Strain identifier

BacDive ID: 2086

Type strain: Yes

Species: Ralstonia syzygii

Strain Designation: R001

Strain history: <- NCPPB <- S.J. Roberts

NCBI tax ID(s): 28097 (species)

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General

@ref: 3136

BacDive-ID: 2086

DSM-Number: 7385

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

description: Ralstonia syzygii R001 is an aerobe, mesophilic, Gram-negative plant pathogen that was isolated from xylem tissue of the clove tree Syzygium aromaticum.

NCBI tax id

  • NCBI tax id: 28097
  • Matching level: species

strain history

  • @ref: 3136
  • history: <- NCPPB <- S.J. Roberts

doi: 10.13145/bacdive2086.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Burkholderiaceae
  • genus: Ralstonia
  • species: Ralstonia syzygii
  • full scientific name: Ralstonia syzygii (Roberts et al. 1990) Vaneechoutte et al. 2004

  • synonyms

    • @ref: 20215
    • synonym: Pseudomonas syzygii

@ref: 3136

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Ralstonia

species: Ralstonia syzygii

full scientific name: Ralstonia syzygii (Roberts et al. 1990) Vaneechoutte et al. 2004 emend. Safni et al. 2014

strain designation: R001

type strain: yes

Morphology

cell morphology

  • @ref: 23167
  • gram stain: negative
  • cell length: 1.5-3.0 µm
  • cell width: 1.0 µm
  • cell shape: rod-shaped

colony morphology

  • @ref: 23167
  • incubation period: 5-7 days
  • medium used: CA

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3136HETEROTROPHIC MEDIUM H3P (DSMZ Medium 428)yeshttps://mediadive.dsmz.de/medium/428Name: HETEROTROPHIC MEDIUM H3P (DSMZ Medium 428) Composition: Agar 19.802 g/l Na2HPO4 x 2 H2O 2.87129 g/l KH2PO4 2.27723 g/l D-Glucose 1.9802 g/l Na-lactate 0.990099 g/l Na-pyruvate 0.990099 g/l D-Mannitol 0.990099 g/l DL-Malate 0.990098 g/l Na-acetate 0.990098 g/l Yeast extract 0.990098 g/l NH4Cl 0.990098 g/l Disodium succinate 0.990098 g/l MgSO4 x 7 H2O 0.495049 g/l Ferric ammonium citrate 0.049505 g/l CaCl2 x 2 H2O 0.00990098 g/l NaVO3 x H2O 0.00495049 g/l Thiamine-HCl x 2 H2O 0.00247525 g/l Nicotinic acid 0.00247525 g/l Pyridoxine hydrochloride 0.00247525 g/l Calcium pantothenate 0.00247525 g/l H3BO3 0.00148515 g/l CoCl2 x 6 H2O 0.000990099 g/l Riboflavin 0.00049505 g/l ZnSO4 x 7 H2O 0.00049505 g/l MnCl2 x 4 H2O 0.000148515 g/l Na2MoO4 x 2 H2O 0.000148515 g/l NiCl2 x 6 H2O 9.90099e-05 g/l CuCl2 x 2 H2O 4.95049e-05 g/l Vitamin B12 4.95049e-05 g/l Folic acid 9.90099e-06 g/l Biotin 4.9505e-06 g/l Distilled water
3136NUTRIENT 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
23167CAyes
36586MEDIUM 328- for nutrient agaryesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
3136R2A 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
3136BOSEA MEDIUM (DSMZ Medium 1052)yeshttps://mediadive.dsmz.de/medium/1052Name: BOSEA MEDIUM (DSMZ Medium 1052) Composition: Agar 15.0 g/l ACES 10.0 g/l Yeast extract 10.0 g/l Activated charcoal 2.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
3136positivegrowth28mesophilic
23167positivegrowth28mesophilic
36586positivegrowth30mesophilic
51180positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 51180
  • oxygen tolerance: aerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2316728757fructose-builds acid from
2316717716lactose-builds acid from
2316717306maltose-builds acid from
2316715971L-histidine-carbon source
2316724996lactate-carbon source
2316727082trehalose-carbon source
2316753423tween 40-carbon source
2316728017starch-hydrolysis
23167181014-hydroxyphenylacetic acid-respiration
2316730089acetate-respiration
2316717784D-glucosaminic acid-respiration
2316715748D-glucuronate-respiration
2316716551D-trehalose-respiration
2316716865gamma-aminobutyric acid-respiration
2316717859glutaric acid-respiration
2316715971L-histidine-respiration
2316724996lactate-respiration
2316717272propionate-respiration
2316753423tween 40-respiration
2316773706bromosuccinate+carbon source
2316717634D-glucose+carbon source
2316717196L-asparagine+carbon source
2316729991L-aspartate+carbon source
2316729985L-glutamate+carbon source
2316717203L-proline+carbon source
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
6836916199urea+hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

