Fishing for Viruses in the Marine Environment

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Fishing for Viruses in the Marine Environment

• Shannon J. Williamson
• J. Craig Venter Institute
• January 23rd, 2009

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Overview

• The J. Craig Venter Institute (JCVI)
• Marine Research
• Microbial and Viral Ecology
• Metagenomics
• Where we sample
• Technology
• Surface water sampling
• Deep water sampling Large Volume Water Sampler
  (LVWS)

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J. Craig Venter Institute (JCVI)
I started here
JCVI East Rockville, Maryland
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J. Craig Venter Institute (JCVI)
and now Im here
JCVI West San Diego/La Jolla
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J. Craig Venter Institute (JCVI)
and someday here
Future JCVI West La Jolla
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JCVI - Organization
www.jcvi.org
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Marine Research

• Microbial/Viral Ecology
• Understand how microbes shape marine ecosystems
• Viruses, Bacteria and Eukaryotic phytoplankton
  (diatoms, dinoflagellates)
• Why? - Form the foundation of ALL marine
  ecosystems
• Metagenomics
• The study of genetic material recovered directly
  from environmental samples
• Collect microbes from various marine ecosystems
• Extract DNA and cut it up
• Sequence (Sanger, 454)
• Assembly put the puzzle pieces back together
• Analysis Who is there? What are they doing?

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Marine projects

• Global Ocean Sampling Expedition (GOS)
• Surface water profiling (5m)
• Objective Characterize marine microbial diversity

Sorcerer II
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Surface Water Sampling Sorcerer II
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Size Fractionation of Microbes
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Marine projects

• Deep Ocean (2,500 meters)
• Hydrothermal vents and surrounding cold waters
• Objective Size fractionate microbial community
  in-situ

Original Model
Current Model
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Evolution of the Large Volume Water Sampler (LVWS)

• Current Model
• Size fractionation of microbes and concentration
  of viruses 210 L
• DSPL battery (12V)
• 2 Seabird pumps (SBE 5T)
• Control panel (modified)
• Sampling port
• Silicone tubing
• One-way check valves
• Over-pressure valves
• 3 Stainless steel filter housings
• Pellicon (TFF)
• Tedlar bags
• 3 Nalgene boxes

• Original Model
• Water collection only 120 L
• DSPL battery (12V)
• Seabird pump (SBE 5T)
• Control panel
• Sampling port
• Gum rubber tubing
• One-way check valves
• Over-pressure valves
• Tedlar bags
• 2 Nalgene boxes

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Control panel
3-way valve
Nalgene box
CTD pump
Sampling port
One-way check valve
Honeycomb platform
Extra weights
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Filter housings
Battery
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Power cable
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Deployment
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Weights
Float pack
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Release
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Technical Challenges

• Time efficiency Transition for membrane
  filtration to virus concentration
• Requires ALVIN and consumes bottom time
• How can we make this automatic?
• Acoustical signal?
• Timers?
• Turning it off Low-tech approach dive weight
• Doesnt always work ruins the sample
• Alternatives?

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Acknowledgements

• University of Delaware
• Eric Wommack
• Craig Cray
• Art Sundberg
• Bekki Helton
• Shawn Polson
• Danielle Winget
• Shellie Bench

• JCVI
• Lisa Zeigler
• Kurt Williamson
• Doug Fadrosh
• UCSD/SIO
• Eddie Kisfaludy
• National Science Foundation
• Gordon and Betty Moore Foundation
• Department of Energy

• WHOI
• Gavin Eppard (ALVIN)

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Contact Information

• Email swilliamson_at_jcvi.org
• Phone [phone]