Name: Arcicella aurantiaca TNR-18
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 3766

Type strain:

Species: Arcicella aurantiaca

Strain Designation: TNR-18

Culture col. no.: DSM 22214, BCRC 17969, LMG 25207

Strain history: <- J.-H. Chou, Natl. Kaohsiung Marine Univ. Taiwan <- W.-M. Chen; TNR-18

NCBI tax ID(s): 591202 (species)

SI-ID 360697

LMG 25207, BCRC 17969, DSM 22214

Section

Arcicella aurantiaca TNR-18 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from stream water.

Gram-negative
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	*Bacteroidota*
	Class	*Cytophagia*
	Order	*Cytophagales*
	Family	*Spirosomataceae*
	Genus	*Arcicella*
	Species	**Arcicella aurantiaca**
	Full Scientific Name (LPSN)	Arcicella aurantiaca Sheu et al. 2010

Information on morphological and physiological properties Morphology

[Ref.: #29806]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.999

[Ref.: #29806]	Cell length	01-03 µm

[Ref.: #29806]	Cell width	0.5-0.6 µm

[Ref.: #29806]	Cell shape	rod-shaped

[Ref.: #29806]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %91.192

[Ref.: #29806]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16206]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #16206]

Culture medium growth

[Ref.: #16206]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16206]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #16206]	growth	28 °C
[Ref.: #29806]	growth	10-30 °C
[Ref.: #29806]	optimum	25 °C

[Ref.: #16206]	Temperature range	mesophilic
[Ref.: #29806]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #29806]			optimum	7
[Ref.: #29806]			growth	06-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29806]

Oxygen tolerance

aerobe

[Ref.: #29806]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.994

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29806]		NaCl		growth	0-0.2	%

[Ref.: #29806]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29806]	alanine ChEBI	+	carbon source
[Ref.: #29806]	aspartate ChEBI	+	carbon source
[Ref.: #29806]	cellobiose ChEBI	+	carbon source
[Ref.: #29806]	dextrin ChEBI	+	carbon source
[Ref.: #29806]	esculin ChEBI	+	hydrolysis
[Ref.: #29806]	fructose ChEBI	+	carbon source
[Ref.: #29806]	fucose ChEBI	+	carbon source
[Ref.: #29806]	galactose ChEBI	+	carbon source
[Ref.: #29806]	glucose ChEBI	+	carbon source
[Ref.: #29806]	glutamate ChEBI	+	carbon source
[Ref.: #29806]	glycogen ChEBI	+	carbon source
[Ref.: #29806]	lactose ChEBI	+	carbon source
[Ref.: #29806]	maltose ChEBI	+	carbon source
[Ref.: #29806]	mannose ChEBI	+	carbon source
[Ref.: #29806]	melibiose ChEBI	+	carbon source
[Ref.: #29806]	methyl pyruvate ChEBI	+	carbon source
[Ref.: #29806]	nitrate ChEBI	+	reduction
[Ref.: #29806]	raffinose ChEBI	+	carbon source
[Ref.: #29806]	rhamnose ChEBI	+	carbon source
[Ref.: #29806]	serine ChEBI	+	carbon source
[Ref.: #29806]	sorbitol ChEBI	+	carbon source
[Ref.: #29806]	sucrose ChEBI	+	carbon source
[Ref.: #29806]	trehalose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #29806]		catalase	+	1.11.1.6
[Ref.: #29806]		cytochrome oxidase	+	1.9.3.1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	quinate degradation	100	2 of 2
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	serine metabolism	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]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	heme metabolism	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]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	methylglyoxal degradation	80	4 of 5
[Ref.: #66794]	starch degradation	80	8 of 10
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	3-chlorocatechol degradation	80	4 of 5
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	77.78	7 of 9
[Ref.: #66794]	lipid metabolism	77.42	24 of 31
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	glutamate and glutamine metabolism	75	21 of 28
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	degradation of sugar alcohols	75	12 of 16
[Ref.: #66794]	purine metabolism	73.4	69 of 94
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	methionine metabolism	73.08	19 of 26
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	glutathione metabolism	71.43	10 of 14
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	pyrimidine metabolism	68.89	31 of 45
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	lysine metabolism	66.67	28 of 42
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	histidine metabolism	65.52	19 of 29
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	degradation of sugar acids	64	16 of 25
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	degradation of hexoses	61.11	11 of 18
[Ref.: #66794]	degradation of pentoses	60.71	17 of 28
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	arachidonate biosynthesis	60	3 of 5
[Ref.: #66794]	coenzyme M biosynthesis	60	6 of 10
[Ref.: #66794]	non-pathway related	57.89	22 of 38
[Ref.: #66794]	tyrosine metabolism	57.14	8 of 14
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	aspartate and asparagine metabolism	55.56	5 of 9
[Ref.: #66794]	tryptophan metabolism	55.26	21 of 38
[Ref.: #66794]	carotenoid biosynthesis	54.55	12 of 22
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	3-phenylpropionate degradation	53.33	8 of 15
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	resorcinol degradation	50	1 of 2
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	polyamine pathway	47.83	11 of 23
[Ref.: #66794]	phenylpropanoid biosynthesis	46.15	6 of 13
[Ref.: #66794]	arginine metabolism	45.83	11 of 24
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	oxidative phosphorylation	45.05	41 of 91
[Ref.: #66794]	phenol degradation	45	9 of 20
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	phenylacetate degradation (aerobic)	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	ascorbate metabolism	36.36	8 of 22
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	chlorophyll metabolism	33.33	6 of 18
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	urea cycle	30.77	4 of 13
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	vitamin B12 metabolism	23.53	8 of 34
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	allantoin degradation	22.22	2 of 9
		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.: #16206]	Sample type/isolated from	stream water
[Ref.: #16206]	Geographic location (country and/or sea, region)	Kaohsiung Prefecture
[Ref.: #16206]	Country	Taiwan
[Ref.: #16206]	Country ISO 3 Code	TWN
[Ref.: #16206]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#River (Creek)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence FJ593908 (>99% sequence identity) for Arcicella aurantiaca subclade from Microbeatlas

