C-DEBI Newsletter – April 15, 2014
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Activities, Workshops and Courses

Submit your abstracts to sessions such as "Astrobiology/Microbiology of Extreme Subsurface Environments" chaired by Tori Hoehler and Karsten Pedersen at the forthcoming International Symposium on Subsurface Microbiology meeting, which will be held at Asilomar this October, right after and near the C-DEBI Annual Meeting (note: the Annual Meeting is by invite only, details to come soon). Abstracts due April 21. See submission instructions at

MARUM: ECORD Summer School, "Subseafloor Biosphere: Current Advances and Future Challenges," September 22 - October 2, Bremen, Germany
The deep subseafloor biosphere may be one of the largest ecosystems on our planet, driving subseafloor geochemical processes that affect ocean chemistry, the global carbon cycle, and the alteration of sediment and rocks. Its exploration means investigation of microbial communities at the limit of life and requires advancement of microbiological and biogeochemical methods. This summer school will address the latest developments in the investigation of the deep marine biosphere. This summer school will combine lab exercises on IODP-style shipboard methodologies (”virtual ship”) as well as interactive lectures by world-leading scientists in the fields of geomicrobiology and biogeochemistry. Participation will prepare you for future involvement in IODP and for research on the deep sub-seafloor biosphere. The summer school will take advantage of the unique and integrated facilities offerred by the IODP Bremen Core Repository and the MARUM laboratories. Applications due May 9, 2014.

C-MORE: Ecological Dissertations in the Aquatic Sciences (Eco-DAS) XI, October 19-25, 2014, Honolulu, HI
Applications are due by April 21, 2014.

ECORD/ICDP MagellanPlus Workshop: Advancing Sub-surface Biosphere and Paleoclimate Research
The workshop is scheduled on 21st-23rd August 2014 in Seoul, South Korea, prior to the ISME conference (24th-29th August 2014 in Seoul). Scientists who wish to participate in this workshop are requested to contact Jan W. de Leeuw before May 5th 2014.

Ocean Leadership: Apply to Host Deep Biosphere IODP Distinguished Lecturer Beth Orcutt
Applications due June 1, 2014.

Proposal Calls

L'Oreal For Women in Science: Five Postdoctoral Grants
Are you a woman in a STEM field who is committed to serving as a role model for younger generations? The L’Oréal For Women in Science program is seeking women like you to help encourage females to pursue careers in science. The program will award five post‐doctoral women scientists in the United States this year with grants of up to $60,000 each. Applicants are welcome from a variety of fields, including the life and physical/material sciences, technology (including computer science), engineering, and mathematics. Applications are due on Monday, May 19, 2014.

IODP: Apply to Sail for Expeditions 355 and 356
The International Ocean Discovery Program (IODP) has begun accepting applications for two expeditions aboard the JOIDES Resolution: Expedition 355 (Arabian Sea Monsoon) and Expedition 356 (Indonesian Throughflow). The deadline to apply is May 1, 2014.

National Academies Research Associateships for Graduate, Postdoctoral and Senior Researchers
There are four annual review cycles and the next closes May 1.

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, 2014, related to the International Ocean Discovery Program (IODP).

NSF: Critical Techniques and Technologies for Advancing Big Data Science & Engineering (BIGDATA) Program Solicitation
Full Proposal Deadline: June 9, 2014.

