Name: Paracoccus pantotrophus GB 17
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 13706

Type strain:

Species: Paracoccus pantotrophus

Strain Designation: GB 17

Culture col. no.: DSM 2944, DSM 3967, LMD 82.5, JCM 21485, ATCC 35512, CIP 106514, IAM 15022, NBRC 102493, NCCB 82005

Strain history: CIP <- 2000, ATCC <- L.A. Robertson: strain GB 17

NCBI tax ID(s): 82367 (species)

SI-ID 41128

ATCC 35512, CIP 106514, DSM 2944, NCIMB 13217, LMD 82.5, NCCB 82005, BCRC 14341, CCRC 14341, IAM 15022, KCTC 12140, NBRC 102493, JCM 21485

Special Collections

Other strains from Paracoccus pantotrophus

Section

Paracoccus pantotrophus GB 17 is an obligate aerobe, Gram-negative, ovoid-shaped bacterium that was isolated from denitrifying, sulfide-oxidizing effluent-treatment plant.

Gram-negative
ovoid-shaped
obligate 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 pantotrophus**
	Full Scientific Name (LPSN)	Paracoccus pantotrophus (Robertson and Kuenen 1984) Rainey et al. 1999

Synonym

Thiosphaera pantotropha

Information on morphological and physiological properties Morphology

[Ref.: #121536]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %98

[Ref.: #121536]	Cell shape	ovoid-shaped

[Ref.: #121536]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #1255]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #1255]

Culture medium growth

[Ref.: #1255]

Culture medium link

Medium recipe at MediaDive

[Ref.: #1255]

Culture medium composition

expand / minimize

[Ref.: #34087]

Culture medium

MEDIUM 3 - Columbia agar

[Ref.: #34087]

Culture medium growth

[Ref.: #34087]

Culture medium composition

expand / minimize

[Ref.: #121536]

Culture medium

CIP Medium 3

[Ref.: #121536]

Culture medium growth

[Ref.: #121536]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #1255]		growth	28 °C
[Ref.: #34087]		growth	37 °C
[Ref.: #67770]		growth	37 °C
[Ref.: #121536]		growth	25-41 °C
[Ref.: #121536]	no	growth	5 °C
[Ref.: #121536]	no	growth	10 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #121536]

Oxygen tolerance

obligate aerobe

[Ref.: #69480]

Ability of spore formation

no Confidence in %91.59

	Salt	Tested relation		Salt conc.
[Ref.: #121536]	NaCl		growth	0-6	%
[Ref.: #121536]	NaCl	no	growth	8	%
[Ref.: #121536]	NaCl	no	growth	10	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #121536]	esculin ChEBI	-	hydrolysis
[Ref.: #121536]	nitrate ChEBI	+	reduction
[Ref.: #121536]	nitrate ChEBI	+	respiration
[Ref.: #121536]	nitrite ChEBI	+	reduction

	Metabolite production	Metabolite	Production
[Ref.: #121536]		indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test
[Ref.: #121536]		acetoin ChEBI	-

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	-	3.1.3.2	* from API zym
[Ref.: #121536]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #121536]	amylase	-
[Ref.: #121536]	beta-galactosidase	-	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #121536]	caseinase	-	3.4.21.50
[Ref.: #121536]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #121536]	DNase	-
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #121536]	gelatinase	-
[Ref.: #121536]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	-	3.4.11.1	* from API zym
[Ref.: #121536]	lipase	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #121536]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #121536]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #121536]	oxidase	+
[Ref.: #121536]	protease	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #121536]	tween esterase	-
[Ref.: #121536]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® Biotype100:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
[Ref.: #121536]	1730	not determinedn.d.	+	+	-	+	+	-	-	+	-	+	+	-	-	-	-	-	-	-	-	+	-	-	+	-	-	+	+	+	+	-	-	+	+	+	+	+	+	+	-	-	-	+	-	-	-	-	-	-	+	+	-	-	-	-	+	-	+	+	-	+	+	+	+	+	+	-	-	+	-	-	-	+	-	+	-	+	-	-	+	+	+	+	+	+	-	-	+	-	+	+	+	+	+	+	+	+	+	+	-

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #121536]	9571	-	+	+	+	-	-	-	-	-	-	-	+	-	-	-	+	-	-	-	-

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

[Ref.: #1255]	Sample type/isolated from	denitrifying, sulfide-oxidizing effluent-treatment plant
[Ref.: #1255]	Geographic location (country and/or sea, region)	Delft
[Ref.: #1255]	Country	Netherlands
[Ref.: #1255]	Country ISO 3 Code	NLD
[Ref.: #1255]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Waste treatment plant
[Ref.: #67770]	Country	Netherlands
[Ref.: #67770]	Country ISO 3 Code	NLD
[Ref.: #67770]	Continent	Europe

