Name: Halogeometricum rufum RO1-4
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133607

Type strain:

Species: Halogeometricum rufum

Strain Designation: RO1-4

Culture col. no.: CGMCC 1.7736, JCM 15770

Strain history: H.-L. Cui RO1-4.

NCBI tax ID(s): 553469 (species)

Section

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

Gram-negative
motile
ovoid-shaped
aerobe
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	*Haloferacales*
	Family	*Haloferacaceae*
	Genus	*Halogeometricum*
	Species	**Halogeometricum rufum**
	Full Scientific Name (LPSN)	Halogeometricum rufum Cui et al. 2010

Information on morphological and physiological properties Morphology

[Ref.: #29723]	Gram stain	negative

[Ref.: #29723]	Cell shape	ovoid-shaped

[Ref.: #29723]	Motility	yes

[Ref.: #29723]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

		Temperature
[Ref.: #29723]	growth	25-55 °C
[Ref.: #29723]	optimum	40-42 °C
[Ref.: #67770]	growth	37 °C

[Ref.: #29723]	Temperature range	thermophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #29723]			optimum	7
[Ref.: #29723]			growth	6-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29723]

Oxygen tolerance

aerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29723]		NaCl		growth	11-27	%
[Ref.: #29723]		NaCl		optimum	21	%

[Ref.: #29723]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29723]	acetate ChEBI	+	carbon source
[Ref.: #29723]	alanine ChEBI	+	carbon source
[Ref.: #29723]	arginine ChEBI	+	carbon source
[Ref.: #29723]	aspartate ChEBI	+	carbon source
[Ref.: #29723]	galactose ChEBI	+	carbon source
[Ref.: #29723]	glucose ChEBI	+	carbon source
[Ref.: #29723]	glutamate ChEBI	+	carbon source
[Ref.: #29723]	glycerol ChEBI	+	carbon source
[Ref.: #29723]	lactate ChEBI	+	carbon source
[Ref.: #29723]	lactose ChEBI	+	carbon source
[Ref.: #29723]	malate ChEBI	+	carbon source
[Ref.: #29723]	maltose ChEBI	+	carbon source
[Ref.: #29723]	mannitol ChEBI	+	carbon source
[Ref.: #29723]	mannose ChEBI	+	carbon source
[Ref.: #29723]	ornithine ChEBI	+	carbon source
[Ref.: #29723]	pyruvate ChEBI	+	carbon source
[Ref.: #29723]	sorbitol ChEBI	+	carbon source
[Ref.: #29723]	succinate ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #29723]		hydrogen sulfide ChEBI	yes
[Ref.: #29723]		indole ChEBI	yes

	Physiological tests	Metabolite	Indole test
[Ref.: #29723]		indole ChEBI	+

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #29723]		catalase	+	1.11.1.6
[Ref.: #29723]		cytochrome oxidase	+	1.9.3.1

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

[Ref.: #29723]	Sample type/isolated from	marine solar saltern

[Ref.: #67770]	Sample type/isolated from	Marine solar saltern in Jiangsu
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #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

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.: #29723]	Halogeometricum rufum strain RO1-4 16S ribosomal RNA gene, complete sequence	EU887286	1472	GenBank	553469 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Halogeometricum rufum CGMCC 1.7736	GCA_900112175	contig	GenBank	553469 tax ID
[Ref.: #66792]	Halogeometricum rufum CGMCC 1.7736	2617270920	draft	JGI IMG/M	553469 tax ID	*
[Ref.: #66792]	Halogeometricum rufum strain CGMCC 1.7736	553469.3	wgs	PATRIC	553469 tax ID	*

[Ref.: #29723]	GC-content	64.9 mol%
[Ref.: #67770]	GC-content	64.9 mol%	high performance liquid chromatography (HPLC)

Availability in culture collections External links

[Ref.: #29723]

Culture collection no.

CGMCC 1.7736, JCM 15770

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	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 )

#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 (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 .

#26106

IJSEM 2613 2010 ( DOI 10.1099/ijs.0.019463-0 , PubMed 20023063 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Halogeometricum rufum in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF