Strain identifier

BacDive ID: 2891

Type strain: Yes

Species: Acidovorax avenae

Strain history: CIP <- 2000, CCUG <- K. Kersters, LMG, Gent, Belgium <- NCPPB <- ICPB <- A. Ullstrup

NCBI tax ID(s): 80867 (species)

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General

@ref: 3062

BacDive-ID: 2891

DSM-Number: 7227

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

description: Acidovorax avenae DSM 7227 is an obligate aerobe, mesophilic, motile plant pathogen that was isolated from Zea mays.

NCBI tax id

  • NCBI tax id: 80867
  • Matching level: species

strain history

@refhistory
3062<- NCPPB <- ICPB <- A.J. Ullstrup
67770IAM 13658 <-- NCPPB 1011 ("Pseudomonas alboprecipitans") <-- M. Starr PA 117 <-- A. J. Ullstrup.
116660CIP <- 2000, CCUG <- K. Kersters, LMG, Gent, Belgium <- NCPPB <- ICPB <- A. Ullstrup

doi: 10.13145/bacdive2891.20230509.8.1

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 avenae
  • full scientific name: Acidovorax avenae (Manns 1909) Willems et al. 1992

  • synonyms

    @refsynonym
    20215Phytomonas rubrilineans
    20215Paracidovorax avenae
    20215Pseudomonas avenae
    20215Pseudomonas rubrilineans

@ref: 3062

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Acidovorax

species: Acidovorax avenae

full scientific name: Acidovorax avenae (Manns 1909) Willems et al. 1992 emend. Schaad et al. 2008

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes97.608
6948099.997negative
116660yesnegativerod-shaped

pigmentation

  • @ref: 116660
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3062REACTIVATION 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
39547MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
116660CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
3062positivegrowth25mesophilic
39547positivegrowth30mesophilic
67770positivegrowth25mesophilic
116660positivegrowth25-41
116660nogrowth5psychrophilic
116660nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116660
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no97
69480no99.994

halophily

@refsaltgrowthtested relationconcentration
116660NaClpositivegrowth0-2 %
116660NaClnogrowth4 %
116660NaClnogrowth6 %
116660NaClnogrowth8 %
116660NaClnogrowth10 %

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
11666016947citrate+carbon source
1166604853esculin-hydrolysis
11666017632nitrate+reduction
11666016301nitrite-reduction
11666017632nitrate-respiration

antibiotic resistance

  • @ref: 116660
  • 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
11666035581indoleno

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
116660oxidase+
116660beta-galactosidase-3.2.1.23
116660alcohol dehydrogenase-1.1.1.1
116660gelatinase-
116660amylase+
116660DNase-
116660caseinase+3.4.21.50
116660catalase+1.11.1.6
116660tween esterase+
116660lecithinase+
116660lipase-
116660lysine decarboxylase-4.1.1.18
116660ornithine decarboxylase-4.1.1.17
116660protease+
116660tryptophan deaminase-
116660urease+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
116660-+++++----++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
3062+---+---++-+--++++--+
3062+---+---++-+--++++--+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116660+++----------------+++--+-+----+-+--+---------+-++++-++---+-+----+-------+-++-++++-+----+++++++-+++

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentsampling dateisolation date
3062Zea maysZea maysUSAUSANorth America
46359Zea maysUSAUSANorth America1958
67770Zea maysZea maysUSAUSANorth America
116660Zea maysUnited States of AmericaUSANorth America1958

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_1323.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_491;97_560;98_1048;99_1323&stattab=map
  • Last taxonomy: Acidovorax
  • 16S sequence: JQ743862
  • Sequence Identity:
  • Total samples: 45753
  • soil counts: 16355
  • aquatic counts: 12286
  • animal counts: 6685
  • plant counts: 10427

Safety information

risk assessment

@refpathogenicity plantbiosafety levelbiosafety level comment
3062yes1Risk group (German classification)
1166601Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Acidovorax avenae subsp. avenae 16S ribosomal RNA gene, partial sequenceAF0787591513ena643561
20218Acidovorax avenae subsp. avenae strain ATCC19860 16S-23S internal transcribed spacer, complete sequenceAY080997619ena643561
20218Acidovorax avenae subsp. avenae strain FC-320 16S ribosomal RNA gene and 16S-23S ribosomal RNA intergenic spacer, partial sequenceEU368726615ena643561
20218Acidovorax avenae subsp. avenae strain CIP 106500 16S ribosomal RNA gene, partial sequenceEU0241341314ena80870
20218Acidovorax avenae subsp. avenae 16S ribosomal RNA gene, partial sequenceAF1375051481ena80870
20218Acidovorax avenae strain ICMP 3183 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceGU339096898ena80867
20218Acidovorax avenae subsp. avenae strain BC523 16S ribosomal RNA gene, partial sequenceJQ7438621426ena80870
20218Acidovorax avenae subsp. avenae strain BC523 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceJQ743875673ena80870

