# Pyrococcus abyssi
**Pyrococcus abyssi** is a hyperthermophilic, anaerobic euryarchaeon isolated from deep-sea hydrothermal vents in the [North Fiji Basin](https://www.edgepedia.org/north-fiji-basin) at a depth of 2,000 m, described by Erauso and colleagues in 1993 and kept as the type strain GE5 (also CNCM I-1302 and JCM 18155).[1](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=29292&mode=info) • [2](https://www.kegg.jp/kegg-bin/show_organism?org=T00024) It grows optimally near 96 °C, doubles in about 33 minutes, and has become a model organism for archaeal [DNA replication](https://www.edgepedia.org/dna-replication), genome maintenance, and the biotechnology of thermostable enzymes.[3](https://onlinelibrary.wiley.com/doi/full/10.1046/j.1365-2958.2003.03381.x)
| Key fact | Detail |
|---|---|
| Classification | Archaea; Methanobacteriota; Thermococci; Thermococcales; Thermococcaceae; *Pyrococcus*; type strain GE5[1](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=29292&mode=info) |
| Habitat | Hydrothermal vents, North Fiji Basin, SW Pacific, 2,000 m depth[2](https://www.kegg.jp/kegg-bin/show_organism?org=T00024) |
| Growth | 67–102 °C under atmospheric pressure, optimum 96 °C, doubling time 33 min; obligate anaerobe[3](https://onlinelibrary.wiley.com/doi/full/10.1046/j.1365-2958.2003.03381.x) • [4](https://bacdive.dsmz.de/strain/162185) |
| Pressure tolerance | Optimum 21 MPa, range below 0.1 to 40 MPa; tolerates up to 50 MPa[5](https://pmc.ncbi.nlm.nih.gov/articles/PMC2816203/) |
| Genome | 1,765,118 bp circular chromosome plus plasmid pGT5; 1,784 protein genes, 97 RNA genes; GC content 44.3 mol% (Tm) or 45.2 mol% (HPLC)[2](https://www.kegg.jp/kegg-bin/show_organism?org=T00024) • [6](https://www.jcm.riken.jp/cgi-bin/jcm/jcm_number?JCM=18155) |
| Replication enzymes | Two replicative DNA polymerases, family B (PabpolB) and family D (PabpolD), both likely required at the replication fork[7](https://pubmed.ncbi.nlm.nih.gov/15922358/) |
| Biotechnology | Pab B-family polymerase sold as Isis DNA polymerase, half-life 5 h at 100 °C[8](https://pmc.ncbi.nlm.nih.gov/articles/PMC6172850/) |
## Discovery and habitat
Strain GE5 was collected in 1989 and later cruises of the French-Japanese Starmer program, from smoker material and fluids sampled by the submersible Nautile at 2,000 m in the North Fiji Basin. Among about 20 isolates representing roughly six genomic species, GE5 was selected for full description because it carried a small multicopy plasmid, pGT5, and was named *P. abyssi* in 1993.[3](https://onlinelibrary.wiley.com/doi/full/10.1046/j.1365-2958.2003.03381.x) The species name and description are credited to Erauso et al. 1993, though the name has been effectively rather than validly published under the Bacteriological Code.[1](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=29292&mode=info)
**Pressure physiology.** The organism lives under about 22 MPa of hydrostatic pressure and tolerates up to 50 MPa, making it a piezotolerant deep-sea species in contrast to the shallow-vent *P. furiosus*, which grows best below 20 MPa.[5](https://pmc.ncbi.nlm.nih.gov/articles/PMC2816203/) Incubation under in situ pressure (20 MPa) or 40 MPa raises both the maximal and minimal growth temperatures by 4 °C, and pressure improves survival at lethal high temperatures of 106 to 112 °C.[9](https://journals.asm.org/doi/10.1128/aem.63.4.1230-1236.1997) Oxygen is toxic at growth temperatures, but cells survive several weeks at 4 °C, and starvation in minimal medium has little effect for at least a month at 4 °C.[9](https://journals.asm.org/doi/10.1128/aem.63.4.1230-1236.1997)
## Metabolism and growth
*P. abyssi* is an obligate heterotroph that ferments peptides or mixtures of amino acids, producing acetate, isovalerate, isobutyrate, propionate, hydrogen, and carbon dioxide, with hydrogen sulfide formed when elemental sulfur or cysteine is present.[3](https://onlinelibrary.wiley.com/doi/full/10.1046/j.1365-2958.2003.03381.x) In continuous culture in a gas-lift bioreactor, proteinaceous substrates such as peptone or amino acids in the presence of sulfur supported growth, whereas the disaccharides maltose and cellobiose did not.[10](https://pmc.ncbi.nlm.nih.gov/articles/PMC2685559/) It is a Gram-negative, highly motile coccus.[3](https://onlinelibrary.wiley.com/doi/full/10.1046/j.1365-2958.2003.03381.x)
