Strain identifier

BacDive ID: 13153

Type strain: Yes

Species: Pseudomonas delhiensis

Strain Designation: RLD-1

Strain history: CIP <- 2007, CCM <- R. Lal, Delhi Univ., Delhi, India: strain RLD-1

NCBI tax ID(s): 366289 (species)

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General

@ref: 7766

BacDive-ID: 13153

DSM-Number: 18900

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

description: Pseudomonas delhiensis RLD-1 is an aerobe, Gram-negative, motile bacterium that was isolated from soil sample contaminated by polycylic aromatic compounds of fly ash dumping site.

NCBI tax id

  • NCBI tax id: 366289
  • Matching level: species

strain history

@refhistory
7766<- R. Lal, Zoology, Univ. Delhi; RLD-1
118885CIP <- 2007, CCM <- R. Lal, Delhi Univ., Delhi, India: strain RLD-1

doi: 10.13145/bacdive13153.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Pseudomonadales
  • family: Pseudomonadaceae
  • genus: Pseudomonas
  • species: Pseudomonas delhiensis
  • full scientific name: Pseudomonas delhiensis Prakash et al. 2007

@ref: 7766

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas delhiensis

full scientific name: Pseudomonas delhiensis Prakash et al. 2007

strain designation: RLD-1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31831negative1.5 µm0.5 µmrod-shapedyes
69480yes97.189
69480negative99.999
118885negativerod-shapedno

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
37756MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
118885CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
31831positivegrowth04-40
31831positiveoptimum37mesophilic
37756positivegrowth37mesophilic
60717positivegrowth30-37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31831aerobe
60717aerobe
118885obligate aerobe

spore formation

@refspore formationconfidence
31831no
69481no100
69480no99.988

halophily

  • @ref: 31831
  • salt: NaCl
  • growth: positive
  • tested relation: optimum
  • concentration: 5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3183115963ribitol+carbon source
3183122599arabinose+carbon source
3183117057cellobiose+carbon source
3183123652dextrin+carbon source
3183128757fructose+carbon source
3183128260galactose+carbon source
3183117234glucose+carbon source
3183117754glycerol+carbon source
3183117716lactose+carbon source
3183129864mannitol+carbon source
3183133942ribose+carbon source
3183130911sorbitol+carbon source
3183117992sucrose+carbon source
3183127082trehalose+carbon source
3183153426tween 80+carbon source
3183118222xylose+carbon source
3183117632nitrate+reduction
11888517632nitrate+reduction
11888516301nitrite+reduction

metabolite production

  • @ref: 118885
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31831catalase+1.11.1.6
31831cytochrome oxidase+1.9.3.1
31831urease+3.5.1.5
118885oxidase+
118885catalase+1.11.1.6
118885urease-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
118885-+++-+--+-++--------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dategeographic location
7766soil sample contaminated by polycylic aromatic compounds of fly ash dumping siteIndiaINDAsia
60717Fly ash dumping site of a thermal power plantIndiaINDAsia2006Delhi
118885Thermal power plant, fly ash dumping siteIndiaINDAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination
#Engineered#Waste#Dust (Ash)
#Environmental#Terrestrial#Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
77661Risk group (German classification)
1188851Risk group (French classification)

Sequence information

16S sequences

  • @ref: 31831
  • description: Pseudomonas delhiensis strain RLD-1 16S ribosomal RNA gene, partial sequence
  • accession: DQ339153
  • length: 1505
  • database: nuccore
  • NCBI tax ID: 366289

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas delhiensis RLD-1GCA_900187975contigncbi366289
66792Pseudomonas delhiensis CCM 7361GCA_900099945scaffoldncbi366289
66792Pseudomonas delhiensis strain CCM 7361366289.8wgspatric366289
66792Pseudomonas delhiensis RLD-12706795031draftimg366289

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes90.159yes
flagellatedyes78.992no
gram-positiveno98.266yes
anaerobicno97.341no
aerobicyes89.291yes
halophileno84.797no
spore-formingno94.131yes
glucose-fermentno90.446no
thermophileno99.796yes
glucose-utilyes89.714yes

External links

@ref: 7766

culture collection no.: DSM 18900, CCUG 55753, CCM 7361, MTCC 7601, CIP 109527

straininfo link

  • @ref: 82361
  • straininfo: 297307

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17329778Pseudomonas delhiensis sp. nov., from a fly ash dumping site of a thermal power plant.Prakash O, Kumari K, Lal RInt J Syst Evol Microbiol10.1099/ijs.0.64456-02007Acyclic Monoterpenes, *Carbon, Coal Ash, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, India, Molecular Sequence Data, Monoterpenes/metabolism, *Particulate Matter, Phenanthrenes/metabolism, Phylogeny, *Power Plants, Pseudomonas/*classification/genetics/isolation & purification/metabolism, RNA, Ribosomal, 16S/geneticsMetabolism
Phylogeny18523175Pseudomonas panipatensis sp. nov., isolated from an oil-contaminated site.Gupta SK, Kumari R, Prakash O, Lal RInt J Syst Evol Microbiol10.1099/ijs.0.65401-02008Bacterial Typing Techniques, Base Sequence, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, India, Molecular Sequence Data, Nucleic Acid Hybridization, *Petroleum, Phenotype, Phylogeny, Pseudomonas/*classification/genetics/*isolation & purification/physiology, RNA, Ribosomal, 16S/chemistry/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Soil Pollutants, Species SpecificityGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7766Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18900)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18900
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
31831Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2809728776041
37756Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7280
60717Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 55753)https://www.ccug.se/strain?id=55753
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
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
82361Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297307.1StrainInfo: A central database for resolving microbial strain identifiers
118885Curators of the CIPCollection of Institut Pasteur (CIP 109527)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109527