C-DEBI Newsletter – February 15, 2017
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Message from the Director

Our 2017 Networked Speaker Series speakers have been selected!  Please mark your calendars for this online seminar series to connect all of us interested "deeply" or broadly in the deep biosphere. Next month's talk is by Dr. Annie Rowe at the University of Southern California, who will present "Eating rocks! Investigating microbial energy conservation with microbes that utilize solid mineral electron donors" on 3/9/17 at 9:30AM Hawaii Time/12:30PM PST/3:30PM EST. 

Congratulations to the proponents of proposals selected for funding in our 2016 December call for research and education grants and fellowships. Stay tuned on our funded projects webpage for their exciting work in Phase 2 of C-DEBI!

  • Graduate Fellowship: Lilja Strang (Advisor: Craig Moyer, Western Washington University)
    Insights into the genomics of deep subsurface vs. near surface Thermococcus isolates
  • Postdoctoral Fellowship: Jeanine Ash (Advisor: Caroline Masiello, Rice University)
    Tracing deep biosphere methane cycling with clumped isotopes
  • Postdoctoral Fellowship: Jesse Colangelo-Lillis (Advisor: Boswell Wing, University of Colorado Boulder)
    MEGA Analogue for Subsurface Sedimentary In-Vivo Evolution (MASSIVE) Plate
  • Postdoctoral Fellowship: Abhiney Jain (Advisor: Jeff Gralnick, University of Minnesota)
    Taming a Zetaproteobacteria using genetics to understand iron cycling in the deep ocean biosphere: Mariprofundus ferrooxydans PV-1 as a model organism
  • Postdoctoral Fellowship: Alma Parada (Advisor: Anne Dekas, Stanford University)
    Linking genetic diversity in benthic marine archaea to functional variability and contributions to carbon cycling
  • Research Grant: John Dore and Eric Boyd, Montana State University
    Microbial anabolism in subseafloor sediments of the North Atlantic subtropical gyre: carbon vs. phosphorus limitation
  • Research Grant: Dionysis Foustoukos and Costantino Vetriani, Carnegie Institution of Washington and Rutgers University
    Symbiotic Growth of Piezophilic Deep-sea Vent Bacteria
  • Research Grant: Jessica Labonte and Peter van Hengstum, Texas A&M University Galveston
    Subseafloor prokaryotic and viral communities and interactions in anoxic marine basins: a case study from a 3000-year old stratigraphic succession
  • Education Grant: Sharon Cooper, LDEO-Columbia University
    Stories from the Deep Biosphere: An Interactive Science Experience

We anticipate our next call to be due in December, and we look forward to receiving another strong group of proposals.  And good luck to all with your NSF proposals due today!  


Jan Amend
C-DEBI Director



Frontiers in Microbiology
Improved measurement of extracellular enzymatic activities in subsurface sediments using competitive desorption treatment NEW!
Adrienne Hoarfrost*, Rachel Snider and Carol Arnosti
*C-DEBI Contribution 355

Extracellular enzymatic activities initiate microbially-driven heterotrophic carbon cycling in subsurface sediments. While measurement of hydrolytic activities in sediments is fundamental to our understanding of carbon cycling, these measurements are often technically difficult due to sorption of organic substrates to the sediment matrix. Most methods that measure hydrolysis of organic substrates in sediments rely on recovery of a fluorophore or fluorescently-labeled target substrate from a sediment incubation. The tendency for substrates to sorb to sediments results in lower recovery of an added substrate, and can result in data that are unusable or difficult to interpret. We developed a treatment using competitive desorption of a fluorescently-labeled, high molecular weight organic substrate that improves recovery of the labeled substrate from sediment subsamples. Competitive desorption treatment improved recovery of the fluorescent substrate by a median of 66%, expanded the range of sediments for which activity measurements could be made, and was effective in sediments from a broad range of geochemical contexts. More reliable measurements of hydrolytic activities in sediments will yield usable and more easily interpretable data from a wider range of sedimentary environments, enabling better understanding of microbially-catalyzed carbon cycling in subsurface environments.

