Strain identifier
BacDive ID: 2891
Type strain:
Species: Acidovorax avenae
Strain history: CIP <- 2000, CCUG <- K. Kersters, LMG, Gent, Belgium <- NCPPB <- ICPB <- A. Ullstrup
NCBI tax ID(s): 80867 (species)
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
@ref | history |
---|---|
3062 | <- NCPPB <- ICPB <- A.J. Ullstrup |
67770 | IAM 13658 <-- NCPPB 1011 ("Pseudomonas alboprecipitans") <-- M. Starr PA 117 <-- A. J. Ullstrup. |
116660 | CIP <- 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
@ref synonym 20215 Phytomonas rubrilineans 20215 Paracidovorax avenae 20215 Pseudomonas avenae 20215 Pseudomonas 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
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | yes | 97.608 | ||
69480 | 99.997 | negative | ||
116660 | yes | negative | rod-shaped |
pigmentation
- @ref: 116660
- production: no
- name: Pyocyanin
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
3062 | REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) | yes | https://mediadive.dsmz.de/medium/1a | Name: 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 |
39547 | MEDIUM 3 - Columbia agar | yes | Columbia agar (39.000 g);distilled water (1000.000 ml) | |
116660 | CIP Medium 3 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
3062 | positive | growth | 25 | mesophilic |
39547 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 25 | mesophilic |
116660 | positive | growth | 25-41 | |
116660 | no | growth | 5 | psychrophilic |
116660 | no | growth | 10 | psychrophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 116660
- oxygen tolerance: obligate aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 97 |
69480 | no | 99.994 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
116660 | NaCl | positive | growth | 0-2 % |
116660 | NaCl | no | growth | 4 % |
116660 | NaCl | no | growth | 6 % |
116660 | NaCl | no | growth | 8 % |
116660 | NaCl | no | growth | 10 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68369 | 25115 | malate | + | assimilation |
68369 | 17128 | adipate | + | assimilation |
68369 | 27689 | decanoate | + | assimilation |
68369 | 24265 | gluconate | + | assimilation |
68369 | 17306 | maltose | - | assimilation |
68369 | 59640 | N-acetylglucosamine | - | assimilation |
68369 | 16899 | D-mannitol | + | assimilation |
68369 | 16024 | D-mannose | - | assimilation |
68369 | 30849 | L-arabinose | + | assimilation |
68369 | 17634 | D-glucose | + | assimilation |
68369 | 5291 | gelatin | - | hydrolysis |
68369 | 4853 | esculin | - | hydrolysis |
68369 | 16199 | urea | + | hydrolysis |
68369 | 29016 | arginine | - | hydrolysis |
68369 | 17634 | D-glucose | - | fermentation |
68369 | 27897 | tryptophan | - | energy source |
68369 | 17632 | nitrate | + | reduction |
116660 | 16947 | citrate | + | carbon source |
116660 | 4853 | esculin | - | hydrolysis |
116660 | 17632 | nitrate | + | reduction |
116660 | 16301 | nitrite | - | reduction |
116660 | 17632 | nitrate | - | 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
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68369 | 35581 | indole | no |
116660 | 35581 | indole | no |
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68369 | cytochrome oxidase | + | 1.9.3.1 |
68369 | gelatinase | - | |
68369 | beta-glucosidase | - | 3.2.1.21 |
68369 | urease | + | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
116660 | oxidase | + | |
116660 | beta-galactosidase | - | 3.2.1.23 |
116660 | alcohol dehydrogenase | - | 1.1.1.1 |
116660 | gelatinase | - | |
116660 | amylase | + | |
116660 | DNase | - | |
116660 | caseinase | + | 3.4.21.50 |
116660 | catalase | + | 1.11.1.6 |
116660 | tween esterase | + | |
116660 | lecithinase | + | |
116660 | lipase | - | |
116660 | lysine decarboxylase | - | 4.1.1.18 |
116660 | ornithine decarboxylase | - | 4.1.1.17 |
116660 | protease | + | |
116660 | tryptophan deaminase | - | |
116660 | urease | + | 3.5.1.5 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
116660 | - | + | + | + | + | + | - | - | - | - | + | + | - | - | - | - | - | - | - | - |
API 20NE
@ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
3062 | + | - | - | - | + | - | - | - | + | + | - | + | - | - | + | + | + | + | - | - | + |
