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 enhanced survival of the Gorda Ridge clade in the deep-subsurface as compared to representative Thermococcus isolates from shallow subsurface habitats. This was accomplished through a pangenomic analysis of isolates from within this clade along with other representatives 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). This group was also enriched for the 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. This suggests that Thermococcus populations inhabiting deep-subsurface fluid reservoirs require the 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.
The opportunity to sequence, analyze and compare genomes from within the Gorda Ridge megaplume group along with other Thermococcus isolates has revealed several functional adaptations unique to isolates from the deep-subsurface habitat. These functions largely represent either DNA repair mechanisms, high-temperature protein folding capabilities, and/or strategies for amino acid utilization.