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18S rRNA clone library of phytoplankton in the Columbia River and its coastal zone. http://www.mapwatch.com/news-blog/images/phytoplankton.jpg. By Pete Kahn Mentors: Lydie Herfort and Peter Zuber. Significance of phytoplankton. Major primary producers: O 2 : 90%
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By Pete Kahn
Mentors: Lydie Herfort and
“Competition” for NO32- and NH3?
Filtering for chlorophyll a
Savin, M. C., Martin, J. L., LeGresley, M., Giewat, M. & Rooney-Varga, J. (2004). Plankton diversity in the Bay of Fundy as measured by
morphological andmolecular methods. Microbial Ecology 48, 51-65.
April: Wecoma & Forerunner: salinity gradient
Wecoma (CR4s, CR15s, CR30s, CR40s):
20-32 psu; coastal surface samples
Forerunner (St 1-5): estuary samples
0-20 psu, inc. of 5
June & July: Forerunner: 0 psu & 30 psu from estuary
Wecoma April 2007
Forerunner April 2007
Forerunner June 2007
Forerunner July 2007
-Good clone library of phytoplankton
-Determining good primers for isolating 18S rRNA
-Understand changes in populations between seasons and locations
-Better understand unexpected changes in
community: monitor ecosystem health
-Bacteria & Archaea relationships/ interactions (Dan Murphy)
-Better understanding of microbial ecosystem as
Asterionella formosa: most abundant diatom
April Wecoma & Forerunner: Freshwater << Surface Coastal
Water sample => Sterivex on site
Total nucleic acid extraction from sterivex in lab
Amplification through PCR
TOPO cloning/ transformation
96 well plates?
Plasmid isolation (Miniprep)
Water samples pass through sterivex filter
BLAST=> Clone library
DNA not removed
Gel after extraction & DNA removal
Gel after PCR
Diez, B., Pedros-Alio, C. & Massana, R. (2001). Study of genetic diversity of eukaryotic picoplankton in different oceanic regions by small-subunit rRNA gene cloning and sequencing. Applied and Environmental Microbiology67, 2932-2941.
-Selective: cells gain ampicillin resistance from
-Differential: cells w/plasmid insert turn white
cells w/ no insert turn blue
Gel from miniprep
St 4 (15 psu): Pseudopedinella elastica; Protperidinium leonis; Katablepharis japonica
CR4s (27 psu): Asterionella kariana*; Thalassiosira aestivalis*
CR 15s (20 psu): Thalassiosira pseudonana*:Sequences from April
Diatom: 1st to have genome sequenced
-Diatom; extremely abundant in temperate areas
-eutrophic freshwater diatom
-river diatom; areas of high conductivity