Name: Halomonas hydrothermalis 1878c
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 6041

Type strain:

Species: Halomonas hydrothermalis

Strain Designation: 1878c, Slthf2

Culture col. no.: DSM 15725, ATCC BAA-800, CECT 5814, CIP 108044

Strain history: CIP <- 2003, C. Marquez, Sevilla Univ., Sevilla, Spain: strain Slthf2, 1878c <- J. Kaye, Washington Univ., Washington, USA

NCBI tax ID(s): 115561 (species)

SI-ID 131419

ATCC BAA-800, CECT 5814, DSM 15725, CCM 7104, CIP 108044, LMG 28987

Section

Halomonas hydrothermalis 1878c is a facultative aerobe, mesophilic, Gram-negative bacterium that was isolated from low-temperature hydrothermal fluid.

Gram-negative
motile
rod-shaped
facultative aerobe
mesophilic
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 hydrothermalis**
	Full Scientific Name (LPSN)	Halomonas hydrothermalis Kaye et al. 2004

Information on morphological and physiological properties Morphology

[Ref.: #29992]	Gram stain	negative
[Ref.: #120011]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.997

[Ref.: #29992]	Cell length	2.5 µm

[Ref.: #29992]	Cell width	1.5 µm

[Ref.: #29992]	Cell shape	rod-shaped
[Ref.: #120011]	Cell shape	rod-shaped

[Ref.: #29992]	Motility	yes
[Ref.: #120011]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %98.882

[Ref.: #29992]

Pigment production

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6083]

Culture medium

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

[Ref.: #6083]

Culture medium growth

[Ref.: #6083]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6083]

Culture medium composition

expand / minimize

[Ref.: #37405]

Culture medium

Marine agar (MA)

[Ref.: #37405]

Culture medium growth

[Ref.: #37405]

Culture medium composition

expand / minimize

[Ref.: #120011]

Culture medium

CIP Medium 13

[Ref.: #120011]

Culture medium growth

[Ref.: #120011]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #120011]

Culture medium

CIP Medium 72

[Ref.: #120011]

Culture medium growth

[Ref.: #120011]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #6083]		growth	28 °C
[Ref.: #29992]		growth	02-40 °C
[Ref.: #29992]		optimum	30 °C
[Ref.: #37405]		growth	30 °C
[Ref.: #120011]		growth	15-30 °C
[Ref.: #120011]	no	growth	5 °C
[Ref.: #120011]	no	growth	37 °C
[Ref.: #120011]	no	growth	41 °C
[Ref.: #120011]	no	growth	45 °C

[Ref.: #6083]	Temperature range	mesophilic
[Ref.: #29992]	Temperature range	mesophilic
[Ref.: #37405]	Temperature range	mesophilic
[Ref.: #120011]	Temperature range	psychrophilic
[Ref.: #120011]	Temperature range	mesophilic
[Ref.: #120011]	Temperature range	thermophilic

	pH	Kind of pH		pH
[Ref.: #29992]			optimum	7.5
[Ref.: #29992]			growth	05-12

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29992]	Oxygen tolerance	facultative aerobe
[Ref.: #120011]	Oxygen tolerance	obligate aerobe

[Ref.: #29992]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.958

	Salt	Tested relation		Salt conc.
[Ref.: #29992]	NaCl		growth	0.5-22	%
[Ref.: #29992]	NaCl		optimum	5.5	%
[Ref.: #120011]	NaCl		growth	2-10	%
[Ref.: #120011]	NaCl	no	growth	0	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29992]	acetate ChEBI	+	carbon source
[Ref.: #29992]	arabinose ChEBI	+	carbon source
[Ref.: #29992]	arginine ChEBI	+	carbon source
[Ref.: #29992]	asparagine ChEBI	+	carbon source
[Ref.: #29992]	citrate ChEBI	+	carbon source
[Ref.: #120011]	citrate ChEBI	-	carbon source
[Ref.: #120011]	esculin ChEBI	-	hydrolysis
[Ref.: #29992]	fructose ChEBI	+	carbon source
[Ref.: #29992]	galactose ChEBI	+	carbon source
[Ref.: #29992]	glucose ChEBI	+	carbon source
[Ref.: #29992]	glycerol ChEBI	+	carbon source
[Ref.: #120011]	hippurate ChEBI	+	hydrolysis
[Ref.: #29992]	malate ChEBI	+	carbon source
[Ref.: #29992]	malonate ChEBI	+	carbon source
[Ref.: #120011]	malonate ChEBI	-	assimilation
[Ref.: #29992]	maltose ChEBI	+	carbon source
[Ref.: #29992]	mannitol ChEBI	+	carbon source
[Ref.: #29992]	mannose ChEBI	+	carbon source
[Ref.: #29992]	nitrate ChEBI	+	reduction
[Ref.: #120011]	nitrate ChEBI	+	reduction
[Ref.: #120011]	nitrate ChEBI	-	respiration
[Ref.: #120011]	nitrite ChEBI	-	reduction
[Ref.: #29992]	proline ChEBI	+	carbon source
[Ref.: #29992]	propionate ChEBI	+	carbon source
[Ref.: #29992]	sucrose ChEBI	+	carbon source
[Ref.: #29992]	trehalose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #120011]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	-	3.1.3.2	* from API zym
[Ref.: #120011]	alcohol dehydrogenase	-	1.1.1.1
[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.: #120011]	amylase	+
[Ref.: #120011]	beta-galactosidase	-	3.2.1.23
[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.: #120011]	caseinase	-	3.4.21.50
[Ref.: #29992]	catalase	+	1.11.1.6
[Ref.: #120011]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #29992]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68382]	esterase (C 4)	-		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	-		* from API zym
[Ref.: #120011]	gamma-glutamyltransferase	+	2.3.2.2
[Ref.: #120011]	gelatinase	-
[Ref.: #120011]	lecithinase	+
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #120011]	lipase	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #120011]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #120011]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #120011]	oxidase	+
[Ref.: #120011]	phenylalanine ammonia-lyase	+	4.3.1.24
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #120011]	tryptophan deaminase	-
[Ref.: #120011]	tween esterase	+
[Ref.: #120011]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

