Name: Paracoccus contaminans WPAn02
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133282

Type strain:

Species: Paracoccus contaminans

Strain Designation: WPAn02, RKI16-01929

Culture col. no.: RKI 16-01929, LMG 29738, CCM 8701, CIP 111112

Strain history: CIP <- 2016, P. Kämpfer, Giessen Univ., Giessen, Germany: strain WPAn02

NCBI tax ID(s): 1945662 (species)

SI-ID 412579

CIP 111112

Section

Paracoccus contaminans WPAn02 is an aerobe, Gram-negative, coccus-shaped bacterium that was isolated from contaminated axenic water microcosm.

coccus-shaped
Gram-negative
aerobe
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	*Alphaproteobacteria*
	Order	*Rhodobacterales*
	Family	*Paracoccaceae*
	Genus	*Paracoccus*
	Species	**Paracoccus contaminans**
	Full Scientific Name (LPSN)	Paracoccus contaminans Kämpfer et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #25118]	Gram stain	negative
[Ref.: #118738]	Gram stain	positive

[Ref.: #25118]	Cell length	1 µm

[Ref.: #25118]	Cell width	1 µm

[Ref.: #25118]	Cell shape	coccus-shaped
[Ref.: #118738]	Cell shape	coccus-shaped

[Ref.: #25118]	Motility	no
[Ref.: #118738]	Motility	yes

[Ref.: #25118]	Colony size	2 mm
[Ref.: #25118]	Colony color	beige
[Ref.: #25118]	Incubation period	2 days
[Ref.: #25118]	Cultivation medium used	NA (Nutrient Agar)

Information on culture and growth conditions Culture and growth conditions

[Ref.: #25118]

Culture medium

NA (Nutrient Agar)

[Ref.: #25118]

Culture medium growth

[Ref.: #25118]

Culture medium

brain–heart infusion agar

[Ref.: #25118]

Culture medium growth

[Ref.: #25118]

Culture medium

TSA (Trypticase soy agar)

[Ref.: #25118]

Culture medium growth

[Ref.: #25118]

Culture medium

Reasoner's 2A agar (R2A)

[Ref.: #25118]

Culture medium growth

[Ref.: #25118]

Culture medium

MacConkey agar

[Ref.: #25118]

Culture medium growth

[Ref.: #42176]

Culture medium

MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromati

[Ref.: #42176]

Culture medium growth

[Ref.: #42176]

Culture medium composition

expand / minimize

[Ref.: #118738]

Culture medium

CIP Medium 566

[Ref.: #118738]

Culture medium growth

[Ref.: #118738]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #25118]		growth	10.0-45.0 °C
[Ref.: #25118]	no	growth	4 °C
[Ref.: #25118]	no	growth	45 °C
[Ref.: #42176]		growth	25 °C

[Ref.: #25118]	Temperature range	psychrophilic
[Ref.: #25118]	Temperature range	thermophilic
[Ref.: #42176]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #25118]			growth	5.0-7.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #25118]

