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Genomic Insights and Ecological Adaptations of Deep-Subsurface and Near Subsurface Thermococcus Isolates
Date Permissions Signed
Date of Award
Department or Program Affiliation
Master of Science (MS)
Moyer, Craig L.
Schwarz, Dietmar, 1974-
Young, Jeff C. (Jeffery C.)
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
Subject – LCSH
Thermophilic microorganisms--Pacific Ocean--Genetics; Hydrothermal vent ecology--Pacific Ocean
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Strang, Lilja Caitlin, "Genomic Insights and Ecological Adaptations of Deep-Subsurface and Near Subsurface Thermococcus Isolates" (2020). WWU Graduate School Collection. 926.