Strain identifier

BacDive ID: 14174

Type strain: Yes

Species: Sphingobium chlorophenolicum

Strain history: CIP <- 1996, L. Nohynek, Helsinki Univ., Finland <- R. Müller, Hamburg Univ., Germany <- ATCC, Arthrobacter sp. <- R.U. Edgehill

NCBI tax ID(s): 1219044 (strain), 46429 (species)

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General

@ref: 2984

BacDive-ID: 14174

DSM-Number: 7098

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

description: Sphingobium chlorophenolicum DSM 7098 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil; pentachlorophenol contaminated.

NCBI tax id

NCBI tax idMatching level
46429species
1219044strain

strain history

@refhistory
2984<- ATCC <- R.U. Edgehill (Arthrobacter sp.)
67770E. Yabuuchi EY4219 <-- ATCC 33790 <-- R. U. Edgehill.
118242CIP <- 1996, L. Nohynek, Helsinki Univ., Finland <- R. Müller, Hamburg Univ., Germany <- ATCC, Arthrobacter sp. <- R.U. Edgehill

doi: 10.13145/bacdive14174.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Sphingomonadaceae
  • genus: Sphingobium
  • species: Sphingobium chlorophenolicum
  • full scientific name: Sphingobium chlorophenolicum (Nohynek et al. 1996) Takeuchi et al. 2001

  • synonyms

    • @ref: 20215
    • synonym: Sphingomonas chlorophenolica

@ref: 2984

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingobium

species: Sphingobium chlorophenolicum

full scientific name: Sphingobium chlorophenolicum (Nohynek et al. 1996) Takeuchi et al. 2001

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.992
118242negativerod-shapedyes

pigmentation

  • @ref: 118242
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2984NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
2984CORYNEBACTERIUM AGAR (DSMZ Medium 53)yeshttps://mediadive.dsmz.de/medium/53Name: CORYNEBACTERIUM AGAR (DSMZ Medium 53) Composition: Agar 15.0 g/l Casein peptone 10.0 g/l NaCl 5.0 g/l Glucose 5.0 g/l Yeast extract 5.0 g/l Distilled water
2984MINERAL MEDIUM (BRUNNER) (DSMZ Medium 457)yeshttps://mediadive.dsmz.de/medium/457Name: MINERAL MEDIUM (BRUNNER) (DSMZ Medium 457) Composition: Na2HPO4 2.44 g/l KH2PO4 1.52 g/l (NH4)2SO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l CaCl2 x 2 H2O 0.05 g/l EDTA 0.005 g/l FeSO4 x 7 H2O 0.002 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.0002 g/l ZnSO4 x 7 H2O 0.0001 g/l MnCl2 x 4 H2O 3e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Distilled water
40668MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
118242CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
2984positivegrowth30mesophilic
40668positivegrowth30mesophilic
60942positivegrowth30mesophilic
67770positivegrowth26mesophilic
118242positivegrowth25-37mesophilic
118242nogrowth5psychrophilic
118242nogrowth10psychrophilic
118242nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
60942aerobe
118242obligate aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.982

compound production

  • @ref: 2984
  • compound: pentachlorophenol-dehalogenase

halophily

@refsaltgrowthtested relationconcentration
118242NaClpositivegrowth0 %
118242NaClnogrowth2 %
118242NaClnogrowth4 %
118242NaClnogrowth6 %
118242NaClnogrowth8 %
118242NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: Q-10

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
68369malate-assimilation25115
68369adipate-assimilation17128
68369decanoate-assimilation27689
68369gluconate-assimilation24265
68369maltose-assimilation17306
68369N-acetylglucosamine-assimilation59640
68369D-mannitol-assimilation16899
68369D-mannose-assimilation16024
68369L-arabinose-assimilation30849
68369D-glucose+assimilation17634
68369gelatin-hydrolysis5291
68369esculin+hydrolysis4853
68369urea-hydrolysis16199
68369arginine-hydrolysis29016
68369D-glucose-fermentation17634
68369tryptophan-energy source27897
68369nitrate-reduction17632
118242citrate-carbon source16947
118242esculin+hydrolysis4853
118242nitrate-reduction17632
118242nitrite-reduction16301
118242phenol-degradation15882
118242nitrate-respiration17632

antibiotic resistance

  • @ref: 118242
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
11824235581indoleno

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
118242oxidase+
118242beta-galactosidase-3.2.1.23
118242alcohol dehydrogenase-1.1.1.1
118242gelatinase-
118242amylase-
118242DNase-
118242caseinase-3.4.21.50
118242catalase-1.11.1.6
118242tween esterase-
118242lecithinase-
118242lipase-
118242lysine decarboxylase-4.1.1.18
118242ornithine decarboxylase-4.1.1.17
118242tryptophan deaminase-
118242urease-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
118242-+++-++---++---++---

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
2984-----+--+-----------+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118242-------------------------------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118242+--------------++--+-----------------------------+------------++---------------++-------+-------+--

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
2984soil; pentachlorophenol contaminatedUSAUSANorth America
60942Soil,pentachlorophenol contaminated
67770Pentachlorophenol-contaminated soil
118242Environment, Pentachlorophenol contaminated soilUnited States of AmericaUSANorth America

