Halogeometricum limi (CGMCC 1.8711, JCM 16054, RO1-6)

Name: Halogeometricum limi (CGMCC 1.8711, JCM 16054, RO1-6)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133594

Type strain

Strain Designation RO1-6

Culture col. no. CGMCC 1.8711 JCM 16054 RO1-6

NCBI tax ID(s) 555875

Special Collections JCM Literature strains

History H.-L. Cui RO1-6.

Links

Halogeometricum limi RO1-6 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 28301

JCM 16054

@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 limi

Full scientific name Halogeometricum limi (Cui et al. 2010) Qiu et al. 2013

Synonyms (1)

Halosarcina limi

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility
29684	negative	ovoid-shaped

Pigmentation

29684

Productionyes

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)
29684	positive	growth	20-50
29684	positive	optimum	37
67770	positive	growth	37

Culture pH

@ref	Ability	Type	PH
29684	positive	optimum	7
29684	positive	growth	6.5-8

Physiology and metabolism

Oxygen tolerance

29684

Oxygen toleranceaerobe

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29684	NaCl	positive	growth	12.18-30 %
29684	NaCl	positive	optimum	22.62 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29684	30089 ChEBI	acetate	+	carbon source
29684	16449 ChEBI	alanine	+	carbon source
29684	28260 ChEBI	galactose	+	carbon source
29684	17234 ChEBI	glucose	+	carbon source
29684	29987 ChEBI	glutamate	+	carbon source
29684	17754 ChEBI	glycerol	+	carbon source
29684	24996 ChEBI	lactate	+	carbon source
29684	17716 ChEBI	lactose	+	carbon source
29684	37684 ChEBI	mannose	+	carbon source
29684	17632 ChEBI	nitrate	+	reduction
29684	15361 ChEBI	pyruvate	+	carbon source
29684	17992 ChEBI	sucrose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
29684	16136 ChEBI	hydrogen sulfide

Enzymes

@ref	Value	Activity	Ec
29684	catalase	+	1.11.1.6
29684	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	Geographic location	Country	Country ISO 3 Code	Continent
29684	marine solar saltern
67770	Rudong solar saltern	Jiangsu	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB663428 (>99% sequence identity) for Halogeometricum limi subclade from Microbeatlas

Aquatic Samples	10
Soil Samples
Animal Samples
Plant Samples
Total Samples	10

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 2617270895 annotated assembly for Halogeometricum limi CGMCC 1.8711	scaffold	GCA_900115785	555875.3	2617270895	555875	76.73

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
29684	Halosarcina limi strain RO1-6 16S ribosomal RNA gene, complete sequence	EU931577	1473		555875
67770	Halosarcina limi gene for 16S rRNA, complete sequence, strain: JCM 16054	AB663428	1473		555875

GC content

@ref	GC-content (mol%)	Method
29684	61.2
67770	61.2	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 limi CGMCC 1.8711
NCBI: GCA_900115785

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	88.50	no
125439	motility	BacteriaNetⓘ	yes	50.40	no
125439	gram_stain	BacteriaNetⓘ	positive	72.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	74.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
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	Halosarcina limi sp. nov., a halophilic archaeon from a marine solar saltern, and emended description of the genus Halosarcina.	Cui HL, Gao X, Li XY, Xu XW, Zhou YG, Liu HC, Zhou PJ	Int J Syst Evol Microbiol	10.1099/ijs.0.018697-0	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 )
#26069	IJSEM 2462 2010 ( DOI 10.1099/ijs.0.018697-0 , PubMed 19946053 )
#29684	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 #26069
#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 .
#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 limi (CGMCC 1.8711, JCM 16054, RO1-6)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Halophily

Metabolite utilization

Metabolite production

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_900115785

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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