Pyrobaculum arsenaticum (DSM 13514, JCM 11321, PZ6)*

Name: Pyrobaculum arsenaticum (DSM 13514, JCM 11321, PZ6*)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17028

Type strain

Strain Designation PZ6*

Culture col. no. DSM 13514 JCM 11321 PZ6* ATCC 700994

NCBI tax ID(s) 340102 121277

Special Collections DSMZ JCM

Links

Pyrobaculum arsenaticum PZ6Pyrobaculum arsenaticum is an anaerobe, hyperthermophilic prokaryote that was isolated from hot sediment.

anaerobe hyperthermophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 49480

DSM 13514,JCM 11321,ATCC 700994

@ref 20215

Last LPSN update 2025-12-16 09:50:59

Domain Thermoproteati

Phylum Thermoproteota

Class Thermoprotei

Order Thermoproteales

Family Thermoproteaceae

Genus Pyrobaculum

Species Pyrobaculum arsenaticum

Full scientific name Pyrobaculum arsenaticum Huber et al. 2001

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
5070	PYROBACULUM MEDIUM (DSMZ Medium 390)		Medium recipe at MediaDive	Name: PYROBACULUM MEDIUM (DSMZ Medium 390; with strain-specific modifications) Composition: Na2S2O3 x 5 H2O 1.9802 g/l (NH4)2SO4 1.28713 g/l Na2S x 9 H2O 0.49505 g/l Trypticase peptone 0.49505 g/l KH2PO4 0.277228 g/l MgSO4 x 7 H2O 0.247525 g/l Yeast extract 0.19802 g/l CaCl2 x 2 H2O 0.0693069 g/l FeCl3 x 6 H2O 0.019802 g/l Na2B4O7 x 10 H2O 0.00445545 g/l MnCl2 x 4 H2O 0.00178218 g/l Sodium resazurin 0.00049505 g/l ZnSO4 x 7 H2O 0.000217822 g/l CuCl2 x 2 H2O 4.95049e-05 g/l Na2MoO4 x 2 H2O 2.9703e-05 g/l VOSO4 x 2 H2O 2.9703e-05 g/l CoSO4 x 7 H2O 9.90099e-06 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
5070	positive	growth	95	hyperthermophilic
67770	positive	growth	95	hyperthermophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
5070	anaerobe
125439	anaerobe

Spore formation

@ref	Spore formation	Confidence
125438		92.631

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Sediment
#Condition	#Thermophilic (>45°C)	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
5070	hot sediment	Naples, Pisciarelli Solfatara	Italy	ITA	Europe
67770	Hot spring at Pisciarelli Solfatara	Naples	Italy	ITA	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
5070	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1638v1 assembly for Pyrobaculum arsenaticum DSM 13514	complete	GCA_000016385	340102.8	640427135	340102	99.45

Genome browser: GCA_000016385

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
5070	Pyrobaculum arsenaticum 16S rRNA gene, strain PZ6	AJ277124	1418		121277

GC content

@ref	GC-content (mol%)
5070	58.3
67770	58.3

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pyrobaculum arsenaticum DSM 13514
NCBI: GCA_000016385

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	64.50	no
125439	motility	BacteriaNetⓘ	no	88.90	no
125439	gram_stain	BacteriaNetⓘ	positive	80.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	99.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pyrobaculum arsenaticum DSM 13514 DSM 13514
NCBI: GCA_000016385.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	78.76	no
125438	anaerobic	anaerobicⓘ	yes	70.99	yes
125438	aerobic	aerobicⓘ	no	65.27	yes
125438	spore-forming	spore-formingⓘ	no	92.63	no
125438	thermophilic	thermophileⓘ	yes	80.57	yes
125438	flagellated	motile2+ⓘ	no	83.63	no

