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Strain identifier

BacDive ID: 1905

Type strain: Yes

Species: Trinickia caryophylli

Strain Designation: 720, ICBPC 113

Strain history: LMG 2155 <-- NCPPB 2151 <-- ICPB PC113 <-- N. A. MacLean.

NCBI tax ID(s): 28094 (species)

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

@ref: 12714

BacDive-ID: 1905

DSM-Number: 50341

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

description: Trinickia caryophylli 720 is a mesophilic plant pathogen that was isolated from carnation .

NCBI tax id

  • NCBI tax id: 28094
  • Matching level: species

strain history

doi: 10.13145/bacdive1905.20221219.7.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Burkholderiaceae
  • genus: Trinickia
  • species: Trinickia caryophylli
  • full scientific name: Trinickia caryophylli (Burkholder 1942) Estrada-de Los Santos et al. 2018
  • synonyms

    @refsynonym
    20215Pseudomonas caryophylli
    20215Burkholderia caryophylli
    20215Phytomonas caryophylli
    20215Paraburkholderia caryophylli

@ref: 12714

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Trinickia

species: Trinickia caryophylli

full scientific name: Trinickia caryophylli (Burkholder 1942) Estrada-de Los Santos et al. 2018

strain designation: 720, ICBPC 113

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 98.2

Culture and growth conditions

culture medium

  • @ref: 12714
  • 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
12714positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 96.844

halophily

  • @ref: 69480
  • halophily level: non-halophilic
  • confidence: 97.883

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate+builds acid from
68371gluconate+builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol+builds acid from18333
68371L-fucose+builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose+builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol+builds acid from17924
68371D-mannitol+builds acid from16899
68371myo-inositol+builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose+builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose+builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371L-xylose-builds acid from65328
68371D-xylose+builds acid from65327
68371L-arabinose+builds acid from30849
68371D-arabinose+builds acid from17108
68371erythritol-builds acid from17113
68369malate+assimilation25115
68369adipate-assimilation17128
68369gluconate+assimilation24265
68369maltose-assimilation17306
68369N-acetylglucosamine+assimilation59640
68369D-mannitol+assimilation16899
68369D-mannose+assimilation16024
68369L-arabinose+assimilation30849
68369D-glucose+assimilation17634
68369gelatin-hydrolysis5291
68369esculin-hydrolysis4853
68369urea-hydrolysis16199
68369arginine-hydrolysis29016
68369D-glucose-fermentation17634
68369tryptophan-energy source27897
68369nitrate+reduction17632

metabolite production

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

metabolite tests

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

enzymes

@refvalueactivityec
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
12714+------++++++-++-+-+/-+
12714+------++++++-+--+--+
12714+------++++++-+--+--+
12714+------++++++-++-+--+
12714+------++++++-+--+--+

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
12714-+/--+++/-+-+/--++++-+-+++--+--------+------+/------++-++-

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentsampling date
12714carnation (Dianthus caryophyllus)Dianthus caryophyllusUSAUSANorth America
47209Dianthus caryophyllusUSAUSANorth America1951
67770Dianthus caryophyllus (carnation)Dianthus caryophyllus

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants
  • Cat3: #Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_3683.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_18;97_2288;98_2816;99_3683&stattab=map
  • Last taxonomy: Burkholderia
  • 16S sequence: AB021423
  • Sequence Identity:
  • Total samples: 166
  • soil counts: 81
  • aquatic counts: 10
  • animal counts: 16
  • plant counts: 59

Safety information

risk assessment

  • @ref: 12714
  • pathogenicity plant: yes
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218P.caryophylli 16S ribosomal RNAX670391453ena28094
12714Burkholderia caryophylli gene for 16S rRNA, strain: ATCC 25418AB0214231448ena28094

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Trinickia caryophylli LMG 2155GCA_902833925scaffoldncbi28094
66792Paraburkholderia caryophylli strain Ballard 72028094.5wgspatric28094
66792Trinickia caryophylli strain DSM 5034128094.8wgspatric28094
66792Trinickia caryophylli strain LMG 215528094.9wgspatric28094
67770Trinickia caryophylli DSM 50341GCA_007097545contigncbi28094
66792Klebsiella pneumoniae 4300STDY6636992GCA_900493125scaffoldpatric573

External links

@ref: 12714

culture collection no.: DSM 50341, ATCC 25418, CCUG 20834, CFBP 2429, CFBP 3818, CIP 105770, HAMBI 2159, ICMP 512, NCPPB 2151, LMG 2155, JCM 10488, BCRC 12862, BCRC 13908, CCEB 861, CCM 4971, ICPB PC113, JCM 9310, KCTC 2965, VKM B-1295, VTT E-991296

straininfo link

@refpassport
20218http://www.straininfo.net/strains/16782
20218http://www.straininfo.net/strains/16778
20218http://www.straininfo.net/strains/129534
20218http://www.straininfo.net/strains/149468
20218http://www.straininfo.net/strains/621183
20218http://www.straininfo.net/strains/149467
20218http://www.straininfo.net/strains/536673
20218http://www.straininfo.net/strains/16783

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17220453Burkholderia soli sp. nov., isolated from soil cultivated with Korean ginseng.Yoo SH, Kim BY, Weon HY, Kwon SW, Go SJ, Stackebrandt EInt J Syst Evol Microbiol10.1099/ijs.0.64471-02007Agriculture, Bacterial Typing Techniques, Burkholderia/chemistry/*classification/genetics/isolation & purification, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Panax/*growth & development, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny22081715Burkholderia symbiotica sp. nov., isolated from root nodules of Mimosa spp. native to north-east Brazil.Sheu SY, Chou JH, Bontemps C, Elliott GN, Gross E, James EK, Sprent JI, Young JPW, Chen WMInt J Syst Evol Microbiol10.1099/ijs.0.037408-02011Bacterial Typing Techniques, Base Composition, Brazil, Burkholderia/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/analysis, Mimosa/*microbiology, Molecular Sequence Data, Phospholipids/analysis, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiology, Sequence Analysis, DNAGenetics
Pathogenicity31605027Structure elucidation and biosynthetic locus of trinickiabactin from the plant pathogenic bacterium Trinickia caryophylli.Jiao J, Du J, Frediansyah A, Jahanshah G, Gross HJ Antibiot (Tokyo)10.1038/s41429-019-0246-02019Anti-Bacterial Agents/*biosynthesis/*chemistry/pharmacology, Computer Simulation, Drug Discovery, Gram-Negative Bacteria/drug effects, Magnetic Resonance Spectroscopy, Microbial Sensitivity Tests, Multigene Family, Plant Diseases/*microbiology, Proteobacteria/*chemistry/genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
12714Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 50341)https://www.dsmz.de/collection/catalogue/details/culture/DSM-50341
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
47209Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 20834)https://www.ccug.se/strain?id=20834
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
68371Automatically annotated from API 50CH acid
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)