Date Awarded


Document Type


Degree Name

Doctor of Philosophy (Ph.D.)


Virginia Institute of Marine Science


Jian Shen

Committee Member

Mark J. Brush

Committee Member

Marjorie A.M. Friedrichs

Committee Member

Kimberly S. Reece

Committee Member

Kyeong Park


The spatial and temporal variability of phytoplankton biomass in estuaries is determined by both local processes and transport processes. Local processes include biological processes (e.g., photosynthesis, respiration/excretion, and grazing) and settling, whereas transport processes include advective and diffusive transports. Transport processes have been demonstrated to regulate phytoplankton dynamics significantly by distributing both phytoplankton and other dissolved and particulate substances (e.g., nutrients, salts, sediments, and chromophoric dissolved organic matter). Yet, these transport properties lack a framework that unifies the pieced description of their various effects, and quantification of their importance under various environmental conditions. This dissertation highlights the role of horizontal transport processes on phytoplankton dynamics in estuaries, including the initiation of harmful algal blooms (HABs). in Chapter 2, the flushing effect of transport processes and its interaction with local processes are exclusively examined, and its relative importance on the variability of phytoplankton biomass is quantified and compared to that of the local processes over timescales from hours to years, using an introduced concept of transport rate that can be numerically computed. in Chapter 3, a simple yet inclusive mathematical model is developed to examine the temporal and spatial variabilities in phytoplankton biomass in response to the various effects of physical transport, under nutrient and light limiting conditions. For estuaries whose dominant nutrient loading is from river input, three basic patterns are revealed for the relationships between phytoplankton biomass and flushing time under various environmental conditions. in Chapters 4 and 5, the flushing effect of transport processes on the initiation of harmful algal blooms (HABs) in estuaries is investigated, which is then applied to examine the location and timing of the initiation of an annual Cochlodinium (recently renamed Margalefidinium) polykrikoides bloom in the lower James River. Theoretical analysis shows that the flushing is the key factor that affects HAB initiation in multiple interconnected systems, and a relatively long period of time (weeks) is required for a successful bloom. A HAB tends to be observed first in locations with relatively long residence time, such as tributaries or areas with large eddies. Multiple unconnected originating locations can co-exist within an estuary that highly depends on hydrodynamics and salinity. A numerical module for C. polykrikoides bloom is developed and built into a 3D numerical model - EFDC, which considers the competitive advantages of C. polykrikoides such as mixotrophic growth, swimming, grazing suppression, and resting cyst germination. Numerical model results show that the flushing effect determines the origins of C. polykrikoides blooms in the lower James River, and the sub-tributary of Lafayette River, which is characterized by relatively long residence time, is favorable for the first bloom to occur, regardless of the cyst distribution. A further investigation of various environmental conditions for the C. polykrikoides bloom reveals that temperature and physical transport control the interannual variability in the timing of its initiation, and individual perturbations by southerly wind, heavy rainfall, and spring tide can cause strong flushing capable of interrupting, or even terminating, initiation of a HAB event in the lower James River.




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