Strain identifier

BacDive ID: 14184

Type strain: Yes

Species: Sphingobium indicum

Strain Designation: B90A

Strain history: CIP <- 2005, CCM <- 2005, R. Lal, Dehli Univ., Delhi, India: strain B90A

NCBI tax ID(s): 332055 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 6438

BacDive-ID: 14184

DSM-Number: 16412

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

description: Sphingobium indicum B90A is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from sugarcane rhizosphere soil.

NCBI tax id

  • NCBI tax id: 332055
  • Matching level: species

strain history

@refhistory
6438<- R. Lal, Univ. New Delhi; B90A <- N. Sethunathan
120083CIP <- 2005, CCM <- 2005, R. Lal, Dehli Univ., Delhi, India: strain B90A

doi: 10.13145/bacdive14184.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Sphingomonadaceae
  • genus: Sphingobium
  • species: Sphingobium indicum
  • full scientific name: Sphingobium indicum Pal et al. 2005

  • synonyms

    @refsynonym
    20215Sphingobium chinhatense
    20215Sphingobium japonicum
    20215Sphingobium francense
    20215Sphingobium lucknowense

@ref: 6438

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingobium

species: Sphingobium indicum

full scientific name: Sphingobium indicum Pal et al. 2005

strain designation: B90A

type strain: yes

Morphology

cell morphology

  • @ref: 120083
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 120083

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
38370MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120083CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

  • @ref: 38370
  • growth: positive
  • type: growth
  • temperature: 30
  • range: mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120083
  • oxygen tolerance: facultative anaerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12008317632nitrate+reduction
12008316301nitrite-reduction

metabolite production

  • @ref: 120083
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
120083oxidase+
120083alcohol dehydrogenase-1.1.1.1
120083catalase-1.11.1.6
120083lysine decarboxylase-4.1.1.18
120083ornithine decarboxylase-4.1.1.17
120083urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120083-++--++-++++---+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6438sugarcane rhizosphere soilCuttackIndiaINDAsia
120083Environment, Rice rhizosphereCuttackIndiaINDAsia

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
64381Risk group (German classification)
1200831Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6438
  • description: Sphingobium indicum strain B90A 16S ribosomal RNA gene, partial sequence
  • accession: AY519129
  • length: 1452
  • database: ena
  • NCBI tax ID: 861109

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingobium indicum B90A861109.7plasmidpatric861109
66792Sphingobium indicum B90A861109.5plasmidpatric861109
66792Sphingobium indicum B90A861109.3wgspatric861109
66792Sphingobium indicum B90A861109.6plasmidpatric861109
66792Sphingobium indicum B90A2775507255completeimg861109
66792Sphingobium indicum B90AGCA_000264945completencbi861109

External links

@ref: 6438

culture collection no.: DSM 16412, CCM 7286, MTCC 6364, CIP 108929

straininfo link

  • @ref: 83347
  • straininfo: 265629

literature

  • topic: Phylogeny
  • Pubmed-ID: 16166696
  • title: Hexachlorocyclohexane-degrading bacterial strains Sphingomonas paucimobilis B90A, UT26 and Sp+, having similar lin genes, represent three distinct species, Sphingobium indicum sp. nov., Sphingobium japonicum sp. nov. and Sphingobium francense sp. nov., and reclassification of [Sphingomonas] chungbukensis as Sphingobium chungbukense comb. nov.
  • authors: Pal R, Bala S, Dadhwal M, Kumar M, Dhingra G, Prakash O, Prabagaran SR, Shivaji S, Cullum J, Holliger C, Lal R
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63201-0
  • year: 2005
  • mesh: Bacterial Proteins/*genetics/metabolism, Bacterial Typing Techniques, Biodegradation, Environmental, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Hexachlorocyclohexane/*metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sphingomonadaceae/*classification/enzymology/genetics/physiology, Sphingomonas/*classification/enzymology/genetics/physiology
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitle
6438Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16412)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16412
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
38370Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6613
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)
68382Automatically annotated from API zym
83347Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID265629.1StrainInfo: A central database for resolving microbial strain identifiers
120083Curators of the CIPCollection of Institut Pasteur (CIP 108929)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108929