Name: Halomonas aquamarina DSM 5425
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 6020

Type strain:

Species: Halomonas aquamarina

Culture col. no.: DSM 5425, ACAM 246, ATCC 49692, KCTC 22196, UQM 3352, CIP 104043, IFO (now NBRC) 15608

Strain history: CIP <- 1994, ACAM <- St James <- R. Garrick and J. Gibson: strain UQM 3352

NCBI tax ID(s): 77097 (species)

SI-ID 34618

ATCC 496, ATCC 49692, ACM 3352, CIP 104043, DSM 5425, NCIMB 13119, IFO 15608, NCIMB 13859, NBRC 15608, NCIMB 13958, NCIMB 13961

Special Collections

Other strains from Halomonas aquamarina

Section

When using BacDive for research please cite our paper

Halomonas aquamarina DSM 5425 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from organic lake.

Gram-negative
aerobe
mesophilic
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Oceanospirillales*
	Family	*Halomonadaceae*
	Genus	*Halomonas*
	Species	**Halomonas aquamarina**
	Full Scientific Name (LPSN)	Halomonas aquamarina (ZoBell and Upham 1944) Dobson and Franzmann 1996

	Synonym	Alcaligenes faecalis subsp. homari
	Synonym	Deleya aesta
	Synonym	Halomonas meridiana
	Synonym	Halomonas axialensis
	Synonym	Alcaligenes aquamarinus
	Synonym	"Achromobacter* aquamarinus"*
	Synonym	Vreelandella aquamarina
	Synonym	Deleya aquamarina
	Synonym	Alcaligenes aestus

Information on morphological and physiological properties Morphology

[Ref.: #67771]	Gram stain	negative
[Ref.: #120897]	Gram stain	negative
[Ref.: #125438]	Gram stain	negative Confidence in %98.5
[Ref.: #125439]	Gram stain	negative Confidence in %97.2

[Ref.: #120897]	Cell shape	rod-shaped

[Ref.: #120897]	Motility	yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #2162]

Culture medium

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

[Ref.: #2162]

Culture medium growth

[Ref.: #2162]

Culture medium link

Medium recipe at MediaDive

[Ref.: #2162]

Culture medium composition

expand / minimize

[Ref.: #34491]

Culture medium

MEDIUM 110 - for Halomonas meridiana

[Ref.: #34491]

Culture medium growth

[Ref.: #34491]

Culture medium composition

expand / minimize

[Ref.: #120897]

Culture medium

CIP Medium 255

[Ref.: #120897]

Culture medium growth

[Ref.: #120897]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #120897]

Culture medium

CIP Medium 110

[Ref.: #120897]

Culture medium growth

[Ref.: #120897]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #2162]		growth	28 °C
[Ref.: #34491]		growth	25 °C
[Ref.: #67771]		growth	28 °C
[Ref.: #120897]		growth	10-37 °C
[Ref.: #120897]	negative	growth	5 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #67771]	Oxygen tolerance	aerobe
[Ref.: #120897]	Oxygen tolerance	obligate aerobe

[Ref.: #125438]	Ability of spore formation	no Confidence in %91.516
[Ref.: #125439]	Ability of spore formation	no Confidence in %98.3

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #120897]		nitrate ChEBI	+	reduction
[Ref.: #120897]		nitrite ChEBI	-	reduction

	Metabolite production	Metabolite	Production
[Ref.: #120897]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #120897]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #120897]	beta-galactosidase	-	3.2.1.23
[Ref.: #120897]	catalase	+	1.11.1.6
[Ref.: #120897]	lysine decarboxylase	-	4.1.1.18
[Ref.: #120897]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #120897]	oxidase	+
[Ref.: #120897]	urease	-	3.5.1.5

API® Biotype100:

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

	API ID	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
[Ref.: #120897]	535	not determinedn.d.	+	+	-	+	-	-	-	+	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	+	-	+	-	+	+	-	-	-	+	-	-	-	-	+	-	+	+	+	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	+	-	+	-	-	-	+	+	-	+	-	-	-	-	-	+	+	+	+	-	+	-	-	+	-	-

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

[Ref.: #2162]	Sample type/isolated from	organic lake
[Ref.: #2162]	Continent	Australia and Oceania

[Ref.: #67771]	Sample type/isolated from	From organic lake
[Ref.: #67771]	Country	Antarctica
[Ref.: #67771]	Country ISO 3 Code	ATA
[Ref.: #67771]	Continent	Australia and Oceania

