Pyrobaculum

Pyrobaculum
Scientific classification
Domain:
Archaea
Kingdom:
Crenarchaeota
Phylum:
Crenarchaeota
Class:
Thermoprotei
Order:
Thermoproteales
Family:
Thermoproteaceae
Genus:
Pyrobaculum

Huber, Kristjansson & Stetter 1988
Type species
Pyrobaculum islandicum
Huber, Kristjansson & Stetter 1988
Species

Pyrobaculum is a genus of the Thermoproteaceae.

Description and significance

As its Latin name Pyrobaculum (the "fire stick") suggests, the archaeon is rod-shaped and isolated from locations with high temperatures. It is Gram-negative and its cells are surrounded by an S-layer of protein subunits.

P. aerophilum is a hyperthermophilic and metabolically versatile organism. Different from other hyperthermophiles, it can live in the presence of oxygen and grows efficiently in microaerobic conditions.

Pyrobaculum yellowstonensis strain WP30 was obtained from an elemental sulfur sediment (Joseph's Coat Hot Spring [JCHS], 80 °C, pH 6.1, 135 μM As) in Yellowstone National Park (YNP), USA and is a chemoorganoheterotroph and requires elemental sulfur and/or arsenate as an electron acceptor. Growth in the presence of elemental sulfur and arsenate resulted in the formation of thioarsenates and polysulfides. The complete genome of this organism was sequenced (1.99 Mb, 58% G+C content), revealing numerous metabolic pathways for the degradation of carbohydrates, amino acids, and lipids. Multiple dimethyl sulfoxide-molybdopterin (DMSO-MPT) oxidoreductase genes, which are implicated in the reduction of sulfur and arsenic, were identified. Pathways for the de novo synthesis of nearly all required cofactors and metabolites were identified. The comparative genomics of P. yellowstonensis and the assembled metagenome sequence from JCHS showed that this organism is highly related (∼95% average nucleotide sequence identity) to in situ populations. The physiological attributes and metabolic capabilities of P. yellowstonensis provide an important foundation for developing an understanding of the distribution and function of these populations in YNP.

Genome structure

The first Pyrobaculum species to be sequenced was P. aerophilum. Its circular genome sequence is 2,222,430 Bp in length and contains 2605 protein-encoding sequences (CDS).

Cell structure and metabolism

Under anaerobic conditions, the archaeon reduces nitrate to molecular nitrogen via the denitrification pathway. Most species grow either chemolithoautotrophically by sulfur reduction or organotrophically by sulfur respiration or by fermentation. Cells are rod-shaped with almost rectangular ends and are about 1.5–8 * 0.5–0.6 µm. Pyrobaculum is motile because of peritrichous or bipolar polytrichous flagellation, and its colonies are round and grey to greenish black. The species are either faculatively aerobic or strictly anaerobic. The growth was observed on yeast extract, peptone, extract of meat, but not on galactose, glucose, maltose, starch glycogen, ethanol, methanol, formamide, formate, malate, propionate, lactate, acetate, and casamino acids.

The first of the Pyrobaculum species to be genetically sequenced, P. aerophilum (rod-shaped, 3–8 * 0.6 µm), has a rare characteristic for an archaeon because it is capable of aerobic respiration (aerophilum = "air-loving"). This is evident from the fact that the archaeon grew only in the presence of oxygen when nitrate was absent. It produces colonies that are round and greyish yellow. It utilizes both organic (maximal cell densities were observed with complex organics such as yeast extract, meat extract, tryptone, and peptone as substrates) and inorganic compounds during aerobic and anaerobic respiration. Also, use of elemental sulphur for growth was observed. Further, P. aerophilum grows between 75 and 104 °C with an optimal growth temperature at 100 °C.

Ecology

To this date, the strains of Pyrobaculum have been isolated from neutral to slightly alkaline boiling solfataric waters and shallow marine hydrothermal systems. P. aerophilum was isolated from a boiling marine water hole at Maronti Beach, Ischia, Italy. Further studies show that P. aerophilum grows under strictly anaerobic conditions with nitrate as the electron acceptor.[1]

Phylogeny

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) [2] and National Center for Biotechnology Information (NCBI)[3]

16S rRNA-based LTP release 132 by The All-Species Living Tree Project[4] Annotree v1.2.0.[5][6] which uses the GTDB 05-RS95 (Genome Taxonomy Database).[7][8]
 
 

P. aerophilum

 
 
 

P. calidifontis

 
 
 
 

P. neutrophilum

 
 

P. ferrireducens

 
 
 
 

P. arsenaticum

 
 

P. oguniense

 
 
 
 
 
 
 

P. calidifontis Amo et al. 2008

 
 
 
 

P. islandicum Huber, Kristjansson & Stetter 1988

 
 

P. neutrophilum (Stetter & Zillig 1989) Chan, Cozen & Lowe 2012

 
 
 
 
 

P. aerophilum Völkl, Huber & Stetter 1996

 
 

P. ferrireducens Slobodkina et al. 2015

 
 
 
 

P. arsenaticum Huber et al. 2001

 
 

P. oguniense Sako, Nunoura & Uchida 2001

 
 
 
 
 

See also

  • Pyrobaculum asR3 small RNA

References

  1. ↑ See the NCBI webpage on Pyrobaculum. Data extracted from the "NCBI taxonomy resources". National Center for Biotechnology Information. Retrieved 2007-03-19.
  2. ↑ J.P. Euzéby. "Thermoproteaceae". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2021-05-15.
  3. ↑ Sayers; et al. "Thermoproteaceae". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2011-06-05.
  4. ↑ All-Species Living Tree Project."16S rRNA-based LTP release 132". Silva Comprehensive Ribosomal RNA Database. Retrieved 2015-08-20.
  5. ↑ "AnnoTree v1.2.0". AnnoTree.
  6. ↑ Mendler, K; Chen, H; Parks, DH; Hug, LA; Doxey, AC (2019). "AnnoTree: visualization and exploration of a functionally annotated microbial tree of life". Nucleic Acids Research. 47 (9): 4442–4448. doi:10.1093/nar/gkz246. PMC 6511854. PMID 31081040.
  7. ↑ "GTDB release 05-RS95". Genome Taxonomy Database.
  8. ↑ Parks, DH; Chuvochina, M; Chaumeil, PA; Rinke, C; Mussig, AJ; Hugenholtz, P (September 2020). "A complete domain-to-species taxonomy for Bacteria and Archaea". Nature Biotechnology. 38 (9): 1079–1086. bioRxiv 10.1101/771964. doi:10.1038/s41587-020-0501-8. PMID 32341564. S2CID 216560589.

Further reading

Scientific journals

Scientific books

Scientific databases


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