Strain identifier

BacDive ID: 14228

Type strain: Yes

Species: Rhizorhabdus wittichii

Strain Designation: RW1

Strain history: CIP <- 2001, A. Hiraishi, Toyohashi Univ., Aichi-Ken, Japan, strain: RW1 <- DSMZ <- RM Wittich: strain RW1

NCBI tax ID(s): 160791 (species)

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General

@ref: 2419

BacDive-ID: 14228

DSM-Number: 6014

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative, motile, rod-shaped

description: Rhizorhabdus wittichii RW1 is a mesophilic, Gram-negative, motile bacterium that was isolated from water samples.

NCBI tax id

  • NCBI tax id: 160791
  • Matching level: species

strain history

@refhistory
2419<- R.M. Wittich; RW1
67770DSM 6014 <-- R. M. Wittich RW1.
123953CIP <- 2001, A. Hiraishi, Toyohashi Univ., Aichi-Ken, Japan, strain: RW1 <- DSMZ <- RM Wittich: strain RW1

doi: 10.13145/bacdive14228.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Sphingomonadaceae
  • genus: Rhizorhabdus
  • species: Rhizorhabdus wittichii
  • full scientific name: Rhizorhabdus wittichii (Yabuuchi et al. 2001) Hördt et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Sphingomonas wittichii

@ref: 2419

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Rhizorhabdus

species: Rhizorhabdus wittichii

full scientific name: Rhizorhabdus wittichii (Yabuuchi et al. 2001) Hördt et al. 2020

strain designation: RW1

type strain: yes

Morphology

cell morphology

  • @ref: 123953
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 123953
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2419NUTRIENT 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
2419MINERAL 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
37289MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123953CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
2419positivegrowth30mesophilic
37289positivegrowth30mesophilic
67770positivegrowth30mesophilic
123953positivegrowth25-37mesophilic
123953nogrowth5psychrophilic
123953nogrowth10psychrophilic
123953nogrowth41thermophilic

Physiology and metabolism

compound production

@refcompound
2419hydrolases
24192,2',3 trihydroxybiphenyl dioxygenase
2419dibenzofuran-4,4a-dioxygenase

halophily

@refsaltgrowthtested relationconcentration
123953NaClpositivegrowth0 %
123953NaClnogrowth2 %
123953NaClnogrowth4 %
123953NaClnogrowth6 %
123953NaClnogrowth8 %
123953NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate+assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol+assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose+assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
12395316947citrate-carbon source
1239534853esculin-hydrolysis
12395317632nitrate+reduction
12395316301nitrite-reduction
12395315792malonate+assimilation
12395317632nitrate-respiration

antibiotic resistance

  • @ref: 123953
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12395335581indoleno

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
123953oxidase+
123953beta-galactosidase-3.2.1.23
123953alcohol dehydrogenase-1.1.1.1
123953gelatinase-
123953amylase-
123953DNase-
123953caseinase-3.4.21.50
123953catalase+1.11.1.6
123953tween esterase-
123953lecithinase-
123953lipase-
123953lysine decarboxylase-4.1.1.18
123953ornithine decarboxylase-4.1.1.17
123953protease+
123953tryptophan deaminase-
123953urease-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
123953-+++-+--+-++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
2419---------+-+-++----++

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123953-------------------+-----------------------------+----+------+---+-------+-+---++----+--+++++++++++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
2419water samplesElbe river near HamburgGermanyDEUEurope
50470Water,enrichment with dibenzo-p-dioxinElbe,downstream Hamburg harbourGermanyDEUEurope
67770Water of the River ElbeGermanyDEUEurope
123953Environment, Water samplesGermanyDEUEurope

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic

taxonmaps

  • @ref: 69479
  • File name: preview.99_1380.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_798;97_929;98_1089;99_1380&stattab=map
  • Last taxonomy: Sphingomonas
  • 16S sequence: LC508800
  • Sequence Identity:
  • Total samples: 656
  • soil counts: 335
  • aquatic counts: 171
  • animal counts: 94
  • plant counts: 56

