Nitratiruptor tergarcus (DSM 16512, JCM 12459, MI55-1)

Name: Nitratiruptor tergarcus (DSM 16512, JCM 12459, MI55-1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 10424

Type strain

Strain Designation MI55-1

Culture col. no. DSM 16512 JCM 12459 MI55-1

NCBI tax ID(s) 1069081 269259

Special Collections DSMZ JCM Literature strains

Links

Nitratiruptor tergarcus MI55-1 is a facultative anaerobe, thermophilic, Gram-negative prokaryote that was isolated from deep-sea hydrothermal vent chimney.

Gram-negative rod-shaped facultative anaerobe thermophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 138024

DSM 16512,JCM 12459

@ref 20215

Last LPSN update 2025-12-16 09:49:20

Domain Pseudomonadati

Phylum Pseudomonadota

Class Epsilonproteobacteria

Order [Epsilonproteobacteria, not assigned to order]

Family Nitratiruptoraceae

Genus Nitratiruptor

Species Nitratiruptor tergarcus

Full scientific name Nitratiruptor tergarcus Nakagawa et al. 2005

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
31405	negative	2.5 µm	0.8 µm	rod-shaped
125438	negative					97.983

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
6385	NITRATIRUPTOR AND NITRATIFACTOR MEDIUM (DSMZ Medium 1024)		Medium recipe at MediaDive	Name: NITRATIRUPTOR AND NITRATIFRACTOR MEDIUM (DSMZ Medium 1024) Composition: MgCl2 x 6 H2O 418.0 g/l KCl 33.0 g/l NH4Cl 25.0 g/l K2HPO4 14.0 g/l Sulfur powder 3.0 g/l MgSO4 x 7 H2O 3.0 g/l C6H9NO6 1.5 g/l Fe(NH4)2(SO4)2 x 6 H2O 1.0 g/l NaCl 1.0 g/l Na2S2O3 x 5 H2O 1.0 g/l NaHCO3 1.0 g/l NaNO3 1.0 g/l MnSO4 x 2 H2O 0.5 g/l CoSO4 x 7 H2O 0.18 g/l ZnSO4 x 7 H2O 0.18 g/l FeSO4 x 7 H2O 0.1 g/l CaCl2 x 2 H2O 0.1 g/l NiCl2 x 6 H2O 0.025 g/l AlK(SO4)2 x 12 H2O 0.02 g/l Nitrilotriacetic acid 0.015 g/l Na2MoO4 x 2 H2O 0.01 g/l CuSO4 x 5 H2O 0.01 g/l H3BO3 0.01 g/l MnSO4 x H2O 0.005 g/l Na2SeO3 x 5 H2O 0.0003 g/l Pyridoxine hydrochloride 0.0001 g/l Calcium D-(+)-pantothenate 5e-05 g/l p-Aminobenzoic acid 5e-05 g/l Thiamine HCl 5e-05 g/l (DL)-alpha-Lipoic acid 5e-05 g/l Riboflavin 5e-05 g/l Nicotinic acid 5e-05 g/l Folic acid 2e-05 g/l Biotin 2e-05 g/l Na2WO4 x 2 H2O 4e-06 g/l Vitamin B12 1e-06 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
6385	positive	growth	55	thermophilic
31405	positive	growth	40-57	thermophilic
31405	positive	optimum	55	thermophilic
67770	positive	growth	55	thermophilic

Culture pH

@ref	Ability	Type	PH
31405	positive	optimum	6.4
31405	positive	growth	5.4-6.9

Physiology and metabolism

Oxygen tolerance

31405

Oxygen tolerancefacultative anaerobe

Spore formation

@ref	Spore formation	Confidence
31405
125438		95.41

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31405	NaCl	positive	growth	1.5-4.0 %
31405	NaCl	positive	optimum	2.5 %

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Hydrothermal vent
#Environmental	#Aquatic	#Marine
#Condition	#Thermophilic (>45°C)	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
6385	deep-sea hydrothermal vent chimney	Iheya North hydrothermal field in the Mid-Okinawa Trough	Japan	JPN	Asia
67770	Deep-sea hydrothermal vent chimney structures at the Iheya North hydrothermal field in the Mid-Okinawa Trough		Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB175499 (>99% sequence identity) for Nitratiruptor tergarcus subclade from Microbeatlas

