Strain identifier

BacDive ID: 17622

Type strain: Yes

Species: Xylella fastidiosa

Strain Designation: 2683 PCE-RR

Strain history: <- ATCC <- J. M. Wells; 2683 PCE-RR <- B. C. Raju

NCBI tax ID(s): 2371 (species)

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General

@ref: 3785

BacDive-ID: 17622

DSM-Number: 10026

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, plant pathogen

description: Xylella fastidiosa 2683 PCE-RR is a mesophilic plant pathogen that was isolated from grapevine.

NCBI tax id

  • NCBI tax id: 2371
  • Matching level: species

strain history

  • @ref: 3785
  • history: <- ATCC <- J. M. Wells; 2683 PCE-RR <- B. C. Raju

doi: 10.13145/bacdive17622.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Lysobacterales
  • family: Lysobacteraceae
  • genus: Xylella
  • species: Xylella fastidiosa
  • full scientific name: Xylella fastidiosa Wells et al. 1987

  • synonyms

    • @ref: 20215
    • synonym: Xylella fastidiosa subsp. piercei

@ref: 3785

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Xanthomonadales

family: Lysobacteraceae

genus: Xylella

species: Xylella fastidiosa

full scientific name: Xylella fastidiosa Wells et al. 1987

strain designation: 2683 PCE-RR

type strain: yes

Morphology

colony morphology

  • @ref: 3785
  • incubation period: 8-14 days

Culture and growth conditions

culture medium

  • @ref: 3785
  • name: BOSEA MEDIUM (DSMZ Medium 1052)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1052
  • composition: Name: 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

  • @ref: 3785
  • growth: positive
  • type: growth
  • temperature: 26
  • range: mesophilic

Isolation, sampling and environmental information

isolation

  • @ref: 3785
  • sample type: grapevine
  • geographic location: Florida
  • country: USA
  • origin.country: USA
  • continent: North America

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Fermented
#Host Body-Site#Plant#Fruit (Seed)
#Engineered#Food production#Beverage

taxonmaps

  • @ref: 69479
  • File name: preview.99_205.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17;96_145;97_156;98_174;99_205&stattab=map
  • Last taxonomy: Xylella fastidiosa
  • 16S sequence: AF203391
  • Sequence Identity:
  • Total samples: 3878
  • soil counts: 540
  • aquatic counts: 1022
  • animal counts: 2029
  • plant counts: 287

Safety information

risk assessment

  • @ref: 3785
  • pathogenicity plant: yes
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Xylella fastidiosa strain GR.8935 16S ribosomal RNA gene, partial sequenceAF2033911534ena2371
20218Xylella fastidiosa strain GR.8935 16S-23S ribosomal RNA intergenic spacer, complete sequenceAF203397512ena2371
20218Xylella fastidiosa 16S ribosomal RNA gene, partial sequence; tRNA-Ala and tRNA-Ile genes, complete sequence; and 23S ribosomal RNA gene, partial sequenceAF272834942ena2371
20218Xylella fastidiosa 16S ribosomal RNA gene, partial sequenceDQ9874771537ena2371
20218Xylella fastidiosa strain ATCC 35879 16S-23S ribosomal RNA intergenic spacer, complete sequenceDQ991169512ena2371
3785Xylella fastidiosa 16S ribosomal RNA, complete sequenceAF1923431537ena2371

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Xylella fastidiosa ATCC 35879GCA_011801475completencbi2371
66792Xylella fastidiosa ATCC 35879GCA_000767565contigncbi2371
66792Xylella fastidiosa DSM 10026GCA_900129695scaffoldncbi2371
66792Xylella fastidiosa subsp. fastidiosa CFBP7970GCA_004016315contigncbi644356
66792Xylella fastidiosa ATCC 358792371.35wgspatric2371
66792Xylella fastidiosa strain ATCC 358792371.472completepatric2371
66792Xylella fastidiosa strain DSM 100262371.167wgspatric2371
66792Xylella fastidiosa subsp. fastidiosa strain CFBP7970644356.17wgspatric644356
66792Xylella fastidiosa DSM 100262595698223draftimg2371
66792Xylella fastidiosa ATCC 358792645728018draftimg2371

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno81.402no
flagellatedno97.089no
gram-positiveno98.521no
anaerobicno97.363no
aerobicno59.502no
halophileno91.706no
spore-formingno96.493no
glucose-utilyes81.639no
thermophileno92.278no
glucose-fermentno80.55no

External links

@ref: 3785

culture collection no.: DSM 10026, ATCC 35879, CFBP 7970, LMG 17159

straininfo link

  • @ref: 86614
  • straininfo: 10333

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11142410Evidence for conserved tRNA genes in the 16S-23S rDNA spacer sequence and two rrn operons of Xylella fastidiosa.Chen J, Banks D, Jarret RL, Jones JBCan J Microbiol10.1139/w00-1142000Base Sequence, Blotting, Southern, Conserved Sequence, DNA, Ribosomal Spacer/*genetics, Gammaproteobacteria/*genetics, *Genes, Bacterial, Molecular Sequence Data, RNA, Ribosomal, 16S/genetics, RNA, Ribosomal, 23S/genetics, RNA, Transfer/*genetics, RNA, Transfer, Ala, RNA, Transfer, Ile/genetics, *rRNA OperonGenetics
Genetics32179972Whole Genome Sequence of Xylella fastidiosa ATCC 35879(T) and Detection of Genome Rearrangements Within Subsp. fastidiosa.Chen J, O'Leary M, Burbank L, Zheng Z, Deng XCurr Microbiol10.1007/s00284-020-01937-02020Bacterial Typing Techniques, DNA, Bacterial/genetics, *Gene Rearrangement, *Genome, Bacterial, Plant Diseases/microbiology, Sequence Analysis, DNA, *Whole Genome Sequencing, Xylella/classification/*geneticsTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3785Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10026)https://www.dsmz.de/collection/catalogue/details/culture/DSM-10026
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
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)
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
86614Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10333.1StrainInfo: A central database for resolving microbial strain identifiers