Name: Haloarcula japonica TR-1
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 5905

Type strain:

Species: Haloarcula japonica

Strain Designation: TR-1

Culture col. no.: DSM 6131, ATCC 49778, JCM 7785, CGMCC 1.3717, CGMCC 1.6162, NBRC 101032, NCIMB 13157, VKM B-2009

Strain history: T. Takashina TR-1.

NCBI tax ID(s): 1227453 (strain), 29282 (species)

SI-ID 45242

ATCC 49778, JCM 7785, DSM 6131, NCIMB 13157, VKM B-2009, NBRC 101032

Special Collections

DSMZ
JCM

Section

Haloarcula japonica TR-1 is an archaeon that was isolated from saltern soil.

16S sequence
Archaea
genome sequence

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Archaea"
	Phylum	*Methanobacteriota*
	Class	*Halobacteria*
	Order	*Halobacteriales*
	Family	*Haloarculaceae*
	Genus	*Haloarcula*
	Species	**Haloarcula japonica**
	Full Scientific Name (LPSN)	Haloarcula japonica Takashina et al. 1991

Information on culture and growth conditions Culture and growth conditions

[Ref.: #2497]

Culture medium

HALOBACTERIA MEDIUM (DSMZ Medium 372)

[Ref.: #2497]

Culture medium growth

[Ref.: #2497]

Culture medium link

Medium recipe at MediaDive

[Ref.: #2497]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #2497]			growth	37 °C
[Ref.: #67770]			growth	37 °C

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

[Ref.: #2497]	Sample type/isolated from	saltern soil
[Ref.: #2497]	Geographic location (country and/or sea, region)	Nato Peninsula
[Ref.: #2497]	Country	Japan
[Ref.: #2497]	Country ISO 3 Code	JPN
[Ref.: #2497]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Saltern soil at Noto Peninsula
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Soil
#Condition	#Saline	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB355986 (>99% sequence identity) for Haloarcula from Microbeatlas

Aquatic Samples	11
Soil Samples	13
Animal Samples	2
Plant Samples
Total Samples	26

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

[Ref.: #2497]

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:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #124043]	Haloarcula japonica gene for 16S ribosomal RNA, partial sequence, strain: JCM7785, note: rrsA.	LC085248	1405	GenBank ENA	29282 tax ID	*
[Ref.: #124043]	Haloarcula japonica gene for 16S ribosomal RNA, partial sequence, strain: JCM7785, note: rrsC.	LC085249	1405	GenBank ENA	29282 tax ID	*
[Ref.: #20218]	Haloarcula japonica gene for 16S ribosomal RNA, partial sequence, strain: JCM 7785	AB355986	1472	GenBank ENA	29282 tax ID	*
[Ref.: #20218]	Haloarcula japonica gene for 16S rRNA, complete sequence, strain: JCM 7785	AB663353	1472	GenBank ENA	29282 tax ID	*
[Ref.: #20218]	Haloarcula japonica strain JCM7785 16S ribosomal RNA (rrnA) gene, complete sequence	EF645684	1472	GenBank ENA	29282 tax ID	*
[Ref.: #20218]	Haloarcula japonica strain JCM7785 16S ribosomal RNA (rrnB) gene, complete sequence	EF645685	1472	GenBank ENA	29282 tax ID	*
[Ref.: #20218]	Haloarcula japonica strain JCM7785 16S ribosomal RNA (rrnC) gene, complete sequence	EF645686	1472	GenBank ENA	29282 tax ID	*
[Ref.: #20218]	Haloarcula japonica gene for 16S ribosomal RNA, partial sequence	D28872	1424	GenBank ENA	29282 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Haloarcula japonica DSM 6131	GCA_000336635	contig	GenBank ENA	1227453 tax ID
[Ref.: #66792]	Haloarcula japonica DSM 6131	2534681902	draft	JGI IMG/M	1227453 tax ID	*
[Ref.: #66792]	Haloarcula japonica DSM 6131	1227453.3	wgs	PATRIC	1227453 tax ID	*

[Ref.: #67770]

GC-content

63.3 mol%

Buoyant density centrifugation (BD)

Availability in culture collections External links

[Ref.: #2497]

Culture collection no.

