C-DEBI Newsletter – May 16, 2016
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A hearty congratulations to C-DEBI ExCom member / Senior Scientist Victoria J. Orphan for being appointed as James Irvine Professor of Environmental Science and Geobiology at Caltech! Also, be sure to check out this series of IODP Expedition 365 videos aboard the Chikyu featuring next week's Networked Speaker Series speaker, Stephanie Carr, as the expedition microbiologist!



Frontiers in Microbiology
Nitrogen Stimulates the Growth of Subsurface Basalt-associated Microorganisms at the Western Flank of the Mid-Atlantic Ridge
Xinxu Zhang, Jing Fang, Wolfgang Bach, Katrina J. Edwards*, Beth N. Orcutt* and Fengping Wang
*C-DEBI Contribution 324

Oceanic crust constitutes the largest aquifer system on Earth, and microbial activity in this environment has been inferred from various geochemical analyses. However, empirical documentation of microbial activity from subsurface basalts is still lacking, particularly in the cool (<25°C) regions of the crust, where are assumed to harbor active iron-oxidizing microbial communities. To test this hypothesis, we report the enrichment and isolation of crust-associated microorganisms from North Pond, a site of relatively young and cold basaltic basement on the western flank of the Mid-Atlantic Ridge that was sampled during Expedition 336 of the Integrated Ocean Drilling Program. Enrichment experiments with different carbon (bicarbonate, acetate, methane) and nitrogen (nitrate and ammonium) sources revealed significant cell growth (one magnitude higher cell abundance), higher intracellular DNA content, and increased Fe3+/ΣFe ratios only when nitrogen substrates were added. Furthermore, a Marinobacter strain with neutrophilic iron-oxidizing capabilities was isolated from the basalt. This work reveals that basalt-associated microorganisms at North Pond had the potential for activity and that microbial growth could be stimulated by in vitro nitrogen addition. Furthermore, iron oxidation is supported as an important process for microbial communities in subsurface basalts from young and cool ridge flank basement.

Nature Microbiology
Genomic and enzymatic evidence for acetogenesis among multiple lineages of the archaeal phylum Bathyarchaeota widespread in marine sediments
Y. He, M. Li, V. Perumal, X. Feng, J. Fang, J. Xie, S. M. Sievert & F. Wang

Members of the archaeal phylum Bathyarchaeota are widespread and abundant in the energy-deficient marine subsurface sediments. However, their life strategies have remained largely elusive. Here, we provide genetic evidence that some lineages of Bathyarchaeota are acetogens, being capable of homoacetogenesis, a metabolism so far restricted to the domain Bacteria. Metabolic reconstruction based on genomic bins assembled from the metagenome of deep-sea subsurface sediments shows that the metabolism of some lineages of Bathyarchaeota is similar to that of bona fide bacterial homoacetogens, by having pathways for acetogenesis and for the fermentative utilization of a variety of organic substrates. Heterologous expression and activity assay of the acetate kinase gene ack from Bathyarchaeota, demonstrate further the capability of these Bathyarchaeota to grow as acetogens. The presence and expression of bathyarchaeotal genes indicative of active acetogenesis was also confirmed in Peru Margin subsurface sediments where Bathyarchaeota are abundant. The analyses reveal that this ubiquitous and abundant subsurface archaeal group has adopted a versatile life strategy to make a living under energy-limiting conditions. These findings further expand the metabolic potential of Archaea and argue for a revision of the role of Archaea in the carbon cycle of marine sediments.


Meetings & Activities

C-DEBI 2015-2016 Networked Speaker Series: Thursday, May 26, 2016, 12:30pm PT online!

Stephanie Carr, Bigelow Laboratory for Ocean Sciences
Methanosaeta, are you my methanogen?
Add to:  iCal  •  gCal  •  Outlook  •  Outlook Online  •  Yahoo!

The Adélie Basin, located ~100km off shore of Antarctica’s Wilkes Land Margin, is an anoxic, eutrophic sedimentary environment. During IODP Expedition 318, a 103 m sediment core was collected for microbiological and geochemical studies. Stable carbon isotope analysis of dissolved CO2 indicates an enrichment of δ13C values with depth. This enrichment is indicative of the autotrophic selection of dissolved 12CO2 over 13CO2 , which corresponds to increasing methane concentrations suggesting methanogenesis (a maximum of 12.8 mM at 18 meters below sea floor). Surprisingly, previous pyrosequencing of SSU rRNA gene amplicons identified relatively low amounts of known archaea (<7%) and very few sequences from known methanogens (<0.2%). An additional PCR screen for the gene mcrA also failed to recognize the presence of potential methanogens. This unsatisfying dearth of genomic evidence for methanogens precludes a deeper understanding of CH4 cycling in this environment. To better identify the missing methanogenic community of this basin, an integrated approach of metagenomics, single cell genomics, and stable carbon isotope analysis of intact polar lipid techniques was applied to these sediments. Lipid analyses identified isotopically light hydroxyarchaeol and glycerol dialkyl glycerol tetraether (GDGT) phospholipids, both suspected to be of methanogenic origin. Metagenomic analyses identified coding regions for both acetoclastic and autotrophic methanogenesis pathways. The majority of these coding regions were classified to the genus Methanosaeta, a well-known acetoclastic methanogen. This presentation takes a thorough look at the genus Methanosaeta, especially their methanogenic potential and their role in these and other marine subsurface environments.

If you missed either of this season's previous talks, Dr. Katrina Twing: Microbial diversity and metabolic potential of the serpentinite subsurface environment and Dr. Olivia Nigro: Viruses in the oceanic basement : An integral component of microbial life, you can watch them now online.