## Genome
The complete genome of strain GE5 was sequenced at Genoscope in 1998 and released before formal publication, an early move that enabled the first experimental identification of a replication origin in any archaeon (a microbe group distinct from bacteria, often extremophile).[3](https://onlinelibrary.wiley.com/doi/full/10.1046/j.1365-2958.2003.03381.x) The circular chromosome is 1,765,118 bp with 1,784 protein-coding genes and 97 RNA genes, and the cell also carries the circular plasmid pGT5.[2](https://www.kegg.jp/kegg-bin/show_organism?org=T00024) A later re-annotation raised the gene count to 1,788 and cut the number of genes without assigned function from 864 to 580.[3](https://onlinelibrary.wiley.com/doi/full/10.1046/j.1365-2958.2003.03381.x) Comparison with the other two sequenced *Pyrococcus* species shows an average amino acid identity of 77% between *P. abyssi* and *P. horikoshii* orthologs and 72% between *P. abyssi* and *P. furiosus*, confirming that *P. abyssi* and *P. horikoshii* are the closer pair.[11](https://pmc.ncbi.nlm.nih.gov/articles/PMC311118/)
## DNA replication as a model system
*P. abyssi* is used as a model to understand the molecular basis of DNA replication.[12](https://pmc.ncbi.nlm.nih.gov/articles/PMC6559790/) [Two-dimensional gel electrophoresis](https://www.edgepedia.org/two-dimensional-gel-electrophoresis) positioned a single replication origin (oriC) within 1 kb of chromosomal DNA, physically linked to the cdc6 gene, and chromatin immunoprecipitation showed that Cdc6 and MCM proteins bind preferentially to the origin in growing cells.[13](https://pmc.ncbi.nlm.nih.gov/articles/PMC58699/)
**Two replicative polymerases.** The genome encodes two replicative DNA polymerases, the family B enzyme PabpolB and the family D enzyme PabpolD, both functionally and structurally characterized.[12](https://pmc.ncbi.nlm.nih.gov/articles/PMC6559790/) Biochemical work showed that PolD is a primer-directed polymerase regardless of primer composition, whereas PolB uses only DNA primers; PolD requires the sliding clamp PabPCNA for efficient synthesis while PolB does not; PolD alone shows strand displacement activity, and both enzymes gain it in the presence of PCNA. The authors concluded that archaea likely require two DNA polymerases at the replication fork.[7](https://pubmed.ncbi.nlm.nih.gov/15922358/) Both enzymes carry exonuclease domains and high nucleotide selectivity, and PolB has been described as one of the most accurate and processive enzymes known.[12](https://pmc.ncbi.nlm.nih.gov/articles/PMC6559790/) A 2025 fidelity analysis found PolD, the major replicative polymerase in *P. abyssi*, has about 6-fold lower fidelity than the accessory PolB.[14](https://academic.oup.com/nar/article/53/21/gkaf1143/8328382)
**Damage tolerance.** The organism shows extreme resistance to ionizing radiation and withstands a moderate level of genomic abasic site damage, about 25 abasic sites per 100,000 bp.[12](https://pmc.ncbi.nlm.nih.gov/articles/PMC6559790/) Both replicative polymerases stall at abasic sites, but PolB can incorporate opposite the damage and complete full-length synthesis under running-start conditions, while PolD bypass is strictly inhibited; exonuclease-deficient versions of both enzymes show effective translesion synthesis, tying the block to proofreading.[15](https://pubmed.ncbi.nlm.nih.gov/18826407/) PolB and PolD also slip in vitro during replication of templates carrying hairpin structures and short direct repeats, a mechanism that can produce microsatellite instability.[16](https://pmc.ncbi.nlm.nih.gov/articles/PMC4134008/)
## Biotechnological enzymes
The B-family DNA polymerase from *P. abyssi*, marketed as Isis DNA polymerase, has a half-life of 5 hours at 100 °C and, like other archaeal B-family polymerases, carries 3′–5′ proofreading exonuclease activity with an error rate about tenfold lower than [Taq polymerase](https://www.edgepedia.org/taq-polymerase).[8](https://pmc.ncbi.nlm.nih.gov/articles/PMC6172850/) Replacing Mg²⁺ with Ca²⁺ in the Pab reaction slows phosphodiester bond formation but improves nucleotide selectivity and eliminates exonuclease degradation of terminal nucleotides.