Name: Halomonas ilicicola Sp8
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 6063

Type strain:

Species: Halomonas ilicicola

Strain Designation: Sp8

Culture col. no.: DSM 19980, CCM 7522, CECT 7331

Strain history: <- J. Soliveri and J. L. Copa-Patiño, Univ. Alcalá de Henares, Madrid; SP8 <- J. Soliveri, M. Arenas, P. Bañón and J. L. Copa-Patiño

NCBI tax ID(s): 1121942 (strain), 480814 (species)

SI-ID 361153

CCM 7522, CECT 7331, DSM 19980

Section

Halomonas ilicicola Sp8 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from Saline water from a solar saltern.

Gram-negative
motile
rod-shaped
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 ilicicola**
	Full Scientific Name (LPSN)	Halomonas ilicicola Arenas et al. 2009

Synonym

"Modicisalibacter ilicicola"

Information on morphological and physiological properties Morphology

[Ref.: #29003]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.999

[Ref.: #29003]	Cell length	0.8-1.1 µm

[Ref.: #29003]	Cell width	0.5-0.6 µm

[Ref.: #29003]	Cell shape	rod-shaped

[Ref.: #29003]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %99.071

[Ref.: #29003]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8352]

Culture medium

HALF STRENGTH BACTO MARINE BROTH (DSMZ Medium 514a)

[Ref.: #8352]

Culture medium growth

[Ref.: #8352]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8352]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #8352]	growth	28 °C
[Ref.: #29003]	growth	25-42 °C
[Ref.: #29003]	optimum	37 °C

[Ref.: #8352]	Temperature range	mesophilic
[Ref.: #29003]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #29003]			optimum	6.5
[Ref.: #29003]			growth	6.0-9.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29003]

Oxygen tolerance

aerobe

[Ref.: #29003]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.96

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29003]		NaCl		growth	2-17.5	%
[Ref.: #29003]		NaCl		optimum	10	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29003]	5-dehydro-D-gluconate ChEBI	+	carbon source
[Ref.: #29003]	acetate ChEBI	+	carbon source
[Ref.: #29003]	alanine ChEBI	+	carbon source
[Ref.: #29003]	citrate ChEBI	+	carbon source
[Ref.: #29003]	esculin ChEBI	+	hydrolysis
[Ref.: #29003]	fructose ChEBI	+	carbon source
[Ref.: #29003]	fucose ChEBI	+	carbon source
[Ref.: #29003]	galactose ChEBI	+	carbon source
[Ref.: #29003]	gluconate ChEBI	+	carbon source
[Ref.: #29003]	glucose ChEBI	+	carbon source
[Ref.: #29003]	mannitol ChEBI	+	carbon source
[Ref.: #29003]	nitrate ChEBI	+	reduction
[Ref.: #29003]	propionate ChEBI	+	carbon source
[Ref.: #29003]	sorbitol ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #29003]		catalase	+	1.11.1.6
[Ref.: #29003]		gelatinase	+

