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{{Short description|Genus of archaea}}
{{more citations needed|date=July 2012}}
{{Automatic taxobox
| taxon = Pyrobaculum
| authority = Huber, Kristjansson & Stetter 1988
| type_species = ''Pyrobaculum islandicum''
| type_species_authority = Huber, Kristjansson & Stetter 1988
| subdivision_ranks = Species
| subdivision =
* ''[[Pyrobaculum aerophilum|P. aerophilum]]''
* ''[[Pyrobaculum arsenaticum|P. arsenaticum]]''
* ''[[Pyrobaculum calidifontis|P. calidifontis]]''
* ''[[Pyrobaculum ferrireducens|P. ferrireducens]]''
* ''[[Pyrobaculum igneiluti|P. igneiluti]]''
* ''[[Pyrobaculum islandicum|P. islandicum]]''
* ''[[Pyrobaculum neutrophilum|P. neutrophilum]]''
* ''[[Pyrobaculum oguniense|P. oguniense]]''
* ''[[Pyrobaculum organotrophum|P. organotrophum]]''
}}

'''''Pyrobaculum''''' is a [[genus]] of [[archaea]]ns in the family [[Thermoproteaceae]].

== Description and significance ==
As its Latin name ''Pyrobaculum'' (the "fire stick") suggests, the [[archaeon]] is rod-shaped and [[Isolation (microbiology)|isolated]] from locations with high temperatures. It is [[Gram-negative]] and its cells are surrounded by an [[S-layer]] of [[protein subunit]]s.

''P. aerophilum'' is a [[Hyperthermophile|hyperthermophilic]] and [[metabolic]]ally versatile organism. Different from other hyperthermophiles, it can live in the presence of [[oxygen]] and grows efficiently in [[microaerophile|microaerobic]] conditions.

''Pyrobaculum yellowstonensis'' [[Strain (biology)|strain]] WP30 was obtained from an [[sulfur|elemental sulfur]] [[sediment]] ([[Joseph's Coat Hot Spring]] [JCHS], 80 °C, [[pH value|pH]] 6.1, 135 [[Molar concentration|μM]] As) in [[Yellowstone National Park]] (YNP), USA and is a [[Chemotroph|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 [[thioarsenate]]s and [[polysulfide]]s. The complete [[genome]] of this organism was [[Sequencing|sequenced]] (1.99 [[Mega base pairs|Mb]], 58% [[G+C content]]), revealing numerous [[metabolic pathway]]s for the degradation of [[carbohydrate]]s, [[amino acid]]s, and [[lipid]]s. Multiple [[dimethyl sulfoxide]]-[[molybdopterin]] (DMSO-MPT) [[oxidoreductase]] [[gene]]s, which are implicated in the reduction of sulfur and arsenic, were identified. Pathways for the ''de novo'' synthesis of nearly all required [[Cofactor (biochemistry)|cofactors]] and [[metabolite]]s 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'' [[Population dynamics|populations]]. The [[Physiology|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 facultatively 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]], [[formic acid|formate]], [[malic acid|malate]], [[propionic acid|propionate]], [[Lactic acid|lactate]], [[acetic acid|acetate]], and [[casamino acid]]s.

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.

In stationary phase cultures, ''Pyrobaculum calidifontis'' cells were observed to aggregate.<ref>{{cite journal |last1=Amo |first1=T |last2=Paje |first2=ML |last3=Inagaki |first3=A |last4=Ezaki |first4=S |last5=Atomi |first5=H |last6=Imanaka |first6=T |title=Pyrobaculum calidifontis sp. nov., a novel hyperthermophilic archaeon that grows in atmospheric air. |journal=Archaea |date=2002 |volume=1 |issue=2 |pages=113–21 |doi=10.1155/2002/616075 |pmid=15803649|pmc=2685560 |doi-access=free }}</ref> The aggregation is likely to be mediated by archaeal bundling pili (ABP), which assemble into highly ordered bipolar bundles.<ref name=Wang2022PNAS>{{cite journal |last1=Wang |first1=F |last2=Cvirkaite-Krupovic |first2=V |last3=Krupovic |first3=M |last4=Egelman |first4=EH |title=Archaeal bundling pili of ''Pyrobaculum calidifontis'' reveal similarities between archaeal and bacterial biofilms. |journal=Proceedings of the National Academy of Sciences of the United States of America |date=2022 |volume=119 |issue=26 |pages=e2207037119 |doi=10.1073/pnas.2207037119 |doi-access=free |pmid=35727984 |pmc=9245690 |bibcode=2022PNAS..11907037W }}</ref> The bipolar nature of these bundles most likely arises from the association of filaments from at least two or more different cells. The component protein, AbpA, shows homology, both at the sequence and structural level, to the bacterial protein TasA, a major component of the extracellular matrix in bacterial [[biofilms]], contributing to biofilm stability.<ref name=Wang2022PNAS />

