Date of Award


Semester of Degree


Document Type

Open Access Dissertation

Degree Name

Ph.D. in Chemistry



Major Professor

Gregory Boyer

Steering Committee Member

John Hassett

Steering Committee Member

David Kieber

Steering Committee Member

Kimberly Schulz

Steering Committee Member

Kelley Donaghy


Multiple areas in Lake Ontario, labeled Areas of Concern (AOCs), have experienced impairments in use due to algal blooms. Cyanobacteria are of particular concern because many species produce metabolites that are toxic to humans and animals. One method for monitoring the distribution of cyanobacteria and other phytoplankton is the measurement of in vivo pigment fluorescence. Several commercial fluorometers were evaluated for their use in a shipboard flow-through system to provide real-time continuous data on chlorophyll and phycocyanin concentrations throughout the lake. These instruments feature both single-wavelength excitation in the Turner Designs AlgaeWatch and CyanoWatch and multi-wavelength excitation in the bbe FluoroProbe. To account for cellular and instrumental variability, in vivo pigment measurements needed to be calibrated using extracted pigment concentrations. A method was developed to optimize extraction of phycocyanin from cyanobacterial cells. Extraction in phosphate buffer with freeze-thaw cycles maximized extraction percentages and minimized chlorophyll coextraction. Chlorophyll calibration curves for the AlgaeWatch were split into two separate regressions for cyanobacteria and non-cyanobacteria based on cut-off phycocyanin fluorescence values. These split curves offered a better representation of the lower fluorescent response of cyanobacteria in both a laboratory and field setting. Pigment fluorometers were deployed on Lake Ontario as part of a flow-through system for seven weeklong cruises in the offshore and six short evaluations of the nearshore. Calibration curves allowed the successful conversion of relative in vivo chlorophyll data into extracted pigment concentrations, although there were some calibration issues when pigment concentrations were low in situ. Mapping of continuous chlorophyll measurements allowed for fine-scale illustrations of phytoplankton distribution. Higher concentrations in the nearshore were associated with the spring thermocline and river outlets. Algal growth in the offshore was very patchy. These findings indicate that in vivo pigment fluorescence, as part of a flow-through system, is an effective method for monitoring phytoplankton biomass as long as the instruments are calibrated appropriately post-deployment.