Oxygen tolerance

aerobe

[Ref.: #25118]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #25118]		NaCl		growth	0.0-1.0	%(w/v)
[Ref.: #25118]		NaCl	no	growth	2	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #25118]	2-oxoglutarate ChEBI	-	carbon source
[Ref.: #25118]	3-hydroxybenzoate ChEBI	-	carbon source
[Ref.: #25118]	3-hydroxybutyrate ChEBI	-	carbon source
[Ref.: #25118]	4-hydroxybenzoate ChEBI	-	carbon source
[Ref.: #25118]	acetate ChEBI	+	carbon source
[Ref.: #25118]	adipate ChEBI	-	carbon source
[Ref.: #25118]	arbutin ChEBI	-	carbon source
[Ref.: #25118]	aspartate ChEBI	-	carbon source
[Ref.: #25118]	azelaate ChEBI	-	carbon source
[Ref.: #25118]	cellobiose ChEBI	-	carbon source
[Ref.: #25118]	cis-aconitate ChEBI	-	carbon source
[Ref.: #25118]	citrate ChEBI	-	carbon source
[Ref.: #25118]	D-fructose ChEBI	+	carbon source
[Ref.: #25118]	D-galactose ChEBI	+	carbon source
[Ref.: #25118]	D-glucose ChEBI	+	carbon source
[Ref.: #25118]	D-mannitol ChEBI	-	carbon source
[Ref.: #25118]	D-mannose ChEBI	+	carbon source
[Ref.: #25118]	D-ribose ChEBI	+	carbon source
[Ref.: #25118]	D-sorbitol ChEBI	+	carbon source
[Ref.: #25118]	D-trehalose ChEBI	-	carbon source
[Ref.: #25118]	D-xylose ChEBI	-	carbon source
[Ref.: #25118]	fumarate ChEBI	+	carbon source
[Ref.: #25118]	gamma-aminobutyric acid ChEBI	-	carbon source
[Ref.: #25118]	gluconate ChEBI	-	carbon source
[Ref.: #25118]	glutaric acid ChEBI	-	carbon source
[Ref.: #25118]	itaconate ChEBI	-	carbon source
[Ref.: #25118]	L-alanine ChEBI	+	carbon source
[Ref.: #25118]	L-arabinose ChEBI	+	carbon source
[Ref.: #25118]	L-histidine ChEBI	+	carbon source
[Ref.: #25118]	L-leucine ChEBI	-	carbon source
[Ref.: #25118]	L-ornithine ChEBI	-	carbon source
[Ref.: #25118]	L-phenylalanine ChEBI	-	carbon source
[Ref.: #25118]	L-rhamnose ChEBI	-	carbon source
[Ref.: #25118]	L-serine ChEBI	+	carbon source
[Ref.: #25118]	L-tryptophan ChEBI	-	carbon source
[Ref.: #25118]	lactate ChEBI	+	carbon source
[Ref.: #25118]	maltitol ChEBI	-	carbon source
[Ref.: #25118]	maltose ChEBI	+	carbon source
[Ref.: #25118]	melibiose ChEBI	-	carbon source
[Ref.: #25118]	mesaconate ChEBI	-	carbon source
[Ref.: #25118]	myo-inositol ChEBI	-	carbon source
[Ref.: #25118]	N-acetylgalactosamine ChEBI	-	carbon source
[Ref.: #25118]	N-acetylglucosamine ChEBI	-	carbon source
[Ref.: #25118]	phenylacetate ChEBI	-	carbon source
[Ref.: #25118]	propionate ChEBI	-	carbon source
[Ref.: #25118]	putrescine ChEBI	-	carbon source
[Ref.: #25118]	pyruvate ChEBI	+	carbon source
[Ref.: #25118]	ribitol ChEBI	-	carbon source
[Ref.: #25118]	salicin ChEBI	-	carbon source
[Ref.: #25118]	suberic acid ChEBI	-	carbon source
[Ref.: #25118]	sucrose ChEBI	-	carbon source
[Ref.: #25118]	trans-aconitate ChEBI	-	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #25118]		catalase	+	1.11.1.6
[Ref.: #25118]		cytochrome oxidase	+	1.9.3.1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	molybdenum cofactor biosynthesis	100	9 of 9
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	octane oxidation	100	3 of 3
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	allantoin degradation	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	methylglyoxal degradation	80	4 of 5
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	vitamin B12 metabolism	79.41	27 of 34
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	pyrimidine metabolism	77.78	35 of 45
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	purine metabolism	76.6	72 of 94
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	lactate fermentation	75	3 of 4
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	glutamate and glutamine metabolism	75	21 of 28
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	peptidoglycan biosynthesis	73.33	11 of 15
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	histidine metabolism	72.41	21 of 29
[Ref.: #66794]	lysine metabolism	71.43	30 of 42
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	tyrosine metabolism	71.43	10 of 14
[Ref.: #66794]	threonine metabolism	70	7 of 10
[Ref.: #66794]	myo-inositol biosynthesis	70	7 of 10
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	oxidative phosphorylation	67.03	61 of 91
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	4-hydroxymandelate degradation	66.67	6 of 9
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	methionine metabolism	65.38	17 of 26
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	64.29	9 of 14
[Ref.: #66794]	degradation of pentoses	64.29	18 of 28
[Ref.: #66794]	pentose phosphate pathway	63.64	7 of 11
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	non-pathway related	63.16	24 of 38
[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 sugar alcohols	62.5	10 of 16
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	sulfate reduction	61.54	8 of 13
[Ref.: #66794]	tryptophan metabolism	60.53	23 of 38
[Ref.: #66794]	propionate fermentation	60	6 of 10
[Ref.: #66794]	vitamin K metabolism	60	3 of 5
[Ref.: #66794]	phenol degradation	60	12 of 20
[Ref.: #66794]	3-chlorocatechol degradation	60	3 of 5
[Ref.: #66794]	degradation of sugar acids	60	15 of 25
[Ref.: #66794]	alanine metabolism	58.62	17 of 29
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	lipid metabolism	58.06	18 of 31
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	resorcinol degradation	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	3-phenylpropionate degradation	46.67	7 of 15
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	propanol degradation	42.86	3 of 7
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	ascorbate metabolism	40.91	9 of 22
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	hydrogen production	40	2 of 5
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	androgen and estrogen metabolism	37.5	6 of 16
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of hexoses	33.33	6 of 18
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	30.77	4 of 13
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
		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.: #25118]	Sample type/isolated from	contaminated axenic water microcosm
[Ref.: #25118]	Enrichment culture	R2A agar (Reasoner's 2A agar)

