Strain identifier

BacDive ID: 2899

Type strain: Yes

Species: Acidovorax valerianellae

Strain history: CIP <- 2003, M. Le Saux, INRA, Beaucouze, France

NCBI tax ID(s): 187868 (species)

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General

@ref: 6527

BacDive-ID: 2899

DSM-Number: 16619

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

description: Acidovorax valerianellae DSM 16619 is an obligate aerobe, mesophilic, Gram-negative plant pathogen that was isolated from lamb's lettuce .

NCBI tax id

  • NCBI tax id: 187868
  • Matching level: species

strain history

@refhistory
6527<- CFBP <- L. Gardan
366742003, M. Le Saux, Beaucouze, France
123786CIP <- 2003, M. Le Saux, INRA, Beaucouze, France

doi: 10.13145/bacdive2899.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Comamonadaceae
  • genus: Acidovorax
  • species: Acidovorax valerianellae
  • full scientific name: Acidovorax valerianellae Gardan et al. 2003

  • synonyms

    • @ref: 20215
    • synonym: Paracidovorax valerianellae

@ref: 6527

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Acidovorax

species: Acidovorax valerianellae

full scientific name: Acidovorax valerianellae Gardan et al. 2003

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
123786negativerod-shapedyes
125439negative98.9
125438negative97

pigmentation

  • @ref: 123786
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6527REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)yeshttps://mediadive.dsmz.de/medium/1aName: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
36674MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123786CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
123786CIP Medium 568yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=568

culture temp

@refgrowthtypetemperature
6527positivegrowth28
36674positivegrowth25
123786positivegrowth10-30
123786nogrowth5
123786nogrowth37
123786nogrowth41

Physiology and metabolism

oxygen tolerance

  • @ref: 123786
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 98.8

halophily

@refsaltgrowthtested relationconcentration
123786NaClpositivegrowth0-2 %
123786NaClnogrowth4 %
123786NaClnogrowth6 %
123786NaClnogrowth8 %
123786NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12378616947citrate-carbon source
1237864853esculin-hydrolysis
12378617632nitrate-reduction
12378616301nitrite-reduction
12378617632nitrate-respiration
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

antibiotic resistance

  • @ref: 123786
  • 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
12378635581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382beta-glucuronidase-3.2.1.31
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase-3.1.3.2
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382lipase (C 14)-
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
123786oxidase+
123786beta-galactosidase-3.2.1.23
123786alcohol dehydrogenase+1.1.1.1
123786gelatinase-
123786amylase+
123786DNase-
123786caseinase+3.4.21.50
123786catalase+1.11.1.6
123786tween esterase+
123786lecithinase-
123786lipase-
123786lysine decarboxylase-4.1.1.18
123786ornithine decarboxylase-4.1.1.17
123786protease+
123786tryptophan deaminase-
123786urease+3.5.1.5
68369gelatinase-
68382esterase lipase (C 8)+
68369cytochrome oxidase+1.9.3.1
68369beta-glucosidase-3.2.1.21
68369urease+3.5.1.5
68369arginine dihydrolase-3.5.3.6

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123786-+++-+-----+--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6527----+---------+-++--+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123786-+-----------------------------+----------------++----------+--------------+--++++------++++--+--++

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentisolation date
6527lamb's lettuce (Valerianella locusta)Valerianella locustaFranceFRAEurope
123786Valerianella locustaFranceFRAEurope1993

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants
  • Cat3: #Herbaceous plants (Grass,Crops)

Safety information

risk assessment

@refpathogenicity plantbiosafety levelbiosafety level comment
6527yes1Risk group (German classification)
1237861Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Acidovorax valerianellae strain DSM 16619 16S ribosomal RNA gene, partial sequenceKF9311501520nuccore187868
20218Acidovorax valerianellae strain DSM 16619 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceKF931155691nuccore187868
6527Acidovorax valerianelle partial 16S rRNA gene, strain CFBP 4730AJ4317311492nuccore187868

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paracidovorax valerianellae DSM 16619GCA_900102625scaffoldncbi187868
66792Acidovorax valerianellae strain DSM 16619187868.3wgspatric187868
66792Acidovorax valerianellae DSM 166192615840716draftimg187868

GC content

  • @ref: 6527
  • GC-content: 64.5

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno97no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no98.205yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes86.422no
125438spore-formingspore-formingAbility to form endo- or exosporesno87.619no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno97.324yes
125438motile2+flagellatedAbility to perform flagellated movementyes78.547no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno98.8
125439BacteriaNetmotilityAbility to perform movementyes82.8
125439BacteriaNetgram_stainReaction to gram-stainingnegative98.9
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe83.1

External links

@ref: 6527

culture collection no.: DSM 16619, CFBP 4730, NCPPB 4283, CIP 107997

straininfo link

  • @ref: 72422
  • straininfo: 87882

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12807202Acidovorax valerianellae sp. nov., a novel pathogen of lamb's lettuce [Valerianella locusta (L.) Laterr].Gardan L, Stead DE, Dauga C, Gillis MInt J Syst Evol Microbiol10.1099/ijs.0.02404-02003Bacterial Typing Techniques, Base Composition, Betaproteobacteria/chemistry/*classification/genetics/*pathogenicity, DNA, Ribosomal/analysis, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Plant Diseases/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Valerianella/*microbiology, VirulenceGenetics
Phylogeny29627890Acidovorax monticola sp. nov., isolated from soil.Chaudhary DK, Kim JAntonie Van Leeuwenhoek10.1007/s10482-018-1083-z2018Base Composition, Betaproteobacteria/*classification/genetics/isolation & purification, Forests, Metabolomics/methods, Molecular Typing, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Soil MicrobiologyPhenotype

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6527Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16619)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16619
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
36674Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5569
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
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
72422Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID87882.1StrainInfo: A central database for resolving microbial strain identifiers
123786Curators of the CIPCollection of Institut Pasteur (CIP 107997)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107997
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1