Name: Parapedobacter pyrenivorans P-4
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 132159

Type strain:

Species: Parapedobacter pyrenivorans

Strain Designation: P-4

Culture col. no.: DSM 102942, CGMCC 1.12195, NBRC 109113

Strain history: <- NBRC <- CGMCC <- Li, X.-M., State Key Lab. Microbial Resources, Inst. Microbiol., Chinese Academy of Sciences, Beijing, China

NCBI tax ID(s): 1305674 (species)

SI-ID 402734

DSM 102942

Section

Parapedobacter pyrenivorans P-4 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from polluted soil of a coking chemical plan.

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	*Sphingobacteriia*
	Order	*Sphingobacteriales*
	Family	*Sphingobacteriaceae*
	Genus	*Parapedobacter*
	Species	**Parapedobacter pyrenivorans**
	Full Scientific Name (LPSN)	Parapedobacter pyrenivorans Zhao et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #31095]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.951

[Ref.: #31095]	Cell length	0.95 µm

[Ref.: #31095]	Cell width	0.35 µm

[Ref.: #31095]	Cell shape	rod-shaped

[Ref.: #31095]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %95.155

[Ref.: #31095]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #23948]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #23948]

Culture medium growth

[Ref.: #23948]

Culture medium link

Medium recipe at MediaDive

[Ref.: #23948]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #23948]	growth	28 °C
[Ref.: #31095]	growth	15-45 °C
[Ref.: #31095]	optimum	37 °C

[Ref.: #23948]	Temperature range	mesophilic
[Ref.: #31095]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31095]			optimum	8.5
[Ref.: #31095]			growth	6.0-9.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31095]

Oxygen tolerance

aerobe

[Ref.: #31095]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.998

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31095]		NaCl		growth	0-4	%

[Ref.: #31095]

Observation

aggregates in clumps

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #31095]	arabinose ChEBI	+	carbon source
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	+	fermentation	* from API 20NE
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-mannose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #31095]	esculin ChEBI	+	hydrolysis
[Ref.: #68369]	esculin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #31095]	glucose ChEBI	+	carbon source
[Ref.: #31095]	glycogen ChEBI	+	carbon source
[Ref.: #68369]	L-arabinose ChEBI	+	assimilation	* from API 20NE
[Ref.: #31095]	malate ChEBI	+	carbon source
[Ref.: #68369]	malate ChEBI	-	assimilation	* from API 20NE
[Ref.: #31095]	maltose ChEBI	+	carbon source
[Ref.: #68369]	maltose ChEBI	+	assimilation	* from API 20NE
[Ref.: #31095]	mannose ChEBI	+	carbon source
[Ref.: #31095]	melibiose ChEBI	+	carbon source
[Ref.: #31095]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #68369]	N-acetylglucosamine ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #31095]	proline ChEBI	+	carbon source
[Ref.: #31095]	rhamnose ChEBI	+	carbon source
[Ref.: #31095]	ribose ChEBI	+	carbon source
[Ref.: #31095]	salicin ChEBI	+	carbon source
[Ref.: #31095]	sucrose ChEBI	+	carbon source
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Physiological tests	Metabolite	Indole test
[Ref.: #68369]		indole ChEBI	-	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #31095]	acid phosphatase	+	3.1.3.2
[Ref.: #31095]	alkaline phosphatase	+	3.1.3.1
[Ref.: #31095]	alpha-galactosidase	+	3.2.1.22
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68369]	beta-glucosidase	+	3.2.1.21	* from API 20NE
[Ref.: #31095]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #31095]	gelatinase	+
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE

API® 20NE:

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

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #23948]	24430	-	-	+	-	-	+	-	+	+	+	+	-	+	+	-	-	-	-	-	-	+

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

[Ref.: #23948]	Sample type/isolated from	polluted soil of a coking chemical plan
[Ref.: #23948]	Geographic location (country and/or sea, region)	Beijing
[Ref.: #23948]	Country	China
[Ref.: #23948]	Country ISO 3 Code	CHN
[Ref.: #23948]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Contamination	-
#Engineered	#Industrial	#Plant (Factory)
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KC684529 (>99% sequence identity) for Parapedobacter pyrenivorans subclade from Microbeatlas

Aquatic Samples	105
Soil Samples	145
Animal Samples	90
Plant Samples	35
Total Samples	375

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

[Ref.: #23948]

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.: #23948]	Parapedobacter pyrenivorans strain P-4 16S ribosomal RNA gene, partial sequence	KC684529	1490	ENA	1305674 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Parapedobacter pyrenivorans CGMCC 1.12195	GCA_014636865	scaffold	GenBank	1305674 tax ID	*
[Ref.: #66792]	Parapedobacter pyrenivorans strain CGMCC 1.12195	1305674.6	wgs	PATRIC	1305674 tax ID	*

[Ref.: #23948]

GC-content

45.4 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: Parapedobacter pyrenivorans CGMCC 1.12195 NCBI: GCA_014636865.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Parapedobacter pyrenivorans CGMCC 1.12195 NCBI: GCA_014636865.1
[Ref.: #69480]	flagellated	no	97.235	yes
[Ref.: #69480]	gram-positive	no	97.012	yes
[Ref.: #69480]	anaerobic	no	99.027	no
[Ref.: #69480]	aerobic	yes	83.351	yes
[Ref.: #69480]	halophile	no	86.378	no
[Ref.: #69480]	spore-forming	no	94.572	no
[Ref.: #69480]	thermophile	no	98.837	yes
[Ref.: #69480]	glucose-util	yes	90.42	yes
[Ref.: #69480]	motile	no	93.857	yes
[Ref.: #69480]	glucose-ferment	no	80.642	yes

Availability in culture collections External links

[Ref.: #23948]

Culture collection no.

DSM 102942, CGMCC 1.12195, NBRC 109113

[Ref.: #90515]

SI-ID 402734

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Parapedobacter pyrenivorans sp. nov., isolated from a pyrene-degrading microbial enrichment, and emended description of the genus Parapedobacter.	Zhao JK, Li XM, Zhang MJ, Jin JH, Jiang CY, Liu SJ	Int J Syst Evol Microbiol	10.1099/ijs.0.051938-0	2013	*

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 )

#23948

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 102942

#31095

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 #27424 (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) .

#68369

Automatically annotated from API 20NE .

#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 )

#90515

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-ID402734.1 )

#27424

IJSEM 3994 2013 ( DOI 10.1099/ijs.0.051938-0 , PubMed 23710053 )

* These data were automatically processed and therefore are not curated

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Parapedobacter pyrenivorans CGMCC 1.12195

Parapedobacter pyrenivorans CGMCC 1.12195

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