DOI: 10.25549/usctheses-c40-360936
title: Studies of protistan communities at large- and small-scales: global diversity, small-scale dynamics, and functional roles of mixotrophic algae

description: Protists are a hugely diverse group of organisms that perform a wide range of ecological roles, and are thus essential in ecosystem function and biogeochemical cycles. Their communities can have different impact in the ecosystem depending on what species are present, so a thorough understanding of the role of protistan communities in the ecosystem requires knowledge on the community composition, how it can vary, as well as the functional roles of individual members. This thesis first explored protistan species richness on a global scale, then investigated how community composition can vary on small temporal and spatial scales, and finally studied the functional roles of mixotrophs in the community with the goal of providing new insights into protistan community structure and function. ❧ The use of specific genes to characterize entire microbial communities has advanced tremendously over the last decade due to the advent of next generation sequencing (NGS), but few comparisons have been made as the field moves from using long but limited numbers of sequences generated from Sanger sequencing to the massive number of short sequences from NGS. Therefore, I obtained both Sanger and NGS sequences from the same DNA samples collected from a number of oceanic sites around the world, and in addition to comparing species compositions on a global scale, I also compared results yielded from the 2 different sequencing technologies. The sequence similarity threshold used to form operational taxonomic units (OTUs) and the presence of OTUs containing only 1 sequence (singleton OTUs) strongly influenced species richness estimated from NGS sequences, but did not affect the relative composition of different taxonomic groups. OTUs generated from NGS sequences may not have enough resolution to distinguish between species, as 1 NGS OTU contained sequences that matched perfectly to multiple OTUs generated from Sanger sequences. However, a comparison of beta diversity analysis using the 2 type of sequences led to similar interpretation of community structure. Therefore, I have demonstrated that short NGS sequences can provide holistic assessments of protistan communities. ❧ Studies on the small-scale variability in protistan community composition are rare even though protists can have rapid growth rates on the scale of days or even hours. Hence, I collected daily samples from the USC San Pedro Ocean Time-series (SPOT) station over 12 consecutive days, and an additional 16 closely located stations surrounding the SPOT station on 1 of the 12 sampling days. Communities collected 0 –12 km apart had an average similarity value of 63% while communities collected 1 – 9 days apart had an average similarity of 58%, and the similarity between communities tended to decrease as time between collection increased. However, comparison of my dataset to a 10-year monthly dataset collected at the same station indicated that communities collected within a small area or 12 days were significantly more similar to each other than the similarity between communities collected a month or more apart. Thus, small-scale variability was minor compared to monthly, seasonal, and interannual variability. ❧ Mixotrophic protists obtain nutrients and energy via multiple trophic modes (phototrophy and heterotrophy), and such flexibility in nutrition can confound their functional roles in the community as they can be either producers or consumers depending on the environment. I investigated how the availability of light and bacterial prey affected the gene expression of a freshwater mixotrophic chrysophyte, Ochromonas sp. strain BG-1. The growth of this species was similar with or without light as long as it had prey, and transcriptomic results corroborated their predominately phagotrophic nature as light had relatively low impact on their overall gene expression. I then examined how light and bacterial prey affected gene expression of a marine Ochromonas sp. strain CCMP1393 that is obligately phototrophic (will not grow in continuous darkness). Comparison of the transcriptomes between these two Ochromonas spp. revealed major differences in their carbon and nitrogen metabolism under the same environmental conditions. Strain BG-1 incorporated bacterial carbon through glycolysis, tricarboxylic acid cycle, and the enzyme phosphoenolpyruvate carboxykinase, and had reduced photosynthetic activities in the presence of prey. Contrastingly, strain CCMP1393 did not appear to incorporate bacterial carbon using the same processes as strain BG-1, and instead increased in photosynthetic activities in the presence of prey as indicated by the upregulation of genes related to photosynthesis, pigment synthesis, and carbon fixation. These results, therefore, implied that phagotrophy might enhance phototrophy in the obligately phototrophic strain CCMP1393. Overall, my studies provided molecular details on how resource availability affects the metabolism of two mixotrophic congeners, and how their functional roles in the community differ as a result of their contrasting nutritional strategies.