IODP: Volunteer for an IODP Panel
The U.S. Science Support Program (USSSP), in association with the International Ocean Discovery Program (IODP), is seeking new U.S.-based members for the JOIDES Resolution Facility Science Evaluation Panel (SEP) and Environmental Protection and Safety Panel (EPSP). New members will serve three-year terms beginning in October 2016. Scientists interested in volunteering for these opportunities should send a cover letter and a two-page CV to by July 8, 2016. Letters should clearly indicate your primary field of expertise, briefly document any previous committee/panel experience, describe your interests in the scientific ocean drilling programs, and identify your preferred panel assignment. We strongly encourage the involvement of early career scientists, as well as those with more experience.

Kyoto University: 5th International Workshop on Deep Sea Microbiology, September 10-11, 2016
The aim of the workshop is to gather international experts in the field of deep-sea microbiology, and provide the participants the opportunity to present very recent data, and to discuss future cooperative works, in a friendly atmosphere. Oral presentations are basically made by selected scientists, but the meeting is open to a broad audience including PhD students and Post-docs. This will give young scientists the opportunity to listen to up to date talks, and meet and discuss with experts during the breaks. Just after this workshop, you can join the Extremophiles 2016 Kyoto congress (September 12-16). Abstract submission deadline: July 23, 2016.

Goldschmidt/DCO/Jamstec: IODP "T-Limit" Project Workshop - Expedition 370: T-Limit of the Deep Biosphere off Muroto
Please register online by June 21, 2016. Registration may close sooner if the maximum number of participants have registered. Participation is limited to 50 scientists (including guests, operators, etc.).

DCO Symposium in Yokohama: Deep Life, Deep Energy, Reservoirs and Flues, and Extreme Physics and Chemistry, June 26, 2016
Register by June 21, 2016.

IODP-USSP: Host An Ocean Discovery Lecture
Are you interested in having an Ocean Discovery Lecturer like C-DEBI researchers Andy Fisher and Jason Sylvan speak at your institution? We accept applications from any U.S. college, university, or nonprofit organization, and the application period is open until May 20, 2016.


Proposal Calls

DCO: Second Call for Proposals: Deep Energy Community
The Deep Energy Community (DEC) of the Deep Carbon Observatory invites proposals for short- term funding of projects and/or activities aimed at addressing the DEC’s decadal goals and/or strengthening the international DEC community and its abilities to generate funding for new and ongoing initiatives. The DEC is dedicated to quantifying the environmental conditions and processes from the molecular to the global scale that control the origins, forms, quantities and movements of reduced carbon compounds derived from deep carbon through deep geologic time. The DEC has identified a number of guiding questions and the DEC Steering Committee encourages submission of ideas for modest short-term support that will address these and other relevant / meritorious efforts with high potential to attract new funding. Examples of supported activities include 1) laboratory research, 2) travel to field sites to collect samples of key importance, 3) support of working groups and workshops to synthesize data for publication of Deep Energy research, and/or to develop interdisciplinary collaborations, 4) travel to work with collaborators on the preparation of new proposals, or 5) other activities that would advance Deep Energy Goals. Deadline July 20, 2016.

IODP: Apply to Sail: Expedition 370, T-Limit of the Deep Biosphere off Muroto
U.S.-affiliated scientists interested in participating in this expedition should apply to sail through the U.S. Science Support Program, by visiting The deadline to apply is June 10, 2016.

IODP: Call for Sample Requests, Expedition 365
Details for requesting samples/data can be found at: The deadline for requests is May 20, 2016.

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 call due June 01, 2016), related to the International Ocean Discovery Program (IODP).

Shell: Ocean Discovery XPRIZE
Regular registration deadline: June 30, 2016.


Bigelow: Postdoctoral Research Scientist 
The Bigelow Laboratory for Ocean Sciences is seeking a qualified and highly motivated individual for a postdoctoral research scientist position in the laboratory of Dr. Beth Orcutt. The research will be related to the study of the marine deep biosphere, focusing on the use of subseafloor observatories to study microbial processes, building off international ocean drilling program field sites on the Juan de Fuca Ridge flank, the Mid-Atlantic Ridge Flank and/or the Atlantis Massif. Highly successful candidates would have experience with environmental science and/or microbiology or biogeochemistry, with working knowledge of molecular biology techniques (such as DNA extraction, amplification, and sequencing or bioinformatics), microscopy, or stable isotope techniques considered as highly desirable. Applicants must have at least a Ph.D in marine sciences, oceanography, environmental microbiology or similar field with a proven publication record. Experience with project management or fieldwork also desired. Research will be conducted primarily at the Bigelow Laboratory for Ocean Sciences in East Boothbay, Maine, but opportunities may be available for fieldwork. The position is offered for two years. The position has an expected start date of September 2016, but this may be negotiated. Salary will be commensurate with prior experience. Review of applicants will begin immediately and proceed until the position is filled.

Rutgers University Deep Sea Microbiology Lab: Bioinformatics Postdoctoral Position
The postdoc will participate in a project to investigate the evolution of early and acquired metabolism in T. ammonificans, a thermophilic, chemolithoautotrophic bacterium that we isolated in my laboratory from a deep-sea hydrothermal vent. Experience with bioinformatics (and some microbiology background) is an essential requirement, as this project entails the analyses large sequence data. The position is available immediately and potential candidates should contact group leader Constantino Vetriani directly at

Montana State University, Thermal Biology Institute: Two Postdoctoral Scholar Positions Open
Applications will be reviewed starting March 21, 2016 and will continue until positions are filled.

IODP at Texas A&M: Assistant Research Scientist
We will begin reviewing applications on May 16, 2016, but will continue to accept applications until candidates are selected for interviews.

Station Biologique de Roscoff (SBR) 2 PhD positions 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!

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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