Strain identifier

BacDive ID: 133073

Type strain: Yes

Species: Rugosibacter aromaticivorans

Strain Designation: Ca6

Strain history: <- E. Corteselli, University of North Carolina, Gillings School of Global Public Health, Environmental Sciences and Engineering, Chapel Hill, USA; Ca6 <- D. R. Singleton, Univ. of North Carolina

NCBI tax ID(s): 1565605 (species)

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General

@ref: 24861

BacDive-ID: 133073

DSM-Number: 103039

keywords: genome sequence, Bacteria, aerobe, heterotroph, Gram-negative, rod-shaped, colony-forming

description: Rugosibacter aromaticivorans Ca6 is an aerobe, heterotroph, Gram-negative bacterium that forms circular colonies and was isolated from PAH contaminated soil from a former manufactured gas plant.

NCBI tax id

  • NCBI tax id: 1565605
  • Matching level: species

strain history

  • @ref: 24861
  • history: <- E. Corteselli, University of North Carolina, Gillings School of Global Public Health, Environmental Sciences and Engineering, Chapel Hill, USA; Ca6 <- D. R. Singleton, Univ. of North Carolina

doi: 10.13145/bacdive133073.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Rhodocyclales
  • family: Rhodocyclaceae
  • genus: Rugosibacter
  • species: Rugosibacter aromaticivorans
  • full scientific name: Rugosibacter aromaticivorans Corteselli et al. 2017

@ref: 24861

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Rhodocyclales

family: Rhodocyclaceae

genus: Rugosibacter

species: Rugosibacter aromaticivorans

full scientific name: Rugosibacter aromaticivorans Corteselli et al. 2017

strain designation: Ca6

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
25209negative0.77-1.15 µm0.23-0.27 µmrod-shapedno
69480negative99.998

colony morphology

  • @ref: 25209
  • colony size: 0.5-0.8 mm
  • colony color: yellow-white
  • colony shape: circular
  • incubation period: 14 days
  • medium used: sRB1-agar plates

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
25209sRB1-agar platesyeswith pyruvate
24861RUGOSIBACTER MEDIUM (DSMZ Medium 1622)yesName: RUGOSIBACTER MEDIUM (DSMZ Medium 1622) Composition: Na-pyruvate 2.0 g/l Na2HPO4 x 2 H2O 0.72 g/l NH4NO3 0.4 g/l MgSO4 x 7 H2O 0.24 g/l CaCl2 x 2 H2O 0.15 g/l KH2PO4 0.12 g/l HCl 0.0025 g/l FeCl2 x 4 H2O 0.0015 g/l CoCl2 x 6 H2O 0.00019 g/l MnCl2 x 4 H2O 0.0001 g/l ZnCl2 7e-05 g/l Na2MoO4 x 2 H2O 3.6e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l H3BO3 6e-06 g/l CuCl2 x 2 H2O 2e-06 g/l Vitamin B12 Distilled waterhttps://mediadive.dsmz.de/medium/1622
24861R2A MEDIUM (DSMZ Medium 830)yesName: 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 waterhttps://mediadive.dsmz.de/medium/830

culture temp

@refgrowthtypetemperaturerange
25209positivegrowth20.0-35.0
25209positiveoptimum30.0-34.0mesophilic
24861positivegrowth28mesophilic

culture pH

@refabilitytypepH
25209positivegrowth6.5-7.5
25209positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

  • @ref: 25209
  • oxygen tolerance: aerobe

nutrition type

  • @ref: 25209
  • type: heterotroph

spore formation

@refspore formationconfidence
69481no100
69480no99.999

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
252095291gelatin-hydrolysis
2520917632nitrate-reduction
2520928017starch-hydrolysis
2520917632nitrate+nitrogen source

enzymes

@refvalueactivityec
25209catalase-1.11.1.6
25209cellulase-3.2.1.4
25209cytochrome oxidase+1.9.3.1
25209lipase+
25209urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    25209C10:0 3OH3.9
    25209C12:03
    25209C16:036.7
    25209C16:1ω7c / C16:1ω6c42.5
    25209C18:1ω7c4.9
    25209Cyclo C17:06.5
  • type of FA analysis: whole cell analysis
  • incubation medium: sRB1 with pyruvate
  • agar/liquid: agar
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture composition
24861PAH contaminated soil from a former manufactured gas plantCharlotte, North CarolinaUSAUSANorth America35.194-80.837
25209(polycyclic aromatic hydrocarbon) PAH-contaminated soilmodified sk43HT isolation mediumcontained 5 mM sodium-potassium phosphate buffer (pH 7.0) and 5 mM NH4NO3, 1 mM MgSO4.7H2O, 1 mM CaCl2.2H2O, 1 ml trace element solution l-1 [containing per litre; 12.5 ml HCl (25 %), 2.1g FeSO4.7H2O, 30 mg H3BO3 , 100 mg MnCl2.4H2O, 190 mg CoCl2.6H2O, 24 mg NaCl2.6H2O, 2 mg CuCl2.2H2O, 144 mg ZnSO4.7H2O, 36 mg Na2MoO4.2H2O] and 1 ml selenium-tungsten solution l-1 (containing per litre; 0.4 g NaOH, 6 mg Na2SeO3.5H2O, 8 mg Na2WO4.2H2O). After autoclaving following filter-sterilized solutions (0.

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination
#Engineered#Industrial#Plant (Factory)
#Environmental#Terrestrial#Soil

Safety information

risk assessment

  • @ref: 24861
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

Genome sequences

  • @ref: 66792
  • description: Rugosibacter aromaticivorans Ca6
  • accession: GCA_000934545
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 1565605

GC content

@refGC-contentmethod
2520955.14genome sequence analysis
2486155.14sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno83.408yes
flagellatedno91.892no
gram-positiveno98.63yes
anaerobicno94.667yes
aerobicno51.381yes
halophileno95.672no
spore-formingno94.803no
glucose-utilno68.44no
thermophileno91.467yes
glucose-fermentno93.464no

External links

@ref: 24861

culture collection no.: DSM 103039, ATCC TSD-59

straininfo link

  • @ref: 91338
  • straininfo: 402305

literature

  • topic: Phylogeny
  • Pubmed-ID: 27902243
  • title: Rugosibacter aromaticivorans gen. nov., sp. nov., a bacterium within the family Rhodocyclaceae, isolated from contaminated soil, capable of degrading aromatic compounds.
  • authors: Corteselli EM, Aitken MD, Singleton DR
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001622
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, North Carolina, *Phylogeny, Polycyclic Aromatic Hydrocarbons, RNA, Ribosomal, 16S/genetics, Rhodocyclaceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, *Soil Microbiology, *Soil Pollutants
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
24861Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-103039Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103039)
25209E. M. A. Corteselli, M. D.,Singleton, D. R.Rugosibacter aromaticivorans gen. nov., sp. nov., a bacterium within the family Rhodocyclaceae, isolated from contaminated soil, capable of degrading aromatic compounds10.1099/ijsem.0.001622IJSEM 67: 311-318 201727902243
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
91338Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID402305.1