Proceedings of the IODP Volume 357
Atlantis Massif Serpentinization and Life
Früh-Green, G.L., Orcutt, B.N., Green, S.L., Cotterill, C., and the Expedition 357 Scientists

International Ocean Discovery Program (IODP) Expedition 357 successfully cored an east–west transect across the southern wall of Atlantis Massif on the western flank of the Mid-Atlantic Ridge (MAR) to study the links between serpentinization processes and microbial activity in the shallow subsurface of highly altered ultramafic and mafic sequences that have been uplifted to the seafloor along a major detachment fault zone. The primary goals of this expedition were to (1) examine the role of serpentinization in driving hydrothermal systems, sustaining microbial communities, and sequestering carbon; (2) characterize the tectonomagmatic processes that lead to lithospheric heterogeneities and detachment faulting; and (3) assess how abiotic and biotic processes change with variations in rock type and progressive exposure on the seafloor. To accomplish these objectives, we developed a coring and sampling strategy centered on the use of seabed drills—the first time that such systems have been used in the scientific ocean drilling programs. This technology was chosen in the hope of achieving high recovery of the carbonate cap sequences and intact contact and deformation relationships. The expedition plans also included several engineering developments to assess geochemical parameters during drilling; sample bottom water before, during, and after drilling; supply synthetic tracers during drilling for contamination assessment; acquire in situ electrical resistivity and magnetic susceptibility measurements for assessing fractures, fluid flow, and extent of serpentinization; and seal boreholes to provide opportunities for future experiments.

Limnology and Oceanography Methods
A simple and inexpensive technique for assessing contamination during drilling operations NEW!

André Friese, Jens Kallmeyer, Jan Axel Kitte, Ivan Montaño Martínez, Satria Bijaksana, Dirk Wagner, the ICDP Lake Chalco Drilling Science Team and the ICDP Towuti Drilling Science Team

Subsurface exploration relies on drilling. Normally drilling requires a drilling fluid that will infiltrate into the drill core. Drilling fluid contains non-indigenous materials and microbes from the surface, so its presence renders a sample unsuitable for microbiological and many other analyses. Because infiltration cannot be avoided, it is of paramount importance to assess the degree of contamination to identify uncontaminated samples for geomicrobiological investigations. To do this, usually a tracer is mixed into the drilling fluid. In past drilling operations a variety of tracers have been used, each has specific strengths and weaknesses. For microspheres the main problem was the high price, which limited their use to spot checks or drilling operations that require only small amounts of drilling fluid. Here, we present a modified microsphere tracer approach that uses an aqueous fluorescent pigment dispersion with a similar concentration of fluorescent particles as previously used microsphere tracers. However, it costs four orders of magnitude less, allowing for a more liberal use even in large operations. Its applicability for deep drilling campaigns was successfully tested during two drilling campaigns of the International Continental Drilling Program (ICDP) at Lake Towuti, Sulawesi, Indonesia, and Lake Chalco, Mexico. Quantification of the tracer requires only a fluorescence microscope or a flow cytometer. The latter allowing for high-resolution data to be obtained directly on-site within minutes and with minimal effort, decreasing sample processing times substantially relative to traditional tracer methods. This approach offers an inexpensive, rapid, but powerful alternative technique for contamination assessment during drilling campaigns.

Proposal Calls

NSF: Dimensions of Biodiversity Program Solicitation
Full proposal deadline date: February 21, 2017.

The National Academies: Gulf Research Program Early-Career Research Fellowships
Applications due February 22, 2017.

IODP: Apply to Sail: Expedition 381 Corinth Active Rift Development
The U.S. deadline to apply is March 3, 2017.

AGU: Nominate an individual for the Asahiko Taira International Scientific Ocean Drilling Research Prize
Nominations due March 15, 2017.

