The GeoMICROBE sled in deployment. Image courtesy Brian Glazer.

Facilities, Equipment & Technology

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C-DEBI Shared Facilities and Equipment

Members of the C-DEBI community have access to a wide range of experimental, analytical, sequencing, field, sampling, and computer equipment that is housed in the laboratories of individual faculty members, in shared departmental facilities, or in core facilities and centers. Here, we list some of these laboratories and facilities, highlighting those that are most germane to the exploration of the subseafloor biosphere, but omitting some that are common at many institutions. We first list the equipment available at USC, starting with core facilities and centers, followed by shared facilities in the Departments of Biological Sciences and Earth Sciences, and then laboratories of individual faculty members, including C-DEBI Director (Amend) and several Collaborators (Heidelberg, Corsetti, Nealson, El-Naggar, Meng). C-DEBI members also have access to facilities and laboratories at our partner institutions; here, we list some of the most pertinent resources for subseafloor biosphere research available through ExCom members Huber (WHOI), D’Hondt (URI), Fisher (UCSC), and Wheat (UAF).

USC Core Facilities and Centers

  • USC Center for Electron Microscopy and Microanalysis (CEMMA)
  • USC DNA Sequencing Core/Molecular Genomics Core Facility/Epigenome Center
  • USC Translational Imaging Center (TIC) & Light Microscopy Imaging Center Resources
  • USC NanoBiophysics Core
  • USC W. M. Keck Photonic Laboratory
  • USC Robotic Embedded Systems Laboratory
  • Polymorphic Robotics Laboratory, The Information Sciences Institute (ISI)

USC Department of Earth Sciences Shared Facilities and Equipment

  • Paleomagnetism and Rock Magnetism Laboratory (PRML)

USC Department of Biological Sciences Shared Facilities and Equipment

  • Major Equipment
  • Trace metal clean laboratory – ICPMS

USC Faculty Laboratories

  • Dr. Jan Amend (Director), Departments of Earth Sciences and Biological Sciences
  • Dr. John Heidelberg (Collaborator), Department of Biological Sciences
  • Dr. Frank Corsetti (Collaborator), Department of Earth Sciences
  • Dr. Kenneth Nealson (Collaborator), Departments of Earth Sciences and Biological Sciences
  • Dr. Moh El-Naggar (Collaborator), Department of Physics & Astronomy
  • Dr. Ellis Meng (Collaborator), Department of Biomedical Engineering

Facilities and Laboratories at our Partner Institutions

  • Dr. Julie Huber (Associate Director), Woods Hole Oceanographic Institution
  • Dr. Steven D’Hondt (ExCom), University of Rhode Island
  • Dr. Andrew Fisher (ExCom), University of California, Santa Cruz
  • Dr. C. Geoffrey Wheat (ExCom), University of Alaska, Fairbanks

C-DEBI-Developed Equipment, Techniques and Technology

C-DEBI maintains a core goal of implementing effective pathways for facilitating intellectual exchange of knowledge, information, and application of new technologies to its various partners and the community at large. This philosophy includes the establishment of an open access policy for all of the new tools, innovations, laboratory techniques and software developed by C-DEBI. At the start of C-DEBI most of the technological advances were in the form of hardware, driven by a wave of sea-going operations that expanded the bounds of subseafloor observation and sample collection. C-DEBI is continuing its sea-going operations, but is now also expanding its developmental emphasis into laboratory advances. Below we list each of the new developments through C-DEBI. Finished developments are described in published literature, some complete with machine and electrical drawings. Other developments are ongoing by research scientists, engineers, students, post-doctoral fellows, and commercial enterprises. Some of the developments are now available commercially and others have potential commercial value.

Sensors

  • DEBI-DOT
  • DEBI-t and DEBI-pt
  • Well-Head Flow Meter
  • Miniaturized E-Chem Sensors

Samplers

  • GeoMICROBE Sled
  • The Mobile Pumping and Sampling system (MPS) and Medium Volume Bag Sampler (MVBS)
  • OsmoSampler derivatives such as the Flow-Through Osmo Colonization System (FLOCS), the Enrichment OsmoSampler, and the Biological OsmoSampler System (BOSS)
  • Mega-Fast Flow Osmo pump
  • Syringe-based fluid samplers
A. %image_alt% B. %image_alt% C. %image_alt%

Various C-DEBI inventions at use at North Pond. A. DEBI-DOT before deployment, B. GeoMicrobe Sled at North Pond CORK 1383C, and C. Deployment of CORK-LITE at North Pond.

Platforms

  • Subseafloor observatory systems (CORKs)
  • CORK-Lite
  • Jannasch Connector
  • DEBI-SELECT
  • Heat Flow Probe Insertion Guide
  • “Catalina” ROV

Laboratory Techniques

  • Sample processing for RNA and DNA characterization
  • Cathodic culturing
  • Heterotrophic enzyme activity measurement
  • High-pressure controls on microbial activity
  • Preparation of thin sections
  • IODP borehole gamma core log analysis

Computer Models and Software

  • Microbial activity simulation educational models
  • Cell abundance data analysis
  • Geochemical and hydrological calculation software

Additional Partnerships

Here, we list additional partnerships (in alphabetical order) outside of our primary partner institutions that provide experimental and educational expertise, and facilities that we have used in the past and will rely on in the future for investigations of the deep biosphere.

  • Aarhus University, Center for Geomicrobiology
  • The Agouron Institute
  • Deep Carbon Observatory (DCO)
  • International Continental Scientific Drilling Program (ICDP)
  • International Ocean Discovery Program (IODP)
  • Japan Agency for Marine Earth Science and Technology (JAMSTEC)
  • Monterey Bay Aquarium Research Institute (MBARI)
  • NASA Astrobiology Institute (NAI)
  • Ocean Observatory Initiative (OOI)
  • Schmidt Ocean Institute (SOI)
  • University of Bremen
  • USC Wrigley Institute for Environmental Studies (WIES)
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