== 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.<ref name=NCBI></ref>

==Phylogeny==
The currently accepted taxonomy is based on the [[List of Prokaryotic names with Standing in Nomenclature]] (LPSN) <ref>{{cite web | author=J.P. Euzéby | url=https://lpsn.dsmz.de/genus/pyrobaculum | title=Pyrobaculum |access-date=2023-06-10 | publisher=[[List of Prokaryotic names with Standing in Nomenclature]] (LPSN)}}</ref> and [[National Center for Biotechnology Information]] (NCBI)<ref name=NCBI>{{cite web |author = Sayers|display-authors = etal| url=https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=2276&lvl=3&lin=f&keep=1&srchmode=1&unlock |title=Pyrobaculum |access-date=2023-06-10 |publisher=[[National Center for Biotechnology Information]] (NCBI) taxonomy database}}</ref>

{| class="wikitable"
|-
! colspan=1 | 16S rRNA based [[The All-Species Living Tree Project|LTP]]_06_2022<ref>{{cite web|title=The LTP |url=https://imedea.uib-csic.es/mmg/ltp/#LTP| access-date=10 May 2023}}</ref><ref>{{cite web|title=LTP_all tree in newick format| url=https://imedea.uib-csic.es/mmg/ltp/wp-content/uploads/ltp/LTP_all_06_2022.ntree |access-date=10 May 2023}}</ref><ref>{{cite web|title=LTP_06_2022 Release Notes| url=https://imedea.uib-csic.es/mmg/ltp/wp-content/uploads/ltp/LTP_06_2022_release_notes.pdf |access-date=10 May 2023}}</ref>
! colspan=1 | 53 marker proteins based [[Genome Taxonomy Database|GTDB]] 08-RS214<ref name="about">{{cite web |title=GTDB release 08-RS214 |url=https://gtdb.ecogenomic.org/about#4%7C |website=[[Genome Taxonomy Database]]|access-date=10 May 2023}}</ref><ref name="tree">{{cite web |title=ar53_r214.sp_label |url=https://data.gtdb.ecogenomic.org/releases/release214/214.0/auxillary_files/ar53_r214.sp_labels.tree |website=[[Genome Taxonomy Database]]|access-date=10 May 2023}}</ref><ref name="taxon_history">{{cite web |title=Taxon History |url=https://gtdb.ecogenomic.org/taxon_history/ |website=[[Genome Taxonomy Database]]|access-date=10 May 2023}}</ref>
|-
| style="vertical-align:top|
{{Clade|style=font-size:90%; line-height:90%
|label1=''Pyrobaculum''
|1={{clade
|1=''P. calidifontis'' Amo et al. 2008
|2={{clade
|1=''[[Pyrobaculum aerophilum|P. aerophilum]]'' Völkl, Huber & Stetter 1996
|2={{clade
|1={{clade
|1=''P. igneiluti'' Lee et al. 2017
|2={{clade
|1=''P. arsenaticum'' Huber et al. 2001
|2=''P. oguniense'' Sako, Nunoura & Uchida 2001
}}
}}
|2={{clade
|1=''P. neutrophilum'' (Stetter & Zillig 1989) Chan, Cozen & Lowe 2012
|2={{clade
|1=''P. ferrireducens'' Slobodkina et al. 2015
|2={{clade
|1=''P. islandicum'' Huber, Kristjansson & Stetter 1988
|2=''P. organotrophum'' Huber, Kristjansson & Stetter 1988
}}
}}
}}
}}
}}
}}
}}
|
{{Clade|style=font-size:90%; line-height:90%
|label1=''Pyrobaculum''
|1={{clade
|1=''P. calidifontis''
|2={{clade
|1={{clade
|1=''P. islandicum''
|2=''P. neutrophilum''
}}
|2={{clade
|1={{clade
|1=''[[Pyrobaculum aerophilum|P. aerophilum]]''
|2=''P. ferrireducens''
}}
|2={{clade
|1=''P. arsenaticum''
|2=''P. oguniense''
}}
}}
}}
}}
}}
|}