Literature

Title	Authors	Journal	DOI	Year
New virus isolates from Italian hydrothermal environments underscore the biogeographic pattern in archaeal virus communities.	Baquero DP, Contursi P, Piochi M, Bartolucci S, Liu Y, Cvirkaite-Krupovic V, Prangishvili D, Krupovic M.	ISME J	10.1038/s41396-020-0653-z	2020
P finder: genomic and metagenomic annotation of RNase P RNA gene (rnpB).	Ellis JC.	BMC Genomics	10.1186/s12864-020-6615-z	2020
Comparative analysis of amino acid sequences from mesophiles and thermophiles in respective of carbon-nitrogen hydrolase family.	Devi S, Sharma N, Savitri, Bhalla TC.	3 Biotech	10.1007/s13205-012-0111-3	2013
Comparison between Some Phenotypic and Genotypic Methods for Assessment of Antimicrobial Resistance Trend of Bovine Mastitis Staphylococcus aureus Isolates from Bulgaria.	Rusenova N, Vasilev N, Rusenov A, Milanova A, Sirakov I.	Vet Sci	10.3390/vetsci9080401	2022
RecJ3/4-aRNase J form a Ubl-associated nuclease complex functioning in survival against DNA damage in Haloferax volcanii.	Jia H, Dantuluri S, Margulies S, Smith V, Lever R, Allers T, Koh J, Chen S, Maupin-Furlow JA.	mBio	10.1128/mbio.00852-23	2023
Complete genome sequence of Pyrobaculum oguniense.	Bernick DL, Karplus K, Lui LM, Coker JK, Murphy JN, Chan PP, Cozen AE, Lowe TM.	Stand Genomic Sci	10.4056/sigs.2645906	2012
Novel Transcriptional Regulons for Autotrophic Cycle Genes in Crenarchaeota.	Leyn SA, Rodionova IA, Li X, Rodionov DA.	J Bacteriol	10.1128/jb.00249-15	2015
Computational identification of a new SelD-like family that may participate in sulfur metabolism in hyperthermophilic sulfur-reducing archaea.	Li GP, Jiang L, Ni JZ, Liu Q, Zhang Y.	BMC Genomics	10.1186/1471-2164-15-908	2014
Phylogeny and Taxonomy of Archaea: A Comparison of the Whole-Genome-Based CVTree Approach with 16S rRNA Sequence Analysis.	Zuo G, Xu Z, Hao B.	Life (Basel)	10.3390/life5010949	2015
Sequence evidence in the archaeal genomes that tRNAs emerged through the combination of ancestral genes as 5' and 3' tRNA halves.	Fujishima K, Sugahara J, Tomita M, Kanai A.	PLoS One	10.1371/journal.pone.0001622	2008
Constraints on anaerobic respiration in the hyperthermophilic Archaea Pyrobaculum islandicum and Pyrobaculum aerophilum.	Feinberg LF, Srikanth R, Vachet RW, Holden JF.	Appl Environ Microbiol	10.1128/aem.02033-07	2008
Evolution of introns in the archaeal world.	Tocchini-Valentini GD, Fruscoloni P, Tocchini-Valentini GP.	Proc Natl Acad Sci U S A	10.1073/pnas.1100862108	2011
A virus of hyperthermophilic archaea with a unique architecture among DNA viruses.	Rensen EI, Mochizuki T, Quemin E, Schouten S, Krupovic M, Prangishvili D.	Proc Natl Acad Sci U S A	10.1073/pnas.1518929113	2016
An uncharacterized member of the ribokinase family in Thermococcus kodakarensis exhibits myo-inositol kinase activity.	Sato T, Fujihashi M, Miyamoto Y, Kuwata K, Kusaka E, Fujita H, Miki K, Atomi H.	J Biol Chem	10.1074/jbc.m113.457259	2013
Network analyses structure genetic diversity in independent genetic worlds.	Halary S, Leigh JW, Cheaib B, Lopez P, Bapteste E.	Proc Natl Acad Sci U S A	10.1073/pnas.0908978107	2010
The CMG (CDC45/RecJ, MCM, GINS) complex is a conserved component of the DNA replication system in all archaea and eukaryotes.	Makarova KS, Koonin EV, Kelman Z.	Biol Direct	10.1186/1745-6150-7-7	2012
The dispersed archaeal eukaryome and the complex archaeal ancestor of eukaryotes.	Koonin EV, Yutin N.	Cold Spring Harb Perspect Biol	10.1101/cshperspect.a016188	2014
Identification and genomic analysis of transcription factors in archaeal genomes exemplifies their functional architecture and evolutionary origin.	Perez-Rueda E, Janga SC.	Mol Biol Evol	10.1093/molbev/msq033	2010
Whole-genome based Archaea phylogeny and taxonomy: A composition vector approach.	Sun J, Xu Z, Hao B.	Chin Sci Bull	10.1007/s11434-010-3008-8	2010