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

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369urease+3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
3136----++/------------+--+

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcontinentcountryorigin.countrysampling date
3136xylem tissue of the clove tree Syzygium aromaticumSyzygium aromaticumSumatra (westside)Asia
23167plant pathogen from xylem tissues of the clove tree (Syzygium aromaticum)West SumatraAsiaIndonesiaIDN
51180The clove tree,xylem tissues (Syzygium aromaticum)West SumatraAsiaIndonesiaIDN1980

isolation source categories

Cat1Cat2Cat3
#Host#Other
#Host#Plants#Tree

Safety information

risk assessment

  • @ref: 3136
  • pathogenicity plant: yes
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Ralstonia syzygii gene for 16S rRNA, strain: ATCC 49543AB0214031513ena28097
20218Ralstonia syzygii subsp. syzygii strain LMG10661T 16S-23S ribosomal RNA intergenic spacer, partial sequenceKC756977506ena1310166
20218Pseudomonas syzygii partial 16S rRNA gene, strain RAL10AJ270252469ena28097
2316716S-23S rRNA ITSKC756077nuccore
3136Pseudomonas syzygii strain R001 16S ribosomal RNA gene, partial sequenceU282371445ena28097

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Ralstonia syzygii subsp. syzygii LMG 10661GCA_919592095contigncbi1310166
66792Ralstonia syzygii subsp. syzygii strain LMG 106611310166.3wgspatric1310166

GC content

@refGC-contentmethod
2316765.5high performance liquid chromatography (HPLC)
313665.2high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno89.216no
flagellatedno90.092no
gram-positiveyes88.767yes
anaerobicno99.26no
aerobicyes93.177yes
halophileyes96.769no
spore-formingno90.991no
glucose-utilyes89.08no
glucose-fermentyes84.773no
thermophileno99.875yes

External links

@ref: 3136

culture collection no.: CCUG 32781, CIP 108366, DSM 7385, ATCC 49543, LMG 10661, NCPPB 3446

straininfo link

  • @ref: 71733
  • straininfo: 4590

literature

  • topic: Phylogeny
  • Pubmed-ID: 24944341
  • title: Polyphasic taxonomic revision of the Ralstonia solanacearum species complex: proposal to emend the descriptions of Ralstonia solanacearum and Ralstonia syzygii and reclassify current R. syzygii strains as Ralstonia syzygii subsp. syzygii subsp. nov., R. solanacearum phylotype IV strains as Ralstonia syzygii subsp. indonesiensis subsp. nov., banana blood disease bacterium strains as Ralstonia syzygii subsp. celebesensis subsp. nov. and R. solanacearum phylotype I and III strains as Ralstonia pseudosolanacearum sp. nov.
  • authors: Safni I, Cleenwerck I, De Vos P, Fegan M, Sly L, Kappler U
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.066712-0
  • year: 2014
  • mesh: Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal Spacer/genetics, Fatty Acids/chemistry, Indonesia, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Plant Diseases/microbiology, RNA, Ribosomal, 16S/genetics, RNA, Ribosomal, 23S/genetics, Ralstonia/*classification, Ralstonia solanacearum/*classification, Sequence Analysis, DNA
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3136Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7385)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7385
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
23167Irda Safni, Ilse Cleenwerck, Paul De Vos, Mark Fegan, Lindsay Sly, Ulrike Kappler10.1099/ijs.0.066712-0Polyphasic taxonomic revision of the Ralstonia solanacearum species complex: proposal to emend the descriptions of Ralstonia solanacearum and Ralstonia syzygii and reclassify current R. syzygii strains as Ralstonia syzygii subsp. syzygii subsp. nov., R. solanacearum phylotype IV strains as Ralstonia syzygii subsp. indonesiensis subsp. nov., banana blood disease bacterium strains as Ralstonia syzygii subsp. celebesensis subsp. nov. and R. solanacearum phylotype I and III strains as Ralstonia pseudosolanacearum sp. nov.IJSEM 64: 3087-3103 201424944341
36586Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5980
51180Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 32781)https://www.ccug.se/strain?id=32781
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)
68369Automatically annotated from API 20NE
71733Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID4590.1StrainInfo: A central database for resolving microbial strain identifiers