Strain identifier

BacDive ID: 2898

Type strain: Yes

Species: Acidovorax defluvii

Strain history: CIP <- 2000, DSMZ <- S. Spring: strain BSB411

NCBI tax ID(s): 86669 (species)

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General

@ref: 4777

BacDive-ID: 2898

DSM-Number: 12644

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, motile

description: Acidovorax defluvii DSM 12644 is an aerobe, mesophilic, motile bacterium that was isolated from activated sludge of the municipal wastewater treatment plant München I.

NCBI tax id

  • NCBI tax id: 86669
  • Matching level: species

strain history

@refhistory
4777<- S. Spring; BSB411
118864CIP <- 2000, DSMZ <- S. Spring: strain BSB411

doi: 10.13145/bacdive2898.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Comamonadaceae
  • genus: Acidovorax
  • species: Acidovorax defluvii
  • full scientific name: Acidovorax defluvii Schulze et al. 1999

@ref: 4777

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Acidovorax

species: Acidovorax defluvii

full scientific name: Acidovorax defluvii Schulze et al. 1999

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes92.371
69480100negative
118864yesnegativerod-shaped

pigmentation

  • @ref: 118864
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4777REACTIVATION 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
39593MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
118864CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
118864CIP Medium 228yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=228

culture temp

@refgrowthtypetemperaturerange
4777positivegrowth30mesophilic
39593positivegrowth30mesophilic
58444positivegrowth30mesophilic
118864positivegrowth5-30
118864nogrowth37mesophilic
118864nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
58444aerobe
118864facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no100

halophily

@refsaltgrowthtested relationconcentration
118864NaClpositivegrowth0 %
118864NaClnogrowth2 %
118864NaClnogrowth4 %
118864NaClnogrowth6 %
118864NaClnogrowth8 %
118864NaClnogrowth10 %

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
11886416947citrate-carbon source
1188644853esculin-hydrolysis
11886417632nitrate+reduction
11886416301nitrite+reduction
11886417632nitrate+respiration

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
11886435581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase-
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
118864oxidase+
118864beta-galactosidase-3.2.1.23
118864alcohol dehydrogenase-1.1.1.1
118864gelatinase+/-
118864amylase-
118864DNase-
118864caseinase-3.4.21.50
118864catalase+1.11.1.6
118864tween esterase+
118864lecithinase+
118864lipase-
118864lysine decarboxylase-4.1.1.18
118864ornithine decarboxylase-4.1.1.17
118864protease-
118864tryptophan deaminase-
118864urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118864-+++-+--------------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
4777+---------------+---+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118864-------------------------------+-------------------------------------------+---+-+------+-++-+-----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
4777activated sludge of the municipal wastewater treatment plant München IGroßlappen near MunichGermanyDEUEurope
58444Activated sludgeMünchenGermanyDEUEurope1995
118864Environment, Activated sludgeMünchenGermanyDEUEurope1995

isolation source categories

Cat1Cat2Cat3
#Engineered#Waste#Activated sludge
#Engineered#Waste#Water treatment plant

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
47771Risk group (German classification)
1188641Risk group (French classification)

Sequence information

16S sequences

  • @ref: 4777
  • description: Acidovorax defluvii 16S rRNA gene
  • accession: Y18616
  • length: 1526
  • database: ena
  • NCBI tax ID: 86669

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Acidovorax defluvii strain DSM 1264486669.4wgspatric86669
66792Acidovorax defluvii DSM 126442756170235draftimg86669

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno61.332no
flagellatedno68.793no
gram-positiveno98.687no
anaerobicno97.438yes
halophileno94.943no
spore-formingno95.821no
glucose-utilno77.332yes
aerobicyes91.067yes
glucose-fermentno91.19no
thermophileno98.548yes

External links

@ref: 4777

culture collection no.: DSM 12644, CIP 106824, CCUG 49021, BSB 411

straininfo link

  • @ref: 72421
  • straininfo: 49332

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10390871Genotypic diversity of Acidovorax strains isolated from activated sludge and description of Acidovorax defluvii sp. nov.Schulze R, Spring S, Amann R, Huber I, Ludwig W, Schleifer KH, Kampfer PSyst Appl Microbiol10.1016/S0723-2020(99)80067-81999Base Sequence, DNA, Bacterial/chemistry, Genotype, Gram-Negative Aerobic Rods and Cocci/classification/*genetics/isolation & purification, Guanine, In Situ Hybridization, Fluorescence/methods, Molecular Sequence Data, Nitrates/metabolism, Oligonucleotide Probes/*genetics, Phenotype, Phylogeny, RNA, Bacterial/analysis, RNA, Ribosomal, 16S/analysis, Sewage/*microbiology, Species SpecificityGenetics
Phylogeny29939126Simplicispira suum sp. nov., isolated from a dust collector at a pig farm.Cho HY, Heo J, Hong SB, Kim JS, Kwon SW, Kim SJInt J Syst Evol Microbiol10.1099/ijsem.0.0028742018Animals, Bacterial Typing Techniques, Base Composition, Comamonadaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, *Dust, *Farms, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Swine, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitle
4777Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12644)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12644
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
39593Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18997
58444Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 49021)https://www.ccug.se/strain?id=49021
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
68382Automatically annotated from API zym
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
72421Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49332.1StrainInfo: A central database for resolving microbial strain identifiers
118864Curators of the CIPCollection of Institut Pasteur (CIP 106824)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106824