# Thermococcales
**Thermococcales** is an order of heterotrophic, hyperthermophilic archaea in the phylum Euryarchaeota that ferment peptides and carbohydrates and reduce elemental sulfur, and that live mainly in marine hydrothermal vents and shallow thermal springs.[1](https://academic.oup.com/femsre/article/37/2/182/623243) • [2](https://academic.oup.com/femsre/article/35/4/577/629194) The order is recognized in the Genome Taxonomy Database as o__Thermococcales.[3](https://onlinelibrary.wiley.com/doi/10.1002/9781118960608.obm00054) Because its members grow rapidly, tolerate extreme heat, and accept genetic manipulation, Thermococcales have become key model organisms for studying life at extreme temperatures.[4](https://pmc.ncbi.nlm.nih.gov/articles/PMC12713403/)
| Key fact | Detail |
|---|---|
| Classification | An order of Euryarchaeota; classically three genera, Pyrococcus, Thermococcus, and Palaeococcus[2](https://academic.oup.com/femsre/article/35/4/577/629194) |
| Metabolism | Obligate anaerobic heterotrophs that ferment peptides and carbohydrates and reduce elemental sulfur (S0) to H2S[1](https://academic.oup.com/femsre/article/37/2/182/623243) • [2](https://academic.oup.com/femsre/article/35/4/577/629194) |
| Fermentation products | On sugars such as maltose, mainly H2, CO2, and acetate[1](https://academic.oup.com/femsre/article/37/2/182/623243) |
| Key enzyme | Mbh, a 14-subunit membrane-bound [NiFe] hydrogenase that makes H2 while pumping ions, with an estimated yield of 0.3 mol ATP per mol H2[1](https://academic.oup.com/femsre/article/37/2/182/623243) |
| Genome | Single chromosome of roughly 1.5 to 3 Mbp; more than 30% of the predicted proteome has no assigned function[4](https://pmc.ncbi.nlm.nih.gov/articles/PMC12713403/) |
| Diversity | More than 40 reported species, mostly in the genus Thermococcus; a 2026 pangenome analysis resolved 70 species across five genus-level clades[5](https://pmc.ncbi.nlm.nih.gov/articles/PMC3737323/) • [6](https://sciety.org/articles/activity/10.64898/2026.09.28.752058) |
| Biotechnology | Described as superior organisms for dark fermentative hydrogen production[7](https://www.sciencedirect.com/science/article/abs/pii/S073497501830168X) |
## Classification and diversity
The order was built around two genera, *Thermococcus* (Zillig et al., 1983) and *Pyrococcus* (Fiala & Stetter, 1986), with *Palaeococcus* (Takai et al., 2000) added later.[2](https://academic.oup.com/femsre/article/35/4/577/629194) 16S rRNA sequencing showed that *Palaeococcus* represents a lineage that likely diverged early in the evolution of the order, perhaps preceding both *Thermococcus* and *Pyrococcus*.[4](https://pmc.ncbi.nlm.nih.gov/articles/PMC12713403/) The first *Thermococcus* described was *T. celer*; many species have followed, including *T. kodakarensis*, *T. gammatolerans*, *T. barophilus*, *T. onnurineus*, and *T. sibiricus*.[4](https://pmc.ncbi.nlm.nih.gov/articles/PMC12713403/) Most species described so far belong to *Thermococcus*, which includes freshwater as well as marine isolates.[4](https://pmc.ncbi.nlm.nih.gov/articles/PMC12713403/)
**Genome-based revision.** [Classification](https://www.edgepedia.org/classification) criteria have changed over time; for example, *Pyrococcus kodakaraensis* was reclassified as *Thermococcus kodakaraensis* before the species spelling was corrected to *kodakarensis*.[4](https://pmc.ncbi.nlm.nih.gov/articles/PMC12713403/) A 2026 pangenome analysis combining genome-scale metrics resolved 70 species across five genus-level clades, proposing the new genera *Oleococcus* and *Piezococcus* alongside the canonical *Pyrococcus*, *Palaeococcus*, and *Thermococcus*.[6](https://sciety.org/articles/activity/10.64898/2026.09.28.752058)
## Metabolism
Thermococcales are obligate anaerobes and heterotrophs that assimilate amino acids, peptides, pyruvate, and oligosaccharides, coupled with sulfur reduction or hydrogen fermentation.[2](https://academic.oup.com/femsre/article/35/4/577/629194) During growth on sugars such as the disaccharide maltose, the main fermentation products are H2, CO2, and acetate; the absence of lactate or ethanol indicates that all reducing equivalents are disposed of as H2.[1](https://academic.oup.com/femsre/article/37/2/182/623243) Many species can also grow on carbohydrates without sulfur present.[1](https://academic.oup.com/femsre/article/37/2/182/623243)