Aquatic Samples	77
Soil Samples	15
Animal Samples	5
Plant Samples	1
Total Samples	98

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6385	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	ASM2794617v1 assembly for Nitratiruptor tergarcus DSM 16512	complete	GCA_027946175	1069081.13	8118737473	1069081	98.26
67770	IMG-taxon 2516493030 annotated assembly for Nitratiruptor tergarcus DSM 16512	scaffold	GCA_900176045	1069081.3	2516493030	1069081	74.43

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6385	Nitratiruptor tergarcus gene for 16S rRNA, partial sequence	AB175499	1409		1069081

GC content

6385

GC-content (mol%)29.6

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Nitratiruptor tergarcus DSM 16512
NCBI: GCA_027946175

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	88.80	no
125439	gram_stain	BacteriaNetⓘ	variable	67.40	no
125439	motility	BacteriaNetⓘ	no	65.60	no
125439	spore_formation	BacteriaNetⓘ	no	83.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Nitratiruptor tergarcus DSM 16512 DSM 16512
NCBI: GCA_027946175.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.98	yes
125438	anaerobic	anaerobicⓘ	no	67.10	yes
125438	aerobic	aerobicⓘ	no	80.30	no
125438	spore-forming	spore-formingⓘ	no	95.41	yes
125438	thermophilic	thermophileⓘ	yes	52.10	yes
125438	flagellated	motile2+ⓘ	yes	64.58	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Emergence of colistin-resistant Enterobacter cloacae and Raoultella ornithinolytica carrying the phosphoethanolamine transferase gene, mcr-9, derived from vegetables in Japan.	Xedzro C, Shimamoto T, Yu L, Zuo H, Sugawara Y, Sugai M, Shimamoto T.	Microbiol Spectr	10.1128/spectrum.01063-23	2023
Enzymology	Horizontal acquisition of hydrogen conversion ability and other habitat adaptations in the Hydrogenovibrio strains SP-41 and XCL-2.	Gonnella G, Adam N, Perner M.	BMC Genomics	10.1186/s12864-019-5710-5	2019
Metabolism	Insights into the genome structure of four acetogenic bacteria with specific reference to the Wood-Ljungdahl pathway.	Esposito A, Tamburini S, Triboli L, Ambrosino L, Chiusano ML, Jousson O.	Microbiologyopen	10.1002/mbo3.938	2019
	Biogeochemical Implications of N₂O-Reducing Thermophilic Campylobacteria in Deep-Sea Vent Fields, and the Description of Nitratiruptor labii sp. nov.	Fukushi M, Mino S, Tanaka H, Nakagawa S, Takai K, Sawabe T.	iScience	10.1016/j.isci.2020.101462	2020
Phylogeny	Nitrosophilus alvini gen. nov., sp. nov., a hydrogen-oxidizing chemolithoautotroph isolated from a deep-sea hydrothermal vent in the East Pacific Rise, inferred by a genome-based taxonomy of the phylum "Campylobacterota".	Shiotani T, Mino S, Sato W, Nishikawa S, Yonezawa M, Sievert SM, Sawabe T.	PLoS One	10.1371/journal.pone.0241366	2020
Phylogeny	Nitratiruptor tergarcus gen. nov., sp. nov. and Nitratifractor salsuginis gen. nov., sp. nov., nitrate-reducing chemolithoautotrophs of the epsilon-Proteobacteria isolated from a deep-sea hydrothermal system in the Mid-Okinawa Trough.	Nakagawa S, Takai K, Inagaki F, Horikoshi K, Sako Y	Int J Syst Evol Microbiol	10.1099/ijs.0.63480-0	2005

References

#6385	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16512
#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 )
#27714	IJSEM 925 2005 ( DOI 10.1099/ijs.0.63480-0 , PubMed 15774687 )
#31405	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #27714
#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;
#69479	João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .
#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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Nitratiruptor tergarcus (DSM 16512, JCM 12459, MI55-1)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_027946175

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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