Using molecular techniques to explore the diversity, ecology and physiology of important protistan species, with an emphasis on the Prymnesiophyceae

• Main Author: Koid, Amy E.
• Format: Dataset
• Language: English
• Published: University of Southern California Digital Library (USC.DL) 2016
• Subjects: Marine and Environmental Biology; bioinformatics; transcriptomics; comparative transcriptomics; nutrient limitation; prymnesiophytes; Antarc*; Antarctica
• Online Access: https://dx.doi.org/10.25549/usctheses-c3-421640; https://digitallibrary.usc.edu/asset-management/2A3BF16ILKN9

Protists are diverse unicellular eukaryotes that are widespread and ecologically important in aquatic and terrestrial environments. As phototrophs, they can be responsible for a significant proportion of carbon fixation, and as heterotrophs they transfer organic matter higher up the food chain and also remineralize nutrients for further use by other organisms. Increasingly, more protistan species are being recognized as mixotrophs, which are able to function both as phototrophs and heterotrophs, but very little is known about the underlying physiology of this nutritional mode. In this dissertation, I investigated the effects of different 18S rRNA or rDNA sample processing techniques to evaluate both species diversity and activity of marine microbial eukaryotes at the San Pedro Ocean Time‐series (SPOT) off the coast of Los Angeles, CA. The results of this study indicated that some taxonomic groups that do not comprise significant fractions of 18S rRNA libraries may well be active and important components of the environment at sampling time. I also used a comparative transcriptomics approach to evaluate functional and physiological differences between the transcriptomes of four prymnesiophytes: Prymnesium parvum, Chrysochromulina brevifilum, Chrysochromulina ericina and Phaeocystis antarctica, the first three of which are mixotrophic species. My analysis revealed the presence of a set of core genes as well as differences in genes involved in secondary metabolite pathways. A larger comparison of gene content with other microbial eukaryotic groups revealed distinct differences in the distribution of functional genes among phototrophic, heterotrophic and mixotrophic species. Finally, I undertook a comparative transcriptomic analysis of P. parvum, a toxigenic, bloom‐forming mixotrophic species that is common in both marine and freshwater ecosystems. This species displayed a robust transcriptomic response when exposed to nitrogen (N) and phosphorus (P) limitation, relative to a nutrient‐replete condition. The response to N‐ and P‐limitation included the increased relative expression of transporters for nitrogen and phosphorus respectively. Additionally, genes involved in protein synthesis and turnover, TCA cycle and fatty acid synthesis were also relatively upregulated under both nutrient limited conditions. Under N‐limitation, genes involved in the intracellular processing of organic nitrogen were more highly expressed relative to the replete condition. Under P‐limitation, photosynthesis genes and polyketide synthase genes were more highly expressed than in the replete treatment. Together, these studies show how molecular data in the form of DNA or RNA sequences can reveal important insights for protistan species diversity and the molecular underpinnings of different nutritional modes and cellular and physiological responses to different nutrient conditions.