C-DEBI Newsletter – December 17, 2018
This newsletter is also accessible via our website.


Message from the Director:

AGU Fellow and C-DEBI Co-I Andy Fisher flanked by C-DEBI Co-Is Julie Huber and Geoff Wheat.

Congratulations again to C-DEBI co-Investigator Andy Fisher who was honored as an AGU Fellow last week! Hope those that attended the American Geophysical Union Fall Meeting in DC had a terrific week of deep biosphere sessions!


Jan Amend
C-DEBI Director


Publications & Press

Frontiers in Microbiology
Minimal Influence of Extracellular DNA on Molecular Surveys of Marine Sedimentary Communities  - NEW!
Gustavo A. Ramírez*, Steffen L. Jørgensen, Rui Zhao, Steven L. D’Hondt*
*C-DEBI Contribution 446

Extracellular DNA has been reported to comprise a large fraction of total DNA in near-seafloor sediment. However, the potential effect of extracellular DNA, arising from dead or moribund cells, on sequencing surveys is a critical concern that has largely not been addressed for marine sedimentary habitats. To address this concern, we interrogated freshly collected Arctic and Pacific sediment for extracellular 16S rRNA genes using the photoactive DNA-binding dye Propidium Monoazide. Significant differences between relative abundances of total (intracellular + extracellular) Bacterial 16S rRNA genes and relative abundances of intracellular Bacterial 16S rRNA genes are only detected in three of twelve shallow [10 cm below seafloor (cmbsf)] samples. Relative abundances of total Bacterial 16S rRNA genes are statistically indistinguishable from relative abundances of intracellular Bacterial 16S rRNA genes in all interrogated samples from depths greater than 10 cmbsf. 16S rRNA gene sequencing shows that even where significantly higher abundances of extracellular genes are detected, they have little or no influence on prokaryote community composition. Taxon-level analyses suggest that extracellular DNA, arising from in situdeath, may be sourced from different organisms in sediment of different ages. However, the overall effect of extracellular genes on sequencing surveys of marine sedimentary prokaryotes is minimal.

Frontiers in Microbiology
Ecological Succession of Sulfur-Oxidizing Epsilon- and Gammaproteobacteria During Colonization of a Shallow-Water Gas Vent  - NEW!
Sushmita Patwardhan, Dionysis I. Foustoukos*, Donato Giovannelli, Mustafa Yücel, Costantino Vetriani*
*C-DEBI Contribution 447

In this study, we integrated geochemical measurements, microbial diversity surveys and physiological characterization of laboratory strains to investigate substrate-attached filamentous microbial biofilms at Tor Caldara, a shallow-water gas vent in the Tyrrhenian Sea. At this site, the venting gases are mainly composed of CO2 and H2S and the temperature at the emissions is the same as that of the surrounding water. To investigate the composition of the total and active fraction of the Tor Caldara biofilm communities, we collected established and newly formed filaments and we sequenced the 16S rRNA genes (DNA) and the 16S rRNA transcripts (cDNA). Chemoautotrophic sulfur-oxidizing members of the Gammaproteobacteria (predominantly Thiotrichales) dominate the active fraction of the established microbial filaments, while Epsilonproteobacteria (predominantly Sulfurovum spp.) are more prevalent in the young filaments. This indicates a succession of the two communities, possibly in response to age, sulfide and oxygen concentrations. Growth experiments with representative laboratory strains in sulfide gradient medium revealed that Sulfurovum riftiae (Epsilonproteobacteria) grew closer to the sulfide source than Thiomicrospirasp. (Gammaproteobacteria, Thiotrichales). Overall, our findings show that sulfur-oxidizing Epsilonproteobacteria are the dominant pioneer colonizers of the Tor Caldara biofilm communities and that Gammaproteobacteria become prevalent once the community is established. This succession pattern appears to be driven - among other factors - by the adaptation of Epsilon- and Gammaproteobacteria to different sulfide concentrations.

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!


Meetings & Activities

C-DEBI now has a company page on LinkedIn - join us! - NEW!
Use LinkedIn for professional networking or job discovery? Add our job announcements and other relevant news to your feed by “following” C-DEBI’s company page, and link your profile via the Work Experience section (e.g., “Postdoctoral Fellow at C-DEBI: Center for Dark Energy Biosphere Investigations”).

EGU: General Assembly 2019: Session BG4.2 - NEW!
We are organizing a session on organic matter recycling and diagenesis in sedimentary environment at the next European Geoscience Meeting in Vienna (Austria). We invite all people who are interested in sharing geomicrobiology related work, in soil, lake or ocean sediments. We would like to foster the collaboration between deep biosphere lovers and geoscientists-paleoclimatologists working on environmental reconstructions. For more information, contact session convener Camille Thomas (University of Geneva). The abstract submission deadline is January 10, 2019.

DCO Webinar: Breaking the mold of the traditional field expedition: Biology Meets Subduction
The live webinar with Peter Barry (University of Oxford, UK), Karen Lloyd (University of Tennessee Knoxville, USA), and Donato Giovannelli (CNR-IRBIM, Italy and Rutgers University, USA) will be held January 23, 2019 at 11am PT / 2pm ET.

