Archive BacDiveID:10.13145/bacdive14103.20230509.8.1

Strain identifier

BacDive ID: 14103

Type strain:

Species: Pedobacter rhizosphaerae

Strain Designation: 01-96

Variant: Isotype of BacDive ID 131130

Strain history: <- H.-Y. Weon, KACC; 01-96

NCBI tax ID(s): 390241 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 7624

BacDive-ID: 14103

DSM-Number: 18610

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

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

NCBI tax id

NCBI tax id: 390241
Matching level: species

strain history

@ref: 7624
history: <- H.-Y. Weon, KACC; 01-96

doi: 10.13145/bacdive14103.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/bacteroidota
domain: Bacteria
phylum: Bacteroidota
class: Sphingobacteriia
order: Sphingobacteriales
family: Sphingobacteriaceae
genus: Pedobacter
species: Pedobacter rhizosphaerae
full scientific name: Pedobacter rhizosphaerae Kwon et al. 2011

@ref: 7624

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Pedobacter

species: Pedobacter rhizosphaerae

full scientific name: Pedobacter rhizosphaerae Kwon et al. 2011

strain designation: 01-96

variant: Isotype of BacDive ID 131130

type strain: yes

Morphology

cell morphology

@ref	motility	confidence	gram stain
69480	no	91.418
69480		99.977	negative

Culture and growth conditions

culture medium

@ref: 7624
name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)
growth: yes
link: https://mediadive.dsmz.de/medium/545
composition: Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water

culture temp

@ref: 7624
growth: positive
type: growth
temperature: 28
range: mesophilic

Physiology and metabolism

spore formation

@ref	spore formation	confidence
69481	no	100
69480	no	99.991

Isolation, sampling and environmental information

isolation

@ref: 7624
sample type: rhizosphere soil of Chinese cabbage (Brassica campestris L.)
host species: Brassica campestris
geographic location: Suwon (37° 16' 38.50'' N 126° 58' 59.60'' E)
country: Republic of Korea
origin.country: KOR
continent: Asia
latitude: 37.2774
longitude: 126.983

isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Rhizosphere

Safety information

risk assessment

@ref: 7624
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 7624
description: Pedobacter rhizosphaerae partial 16S rRNA gene, type strain 01-96T
accession: AM279214
length: 1486
database: ena
NCBI tax ID: 390241

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Pedobacter rhizosphaerae DSM 18610	GCA_900111155	scaffold	ncbi	390241
66792	Pedobacter rhizosphaerae strain DSM 18610	390241.6	wgs	patric	390241
66792	Pedobacter rhizosphaerae DSM 18610	2622736586	draft	img	390241

GC content

@ref: 7624
GC-content: 37.8
method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	100	no
motile	no	87.9	no
flagellated	no	96.104	no
gram-positive	no	97.431	no
anaerobic	no	99.407	no
aerobic	yes	88.12	no
halophile	no	96.544	no
spore-forming	no	94.837	no
glucose-ferment	no	87.707	no
thermophile	no	99.537	yes
glucose-util	yes	86.853	no

External links

@ref: 7624

culture collection no.: DSM 18610, KACC 14938, NBRC 107690

straininfo link

@ref: 83270
straininfo: 412344

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	21257686	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	Base Composition, Brassica/microbiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Pedobacter/classification/genetics/isolation & purification/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizosphere, Soil Microbiology	Metabolism
Phylogeny	23456708	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	Aerobiosis, Bacteroidetes/classification/genetics/isolation & purification/physiology, Base Composition, Brassica/growth & development, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Korea, Molecular Sequence Data, Phylogeny, Pigments, Biological/metabolism, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Temperature	Genetics
Phylogeny	25563921	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	Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lycopersicon esculentum/microbiology, Molecular Sequence Data, Pedobacter/classification/genetics/isolation & purification, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analogs & derivatives/chemistry, Vitamin K 2/analogs & derivatives/chemistry	Genetics

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
7624	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18610)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-18610
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	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		10.1093/nar/gkaa1025	BRENDA, the ELIXIR core data resource in 2021: new developments and updates	Nucleic Acids Res. 49: D498-D508 2020	33211880
69480	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	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		10.21203/rs.3.rs-2527258/v1	Predictions based on the model GenomeNet Sporulation v. 1
83270	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID412344.1	StrainInfo: A central database for resolving microbial strain identifiers