Pyrobaculum ferrireducens (DSM 28942, VKM B-2856, 1860)

Name: Pyrobaculum ferrireducens (DSM 28942, VKM B-2856, 1860)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 130743

Type strain

Strain Designation 1860

Culture col. no. DSM 28942 VKM B-2856 1860

NCBI tax ID(s) 1104324

Special Collections DSMZ

History <- G. Slobodkina, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; 1860 <- A. Slobodkin and G. Slobodkina {2009}

Links

Pyrobaculum ferrireducens 1860 is an anaerobe, hyperthermophilic prokaryote that was isolated from sediment from the bottom of a terrestrial hot spring.

anaerobe hyperthermophilic genome sequence

Name and taxonomic classification

SI-ID 404802

VKM B-2856,DSM 28942

@ref 20215

Last LPSN update 2025-12-16 10:01:04

Domain Thermoproteati

Phylum Thermoproteota

Class Thermoprotei

Order Thermoproteales

Family Thermoproteaceae

Genus Pyrobaculum

Species Pyrobaculum ferrireducens

Full scientific name Pyrobaculum ferrireducens Slobodkina et al. 2015

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	positive	94.9

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
21926	PYROBACULUM FERRIREDUCENS MEDIUM (DSMZ Medium 1579)		Medium recipe at MediaDive	Name: PYROBACULUM FERRIREDUCENS MEDIUM (DSMZ Medium 1579) Composition: NaHCO3 1.99402 g/l KNO3 0.997009 g/l Yeast extract 0.997009 g/l NH4Cl 0.329013 g/l CaCl2 x 2 H2O 0.329013 g/l MgCl2 x 6 H2O 0.329013 g/l KH2PO4 0.329013 g/l KCl 0.329013 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l NaOH 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l MnCl2 x 4 H2O 9.97009e-05 g/l Pyridoxine hydrochloride 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l Thiamine HCl 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Biotin 1.99402e-05 g/l Folic acid 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Vitamin B12 9.97009e-07 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
21926	positive	growth	90	hyperthermophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
21926	anaerobe
125439	anaerobe	99.7

Spore formation

@ref	Spore formation	Confidence
125438		91.685

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Sediment
#Environmental	#Aquatic	#Thermal spring
#Condition	#Thermophilic (>45°C)	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
21926	sediment from the bottom of a terrestrial hot spring	Kamchatka, Uzon Kaldera, Kronotsky Nature Reserve, 'Fumarolnoye' field, (54° 30.115' N 159° 59.279' E, elevation 656 m)	Russia	RUS	Asia	54.5019	159.502 54.5019/159.502

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
21926	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM23480v1 assembly for Pyrobaculum ferrireducens 1860	complete	GCA_000234805	1104324.8	2511231117	1104324	99.1

GC content

@ref	GC-content (mol%)	Method
21926	56.97	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pyrobaculum ferrireducens 1860
NCBI: GCA_000234805

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	77.40	no
125439	motility	BacteriaNetⓘ	no	87.30	no
125439	gram_stain	BacteriaNetⓘ	positive	94.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	99.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pyrobaculum ferrireducens 1860
NCBI: GCA_000234805.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	75.17	no
125438	anaerobic	anaerobicⓘ	yes	66.46	yes
125438	aerobic	aerobicⓘ	no	63.92	yes
125438	spore-forming	spore-formingⓘ	no	91.69	no
125438	thermophilic	thermophileⓘ	yes	81.96	no
125438	flagellated	motile2+ⓘ	no	81.75	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Enzymatic Nitrogen Incorporation Using Hydroxylamine.	Gao S, Das A, Alfonzo E, Sicinski KM, Rieger D, Arnold FH.	J Am Chem Soc	10.1021/jacs.3c08053	2023
	Mesophiles vs. Thermophiles: Untangling the Hot Mess of Intrinsically Disordered Proteins and Growth Temperature of Bacteria.	Kruglikov A, Xia X.	Int J Mol Sci	10.3390/ijms25042000	2024
Genetics	Biodegradation of sodium selenite by a highly tolerant strain Rhodococcus qingshengii PM1: Biochemical characterization and comparative genome analysis.	Wang Z, Hou X, Guo Z, Lei X, Peng M.	Curr Res Microb Sci	10.1016/j.crmicr.2025.100426	2025
Genetics	Environmental activity-based protein profiling for function-driven enzyme discovery from natural communities.	Ninck S, Klaus T, Kochetkova TV, Esser SP, Sewald L, Kaschani F, Brasen C, Probst AJ, Kublanov IV, Siebers B, Kaiser M.	Environ Microbiome	10.1186/s40793-024-00577-2	2024
Metabolism	Phylogenomic Analysis of beta-Lactamase in Archaea and Bacteria Enables the Identification of Putative New Members.	Keshri V, Panda A, Levasseur A, Rolain JM, Pontarotti P, Raoult D.	Genome Biol Evol	10.1093/gbe/evy028	2018
Phylogeny	Pyrobaculum ferrireducens sp. nov., a hyperthermophilic Fe(III)-, selenate- and arsenate-reducing crenarchaeon isolated from a hot spring.	Slobodkina GB, Lebedinsky AV, Chernyh NA, Bonch-Osmolovskaya EA, Slobodkin AI	Int J Syst Evol Microbiol	10.1099/ijs.0.000027	2014

References

#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 )
#21926	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28942
#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) .
#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 ferrireducens (DSM 28942, VKM B-2856, 1860)

Name and taxonomic classification

Morphology

Cell 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_000234805

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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