Name: Halorubrum lipolyticum 9-3
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5951

Type strain:

Species: Halorubrum lipolyticum

Strain Designation: 9-3

Culture col. no.: DSM 21995, CGMCC 1.5332, JCM 13559, KCTC 4069

Strain history: S. Liu 9-3.

NCBI tax ID(s): 1227482 (strain), 368624 (species)

SI-ID 297208

CGMCC 1.5332, JCM 13559, DSM 21995

Section

Halorubrum lipolyticum 9-3 is an aerobe, mesophilic, Gram-negative archaeon that was isolated from sediments of Aibi salt lake.

Gram-negative
motile
rod-shaped
aerobe
mesophilic
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	*Halorubraceae*
	Genus	*Halorubrum*
	Species	**Halorubrum lipolyticum**
	Full Scientific Name (LPSN)	Halorubrum lipolyticum Cui et al. 2006

Information on morphological and physiological properties Morphology

[Ref.: #31797]	Gram stain	negative

[Ref.: #31797]	Cell length	1.8-5.5 µm

[Ref.: #31797]	Cell width	0.9-1.2 µm

[Ref.: #31797]	Cell shape	rod-shaped

[Ref.: #31797]	Motility	yes

[Ref.: #31797]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16088]

Culture medium

HALOBACTERIA MEDIUM (DSMZ Medium 372)

[Ref.: #16088]

Culture medium growth

[Ref.: #16088]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16088]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #16088]	growth	37 °C
[Ref.: #31797]	growth	25-58 °C
[Ref.: #31797]	optimum	45-48 °C
[Ref.: #67770]	growth	37 °C

[Ref.: #16088]	Temperature range	mesophilic
[Ref.: #31797]	Temperature range	thermophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31797]			optimum	7.5
[Ref.: #31797]			growth	07-09

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31797]

Oxygen tolerance

aerobe

[Ref.: #31797]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31797]		NaCl		growth	9.86-27.84	%
[Ref.: #31797]		NaCl		optimum	15	%

[Ref.: #31797]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31797]	fructose ChEBI	+	carbon source
[Ref.: #31797]	galactose ChEBI	+	carbon source
[Ref.: #31797]	glucose ChEBI	+	carbon source
[Ref.: #31797]	maltose ChEBI	+	carbon source
[Ref.: #31797]	mannose ChEBI	+	carbon source
[Ref.: #31797]	nitrate ChEBI	+	reduction
[Ref.: #31797]	sucrose ChEBI	+	carbon source

	Enzyme	Enzyme activity	EC number
[Ref.: #31797]	catalase	+	1.11.1.6
[Ref.: #31797]	cytochrome oxidase	+	1.9.3.1
[Ref.: #31797]	gelatinase	+

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

[Ref.: #16088]	Sample type/isolated from	sediments of Aibi salt lake
[Ref.: #16088]	Geographic location (country and/or sea, region)	Xin-Jiang
[Ref.: #16088]	Country	China
[Ref.: #16088]	Country ISO 3 Code	CHN
[Ref.: #16088]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Aibi salt lake in Xin-Jiang
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Lake (large)
#Environmental	#Aquatic	#Sediment
#Condition	#Saline	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB663415 (>99% sequence identity) for Halorubrum from Microbeatlas

Aquatic Samples	18
Soil Samples	3
Animal Samples
Plant Samples
Total Samples	21

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

[Ref.: #16088]

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:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #16088]	Halorubrum lipolyticum strain 9-3 16S ribosomal RNA gene, partial sequence	DQ355814	1470	ENA	368624 tax ID
[Ref.: #20218]	Halorubrum lipolyticum gene for 16S ribosomal RNA, partial sequence, strain: JCM 13559	AB477978	1430	ENA	368624 tax ID	*
[Ref.: #20218]	Halorubrum lipolyticum gene for 16S rRNA, complete sequence, strain: JCM 13559	AB663415	1470	ENA	368624 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Halorubrum lipolyticum DSM 21995	GCA_000337375	contig	GenBank	1227482 tax ID
[Ref.: #66792]	Halorubrum lipolyticum DSM 21995	2534682115	draft	JGI IMG/M	1227482 tax ID	*
[Ref.: #66792]	Halorubrum lipolyticum DSM 21995	1227482.3	wgs	PATRIC	1227482 tax ID	*

[Ref.: #16088]	GC-content	65.9 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #31797]	GC-content	65.9 mol%

Availability in culture collections External links

[Ref.: #16088]

Culture collection no.

DSM 21995, CGMCC 1.5332, JCM 13559, KCTC 4069

[Ref.: #75440]

SI-ID 297208

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Halorubrum gandharaense sp. nov., an alkaliphilic haloarchaeon from commercial rock salt.	Kondo Y, Minegishi H, Echigo A, Shimane Y, Kamekura M, Itoh T, Ohkuma M, Takahashi-Ando N, Fukushima Y, Yoshida Y, Usami R	Int J Syst Evol Microbiol	10.1099/ijs.0.000261	2015	*
Phylogeny	Halorubrum salinum sp. nov., isolated from a marine solar saltern.	Zhang WJ, Cui HL	Arch Microbiol	10.1007/s00203-014-0975-1	2014	*
Phylogeny	Halorubrum lipolyticum sp. nov. and Halorubrum aidingense sp. nov., isolated from two salt lakes in Xin-Jiang, China.	Cui HL, Tohty D, Zhou PJ, Liu SJ	Int J Syst Evol Microbiol	10.1099/ijs.0.64305-0	2006	*

References

#16088

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21995

#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 )

#31797

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 #28068 (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 .

#75440

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-ID297208.1 )

#28068

IJSEM 1631 2006 ( DOI 10.1099/ijs.0.64305-0 , PubMed 16825640 )

* These data were automatically processed and therefore are not curated

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