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	molybdenum cofactor biosynthesis	100	9 of 9
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	lipoate biosynthesis	100	5 of 5
[Ref.: #66794]	phenylmercury acetate degradation	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	ubiquinone biosynthesis	100	7 of 7
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	photosynthesis	92.86	13 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	89.29	25 of 28
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	allantoin degradation	88.89	8 of 9
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	ketogluconate metabolism	87.5	7 of 8
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	citric acid cycle	85.71	12 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	vitamin B6 metabolism	81.82	9 of 11
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	3-chlorocatechol degradation	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	arginine metabolism	79.17	19 of 24
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	pyrimidine metabolism	77.78	35 of 45
[Ref.: #66794]	purine metabolism	77.66	73 of 94
[Ref.: #66794]	lipid metabolism	77.42	24 of 31
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	alginate biosynthesis	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	glutathione metabolism	71.43	10 of 14
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	degradation of sugar alcohols	68.75	11 of 16
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	oxidative phosphorylation	65.93	60 of 91
[Ref.: #66794]	non-pathway related	63.16	24 of 38
[Ref.: #66794]	lysine metabolism	61.9	26 of 42
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	tryptophan metabolism	60.53	23 of 38
[Ref.: #66794]	creatinine degradation	60	3 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	degradation of sugar acids	60	15 of 25
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	cellulose degradation	60	3 of 5
[Ref.: #66794]	histidine metabolism	58.62	17 of 29
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	polyamine pathway	56.52	13 of 23
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	53.85	7 of 13
[Ref.: #66794]	methionine metabolism	53.85	14 of 26
[Ref.: #66794]	myo-inositol biosynthesis	50	5 of 10
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	glycogen biosynthesis	50	2 of 4
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	phenol degradation	50	10 of 20
[Ref.: #66794]	degradation of pentoses	46.43	13 of 28
[Ref.: #66794]	degradation of hexoses	44.44	8 of 18
[Ref.: #66794]	arachidonic acid metabolism	44.44	8 of 18
[Ref.: #66794]	4-hydroxymandelate degradation	44.44	4 of 9
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	40	2 of 5
[Ref.: #66794]	3-phenylpropionate degradation	40	6 of 15
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	glycogen metabolism	40	2 of 5
[Ref.: #66794]	androgen and estrogen metabolism	37.5	6 of 16
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	37.5	3 of 8
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	tyrosine metabolism	35.71	5 of 14
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	ascorbate metabolism	27.27	6 of 22
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	23.53	4 of 17
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #8352]	Sample type/isolated from	Saline water from a solar saltern
[Ref.: #8352]	Geographic location (country and/or sea, region)	Alicante, Santa Pola (38° 11' 35'' N 0° 35' 45'' W)
[Ref.: #8352]	Country	Spain
[Ref.: #8352]	Country ISO 3 Code	ESP
[Ref.: #8352]	Continent	Europe
[Ref.: #8352]	Geographic location	38.1931°/-0.5958°
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	-
#Condition	#Saline	-

What are isolation sources categories?

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

[Ref.: #8352]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #8352]	Halomonas ilicicola strain SP8 16S ribosomal RNA gene, partial sequence	EU218533	1423	ENA	480814 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Halomonas ilicicola DSM 19980	GCA_900128925	scaffold	GenBank	1121942 tax ID	*
[Ref.: #66792]	Halomonas ilicicola DSM 19980	1121942.4	wgs	PATRIC	1121942 tax ID	*
[Ref.: #66792]	Halomonas ilicicola DSM 19980	2582581268	draft	JGI IMG/M	1121942 tax ID	*

[Ref.: #8352]	GC-content	66.9 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #29003]	GC-content	66.9 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 ilicicola DSM 19980 DSM 19980 NCBI: GCA_900128925.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Halomonas ilicicola DSM 19980 DSM 19980 NCBI: GCA_900128925.1
[Ref.: #69480]	motile	yes	90.312	no
[Ref.: #69480]	flagellated	no	58.98	no
[Ref.: #69480]	gram-positive	no	99.017	yes
[Ref.: #69480]	anaerobic	no	98.175	no
[Ref.: #69480]	aerobic	yes	84.695	no
[Ref.: #69480]	halophile	yes	93.159	yes
[Ref.: #69480]	spore-forming	no	95.695	yes
[Ref.: #69480]	glucose-ferment	no	75.507	no
[Ref.: #69480]	thermophile	no	97.367	no
[Ref.: #69480]	glucose-util	yes	89.294	yes

Availability in culture collections External links

[Ref.: #8352]

Culture collection no.

DSM 19980, CCM 7522, CECT 7331

[Ref.: #75550]

SI-ID 361153

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Halomonas ilicicola sp. nov., a moderately halophilic bacterium isolated from a saltern.	Arenas M, Banon PI, Copa-Patino JL, Sanchez-Porro C, Ventosa A, Soliveri J	Int J Syst Evol Microbiol	10.1099/ijs.0.003509-0	2009	*

References

#8352

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19980

#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 )

#29003

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 #25436 (see below)

#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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#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 )

#75550

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-ID361153.1 )

#25436

IJSEM 578 2009 ( DOI 10.1099/ijs.0.003509-0 , PubMed 19244445 )

* These data were automatically processed and therefore are not curated

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Halomonas ilicicola DSM 19980 DSM 19980

Halomonas ilicicola DSM 19980 DSM 19980

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