Genetic Characterization Of Microbial Eukaryotic Diversity And Metabolic Potential
Creators: name: Hu, Sarah K
Publisher: name: Zenodo
Year: 2018
Subjects: microbial eukaryotes
protist
microbial ecology
microbial diversity
tag-sequencing
18S rRNA gene
metatranscriptome

description: For questions, please contact sarah.hu@usc.edu.

<em>Associated publications:</em>


	<strong>Sarah K. Hu</strong>, Zhenfeng Liu, Alle A. Y. Lie, Peter D. Countway, Diane Y. Kim, Adriane C. Jones, Rebecca J. Gast, S. Craig Cary, Evelyn B. Sherr, Barry F. Sherr, &amp; David A. Caron. (2015). <em>Estimating Protistan Diversity using High-throughput Sequencing</em>. J Eukaryot Microbiol. 62(5): 688-693. doi:10.1111/jeu.12217.
	<strong>Sarah K. Hu</strong>, Victoria Campbell, Paige Connell, Alyssa Gellene, Zhenfeng Liu, Ramon Terrado, &amp; David A. Caron. <em>Protistan diversity and activity inferred from RNA and DNA at a coastal ocean site in the eastern North Pacific</em>. (2016). FEMS Microbiol Ecol. 92(4) doi: 10.1093/femsec/fiw050.
	<strong>Sarah K. Hu</strong>, Lisa Mesrop, Paige Connell, &amp; David A. Caron. <em>A Hard Day’s Night: Shifts in microbial eukaryotic activity in the North Pacific Subtropical Gyre</em>. In prep. Expected submission March 2018.
	<strong>Sarah K. Hu</strong>, Zhenfeng Liu, Harriet Alexander, Victoria Campbell, Paige Connell, Karla B. Heidelberg, Sonya Dyhrman, &amp; David A. Caron. <em>Shifting metabolic priorities among key protistan taxonomic groups within and below the euphotic zone</em>. In revision.


 

<strong>Dissertation Abstract</strong>:

Single-celled microbial eukaryotes (protists) mediate critical elemental transformations that support ecosystem function. An overarching goal in microbial ecology is to link the metabolic roles of individual microbes to food web structure, when will enable a better understanding of the biogeochemical processes driving marine ecosystems. The central goal of my dissertation work was to characterize protistan community structure and diversity in two regions in the Pacific Ocean: off the coast of California in the San Pedro Channel and northeast of Hawai’i in the North Pacific Subtropical Gyre. I used molecular techniques and bioinformatics to improve how we describe the diversity and activity of in situ protistan communities. By pairing traditional DNA-based tag sequencing with ribosomal RNA sequences, changes in protistan community structure and activity were found to correspond to depth, proximity to coastline, season, or time of day. Further, a metatranscriptome survey provided one of the first accounts of protistan physiological ecology across a depth gradient. Comparing transcript abundances (mRNA) among euphotic and sub-euphotic zone depths revealed the metabolic flexibility among key protistan lineages to rely on alternate metabolic modes/nutritional strategies (e.g. phototrophy at the surface, heterotrophy below the euphotic zone). This dissertation work addressed long-standing ecological questions regarding the metabolic roles of protists that we otherwise have no other way of observing in situ by using RNA-derived sequence information to characterize protistan diversity and metabolic potential. 

 

A Dissertation Presented to the Faculty of the

USC GRADUATE SCHOOL

UNIVERSITY OF SOUTHERN CALIFORNIA

In Partial Fulfillment of the Requirement for the Degree

DOCTOR OF PHILOSOPHY

(BIOLOGICAL SCIENCES)

MAY 2018