Strain identifier

BacDive ID: 1917

Type strain: Yes

Species: Burkholderia plantarii

Strain Designation: AZ 8201

Strain history: CIP <- 1998, CFBP

NCBI tax ID(s): 41899 (species)

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General

@ref: 3621

BacDive-ID: 1917

DSM-Number: 9509

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-negative, rod-shaped, plant pathogen

description: Burkholderia plantarii AZ 8201 is an obligate aerobe, mesophilic, Gram-negative plant pathogen that was isolated from rice seedling.

NCBI tax id

  • NCBI tax id: 41899
  • Matching level: species

strain history

@refhistory
3621<- JCM <- K. Azegami; AZ 8201
419411998, CFBP
67770K. Azegami AZ8201.
121853CIP <- 1998, CFBP

doi: 10.13145/bacdive1917.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Burkholderiaceae
  • genus: Burkholderia
  • species: Burkholderia plantarii
  • full scientific name: Burkholderia plantarii (Azegami et al. 1987) Urakami et al. 1994

  • synonyms

    @refsynonym
    20215Burkholderia vandii
    20215Pseudomonas plantarii

@ref: 3621

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Burkholderia

species: Burkholderia plantarii

full scientific name: Burkholderia plantarii (Azegami et al. 1987) Urakami et al. 1994

strain designation: AZ 8201

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
121853negativerod-shapedno
125438negative97
125439negative94.1

colony morphology

  • @ref: 3621
  • incubation period: 1-2 days

pigmentation

  • @ref: 121853
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3621NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
41941MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121853CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
121853CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperature
3621positivegrowth30
41941positivegrowth30
47799positivegrowth28
67770positivegrowth30
121853positivegrowth25-37
121853nogrowth5
121853nogrowth10
121853nogrowth41

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
121853obligate aerobe
125439obligate aerobe97.4

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 94.4

compound production

  • @ref: 3621
  • compound: tropolone

observation

  • @ref: 67770
  • observation: quinones: Q-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12185316947citrate+carbon source
1218534853esculin-hydrolysis
12185317632nitrate+reduction
12185316301nitrite-reduction
12185317632nitrate-respiration
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate+assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol+assimilation
6836916024D-mannose+assimilation
6836917634D-glucose+assimilation
683695291gelatin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction

antibiotic resistance

  • @ref: 121853
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12185335581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
3621catalase+1.11.1.6
3621cytochrome-c oxidase+1.9.3.1
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382cystine arylamidase-3.4.11.3
68382lipase (C 14)+
68382leucine arylamidase+3.4.11.1
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
121853oxidase+
121853beta-galactosidase+3.2.1.23
121853alcohol dehydrogenase-1.1.1.1
121853gelatinase+/-
121853amylase-
121853DNase-
121853caseinase+3.4.21.50
121853catalase+1.11.1.6
121853tween esterase-
121853lecithinase+
121853lipase+
121853lysine decarboxylase-4.1.1.18
121853ornithine decarboxylase-4.1.1.17
121853protease+
121853tryptophan deaminase-
121853urease-3.5.1.5
68369urease-3.5.1.5
68382valine arylamidase-
68369cytochrome oxidase+1.9.3.1
68369gelatinase+
68369arginine dihydrolase-3.5.3.6

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121853-+++++----++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
3621+----++++++++-+/-+-+++/-+
3621+-----+-++/-+++--+-+--+
3621+-----+++++++-++-++-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121853+++++---------------++-++-+--+--++--+------++++--++--+--+--++-+++------+-+--+++++-+-----++++-++++--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
3621rice seedlingOmigawaJapanJPNAsia
47799Oryza sativa cv. KoshihikariJapanJPNAsia1982
67770Rice seedlingOmigawa,ChibaJapanJPNAsia
121853Oryza sativaJapanJPNAsia1982

isolation source categories

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

Safety information

risk assessment

@refpathogenicity plantbiosafety levelbiosafety level comment
3621yes1Risk group (German classification)
1218531Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Burkholderia plantarii strain LMG 9035 16S ribosomal RNA gene, partial sequenceHQ8490981124nuccore41899
3621Burkholderia plantarii 16S ribosomal RNA gene, partial sequenceU969331549nuccore41899
124043Burkholderia plantarii gene for 16S rRNA, partial sequence, strain: NBRC 104884.AB6822181458nuccore41899
124043Burkholderia plantarii strain NCPPB 3590 16S ribosomal RNA gene, partial sequence.KC188308755nuccore41899

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Burkholderia plantarii ATCC 43733GCA_001411805completencbi41899
66792Burkholderia plantarii LMG 9035GCA_902832905scaffoldncbi41899
66792Burkholderia plantarii strain ATCC 4373341899.12plasmidpatric41899
66792Burkholderia plantarii strain ATCC 4373341899.3completepatric41899
66792Burkholderia plantarii strain LMG 903541899.18wgspatric41899
66792Burkholderia plantarii ATCC 437332687453568completeimg41899

GC content

@refGC-contentmethod
362164.8Buoyant density centrifugation (BD)
362168.7
6777068.7high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno97no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.56yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes88.799yes
125438spore-formingspore-formingAbility to form endo- or exosporesno87.001no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno95.477yes
125438motile2+flagellatedAbility to perform flagellated movementyes83.505no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno94.4
125439BacteriaNetmotilityAbility to perform movementyes75.9
125439BacteriaNetgram_stainReaction to gram-stainingnegative94.1
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe97.4

External links

@ref: 3621

culture collection no.: DSM 9509, ATCC 43733, ICMP 9424, JCM 5492, LMG 9035, CCUG 23368, NIAES 1723, CIP 105769, KACC 10679, KCTC 2972, NBRC 104884, NCCB 95038, NCPPB 3590, CFBP 3997

straininfo link

  • @ref: 71561
  • straininfo: 4203

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny33555242Paraburkholderia acidiphila sp. nov., Paraburkholderia acidisoli sp. nov. and Burkholderia guangdongensis sp. nov., isolated from forest soil, and reclassification of Burkholderia ultramafica as Paraburkholderia ultramafica comb. nov.Gao ZH, Zhang QM, Lv YY, Wang YQ, Zhao BN, Qiu LHInt J Syst Evol Microbiol10.1099/ijsem.0.0046902021
Phylogeny34287810Burkholderia perseverans sp. nov., a bacterium isolated from the Restinga ecosystem, is a producer of volatile and diffusible compounds that inhibit plant pathogens.Andrade JP, de Souza HG, Ferreira LC, Cnockaert M, De Canck E, Wieme AD, Peeters C, Gross E, De Souza JT, Marbach PAS, Goes-Neto A, Vandamme PBraz J Microbiol10.1007/s42770-021-00560-w2021Agaricales/drug effects/physiology, *Antibiosis/physiology, Aspergillus/drug effects/physiology, Bacterial Typing Techniques, Brazil, *Burkholderia/chemistry/classification/genetics, DNA, Bacterial/genetics, *Ecosystem, Phospholipids/analysis, Phylogeny, Phytophthora/drug effects/physiology, Plant Leaves/microbiology, RNA, Ribosomal, 16S/genetics, Species Specificity, Volatile Organic Compounds/metabolism/pharmacologyPathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3621Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 9509)https://www.dsmz.de/collection/catalogue/details/culture/DSM-9509
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
41941Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17825
47799Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 23368)https://www.ccug.se/strain?id=23368
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
71561Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID4203.1StrainInfo: A central database for resolving microbial strain identifiers
121853Curators of the CIPCollection of Institut Pasteur (CIP 105769)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105769
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1