Save the Date: 16th SoCal Geobiology Symposium @ CalTech, April 6, 2019 - NEW!
Now in its 16th year, the Symposium is a regional conference which provides opportunities for students and post-docs studying one of the myriad facets of geobiology to come together and share their findings. The symposium is just one day long but will include both oral and poster presentations. Breakfast, lunch, and dinner are provided to attendees and registration is free. Although only presentations from students and post-docs will be accepted, faculty are welcome and encouraged to attend. A registration website will be available soon.

Ongoing Activities:


Education & Outreach

C-DEBI: Latest Professional Development Webinar Now Online!
Missed the last Professional Development Webinar on “Scientific editing as a career” with Delphine Defforey (Nature Communications)? Watch it on YouTube.

UNLV: Graduate Research Assistantships in Deep Biosphere and Cave Research - NEW!
The Environmental Microbiology and Astrobiology Labs of the Desert Research Institute (DRI) in Las Vegas, NV, in partnership with the School of Life Sciences (SoLS) at the University of Nevada Las Vegas (UNLV), invite applications for graduate studies beginning in Fall of 2019. These joint positions will based at DRI, but coursework, academic advisement, and degrees will be provided through UNLV. We seek highly motivated individuals to contribute to NASA- and NSF-funded research at the interface between environmental science, cultivation-based microbiology, and genomics. The successful applicant will join a dynamic research team with primary collaborators from the Single Cell Genomics Center (Bigelow Lab, ME), the Universities of New Hampshire and New Mexico, and NASA in Silicon Valley (NASA Ames). Major field activities will focus on caves at Lava Beds National Monument, deep boreholes associated with Death Valley, and other (often) extreme desert environments. Open until filled, UNLV application deadline – January 15, 2019.

MARUM: ECORD Training Course, March 25-29, 2019 - NEW!
As host to one of only three IODP core re­pos­it­or­ies in the world – the only one in Europe – the MARUM in Bre­men is an im­port­ant hub for mar­ine geoscient­ists. Tak­ing ad­vant­age of this set­ting, the new ECORD Train­ing Course will provide a “Vir­tual Drill­ship Ex­per­i­ence” for sci­ent­ists from aca­demia and in­dustry. The participants will be early ca­reer and es­tab­lished sci­ent­ists from aca­demia and in­dustry from all over the world who have an interest in sci­entific drilling and de­vel­op­ment of pro­fes­sional skills in core ana­lysis. This one week course of­fers a ba­sic train­ing fo­cus­ing on the IODP core flow pro­ced­ures, pre­par­ing the par­ti­cipants for par­ti­cip­at­ing in an off­shore drill­ship ex­ped­i­tion, and in­stilling them with an ap­pre­ci­ation for high stand­ards in all kinds of cor­ing pro­jects. IODP‐style lab ex­er­cises will form the found­a­tion of the ECORD Train­ing Course fol­low­ing the pat­tern of the unique “Vir­tual Ship” ap­proach de­veloped for the Bre­men ECORD Sum­mer Schools. Application deadline: January 18, 2019.

CalTech: Geobiology 2019: An International Training Course in a Rapidly Evolving Field
Applications are due by February 8, 2019.


Proposal Calls

NOPP: FY2019 Broad Agency Announcement
Proposal deadlines of December 21, 2018 and January 18, 2019.

NSF: Understanding the Rules of Life (URoL): Epigenetics
Full proposal deadline: February 1, 2019.

IODP-USSSP: Apply to Sail on Expedition 387: Amazon Margin
The deadline to apply is March 1, 2019.

IODP-USSSP: Apply to Sail on Expedition 388: Equatorial Atlantic Gateway
The deadline to apply is April 1, 2019.

NSF: Opportunities for Promoting Understanding through Synthesis (OPUS)
Full proposal deadline: August 5, 2019.

Rolling Calls:




Assistant / Associate Professor of Microbiology - NEW!
The Department of Biological Sciences is searching for a tenure-track Assistant or Associate Professor to start August 21, 2019. California State University, Chico seeks faculty who are competent in their field, collaborative with colleagues and staff, and committed to student success. The minimum education requirement for appointment to this position is a PhD in microbiology or a related field, with a specialization in prokaryotic or eukaryotic (protist or fungal) microbial pathogenesis, food or industrial microbiology, or microbial ecology. A demonstrated ability or potential to establish externally-funded research, a record of publication, and a strong interest in teaching excellence and enthusiasm for mentoring undergraduate and graduate students in research are also required. The successful candidate should provide evidence of their commitment to or experience promoting and fostering a learning environment that is supportive of individuals from diverse backgrounds. Review of applications will begin on January 10, 2019 and continue until the position is filled.

U Oldenburg: Professorship in Benthic Microbiology
Applications should be submitted by no later than January 15, 2019.

USGS: Mendenhall Research Fellowship Program
The deadline for submission is Friday, January 18, 2019.

MSU: Assistant/Associate Professor of Environmental Microbiology
Screening of applications will begin on February 1, 2019; however, applications will continue to be accepted until an adequate applicant pool has been established.

U Toronto: Postdoctoral Positions in Fluid-Rock Interactions and Deep Subsurface Life

UNC Chapel Hill: Guaymas Basin postdoc opportunity

TAMU: Instructional Assistant Professor

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!


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.

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