Halomonas halodenitrificans (DSM 735, ATCC 13511, CCM 286)

Name: Halomonas halodenitrificans (DSM 735, ATCC 13511, CCM 286)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6014

Type strain

Culture col. no. DSM 735 ATCC 13511 CCM 286 NCMB 700 CIP 105456 4 more

NCBI tax ID(s) 1121941 28252

Special Collections DSMZ CIP

History DSMZ <- CCM <- N.E. Gibbons (Micrococcus halodenitrificans) CIP <- 1998, NCIMB <- M. Ingram <- N.E. Gibbons, Micrococcus halodenitrificans

Links

Halomonas halodenitrificans DSM 735 is a Gram-negative, oval-shaped bacterium that was isolated from wiltshire bacon curing brine.

Gram-negative oval-shaped genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 35825

ATCC 13511,DSM 735,CCM 286,NCMB 700,CIP 105456,IAM 13950,IFO 14912,NCIMB 700,CECT 5012,NBRC 14912,KCTC 5069

@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 halodenitrificans

Full scientific name Halomonas halodenitrificans (Robinson and Gibbons 1952) Dobson and Franzmann 1996

Synonyms (2)

Paracoccus halodenitrificans
"Micrococcus halodenitrificans"

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
119801	negative	oval-shaped
125439	negative		98.624
125438	negative		99.5

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
379	MEDIUM 514 PLUS ADDITIONAL SALT (DSMZ Medium 514b)	Medium recipe at MediaDive	Name: MEDIUM 514 plus additional salt (DSMZ Medium 514b) Composition: NaCl 19.45 g/l Agar 17.5 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
39298	MEDIUM 192 - for Alteromonas rubra		Distilled water make up to (250.000 ml);Agar (15.000 g);Yeast extract (3.000 g);Peptone (5.000 g);Synthetic sea solution - M0216 (750.000 ml)
119801	CIP Medium 192	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
379	positive	growth	28
39298	positive	growth	25
119801	positive	growth	15-30
119801	negative	growth	5
119801	negative	growth	37
119801	negative	growth	41
119801	negative	growth	45

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125438		90.246
125439		99.927

Halophily

@ref	Salt	Growth	Tested relation	Concentration
119801	NaCl	positive	growth	2-10 %
119801	NaCl		growth	0 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
119801	4853 ChEBI	esculin	-	hydrolysis
119801	17234 ChEBI	glucose	-	degradation
119801	606565 ChEBI	hippurate	-	hydrolysis
119801	15792 ChEBI	malonate	-	assimilation
119801	17632 ChEBI	nitrate	-	builds gas from
119801	17632 ChEBI	nitrate	+	reduction
119801	16301 ChEBI	nitrite	-	builds gas from
119801	16301 ChEBI	nitrite	-	reduction

Metabolite production

@ref	Chebi-ID	Metabolite	Production
119801	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
119801	15688 ChEBI	acetoin	-
119801	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
119801	alcohol dehydrogenase	-	1.1.1.1
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
119801	amylase	-
68382	beta-galactosidase	-	3.2.1.23	from API zym
119801	beta-galactosidase	-	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
119801	caseinase	-	3.4.21.50
119801	catalase	-	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	-		from API zym
119801	gamma-glutamyltransferase	+	2.3.2.2
119801	gelatinase	-
119801	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
119801	lipase	-
68382	lipase (C 14)	-		from API zym
119801	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
119801	ornithine decarboxylase	-	4.1.1.17
119801	oxidase	-
119801	phenylalanine ammonia-lyase	-	4.3.1.24
68382	trypsin	-	3.4.21.4	from API zym
119801	tryptophan deaminase	-
119801	tween esterase	-
119801	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
119801	-	-	+	-	-	+	-	-	-	-	-	+	-	-	-	+	-	-	-	-

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
119801	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Food production	#Meat
#Condition	#Saline	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
379	wiltshire bacon curing brine		Canada	CAN	North America
119801	Bacon curing brine	Wiltshire	United Kingdom	GBR	Europe

Taxonmaps

69479

Global distribution of 16S sequence L04942 (>99% sequence identity) for Halomonas from Microbeatlas

Aquatic Samples	19
Soil Samples	8
Animal Samples	12
Plant Samples	7
Total Samples	46

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
379	1	Risk group (German classification) According to TRBA 466
119801	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM62004v1 assembly for Halomonas halodenitrificans DSM 735	scaffold	GCA_000620045	1121941.3	2556921012	1121941	68.16

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
379	Paracoccus halodenitrificans 16S ribosomal RNA sequence	L04942	1531		28252

