Strain identifier

BacDive ID: 8364

Type strain: Yes

Species: Mycobacterium chlorophenolicum

Strain Designation: PCP-1

Strain history: CIP <- 1994, JCM <- DSM <- J.H.A. Apajalahti, Helsinki Univ., Finland: PCP-I, Rhodococcus chlorophenolicus

NCBI tax ID(s): 1303685 (strain), 37916 (species)

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General

@ref: 11297

BacDive-ID: 8364

DSM-Number: 43826

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-positive

description: Mycobacterium chlorophenolicum PCP-1 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from mixed culture that originated from a chlorophenol-contaminated lake sediment sample.

NCBI tax id

NCBI tax idMatching level
1303685strain
37916species

strain history

@refhistory
11297<- J.H.A. Apajalahti, Univ. Helsinki, PCP-1
67770DSM 43826 <-- J. H. A. Apajalahti et al. PCP-I.
118241CIP <- 1994, JCM <- DSM <- J.H.A. Apajalahti, Helsinki Univ., Finland: PCP-I, Rhodococcus chlorophenolicus

doi: 10.13145/bacdive8364.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Mycobacteriales
  • family: Mycobacteriaceae
  • genus: Mycobacterium
  • species: Mycobacterium chlorophenolicum
  • full scientific name: Mycobacterium chlorophenolicum (Apajalahti et al. 1986) Häggblom et al. 1994

  • synonyms

    @refsynonym
    20215Mycolicibacterium chlorophenolicum
    20215Mycobacterium chlorophenolicum
    20215Rhodococcus chlorophenolicus

@ref: 11297

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium chlorophenolicum

full scientific name: Mycobacterium chlorophenolicum (Apajalahti et al. 1986) Häggblom et al. 1994 emend. Nouioui et al. 2018

strain designation: PCP-1

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
118241rod-shapedno

multimedia

  • @ref: 11297
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_43826.jpg
  • caption: Medium 645 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11297GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
11297MIDDLEBROOK MEDIUM (DSMZ Medium 645)yeshttps://mediadive.dsmz.de/medium/645Name: MIDDLEBROOK MEDIUM (DSMZ Medium 645) Composition: Bacto Middlebrook 7H10 agar 20.9945 g/l Glycerol Distilled water
39745MEDIUM 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)
118241CIP Medium 116yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=116
118241CIP Medium 194yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=194

culture temp

@refgrowthtypetemperaturerange
11297positivegrowth28mesophilic
39745positivegrowth30mesophilic
67770positivegrowth28mesophilic
118241positivegrowth25-37mesophilic
118241nogrowth10psychrophilic
118241nogrowth41thermophilic
118241nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 118241
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.771

observation

@refobservation
20216Degrades chlorophenols
67770quinones: MK-9(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836927689decanoate-assimilation
6836924265gluconate+assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol+assimilation
6836916024D-mannose-assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
118241606565hippurate-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
11824135581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836935581indole-
11824115688acetoin-
11824117234glucose-

enzymes

@refvalueactivityec
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
118241oxidase-
118241beta-galactosidase-3.2.1.23
118241alcohol dehydrogenase-1.1.1.1
118241gelatinase-
118241DNase-
118241caseinase-3.4.21.50
118241catalase+1.11.1.6
118241gamma-glutamyltransferase-2.3.2.2
118241lecithinase-
118241lysine decarboxylase-4.1.1.18
118241ornithine decarboxylase-4.1.1.17
118241urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
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
11297-+++-++/-+/---++/----+----
118241-++++++++-++---+----

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
11297--------+/-+/--+--+-+/-+--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118241++-++--+-----------+++-+--+++---++--++--+--------+----------+-+++--+----++-+---++--+--+-+-------+-+

Isolation, sampling and environmental information

isolation

@refsample type
11297mixed culture that originated from a chlorophenol-contaminated lake sediment sample
67770Lake sediment
118241Environment, Lake sediment

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination
#Engineered#Laboratory#Lab enrichment
#Environmental#Aquatic#Lake (large)
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_6383.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_115;97_219;98_419;99_6383&stattab=map
  • Last taxonomy: Mycolicibacterium
  • 16S sequence: X81926
  • Sequence Identity:
  • Total samples: 4905
  • soil counts: 1619
  • aquatic counts: 1667
  • animal counts: 1470
  • plant counts: 149

