C-DEBI Newsletter – May 1, 2015
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Frontiers in Extreme Microbiology
A modular method for the extraction of DNA and RNA, and the separation of DNA pools from diverse environmental sample types

Mark A. Lever, Andrea Torti, Philip Eickenbusch, Alexander B. Michaud, Tina Šantl-Temkiv and Bo B. Jørgensen
C-DEBI Contribution 263, Graduate Fellowship

A method for the extraction of nucleic acids from a wide range of environmental samples was developed. This method consists of several modules, which can be individually modified to maximize yields in extractions of DNA and RNA or separations of DNA pools. Modules were designed based on elaborate tests, in which permutations of all nucleic acid extraction steps were compared. The final modular protocol is suitable for extractions from igneous rock, air, water, and sediments. Sediments range from high-biomass, organic rich coastal samples to samples from the most oligotrophic region of the world’s oceans and the deepest borehole ever studied by scientific ocean drilling. Extraction yields of DNA and RNA are higher than with widely used commercial kits, indicating an advantage to optimizing extraction procedures to match specific sample characteristics. The ability to separate soluble extracellular DNA pools without cell lysis from intracellular and particle-complexed DNA pools may enable new insights into the cycling and preservation of DNA in environmental samples in the future. A general protocol is outlined, along with recommendations for optimizing this general protocol for specific sample types and research goals.

Proceedings of the IODP, vol. 336
Data report: cultivation of microorganisms from basaltic rock and sediment cores from the North Pond on the western flank of the Mid-Atlantic Ridge, IODP Expedition 336

Hisako Hirayama, Mariko Abe, Junichi Miyazaki, Sanae Sakai, Yuriko Nagano, and Ken Takai

Cultivation experiments targeting chemolithoautotrophic microorganisms were performed using subseafloor basaltic cores (the deepest sample is from 315 meters below seafloor [mbsf] and overlying sediment cores (the deepest sample is from 91.4 mbsf) from North Pond on the western flank of the Mid-Atlantic Ridge. The cores were recovered by the R/V JOIDES Resolution during Integrated Ocean Drilling Program Expedition 336. Different bacteria were grown under different media and temperature conditions. In the enrichment cultures of the basaltic cores under aerobic conditions, frequently detected bacteria at 8°C and 25°C were members of the genera Ralstonia (the class Betaproteobacteria) and Pseudomonas (Gammaproteobacteria), whereas members of the genera Paenibacillus (Bacilli) and Acidovorax (Betaproteobacteria) were conspicuous at 37°C. Bacillus spp. (Bacilli) were outstanding at 37°C under anaerobic conditions. In the enriched cultures of the sediment cores, bacterial growth was observed at 15°C but not at 37°C, and the bacteria detected at 15°C mostly belonged to gammaproteobacterial genera such as Pseudomonas, Halomonas, and Marinobacter. All of the bacteria detected in this study were enriched only, and subcultivation of the enriched cultures in the respective original media did not succeed. The presence of hydrogenotrophic methanogens was examined by a culture-dependent or a culture-independent analysis in the basalt and sediment cores but was not proven. A fungal isolate was obtained from a single basaltic core and belonged to the genus Exophiala of the order Chaetothyriales.


Education & Outreach

USC / Sea Grant / C-DEBI / Wrigley Institute: Summer Science Programs applications now open
Weeklong Summer Science Programs provide middle school and high school students the opportunity to visit the USC Phillip K. Wrigley Wrigley Institute for Environmental Studies on Catalina Island, and other coastal sites. Over the course of a week, students get amazing opportunities to work with local researchers, conduct their own research projects, learn about careers in marine science, build their own ROVs and explore the marine protected areas around the island. Applications for Summer 2015 are now available! Program dates are July 23- 29, 2015. The program is FREE to the students including transportation and will be limited to twenty applicants. It is offered in partnership by USC Sea Grant Program, Center for Dark Energy Biosphere Investigations, and Wrigley Institute for Environmental Studies. Applications are due by March 20, 2015.

