Name: Nitratiruptor tergarcus MI55-1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 10424

Type strain:

Species: Nitratiruptor tergarcus

Strain Designation: MI55-1

Culture col. no.: DSM 16512, JCM 12459

Strain history: S. Nakagawa MI55-1.

NCBI tax ID(s): 1069081 (strain), 269259 (species)

SI-ID 138024

DSM 16512, JCM 12459

Section

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Epsilonproteobacteria*
	Order	[Epsilonproteobacteria, not assigned to order]
	Family	*Nitratiruptoraceae*
	Genus	*Nitratiruptor*
	Species	**Nitratiruptor tergarcus**
	Full Scientific Name (LPSN)	Nitratiruptor tergarcus Nakagawa et al. 2005

Information on morphological and physiological properties Morphology

[Ref.: #31405]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %100

[Ref.: #31405]	Cell length	2.5 µm

[Ref.: #31405]	Cell width	0.8 µm

[Ref.: #31405]	Cell shape	rod-shaped

[Ref.: #31405]	Motility	no
[Ref.: #69480]	Motility	yes Confidence in %94.989

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6385]

Culture medium

NITRATIRUPTOR AND NITRATIFACTOR MEDIUM (DSMZ Medium 1024)

[Ref.: #6385]

Culture medium growth

[Ref.: #6385]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6385]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #6385]	growth	55 °C
[Ref.: #31405]	growth	40-57 °C
[Ref.: #31405]	optimum	55 °C
[Ref.: #67770]	growth	55 °C

[Ref.: #6385]	Temperature range	thermophilic
[Ref.: #31405]	Temperature range	thermophilic
[Ref.: #67770]	Temperature range	thermophilic
[Ref.: #69480]	Temperature range	thermophilic Confidence in %97.557

	pH	Kind of pH		pH
[Ref.: #31405]			optimum	6.4
[Ref.: #31405]			growth	5.4-6.9

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31405]

Oxygen tolerance

facultative anaerobe

[Ref.: #31405]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.976

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31405]		NaCl		growth	1.5-4.0	%
[Ref.: #31405]		NaCl		optimum	2.5	%

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #6385]	Sample type/isolated from	deep-sea hydrothermal vent chimney
[Ref.: #6385]	Geographic location (country and/or sea, region)	Iheya North hydrothermal field in the Mid-Okinawa Trough
[Ref.: #6385]	Country	Japan
[Ref.: #6385]	Country ISO 3 Code	JPN
[Ref.: #6385]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Deep-sea hydrothermal vent chimney structures at the Iheya North hydrothermal field in the Mid-Okinawa Trough
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #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

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #6385]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #6385]	Nitratiruptor tergarcus gene for 16S rRNA, partial sequence	AB175499	1409	ENA	1069081 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Nitratiruptor tergarcus DSM 16512	GCA_900176045	scaffold	GenBank	1069081 tax ID
[Ref.: #66792]	Nitratiruptor tergarcus DSM 16512 strain DSM 16512	1069081.3	wgs	PATRIC	1069081 tax ID	*
[Ref.: #66792]	Nitratiruptor tergarcus DSM 16512	2516493030	draft	JGI IMG/M	1069081 tax ID	*
[Ref.: #66792]	Nitratiruptor tergarcus DSM 16512	GCA_027946175	complete	GenBank	1069081 tax ID	*

[Ref.: #6385]

GC-content

29.6 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Nitratiruptor tergarcus DSM 16512 DSM 16512 NCBI: GCA_900176045.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Nitratiruptor tergarcus DSM 16512 DSM 16512 NCBI: GCA_027946175.1
[Ref.: #69480]	motile	yes	81.282	yes
[Ref.: #69480]	flagellated	no	71.68	yes
[Ref.: #69480]	gram-positive	no	99.335	yes
[Ref.: #69480]	anaerobic	yes	53.643	yes
[Ref.: #69480]	aerobic	no	97.112	yes
[Ref.: #69480]	halophile	no	87.097	no
[Ref.: #69480]	spore-forming	no	95.845	no
[Ref.: #69480]	glucose-ferment	no	87.04	no
[Ref.: #69480]	thermophile	yes	99.687	yes
[Ref.: #69480]	glucose-util	no	63.985	no

Availability in culture collections External links

[Ref.: #6385]

Culture collection no.

DSM 16512, JCM 12459

[Ref.: #79706]

SI-ID 138024

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 )

#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 (see below)

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#79706

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID138024.1 )

#27714

IJSEM 925 2005 ( DOI 10.1099/ijs.0.63480-0 , PubMed 15774687 )

* These data were automatically processed and therefore are not curated

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Nitratiruptor tergarcus DSM 16512 DSM 16512

Nitratiruptor tergarcus DSM 16512 DSM 16512

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