Arenicella xantha (DSM 24032, KMM 3895, NRIC 0759)

Name: Arenicella xantha (DSM 24032, KMM 3895, NRIC 0759)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17916

Type strain

Strain Designation Sd2-39

Culture col. no. DSM 24032 KMM 3895 NRIC 0759 Sd2-39 JCM 16153

NCBI tax ID(s) 644221

Special Collections DSMZ JCM Literature strains

History <- N. Tanaka, NRIC <- L. A. Romanenko, KMM; Sd2-39 N. Tanaka <-- L. A. Romanenko Sd2-39 (=KMM 3895).

Links

Arenicella xantha Sd2-39 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from offshore marine sandy sample.

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

Name and taxonomic classification

SI-ID 403893

JCM 16153,DSM 24032

@ref 20215

Last LPSN update 2026-02-09 11:22:20

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Arenicellales

Family Arenicellaceae

Genus Arenicella

Species Arenicella xantha

Full scientific name Arenicella xantha Romanenko et al. 2010

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
29623	negative	3.5 µm	0.55 µm	rod-shaped
125438	negative				98.5
125439	negative				99.8

Pigmentation

29623

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
17481	REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c)		Medium recipe at MediaDive	Name: REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c) Composition: NaCl 19.45 g/l Agar 18.0 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 Na2CO3 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

Culture temp

@ref	Growth	Type	Temperature (°C)
17481	positive	growth	28
29623	positive	growth	05-35
29623	positive	optimum	26.5
67770	positive	growth	25

Culture pH

@ref	Ability	Type	PH	PH range
29623	positive	optimum	9
29623	positive	growth	06-11	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29623	aerobe
125439	obligate aerobe	97.9

Spore formation

@ref	Spore formation	Confidence
125438		92.42
125439		98.8

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29623	NaCl	positive	growth	01-05 %
29623	NaCl	positive	optimum	2.5 %

Observation

67770

Observationquinones: Q-8

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29623	16449 ChEBI	alanine	+	carbon source
29623	22599 ChEBI	arabinose	+	carbon source
29623	4853 ChEBI	esculin	+	hydrolysis
29623	17234 ChEBI	glucose	+	carbon source
29623	28053 ChEBI	melibiose	+	carbon source
29623	33942 ChEBI	ribose	+	carbon source
29623	18222 ChEBI	xylose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
29623	alkaline phosphatase	+	3.1.3.1
29623	catalase	+	1.11.1.6
29623	cytochrome oxidase	+	1.9.3.1
29623	gelatinase	+

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	Entner Doudoroff pathway	100	10 of 10
66794	adipate degradation	100	2 of 2
66794	cardiolipin biosynthesis	100	7 of 7
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	octane oxidation	100	3 of 3
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	molybdenum cofactor biosynthesis	100	9 of 9
66794	palmitate biosynthesis	100	22 of 22
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	L-lactaldehyde degradation	100	3 of 3
66794	ppGpp biosynthesis	100	4 of 4
66794	biotin biosynthesis	100	4 of 4
66794	suberin monomers biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	threonine metabolism	90	9 of 10
66794	lipid A biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	gluconeogenesis	87.5	7 of 8
66794	glutamate and glutamine metabolism	85.71	24 of 28
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	phenylalanine metabolism	84.62	11 of 13
66794	leucine metabolism	84.62	11 of 13
66794	pyrimidine metabolism	84.44	38 of 45
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	alanine metabolism	82.76	24 of 29
66794	purine metabolism	81.91	77 of 94
66794	cellulose degradation	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	propionate fermentation	80	8 of 10
66794	3-phenylpropionate degradation	80	12 of 15
66794	flavin biosynthesis	80	12 of 15
66794	gallate degradation	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	heme metabolism	78.57	11 of 14
66794	photosynthesis	78.57	11 of 14
66794	serine metabolism	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	d-mannose degradation	77.78	7 of 9
66794	glycolysis	76.47	13 of 17
66794	cyclohexanol degradation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	butanoate fermentation	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	lipid metabolism	74.19	23 of 31
66794	propanol degradation	71.43	5 of 7
66794	tyrosine metabolism	71.43	10 of 14
66794	citric acid cycle	71.43	10 of 14
66794	starch degradation	70	7 of 10
66794	histidine metabolism	68.97	20 of 29
66794	tryptophan metabolism	68.42	26 of 38
66794	non-pathway related	68.42	26 of 38
66794	degradation of sugar acids	68	17 of 25
66794	cysteine metabolism	66.67	12 of 18
66794	methane metabolism	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	methionine metabolism	65.38	17 of 26
66794	glutathione metabolism	64.29	9 of 14
66794	lysine metabolism	64.29	27 of 42
66794	proline metabolism	63.64	7 of 11
66794	d-xylose degradation	63.64	7 of 11
66794	pentose phosphate pathway	63.64	7 of 11
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	arginine metabolism	62.5	15 of 24
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	ketogluconate metabolism	62.5	5 of 8
66794	lipoate biosynthesis	60	3 of 5
66794	methylglyoxal degradation	60	3 of 5
66794	degradation of sugar alcohols	56.25	9 of 16
66794	nitrate assimilation	55.56	5 of 9
66794	arachidonic acid metabolism	55.56	10 of 18
66794	vitamin B6 metabolism	54.55	6 of 11
66794	urea cycle	53.85	7 of 13
66794	sulfate reduction	53.85	7 of 13
66794	isoprenoid biosynthesis	53.85	14 of 26
66794	kanosamine biosynthesis II	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	carnitine metabolism	50	4 of 8
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	ribulose monophosphate pathway	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	phenylmercury acetate degradation	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	quinate degradation	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	polyamine pathway	47.83	11 of 23
66794	degradation of pentoses	46.43	13 of 28
66794	metabolism of disaccharids	45.45	5 of 11
66794	phenol degradation	45	9 of 20
66794	vitamin B12 metabolism	44.12	15 of 34
66794	androgen and estrogen metabolism	43.75	7 of 16
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	glycine betaine biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	vitamin K metabolism	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	O-antigen biosynthesis	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	4-hydroxyphenylacetate degradation	40	4 of 10
66794	vitamin B1 metabolism	38.46	5 of 13
66794	oxidative phosphorylation	38.46	35 of 91
66794	ascorbate metabolism	36.36	8 of 22
66794	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
66794	IAA biosynthesis	33.33	1 of 3
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	sphingosine metabolism	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	bile acid biosynthesis, neutral pathway	29.41	5 of 17
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	degradation of hexoses	27.78	5 of 18
66794	cholesterol biosynthesis	27.27	3 of 11
66794	toluene degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	carotenoid biosynthesis	22.73	5 of 22

