Halomonas denitrificans (DSM 18045, CIP 109894, M29)

Name: Halomonas denitrificans (DSM 18045, CIP 109894, M29)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6049

Type strain

Strain Designation M29

Culture col. no. DSM 18045 CIP 109894 M29 KCTC 12665

NCBI tax ID(s) 370769

Special Collections DSMZ CIP Literature strains KCTC

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

Links

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

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

Name and taxonomic classification

SI-ID 302755

DSM 18045,KCTC 12665,CIP 109894

@ref 20215

Last LPSN update 2026-05-29 08:26:18

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Oceanospirillales

Family Halomonadaceae

Genus Halomonas

Species Halomonas denitrificans

Full scientific name Halomonas denitrificans Kim et al. 2007

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31987	negative	1.2-1.6 µm	0.6-0.8 µm	rod-shaped
118897	negative			rod-shaped
125438	negative				98.4
125439	negative				98.017

Pigmentation

31987

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7266	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)	Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514; with strain-specific modifications) Composition: NaCl 80.0 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
7266	R2A MEDIUM (DSMZ Medium 830)	Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
36923	Marine agar (MA)		Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
118897	CIP Medium 13	Medium recipe at CIP
118897	CIP Medium 566	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
7266	positive	growth	28
31987	positive	growth	05-50
31987	positive	optimum	25-35
36923	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
31987	positive	optimum	08-09
31987	positive	growth	07-10	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
31987	aerobe
118897	facultative anaerobe

Spore formation

@ref	Spore formation	Confidence
31987
125439		99.874

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31987	NaCl	positive	growth	02-20 %
31987	NaCl	positive	optimum	08-10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31987	37054 ChEBI	3-hydroxybutyrate	+	carbon source
31987	30089 ChEBI	acetate	+	carbon source
31987	16449 ChEBI	alanine	+	carbon source
31987	16947 ChEBI	citrate	+	carbon source
31987	24996 ChEBI	lactate	+	carbon source
31987	25115 ChEBI	malate	+	carbon source
31987	15792 ChEBI	malonate	+	carbon source
31987	17632 ChEBI	nitrate	+	reduction
118897	17632 ChEBI	nitrate	+	reduction
118897	16301 ChEBI	nitrite	-	reduction
31987	26271 ChEBI	proline	+	carbon source
31987	17272 ChEBI	propionate	+	carbon source
31987	17822 ChEBI	serine	+	carbon source
31987	31011 ChEBI	valerate	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
118897	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
31987	catalase	+	1.11.1.6
118897	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
31987	cytochrome oxidase	+	1.9.3.1
68382	esterase (C 4)	-		from API zym
68382	esterase lipase (C 8)	-		from API zym
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
118897	oxidase	+
68382	trypsin	-	3.4.21.4	from API zym
118897	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
118897	-	+	-	-	-	+	-	-	-	-	+	+	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Condition	#Saline

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7266	solar saltern		Republic of Korea	KOR	Asia
118897	Environment, Solar saltern	Anmyeondo	Republic of Korea	KOR	Asia

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7266	1	Risk group (German classification) According to TRBA 466
118897	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	NCBI tax ID	Score
66792	ASM305630v1 assembly for Halomonas denitrificans DSM 18045	contig	GCA_003056305	370769.4	370769	76.43

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
31987	Halomonas denitrificans partial 16S rRNA gene, type strain M29T	AM229317	1489		370769

GC content

31987

GC-content (mol%)53.8-55.2

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM305630v1 assembly for Halomonas denitrificans DSM 18045
NCBI: GCA_003056305

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	61.90	no
125439	gram_stain	BacteriaNetⓘ	negative	98.02	no
125439	motility	BacteriaNetⓘ	yes	87.38	no
125439	spore_formation	BacteriaNetⓘ	no	99.87	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Halomonas denitrificans strain DSM 18045
PATRIC: 370769.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.40	yes
125438	anaerobic	anaerobicⓘ	no	95.43	yes
125438	spore-forming	spore-formingⓘ	no	86.05	yes
125438	aerobic	aerobicⓘ	yes	79.08	no
125438	thermophilic	thermophileⓘ	no	98.21	yes
125438	flagellated	motile2+ⓘ	yes	82.61	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Antimicrobial Properties of Secondary Metabolites Produced by Halomonas sp.: A Halophilic Bacterium.	Perumal K, Seenuvasan J, Nandhagopal M.	Cureus	10.7759/cureus.69633	2024
	Synthesis, kinetics, mechanisms, and bioactivity evaluations of a novel Zn(ii) complex.	Dey A, Kumar R, Dutta B, Bandopadhyay R, Chakrabortty S, Khan MA, Saratale RG, Saratale GD, Jeon BH, Ghosh AK.	RSC Adv	10.1039/d4ra03356f	2024
	Synthesis, Kinetics, Reaction Mechanism, and Bioactivity Assays of a Dimeric Palladium Complex.	Dey A, Kumar R, Dutta B, Bandopadhyay R, Chakrabortty S, Khan MA, Jeon BH, Ghosh AK.	ACS Omega	10.1021/acsomega.3c05944	2023
Phylogeny	Denitrification as an important taxonomic marker within the genus Halomonas.	Gonzalez-Domenech CM, Martinez-Checa F, Bejar V, Quesada E.	Syst Appl Microbiol	10.1016/j.syapm.2009.12.001	2010
Genetics	A Novel Benthic Phage Infecting Shewanella with Strong Replication Ability.	Wang Z, Zhao J, Wang L, Li C, Liu J, Zhang L, Zhang Y.	Viruses	10.3390/v11111081	2019
	Metatranscriptomic and comparative genomic insights into resuscitation mechanisms during enrichment culturing.	Mu DS, Liang QY, Wang XM, Lu DC, Shi MJ, Chen GJ, Du ZJ.	Microbiome	10.1186/s40168-018-0613-2	2018
	Aerobic Denitrification and Heterotrophic Sulfur Oxidation in the Genus Halomonas Revealed by Six Novel Species Characterizations and Genome-Based Analysis.	Wang L, Shao Z.	Front Microbiol	10.3389/fmicb.2021.652766	2021
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 urmiana sp. nov., a moderately halophilic bacterium isolated from Urmia Lake in Iran.	Khan SA, Zununi Vahed S, Forouhandeh H, Tarhriz V, Chaparzadeh N, Hejazi MA, Jeon CO, Hejazi MS.	Int J Syst Evol Microbiol	10.1099/ijsem.0.004005	2020
Phylogeny	Halomonas aestuarii sp. nov., a moderately halophilic bacterium isolated from a tidal flat.	Koh HW, Rani S, Kim SJ, Moon E, Nam SW, Rhee SK, Park SJ.	Int J Syst Evol Microbiol	10.1099/ijsem.0.001824	2017
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 )
#28241	IJSEM 675 2007 ( DOI 10.1099/ijs.0.64767-0 , PubMed 17392185 )
#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
#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 .
#118897	Collection of Institut Pasteur ; Curators of the CIP; CIP 109894
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#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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Halomonas denitrificans (DSM 18045, CIP 109894, M29)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Enzymes

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003056305

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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