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Date of Award
Fall 2023
Document Type
Masters Thesis
Department or Program Affiliation
Biology
Degree Name
Master of Science (MS)
Department
Biology
First Advisor
Moyer, Craig L.
Second Advisor
Fullerton, Heather
Third Advisor
Arellano, Shawn M.
Abstract
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.
Type
Text
Keywords
microbial mat communities, biogeochemical cycling, targeted amplicon surveys
Publisher
Western Washington University
OCLC Number
1409332354
Subject – LCSH
Microbial mats--Hawaii; Hydrothermal vents--Hawaii; Biogeochemical cycles--Hawaii; Biology--Classification
Geographic Coverage
Hawaii
Format
application/pdf
Genre/Form
masters theses
Language
English
Rights
Copying of this document in whole or in part is allowable only for scholarly purposes. It is understood, however, that any copying or publication of this document for commercial purposes, or for financial gain, shall not be allowed without the author’s written permission.
Recommended Citation
Smith, Lindsey, "Complex Microbial Mat Communities Used to Assess Primer Selection for Targeted Amplicon Surveys" (2023). WWU Graduate School Collection. 1247.
https://cedar.wwu.edu/wwuet/1247