Halogeometricum rufum (CGMCC 1.7736, JCM 15770, RO1-4)

Name: Halogeometricum rufum (CGMCC 1.7736, JCM 15770, RO1-4)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133607

Type strain

Strain Designation RO1-4

Culture col. no. CGMCC 1.7736 JCM 15770 RO1-4

NCBI tax ID(s) 553469

Special Collections JCM Literature strains

History H.-L. Cui RO1-4.

Links

Halogeometricum rufum RO1-4 is an aerobe, Gram-negative, motile archaeon that was isolated from marine solar saltern.

Gram-negative motile ovoid-shaped aerobe genome sequence 16S sequence Archaea

Name and taxonomic classification

SI-ID 132960

JCM 15770

@ref 20215

Last LPSN update 2026-02-09 11:31:59

Domain Archaea

Phylum Methanobacteriota

Class Halobacteria

Order Halobacteriales

Family Haloferacaceae

Genus Halogeometricum

Species Halogeometricum rufum

Full scientific name Halogeometricum rufum Cui et al. 2010

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility
29723	negative	ovoid-shaped

Pigmentation

29723

Productionyes

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)
29723	positive	growth	25-55
29723	positive	optimum	40-42
67770	positive	growth	37

Culture pH

@ref	Ability	Type	PH	PH range
29723	positive	optimum	7
29723	positive	growth	6-8.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

29723

Oxygen toleranceaerobe

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29723	NaCl	positive	growth	11-27 %
29723	NaCl	positive	optimum	21 %

Observation

29723

Observationaggregates in chains

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29723	30089 ChEBI	acetate	+	carbon source
29723	16449 ChEBI	alanine	+	carbon source
29723	29016 ChEBI	arginine	+	carbon source
29723	35391 ChEBI	aspartate	+	carbon source
29723	28260 ChEBI	galactose	+	carbon source
29723	17234 ChEBI	glucose	+	carbon source
29723	29987 ChEBI	glutamate	+	carbon source
29723	17754 ChEBI	glycerol	+	carbon source
29723	24996 ChEBI	lactate	+	carbon source
29723	17716 ChEBI	lactose	+	carbon source
29723	25115 ChEBI	malate	+	carbon source
29723	17306 ChEBI	maltose	+	carbon source
29723	29864 ChEBI	mannitol	+	carbon source
29723	37684 ChEBI	mannose	+	carbon source
29723	18257 ChEBI	ornithine	+	carbon source
29723	15361 ChEBI	pyruvate	+	carbon source
29723	30911 ChEBI	sorbitol	+	carbon source
29723	30031 ChEBI	succinate	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
29723	16136 ChEBI	hydrogen sulfide
29723	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
29723	35581 ChEBI	indole	+

Enzymes

@ref	Value	Activity	Ec
29723	catalase	+	1.11.1.6
29723	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Condition	#Saline	-
#Engineered	#Industrial	#Industrial production
#Environmental	#Terrestrial	#Coast

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
29723	marine solar saltern
67770	Marine solar saltern in Jiangsu	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence EU887286 (>99% sequence identity) for Halogeometricum rufum from Microbeatlas

Aquatic Samples	1
Soil Samples
Animal Samples
Plant Samples
Total Samples	1

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	IMG-taxon 2617270920 annotated assembly for Halogeometricum rufum CGMCC 1.7736	contig	GCA_900112175	553469.3	2617270920	553469	76.6

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
29723	Halogeometricum rufum strain RO1-4 16S ribosomal RNA gene, complete sequence	EU887286	1472		553469
124043	Halogeometricum rufum gene for 16S rRNA, complete sequence, strain: JCM 15770.	AB663385	1472		553469

GC content

@ref	GC-content (mol%)	Method
29723	64.9
67770	64.9	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Halogeometricum rufum CGMCC 1.7736
NCBI: GCA_900112175

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	86.20	no
125439	motility	BacteriaNetⓘ	yes	53.70	no
125439	gram_stain	BacteriaNetⓘ	negative	72.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	86.70	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	The Prodigal Compound: Return of Ribosyl 1,5-Bisphosphate as an Important Player in Metabolism.	Hove-Jensen B, Brodersen DE, Manav MC.	Microbiol Mol Biol Rev	10.1128/mmbr.00040-18	2019
Phylogeny	Taxonomic study of the genera Halogeometricum and Halosarcina: transfer of Halosarcina limi and Halosarcina pallida to the genus Halogeometricum as Halogeometricum limi comb. nov. and Halogeometricum pallidum comb. nov., respectively.	Qiu XX, Zhao ML, Han D, Zhang WJ, Dyall-Smith ML, Cui HL	Int J Syst Evol Microbiol	10.1099/ijs.0.055038-0	2013
Phylogeny	Halogeometricum rufum sp. nov., a halophilic archaeon from a marine solar saltern, and emended description of the genus Halogeometricum.	Cui HL, Yang X, Gao X, Li XY, Xu XW, Zhou YG, Liu HC, Zhou PJ	Int J Syst Evol Microbiol	10.1099/ijs.0.019463-0	2009

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 )
#26106	IJSEM 2613 2010 ( DOI 10.1099/ijs.0.019463-0 , PubMed 20023063 )
#29723	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 #26106
#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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Halogeometricum rufum (CGMCC 1.7736, JCM 15770, RO1-4)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_900112175

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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