The vast majority of theses in this collection are open access and freely available. There are a small number of theses that have access restricted to the WWU campus. For off-campus access to a thesis labeled "Campus Only Access," please log in here with your WWU universal ID, or talk to your librarian about requesting the restricted thesis through interlibrary loan.

Date Permissions Signed


Date of Award

Winter 2020

Document Type

Masters Thesis

Department or Program Affiliation


Degree Name

Master of Science (MS)



First Advisor

Moyer, Craig L.

Second Advisor

Schwarz, Dietmar, 1974-

Third Advisor

Young, Jeff C. (Jeffery C.)

Fourth Advisor

Fullerton, Heather


Members of the Archaeal genus Thermococcus are sulfur-dependent hyperthermophiles found in hydrothermal vents throughout the world. Previous analysis of a Thermococcus culture collection containing isolates from the Juan de Fuca Ridge, Gorda Ridge, and South East Pacific Rise using amplified fragment length polymorphism analysis and multilocus sequence typing revealed a distinct clade of Thermococcus isolated from the 1996 megaplume event at Gorda Ridge, indicating that they originated from a deep-subsurface habitat. The aim of this study was to elucidate the functional adaptations that allow for the survival of the Gorda Ridge clade in a deepsubsurface habitat as compared to representative Thermococcus isolates from shallow subsurface environments. This was accomplished through a pangenomic analysis of representative isolates in this clade and others from this culture collection. The Gorda Ridge megaplume group was enriched for genes relating to DNA repair and stabilization including a predicted endonuclease distantly related to Archaeal Holliday junction resolvase, DNA mismatch repair ATPase mutS, CRISPR/Cas elements, and dnaK (hsp70). The group was also enriched for ABC-type branched-chain amino acid (BCAA) transport system, enzymes for the Shikimate pathway for aromatic amino acid synthesis, as well as TupA for tungstate transport. These findings suggest that Thermococcus inhabiting deep-subsurface fluid reservoir require the added ability to prevent and repair damage to their DNA, presumably due to the energy demands of DNA replication. The enrichment in BCAA and tungstate transporters may indicate the use of an amino acid catabolism pathway followed by fermentation catalyzed by the tungstopterin containing enzymes aldehyde ferredoxin oxidoreductase and alcohol dehydrogenase, suggesting a preference for peptides over carbohydrates as an energy source in the deep-subsurface.




archaea, microbiology, deep-sea, hydrothermal vents, thermococcus, transporters, CRISPR, tungsten


Western Washington University

OCLC Number


Subject – LCSH

Thermophilic microorganisms--Pacific Ocean--Genetics; Hydrothermal vent ecology--Pacific Ocean

Geographic Coverage

Pacific Ocean




masters theses




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.

Included in

Biology Commons