Name: Siphonobacter aquaeclarae P2
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5747

Type strain:

Species: Siphonobacter aquaeclarae

Strain Designation: P2

Culture col. no.: DSM 21668, NCAIM B 02328

Strain history: <- A. Táncsics, Eötvös Loránd Univ. Budapest, Hungary; P2

NCBI tax ID(s): 563176 (species)

SI-ID 371121

DSM 21668

Section

Siphonobacter aquaeclarae P2 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from inner surface of an ultra pure cooling water system in a power plant.

Gram-negative
rod-shaped
facultative anaerobe
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	*Siphonobacter*
	Species	**Siphonobacter aquaeclarae**
	Full Scientific Name (LPSN)	Siphonobacter aquaeclarae Táncsics et al. 2010

Information on morphological and physiological properties Morphology

[Ref.: #29717]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.997

[Ref.: #29717]	Cell length	1.3-2.7 µm

[Ref.: #29717]	Cell width	0.3-0.4 µm

[Ref.: #29717]	Cell shape	rod-shaped

[Ref.: #29717]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %93.208

[Ref.: #29717]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #15875]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #15875]

Culture medium growth

[Ref.: #15875]

Culture medium link

Medium recipe at MediaDive

[Ref.: #15875]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #15875]	growth	28 °C
[Ref.: #29717]	growth	04-37 °C
[Ref.: #29717]	optimum	30-37 °C

[Ref.: #15875]	Temperature range	mesophilic
[Ref.: #29717]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #29717]			optimum	7
[Ref.: #29717]			growth	05-09

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29717]

Oxygen tolerance

facultative anaerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.853

[Ref.: #29717]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29717]	cellobiose ChEBI	+	carbon source
[Ref.: #29717]	fructose ChEBI	+	carbon source
[Ref.: #29717]	fucose ChEBI	+	carbon source
[Ref.: #29717]	galactose ChEBI	+	carbon source
[Ref.: #29717]	glucose ChEBI	+	carbon source
[Ref.: #29717]	lactose ChEBI	+	carbon source
[Ref.: #29717]	maltose ChEBI	+	carbon source
[Ref.: #29717]	mannose ChEBI	+	carbon source
[Ref.: #29717]	melibiose ChEBI	+	carbon source
[Ref.: #29717]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #29717]	raffinose ChEBI	+	carbon source
[Ref.: #29717]	rhamnose ChEBI	+	carbon source
[Ref.: #29717]	sucrose ChEBI	+	carbon source
[Ref.: #29717]	trehalose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #29717]	acid phosphatase	+	3.1.3.2
[Ref.: #29717]	alkaline phosphatase	+	3.1.3.1
[Ref.: #29717]	catalase	+	1.11.1.6

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	quinate degradation	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	molybdenum cofactor biosynthesis	100	9 of 9
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	tetrahydrofolate metabolism	92.86	13 of 14
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	alanine metabolism	86.21	25 of 29
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[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]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	glutathione metabolism	78.57	11 of 14
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	lipid metabolism	77.42	24 of 31
[Ref.: #66794]	purine metabolism	76.6	72 of 94
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	pyrimidine metabolism	75.56	34 of 45
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	biotin biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	75	6 of 8
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	metabolism of disaccharids	72.73	8 of 11
[Ref.: #66794]	degradation of sugar acids	72	18 of 25
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	71.43	20 of 28
[Ref.: #66794]	4-hydroxyphenylacetate degradation	70	7 of 10
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	leucine metabolism	69.23	9 of 13
[Ref.: #66794]	isoprenoid biosynthesis	69.23	18 of 26
[Ref.: #66794]	carotenoid biosynthesis	68.18	15 of 22
[Ref.: #66794]	degradation of pentoses	67.86	19 of 28
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	lysine metabolism	66.67	28 of 42
[Ref.: #66794]	methionine metabolism	65.38	17 of 26
[Ref.: #66794]	tyrosine metabolism	64.29	9 of 14
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	tryptophan metabolism	60.53	23 of 38
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	myo-inositol biosynthesis	60	6 of 10
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	aclacinomycin biosynthesis	57.14	4 of 7
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	aspartate and asparagine metabolism	55.56	5 of 9
[Ref.: #66794]	degradation of hexoses	55.56	10 of 18
[Ref.: #66794]	non-pathway related	55.26	21 of 38
[Ref.: #66794]	histidine metabolism	55.17	16 of 29
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	sphingosine metabolism	50	3 of 6
[Ref.: #66794]	arginine metabolism	50	12 of 24
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	3-phenylpropionate degradation	46.67	7 of 15
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	46.15	6 of 13
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	phenol degradation	45	9 of 20
[Ref.: #66794]	arachidonic acid metabolism	44.44	8 of 18
[Ref.: #66794]	oxidative phosphorylation	43.96	40 of 91
[Ref.: #66794]	androgen and estrogen metabolism	43.75	7 of 16
[Ref.: #66794]	polyamine pathway	43.48	10 of 23
[Ref.: #66794]	vitamin B12 metabolism	41.18	14 of 34
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	ascorbate metabolism	36.36	8 of 22
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	phenylpropanoid biosynthesis	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]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[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.: #15875]	Sample type/isolated from	inner surface of an ultra pure cooling water system in a power plant
[Ref.: #15875]	Geographic location (country and/or sea, region)	Budapest
[Ref.: #15875]	Country	Hungary
[Ref.: #15875]	Country ISO 3 Code	HUN
[Ref.: #15875]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Engineered