IODP: Apply to Sail on IODP Expedition 376
The deadline to apply is April 1, 2017.

IODP: Submit an IODP Drilling Proposal
Next Proposal Submission Deadline: April 3, 2017.

NSF: Arctic Sciences Program Solicitation
Proposals accepted anytime.

NSF: Tribal Colleges and Universities Program (TCUP) Program Solicitation
Preparing for TCUP Implementation proposals accepted anytime.

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).

C-DEBI: Rolling call for Research Exchange proposals

Education & Outreach

C-DEBI: Applications Now Open for the NSF REU: Community College Cultivation Cohort (C4)
Applications due TODAY, February 15, 2017.

Sigma Xi: 2017 Student Research Showcase
Project approval and registration deadline: February 22, 2017.

RGNO Ocean Discovery Camp - Namibia, April 12-May 12, 2017 NEW!
Who: For dedicated early career researchers who care about the Oceans: PhD candidates and honors MSc students majoring in one of the ocean science fields, professors, lecturers and active young scientists holding an equivalent advanced degree with specialization in oceanography. What: Work at sea, and conduct analyses in the laboratory. Sampling, sample preservation, designing and executing experiments, computer-supported exercises, lectures, paper discussions, model development. Application deadline: March 10, 2017.

C-DEBI: Community College Research Internship for Scientific Engagement (CC-RISE)
CC-RISE is an eight-week, paid, summer research internship program for community college students run by the Center for Dark Energy Biosphere Investigations. Students will gain firsthand exposure to the scientific process by working in a faculty-led research lab at the University of California Santa Cruz or at the Woods Hole Oceanographic Institution in Woods Hole, MA. In addition to research, students will participate in activities focusing on how to transition from a two-year college to a university and information on graduate school. At the end of the program, students will present their results to an audience of peers and mentors. Applications are due March 20, 2017 for UCSC and March 24, 2017 for WHOI.

NSF Advanced Training Program in Antarctica for Early-Career Scientists: Biological Adaptations to Environmental Change
Deadline for receipt of completed applications is April 17, 2017.


Meetings & Activities

Onshore-Offshore Drilling and Sampling to Understand Freshwater Resources along the New England Continental Shelf: An IODP-ICDP Workshop
The workshop is open to U.S. and international participants and the deadline to apply is February 17, 2017.

Register and submit abstracts for the 2017 SoCal Geobiology Symposium
Abstract submission is due March 3, 2017.

Geobiology 2017
Abstract deadline: March 15, 2017.

6th International Symposium on Chemosynthesis-Based Ecosystems (CBE6), Woods Hole, Massachusetts, USA, August 27 – September 1, 2017
Abstract submission deadline March 17, 2017.

The 4th International Conference of Geobiology — Rocks, life and climate, June 24-26, 2017, Wuhan, China NEW!
To explore the interaction among rocks, life and climate, we will to hold the 4th International Conference of Geobiology in 2017 at Wuhan, central China. Interaction and co-evolution between organisms and environments at critical periods of geological history and in modern days will be the subject of this meeting. Tentatively, symposia including one session on the deep biosphere are suggested, and more session proposals are encouraged. The deadline for abstract submission is April 1, 2017.

Call for Abstracts: Goldschmidt 2017, Paris, August 13-18
Abstract submissions are due April 1, 2017.

Aarhus University: International Workshop on "Marine Geomicrobiology" in Denmark
Deadline for applications is April 1, 2017.

IODP-USSSP: Call for IODP-ICDP Session Conveners at AGU 2017 Fall Meeting
The provisional dates of the call for session proposal are February 15th – April 19th, 2017.

ISSM 2017: Call for Abstracts
Abstracts due April 24, 2017.

C-DEBI: Rolling call for Community Workshop support


Shanghai Ocean University: Faculty Positions in Bioinformatics and Proteomics at HAST

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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