Characterization of the taxonomic composition and physiological status of natural eukaryotic phytoplankton communities

Contributing around half of global primary production, phytoplankton are a central component to ocean biogeochemical cycles. Changes in physiological status can alter phytoplankton growth, productivity and elemental stoichiometry and consequently affect food web dynamics and the extent of carbon export. The growth of harmful algal bloom species can have substantial ecological and economical impacts. Recent studies have also shown specific phytoplankton can contribute disproportionally to carbon export. Therefore, a complete understanding of the coupling between phytoplankton physiology and taxonomic composition with their environmental surroundings is necessary to decipher their roles in shaping ocean ecology and biogeochemistry. By measuring the abundance of genes and transcripts within phytoplankton, novel molecular approaches are providing a new means to explore their functional and taxonomic profiles within naturally mixed assemblages. The focus of my dissertation is to develop and implement environmental genomics techniques, in combination with conventional taxonomic identification and rate measurements, to provide new insights on eukaryotic phytoplankton metabolic activities and diversity within their natural setting. Algal blooms have become a major nuisance in many estuarine and coastal marine systems worldwide. However, the cellular level changes that occur in blooming algal remain largely unknown. Using metatranscriptomics, we develop a comparative analysis to investigate the underlying molecular mechanisms associated with blooming phytoplankton. Increased expression of genes involved in carbon metabolism, transporters and synthesis of cellular membrane components are indicative of rapidly growing cells, increased nutrient demands and imply bacterial cultivation under bloom condition. Our findings elucidate the molecular mechanisms leading to harmful algal bloom formation and provide potential molecular targets for forecasting future bloom events. Using 18S rDNA amplicon sequencing approaches, I compared results using high-throughput DNA and RNA sequencing techniques to conventional taxonomic identification measures and found inconsistencies among methods in representing phytoplankton composition that should be considered by environmental managers. Furthermore, I identify a major bias in 18S rDNA amplicon sequencing in that eukaryotic plankton may have high variability in gene copy numbers which can lead to highly distorted representations of phytoplankton communities. My findings provide proof of concept for 18S rDNA gene copy number estimates through a read-depth approach and emphasize the importance of incorporating 18S copy number variation in phytoplankton compositional studies. Finally, I revisited phytoplankton biomass and primary productivity in one of the most well-characterized oceanic regions, and provided new estimates of phytoplankton gross primary productivity in Northeast Pacific during summer months. With further sequencing efforts, my findings will aid in elucidating phytoplankton’s role in regulating carbon flux. Collectively, my research has led to improvements on current knowledge of the phytoplankton responses to environmental changes and has provided guidance for further ecosystem management efforts through the utilization of environmental sequencing approaches.Doctor of Philosoph