Strain identifier

BacDive ID: 14222

Type strain: Yes

Species: Rhizorhapis suberifaciens

Strain Designation: CA1, EY 2404, Ca 1

Strain history: CIP <- 1998, A.H.C. van Bruggen, Univ. California, Davis, CA, USA: strain Ca 1 <- C. Waters

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

@ref: 3170

BacDive-ID: 14222

DSM-Number: 7465

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

description: Rhizorhapis suberifaciens CA1 is a mesophilic, Gram-negative plant pathogen that was isolated from Lactuca sativa, corky roots.

NCBI tax id

NCBI tax idMatching level
1219056strain
13656species

strain history

@refhistory
3170<- LMG <- A. van Bruggen Univ. California, USA
67770ATCC 49355 <-- A. H. C. van Bruggen CR-CA1 <-- R. Michelmore <-- C. Waters.
123343CIP <- 1998, A.H.C. van Bruggen, Univ. California, Davis, CA, USA: strain Ca 1 <- C. Waters

doi: 10.13145/bacdive14222.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Sphingomonadaceae
  • genus: Rhizorhapis
  • species: Rhizorhapis suberifaciens
  • full scientific name: Rhizorhapis suberifaciens (van Bruggen et al. 1990) Francis et al. 2014
  • synonyms

    @refsynonym
    20215Sphingobium suberifaciens
    20215Rhizomonas suberifaciens
    20215Sphingomonas suberifaciens

@ref: 3170

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Rhizorhapis

species: Rhizorhapis suberifaciens

full scientific name: Rhizorhapis suberifaciens (van Bruggen et al. 1990) Francis et al. 2014

strain designation: CA1, EY 2404, Ca 1

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.998
123343negativerod-shapedyes

pigmentation

  • @ref: 123343
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3170R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: 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 water
3170RHIZOMONAS SUBERIFACIENS MEDIUM (DSMZ Medium 726)yeshttps://mediadive.dsmz.de/medium/726Name: RHIZOMONAS SUBERIFACIENS MEDIUM (DSMZ Medium 726) Composition: Agar 11.0 g/l Enzymatic digest of casein 5.0 g/l Glucose 2.5 g/l K2HPO4 x 3 H2O 1.3 g/l MgSO4 x 7 H2O 0.5 g/l KNO3 0.5 g/l Ca(NO3)2 x 4 H2O 0.06 g/l Distilled water
36403MEDIUM 254 - for Rhizomonas suberifaciensyesDistilled water make up to (1000.000 ml);Magnesium sulphate heptahydrate (0.500 g);Glucose (2.500 g);Potassium nitrate (0.500 g);Calcium nitrate tetrahydrate (0.060g);Di Potassium monohydrogenophosphate (1.000 g);Casein hydrolysate acid hydrolysed vitamin
123343CIP Medium 254yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=254

culture temp

@refgrowthtypetemperaturerange
3170positivegrowth28mesophilic
36403positivegrowth30mesophilic
67770positivegrowth26mesophilic
123343positivegrowth25-30mesophilic
123343nogrowth5psychrophilic
123343nogrowth10psychrophilic
123343nogrowth37mesophilic
123343nogrowth41thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.99

halophily

@refsaltgrowthtested relationconcentration
123343NaClpositivegrowth0 %
123343NaClnogrowth2 %
123343NaClnogrowth4 %
123343NaClnogrowth6 %
123343NaClnogrowth8 %
123343NaClnogrowth10 %

observation

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

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
12334316947citrate-carbon source
1233434853esculin+hydrolysis
12334317632nitrate+reduction
12334316301nitrite-reduction

antibiotic resistance

  • @ref: 123343
  • 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
12334335581indoleno

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
123343oxidase+
123343beta-galactosidase+3.2.1.23
123343alcohol dehydrogenase-1.1.1.1
123343gelatinase-
123343catalase+1.11.1.6
123343lysine decarboxylase-4.1.1.18
123343ornithine decarboxylase-4.1.1.17
123343phenylalanine ammonia-lyase-4.3.1.24
123343tryptophan deaminase-
123343urease-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
123343-+++-++-+-+--+-++---

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
3170+----+-+-+----------+

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
3170Lactuca sativa, corky rootsLactuca sativaCaliforniaUSAUSANorth America
67770Lettuce rootsCAUSAUSANorth America
123343Plant, Corked lettuce rootsCaliforniaUnited States of AmericaUSANorth America

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root (Rhizome)

taxonmaps

  • @ref: 69479
  • File name: preview.99_87530.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_36340;97_46181;98_60493;99_87530&stattab=map
  • Last taxonomy: Rhizorhapis suberifaciens subclade
  • 16S sequence: KF437561
  • Sequence Identity:
  • Total samples: 24368
  • soil counts: 12941
  • aquatic counts: 5886
  • animal counts: 2084
  • plant counts: 3457