[17](https://doi.org/10.3390/bioengineering10101150) The D-family polymerase has also been shown to be a suitable PCR enzyme.[18](https://pmc.ncbi.nlm.nih.gov/articles/PMC4148896/) A thermostable [DNA ligase](https://www.edgepedia.org/dna-ligase) from *P. abyssi* retains activity for 60 minutes at 90 °C, useful for nick-joining reactions in mutation detection.[8](https://pmc.ncbi.nlm.nih.gov/articles/PMC6172850/) Beyond DNA-processing enzymes, a carbamoyl phosphate synthetase from *P. abyssi* was cloned and expressed in *E. coli* to overcome codon-usage limits, and a recombinant nitrilase from the species has been reported as a potential biocatalyst for the pharmaceutical industry.[10](https://pmc.ncbi.nlm.nih.gov/articles/PMC2685559/) • [19](https://biolres.biomedcentral.com/track/pdf/10.1186/s40659-018-0186-3)
## References
1. [Pyrococcus abyssi Taxonomy Browser, NCBI](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=29292&mode=info)
2. [KEGG Genome: Pyrococcus abyssi GE5](https://www.kegg.jp/kegg-bin/show_organism?org=T00024)
3. [Cohen GN et al. (2003). An integrated analysis of the genome of the hyperthermophilic archaeon Pyrococcus abyssi. Molecular Microbiology](https://onlinelibrary.wiley.com/doi/full/10.1046/j.1365-2958.2003.03381.x)
4. [Pyrococcus abyssi JCM 18155, BacDive](https://bacdive.dsmz.de/strain/162185)
5. [Molecular evolution of the hyperthermophilic archaea of the Pyrococcus genus, PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC2816203/)
6. [JCM 18155 Catalogue entry](https://www.jcm.riken.jp/cgi-bin/jcm/jcm_number?JCM=18155)
7. [Henneke G et al. (2005). The hyperthermophilic euryarchaeota Pyrococcus abyssi likely requires the two DNA polymerases D and B for DNA replication. J Mol Biol](https://pubmed.ncbi.nlm.nih.gov/15922358/)
8. [Biotechnological applications of archaeal enzymes from extreme environments, PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC6172850/)
9. [Marteinsson VT et al. (1997). Physiological Responses to Stress Conditions and Barophilic Behavior of the Hyperthermophilic Vent Archaeon Pyrococcus abyssi. Appl Environ Microbiol](https://journals.asm.org/doi/10.1128/aem.63.4.1230-1236.1997)
10. [Perspectives on biotechnological applications of archaea, PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC2685559/)
11. [Genome Evolution at the Genus Level: Comparison of Three Complete Genomes of Hyperthermophilic Archaea, PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC311118/)
12. [The interplay at the replisome mitigates the impact of oxidative damage on the genetic integrity of hyperthermophilic Archaea, PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC6559790/)
13. [In vivo interactions of archaeal Cdc6/Orc1 and minichromosome maintenance proteins with the replication origin, PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC58699/)
14. [A, B, C, D's of replicative DNA polymerase fidelity, Nucleic Acids Research](https://academic.oup.com/nar/article/53/21/gkaf1143/8328382)
15. [Intrinsic properties of the two replicative DNA polymerases of Pyrococcus abyssi in replicating abasic sites, Molecular Microbiology](https://pubmed.ncbi.nlm.nih.gov/18826407/)
16. [Replication slippage of the thermophilic DNA polymerases B and D from the Euryarchaeota Pyrococcus abyssi, PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC4134008/)
17. [Direct Enzyme Engineering of B Family DNA Polymerases for Biotechnological Approaches, Bioengineering](https://doi.org/10.3390/bioengineering10101150)
18. [DNA polymerases as useful reagents for biotechnology, PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC4148896/)
19. [Biotechnological applications of archaeal enzymes from extreme environments, Biological Research](https://biolres.biomedcentral.com/track/pdf/10.1186/s40659-018-0186-3)
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*Topic: Encyclopedia › Life and health › Microorganisms and fungi › Archaea › Archaeal taxonomy and diversity › Euryarchaeota › Thermococci and Archaeoglobi taxa › Pyrococcus*
*Initially written Sep 17, 2026 · Reviewed: Sep 30, 2026; Oct 21, 2026 · Edited: Sep 30, 2026; Oct 11, 2026; Oct 15, 2026; Oct 21, 2026 · Last review: Oct 21, 2026*
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