Strain identifier

BacDive ID: 133093

Type strain: Yes

Species: Immundisolibacter cernigliae

Strain Designation: TR3.2

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

NCBI tax ID(s): 1810504 (species)

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For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 24881

BacDive-ID: 133093

DSM-Number: 103040

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

description: Immundisolibacter cernigliae TR3.2 is an aerobe, heterotroph, Gram-negative bacterium that forms circular colonies and was isolated from polycyclic aromatic hydrocarbon-contaminated and bioreactor treated soil from the site of a former manufactured gas plant.

NCBI tax id

  • NCBI tax id: 1810504
  • Matching level: species

strain history

  • @ref: 24881
  • history: <- E. Corteselli, Gillings School of Global Public Health, Dep. Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, USA <- D. Singleton, Gillings School, University North Carolina

doi: 10.13145/bacdive133093.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Immundisolibacterales
  • family: Immundisolibacteraceae
  • genus: Immundisolibacter
  • species: Immundisolibacter cernigliae
  • full scientific name: Immundisolibacter cernigliae Corteselli et al. 2017

@ref: 24881

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Immundisolibacterales

family: Immundisolibacteraceae

genus: Immundisolibacter

species: Immundisolibacter cernigliae

full scientific name: Immundisolibacter cernigliae Corteselli et al. 2017

strain designation: TR3.2

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
25270negative0.56 µm0.35 µmoval-shapedno
69480negative100

colony morphology

  • @ref: 25270
  • colony size: 0.5-0.75 mm
  • colony color: yellow-orange
  • colony shape: circular
  • medium used: sRB2 agar

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
25270sRB2 agaryes1 mM MgSO4 , 1 mM CaCl2 , 1 ml/l trace element solution, 1 ml/l vitamin B12 solution, 0.2 % (w/v) sodium pyruvate
24881RUGOSIBACTER 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
24881R2A 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
25270positivegrowth20-36
25270positiveoptimum28-30mesophilic
24881positivegrowth28mesophilic

culture pH

@refabilitytypepH
25270positivegrowth6.5-8.0
25270positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 25270
  • oxygen tolerance: aerobe

nutrition type

  • @ref: 25270
  • type: heterotroph

spore formation

@refspore formationconfidence
69481no100
69480no99.975

halophily

@refsalttested relationconcentrationgrowth
25270NaClmaximum1 %(w/v)
25270NaClgrowth0-1 %(w/v)positive
25270NaCloptimum0 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
252705291gelatin-hydrolysis
2527028017starch-hydrolysis
25270167632-oxobutanoate+assimilation
2527016134ammonia+nitrogen source
2527035298anthracene+carbon source
2527028266fluorene+carbon source
2527017632nitrate+nitrogen source
2527028851phenanthrene+carbon source
2527039106pyrene+carbon source
2527051348tetraphene+carbon source

metabolite production

  • @ref: 25270
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
25270catalase+1.11.1.6
25270cellulase-3.2.1.4
25270cytochrome oxidase+1.9.3.1
25270lipase+
25270skimmed milk protease-
25270urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    25270C18:0 anteiso / C18:2ω6,9c1.6
    25270C10:01.4
    25270C12:02
    25270C12:0 3OH6.4
    25270C14:01.4
    25270C16:029.6
    25270C16:1ω7c / C16:1ω6c12
    25270C17:0 cyclo32.1
    25270C18:1ω7c / C18:1ω6c1.9
    25270C19:0 cyclo ω8c8.3
  • type of FA analysis: whole cell analysis
  • incubation medium: sRB2
  • agar/liquid: agar
  • system: MIS MIDI
  • method/protocol: Sasser 1990
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeisolation procedure
24881polycyclic aromatic hydrocarbon-contaminated and bioreactor treated soil from the site of a former manufactured gas plantNorth Carolina, SalisburyUSAUSANorth America35.6667-80.45
25270aerobic bioreactor-treated, PAH-contaminated soil from a former manufactured gas plantserial dilution method

isolation source categories

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

Safety information

risk assessment

  • @ref: 24881
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Immundisolibacter cernigliae TR3.2GCA_001697225completencbi1810504
66792Immundisolibacter cernigliae TR3.22775507249completeimg1810504

GC content

@refGC-contentmethod
2527067.79genome sequence analysis
2488167.79sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno85.264yes
gram-positiveno98.378yes
anaerobicno96.403yes
halophileno94.432yes
spore-formingno91.155no
glucose-utilno53.446no
aerobicyes64.928no
thermophileno79.396no
motileyes72.705no
glucose-fermentno89.059no

External links

@ref: 24881

culture collection no.: DSM 103040, ATCC TSD-58

straininfo link

  • @ref: 91358
  • straininfo: 400010

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27926817Description of Immundisolibacter cernigliae gen. nov., sp. nov., a high-molecular-weight polycyclic aromatic hydrocarbon-degrading bacterium within the class Gammaproteobacteria, and proposal of Immundisolibacterales ord. nov. and Immundisolibacteraceae fam. nov.Corteselli EM, Aitken MD, Singleton DRInt J Syst Evol Microbiol10.1099/ijsem.0.0017142017Bacterial Typing Techniques, Base Composition, Bioreactors/microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gammaproteobacteria/*classification/genetics/isolation & purification, North Carolina, *Phylogeny, Polycyclic Aromatic Hydrocarbons/*metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome
Phylogeny28401633Functional soil metagenomics: elucidation of polycyclic aromatic hydrocarbon degradation potential following 12 years of in situ bioremediation.Duarte M, Nielsen A, Camarinha-Silva A, Vilchez-Vargas R, Bruls T, Wos-Oxley ML, Jauregui R, Pieper DHEnviron Microbiol10.1111/1462-2920.137562017Base Sequence, *Biodegradation, Environmental, Biphenyl Compounds/chemistry, Catechols/chemistry, DNA, Bacterial/genetics, Gammaproteobacteria/classification/genetics/*isolation & purification/*metabolism, High-Throughput Nucleotide Sequencing, Metagenomics/methods, Oxygenases/genetics, Phylogeny, Polycyclic Aromatic Hydrocarbons/*metabolism, Rhodocyclaceae/classification/genetics/*isolation & purification/*metabolism, Soil, Soil MicrobiologyMetabolism

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
24881Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-103040Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103040)
25270E. M. A. Corteselli, M. D.,Singleton, D. R.Description of Immundisolibacter cernigliae gen. nov., sp. nov., a high-molecular-weight polycyclic aromatic hydrocarbon-degrading bacterium within the class Gammaproteobacteria, and proposal of Immundisolibacterales ord. nov. and Immundisolibacteraceae fam. nov10.1099/ijsem.0.001714IJSEM 67: 925-931 201727926817
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
91358Reimer, 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-ID400010.1