Hot Off the Press: Microbial Life of the Deep Biosphere (Eds. Kallmeyer and Wagner) in Life in Extreme Environments
Over the last two decades, exploration of the deep subsurface biosphere has developed into a major research area. New findings constantly challenge our concepts of global biogeochemical cycles and the ultimate limits to life. In order to explain our observations from deep subsurface ecosystems it is necessary to develop truly interdisciplinary approaches, ranging from microbiology and geochemistry to physics and modeling. This book aims to bring together a wide variety of topics, covering the broad range of issues that are associated with deep biosphere exploration. Not only does the book present case studies of selected projects, but also treats questions arising from our current knowledge. Despite nearly two decades of research, there are still many boundaries to exploration caused by technical limitations and one section of the book is devoted to these technical challenges and the latest developments in this field. This volume will be of high interest to biologists, chemists and earth scientists all working on the deep biosphere. Chapters include:
  • C-DEBI Former Postdoc Committee Chair Biddle, Graduate Fellow Jungbluth, Networked Speaker Lever and Co-PI Rappé, "Life in the oceanic crust" (C-DEBI Contribution 196)
  • C-DEBI Research Grantee Lloyd, "Quantifying microbes in the marine subseafloor: some notes of caution"
  • C-DEBI Extent Theme Team Leader Teske, "Archaea in deep marine subsurface sediments" (C-DEBI Contribution 199)
  • C-DEBI Research Grantees Edgcomb, Orsi and Biddle, "Fungi in the marine subsurface"
  • C-DEBI Postdoc Fellow LaRowe and Director Amend, "Energetic constraints on life in marine deep sediments" (C-DEBI Contribution 169)
Phylogenetic diversity of microorganisms in subseafloor crustal fluids from Holes 1025C and 1026B along the Juan de Fuca Ridge flank, in Frontiers in Microbiology
To expand investigations into the phylogenetic diversity of microorganisms inhabiting the subseafloor biosphere, basalt-hosted crustal fluids were sampled from Circulation Obviation Retrofit Kits (CORKs) affixed to Holes 1025C and 1026B along the Juan de Fuca Ridge (JdFR) flank using a clean fluid pumping system. These boreholes penetrate the crustal aquifer of young ocean crust (1.24 and 3.51 million years old, respectively), but differ with respect to borehole depth and temperature at the sediment-basement interface (147 m and 39°C vs. 295 m and 64°C, respectively). Cloning and sequencing of PCR-amplified small subunit ribosomal RNA genes revealed that fluids retrieved from Hole 1025C were dominated by relatives of the genus Desulfobulbus of theDeltaproteobacteria (56% of clones) and Candidatus Desulforudis of the Firmicutes (17%). Fluids sampled from Hole 1026B also contained plausible deep subseafloor inhabitants amongst the most abundant clone lineages; however, both geochemical analysis and microbial community structure reveal the borehole to be compromised by bottom seawater intrusion. Regardless, this study by C-DEBI Graduate Fellow Jungbluth, postdoc Lin, former Co-PI Cowen, Research Grantee Glazer and Co-PI Rappé provides independent support for previous observations seeking to identify phylogenetic groups of microorganisms common to the deep ocean crustal biosphere, and extends previous observations by identifying additional lineages that may be prevalent in this unique environment.

Pan-genome analyses identify lineage- and niche-specific markers of evolution and adaptation in Epsilonproteobacteria, in Frontiers in Microbiology
The rapidly increasing availability of complete bacterial genomes has created new opportunities for reconstructing bacterial evolution, but it has also highlighted the difficulty to fully understand the genomic and functional variations occurring among different lineages. Using the class Epsilonproteobacteria as a case study, Zhang and Sievert investigated the composition, flexibility, and function of its pan-genomes. Models were constructed to extrapolate the expansion of pan-genomes at three different taxonomic levels. The results show that, for Epsilonproteobacteria the seemingly large genome variations among strains of the same species are less noticeable when compared with groups at higher taxonomic ranks, indicating that genome stability is imposed by the potential existence of taxonomic boundaries. The analyses of pan-genomes has also defined a set of universally conserved core genes, based on which a phylogenetic tree was constructed to confirm that thermophilic species from deep-sea hydrothermal vents represent the most ancient lineages of Epsilonproteobacteria. Moreover, by comparing the flexible genome of a chemoautotrophic deep-sea vent species to (1) genomes of species belonging to the same genus, but inhabiting different environments, and (2) genomes of other vent species, but belonging to different genera, they were able to delineate the relative importance of lineage-specific versus niche-specific genes. This result not only emphasizes the overall importance of phylogenetic proximity in shaping the variable part of the genome, but also highlights the adaptive functions of niche-specific genes. Overall, by modeling the expansion of pan-genomes and analyzing core and flexible genes, this study provides snapshots on how the complex processes of gene acquisition, conservation, and removal affect the evolution of different species, and contribute to the metabolic diversity and versatility of Epsilonproteobacteria.