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paracidovorax avenae ATCC 19860GCA_000176855completencbi643561
66792Acidovorax avenae subsp. avenae ATCC 19860643561.4completepatric643561
66792Acidovorax avenae avenae ATCC 19860650716004completeimg643561

GC content

  • @ref: 3062
  • GC-content: 69.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno97no
motileyes89.857no
flagellatedyes69.178no
gram-positiveno98.512no
anaerobicno98.206no
aerobicyes93.536no
halophileno95.871no
spore-formingno92.371no
thermophileno99.284no
glucose-utilyes75.78yes
glucose-fermentno90.408yes

External links

@ref: 3062

culture collection no.: DSM 7227, ATCC 19860, ICMP 3183, ICPB PA117, NCPPB 1011, CCUG 15838, LMG 2117, CIP 106500, JCM 20985, CFBP 2425, IAM 13658

straininfo link

  • @ref: 72414
  • straininfo: 97

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23148096Description of Acidovorax wautersii sp. nov. to accommodate clinical isolates and an environmental isolate, most closely related to Acidovorax avenae.Vaneechoutte M, Janssens M, Avesani V, Delmee M, Deschaght PInt J Syst Evol Microbiol10.1099/ijs.0.046102-02012Bacterial Typing Techniques, Base Composition, Comamonadaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Genotype, Humans, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny28553696Acidovorax lacteus sp. nov., isolated from a culture of a bloom-forming cyanobacterium (Microcystis sp.).Chun SJ, Cui Y, Ko SR, Lee HG, Srivastava A, Oh HM, Ahn CYAntonie Van Leeuwenhoek10.1007/s10482-017-0892-92017Base 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 SpecificityEnzymology
30704011First Report of Corn Bacterial Leaf Stripe Caused by Acidovorax avenae in Guangdong Province, China.Ji C, Ou J, Xu D, Pan RPlant Dis10.1094/PDIS-03-14-0334-PDN2014
30708509First Report of Acidovorax avenae subsp. avenae Causing Sugarcane Red Stripe in Gabon.Girard JC, Noell J, Larbre F, Roumagnac P, Rott PPlant Dis10.1094/PDIS-09-13-0914-PDN2014
30731750First Report of Acidovorax avenae subsp. avenae Causing Bacterial Leaf Stripe of Strelitzia nicolai.Seijo TE, Peres NAPlant Dis10.1094/PDIS-03-11-01602011
Metabolism30985034Substrate and metabolic promiscuities of d-altronate dehydratase family proteins involved in non-phosphorylative d-arabinose, sugar acid, l-galactose and l-fucose pathways from bacteria.Watanabe S, Fukumori F, Watanabe YMol Microbiol10.1111/mmi.142592019Amino Acid Sequence/genetics, Arabinose/metabolism, Cloning, Molecular/methods, Fucose/metabolism, Galactose/metabolism, Genome, Bacterial/genetics, Gluconates/metabolism, Herbaspirillum/genetics/metabolism, Hydro-Lyases/*genetics/*metabolism/physiology, Multigene Family/genetics, Sugar Acids/metabolismEnzymology
Metabolism32448506Functional and structural characterization of a novel L-fucose mutarotase involved in non-phosphorylative pathway of L-fucose metabolism.Watanabe Y, Watanabe S, Fukui Y, Nishiwaki HBiochem Biophys Res Commun10.1016/j.bbrc.2020.05.0942020Calorimetry, Carbohydrate Epimerases/*chemistry/*metabolism, Catalytic Domain, Comamonadaceae/enzymology, Crystallography, X-Ray, DNA Mutational Analysis, Evolution, Molecular, Fucose/chemistry/*metabolism, Magnetic Resonance Spectroscopy, Models, Molecular, Phosphorylation, Structure-Activity RelationshipEnzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3062Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7227)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7227
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
39547Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18637
46359Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 15838)https://www.ccug.se/strain?id=15838
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
72414Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID97.1StrainInfo: A central database for resolving microbial strain identifiers
116660Curators of the CIPCollection of Institut Pasteur (CIP 106500)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106500