GC content

379

GC-content (mol%)65.0

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM62004v1 assembly for Halomonas halodenitrificans DSM 735
BV-BRC: 1121941.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	68.91	no
125439	gram_stain	BacteriaNetⓘ	negative	98.62	no
125439	motility	BacteriaNetⓘ	yes	86.15	no
125439	spore_formation	BacteriaNetⓘ	no	99.93	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Halomonas halodenitrificans DSM 735 DSM 735
NCBI: GCA_000620045.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.50	no
125438	anaerobic	anaerobicⓘ	no	96.81	no
125438	aerobic	aerobicⓘ	yes	79.09	no
125438	spore-forming	spore-formingⓘ	no	90.25	no
125438	thermophilic	thermophileⓘ	no	97.60	no
125438	flagellated	motile2+ⓘ	no	68.70	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	1, 4, 5, 6-Tetrahydro-2-methyl-4-pyrimidinecarboxylic acid (THMP) - A novel universal stress protein data from Halomonas species for pharmaceutical applications.	Rekadwad BN.	Data Brief	10.1016/j.dib.2024.110272	2024
	Draft Genome Sequence of Halomonas sp. Strain KAO, a Halophilic Mn(II)-Oxidizing Bacterium.	Lee CJ, Wright MH, Bentley SR, Greene AC.	Microbiol Resour Announc	10.1128/mra.00032-21	2021
Enzymology	Unusual features in the photosynthetic machinery of Halorhodospira halochloris DSM 1059 revealed by complete genome sequencing.	Tsukatani Y, Hirose Y, Harada J, Yonekawa C, Tamiaki H.	Photosynth Res	10.1007/s11120-019-00613-0	2019
Metabolism	Net Charges of the Ribosomal Proteins of the S10 and spc Clusters of Halophiles Are Inversely Related to the Degree of Halotolerance.	Tirumalai MR, Anane-Bediakoh D, Rajesh S, Fox GE.	Microbiol Spectr	10.1128/spectrum.01782-21	2021
	Abundant Sulfitobacter marine bacteria protect Emiliania huxleyi algae from pathogenic bacteria.	Beiralas R, Ozer N, Segev E.	ISME Commun	10.1038/s43705-023-00311-y	2023
Genetics	Beyond the ABCs-Discovery of Three New Plasmid Types in Rhodobacterales (RepQ, RepY, RepW).	Freese HM, Ringel V, Overmann J, Petersen J.	Microorganisms	10.3390/microorganisms10040738	2022
Genetics	The association of group IIB intron with integrons in hypersaline environments.	Sonbol S, Siam R.	Mob DNA	10.1186/s13100-021-00234-2	2021
Genetics	Endozoicomonas genomes reveal functional adaptation and plasticity in bacterial strains symbiotically associated with diverse marine hosts.	Neave MJ, Michell CT, Apprill A, Voolstra CR.	Sci Rep	10.1038/srep40579	2017
	Biological Contamination Prevention for Outer Solar System Moons of Astrobiological Interest: What Do We Need to Know?	Rettberg P, Antunes A, Brucato J, Cabezas P, Collins G, Haddaji A, Kminek G, Leuko S, McKenna-Lawlor S, Moissl-Eichinger C, Fellous JL, Olsson-Francis K, Pearce D, Rabbow E, Royle S, Saunders M, Sephton M, Spry A, Walter N, Wimmer Schweingruber R, Treuet JC.	Astrobiology	10.1089/ast.2018.1996	2019
Phylogeny	Nitrite reductase genes (nirK and nirS) as functional markers to investigate diversity of denitrifying bacteria in pacific northwest marine sediment communities.	Braker G, Zhou J, Wu L, Devol AH, Tiedje JM.	Appl Environ Microbiol	10.1128/aem.66.5.2096-2104.2000	2000
	Biology of moderately halophilic aerobic bacteria.	Ventosa A, Nieto JJ, Oren A.	Microbiol Mol Biol Rev	10.1128/mmbr.62.2.504-544.1998	1998
Enzymology	Nitric oxide reductase (norB) genes from pure cultures and environmental samples.	Braker G, Tiedje JM.	Appl Environ Microbiol	10.1128/aem.69.6.3476-3483.2003	2003
Metabolism	Chip calorimetry for the monitoring of whole cell biotransformation.	Maskow T, Lerchner J, Peitzsch M, Harms H, Wolf G	J Biotechnol	10.1016/j.jbiotec.2005.10.008	2005
Metabolism	Thermokinetic description of anaerobic growth of Halomonas halodenitrificans using a static microcalorimetric ampoule technique.	Maskow T, Babel W	J Biotechnol	10.1016/s0168-1656(02)00341-3	2003
Phylogeny	Sulfitobacter algicola sp. nov., isolated from green algae.	Wang CN, Liu Y, Wang J, Du ZJ, Wang MY.	Arch Microbiol	10.1007/s00203-021-02213-w	2021
Phylogeny	Halomonas icarae sp. nov., a moderately halophilic bacterium isolated from beach soil in India.	Pandiyan K, Kushwaha P, Bagul SY, Chakdar H, Madhaiyan M, Krishnamurthi S, Kumar P, Karthikeyan N, Singh A, Kumar M, Singh UB, Saxena AK	Int J Syst Evol Microbiol	10.1099/ijsem.0.004611	2020

References

#379	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 735
#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 )
#39298	; 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 .
#119801	Collection of Institut Pasteur ; Curators of the CIP; CIP 105456
#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 halodenitrificans (DSM 735, ATCC 13511, CCM 286)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Spore formation

Halophily

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000620045

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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