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.: #120011]	2558	not determinedn.d.	+	+	-	+	-	-	-	+	-	+	+	-	-	-	-	-	-	-	-	-	-	-	+	-	-	+	-	-	-	-	-	+	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	+	+	+	-	+	-	-	+	+	+	+	-	+	+	-	-	-	+	+	+	+	+	+	-	-	+	-	+

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.: #120011]	10842	-	-	-	-	-	+	-	-	-	-	-	+	-	-	-	+	-	-	-	-

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

[Ref.: #6083]	Sample type/isolated from	low-temperature hydrothermal fluid
[Ref.: #6083]	Geographic location (country and/or sea, region)	17°S Southern East Pacific Rise
[Ref.: #6083]	Geographic location	-17.0000°/0.0000°

[Ref.: #120011]	Sample type/isolated from	Hydrothermal fluid
[Ref.: #120011]	Geographic location (country and/or sea, region)	South
[Ref.: #120011]	Country	Pacific Ocean
[Ref.: #120011]	Isolation date	1998
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AF212218 (>99% sequence identity) for Halomonas from Microbeatlas

Aquatic Samples	62
Soil Samples	3
Animal Samples	12
Plant Samples	1
Total Samples	78

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

[Ref.: #6083]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #120011]	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.: #6083]	Halomonas hydrothermalis strain Slthf2 16S ribosomal RNA gene, complete sequence	AF212218	1409	ENA	115561 tax ID
[Ref.: #20218]	Halomonas hydrothermalis genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 958	AB367232	958	ENA	115561 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Halomonas hydrothermalis Slthf2	GCA_011399095	complete	GenBank	115561 tax ID	*
[Ref.: #66792]	Halomonas hydrothermalis strain Slthf2	115561.14	complete	PATRIC	115561 tax ID	*

[Ref.: #29992]

GC-content

56.3 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Halomonas hydrothermalis Slthf2 NCBI: GCA_011399095.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Halomonas hydrothermalis Slthf2 NCBI: GCA_011399095.1
[Ref.: #69480]	motile	yes	93.622	yes
[Ref.: #69480]	flagellated	yes	82.091	no
[Ref.: #69480]	gram-positive	no	98.854	yes
[Ref.: #69480]	anaerobic	no	98.565	yes
[Ref.: #69480]	aerobic	yes	87.598	yes
[Ref.: #69480]	halophile	yes	95.075	yes
[Ref.: #69480]	spore-forming	no	96.198	no
[Ref.: #69480]	glucose-util	yes	89.989	yes
[Ref.: #69480]	thermophile	no	98.308	yes
[Ref.: #69480]	glucose-ferment	no	73.017	no

Availability in culture collections External links

[Ref.: #6083]

Culture collection no.

DSM 15725, ATCC BAA-800, CECT 5814, CIP 108044

[Ref.: #75528]

SI-ID 131419

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Halomonas humidisoli Sp. Nov., Isolated From Saline-Alkaline Soil.	Liu H, Tang L, Zhao J, Miao S, Gong Q, Ma L, Zhang G	Curr Microbiol	10.1007/s00284-020-02291-x	2021	*
Genetics	Complete Genome Sequence of Halomonas hydrothermalis Strain Slthf2, a Halophilic Bacterium Isolated from a Deep-Sea Hydrothermal-Vent Environment.	Takeyama N, Huang M, Sato K, Galipon J, Arakawa K	Microbiol Resour Announc	10.1128/MRA.00294-20	2020	*
Phylogeny	Halomonas lutescens sp. nov., a halophilic bacterium isolated from a lake sediment.	Wang T, Wei X, Xin Y, Zhuang J, Shan S, Zhang J	Int J Syst Evol Microbiol	10.1099/ijsem.0.001413	2016	*
Phylogeny	Halomonas zhaodongensis sp. nov., a slightly halophilic bacterium isolated from saline-alkaline soils in Zhaodong, China.	Jiang J, Pan Y, Meng L, Hu S, Zhang X, Hu B, Meng J, Li C, Huang H, Wang K, Su T	Antonie Van Leeuwenhoek	10.1007/s10482-013-9976-3	2013	*
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 alkaliphila sp. nov., a novel halotolerant alkaliphilic bacterium isolated from a salt pool in Campania (Italy).	Romano I, Lama L, Nicolaus B, Poli A, Gambacorta A, Giordano A	J Gen Appl Microbiol	10.2323/jgam.52.339	2006	*
Phylogeny	Halomonas neptunia sp. nov., Halomonas sulfidaeris sp. nov., Halomonas axialensis sp. nov. and Halomonas hydrothermalis sp. nov.: halophilic bacteria isolated from deep-sea hydrothermal-vent environments.	Kaye JZ, Marquez MC, Ventosa A, Baross JA	Int J Syst Evol Microbiol	10.1099/ijs.0.02799-0	2004	*

References

#6083

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15725

#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 )

#29992

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 #26358 (see below)

#37405 ; 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) .

#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 )

#75528

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-ID131419.1 )

#120011 Collection of Institut Pasteur ; Curators of the CIP; CIP 108044

#26358

IJSEM 499 2004 ( DOI 10.1099/ijs.0.02799-0 , PubMed 15023967 )

* These data were automatically processed and therefore are not curated

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Halomonas hydrothermalis Slthf2

Halomonas hydrothermalis Slthf2

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