Western Washington University: Microbial Ecology Research Opportunity Summer 2015: Two Research Experience for Undergraduates (REU) Internships Available!
The Zeta Hunter Project:

  • Hydrothermal vent microbial communities from Mariana Arc and Backarc Volcanoes will be used for the study of iron-oxidizing bacteria and the microbial iron cycle.
  • Microbial ecology projects will focus on using state-of-the-art molecular microbiological techniques in addition to classical cultivation and enrichment culture strategies to address questions in community structure and diversity.
  • Advanced training offered in molecular techniques such as environmental DNA extraction and purification, NextGen DNA Sequencing, Quantitative-PCR, T-RFLP Metagenomics and extreme culturing techniques.
  • Throughout the summer, we will focus on such skills as keeping good research notes, troubleshooting experiments, and organizing data. In addition, students will read and discuss papers relevant to their projects and to the Zeta Hunter project in general.

Available Resources per Intern: Summer stipend (40 hrs/wk x 12 wks x $12.00/hr = $5,760); tentative effective dates, June 15th through Sept 15th; any and all research expenses included (May consider half-time positions at 20 hrs per week, if necessary). Email application asap to (deadline June 05, 2015) Craig L. Moyer.

C-DEBI Education Grant: An interactive interface for deep biosphere models to promote dialogue between scientists and the public
David Fike and Jen Houghton at Washington University have created an educational simulation for middle- and high school students to investigate chemical mixing and microbial response in subsurface marine environments. Each step in the 2D solute transport model simulation is accompanied by embedded in-depth information, visual displays of 2D change in parameters in real-time, and the ability to interrogate results in 2D. Find teaching strategies and more ways to interact with this project.

The Gates Millenium Scholarship Program
Congratulations to the Class of 2015 Gates Millennium Scholars, including the three winners from Animo Leadership Charter High School (Los Angeles): Esteban Espinoza, Anacarina Gomez, and Jesus Madrid!  Out of 52,000 applicants (the top students in the country) for the Gates Millennium Scholarship only 1000 were chosen to receive a $250,000 educational grant. These students have been integrated with C-DEBI as Rising Deep Scholars interns (Esteban and Anacarina) and leaders of the Animo Marine Biology Club through their tirelessly supportive teacher Mark Friedman. Find out more about the Gates Millennium Scholars Program, funded by a grant from the Bill & Melinda Gates Foundation, established in 1999 to provide outstanding low income African American, American Indian/Alaska Native, Asian Pacific Islander American, and Hispanic American students with an opportunity to complete an undergraduate college education.

ECORD: Summer School 2015: Ocean crust processes: magma, faults, fluxes and life; August 31 - September 11, 2015, Bremen, Germany
The application deadline is April 30, 2015.

The Data Incubator: Data Science Fellowship Opportunity
The next session will be from 06/01/15 to 07/17/15.

Community News
We have heard the community comments and questions on the status of construction completion of the OOI. In these final months leading to construction closeout, I will provide a brief progress status each week on in an effort to keep the community informed about program status. If you have any specific questions, please ask! You can submit questions through the OOI website here. [Read the full message here...]

IODP: Message from the Program Director
On March 23, 2015, the National Science Foundation awarded a five-year Cooperative Agreement to Lamont-Doherty Earth Observatory (LDEO) of Columbia University to manage the U.S. Science Support Office for the International Ocean Discovery Program (USSSP). The USSSP provides travel, salary, and post-expedition awards to U.S. IODP scientists for each expedition, as well as support for IODP workshops and education and outreach efforts. Principal Investigators for this new Cooperative Agreement (USSSP-LDEO) are Carl Brenner, Maureen Raymo, and David Goldberg. The lead PI, Carl Brenner, will also be the Project Director and the primary point of contact for most USSSP-related issues. LDEO succeeds the Consortium for Ocean Leadership, which provided these services to the U.S. drilling community for the past three decades. There will be a transition period over the coming year with most new expedition salary and post-expedition awards for U.S. scientists being handled by USSSP-LDEO and USSSP-COL continuing to handle previously-issued awards expedition salary, travel and post-expedition awards to U.S. scientists. For more information regarding the new USSSP office, please visit their website at

Meetings, Workshops and Activities

Deadline for oral abstracts is closed. Meeting application due June 13, 2015.