**Modified glycolysis.** Sugar degradation runs through a modified Embden-Meyerhof pathway in which the classical enzymes glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and phosphoglycerate kinase (PGK) are replaced by a single ferredoxin-linked enzyme, glyceraldehyde-3-phosphate ferredoxin (iron-sulfur protein carrying electrons in cell metabolism) oxidoreductase (GAPOR), which does not generate ATP by substrate-level phosphorylation.[1](https://academic.oup.com/femsre/article/37/2/182/623243) [Ferredoxin](https://www.edgepedia.org/ferredoxin) is the electron acceptor for all oxidative steps; because its redox potential (−480 mV) lies below that of the H2/H+ couple (−420 mV), hydrogen production with ferredoxin as donor is thermodynamically favorable.[1](https://academic.oup.com/femsre/article/37/2/182/623243) Peptide fermentation uses transaminases and glutamate dehydrogenase together with ferredoxin-linked oxidoreductases not found in mesophilic organisms.[8](https://pubmed.ncbi.nlm.nih.gov/7747936/)
**Formate as an alternative outlet.** Some Thermococcales strains produce formate in the presence of H2 as an alternative to sulfur reduction for disposing of reducing equivalents, using membrane-bound formate-dependent hydrogenases and formate dehydrogenases.[9](https://academic.oup.com/ismej/article/15/12/3423/7474403)
## Hydrogen and sulfur enzyme complexes
The enzyme responsible for H2 formation is the membrane-bound hydrogenase complex Mbh. In *Pyrococcus furiosus*, Mbh is encoded by a 14-gene cluster (PF1423-PF1436, MbhA-N), with MbhL as the catalytic subunit.[1](https://academic.oup.com/femsre/article/37/2/182/623243) Mbh is unique among [NiFe]-hydrogenases in that it both generates molecular H2 and uses the energy of that exergonic reaction to create an ion gradient (H+ or Na+) across the membrane; it has been postulated to represent the simplest form of respiration in modern metabolism.[1](https://academic.oup.com/femsre/article/37/2/182/623243) Ion pumping recovers some of the ATP lost through the missing phosphorylation step of glycolysis, at an estimated 0.3 mol ATP per mol H2 formed.[1](https://academic.oup.com/femsre/article/37/2/182/623243) Deletion studies in *T. kodakarensis* show that Mbh is essential for growth in the absence of S0, when no other route exists for recycling ferredoxin.[1](https://academic.oup.com/femsre/article/37/2/182/623243)
**Mbx and sulfur reduction.** *P. furiosus* also carries a 13-gene cluster, Mbx, highly homologous to Mbh, with a distinct role in S0-dependent growth.[1](https://academic.oup.com/femsre/article/37/2/182/623243) Adding sulfur down-regulates the hydrogenase genes and up-regulates genes for sulfur reduction, including Mbx and the CoA-dependent NADPH elemental sulfur reductase (Nsr).[1](https://academic.oup.com/femsre/article/37/2/182/623243) Mutant data separate the two: deleting MbxL cut cell yield in sulfur-grown cultures by about 70% and eliminated sulfide production above background, while the Nsr deletion showed no obvious growth phenotype, demonstrating that Mbx is an essential component of the S0 reduction system and Nsr is not.[1](https://academic.oup.com/femsre/article/37/2/182/623243) Mbh and Mbx are thus analogous complexes that re-oxidize reduced ferredoxin in the absence and presence of sulfur, respectively.[1](https://academic.oup.com/femsre/article/37/2/182/623243) Two soluble S0-reducing enzymes, sulfhydrogenase and sulfide dehydrogenase, have also been purified from the cytoplasm of a hyperthermophile able to grow with or without sulfur.[8](https://pubmed.ncbi.nlm.nih.gov/7747936/)
## Genomes and mobile elements
*Pyrococcus horikoshii* became the first member of the order with a complete genome sequence in 1998, revealing that nearly half of its roughly 1,000 genes had no obvious homologs outside the Thermococcales.[4](https://pmc.ncbi.nlm.nih.gov/articles/PMC12713403/) Thermococcales carry a single chromosome of about 2 Mb encoding an average of 2,100 proteins, and complete genomes range from about 1.5 to 3 Mbp; despite hundreds of complete genomes, the function of more than 30% of the predicted proteome remains unknown.[10](https://pmc.ncbi.nlm.nih.gov/articles/PMC4640148/) • [4](https://pmc.ncbi.nlm.nih.gov/articles/PMC12713403/) Comparative genomics shows extensive chromosome shuffling mediated by mobile genetic elements, with highly divergent genomes and little synteny beyond a few operons.[5](https://pmc.ncbi.nlm.nih.gov/articles/PMC3737323/) Viral-host interactions have left a marked genomic footprint, including plasmids, expanded CRISPR arrays, and retained viral genomes; natural plasmids of some model strains have been repurposed into expression platforms for ectopic protein production.[4](https://pmc.ncbi.nlm.nih.gov/articles/PMC12713403/)