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_6986.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_32;97_33;98_4284;99_6986&stattab=map
  • Last taxonomy: Sphingobium chlorophenolicum
  • 16S sequence: X87161
  • Sequence Identity:
  • Total samples: 64
  • soil counts: 16
  • aquatic counts: 32
  • animal counts: 11
  • plant counts: 5

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
29841Risk group (German classification)
1182421Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Sphingobium chlorophenolicum gene for 16S rRNA, partial sequence, strain: NBRC 16172AB6810561412ena46429
20218Sphingomonas chlorophenolica strain ATCC 33790 16S rRNA gene, partial sequenceU601711021ena46429
2984S.chlorophenolica 16S rRNA gene, strain ATCC 33790X871611442ena46429

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingobium chlorophenolicum NBRC 161721219044.3wgspatric1219044
66792Sphingobium chlorophenolicum strain NBRC 1617246429.4wgspatric46429
66792Sphingobium chlorophenolicum NBRC 161722585427849draftimg1219044
66792Sphingobium chlorophenolicum NBRC 161722731957704draftimg1219044
67770Sphingobium chlorophenolicum NBRC 16172GCA_001598515contigncbi1219044
67770Sphingobium chlorophenolicum NBRC 16172GCA_000722875contigncbi46429

GC content

  • @ref: 67770
  • GC-content: 66
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno87no
motileyes58.616no
gram-positiveno97.745no
anaerobicno99.098yes
halophileno95.504no
spore-formingno93.727no
thermophileno97.129yes
glucose-utilyes84.568no
flagellatedno85.12no
aerobicyes92.873yes
glucose-fermentno93.8yes

External links

@ref: 2984

culture collection no.: DSM 7098, ATCC 33790, CIP 104885, IFO 16172, NBRC 16172, CCUG 56399, LMG 17937, KCTC 3325, JCM 10275, LMG 17771

straininfo link

  • @ref: 83337
  • straininfo: 10531

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9734064Characterization and reclassification of an aromatic- and chloroaromatic-degrading Pseudomonas sp., strain HV3, as Sphingomonas sp. HV3.Yrjala K, Suomalainen S, Suhonen EL, Kilpi S, Paulin L, Romantschuk MInt J Syst Bacteriol10.1099/00207713-48-3-10571998Base Sequence, Biodegradation, Environmental, DNA, Bacterial/analysis, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Pseudomonas/chemistry/*classification/genetics, Sphingolipids/analysisGenetics
Phylogeny16166696Hexachlorocyclohexane-degrading bacterial strains Sphingomonas paucimobilis B90A, UT26 and Sp+, having similar lin genes, represent three distinct species, Sphingobium indicum sp. nov., Sphingobium japonicum sp. nov. and Sphingobium francense sp. nov., and reclassification of [Sphingomonas] chungbukensis as Sphingobium chungbukense comb. nov.Pal R, Bala S, Dadhwal M, Kumar M, Dhingra G, Prakash O, Prabagaran SR, Shivaji S, Cullum J, Holliger C, Lal RInt J Syst Evol Microbiol10.1099/ijs.0.63201-02005Bacterial Proteins/*genetics/metabolism, Bacterial Typing Techniques, Biodegradation, Environmental, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Hexachlorocyclohexane/*metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sphingomonadaceae/*classification/enzymology/genetics/physiology, Sphingomonas/*classification/enzymology/genetics/physiologyMetabolism
Phylogeny19643879Sphingobium vermicomposti sp. nov., isolated from vermicompost.Vaz-Moreira I, Faria C, Lopes AR, Svensson L, Falsen E, Moore ER, Ferreira AC, Nunes OC, Manaia CMInt J Syst Evol Microbiol10.1099/ijs.0.006163-02009DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Soil/analysis, *Soil Microbiology, Sphingomonadaceae/*classification/genetics/*isolation & purification/metabolismMetabolism
Metabolism30560286Sphingobium aromaticivastans sp. nov., a novel aniline- and benzene-degrading, and antimicrobial compound producing bacterium.Nguyen TM, Kim JArch Microbiol10.1007/s00203-018-1611-22018Aniline Compounds/metabolism, Anti-Bacterial Agents/*metabolism, Base Composition, Benzene/metabolism, DNA, Bacterial/chemistry, Fatty Acids/analysis, Phospholipids/analysis, Spermidine/metabolism, Sphingomonadaceae/chemistry/classification/genetics/*metabolism, Ubiquinone/analogs & derivatives/metabolismPhylogeny
Phylogeny32048985Sphingobium estronivorans sp. nov. and Sphingobium bisphenolivorans sp. nov., isolated from a wastewater treatment plant.Qin D, Ma C, Lv M, Yu CPInt J Syst Evol Microbiol10.1099/ijsem.0.0039782020Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Spermidine/chemistry, Sphingomonadaceae/*classification/isolation & purification, Ubiquinone/analogs & derivatives/chemistry, Waste Water/*microbiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2984Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7098)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7098
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
40668Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16842
60942Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 56399)https://www.ccug.se/strain?id=56399
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
68371Automatically annotated from API 50CH acid
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)
83337Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10531.1StrainInfo: A central database for resolving microbial strain identifiers
118242Curators of the CIPCollection of Institut Pasteur (CIP 104885)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104885