Metagenomes from high-temperature chemotrophic systems reveal geochemical controls on microbial community structure and function.	Inskeep WP, Rusch DB, Jay ZJ, Herrgard MJ, Kozubal MA, Richardson TH, Macur RE, Hamamura N, Jennings Rd, Fouke BW, Reysenbach AL, Roberto F, Young M, Schwartz A, Boyd ES, Badger JH, Mathur EJ, Ortmann AC, Bateson M, Geesey G, Frazier M.	PLoS One	10.1371/journal.pone.0009773	2010
Pre_GI: a global map of ontological links between horizontally transferred genomic islands in bacterial and archaeal genomes.	Pierneef R, Cronje L, Bezuidt O, Reva ON.	Database (Oxford)	10.1093/database/bav058	2015
Stygiolobus rod-shaped virus and the interplay of crenarchaeal rudiviruses with the CRISPR antiviral system.	Vestergaard G, Shah SA, Bize A, Reitberger W, Reuter M, Phan H, Briegel A, Rachel R, Garrett RA, Prangishvili D.	J Bacteriol	10.1128/jb.00795-08	2008
A novel pathway for the biosynthesis of heme in Archaea: genome-based bioinformatic predictions and experimental evidence.	Storbeck S, Rolfes S, Raux-Deery E, Warren MJ, Jahn D, Layer G.	Archaea	10.1155/2010/175050	2010
Pyrobaculum yellowstonensis Strain WP30 Respires on Elemental Sulfur and/or Arsenate in Circumneutral Sulfidic Geothermal Sediments of Yellowstone National Park.	Jay ZJ, Beam JP, Dohnalkova A, Lohmayer R, Bodle B, Planer-Friedrich B, Romine M, Inskeep WP.	Appl Environ Microbiol	10.1128/aem.01095-15	2015
Functional Promiscuity of Homologues of the Bacterial ArsA ATPases.	Castillo R, Saier MH.	Int J Microbiol	10.1155/2010/187373	2010
Discovery and Biotechnological Exploitation of Glycoside-Phosphorylases.	Li A, Benkoulouche M, Ladeveze S, Durand J, Cioci G, Laville E, Potocki-Veronese G.	Int J Mol Sci	10.3390/ijms23063043	2022
Distribution analysis of hydrogenases in surface waters of marine and freshwater environments.	Barz M, Beimgraben C, Staller T, Germer F, Opitz F, Marquardt C, Schwarz C, Gutekunst K, Vanselow KH, Schmitz R, LaRoche J, Schulz R, Appel J.	PLoS One	10.1371/journal.pone.0013846	2010
Archaeal ubiquitin-like proteins: functional versatility and putative ancestral involvement in tRNA modification revealed by comparative genomic analysis.	Makarova KS, Koonin EV.	Archaea	10.1155/2010/710303	2010
Archaeal RNA polymerase and transcription regulation.	Jun SH, Reichlen MJ, Tajiri M, Murakami KS.	Crit Rev Biochem Mol Biol	10.3109/10409238.2010.538662	2011
Archaeology of eukaryotic DNA replication.	Makarova KS, Koonin EV.	Cold Spring Harb Perspect Biol	10.1101/cshperspect.a012963	2013
Transcriptional map of respiratory versatility in the hyperthermophilic crenarchaeon Pyrobaculum aerophilum.	Cozen AE, Weirauch MT, Pollard KS, Bernick DL, Stuart JM, Lowe TM.	J Bacteriol	10.1128/jb.00965-08	2009
Annotation of Protein Domains Reveals Remarkable Conservation in the Functional Make up of Proteomes Across Superkingdoms.	Nasir A, Naeem A, Khan MJ, Nicora HD, Caetano-Anolles G.	Genes (Basel)	10.3390/genes2040869	2011
The nonphosphorylative Entner-Doudoroff pathway in the thermoacidophilic euryarchaeon Picrophilus torridus involves a novel 2-keto-3-deoxygluconate- specific aldolase.	Reher M, Fuhrer T, Bott M, Schonheit P.	J Bacteriol	10.1128/jb.01281-09	2010
A study in entire chromosomes of violations of the intra-strand parity of complementary nucleotides (Chargaff's second parity rule).	Powdel BR, Satapathy SS, Kumar A, Jha PK, Buragohain AK, Borah M, Ray SK.	DNA Res	10.1093/dnares/dsp021	2009
Bioinformatic characterization of the trimeric intracellular cation-specific channel protein family.	Silverio AL, Saier MH.	J Membr Biol	10.1007/s00232-011-9364-8	2011
Respiration of arsenate and selenate by hyperthermophilic archaea.	Huber R, Sacher M, Vollmann A, Huber H, Rose D	Syst Appl Microbiol	10.1016/S0723-2020(00)80058-2	2000

References

#5070	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 13514
#20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Pyrobaculum arsenaticum (DSM 13514, JCM 11321, PZ6)*

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000016385

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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