Strain identifier

BacDive ID: 141040

Type strain: Yes

Species: Parapedobacter lycopersici

Strain Designation: T16R-256

Strain history: S.-W. Kwon; KACC, South Korea; T16R-256.

NCBI tax ID(s): 1864939 (species)

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General

@ref: 43920

BacDive-ID: 141040

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

description: Parapedobacter lycopersici T16R-256 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from rhizosphere soil of tomato plants grown in a greenhouse in Yecheon-gun, Gyeongsangbuk-do, Republic of Korea.

NCBI tax id

  • NCBI tax id: 1864939
  • Matching level: species

strain history

  • @ref: 67770
  • history: S.-W. Kwon; KACC, South Korea; T16R-256.

doi: 10.13145/bacdive141040.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Sphingobacteriia
  • order: Sphingobacteriales
  • family: Sphingobacteriaceae
  • genus: Parapedobacter
  • species: Parapedobacter lycopersici
  • full scientific name: Parapedobacter lycopersici Kim et al. 2017

@ref: 43920

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Parapedobacter

species: Parapedobacter lycopersici

strain designation: T16R-256

type strain: yes

Morphology

cell morphology

  • @ref: 43920
  • gram stain: negative
  • cell length: 0.8-1.1 µm
  • cell width: 0.6 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 43920
  • colony color: light-yellow
  • colony shape: circular
  • medium used: R2A agar

Culture and growth conditions

culture medium

  • @ref: 43920
  • name: Reasoner's 2A agar (R2A)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
43920positivegrowth15-37
43920positiveoptimum28-30mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
43920positivegrowth7.0-9.0alkaliphile
43920positiveoptimum7.0-8.0

Physiology and metabolism

oxygen tolerance

  • @ref: 43920
  • oxygen tolerance: aerobe

halophily

  • @ref: 43920
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-4 %(w/v)

observation

@refobservation
43920quinone MK-7
67770quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
43920161933-hydroxybenzoate-assimilation
43920370543-hydroxybutyrate-assimilation
43920178794-hydroxybenzoate-assimilation
4392017128adipate-assimilation
4392027689decanoate-assimilation
4392016899D-mannitol-assimilation
4392016988D-ribose-assimilation
4392017924D-sorbitol-assimilation
4392028087glycogen-assimilation
4392017268myo-inositol-assimilation
4392017240itaconate-assimilation
43920L-alanine 4-nitroanilide-assimilation
4392030849L-arabinose-assimilation
4392018287L-fucose-assimilation
4392015971L-histidine-assimilation
4392017203L-proline-assimilation
4392062345L-rhamnose-assimilation
4392017115L-serine-assimilation
4392024996lactate-assimilation
4392025115malate-assimilation
4392028053melibiose-assimilation
4392018401phenylacetate-assimilation
43920potassium 2-dehydro-D-gluconate-assimilation
43920potassium 5-dehydro-D-gluconate-assimilation
4392017272propionate-assimilation
4392032954sodium acetate-assimilation
4392053258sodium citrate-assimilation
4392062983sodium malonate-assimilation
439209300suberic acid-assimilation
4392031011valerate-assimilation
4392085146carboxymethylcellulose-hydrolysis
43920casein-hydrolysis
4392017029chitin-hydrolysis
4392016991dna-hydrolysis
439205291gelatin-hydrolysis
4392017368hypoxanthine-hydrolysis
4392028017starch-hydrolysis
4392053426tween 80-hydrolysis
4392018186tyrosine-hydrolysis
4392016199urea-hydrolysis
4392015318xanthine-hydrolysis
4392017632nitrate-reduction
4392017634D-glucose+assimilation
4392016024D-mannose+assimilation
43920maltose hydrate+assimilation
43920506227N-acetylglucosamine+assimilation
4392032032potassium gluconate+assimilation
4392017814salicin+assimilation
4392017992sucrose+assimilation
43920esculin ferric citrate+hydrolysis

