Strain identifier

BacDive ID: 133256

Type strain: Yes

Species: Pedobacter lycopersici

Strain Designation: T16R-88

NCBI tax ID(s): 1911527 (species)

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General

@ref: 25059

BacDive-ID: 133256

keywords: 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped, colony-forming

description: Pedobacter lycopersici T16R-88 is an aerobe, Gram-negative, rod-shaped bacterium that forms irregular colonies and was isolated from rhizosphere soil of a tomato plant.

NCBI tax id

  • NCBI tax id: 1911527
  • Matching level: species

doi: 10.13145/bacdive133256.20230509.8.1

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 lycopersici
  • full scientific name: Pedobacter lycopersici Cho et al. 2016

@ref: 25059

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Pedobacter

species: Pedobacter lycopersici

strain designation: T16R-88

type strain: yes

Morphology

cell morphology

  • @ref: 25059
  • gram stain: negative
  • cell length: 1.2-2.5 µm
  • cell width: 0.6-0.9 µm
  • cell shape: rod-shaped

colony morphology

  • @ref: 25059
  • colony color: white
  • colony shape: irregular

pigmentation

  • @ref: 25059
  • production: no
  • name: no Flexirubin-type pigments

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
25059positivegrowth4-35
25059positiveoptimum28-30mesophilic

culture pH

@refabilitytypepHPH range
25059positivegrowth6.0-9.0alkaliphile
25059positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 25059
  • oxygen tolerance: aerobe

halophily

@refsalttested relationconcentrationgrowth
25059NaCloptimum0 %
25059NaClgrowth0-4.0 %(w/v)positive

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
25059168082-dehydro-D-gluconate-assimilation
25059161933-hydroxybenzoate-assimilation
25059370543-hydroxybutyrate-assimilation
25059178794-hydroxybenzoate-assimilation
25059174265-dehydro-D-gluconate-assimilation
2505917128adipate-assimilation
2505985146carboxymethylcellulose-hydrolysis
25059casein-hydrolysis
2505917029chitin-hydrolysis
2505916899D-mannitol-assimilation
2505916988D-ribose-assimilation
2505917924D-sorbitol-assimilation
2505927689decanoate-assimilation
2505916991dna-hydrolysis
2505917234glucose-fermentation
2505928087glycogen-assimilation
2505917268myo-inositol-assimilation
2505917240itaconate-assimilation
2505916977L-alanine-assimilation
2505930849L-arabinose-assimilation
2505918287L-fucose-assimilation
2505915971L-histidine-assimilation
2505917203L-proline-assimilation
2505962345L-rhamnose-assimilation
2505917115L-serine-assimilation
2505924996lactate-assimilation
2505925115malate-assimilation
2505918401phenylacetate-assimilation
2505932032potassium gluconate-assimilation
2505917272propionate-assimilation
2505932954sodium acetate-assimilation
2505953258sodium citrate-assimilation
2505962983sodium malonate-assimilation
2505928017starch-hydrolysis
250599300suberic acid-assimilation
2505927897tryptophan-energy source
2505953426tween 80-hydrolysis
2505918186tyrosine-hydrolysis
2505916199urea-hydrolysis
2505931011valerate-assimilation
2505917634D-glucose+assimilation
2505916024D-mannose+assimilation
250594853esculin+hydrolysis
250595291gelatin+hydrolysis
2505917368hypoxanthine+hydrolysis
2505917306maltose+assimilation
2505928053melibiose+assimilation
25059506227N-acetylglucosamine+assimilation
2505917632nitrate+reduction
2505917814salicin+assimilation
2505917992sucrose+assimilation
2505915318xanthine+hydrolysis

metabolite production

  • @ref: 25059
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitemethylred-testindole test
2505917234glucose-
2505935581indole-

enzymes

@refvalueactivityec
25059acid phosphatase+3.1.3.2
25059alkaline phosphatase+3.1.3.1
25059alpha-chymotrypsin-3.4.21.1
25059alpha-fucosidase+3.2.1.51
25059alpha-galactosidase+3.2.1.22
25059alpha-glucosidase+3.2.1.20
25059alpha-mannosidase+3.2.1.24
25059arginine dihydrolase-3.5.3.6
25059beta-galactosidase+3.2.1.23
25059beta-glucosidase+3.2.1.21
25059beta-glucuronidase-3.2.1.31
25059catalase+1.11.1.6
25059cystine arylamidase+3.4.11.3
25059cytochrome oxidase+1.9.3.1
25059esterase (C 4)+
25059esterase lipase (C 8)+
25059leucine arylamidase+3.4.11.1
25059lipase (C 14)-
25059N-acetyl-beta-glucosaminidase+3.2.1.52
25059naphthol-AS-BI-phosphohydrolase+
25059trypsin-3.4.21.4
25059tryptophan deaminase-4.1.99.1
25059valine arylamidase+

Isolation, sampling and environmental information

isolation

  • @ref: 25059
  • sample type: rhizosphere soil of a tomato plant
  • geographic location: Buyeo-gun, Chungcheongnam-do
  • country: Republic of Korea
  • origin.country: KOR
  • continent: Asia
  • latitude: 36.275
  • longitude: 126.912
  • isolation date: 2015-04

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Rhizosphere

Sequence information

16S sequences

  • @ref: 25059
  • description: Pedobacter sp. strain T16R-88 16S ribosomal RNA gene, partial sequence
  • accession: KU379664
  • length: 1460
  • database: nuccore
  • NCBI tax ID: 1911527

GC content

  • @ref: 25059
  • GC-content: 35.6
  • method: Thermal denaturation, fluorometry

External links

@ref: 25059

culture collection no.: KACC 18652, NBRC 111984

literature

  • topic: Phylogeny
  • Pubmed-ID: 27902181
  • title: Pedobacterlycopersici sp. nov., isolated from the rhizosphere of tomato plant (Solanum lycopersicum L.).
  • authors: Cho H, Ahn JH, Weon HY, Joa JH, Kwon SW, Kim SJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001532
  • year: 2016
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lycopersicon esculentum/*microbiology, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Sphingolipids/chemistry, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournalpubmed
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
25059H. A. Cho, J. H.,Weon, H. Y.,Joa, J. H.,Kwon, S. W.,Kim, S. J.Pedobacter lycopersici sp. nov., isolated from the rhizosphere of tomato plant (Solanum lycopersicum L.)10.1099/ijsem.0.001532IJSEM 66: 5406-5411 201627902181