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
24191Risk group (German classification)
1239531Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Sphingomonas wittichii gene for 16S rRNA, strain DSM 6014AB0214921481ena392499
2419Sphingomonas sp. partial 16S rRNA geneX727231460ena28214
67770Sphingomonas wittichii JCM 15750 gene for 16S ribosomal RNA, partial sequenceLC5088001409ena160791

Genome sequences

  • @ref: 66792
  • description: Rhizorhabdus wittichii RW1
  • accession: GCA_000016765
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 392499

GC content

  • @ref: 67770
  • GC-content: 67
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes80.52no
flagellatedno90.346no
gram-positiveno96.034no
anaerobicno98.925no
halophileno96.251no
spore-formingno94.81no
thermophileno99.061yes
glucose-utilyes68.821yes
aerobicyes94.863no
glucose-fermentno93.259yes

External links

@ref: 2419

culture collection no.: DSM 6014, JCM 10273, JCM 15750, CCUG 31198, CIP 107293, KCTC 12908, MTCC 7933, NBRC 100425, NBRC 105917

straininfo link

  • @ref: 83387
  • straininfo: 48039

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11321072Proposal of Sphingomonas wittichii sp. nov. for strain RW1T, known as a dibenzo-p-dioxin metabolizer.Yabuuchi E, Yamamoto H, Terakubo S, Okamura N, Naka T, Fujiwara N, Kobayashi K, Kosako Y, Hiraishi AInt J Syst Evol Microbiol10.1099/00207713-51-2-2812001Bacterial Typing Techniques, Ceramides/isolation & purification, DNA, Bacterial, DNA, Ribosomal/genetics, Dioxins/*metabolism, Fatty Acids, Omega-3, Fresh Water, Microbial Sensitivity Tests, Molecular Sequence Data, Nucleic Acid Conformation, Phenotype, RNA, Ribosomal, 16S/genetics, Sphingomonas/*classification/*metabolism/ultrastructure, Terminology as Topic, *Water MicrobiologyMetabolism
Phylogeny19666786Sphingomonas histidinilytica sp. nov., isolated from a hexachlorocyclohexane dump site.Nigam A, Jit S, Lal RInt J Syst Evol Microbiol10.1099/ijs.0.008995-02009Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, *Hexachlorocyclohexane, India, *Insecticides, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Refuse Disposal/*methods, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, Sphingomonas/*classification/genetics/*isolation & purification/physiologyGenetics
Phylogeny22685105Sphingomonas starnbergensis sp. nov., isolated from a prealpine freshwater lake.Chen H, Jogler M, Tindall BJ, Klenk HP, Rohde M, Busse HJ, Overmann JInt J Syst Evol Microbiol10.1099/ijs.0.042887-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Germany, Lakes/*microbiology, Molecular Sequence Data, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spermidine/analogs & derivatives/analysis, Sphingomonas/*classification/genetics/isolation & purification, Water MicrobiologyGenetics
Metabolism22909785Integrated hybrid treatment for the remediation of 2,3,7,8-tetrachlorodibenzo-p-dioxin.Bokare V, Murugesan K, Kim JH, Kim EJ, Chang YSSci Total Environ10.1016/j.scitotenv.2012.07.0792012Biological Availability, Chromatography, High Pressure Liquid, Dioxins/metabolism, Environmental Restoration and Remediation/*methods, Iron/chemistry, Metal Nanoparticles/chemistry, Oxidation-Reduction, Palladium/chemistry, Polychlorinated Dibenzodioxins/analysis/chemistry/*metabolism, Sphingomonas/metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2419Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6014)https://www.dsmz.de/collection/catalogue/details/culture/DSM-6014
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
37289Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4712
50470Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 31198)https://www.ccug.se/strain?id=31198
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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
83387Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID48039.1StrainInfo: A central database for resolving microbial strain identifiers
123953Curators of the CIPCollection of Institut Pasteur (CIP 107293)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107293