C-DEBI Newsletter – August 15, 2018

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 FastDNA^TM 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 FastDNA^TM 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.

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

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