DSM 6131, ATCC 49778, JCM 7785, CGMCC 1.3717, CGMCC 1.6162, NBRC 101032, NCIMB 13157, VKM B-2009

[Ref.: #75385]	SI-ID 45242	*
[Ref.: #75386]	SI-ID 312368	*

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Enzymology	Characterization of 3-isopropylmalate dehydrogenase from extremely halophilic archaeon Haloarcula japonica.	Nagaoka S, Sugiyama N, Yatsunami R, Nakamura S	Biosci Biotechnol Biochem	10.1093/bbb/zbab122	2021	*
Phylogeny	Haloarcula mannanilytica sp. nov., a galactomannan-degrading haloarchaeon isolated from commercial salt.	Enomoto S, Shimane Y, Ihara K, Kamekura M, Itoh T, Ohkuma M, Takahashi-Ando N, Fukushima Y, Yoshida Y, Usami R, Takai K, Minegishi H	Int J Syst Evol Microbiol	10.1099/ijsem.0.004535	2020	*
Enzymology	Halophilic mechanism of the enzymatic function of a moderately halophilic dihydrofolate reductase from Haloarcula japonica strain TR-1.	Miyashita Y, Ohmae E, Ikura T, Nakasone K, Katayanagi K	Extremophiles	10.1007/s00792-017-0928-0	2017	*
Enzymology	Effects of salt on the structure, stability, and function of a halophilic dihydrofolate reductase from a hyperhalophilic archaeon, Haloarcula japonica strain TR-1.	Miyashita Y, Ohmae E, Nakasone K, Katayanagi K	Extremophiles	10.1007/s00792-015-0732-7	2015	*
Phylogeny	Isolation of crtI homolog from extremely halophilic archaeon Haloarcula japonica strain TR-1.	Yatsunami R, Takaichi S, Nakamura S	Nucleic Acids Symp Ser (Oxf)	10.1093/nass/48.1.193	2004	*
Enzymology	Molecular cloning of transducer genes hjtA and hjtC from extremely halophilic archaeon Haloarcula japonica.	Kosaka T, Ozawa T, Yatsunami R, Nakamura S	Nucleic Acids Symp Ser (Oxf)	10.1093/nass/48.1.169	2004	*
Genetics	Gene cloning, expression and partial characterization of cell division protein FtsZ1 from extremely halophilic archaeon Haloarcula japonica strain TR-1.	Ozawa K, Harashina T, Yatsunami R, Nakamura S	Extremophiles	10.1007/s00792-005-0443-6	2005	*
Enzymology	Gene cloning of ftsZ1 homolog from extremely halophilic archaeon Haloarcula japonica.	Ozawa K, Yatsunami R, Nakamura S	Nucleic Acids Res Suppl	10.1093/nass/3.1.313	2003	*
Enzymology	A brp homolog of Haloarcula japonica: gene cloning and transcriptional analysis.	Yatsunami R, Iwamoto M, Ito S, Nakamura S	Nucleic Acids Res Suppl	10.1093/nass/3.1.267	2003	*
Enzymology	Cloning and sequencing of ftsZ homolog from extremely halophilic archaeon Haloarcula japonica strain TR-1.	Kazumichi O, Yatsunami R, Nakamura S	Nucleic Acids Symp Ser	10.1093/nass/44.1.155	2000	*
Enzymology	The gene encoding a novel halorhodopsin-like protein of extremely halophilic archaeon Haloarcula japonica strain TR-1.	Yatsunami R, Aono S, Nakamura S	Nucleic Acids Symp Ser	10.1093/nass/44.1.1	2000	*
Enzymology	Gene clusters encoding ATP synthase of Haloarcula japonica strain TR-1.	Yatsunami R, Iwamoto M, Ihara K, Nakamura S	Nucleic Acids Res Suppl	10.1093/nass/1.1.51	2001	*
Enzymology	Purification and characterization of a ferredoxin from Haloarcula japonica strain TR-1.	Sugimori D, Ichimata T, Ikeda A, Nakamura S	Biometals	10.1023/a:1009260220682	2000	*
Enzymology	A novel bacteriorhodopsin-like protein from Haloarcula japonica strain TR-1: gene cloning, sequencing, and transcript analysis.	Yatsunami R, Kawakami T, Ohtani H, Nakamura S	Extremophiles	10.1007/pl00010710	2000	*
Enzymology	Molecular cloning of A1-ATPase gene from extremely halophilic archaeon Haloarcula japonica strain TR-1.	Yatsunami R, Iwamoto M, Ihara K, Nakamura S	Nucleic Acids Symp Ser	10.1093/nass/42.1.75	1999	*
Cultivation	Transcriptional regulation of cruxrhodopsin gene from extremely halophilic archaeon Haloarcula japonica strain TR-1.	Yatsunami R, Kawakami T, Ohtani H, Nakamura S	Nucleic Acids Symp Ser	10.1093/nass/42.1.73	1999	*
Enzymology	Cloning and sequencing of the gene encoding the cell surface glycoprotein of Haloarcula japonica strain TR-1.	Wakai H, Nakamura S, Kawasaki H, Takada K, Mizutani S, Aono R, Horikoshi K	Extremophiles	10.1007/s007920050012	1997	*
Enzymology	Primary structure of the novel bacterial rhodopsin from extremely halophilic archaeon Haloarcula japonica strain TR-1.	Yatsunami R, Kawakami T, Ohtani H, Nakamura S	Nucleic Acids Symp Ser		1997	*
Enzymology	Molecular cloning of the gene encoding a 2Fe-2S ferredoxin from extremely halophilic archaeon Haloarcula japonica strain TR-1.	Ikeda A, Ichimata T, Sugimori D, Nakamura S	Nucleic Acids Symp Ser		1997	*
Enzymology	Structure and heterologous expression of the gene encoding the cell surface glycoprotein from Haloarcula japonica strain TR-1.	Wakai H, Takada K, Nakamura S, Horikoshi K	Nucleic Acids Symp Ser		1995	*

References

#2497

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 6131

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#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 .

#75385

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-ID45242.1 )

#75386

#124043

Dr. Isabel Schober, Dr. Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .

* These data were automatically processed and therefore are not curated

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