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
112971Risk group (German classification)
1182411Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Mycobacterium chlorophenolicum strain CIP 104189 16S ribosomal RNA gene, partial sequenceAF547911540ena37916
20218M.chlorophenolicum (DSM 43826) 16S rRNA geneX792921466ena37916
20218M.chlorophenolicum 16S rRNA gene (NCIMB 12325T)X819261317ena37916
20218M.chlorophenolicus (PCP-1) 16S rRNA geneX790941532ena37916

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycolicibacterium chlorophenolicum JCM 7439 = NBRC 15527GCA_001313545contigncbi1303685
66792Mycobacterium chlorophenolicum JCM 7439 = NBRC 155271303685.5wgspatric1303685
66792Mycobacterium chlorophenolicum JCM 7439 = NBRC 155271303685.4wgspatric1303685
66792Mycobacterium chlorophenolicum strain DSM 4382637916.4wgspatric37916
66792Mycolicibacterium chlorophenolicum DSM 438262630968674draftimg37916
66792Mycolicibacterium chlorophenolicum NBRC 155272731957580draftimg1303685
66792Mycolicibacterium chlorophenolicum NBRC 155272734481951draftimg1303685
67770Mycolicibacterium chlorophenolicum JCM 7439 = NBRC 15527GCA_001552315contigncbi1303685
67770Mycolicibacterium chlorophenolicum DSM 43826GCA_001044235scaffoldncbi37916

GC content

@refGC-contentmethod
6777068.4genome sequence analysis
6777069.2high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno76no
motileno92.121no
gram-positiveyes89.182no
anaerobicno99.083no
halophileno93.881no
spore-formingno93.484no
thermophileno99.419no
glucose-utilyes82.748no
aerobicyes90.256no
flagellatedno98.391no
glucose-fermentno92.107yes

External links

@ref: 11297

culture collection no.: DSM 43826, ATCC 49826, JCM 7439, NCIMB 123325, NRRL B-16528, BCRC 13726, CECT 4065, CIP 104189, HAMBI 2278, IFO 15527, MTCC 2570, NBRC 15527, NCIMB 12325