Aquatic Samples	41
Soil Samples
Animal Samples
Plant Samples	4
Total Samples	45

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

[Ref.: #16206]

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.: #16206]	Arcicella aurantiaca 16S ribosomal RNA gene, partial sequence	FJ593908	1411	ENA	591202 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Arcicella aurantiaca DSM 22214	GCA_003148625	scaffold	GenBank	591202 tax ID	*
[Ref.: #66792]	Arcicella aurantiaca strain DSM 22214	591202.3	wgs	PATRIC	591202 tax ID	*
[Ref.: #66792]	Arcicella aurantiaca DSM 22214	2595698202	draft	JGI IMG/M	591202 tax ID	*

[Ref.: #16206]	GC-content	39.9 mol%	high performance liquid chromatography (HPLC)
[Ref.: #29806]	GC-content	39.9 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: Arcicella aurantiaca DSM 22214 NCBI: GCA_003148625.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Arcicella aurantiaca DSM 22214 NCBI: GCA_003148625.1
[Ref.: #69480]	flagellated	no	96.938	yes
[Ref.: #69480]	gram-positive	no	98.006	yes
[Ref.: #69480]	anaerobic	no	99.343	yes
[Ref.: #69480]	halophile	no	96.432	yes
[Ref.: #69480]	spore-forming	no	95.154	yes
[Ref.: #69480]	glucose-util	yes	86.404	yes
[Ref.: #69480]	aerobic	yes	90.22	yes
[Ref.: #69480]	thermophile	no	98.249	no
[Ref.: #69480]	motile	no	93.414	yes
[Ref.: #69480]	glucose-ferment	no	89.21	no

Availability in culture collections External links

[Ref.: #16206]

Culture collection no.

DSM 22214, BCRC 17969, LMG 25207

[Ref.: #73278]

SI-ID 360697

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Arcicella rigui sp. nov., isolated from water of a wetland, and emended descriptions of the genus Arcicella, Arcicella aquatica, Arcicella rosea and Arcicella aurantiaca.	Chen WM, Yang SH, Young CC, Sheu SY	Int J Syst Evol Microbiol	10.1099/ijs.0.037242-0	2012	*
Phylogeny	Arcicella aurantiaca sp. nov., isolated from stream water.	Sheu SY, Yang CS, Chen MH, Arun AB, Young CC, Chen WM	Int J Syst Evol Microbiol	10.1099/ijs.0.021527-0	2010	*

References

#16206

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22214

#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 )

#29806

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 #26183 (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 )

#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 )

#73278

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-ID360697.1 )

#26183

IJSEM 2979 2010 ( DOI 10.1099/ijs.0.021527-0 , PubMed 20118286 )

* These data were automatically processed and therefore are not curated

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Arcicella aurantiaca DSM 22214

Arcicella aurantiaca DSM 22214

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