#Industrial

#Plant (Factory)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence FJ177421 (>99% sequence identity) for Siphonobacter aquaeclarae subclade from Microbeatlas

Aquatic Samples	821
Soil Samples	464
Animal Samples	812
Plant Samples	313
Total Samples	2410

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

[Ref.: #15875]

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.: #15875]	Siphonobacter aquaeclarae strain P2 16S ribosomal RNA gene, partial sequence	FJ177421	1351	ENA	563176 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Siphonobacter aquaeclarae DSM 21668	GCA_900103285	scaffold	GenBank	563176 tax ID	*
[Ref.: #66792]	Siphonobacter aquaeclarae strain DSM 21668	563176.3	wgs	PATRIC	563176 tax ID	*
[Ref.: #66792]	Siphonobacter aquaeclarae DSM 21668	2622736636	draft	JGI IMG/M	563176 tax ID	*

[Ref.: #15875]	GC-content	54.5 mol%	high performance liquid chromatography (HPLC)
[Ref.: #29717]	GC-content	54.5 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: Siphonobacter aquaeclarae DSM 21668 NCBI: GCA_900103285.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Siphonobacter aquaeclarae DSM 21668 NCBI: GCA_900103285.1
[Ref.: #69480]	motile	no	93.106	yes
[Ref.: #69480]	flagellated	no	96.619	yes
[Ref.: #69480]	gram-positive	no	98.105	no
[Ref.: #69480]	anaerobic	no	99.517	yes
[Ref.: #69480]	aerobic	yes	86.533	yes
[Ref.: #69480]	halophile	no	96.632	no
[Ref.: #69480]	spore-forming	no	94.57	no
[Ref.: #69480]	glucose-ferment	no	87.867	no
[Ref.: #69480]	thermophile	no	98.85	yes
[Ref.: #69480]	glucose-util	yes	87.16	yes

Availability in culture collections External links

[Ref.: #15875]

Culture collection no.

DSM 21668, NCAIM B 02328

[Ref.: #75226]

SI-ID 371121

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Siphonobacter curvatus sp. nov., isolated from a freshwater river.	Lee Y, Jeon CO	Int J Syst Evol Microbiol	10.1099/ijsem.0.002769	2018	*
Phylogeny	Siphonobacter aquaeclarae gen. nov., sp. nov., a novel member of the family 'Flexibacteraceae', phylum Bacteroidetes.	Tancsics A, Keki Z, Marialigeti K, Schumann P, Toth EM	Int J Syst Evol Microbiol	10.1099/ijs.0.019398-0	2009	*

References

#15875

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21668

#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 )

#29717

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 #26100 (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 )

#75226

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-ID371121.1 )

#26100

IJSEM 2567 2010 ( DOI 10.1099/ijs.0.019398-0 , PubMed 20008110 )

* These data were automatically processed and therefore are not curated

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Siphonobacter aquaeclarae DSM 21668

Siphonobacter aquaeclarae DSM 21668

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