Halarchaeum rubridurum (DSM 22443, CECT 7535, JCM 16108)

Name: Halarchaeum rubridurum (DSM 22443, CECT 7535, JCM 16108)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 24088

Type strain

Strain Designation MH1-16-3

Culture col. no. DSM 22443 CECT 7535 JCM 16108 MH1-16-3

NCBI tax ID(s) 489911

Special Collections DSMZ JCM Literature strains

History DSMZ <- H. Minegishi, Bio-Nano Electronics Res. Centre, Toyo Univ., Kawagoe, Japan; MH1-16-3 JCM <-- H. Minegishi MH1-16-3.

Links

Halarchaeum rubridurum MH1-16-3 is an aerobe, Gram-negative archaeon that was isolated from commercial solar sea salt.

Gram-negative aerobe genome sequence 16S sequence Archaea

Name and taxonomic classification

SI-ID 371184

CECT 7534,DSM 22442,JCM 16109,JCM 16108,CECT 7535,DSM 22443

@ref 20215

Last LPSN update 2026-05-29 08:30:33

Domain Archaea

Phylum Methanobacteriota

Class Halobacteria

Order Halobacteriales

Family Halobacteriaceae

Genus Halarchaeum

Species Halarchaeum rubridurum

Full scientific name Halarchaeum rubridurum Yamauchi et al. 2013

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Motility
30997	negative	1.5 µm	1.5 µm

Pigmentation

30997

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
21215	HALOARCHAEAL MEDIUM MH-1 (DSMZ Medium 1396)		Medium recipe at MediaDive	Name: HALOARCHAEAL MEDIUM MH-1 (DSMZ Medium 1396) Composition: NaCl 249.377 g/l Agar 24.9377 g/l K2SO4 6.23441 g/l Casamino acids 4.98753 g/l L-Glutamic acid 2.49377 g/l Trisodium citrate x 2 H2O 2.49377 g/l Yeast extract 2.49377 g/l NH4Cl 1.24688 g/l KH2PO4 1.24688 g/l Na2S2O3 x 5 H2O 0.00498753 g/l FeSO4 x 6 H2O 0.00498753 g/l CaCl2 x 2 H2O 0.00249377 g/l CoCl2 x 6 H2O 0.00074813 g/l Na2MoO4 x 2 H2O 0.000249377 g/l MnCl2 x 4 H2O 0.000249377 g/l ZnCl2 0.000249377 g/l NiCl2 x 6 H2O 0.000249377 g/l AlCl3 9.97506e-05 g/l H3BO4 4.98753e-05 g/l Na2WO4 x 2 H2O 4.98753e-05 g/l CuCl2 x 6 H2O 2.49377e-05 g/l BaCl2 x 2 H2O 2.49377e-05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
21215	positive	growth	37
30997	positive	growth	20-50
30997	positive	optimum	42.5
67770	positive	growth	37

Culture pH

@ref	Ability	Type	PH
30997	positive	optimum	5.75
30997	positive	growth	4.5-6.8

Physiology and metabolism

Oxygen tolerance

30997

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
125439		95.115

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30997	NaCl	positive	growth	09-30 %
30997	NaCl	positive	optimum	19.5 %

Observation

30997

Observationaggregates in clumps

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30997	17057 ChEBI	cellobiose	+	carbon source
30997	28757 ChEBI	fructose	+	carbon source
30997	28260 ChEBI	galactose	+	carbon source
30997	17234 ChEBI	glucose	+	carbon source
30997	25115 ChEBI	malate	+	carbon source
30997	30031 ChEBI	succinate	+	carbon source

Enzymes

@ref	Value	Activity	Ec
30997	catalase	+	1.11.1.6

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Food production	#Food
#Environmental	#Aquatic	#Marine

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
21215	commercial solar sea salt	Philippines	PHL	Asia
67770	Commercial solar salt sample produced in the Philippines

Taxonmaps

69479

Global distribution of 16S sequence AB372513 (>99% sequence identity) for Halarchaeum rubridurum subclade from Microbeatlas

Aquatic Samples	17
Soil Samples	1
Animal Samples	0
Plant Samples	0
Total Samples	18

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
21215	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	ASM1787377v1 assembly for Halarchaeum rubridurum DSM 22443	contig	GCA_017873775	489911.4	2913406730	489911	74.84
66792	ASM1464711v1 assembly for Halarchaeum rubridurum JCM 16108	contig	GCA_014647115	489911.3	8064871848	489911	73.21

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
21215	Halarchaeum rubridurum gene for 16S ribosomal RNA, complete sequence	AB372513	1476		489911
124043	Halarchaeum rubridurum strain JCM 16108 16S ribosomal RNA gene, partial sequence.	MT760369	1357		489911

GC content

@ref	GC-content (mol%)	Method
21215	63.2	high performance liquid chromatography (HPLC)
30997	63.2

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1787377v1 assembly for Halarchaeum rubridurum DSM 22443
NCBI: GCA_017873775

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	72.62	no
125439	motility	BacteriaNetⓘ	no	63.12	no
125439	gram_stain	BacteriaNetⓘ	positive	56.16	no
125439	spore_formation	BacteriaNetⓘ	no	95.12	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Halarchaeum nitratireducens sp. nov., a moderately acidophilic haloarchaeon isolated from commercial sea salt.	Minegishi H, Yamauchi Y, Echigo A, Shimane Y, Kamekura M, Itoh T, Ohkuma M, Usami R	Int J Syst Evol Microbiol	10.1099/ijs.0.054668-0	2013
Phylogeny	Halarchaeum rubridurum sp. nov., a moderately acidophilic haloarchaeon isolated from commercial sea salt samples.	Yamauchi Y, Minegishi H, Echigo A, Shimane Y, Kamekura M, Itoh T, Ohkuma M, Doukyu N, Inoue A, Usami R	Int J Syst Evol Microbiol	10.1099/ijs.0.049262-0	2013

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 )
#21215	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22443
#27327	IJSEM 3143 2013 ( DOI 10.1099/ijs.0.049262-0 , PubMed 23435243 )
#30997	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 #27327
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Halarchaeum rubridurum (DSM 22443, CECT 7535, JCM 16108)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_017873775

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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