Strain identifier

BacDive ID: 11044

Type strain: Yes

Species: Rhodococcus opacus

Strain Designation: RKJ 300

Strain history: CIP <- 2006, JCM <- 2005, MTCC

NCBI tax ID(s): 37919 (species)

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General

@ref: 12333

BacDive-ID: 11044

DSM-Number: 45091

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, Gram-positive, rod-shaped

description: Rhodococcus opacus RKJ 300 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from pesticide-contaminated soil.

NCBI tax id

  • NCBI tax id: 37919
  • Matching level: species

strain history

@refhistory
12333<- JCM <- R. K. Jain; RKJ 300
67770R. K. Jain RKJ300.
120059CIP <- 2006, JCM <- 2005, MTCC

doi: 10.13145/bacdive11044.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Mycobacteriales
  • family: Nocardiaceae
  • genus: Rhodococcus
  • species: Rhodococcus opacus
  • full scientific name: Rhodococcus opacus Klatte et al. 1995

  • synonyms

    @refsynonym
    20215Rhodococcus percolatus
    20215Rhodococcus imtechensis

@ref: 12333

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Rhodococcus

species: Rhodococcus imtechensis

full scientific name: Rhodococcus imtechensis Ghosh et al. 2006

strain designation: RKJ 300

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
31633positiverod-shapedno
120059positiverod-shapedno
125438no90
125439positive98.4

pigmentation

  • @ref: 31633
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
37515MEDIUM 116 - for Streptomyces, Nocardia, Streptosporangium and Mycobacterium chlorophenolicumyesDistilled water make up to (1000.000 ml);Agar (20.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g)
120059CIP Medium 116yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=116

culture temp

@refgrowthtypetemperature
31633positivegrowth15-37
31633positiveoptimum30
37515positivegrowth30
67770positivegrowth28

culture pH

@refabilitytypepHPH range
31633positivegrowth05-10alkaliphile
31633positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
31633aerobe
120059obligate aerobe
125439obligate aerobe98.5

spore formation

  • @ref: 31633
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
31633NaClpositivegrowth2.5-5 %
31633NaClpositiveoptimum2.5-5 %

observation

@refobservation
31633aggregates in chains
67770quinones: MK-8(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3163330089acetate+carbon source
3163340585alpha-cyclodextrin+carbon source
3163333984fucose+carbon source
3163317272propionate+carbon source
3163327082trehalose+carbon source
12005917632nitrate-reduction
12005916301nitrite-reduction

metabolite production

  • @ref: 120059
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31633catalase+1.11.1.6
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
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+
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382trypsin-3.4.21.4
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
120059oxidase-
120059catalase+1.11.1.6
120059urease+3.5.1.5
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382cystine arylamidase+3.4.11.3

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120059-+++-+++--++++-+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12333pesticide-contaminated soilPunjab SateIndiaINDAsia
67770Pesticide-contaminated soilPunjab StateIndiaINDAsia
120059Environment, SoilPunjabIndiaINDAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_628.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_181;97_445;98_509;99_628&stattab=map
  • Last taxonomy: Rhodococcus
  • 16S sequence: KF410362
  • Sequence Identity:
  • Total samples: 806
  • soil counts: 425
  • aquatic counts: 116
  • animal counts: 152
  • plant counts: 113

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
123331Risk group (German classification)
1200591Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Rhodococcus imtechensis strain DSM 45091 16S ribosomal RNA gene, partial sequenceKF4103621510nuccore262776
12333Rhodococcus imtechensis strain RKJ300 16S ribosomal RNA gene, complete sequenceAY5257851510nuccore1165867

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhodococcus opacus RKJ300 = JCM 13270GCA_001313285contigncbi1165867
66792Rhodococcus imtechensis RKJ300 = JCM 132701165867.3wgspatric1165867
66792Rhodococcus imtechensis RKJ300 = JCM 132701165867.6wgspatric1165867
66792Rhodococcus imtechensis RKJ300, JCM 132702734481939draftimg1165867
67770Rhodococcus opacus RKJ300 = JCM 13270GCA_000260815contigncbi1165867

GC content

@refGC-contentmethod
1233372
6777072thermal denaturation, midpoint method (Tm)
6777067.22genome sequence analysis

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe98.5
125439BacteriaNetgram_stainReaction to gram-stainingpositive98.4
125439BacteriaNetmotilityAbility to perform movementno89.9
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes58.3
125438gram-positivegram-positivePositive reaction to Gram-stainingyes86.556yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.603no
125438spore-formingspore-formingAbility to form endo- or exosporesyes61.927yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes86.844yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno96yes
125438motile2+flagellatedAbility to perform flagellated movementno90yes

External links

@ref: 12333

culture collection no.: DSM 45091, CIP 109333, JCM 13270, MTCC 7085, NCIMB 14316

straininfo link

  • @ref: 80296
  • straininfo: 297304

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16902038Rhodococcus imtechensis sp. nov., a nitrophenol-degrading actinomycete.Ghosh A, Paul D, Prakash D, Mayilraj S, Jain RKInt J Syst Evol Microbiol10.1099/ijs.0.63939-02006Base Composition, Biodegradation, Environmental, DNA, Bacterial/chemistry/genetics, India, Molecular Sequence Data, Nitrophenols/*metabolism, Pesticides, Phylogeny, Rhodococcus/chemistry/*classification/genetics/metabolism, Sequence Homology, Nucleic Acid, Soil Pollutants, Species SpecificityGenetics
Metabolism20050667Degradation of 4-nitrophenol, 2-chloro-4-nitrophenol, and 2,4-dinitrophenol by Rhodococcus imtechensis strain RKJ300.Ghosh A, Khurana M, Chauhan A, Takeo M, Chakraborti AK, Jain RKEnviron Sci Technol10.1021/es903412320102,4-Dinitrophenol/chemistry/*metabolism, *Biodegradation, Environmental, Environmental Pollutants/chemistry/*metabolism, Molecular Structure, Nitrophenols/chemistry/*metabolism, Rhodococcus/classification/*metabolism, Soil MicrobiologyPhylogeny
Metabolism26567304A Two-Component para-Nitrophenol Monooxygenase Initiates a Novel 2-Chloro-4-Nitrophenol Catabolism Pathway in Rhodococcus imtechensis RKJ300.Min J, Zhang JJ, Zhou NYAppl Environ Microbiol10.1128/AEM.03042-152015Bacterial Proteins/chemistry/genetics/*metabolism, Biocatalysis, Hydroquinones/metabolism, Mixed Function Oxygenases/chemistry/genetics/*metabolism, Nitrophenols/chemistry/*metabolism, Rhodococcus/*enzymology/genetics/metabolism, Substrate SpecificityEnzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
12333Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45091)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45091
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
31633Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127916
37515Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7063
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/
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
80296Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297304.1StrainInfo: A central database for resolving microbial strain identifiers
120059Curators of the CIPCollection of Institut Pasteur (CIP 109333)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109333
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