Strain identifier

BacDive ID: 17493

Type strain: Yes

Species: Lysobacter capsici

Strain Designation: YC5194

Strain history: <- YR Chung, Gyeongsang Univ.

NCBI tax ID(s): 435897 (species)

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General

@ref: 7997

BacDive-ID: 17493

DSM-Number: 19286

keywords: 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, rod-shaped

description: Lysobacter capsici YC5194 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from rhizosphere of pepper.

NCBI tax id

  • NCBI tax id: 435897
  • Matching level: species

strain history

@refhistory
7997<- Y. R. Chung, National University Jinju
67771<- YR Chung, Gyeongsang Univ.

doi: 10.13145/bacdive17493.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Lysobacterales
  • family: Lysobacteraceae
  • genus: Lysobacter
  • species: Lysobacter capsici
  • full scientific name: Lysobacter capsici Park et al. 2008

@ref: 7997

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Xanthomonadales

family: Lysobacteraceae

genus: Lysobacter

species: Lysobacter capsici

full scientific name: Lysobacter capsici Park et al. 2008

strain designation: YC5194

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
32305negative11 µm0.4 µmrod-shapedno
67771negative

pigmentation

  • @ref: 32305
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 7997
  • name: NUTRIENT AGAR (DSMZ Medium 1)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1
  • composition: Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
7997positivegrowth28mesophilic
32305positivegrowth04-37
32305positiveoptimum28mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
32305positivegrowth5.5-8.5alkaliphile
32305positiveoptimum7.25

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32305facultative anaerobe
67771aerobe

spore formation

  • @ref: 32305
  • spore formation: no

halophily

  • @ref: 32305
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-2 %

observation

  • @ref: 67771
  • observation: quinones: Q-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3230516947citrate+carbon source
323054853esculin+hydrolysis
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose+assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose+assimilation
683695291gelatin+hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
32305acid phosphatase+3.1.3.2
32305alkaline phosphatase+3.1.3.1
32305catalase+1.11.1.6
32305cytochrome oxidase+1.9.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase+
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
7997-----++++-+-++---+--+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7997rhizosphere of pepperJinjuRepublic of KoreaKORAsia
67771From rhizosphere of pepper in JinjuRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_2461.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17;96_647;97_1577;98_1919;99_2461&stattab=map
  • Last taxonomy: Lysobacter
  • 16S sequence: EF488749
  • Sequence Identity:
  • Total samples: 16578
  • soil counts: 9924
  • aquatic counts: 1340
  • animal counts: 1424
  • plant counts: 3890

Safety information

risk assessment

  • @ref: 7997
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7997
  • description: Lysobacter capsici strain YC5194 16S ribosomal RNA gene, complete sequence
  • accession: EF488749
  • length: 1470
  • database: ena
  • NCBI tax ID: 435897

GC content

  • @ref: 32305
  • GC-content: 65.4

External links

@ref: 7997

culture collection no.: DSM 19286, KCTC 22007

straininfo link

  • @ref: 86490
  • straininfo: 323975

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18218936Lysobacter capsici sp. nov., with antimicrobial activity, isolated from the rhizosphere of pepper, and emended description of the genus Lysobacter.Park JH, Kim R, Aslam Z, Jeon CO, Chung YRInt J Syst Evol Microbiol10.1099/ijs.0.65290-02008Bacterial Typing Techniques, Capsicum/*growth & development/microbiology, DNA, Bacterial/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Korea, Lysobacter/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
Phylogeny19684312Lysobacter soli sp. nov., isolated from soil of a ginseng field.Srinivasan S, Kim MK, Sathiyaraj G, Kim HB, Kim YJ, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.016428-02009Base Composition, Base Sequence, Fatty Acids/analysis, Lysobacter/*classification/genetics/isolation & purification, Molecular Sequence Data, Panax/*microbiology, *Soil MicrobiologyGenetics
Phylogeny20399056Genotypic and phenotypic variation among Lysobacter capsici strains isolated from Rhizoctonia suppressive soils.Postma J, Nijhuis EH, Yassin AFSyst Appl Microbiol10.1016/j.syapm.2010.03.0022010Bacterial Typing Techniques, Cluster Analysis, DNA Fingerprinting, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genotype, Lysobacter/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Netherlands, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizoctonia/*growth & development, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil MicrobiologyGenetics
Phylogeny20952549Lysobacter korlensis sp. nov. and Lysobacter bugurensis sp. nov., isolated from soil.Zhang L, Bai J, Wang Y, Wu GL, Dai J, Fang CXInt J Syst Evol Microbiol10.1099/ijs.0.024448-02010Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Locomotion, Lysobacter/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Phospholipids, Phylogeny, Pigments, Biological/metabolism, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Salts/metabolism, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny32511086Lysobacter profundi sp. nov., isolated from freshwater sediment and reclassification of Lysobacter panaciterrae as Luteimonas panaciterrae comb. nov.Jin CZ, Song X, Sung YJ, Jin FJ, Li T, Oh HM, Lee HG, Jin LInt J Syst Evol Microbiol10.1099/ijsem.0.0042532020Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/*microbiology, Geologic Sediments/*microbiology, Lysobacter/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Ubiquinone/chemistryEnzymology

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7997Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19286)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19286
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
32305Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2854428776041
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68369Automatically annotated from API 20NE
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
86490Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID323975.1StrainInfo: A central database for resolving microbial strain identifiers