Safety information

risk assessment

@refpathogenicity plantbiosafety levelbiosafety level comment
3170yes1Risk group (German classification)
1233431Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
3170Sphingomonas suberifaciens gene for 16S rRNA, partial sequenceD137371415ena1219056
3170Rhizorhapis suberifaciens NBRC 15211 16S ribosomal RNA gene, partial sequenceKF4375611453ena1219056
67770Sphingomonas suberifaciens gene for 16S rRNA, partial sequence, strain: NBRC 15211AB6808131414ena1219056

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhizorhapis suberifaciens DSM 7465GCA_014200045scaffoldncbi13656
66792Rhizorhapis suberifaciens strain DSM 746513656.4wgspatric13656
66792Rhizorhapis suberifaciens DSM 74652829787817draftimg13656

GC content

@refGC-contentmethod
317059
6777058.6-59.2Buoyant density centrifugation (BD)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno83.622no
gram-positiveno97.579no
anaerobicno98.101no
aerobicyes83.327no
halophileno96.734no
spore-formingno90.832no
glucose-utilyes79.631no
thermophileno93.353yes
motileyes71.851no
glucose-fermentno93.127yes

External links

@ref: 3170

culture collection no.: DSM 7465, ATCC 49355, CIP 105429, ICMP 12535, JCM 8521, LMG 11026, LMG 17323, NBRC 15211, NCPPB 3629, IFO 15211, LMG 15574, LMG 15591, LMG 9830

straininfo link

  • @ref: 83381
  • straininfo: 4820

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny8186095Phylogenetic evidence for Sphingomonas and Rhizomonas as nonphotosynthetic members of the alpha-4 subclass of the Proteobacteria.Takeuchi M, Sawada H, Oyaizu H, Yokota AInt J Syst Bacteriol10.1099/00207713-44-2-3081994Bacteriochlorophylls/analysis, Base Sequence, DNA, Bacterial/*genetics, DNA, Ribosomal/*genetics, Fatty Acids/analysis, Gram-Negative Bacteria/chemistry/*classification/genetics, Lipids/analysis, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/*genetics, Sequence Analysis, DNAGenetics
Phylogeny10385200Proposal of Sphingomonas suberifaciens (van Bruggen, Jochimsen and Brown 1990) comb. nov., sphingomonas natatoria (Sly 1985) comb. nov., Sphingomonas ursincola (Yurkov et al. 1997) comb. nov., and emendation of the genus Sphingomonas.Yabuuchi E, Kosako Y, Naka T, Suzuki S, Yano IMicrobiol Immunol10.1111/j.1348-0421.1999.tb02414.x1999Base Composition, DNA, Bacterial, DNA, Ribosomal, Genotype, Glycosphingolipids/analysis, Gram-Negative Aerobic Bacteria/chemistry/*classification/genetics, Microbial Sensitivity Tests, Phylogeny, RNA, Ribosomal, 16SGenetics
Phylogeny22561591Sphingobium limneticum sp. nov. and Sphingobium boeckii sp. nov., two freshwater planktonic members of the family Sphingomonadaceae, and reclassification of Sphingomonas suberifaciens as Sphingobium suberifaciens comb. nov.Chen H, Jogler M, Rohde M, Klenk HP, Busse HJ, Tindall BJ, Sproer C, Overmann JInt J Syst Evol Microbiol10.1099/ijs.0.040105-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, *Fresh Water, Molecular Sequence Data, Myristic Acids/analysis, Nucleic Acid Hybridization, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sphingomonadaceae/*classification/genetics/isolation & purification, *Water MicrobiologyGenetics
Phylogeny24436067Reclassification of rhizosphere bacteria including strains causing corky root of lettuce and proposal of Rhizorhapis suberifaciens gen. nov., comb. nov., Sphingobium mellinum sp. nov., Sphingobium xanthum sp. nov. and Rhizorhabdus argentea gen. nov., sp. nov.Francis IM, Jochimsen KN, De Vos P, van Bruggen AHCInt J Syst Evol Microbiol10.1099/ijs.0.058909-02014Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lettuce/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Plant Diseases/*microbiology, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, Sphingomonadaceae/*classification/genetics/isolation & purificationGenetics
Phylogeny24647265Novel primers and PCR protocols for the specific detection and quantification of Sphingobium suberifaciens in situ.Bull CT, Goldman PH, Martin KJMol Cell Probes10.1016/j.mcp.2014.03.0012014Bacterial Typing Techniques/methods, DNA Primers/*genetics, DNA, Bacterial/chemistry/*genetics, Genetic Variation, Lettuce/microbiology, Molecular Sequence Data, Plant Roots/microbiology, Polymerase Chain Reaction/*methods, RNA, Ribosomal, 16S/*genetics, Reproducibility of Results, Sequence Analysis, DNA, Soil Microbiology, Species Specificity, Sphingomonadaceae/classification/*geneticsGenetics
Phylogeny25385991Sphingobium subterraneum sp. nov., isolated from ground water.Lee JC, Kim SG, Whang KSInt J Syst Evol Microbiol10.1099/ijs.0.069708-02014Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Groundwater/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/analogs & derivatives/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitle
3170Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7465)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7465
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
36403Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17448
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
83381Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID4820.1StrainInfo: A central database for resolving microbial strain identifiers
123343Curators of the CIPCollection of Institut Pasteur (CIP 105429)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105429