[Ref.: #121536]	Sample type/isolated from	Waste treatment plant
[Ref.: #121536]	Country	Netherlands
[Ref.: #121536]	Country ISO 3 Code	NLD
[Ref.: #121536]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Engineered	#Industrial	#Plant (Factory)
#Engineered	#Waste	#Water treatment plant
#Condition	#Sulfuric	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence Y16933 (>99% sequence identity) for Paracoccus from Microbeatlas

Aquatic Samples	2441
Soil Samples	932
Animal Samples	1611
Plant Samples	205
Total Samples	5189

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

[Ref.: #1255]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #121536]	Biosafety level	1	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.: #20218]	Paracoccus pantotrophus 16S rRNA gene, strain ATCC 35512T	Y16933	1395	GenBank ENA	82367 tax ID	*
[Ref.: #20218]	Paracoccus denitrificans partial 16S rRNA gene, strain DSM 2944	AJ288159	1297	GenBank ENA	266 tax ID	*
[Ref.: #20218]	Paracoccus pantotrophus gene for 16S rRNA, partial sequence, strain: NBRC 102493	AB681830	1388	GenBank ENA	82367 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Paracoccus pantotrophus DSM 2944	GCA_003633525	contig	GenBank ENA	82367 tax ID
[Ref.: #66792]	Paracoccus pantotrophus DSM 2944	GCA_008824185	complete	GenBank ENA	82367 tax ID	*
[Ref.: #66792]	Paracoccus pantotrophus strain DSM 2944	82367.27	complete	PATRIC	82367 tax ID	*
[Ref.: #66792]	Paracoccus pantotrophus strain DSM 2944	82367.24	wgs	PATRIC	82367 tax ID	*
[Ref.: #66792]	Paracoccus pantotrophus DSM 2944	2772190981	draft	JGI IMG/M	82367 tax ID	*

[Ref.: #1255]

GC-content

65.8-66.0 mol%

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Paracoccus pantotrophus DSM 2944 NCBI: GCA_008824185.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	89	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Paracoccus pantotrophus DSM 2944 NCBI: GCA_008824185.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	98	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	93.664	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	78.292	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	91.59	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	96.071	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	58.074	no

Availability in culture collections External links

[Ref.: #1255]

Culture collection no.

DSM 2944, DSM 3967, LMD 82.5, JCM 21485, ATCC 35512, CIP 106514, IAM 15022, NBRC 102493, NCCB 82005

[Ref.: #82891]

SI-ID 41128

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Eco-friendly decolorization and degradation of reactive yellow 145 textile dye by Pseudomonas aeruginosa and Thiosphaera pantotropha.	Garg N, Garg A, Mukherji S	J Environ Manage	10.1016/j.jenvman.2020.110383	2020	*
Genetics	Complete Genome Sequence and Annotation of the Paracoccus pantotrophus Type Strain DSM 2944.	Bockwoldt JA, Zimmermann M, Tiso T, Blank LM	Microbiol Resour Announc	10.1128/MRA.01290-19	2020	*
Metabolism	Sulphate production by Paracoccus pantotrophus ATCC 35512 from different sulphur substrates: sodium thiosulphate, sulphite and sulphide.	Meyer DD, Andrino FG, Possedente de Lira S, Fornaro A, Corcao G, Brandelli A	Environ Technol	10.1080/09593330.2015.1081411	2015	*
Metabolism	Paracoccus pantotrophus pseudoazurin is an electron donor to cytochrome c peroxidase.	Pauleta SR, Guerlesquin F, Goodhew CF, Devreese B, Van Beeumen J, Pereira AS, Moura I, Pettigrew GW	Biochemistry	10.1021/bi0491144	2004	*
Genetics	Identification and characterization of transposable elements of Paracoccus pantotrophus.	Bartosik D, Sochacka M, Baj J	J Bacteriol	10.1128/JB.185.13.3753-3763.2003	2003	*
Metabolism	Comparison of aerobic denitrification under high oxygen atmosphere by Thiosphaera pantotropha ATCC 35512 and Pseudomonas stutzeri SU2 newly isolated from the activated sludge of a piggery wastewater treatment system.	Su JJ, Liu BY, Liu CY	J Appl Microbiol	10.1046/j.1365-2672.2001.01265.x	2001	*
Enzymology	Cytochrome cb-type nitric oxide reductase with cytochrome c oxidase activity from Paracoccus denitrificans ATCC 35512.	Fujiwara T, Fukumori Y	J Bacteriol	10.1128/jb.178.7.1866-1871.1996	1996	*

References

#1255

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 2944

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#34087 ; 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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#68382

Automatically annotated from API zym .

#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 )

#82891

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-ID41128.1 )

#121536 Collection of Institut Pasteur ; Curators of the CIP; CIP 106514
* These data were automatically processed and therefore are not curated

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Paracoccus pantotrophus DSM 2944

Paracoccus pantotrophus DSM 2944

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