[Ref.: #120897]	Sample type/isolated from	Environment, Water
[Ref.: #120897]	Geographic location (country and/or sea, region)	Burch lake
[Ref.: #120897]	Country	Antarctica
[Ref.: #120897]	Country ISO 3 Code	ATA
[Ref.: #120897]	Continent	Antarctica
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#Lake (large)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AJ306891 (>99% sequence identity) for Halomonas from Microbeatlas

Aquatic Samples	5177
Soil Samples	435
Animal Samples	4415
Plant Samples	138
Total Samples	10165

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

[Ref.: #2162]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #120897]	Biosafety level	1	Risk group (French classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #2162]	Halomonas meridiana partial 16S rRNA gene, strain DSM 5425	AJ306891	1528	GenBank ENA	29570 tax ID
[Ref.: #20218]	Halomonas meridiana genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 920	AB367234	920	GenBank ENA	29570 tax ID	*
[Ref.: #20218]	Halomonas meridiana genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 1204	AB367235	1204	GenBank ENA	29570 tax ID	*
[Ref.: #20218]	Halomonas meridiana (DSM 5425) 16S ribosomal RNA (16S rRNA) gene	M93356	1475	GenBank ENA	29570 tax ID	*
[Ref.: #20218]	Halomonas meridiana gene for 16S rRNA, partial sequence, strain: NBRC 15608	AB680914	1460	GenBank ENA	29570 tax ID	*
[Ref.: #124043]	Halomonas meridiana clone 6 16S ribosomal RNA gene, partial sequence.	KP150438	1496	GenBank ENA	29570 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Halomonas meridiana ACAM 246	GCA_900129255	contig	GenBank ENA	29570 tax ID	*
[Ref.: #66792]	Halomonas meridiana strain ACAM 246	29570.7	wgs	PATRIC	29570 tax ID	*
[Ref.: #66792]	Halomonas meridiana ACAM 246	2698536813	draft	JGI IMG/M	29570 tax ID	*

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Halomonas meridiana strain ACAM 246 PATRIC: 29570.7
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	98.5	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	95.891	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	91.516	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	83.071	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	98.875	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	80.382	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Halomonas meridiana ACAM 246 NCBI: GCA_900129255
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	98.3
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	69.9
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	97.2
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	facultative aerobe	60.8

Availability in culture collections External links

[Ref.: #2162]

Culture collection no.

DSM 5425, ACAM 246, ATCC 49692, KCTC 22196, UQM 3352, CIP 104043, IFO (now NBRC) 15608

[Ref.: #75506]

SI-ID 34618

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Halomonas piezotolerans sp. nov., a multiple-stress-tolerant bacterium isolated from a deep-sea sediment sample of the New Britain Trench.	Yan F, Fang J, Cao J, Wei Y, Liu R, Wang L, Xie Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.004069	2020	*
Phylogeny	Halomonas songnenensis sp. nov., a moderately halophilic bacterium isolated from saline and alkaline soils.	Jiang J, Pan Y, Hu S, Zhang X, Hu B, Huang H, Hong S, Meng J, Li C, Wang K	Int J Syst Evol Microbiol	10.1099/ijs.0.056499-0	2014	*
Phylogeny	Halomonas andesensis sp. nov., a moderate halophile isolated from the saline lake Laguna Colorada in Bolivia.	Guzman D, Quillaguaman J, Munoz M, Hatti-Kaul R	Int J Syst Evol Microbiol	10.1099/ijs.0.014522-0	2009	*
Phylogeny	Halomonas boliviensis sp. nov., an alkalitolerant, moderate halophile isolated from soil around a Bolivian hypersaline lake.	Quillaguaman J, Hatti-Kaul R, Mattiasson B, Alvarez MT, Delgado O	Int J Syst Evol Microbiol	10.1099/ijs.0.02800-0	2004	*
Enzymology	The alpha-amylase gene amyH of the moderate halophile Halomonas meridiana: cloning and molecular characterization.	Coronado MA, Vargas C, Mellado E, Tegos G, Drainas C, Nieto JNJ, Ventosa A	Microbiology (Reading)	10.1099/00221287-146-4-861	2000	*

References

#2162

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 5425

#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 )

#34491 ; 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) .

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

#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 .

#75506

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-ID34618.1 )

#120897 Collection of Institut Pasteur ; Curators of the CIP; CIP 104043

#124043

Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .

#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 .

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Halomonas meridiana in external resources:
SILVA
BRENDA
PANGAEA
GBIF

Halomonas meridiana strain ACAM 246

Halomonas meridiana ACAM 246

Change proposal

Change proposal