Strain identifier

BacDive ID: 1968

Type strain: Yes

Species: Paraburkholderia terrae

Strain Designation: KMY02, KMY 02

Strain history: CIP <- 2006, KCTC <- ST Lee, KAIST

NCBI tax ID(s): 1218084 (strain), 311230 (species)

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General

@ref: 7195

BacDive-ID: 1968

DSM-Number: 17804

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped

description: Paraburkholderia terrae KMY02 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
1218084strain
311230species

strain history

@refhistory
7195<- S.-T. Lee; KMY 02 <- H.-C. Yang
419862006, KCTC
123462CIP <- 2006, KCTC <- ST Lee, KAIST

doi: 10.13145/bacdive1968.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Burkholderiaceae
  • genus: Paraburkholderia
  • species: Paraburkholderia terrae
  • full scientific name: Paraburkholderia terrae (Yang et al. 2006) Sawana et al. 2015

  • synonyms

    • @ref: 20215
    • synonym: Burkholderia terrae

@ref: 7195

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Paraburkholderia

species: Paraburkholderia terrae

full scientific name: Paraburkholderia terrae (Yang et al. 2006) Sawana et al. 2015

strain designation: KMY02, KMY 02

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31652negative1.6-2 µm0.6-0.8 µmrod-shapedyes
69480yes92.816
69480negative99.973
123462negativerod-shapedyes

colony morphology

  • @ref: 7195
  • incubation period: 1-2 days

pigmentation

  • @ref: 31652
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7195TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
41986MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
123462CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
7195positivegrowth28mesophilic
31652positivegrowth25-30mesophilic
31652positiveoptimum25-30mesophilic
41986positivegrowth25mesophilic
60331positivegrowth30mesophilic

culture pH

@refabilitytypepH
31652positivegrowth7
31652positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31652aerobe
60331aerobe
123462obligate aerobe

spore formation

@refspore formationconfidence
31652no
69481no100
69480no99.983

halophily

@refsaltgrowthtested relationconcentration
31652NaClpositivegrowth0-3 %
31652NaClpositiveoptimum0-1.5 %

observation

  • @ref: 31652
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
31652168082-dehydro-D-gluconate+carbon source
31652370543-hydroxybutyrate+carbon source
31652581435-dehydro-D-gluconate+carbon source
3165222599arabinose+carbon source
3165227689decanoate+carbon source
3165233984fucose+carbon source
3165224265gluconate+carbon source
3165217234glucose+carbon source
3165227570histidine+carbon source
3165224996lactate+carbon source
3165225115malate+carbon source
3165229864mannitol+carbon source
3165237684mannose+carbon source
31652506227N-acetylglucosamine+carbon source
3165218401phenylacetate+carbon source
3165226271proline+carbon source
3165226546rhamnose+carbon source
3165233942ribose+carbon source
3165217822serine+carbon source
3165230911sorbitol+carbon source
316529300suberic acid+carbon source
6836925115malate+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
12346217632nitrate-reduction
12346216301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12346235581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
7195catalase+1.11.1.6
7195cytochrome-c oxidase+1.9.3.1
31652catalase+1.11.1.6
31652cytochrome oxidase+1.9.3.1
31652urease+3.5.1.5
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
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase+3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin+3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)+
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
123462oxidase+
123462alcohol dehydrogenase-1.1.1.1
123462catalase+1.11.1.6
123462lysine decarboxylase-4.1.1.18
123462ornithine decarboxylase-4.1.1.17
123462urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123462-+++++---+++++--+---

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
7195-------++++++-+++/-++/-++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7195soilDaejeon cityRepublic of KoreaKORAsia
60331SoilRepublic of KoreaKORAsia
123462Environment, Forest soilDaejeonRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_7918.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_173;97_511;98_587;99_7918&stattab=map
  • Last taxonomy: Paraburkholderia
  • 16S sequence: AB681300
  • Sequence Identity:
  • Total samples: 3399
  • soil counts: 2594
  • aquatic counts: 205
  • animal counts: 165
  • plant counts: 435

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
71951Risk group (German classification)
1234621Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Burkholderia terrae gene for 16S rRNA, partial sequence, strain: NBRC 100964AB6813001456ena311230
7195Burkholderia terrae gene for 16S rRNA, partial sequence, strain: KMY02AB2012851470ena311230

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paraburkholderia terrae DSM 17804GCA_002902925completencbi311230
66792Paraburkholderia terrae NBRC 100964GCA_000739835contigncbi1218084
66792Burkholderia terrae NBRC 1009641218084.3wgspatric1218084
66792Paraburkholderia terrae strain DSM 17804311230.14completepatric311230
66792Paraburkholderia terrae NBRC 1009642600255059draftimg1218084
66792Paraburkholderia terrae DSM 178042811994987completeimg311230

GC content

  • @ref: 31652
  • GC-content: 62

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno81.967no
gram-positiveno98.054yes
anaerobicno98.804no
aerobicyes92.559yes
halophileno91.975no
spore-formingno93.496no
thermophileno99.56no
glucose-utilyes90.142yes
motileyes87.809yes
glucose-fermentno89.829yes

External links

@ref: 7195

culture collection no.: DSM 17804, KCTC 12388, NBRC 100964, CCUG 54786, CIP 109196

straininfo link

  • @ref: 71613
  • straininfo: 232861

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16449457Burkholderia terrae sp. nov., isolated from a forest soil.Yang HC, Im WT, Kim KK, An DS, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.63968-02006Bacterial Typing Techniques, Burkholderia/chemistry/*classification/genetics/isolation & purification, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Trees/*microbiologyGenetics
Phylogeny22467155Burkholderia diazotrophica sp. nov., isolated from root nodules of Mimosa spp.Sheu SY, Chou JH, Bontemps C, Elliott GN, Gross E, Dos Reis Junior FB, Melkonian R, Moulin L, James EK, Sprent JI, Young JPW, Chen WMInt J Syst Evol Microbiol10.1099/ijs.0.039859-02012Bacterial Typing Techniques, Base Composition, Brazil, Burkholderia/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/analysis, Genes, Bacterial, Mimosa/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiology, Sequence Analysis, DNAGenetics
29896162The Response of Paraburkholderia terrae Strains to Two Soil Fungi and the Potential Role of Oxalate.Haq IU, Zwahlen RD, Yang P, van Elsas JDFront Microbiol10.3389/fmicb.2018.009892018
Phylogeny32068849Delineation of a Subgroup of the Genus Paraburkholderia, Including P. terrae DSM 17804T, P. hospita DSM 17164T, and Four Soil-Isolated Fungiphiles, Reveals Remarkable Genomic and Ecological Features-Proposal for the Definition of a P. hospita Species Cluster.Pratama AA, Jimenez DJ, Chen Q, Bunk B, Sproer C, Overmann J, van Elsas JDGenome Biol Evol10.1093/gbe/evaa0312020Burkholderiaceae/*genetics/growth & development/metabolism, Ecology, Fungi/*genetics/growth & development/metabolism, *Genome, Bacterial, *Genome, Fungal, Genomics/*methods, Phylogeny, Soil Microbiology, Species SpecificityGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
7195Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17804)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17804
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
31652Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127934
41986Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6911
60331Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 54786)https://www.ccug.se/strain?id=54786
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)
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
71613Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID232861.1StrainInfo: A central database for resolving microbial strain identifiers
123462Curators of the CIPCollection of Institut Pasteur (CIP 109196)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109196