Halomonas zhanjiangensis | Type strain | DSM 21076, CCTCC AB 208031, KCTC 22279, JSM 078169 | BacDiveID:6072

Strain identifier

BacDive ID: 6072

Type strain:

Species: Halomonas zhanjiangensis

Culture col. no.: DSM 21076, CCTCC AB 208031, KCTC 22279, JSM 078169

Strain history: <- YG Chen, Yunnan Inst., China

NCBI tax ID(s): 574966 (strain), 1121960 (species)

SI-ID 403840

DSM 21076

Special Collections

Section

Halomonas zhanjiangensis DSM 21076 is an aerobe, Gram-negative, motile bacterium that was isolated from sea urchin Hemicentrotus pulcherrimus.

Gram-negative
motile
rod-shaped
aerobe
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Oceanospirillales*
	Family	*Halomonadaceae*
	Genus	*Halomonas*
	Species	**Halomonas zhanjiangensis**
	Full Scientific Name (LPSN)	Halomonas zhanjiangensis Chen et al. 2009

Synonym

"Vreelandella zhanjiangensis"

Information on morphological and physiological properties Morphology

[Ref.: #29283]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %100

[Ref.: #29283]	Cell length	2 µm

[Ref.: #29283]	Cell width	1.05 µm

[Ref.: #29283]	Cell shape	rod-shaped

[Ref.: #29283]	Motility	yes

Pigment production

yes

Multimedia content

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Information on culture and growth conditions Culture and growth conditions

Culture medium

MEDIUM 514 PLUS ADDITIONAL SALT (DSMZ Medium 514b)

Culture medium growth

Culture medium link

Medium recipe at MediaDive

Culture medium composition

expand / minimize

Culture medium

MODIFIED MEDIUM 514 FOR HALOMONAS SP. (DSMZ Medium 1510)

Culture medium growth

Culture medium link

Medium recipe at MediaDive

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #15543]			growth	28 °C
[Ref.: #29283]			growth	04-40 °C
[Ref.: #29283]			optimum	27.5 °C
[Ref.: #67771]			growth	28 °C

	pH	Kind of pH		pH
[Ref.: #29283]			optimum	7.5
[Ref.: #29283]			growth	6-10.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29283]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #29283]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29283]		NaCl		growth	01-20	%
[Ref.: #29283]		NaCl		optimum	4	%

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29283]		acetate ChEBI	+	carbon source
[Ref.: #29283]		alanine ChEBI	+	carbon source
[Ref.: #29283]		arabinose ChEBI	+	carbon source
[Ref.: #29283]		asparagine ChEBI	+	carbon source
[Ref.: #29283]		citrate ChEBI	+	carbon source
[Ref.: #29283]		fructose ChEBI	+	carbon source
[Ref.: #29283]		glucose ChEBI	+	carbon source
[Ref.: #29283]		glutamate ChEBI	+	carbon source
[Ref.: #29283]		leucine ChEBI	+	carbon source
[Ref.: #29283]		maltose ChEBI	+	carbon source
[Ref.: #29283]		nitrate ChEBI	+	reduction
[Ref.: #29283]		proline ChEBI	+	carbon source
[Ref.: #29283]		pyruvate ChEBI	+	carbon source
[Ref.: #29283]		serine ChEBI	+	carbon source
[Ref.: #29283]		sucrose ChEBI	+	carbon source
[Ref.: #29283]		trehalose ChEBI	+	carbon source
[Ref.: #29283]		tween 60 ChEBI	+	carbon source
		Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #29283]		acid phosphatase	+	3.1.3.2
[Ref.: #29283]		alkaline phosphatase	+	3.1.3.1
[Ref.: #29283]		alpha-galactosidase	+	3.2.1.22
[Ref.: #29283]		catalase	+	1.11.1.6

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

[Ref.: #15543]	Sample type/isolated from	sea urchin Hemicentrotus pulcherrimus
[Ref.: #15543]	Host species	Hemicentrotus pulcherrimus
[Ref.: #15543]	Geographic location (country and/or sea, region)	South China Sea, tidal flat of Naozhou Island near Zhanjiang
[Ref.: #15543]	Country	China
[Ref.: #15543]	Country ISO 3 Code	CHN
[Ref.: #15543]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From sea water
[Ref.: #67771]	Geographic location (country and/or sea, region)	Guangdong province
[Ref.: #67771]	Country	China
[Ref.: #67771]	Country ISO 3 Code	CHN
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host

#Invertebrates (Other)

#Echinodermata

What are isolation sources categories?

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

Biosafety level

1

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.: #15543]	Halomonas sp. JSM 078169 16S ribosomal RNA gene, partial sequence	FJ429198	1446	GenBank ENA	574966 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Halomonas zhanjiangensis DSM 21076	GCA_000377665	scaffold	GenBank ENA	574966 tax ID	*
[Ref.: #66792]	Halomonas zhanjiangensis DSM 21076	574966.4	wgs	PATRIC	574966 tax ID	*
[Ref.: #66792]	Halomonas zhanjiangensis DSM 21076	2517572236	draft	JGI IMG/M	574966 tax ID	*

[Ref.: #15543]	GC-content	55.8 mol%	high performance liquid chromatography (HPLC)
[Ref.: #29283]	GC-content	55.8 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Halomonas zhanjiangensis DSM 21076 DSM 21076 NCBI: GCA_000377665.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Halomonas zhanjiangensis DSM 21076 DSM 21076 NCBI: GCA_000377665.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	100	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	97.138	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	85.397	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	88.739	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	98.228	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	84.252	no

Availability in culture collections External links

Culture collection no.

DSM 21076, CCTCC AB 208031, KCTC 22279, JSM 078169

SI-ID 403840

*

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	High quality draft genome sequence of the slightly halophilic bacterium Halomonas zhanjiangensis type strain JSM 078169(T) (DSM 21076(T)) from a sea urchin in southern China.	Zhou Y, Li R, Gao XY, Lapidus A, Han J, Haynes M, Lobos E, Huntemann M, Pati A, Ivanova NN, Rohde M, Mavromatis K, Tindall BJ, Markowitz V, Woyke T, Klenk HP, Kyrpides NC, Li WJ	Stand Genomic Sci	10.4056/sigs.5449586	2014	*
Phylogeny	[Diversity of culturable bacteria associated with the sea urchin Hemicentrotus pulcherrimus from Naozhou Island].	Huang K, Zhang L, Liu Z, Chen Q, Peng Q, Li W, Cui X, Chen Y	Wei Sheng Wu Xue Bao		2009	*
Phylogeny	Halomonas zhanjiangensis sp. nov., a halophilic bacterium isolated from a sea urchin.	Chen YG, Zhang YQ, Huang HY, Klenk HP, Tang SK, Huang K, Chen QH, Cui XL, Li WJ	Int J Syst Evol Microbiol	10.1099/ijs.0.010173-0	2009	*

References

#15543

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21076

#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 )

#29283

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 #25699 (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) .

#66793

Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#75559

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-ID403840.1 )

#25699

IJSEM 2888 2009 ( DOI 10.1099/ijs.0.010173-0 , PubMed 19628603 )

* These data were automatically processed and therefore are not curated

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