Strain identifier

BacDive ID: 2893

Type strain: Yes

Species: Acidovorax konjaci

Strain Designation: K2

Strain history: CIP <- 2000, CCUG <- 1985, LMG, Pseudomonas pseudoalcaligenes konjaci <- 1983, PDDC: strain 7733 <- M. Goto: strain K2

NCBI tax ID(s): 32040 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 3180

BacDive-ID: 2893

DSM-Number: 7481

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, motile, plant pathogen

description: Acidovorax konjaci K2 is an obligate aerobe, mesophilic, motile plant pathogen that was isolated from Amorphophallus rivieri cv. konjaci.

NCBI tax id

  • NCBI tax id: 32040
  • Matching level: species

strain history

@refhistory
3180<- ATCC <- M. Goto; K2
67770M. Goto strain K2.
120463CIP <- 2000, CCUG <- 1985, LMG, Pseudomonas pseudoalcaligenes konjaci <- 1983, PDDC: strain 7733 <- M. Goto: strain K2

doi: 10.13145/bacdive2893.20230509.8.1

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 konjaci
  • full scientific name: Acidovorax konjaci (Goto 1983) Willems et al. 1992
  • synonyms

    @refsynonym
    20215Paracidovorax konjaci
    20215Pseudomonas pseudoalcaligenes subsp. konjaci
    20215Pseudomonas avenae subsp. konjaci

@ref: 3180

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Acidovorax

species: Acidovorax konjaci

full scientific name: Acidovorax konjaci (Goto 1983) Willems et al. 1992

strain designation: K2

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes98.918
6948099.997negative
120463yesnegativerod-shaped

pigmentation

  • @ref: 120463
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3180NUTRIENT 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
39525MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
120463CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
120463CIP Medium 35yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=35

culture temp

@refgrowthtypetemperaturerange
3180positivegrowth28mesophilic
39525positivegrowth30mesophilic
67770positivegrowth28mesophilic
120463positivegrowth25-37mesophilic
120463nogrowth5psychrophilic
120463nogrowth10psychrophilic
120463nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120463
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.996

halophily

@refsaltgrowthtested relationconcentration
120463NaClpositivegrowth2 %
120463NaClnogrowth4 %
120463NaClnogrowth6 %
120463NaClnogrowth8 %
120463NaClnogrowth10 %

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
12046316947citrate-carbon source
1204634853esculin-hydrolysis
12046317632nitrate+reduction
12046316301nitrite-reduction
12046317632nitrate-respiration

antibiotic resistance

  • @ref: 120463
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12046335581indoleno

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-
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
120463oxidase+
120463beta-galactosidase-3.2.1.23
120463alcohol dehydrogenase-1.1.1.1
120463gelatinase-
120463amylase-
120463DNase-
120463caseinase-3.4.21.50
120463catalase+1.11.1.6
120463tween esterase-
120463lecithinase-
120463lipase-
120463lysine decarboxylase-4.1.1.18
120463ornithine decarboxylase-4.1.1.17
120463protease-
120463tryptophan deaminase-
120463urease+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
46608--++-+--------------
120463-+++-+-+--+---------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
46608+-------+++++++++++-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120463-+-----------------+------+----+-+---------+--++++----+-----+------------+-++--++++-----+++++++++++

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentsampling dateisolation date
3180Amorphophallus rivieri cv. konjaciAmorphophallus rivieriShizuokaJapanJPNAsia
46608Amorphophallus rivieri cv. KonjacJapanJPNAsia1977
67770Amorphophalus rivieri cv. KonjacAmorphophalus rivieri
120463Amorphophallus rivieri cv. KonjacJapanJPNAsia1977

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_10865.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_491;97_560;98_8087;99_10865&stattab=map
  • Last taxonomy: Acidovorax konjaci
  • 16S sequence: AF078760
  • Sequence Identity:
  • Total samples: 943
  • soil counts: 195
  • aquatic counts: 153
  • animal counts: 30
  • plant counts: 565

Safety information

risk assessment

@refpathogenicity plantbiosafety levelbiosafety level comment
3180yes1Risk group (German classification)
1204631Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Acidovorax konjaci 16S ribosomal RNA gene, partial sequenceAF0787601513ena32040
20218Mycobacterium goodii strain CIP 106349 16S ribosomal RNA gene, partial sequenceAF547930544ena134601
20218Acidovorax konjaci 16S rRNA gene, strain DSM 7481AJ4203251490ena32040
20218Acidovorax konjaci 16S ribosomal RNA gene, partial sequenceAF1375071481ena32040
20218Acidovorax konjaci strain ICMP 7733 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceGU339095871ena32040

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Acidovorax konjaci strain DSM 748132040.4wgspatric32040
66792Acidovorax konjaci DSM 74812634166315draftimg32040
67770Paracidovorax konjaci DSM 7481GCA_900112675scaffoldncbi32040

GC content

  • @ref: 3180
  • GC-content: 68.4
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.871no
anaerobicno98.436no
halophileno97.189no
spore-formingno92.528no
glucose-utilyes72.057yes
flagellatedyes62.164no
thermophileno98.546yes
aerobicyes95.839no
motileyes87.427no
glucose-fermentno91.103yes

External links

@ref: 3180

culture collection no.: DSM 7481, ATCC 33996, CCUG 17394, ICMP 7733, LMG 5691, JCM 2397, CIP 106439, CFBP 4460, NCPPB 3698

straininfo link

  • @ref: 72416
  • straininfo: 140

literature

  • topic: Phylogeny
  • Pubmed-ID: 28553696
  • title: Acidovorax lacteus sp. nov., isolated from a culture of a bloom-forming cyanobacterium (Microcystis sp.).
  • authors: Chun SJ, Cui Y, Ko SR, Lee HG, Srivastava A, Oh HM, Ahn CY
  • journal: Antonie Van Leeuwenhoek
  • DOI: 10.1007/s10482-017-0892-9
  • year: 2017
  • mesh: Base Composition, Comamonadaceae/chemistry/*classification/genetics/physiology, Enzymes/analysis, Eutrophication, Lakes/*microbiology, Microcystis/chemistry/classification/genetics/physiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Species Specificity
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3180Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7481)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7481
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
39525Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18570
46608Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 17394)https://www.ccug.se/strain?id=17394
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
72416Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID140.1StrainInfo: A central database for resolving microbial strain identifiers
120463Curators of the CIPCollection of Institut Pasteur (CIP 106439)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106439