straininfo link

  • @ref: 77763
  • straininfo: 42703

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny7520738Phylogenetic evidence for transfer of pentachlorophenol-mineralizing Rhodococcus chlorophenolicus PCP-I(T) to the genus Mycobacterium.Briglia M, Eggen RI, Van Elsas DJ, De Vos WMInt J Syst Bacteriol10.1099/00207713-44-3-4941994Base Sequence, DNA Primers/genetics, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, Bacterial, Molecular Sequence Data, Mycobacterium/*classification/genetics/*metabolism, Nucleic Acid Conformation, Pentachlorophenol/*metabolism, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rhodococcus/*classification/genetics/*metabolism, Sequence Homology, Nucleic Acid, Species Specificity, Terminology as TopicMetabolism
Metabolism7772938Metabolism of halohydroquinones in Rhodococcus chlorophenolicus PCP-1.Uotila JS, Kitunen VH, Coote T, Saastamoinen T, Salkinoja-Salonen M, Apajalahti JHBiodegradation10.1007/BF006953421995Biodegradation, Environmental, Cytochrome P-450 Enzyme System/metabolism, Enzyme Induction, Halogens/chemistry/*metabolism, Hydrolases/antagonists & inhibitors/metabolism, Hydroquinones/chemistry/*metabolism, Mass Spectrometry, Rhodococcus/enzymology/*metabolismEnzymology
Phylogeny8919817Rapid and sensitive method for the detection of Mycobacterium chlorophenolicum PCP-1 in soil based on 16S rRNA gene-targeted PCR.Briglia M, Eggen RI, de Vos WM, van Elsas JDAppl Environ Microbiol10.1128/aem.62.4.1478-1480.19961996Base Sequence, DNA Primers/genetics, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Evaluation Studies as Topic, Gene Targeting, Genes, Bacterial, Molecular Sequence Data, Mycobacterium/classification/*genetics/*isolation & purification, Polymerase Chain Reaction/*methods/statistics & numerical data, RNA, Bacterial/*genetics, RNA, Ribosomal, 16S/*genetics, Sensitivity and Specificity, Sequence Homology, Nucleic Acid, *Soil Microbiology, Species SpecificityGenetics
Metabolism10070720Inefficiency of Mycobacterium chlorophenolicum PCP-1 to enhance mineralization of pentachlorophenol in soil microcosms.Combrisson J, Monrozier LJChemosphere10.1016/s0045-6535(98)00531-11999Biodegradation, Environmental, Carbon Dioxide/analysis, Chlorides/analysis, Environmental Pollutants/analysis/*metabolism, Mycobacterium/*metabolism, Pentachlorophenol/chemistry/*metabolism, *Soil Microbiology
Enzymology10440675Adsorption capacity as a key parameter for enzyme induction and pentachlorophenol degradation in Mycobacterium chlorophenolicum PCP-1.Brandt S, Zeng AP, Deckwer WDBiotechnol Bioeng10.1002/(sici)1097-0290(19991005)65:1<93::aid-bit11>3.0.co;2-51999Adsorption, Biodegradation, Environmental, Biomass, Bioreactors, Environmental Pollutants/metabolism, Enzyme Induction/drug effects, Hydrogen-Ion Concentration, Kinetics, Models, Biological, Mycobacterium/drug effects/*enzymology/*metabolism, Pentachlorophenol/*metabolism/pharmacokinetics/pharmacologyMetabolism
Enzymology16079338Analysis of the nearly identical morpholine monooxygenase-encoding mor genes from different Mycobacterium strains and characterization of the specific NADH : ferredoxin oxidoreductase of this cytochrome P450 system.Sielaff B, Andreesen JRMicrobiology (Reading)10.1099/mic.0.28039-02005Cytochrome P-450 Enzyme System/genetics/isolation & purification/*metabolism, DNA, Bacterial/chemistry/isolation & purification, Ferredoxin-NADP Reductase/genetics/isolation & purification/*metabolism, Ferredoxins/metabolism, Gene Expression, Mixed Function Oxygenases/*genetics/metabolism, Morpholines/*metabolism, Mycobacterium/classification/*enzymology/genetics/metabolism, Oxidoreductases/geneticsMetabolism
18636513Adsorption and desorption of pentachlorophenol on cells of Mycobacterium chlorophenolicum PCP-1.Brandt S, Zeng AP, Deckwer WDBiotechnol Bioeng10.1002/(SICI)1097-0290(19970805)55:3<480::AID-BIT3>3.0.CO;2-81997
Metabolism18754475Microbial O-methylation of the flame retardant tetrabromobisphenol-A.George KW, Haggblom MMEnviron Sci Technol10.1021/es800038q2008Animals, Flame Retardants/*metabolism/toxicity, Gas Chromatography-Mass Spectrometry, Humans, Methylation, Mycobacterium/*metabolism, Polybrominated Biphenyls/chemistry/*metabolism/toxicity, Public Health, Risk Assessment, *Soil Microbiology, Time FactorsPathogenicity
Metabolism24193969Biodegradation of pentachlorophenol in natural soil by inoculatedRhodococcus chlorophenolicus.Middeldorp PJ, Briglia M, Salkinoja-Salonen MSMicrob Ecol10.1007/BF025438721990
Genetics26079817Characterization of Three Mycobacterium spp. with Potential Use in Bioremediation by Genome Sequencing and Comparative Genomics.Das S, Pettersson BM, Behra PR, Ramesh M, Dasgupta S, Bhattacharya A, Kirsebom LAGenome Biol Evol10.1093/gbe/evv1112015Biodegradation, Environmental, Copper/metabolism, Gene Transfer, Horizontal, Genes, Bacterial, *Genome, Bacterial, Genomics, Molecular Sequence Data, Mycobacterium/classification/*genetics/metabolism, Oxygenases/genetics, Phylogeny, RNA, Untranslated/genetics, Sequence Alignment, Sequence Analysis, DNAPhylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11297Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43826)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43826
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
20216Curators of the HKIhttp://www.leibniz-hki.de/de/Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI)
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
39745Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16070
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/
68369Automatically annotated from API 20NE
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
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)
77763Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42703.1StrainInfo: A central database for resolving microbial strain identifiers
118241Curators of the CIPCollection of Institut Pasteur (CIP 104189)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104189