Proposal Calls

IODP: Apply to sail on Expedition 364 Chicxulub Impact Crater
The deadline to apply is May 08, 2015.

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, next submission deadline May 15, 2015, related to the International Ocean Discovery Program (IODP).

DCO: Call for Proposals Census of Deep Life Sequencing Opportunities
Application deadline: June 01, 2015.


Bigelow: Postdoctoral Research Scientist – Geomicrobiology/Microbial Ecology
Bigelow Laboratory for Ocean Sciences in East Boothbay, Maine seeks a Postdoctoral Research Scientist to help carry out a project analyzing the role of bacteria in coastal iron cycling. The position will be in Dr. David Emerson’s laboratory at Bigelow, and is a collaborative project with researchers at Harvard University. Two primary goals of the project are to learn more about specific groups of Fe-oxidizing and Fe-reducing bacteria that play a role in iron cycling in coastal environments, and understand the role that oxygen plays in controlling these dynamics. The project will entail some field work in identifying important populations carrying out these processes, and there will be a significant emphasis on lab work using microcosms with both natural communities and pure cultures to investigate iron cycling dynamics and microbial growth at very low oxygen levels. The overarching goal is to develop a detailed understanding of the ecophysiology of specific iron cycling microbes, and understand how these adaptations impact iron dynamics in the ocean. Techniques specific to this project will be the establishment of microcosms for the study of microbes, cultivation techniques, the use of qPCR for tracking either bacterial populations and/or expression of specific genes, as well as RNA-seq based transcriptome approaches. This position is funded for two years with the possibility of funding for a third year. For full consideration, the application should be received by May 22, 2015.

C-DEBI: Education, Outreach, and Diversity Manager
The Center for Dark Energy Biosphere Investigations (C-DEBI) is seeking a Program Manager to join its team. C-DEBI is a multi-institutional research and education center funded by the National Science Foundation with USC as its headquarters. In addition to the science of exploring microbial life beneath the seafloor, education and diversity are priorities to the Center's efforts to strengthen the STEM pipeline by integrating research and educational programs for diverse future generations. The full-time Program Manager will serve as Education, Outreach, and Diversity Manager, helping to create, coordinate, and lead our education, outreach, and diversity efforts to serve our students, postdocs, faculty, and other participants at USC and across the nation. The Program Manager will also direct day-to-day project operations and administrative activities of C-DEBI at USC. The ideal candidate for the position of C-DEBI Education, Outreach, and Diversity Manager has:

  • 5 years of experience developing and managing educational STEM programs with multiple institutions
  • Leadership and strong oral and written communication skills
  • Experience using social media for professional outreach
  • Research experience at Ph.D. level

See the USC jobs website for more information on this posting ID 1003195:

MBARI: Principle Investigator
The Monterey Bay Aquarium Research Institute (MBARI) seeks a Principal Investigator (PI) to develop and direct a marine carbon cycle research team.

Bermuda Institute of Ocean Sciences: Chemical/Physical/Biological Oceanographer
Review of applications will begin April 15, 2015.

UTK: Professor and Head Department of Microbiology, The College of Arts & Sciences
Review of applications will begin on March 31, 2015 and will continue until the position is filled.

University of Nevada, Las Vegas: Postdoctoral Fellow in microbiology (“microbial dark matter” biology)
The review of materials will begin December 01, 2014, and will continue until the position is filled.

Skidaway Institute of Oceanography: Two Tenure Track Faculty Positions in Oceanography
The committee will begin to review applications on October 24, 014 and will continue until the positions are filled.

Don’t forget to email me with any items you'd like to share in future newsletters! You are what makes our deep biosphere community!
Matthew Janicak
Data Manager
Center for Dark Energy Biosphere Investigations (C-DEBI)
University of Southern California
3616 Trousdale Pkwy, AHF 209, Los Angeles, CA 90089-0371
Phone: 708-691-9563, Fax: 213-740-2437

Exploring life beneath the seafloor and making transformative discoveries that advance science, benefit society, and inspire people of all ages and origins.

C-DEBI is now on Twitter! Follow and tweet to us @deepbiosphere or tag #CDEBI.
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