Strain identifier

BacDive ID: 1934

Type strain: No

Species: Burkholderia sp.

Strain Designation: SJ98

Strain history: R. K. Jain strain SJ98.

NCBI tax ID(s): 36773 (species)

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General

@ref: 16746

BacDive-ID: 1934

DSM-Number: 23195

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

description: Burkholderia sp. SJ98 is a mesophilic bacterium that was isolated from soil from pesticide-contaminated site.

NCBI tax id

  • NCBI tax id: 36773
  • Matching level: species

strain history

@refhistory
16746<- R. K. Jain, MTCC; SJ98
67770R. K. Jain strain SJ98.

doi: 10.13145/bacdive1934.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Burkholderiaceae
  • genus: Burkholderia
  • species: Burkholderia sp.
  • full scientific name: Burkholderia Yabuuchi et al. 1993

@ref: 16746

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Burkholderia

species: Burkholderia sp.

full scientific name: Burkholderia sp.

strain designation: SJ98

type strain: no

Morphology

colony morphology

  • @ref: 16746
  • incubation period: 1-2 days

Culture and growth conditions

culture medium

  • @ref: 16746
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
16746positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
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
16746catalase+1.11.1.6
16746cytochrome-c 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
16746--------+++++-++-+-++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
16746soil from pesticide-contaminated siteAssamIndiaINDAsia
67770Pesticide contaminated soil from Assam agricultural fieldsIndiaINDAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_3955.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_18;97_1155;98_1378;99_3955&stattab=map
  • Last taxonomy: Burkholderia
  • 16S sequence: DQ986324
  • Sequence Identity:
  • Total samples: 11435
  • soil counts: 6263
  • aquatic counts: 545
  • animal counts: 1567
  • plant counts: 3060

Sequence information

16S sequences

  • @ref: 16746
  • description: Burkholderia sp. SJ98 16S ribosomal RNA gene, partial sequence
  • accession: DQ986324
  • length: 1449
  • database: ena
  • NCBI tax ID: 406819

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Burkholderia sp. SJ98406819.9wgspatric406819
66792Burkholderia sp. SJ982531839682draftimg406819
67770Burkholderia sp. SJ98GCA_000256585contigncbi406819

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno98.115no
anaerobicno98.399no
halophileno93.809no
spore-formingno92.465no
glucose-utilyes88.727yes
aerobicyes89.775no
flagellatedno82.064no
thermophileno99.336no
motileyes87.535no
glucose-fermentno90.462yes

External links

@ref: 16746

culture collection no.: DSM 23195, MTCC 10105, JCM 16861

straininfo link

  • @ref: 71579
  • straininfo: 403441

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism21626025Reductive dehalogenation mediated initiation of aerobic degradation of 2-chloro-4-nitrophenol (2C4NP) by Burkholderia sp. strain SJ98.Pandey J, Heipieper HJ, Chauhan A, Arora PK, Prakash D, Takeo M, Jain RKAppl Microbiol Biotechnol10.1007/s00253-011-3254-y2011Aerobiosis, Biotransformation, Burkholderia/*metabolism, Carbon/metabolism, Chlorides/metabolism, Chromatography, High Pressure Liquid, Culture Media/chemistry, Energy Metabolism, Gas Chromatography-Mass Spectrometry, Nitrites/metabolism, Nitrogen/metabolism, Nitrophenols/*metabolism, Spectrometry, Mass, Matrix-Assisted Laser Desorption-IonizationCultivation
Metabolism25085488The gene cluster for para-nitrophenol catabolism is responsible for 2-chloro-4-nitrophenol degradation in Burkholderia sp. strain SJ98.Min J, Zhang JJ, Zhou NYAppl Environ Microbiol10.1128/AEM.02093-142014Bacterial Proteins/genetics/isolation & purification/metabolism, Benzoquinones/chemistry/metabolism, Burkholderia/*genetics/metabolism, Mixed Function Oxygenases/genetics/isolation & purification/metabolism, *Multigene Family, Nitrophenols/chemistry/*metabolism, Quinone Reductases/*genetics/isolation & purification/metabolismEnzymology

Reference

@idauthorscataloguedoi/urltitle
16746Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23195)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23195
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
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
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
71579Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID403441.1StrainInfo: A central database for resolving microbial strain identifiers