## Habitats
The majority of Thermococcales have been isolated from shallow marine thermal springs or deep-sea hydrothermal vents, with exceptions such as the freshwater *Thermococcus waiotapuensis*.[2](https://academic.oup.com/femsre/article/35/4/577/629194) Their abundance in hot aquatic ecosystems, with more than 40 reported species, has made them model organisms for hyperthermophiles in many laboratories.[5](https://pmc.ncbi.nlm.nih.gov/articles/PMC3737323/)
## Model system and biotechnology
Early work in the 1980s isolated vent species that grew rapidly, tolerated extreme heat, and metabolized diverse substrates, making them amenable to laboratory study; their thermostable enzymes and emerging genetic tools supported research on [DNA replication](https://www.edgepedia.org/dna-replication), repair, and transcription at temperatures that challenge most life.[4](https://pmc.ncbi.nlm.nih.gov/articles/PMC12713403/) Early genome availability for three *Pyrococcus* species promoted transcriptomics, proteomics, and structural genomics.[2](https://academic.oup.com/femsre/article/35/4/577/629194)
In biotechnology, Thermococcales have been called the superior organisms for dark fermentative biohydrogen production, with high hydrogen yields and production rates in continuous culture; a 2018 review suggested integrating Thermococcaceae into hydrogen production setups with cell retention systems that allow high biomass density.[7](https://www.sciencedirect.com/science/article/abs/pii/S073497501830168X) Most members of the order contain genes for at least one Mbh and one soluble hydrogenase, the enzymatic basis of their hydrogen metabolism.[11](https://pmc.ncbi.nlm.nih.gov/articles/PMC6454523/)
## References
1. [Schut, G. J., Boyd, E. S., Peters, J. W., Adams, M. W. W. (2013). The modular respiratory complexes involved in hydrogen and sulfur metabolism by heterotrophic hyperthermophilic archaea and their evolutionary implications. FEMS Microbiology Reviews 37(2):182–203.](https://academic.oup.com/femsre/article/37/2/182/623243)
2. [Model organisms for genetics in the domain Archaea: methanogens, halophiles, Thermococcales and Sulfolobales. FEMS Microbiology Reviews 35(4):577.](https://academic.oup.com/femsre/article/35/4/577/629194)
3. [Thermococcales. Wiley Online Library, eLS.](https://onlinelibrary.wiley.com/doi/10.1002/9781118960608.obm00054)
4. [Galyon et al. (2025). The Thermococcales as a model system: historical perspectives and emerging tools. PMC12713403.](https://pmc.ncbi.nlm.nih.gov/articles/PMC12713403/)
5. [Diversity of CRISPR systems in the euryarchaeal Pyrococcales. RNA 10:659. PMC3737323.](https://pmc.ncbi.nlm.nih.gov/articles/PMC3737323/)
6. [Thermococcales pangenome uncovers new genera and modular evolution (2026 preprint).](https://sciety.org/articles/activity/10.64898/2026.09.28.752058)
7. [Ergal et al. (2018). The physiology and biotechnology of dark fermentative biohydrogen production. Biotechnology Advances 36(8):2165–2186.](https://www.sciencedirect.com/science/article/abs/pii/S073497501830168X)
8. [Metabolism in hyperthermophilic microorganisms. PubMed 7747936.](https://pubmed.ncbi.nlm.nih.gov/7747936/)
9. [H2-dependent formate production by hyperthermophilic Thermococcales. The ISME Journal 15(12):3423.](https://academic.oup.com/ismej/article/15/12/3423/7474403)
10. [Comparative genomics reveals conserved positioning of essential genomic clusters in highly rearranged Thermococcales chromosomes. PMC4640148.](https://pmc.ncbi.nlm.nih.gov/articles/PMC4640148/)
11. [Biotechnology of extremely thermophilic archaea. PMC6454523.](https://pmc.ncbi.nlm.nih.gov/articles/PMC6454523/)
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*Topic: Encyclopedia › Life and health › Microorganisms and fungi › Archaea › Archaeal taxonomy and diversity › Euryarchaeota › Thermococci and Archaeoglobi taxa › Thermococcales order-level systematics*
*Initially written Sep 17, 2026 · Reviewed: Oct 21, 2026 · Edited: Oct 11, 2026; Oct 15, 2026; Oct 21, 2026 · Last review: Oct 21, 2026*
*Copyright 2026 EdgeChat AI, a subsidiary of Biostate AI.*
License: Edgepedia Community License 1.0, https://www.edgepedia.org/edgepedia/license