Name: Pedobacter rhizosphaerae 01-96
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 131130

Type strain:

Species: Pedobacter rhizosphaerae

Strain Designation: 01-96

Variant: Isotype of BacDive ID 14103

Culture col. no.: DSM 25732, KACC 14938

Strain history: <- S.-W. Kwon, KACC; 01-96 <- H.-Y. Weon, Rural Development Administration (RDA), Suwon, Republic of Korea

NCBI tax ID(s): 390241 (species)

SI-ID 398975

DSM 25732

Special Collections

DSMZ

Other strains from Pedobacter rhizosphaerae

Section

Pedobacter rhizosphaerae 01-96 is a bacterium that was isolated from rhizosphere soil of Chinese cabbage.

Bacteria

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	*Pedobacter*
	Species	**Pedobacter rhizosphaerae**
	Full Scientific Name (LPSN)	Pedobacter rhizosphaerae Kwon et al. 2011

Information on culture and growth conditions Culture and growth conditions

[Ref.: #22422]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #22422]

Culture medium growth

[Ref.: #22422]

Culture medium link

Medium recipe at MediaDive

[Ref.: #22422]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #22422]			growth	28 °C

Information on physiology and metabolism Physiology and metabolism

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[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]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	pentose phosphate pathway	100	11 of 11
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	100	6 of 6
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glutamate and glutamine metabolism	75	21 of 28
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	purine metabolism	74.47	70 of 94
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	pyrimidine metabolism	71.11	32 of 45
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	leucine metabolism	69.23	9 of 13
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	isoprenoid biosynthesis	69.23	18 of 26
[Ref.: #66794]	histidine metabolism	68.97	20 of 29
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	tryptophan metabolism	65.79	25 of 38
[Ref.: #66794]	alanine metabolism	65.52	19 of 29
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	tyrosine metabolism	64.29	9 of 14
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	d-xylose degradation	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]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	lipid metabolism	61.29	19 of 31
[Ref.: #66794]	degradation of hexoses	61.11	11 of 18
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	arachidonate biosynthesis	60	3 of 5
[Ref.: #66794]	O-antigen biosynthesis	60	3 of 5
[Ref.: #66794]	coenzyme M biosynthesis	60	6 of 10
[Ref.: #66794]	propionate fermentation	60	6 of 10
[Ref.: #66794]	lysine metabolism	59.52	25 of 42
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	methionine metabolism	57.69	15 of 26
[Ref.: #66794]	degradation of pentoses	57.14	16 of 28
[Ref.: #66794]	non-pathway related	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]	urea cycle	53.85	7 of 13
[Ref.: #66794]	oxidative phosphorylation	50.55	46 of 91
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	arginine metabolism	50	12 of 24
[Ref.: #66794]	catecholamine biosynthesis	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	myo-inositol biosynthesis	50	5 of 10
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	androgen and estrogen metabolism	50	8 of 16
[Ref.: #66794]	degradation of sugar acids	48	12 of 25
[Ref.: #66794]	aclacinomycin biosynthesis	42.86	3 of 7
[Ref.: #66794]	ascorbate metabolism	40.91	9 of 22
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	phenol degradation	40	8 of 20
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	polyamine pathway	39.13	9 of 23
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	glycolate and glyoxylate degradation	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	3-phenylpropionate degradation	26.67	4 of 15
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	nitrate assimilation	22.22	2 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
[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.: #22422]	Sample type/isolated from	rhizosphere soil of Chinese cabbage
[Ref.: #22422]	Geographic location (country and/or sea, region)	Suwon (37° 16' 38.50'' N 126° 58' 59.60'' E)
[Ref.: #22422]	Country	Republic of Korea
[Ref.: #22422]	Country ISO 3 Code	KOR
[Ref.: #22422]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Rhizosphere

What are isolation sources categories?

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

[Ref.: #22422]

Biosafety level

Risk group (German classification)
According to TRBA 466

Availability in culture collections External links

[Ref.: #22422]

Culture collection no.

DSM 25732, KACC 14938

[Ref.: #89584]

SI-ID 398975

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pedobacter ureilyticus sp. nov., isolated from tomato rhizosphere soil.	Ngo HTT, Kook M, Yi TH	Int J Syst Evol Microbiol	10.1099/ijs.0.000055	2015	*
Phylogeny	Pedobacter namyangjuensis sp. nov. isolated from soil and reclassification of Nubsella zeaxanthinifaciens Asker et al. 2008 as Pedobacter zeaxanthinifaciens comb. nov.	Kim DU, Kim YJ, Shin DH, Weon HY, Kwon SW, Seong CN, Ka JO	J Microbiol	10.1007/s12275-013-2231-9	2013	*
Phylogeny	Pedobacter rhizosphaerae sp. nov. and Pedobacter soli sp. nov., isolated from rhizosphere soil of Chinese cabbage (Brassica campestris).	Kwon SW, Son JA, Kim SJ, Kim YS, Park IC, Bok JI, Weon HY	Int J Syst Evol Microbiol	10.1099/ijs.0.026781-0	2011	*

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 )

#22422

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25732

#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 )

#89584

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-ID398975.1 )

* These data were automatically processed and therefore are not curated

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