metabolite production

  • @ref: 43920
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
43920catalase+1.11.1.6
43920cytochrome oxidase+1.9.3.1
43920arginine dihydrolase-3.5.3.6
43920alkaline phosphatase+3.1.3.1
43920esterase (C 4)+
43920esterase Lipase (C 8)+
43920leucine arylamidase+3.4.11.1
43920valine arylamidase+
43920cystine arylamidase+3.4.11.3
43920acid phosphatase+3.1.3.2
43920naphthol-AS-BI-phosphohydrolase+
43920alpha-galactosidase+3.2.1.22
43920beta-galactosidase+3.2.1.23
43920alpha-glucosidase+3.2.1.20
43920beta-glucosidase+3.2.1.21
43920N-acetyl-beta-glucosaminidase+3.2.1.52
43920alpha-mannosidase+3.2.1.24
43920lipase (C 14)-
43920trypsin-3.4.21.4
43920alpha-chymotrypsin-3.4.21.1
43920beta-glucuronidase-3.2.1.31
43920alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    43920C15:0 anteiso1.3
    43920C16:01.1
    43920C16:0 3OH1
    43920C15:0 iso38.9
    43920C15:0 iso 2OH / C16:1ω7c23.7
    43920C15:0 iso 3OH3.1
    43920C17:0 iso 3OH22.7
    43920C17:1 iso ω9c2.3
    43920unknown 16.5821.516582
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A agar
  • agar/liquid: agar
  • incubation temperature: 28
  • software version: Sherlock 5.0
  • library/peak naming table: TSBA 5.0
  • system: MIS MIDI
  • instrument: Hewlett Packard 6890 gas chromatograph
  • method/protocol: Sasser, 1990
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment culture
43920rhizosphere soil of tomato plants grown in a greenhouse in Yecheon-gun, Gyeongsangbuk-do, Republic of KoreaYecheon-gun, Gyeongsangbuk-doRepublic of KoreaKORAsia36.7176128.499R2A agar
67770Rhizosphere soil of tomato plants grown in a greenhouse in Yecheon-gunGyeongsangbuk-doRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_28676.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15793;96_14150;97_17247;98_21427;99_28676&stattab=map
  • Last taxonomy: Parapedobacter lycopersici subclade
  • 16S sequence: KX417294
  • Sequence Identity:
  • Total samples: 211
  • soil counts: 68
  • aquatic counts: 28
  • animal counts: 97
  • plant counts: 18

Sequence information

16S sequences

  • @ref: 43920
  • description: 16S rRNA gene sequence
  • accession: KX417294
  • database: nuccore

Genome sequences

  • @ref: 66792
  • description: Parapedobacter lycopersici KACC 18788
  • accession: GCA_024643285
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 1864939

GC content

@refGC-contentmethod
4392055.5real time PCR (RTD-PCR)
6777055.5thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno97.181yes
gram-positiveno98.076no
anaerobicno99.002no
aerobicyes84.681yes
halophileno86.87no
spore-formingno95.396no
glucose-fermentno86.556no
thermophileno96.337no
glucose-utilyes86.421yes
motileno93.63yes

External links

@ref: 43920

culture collection no.: KACC 18788, JCM 31602

literature

  • topic: Phylogeny
  • Pubmed-ID: 28895519
  • title: Parapedobacter lycopersici sp. nov., isolated from the rhizosphere soil of tomato plants (Solanum lycopersicum L.).
  • authors: Kim JM, Lee SA, Cho H, Kim SJ, Joa JH, Kwon SW, Weon HY
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002162
  • year: 2017
  • mesh: Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lycopersicon esculentum/*microbiology, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/chemistry, 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
43920Jeong Myeong Kim, Shin Ae Lee, Hayoung Cho, Soo-Jin Kim, Jae-Ho Joa, Soon-Wo Kwon, Hang-Yeon WeonParapedobacter lycopersici sp. nov., isolated from the rhizosphere soil of tomato plants (Solanum lycopersicum L.)10.1099/ijsem.0.002162IJSEM 67: 3728-3732 201728895519
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69479João 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 betahttps://microbeatlas.org/