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Terrestrial	#Sandy

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
17481	offshore marine sandy sample	Sea of Japan, offshore	Russia	RUS	Asia
67770	Sandy sediment sample collected offshore from the Sea of Japan		Russia	RUS

Taxonmaps

69479

Global distribution of 16S sequence AB500096 (>99% sequence identity) for Arenicella xantha subclade from Microbeatlas

Aquatic Samples	965
Soil Samples	12
Animal Samples	15
Plant Samples	5
Total Samples	997

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17481	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM331524v1 assembly for Arenicella xantha DSM 24032	scaffold	GCA_003315245	644221.3	2770939506	644221	67.94

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
17481	Arenicella xantha gene for 16S ribosomal RNA, partial sequence	AB500096	1506		644221

GC content

@ref	GC-content (mol%)	Method
17481	48.1	thermal denaturation, midpoint method (Tm)
29623	48.1

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Arenicella xantha DSM 24032
NCBI: GCA_003315245

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.80	no
125439	motility	BacteriaNetⓘ	yes	87.40	no
125439	gram_stain	BacteriaNetⓘ	negative	99.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Arenicella xantha strain DSM 24032
PATRIC: 644221.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.50	no
125438	anaerobic	anaerobicⓘ	no	95.70	yes
125438	aerobic	aerobicⓘ	yes	86.99	yes
125438	spore-forming	spore-formingⓘ	no	92.42	no
125438	thermophilic	thermophileⓘ	no	96.65	yes
125438	flagellated	motile2+ⓘ	no	75.07	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
	High wax ester and triacylglycerol biosynthesis potential in coastal sediments of Antarctic and Subantarctic environments.	Galvan V, Pascutti F, Sandoval NE, Lanfranconi MP, Lozada M, Arabolaza AL, Mac Cormack WP, Alvarez HM, Gramajo HC, Dionisi HM.	PLoS One	10.1371/journal.pone.0288509	2023
	Kinetics and scale up of oxygen reducing cathodic biofilms.	Mohamed A, Ha PT, Beyenal H.	Biofilm	10.1016/j.bioflm.2021.100053	2021
Phylogeny	Cuticles of European and American lobsters harbor diverse bacterial species and differ in disease susceptibility.	Whitten MM, Davies CE, Kim A, Tlusty M, Wootton EC, Chistoserdov A, Rowley AF.	Microbiologyopen	10.1002/mbo3.174	2014
Phylogeny	Arenicella xantha gen. nov., sp. nov., a gammaproteobacterium isolated from a marine sandy sediment.	Romanenko LA, Tanaka N, Frolova GM, Mikhailov VV	Int J Syst Evol Microbiol	10.1099/ijs.0.017194-0	2009
Phylogeny	Arenicella chitinivorans sp. nov., a gammaproteobacterium isolated from the sea urchin Strongylocentrotus intermedius.	Nedashkovskaya OI, Cleenwerck I, Zhukova NV, Kim SB, de Vos P	Int J Syst Evol Microbiol	10.1099/ijs.0.051599-0	2013

References

#17481	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24032
#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 )
#26013	IJSEM 1832 2010 ( DOI 10.1099/ijs.0.017194-0 , PubMed 19767361 )
#29623	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 #26013
#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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#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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Arenicella xantha (DSM 24032, KMM 3895, NRIC 0759)

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

Observation

Metabolite utilization

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003315245

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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