Name: Halomonas denitrificans M29
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 6049

Type strain:

Species: Halomonas denitrificans

Strain Designation: M29

Culture col. no.: DSM 18045, CIP 109894, KCTC 12665

Strain history: CIP <- 2008, DSMZ <- K.K. Kim, KAIST, Daejon, Korea: strain M29

NCBI tax ID(s): 370769 (species)

SI-ID 302755

DSM 18045, KCTC 12665, CIP 109894

Special Collections

Section

Halomonas denitrificans M29 is an aerobe, Gram-negative, motile bacterium that was isolated from solar saltern.

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 denitrificans**
	Full Scientific Name (LPSN)	Halomonas denitrificans Kim et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #31987]	Gram stain	negative
[Ref.: #118897]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %98.4

[Ref.: #31987]	Cell length	1.2-1.6 µm

[Ref.: #31987]	Cell width	0.6-0.8 µm

[Ref.: #31987]	Cell shape	rod-shaped
[Ref.: #118897]	Cell shape	rod-shaped

[Ref.: #31987]	Motility	yes
[Ref.: #118897]	Motility	yes

[Ref.: #31987]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7266]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #7266]

Culture medium growth

[Ref.: #7266]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7266]

Culture medium composition

expand / minimize

[Ref.: #7266]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #7266]

Culture medium growth

[Ref.: #7266]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7266]

Culture medium composition

expand / minimize

[Ref.: #36923]

Culture medium

Marine agar (MA)

[Ref.: #36923]

Culture medium growth

[Ref.: #36923]

Culture medium composition

expand / minimize

[Ref.: #118897]

Culture medium

CIP Medium 13

[Ref.: #118897]

Culture medium growth

[Ref.: #118897]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #118897]

Culture medium

CIP Medium 566

[Ref.: #118897]

Culture medium growth

[Ref.: #118897]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #7266]	growth	28 °C
[Ref.: #31987]	growth	05-50 °C
[Ref.: #31987]	optimum	25-35 °C
[Ref.: #36923]	growth	30 °C

	pH	Kind of pH		pH
[Ref.: #31987]			optimum	08-09
[Ref.: #31987]			growth	07-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31987]	Oxygen tolerance	aerobe
[Ref.: #118897]	Oxygen tolerance	facultative anaerobe

[Ref.: #31987]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31987]		NaCl		growth	02-20	%
[Ref.: #31987]		NaCl		optimum	08-10	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31987]	3-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #31987]	acetate ChEBI	+	carbon source
[Ref.: #31987]	alanine ChEBI	+	carbon source
[Ref.: #31987]	citrate ChEBI	+	carbon source
[Ref.: #31987]	lactate ChEBI	+	carbon source
[Ref.: #31987]	malate ChEBI	+	carbon source
[Ref.: #31987]	malonate ChEBI	+	carbon source
[Ref.: #31987]	nitrate ChEBI	+	reduction
[Ref.: #118897]	nitrate ChEBI	+	reduction
[Ref.: #118897]	nitrite ChEBI	-	reduction
[Ref.: #31987]	proline ChEBI	+	carbon source
[Ref.: #31987]	propionate ChEBI	+	carbon source
[Ref.: #31987]	serine ChEBI	+	carbon source
[Ref.: #31987]	valerate ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #118897]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #31987]	catalase	+	1.11.1.6
[Ref.: #118897]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #31987]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68382]	esterase (C 4)	-		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	-		* from API zym
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #118897]	oxidase	+
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #118897]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #118897]	12199	-	+	-	-	-	+	-	-	-	-	+	+	-	-	-	-	-	-	-	-

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

[Ref.: #7266]	Sample type/isolated from	solar saltern
[Ref.: #7266]	Country	Republic of Korea
[Ref.: #7266]	Country ISO 3 Code	KOR
[Ref.: #7266]	Continent	Asia

[Ref.: #118897]	Sample type/isolated from	Environment, Solar saltern
[Ref.: #118897]	Geographic location (country and/or sea, region)	Anmyeondo
[Ref.: #118897]	Country	Republic of Korea
[Ref.: #118897]	Country ISO 3 Code	KOR
[Ref.: #118897]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Condition

#Saline

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AM229317 (>99% sequence identity) for Halomonas from Microbeatlas

Aquatic Samples	505
Soil Samples	68
Animal Samples	1696
Plant Samples	21
Total Samples	2290

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

[Ref.: #7266]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #118897]	Biosafety level	1	Risk group (French classification)

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.: #31987]	Halomonas denitrificans partial 16S rRNA gene, type strain M29T	AM229317	1489	GenBank ENA	370769 tax ID
[Ref.: #20218]	Halomonas denitrificans genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 1089	AB367230	1089	GenBank ENA	370769 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Halomonas denitrificans DSM 18045	GCA_003056305	contig	GenBank ENA	370769 tax ID	*
[Ref.: #66792]	Halomonas denitrificans strain DSM 18045	370769.4	wgs	PATRIC	370769 tax ID	*

[Ref.: #31987]

GC-content

53.8-55.2 mol%

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Halomonas denitrificans strain DSM 18045 PATRIC: 370769.4
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	98.4	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	95.43	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	86.05	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	79.075	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	98.214	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	82.605	no

Availability in culture collections External links

[Ref.: #7266]

Culture collection no.

DSM 18045, CIP 109894, KCTC 12665

[Ref.: #75536]

SI-ID 302755

Literature:

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Biodegradation of Para Amino Acetanilide by Halomonas sp. TBZ3.	Hajizadeh N, Sefidi Heris Y, Zununi Vahed S, Vallipour J, Hejazi MA, Golabi SM, Asadpour-Zeynali K, Hejazi MS	Jundishapur J Microbiol	10.5812/jjm.18622	2015	*
Phylogeny	Halomonas huangheensis sp. nov., a moderately halophilic bacterium isolated from a saline-alkali soil.	Miao C, Jia F, Wan Y, Zhang W, Lin M, Jin W	Int J Syst Evol Microbiol	10.1099/ijs.0.056556-0	2013	*
Phylogeny	Halomonas gomseomensis sp. nov., Halomonas janggokensis sp. nov., Halomonas salaria sp. nov. and Halomonas denitrificans sp. nov., moderately halophilic bacteria isolated from saline water.	Kim KK, Jin L, Yang HC, Lee ST	Int J Syst Evol Microbiol	10.1099/ijs.0.64767-0	2007	*

References

#7266

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18045

#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 )

#31987

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 #28241 (see below)

#36923 ; Curators of the CIP;

#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) .

#68382

Automatically annotated from API zym .

#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 .

#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) .

#75536

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-ID302755.1 )

#118897 Collection of Institut Pasteur ; Curators of the CIP; CIP 109894

#28241

IJSEM 675 2007 ( DOI 10.1099/ijs.0.64767-0 , PubMed 17392185 )

* These data were automatically processed and therefore are not curated

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Halomonas denitrificans strain DSM 18045

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