Date of Award


Document Type


Degree Name

Master of Science (MS)


College of Science and Mathematics



Thesis Sponsor/Dissertation Chair/Project Chair

Lee H. Lee

Committee Member

Meiyin Wu

Committee Member

Kirsten J. Monsen


Harmful algal blooms have been reported in many parts of the world affecting water quality, human and animal health. Timely intervention depends on early detection of bloom-forming algae and cyanobacteria. Water samples were collected from 15 northern New Jersey freshwater bodies and each processed through coarse (3.0um) and fine (0.45um) pore filters which were dried then frozen at -20°C. Five small discs punched from the filters were resuspended in 500ul water for microscopic observation. Many microorganisms-cyanobacteria and algae were detected, whose distinction and identification based on morphology was not conclusive. Two genes of interest (The cyanobacterial phycocyanin and the 16S rDNA genes) were selected for polymerase chain reaction (PCR) analysis using three primers. A quick DNA extraction protocol (using 5% chelex-100) was followed for rapid DNA extraction from filters for laboratory microorganism cultures and water samples from various freshwater bodies followed by PCR based assay. The cyanobacterial phycocyanin cpcBA IGS- intergenic spacer gene was amplified by a pair of primers specifically designed to amplify this gene in cyanobacteria. 16S rDNA gene was amplified by two pairs of primers-one pair was universal, amplifying the gene in all bacteria, cyanobacteria and phototrophs while the other pair was designed to specifically amplify the gene in phototrophs. Cyanobacteria and algae were detected through microscopy and PCR based assay. Results suggest that these primers can be used to quickly determine the presence of cyanobacteria and/or algae in water samples from various waterbodies.

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