18S rRNA clone library of phytoplankton in the Columbia River and its coastal zone

1
18S rRNA clone library of phytoplankton in the
Columbia River and its coastal zone

• By Pete Kahn
• Mentors Lydie Herfort and
• Peter Zuber

http//www.mapwatch.com/news-blog/images/phytoplan
kton.jpg
2
Significance of phytoplankton

• Major producers
• O2 90
• CO2gtC3 50
• Base of aquatic food chain

3
Interactions with other Domains
Bacterioplankton Colonization POCgtDOC
Competition for NO32- and NH3?
http//www.fossilmuseum.net/Tree_of_Life/Domains_A
rchaea_Bacteria/Domains_of_life.jpg
4
Significance Why is CMOP interested in
Phytoplankton?

• Base of aquatic food chain
• Major producers O2 90 CO2gtC3 50
• Interaction with other two Domains
• -Crenarchaeota competition
• -Bacterioplankton colonization
• -POCgtDOC

Marine Phytoplankton bloom off the coast of
Argentina
http//www.mapwatch.com/news-blog/images/phytoplan
kton.jpg
5
Traditional Methods
Flow cytometry
Microscopy Pediastrium

• Microscopy
• Flow Cytometry
• Chlorophyll a
• Photosynthesis
• O2 production
• C14 uptake

http//upload.wikimedia.org/wikipedia/commons/c/c7
/Picoplancton_cytometrie.jpg
http//www.keweenawalgae.mtu.edu/ALGAL_IMAGES/chlo
rophyceans/Pediastrium_n16_dollartow3_402_c.jpg
Filtering for chlorophyll a
6
Objectives

• 18S rRNA clone library for different seasons and
  different locations 0 PSU, 30 PSU for spring and
  summer compare to winter samples
• Compare with Bacteria
• Archaea clone libraries from
• Dan Murphy
• Identify unexpected changes
• Monitor health of ecosystem

Pediastrium
http//www.keweenawalgae.mtu.edu/ALGAL_IMAGES/chlo
rophyceans/Pediastrium_n16_dollartow3_402_c.jpg
7
Methods Overview
Understand Phytoplankton community in estuary
Phylogenetic analysis
Sequence analysis w/ BLAST
Yan, Q. Y., Yu, Y. H. Feng, W. S. (2006).
Genetic fingerprinting of plankton community
provides new insights into aquatic ecology.
Progress in Natural Science 16, 893-898.
8
Methods Overview
Water sample gt Sterivex on site
Total nucleic acid extraction from sterivex in lab
Amplification through PCR
9
Variations in nucleic acid in environmental
samples
Oct 2006
Feb 2007

• Between seasons
• Between locations
• April Wecoma Forerunner Freshwater ltlt
  Surface Coastal

DNA
RNA