==See also ==
* [[Pyrobaculum asR3 small RNA]]
* [[List of Archaea genera]]

==References==
{{Reflist}}

==Further reading==
*{{cite journal | author = Jay, Z.J. | author2 = J.P. Beam | author3 = A. Dohnalkova | author4 = R. Lohmayer | author5 = B. Bodle | author6 = B. Planer-Friedrich | author7 = M. Romine | author8 = W. P. Inskeep | date= 2015 | title = Pyrobaculum yellowstonensis Strain WP30 Respires on Elemental Sulfur and/or Arsenate in Circumneutral Sulfidic Geothermal Sediments of Yellowstone National Park | journal = Appl. Environ. Microbiol. | volume = 81 | pages = 5907–5916 | pmid = 26092468| doi = 10.1128/AEM.01095-15 | issue = 17| pmc = 4551270 | bibcode = 2015ApEnM..81.5907J | doi-access = free }}
* {{cite journal | title = The distribution, diversity, and importance of 16S rRNA gene introns in the order Thermoproteales. | author=Jay ZJ and Inskeep WP. | journal = Biology Direct | date = 2015 | volume = 10 | issue = 35 | pages = 35 | pmid=26156036 | doi=10.1186/s13062-015-0065-6 | pmc=4496867 | doi-access=free }}
*{{cite journal | author = Burggraf S | author2 = Huber H | author3 = Stetter KO | date = 1997 | title = Reclassification of the crenarchael orders and families in accordance with 16S rRNA sequence data | journal = Int. J. Syst. Bacteriol. | volume = 47 | pages = 657–660 | pmid = 9226896 | doi = 10.1099/00207713-47-3-657 | issue = 3| doi-access = free }}
* {{ cite journal | author = Huber R | author2 = Kristjansson JK | author3 = Stetter KO | date = 1987 | title = Pyrobaculum gen. nov., a new genus of neutrophilic, rod-shaped archaebacteria from continental solfataras growing optimally at 100°C | journal = Arch. Microbiol. | volume = 149 | pages = 95–101 | doi = 10.1007/BF00425072 | issue = 2 | s2cid = 27242697 }}
* {{ cite journal | display-authors = 4 | author = Zillig W | author2 = Stetter KO | author3 = Schafer W| author4 = Janekovic D | author5 = Wunderl S| author6 = Holz I | author7 = Palm P | date = 1981 | title = Thermoproteales: a novel type of extremely thermoacidophilic anaerobic archaebacteria isolated from Icelandic solfataras | journal = Zentralbl. Mikrobiol. Parasitenkd. Infektionskr. Hyg. Abt. 1 Orig | volume = C2 | pages = 205–227 }}
* {{cite journal|display-authors=4|last1=Lai|first1=Lien B.|last2=Chan|first2=Patricia P.|last3=Cozen|first3=Aaron E.|last4=Bernick|first4=David L.|last5=Brown|first5=James W.|last6=Gopalan|first6=Venkat|last7=Lowe|first7=Todd M.|title=Discovery of a minimal form of RNase P in Pyrobaculum|date=28 Dec 2010|volume=107|issue=52|pages=22493–22498|doi=10.1073/pnas.1013969107|pmid=21135215|pmc=3012483|journal=Proceedings of the National Academy of Sciences|bibcode=2010PNAS..10722493L|doi-access=free}}
* {{cite journal|last1=Wells|first1=Stephen A.|last2=Crennell|first2=Susan J.|last3=Danson|first3=Michael J.|title=Structures of mesophilic and extremophilic citrate synthases reveal rigidity and flexibility for function|journal=Proteins: Structure, Function, and Bioinformatics|date=Oct 2014|volume=82|issue=10|pages=2657–70|doi=10.1002/prot.24630|pmid=24948467|s2cid=41430703|url=http://opus.bath.ac.uk/40057/1/PDF17214957_291190889.pdf}}

{{Taxonbar|from=Q5363186}}

[[Category:Archaea genera]]
[[Category:Thermophiles]]
[[Category:Thermoproteota]]

Pyrobaculum - Revision history

imported>Ira Leviton: faculatively→facultatively - toolforge:typos