[Ref.: #118738]	Sample type/isolated from	Other, Contaminant of an axenic E. coli culture in 7% NaCl
[Ref.: #118738]	Geographic location (country and/or sea, region)	Weningerode
[Ref.: #118738]	Country	Germany
[Ref.: #118738]	Country ISO 3 Code	DEU
[Ref.: #118738]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Engineered	#Contamination	-
#Environmental	#Aquatic	-
#Host	#Microbial	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KX427102 (>99% sequence identity) for Paracoccus contaminans subclade from Microbeatlas

Aquatic Samples	127
Soil Samples	31
Animal Samples	590
Plant Samples	7
Total Samples	755

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

[Ref.: #118738]

Biosafety level

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.: #25118]	Paracoccus contaminans strain WPAn02 16S ribosomal RNA gene, partial sequence	KX427102	1397	GenBank	1945662 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Paracoccus contaminans strain RKI 16-01929T=LMG 29738T=CCM 8701T=CIP 111112T	1945662.5	plasmid	PATRIC	1945662 tax ID	*
[Ref.: #66792]	Paracoccus contaminans strain RKI 16-01929T=LMG 29738T=CCM 8701T=CIP 111112T	1945662.3	complete	PATRIC	1945662 tax ID	*

[Ref.: #25118]

GC-content

66.1 mol%

thermal denaturation, midpoint method (Tm)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Paracoccus contaminans strain RKI 16-01929T=LMG 29738T=CCM 8701T=CIP 111112T PATRIC: 1945662.3
[Ref.: #69480]	motile	no	73.176	yes
[Ref.: #69480]	gram-positive	no	97.544	yes
[Ref.: #69480]	anaerobic	no	99.075	yes
[Ref.: #69480]	aerobic	yes	92.167	no
[Ref.: #69480]	halophile	no	83.842	yes
[Ref.: #69480]	spore-forming	no	96.56	no
[Ref.: #69480]	glucose-util	yes	84.383	yes
[Ref.: #69480]	flagellated	no	93.949	no
[Ref.: #69480]	thermophile	no	74.787	no
[Ref.: #69480]	glucose-ferment	no	92.201	no

Availability in culture collections External links

[Ref.: #25118]

Culture collection no.

RKI 16-01929, LMG 29738, CCM 8701, CIP 111112

[Ref.: #91401]

SI-ID 412579

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Paracoccus aeridis sp. nov., an indole-producing bacterium isolated from the rhizosphere of an orchid, Aerides maculosa.	Rai A, N S, G S, A S, G D, Ch S, Ch V R	Int J Syst Evol Microbiol	10.1099/ijsem.0.003962	2020	*
Genetics	Genome Sequence of Paracoccus contaminans LMG 29738(T), Isolated from a Water Microcosm.	Aurass P, Karste S, Trost E, Glaeser SP, Kampfer P, Flieger A	Genome Announc	10.1128/genomeA.00487-17	2017	*
Phylogeny	Paracoccus contaminans sp. nov., isolated from a contaminated water microcosm.	Kampfer P, Aurass P, Karste S, Flieger A, Glaeser SP	Int J Syst Evol Microbiol	10.1099/ijsem.0.001478	2016	*

References

#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 )

#25118

P. A. Kämpfer, P.,Karste, S.,Flieger, A.,Glaeser, S. P.: Paracoccus contaminans sp. nov., isolated from a contaminated water microcosm. IJSEM 66: 5101 - 5105 2016 ( DOI 10.1099/ijsem.0.001478 , PubMed 27599853 )

#42176 ; 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) .

#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) .

#91401

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-ID412579.1 )

#118738 Collection of Institut Pasteur ; Curators of the CIP; CIP 111112
* These data were automatically processed and therefore are not curated

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Paracoccus contaminans strain RKI 16-01929T=LMG 29738T=CCM 8701T=CIP 111112T

Change proposal

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