5,000 panels have been submitted to SXSW, yet fewer than 1,000 spots are available. To ensure we’re able to spotlight cutting-edge research, innovations and the men and women who make it happen, please vote for the NSF-submitted panels below and spread the word to encourage other people within your own community to vote. Place your votes by Thursday, August 30, 2018.

C-DEBI: Rolling call for Community Workshop support

C-DEBI: Protocols.io Group Page

C-DEBI: Subseafloor Cultures Database


 

Proposal Calls


NSF: Research Experiences for Undergraduates (REU)
Full Proposal Deadline: August 22, 2018.

NSF: Graduate Research Fellowship Program (GRFP)
Application deadlines: October 22-26, 2018.

NSF: Graduate Research Fellowship Program (GRFP) - Graduate Research Internship Program (GRIP)
GRIP applications are due December 4, 2018.

C-DEBI: Rolling call for Research Exchange proposals

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: 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)



 

Employment

BIOS: Postdoctoral Scholarship in Oceanography - NEW!
A Postdoctoral Scholar award will be offered to a new or recent PhD in the fields of oceanography or closely related subjects. We welcome a broad range of potential topics for study, including physical oceanography process studies at all scales, biogeochemical research with practical experimentation, and system modeling with strong integration of data. We seek a candidate who will take advantage of the opportunities and facilities offered at BIOS which include bi-weekly access to the deep ocean, repeat measurements and long-term monitoring of ocean properties, integration of glider observations with traditional ship-based measurements and laboratory access for chemical and biological measurements and experimentation. The award is designed to further the education and training of the applicant with primary emphasis on supporting the individual’s research promise in his/her chosen area of research. A successful postdoctoral term would offer the opportunity to transition to the BIOS resident scientific staff. Applicants should have received their doctoral degree completed by the start date of the position. The recipient will receive full salary support for an eighteen-month period, with possibility of extension depending on performance success. Support is also available for relocation, travel to scientific meetings, equipment and supplies.

Bigelow: Postdoctoral Research Scientist
Application deadline: September 1, 2018.

U Waterloo (Canada): Assistant/Associate Professor Position in Geomicrobiology
Application deadline: October 1, 2018.

Rice: Wiess and Pan Post-Doctoral Research Fellowships
The applications are due on November 1, 2018.

U South Florida: Two Tenure-Track Faculty Positions in Chemical and Geological Oceanography
The positions are open until filled, however, priority review of applications will begin by August 1, 2018.

U Southern Mississippi: Three Positions (Postdoctoral Researcher, Graduate Student, Research Technician) in Marine Microbial Ecology

UTK: Post-Doctoral Research Associate, Center for Environmental Biotechnology

Karlsruhe Institute of Technology: Ph.D. and Postdoc position available




 
 
 
 
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!


 

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

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