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Date of Award

Fall 2023

Document Type

Masters Thesis

Department or Program Affiliation


Degree Name

Master of Science (MS)



First Advisor

Moyer, Craig L.

Second Advisor

Fullerton, Heather

Third Advisor

Arellano, Shawn M.


The microbiota of hydrothermal vents has been widely implicated in the dynamics of oceanic biogeochemical cycling. Lithotrophic organisms utilize reduced chemicals in the vent effluent for energy, which fuels carbon fixation, and their metabolic byproducts can then support higher trophic levels and high-biomass ecosystems. However, despite the important role these microorganisms play in our oceans, they are difficult to study. Most are resistant to culturing in a lab setting, so culture-independent methods are necessary to examine community composition. Targeted amplicon surveying, in which a marker gene is selected for DNA amplification, has become the standard practice for assessing the structure and diversity of hydrothermal vent microbial communities. The most commonly used marker gene is the small subunit ribosomal RNA (SSU rRNA) gene, due to its ubiquity across all cellular organisms and the presence of both conserved and variable regions. Here, the performance of primer pairs targeting the V3V4 and V4V5 variable regions of the SSU rRNA gene were assessed using environmental samples from microbial mats surrounding iron-dominated hydrothermal vents. Using the amplicon sequence variant (ASV) approach to taxonomic identification, the structure and diversity of microbial communities at Kamaʻehuakanaloa Seamount were elucidated in detail. Both primer pairs generated robust data and comparable alpha diversity profiles. However, several distinct differences in community composition were identified between primer sets, including differential relative abundances of both bacterial and archaeal phyla. The primer choice was determined to be a significant driver of variation among the taxonomic profiles generated. Based on the higher quality of the raw sequences generated and on the breadth of abundant taxa found using the V4V5 primer set, it is determined as the most efficacious primer pair for whole-community surveys of microbial mats at iron-dominated hydrothermal vents.




microbial mat communities, biogeochemical cycling, targeted amplicon surveys


Western Washington University

OCLC Number


Subject – LCSH

Microbial mats--Hawaii; Hydrothermal vents--Hawaii; Biogeochemical cycles--Hawaii; Biology--Classification

Geographic Coverage





masters theses




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