Montana State University, Bozeman: Postdoctoral Researcher in Geomicrobiology
A postdoctoral research position in geomicrobiology is available at Montana State University. This research focuses field- and laboratory investigations to define the role of water rock interactions in supporting terrestrial high temperature ecosystems. Experience and expertise in techniques in microbial ecology and physiology is required, and experience in genomics and transcriptomics is preferred. The position is available immediately, for one year initially, with potential for renewal based upon satisfactory performance and availability of funds. A competitive salary will be offered on the basis of the applicant's qualifications and experience. Full details on the required and preferred qualifications for the position and application procedures can be found at Screening of applications will begin on April 16, 2014 and will continue to be accepted until an adequate candidate pool has been established. We encourage applications from members of underrepresented groups. Montana State University is an institution committed to cultural diversity.

George Mason University, Department of Environmental Science and Policy: Postdoctoral Research Fellow
The George Mason University, Department of Environmental Science and Policy in the College of Science invites applicants for a Postdoctoral Research Fellow position to work on a Bureau of Ocean Energy Management (BOEM)-funded project with Dr. Leila Hamdan. Work on the project is scheduled to begin as early as summer 2014 and will last up to two years. This position will support field and laboratory research on a study to evaluate the impact of oil spills on metal and wood shipwrecks in the northern Gulf of Mexico. Through a comparative study of spill-impacted and un-impacted sites and laboratory experiments, the study will address if exposure to oil and/or dispersants affect the population structure, metabolic activity, and biodiversity of microbial communities which colonize shipwrecks and their surrounding environment. This assessment will address if microbial degradation processes and consequently site degradation are either accelerated or reduced as a result of exposure to hydrocarbon contamination. Applicants must have a Ph.D. in microbial ecology, molecular biology, microbiology, coastal or marine science, biogeochemistry, systems biology, or a related field. Strong preference will be given to candidates with a track record of experience using next generation sequencing techniques, biogeochemistry analytical protocols, and bioinformatic analytical pipelines. For full consideration, apply by May 1, 2014. Contact Leila Hamdan ( with any questions.

Texas A&M, College of Geosciences: 4 Faculty Positions
To significantly advance research and instructional excellence in fields related to scientific ocean drilling, the College of Geosciences at Texas A&M University invites applications for up to 4 faculty positions. We seek outstanding individuals who will complement and expand existing university-wide strengths in scientific ocean drilling, especially through the International Ocean Discovery Program (IODP). The academic appointments will be nine-month, tenure track or tenured positions, and are expected to be at the assistant and/or associate professor level. Candidates with suitable qualifications will be considered for appointment as full professor and an endowed chair. Candidates must have a Ph.D. at the time of appointment in a field related to geoscience. Areas of interest include (but are not limited to) climate and ocean change, basin/margin processes, sedimentary processes, earthquake processes, biogeochemistry, ecosystems and the deep biosphere, geophysics (including down-hole logging), geoinformatics/data science and land­ ocean dynamics. The search committee will commence review of applications starting 1 May and will continue until the positions are filled.

ABYSS: PhD and Post-Doctoral fellowships in Geodynamics, Mineralogy, Hydrodynamics, Thermodynamics and (Bio-)Geochemistry
The ABYSS training and research programme started on March 1, 2014. It brings together 14 European research groups and industrial partners; it focuses on the development of new field, experimental and analytical approaches to measure and model the physical, hydrodynamic and geochemical processes controlling mass and energy transfers at mid-oceanic spreading ridges, and the linkages and feedbacks between these processes and their implications for life and marine resources in the deep-sea. We are now recruiting 10 PhDs and 1 post-doctoral fellow, including PhD position ESR11 in geobiology, "The ocean crust as microbial incubator." The deadline for application is June 1, 2014.
UNC-CH: Tenure-Track Assistant/Associate Professor in Marine Environmental Genomics or Particle Dynamics
To apply for the position, please follow this link: Applications will be reviewed starting January 15, 2014

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

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