3062 | + | - | - | - | + | - | - | - | + | + | - | + | - | - | + | + | + | + | - | - | + |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
116660 | + | + | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | + | + | - | - | + | - | + | - | - | - | - | + | - | + | - | - | + | - | - | - | - | - | - | - | - | - | + | - | + | + | + | + | - | + | + | - | - | - | + | - | + | - | - | - | - | + | - | - | - | - | - | - | - | + | - | + | + | - | + | + | + | + | - | + | - | - | - | - | + | + | + | + | + | + | + | - | + | + | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | country | origin.country | continent | sampling date | isolation date |
---|---|---|---|---|---|---|---|
3062 | Zea mays | Zea mays | USA | USA | North America | ||
46359 | Zea mays | USA | USA | North America | 1958 | ||
67770 | Zea mays | Zea mays | USA | USA | North America | ||
116660 | Zea mays | United States of America | USA | North America | 1958 |
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
@ref | pathogenicity plant | biosafety level | biosafety level comment |
---|---|---|---|
3062 | yes | 1 | Risk group (German classification) |
116660 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Acidovorax avenae subsp. avenae 16S ribosomal RNA gene, partial sequence | AF078759 | 1513 | ena | 643561 |
20218 | Acidovorax avenae subsp. avenae strain ATCC19860 16S-23S internal transcribed spacer, complete sequence | AY080997 | 619 | ena | 643561 |
20218 | Acidovorax avenae subsp. avenae strain FC-320 16S ribosomal RNA gene and 16S-23S ribosomal RNA intergenic spacer, partial sequence | EU368726 | 615 | ena | 643561 |
20218 | Acidovorax avenae subsp. avenae strain CIP 106500 16S ribosomal RNA gene, partial sequence | EU024134 | 1314 | ena | 80870 |
20218 | Acidovorax avenae subsp. avenae 16S ribosomal RNA gene, partial sequence | AF137505 | 1481 | ena | 80870 |
20218 | Acidovorax avenae strain ICMP 3183 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence | GU339096 | 898 | ena | 80867 |
20218 | Acidovorax avenae subsp. avenae strain BC523 16S ribosomal RNA gene, partial sequence | JQ743862 | 1426 | ena | 80870 |
20218 | Acidovorax 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 sequence | JQ743875 | 673 | ena | 80870 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Paracidovorax avenae ATCC 19860 | GCA_000176855 | complete | ncbi | 643561 |
66792 | Acidovorax avenae subsp. avenae ATCC 19860 | 643561.4 | complete | patric | 643561 |
66792 | Acidovorax avenae avenae ATCC 19860 | 650716004 | complete | img | 643561 |
GC content
- @ref: 3062
- GC-content: 69.8
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 97 | no |
motile | yes | 89.857 | no |
flagellated | yes | 69.178 | no |
gram-positive | no | 98.512 | no |
anaerobic | no | 98.206 | no |
aerobic | yes | 93.536 | no |
halophile | no | 95.871 | no |
spore-forming | no | 92.371 | no |
thermophile | no | 99.284 | no |
glucose-util | yes | 75.78 | yes |
glucose-ferment | no | 90.408 | yes |
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
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 23148096 | Description 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 P | Int J Syst Evol Microbiol | 10.1099/ijs.0.046102-0 | 2012 | Bacterial 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 Specificity | Genetics |
Phylogeny | 28553696 | Acidovorax 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 CY | Antonie Van Leeuwenhoek | 10.1007/s10482-017-0892-9 | 2017 | 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 | Enzymology |
30704011 | First Report of Corn Bacterial Leaf Stripe Caused by Acidovorax avenae in Guangdong Province, China. | Ji C, Ou J, Xu D, Pan R | Plant Dis | 10.1094/PDIS-03-14-0334-PDN | 2014 | |||
30708509 | First Report of Acidovorax avenae subsp. avenae Causing Sugarcane Red Stripe in Gabon. | Girard JC, Noell J, Larbre F, Roumagnac P, Rott P | Plant Dis | 10.1094/PDIS-09-13-0914-PDN | 2014 | |||
30731750 | First Report of Acidovorax avenae subsp. avenae Causing Bacterial Leaf Stripe of Strelitzia nicolai. | Seijo TE, Peres NA | Plant Dis | 10.1094/PDIS-03-11-0160 | 2011 | |||
Metabolism | 30985034 | Substrate 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 Y | Mol Microbiol | 10.1111/mmi.14259 | 2019 | Amino 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/metabolism | Enzymology |
Metabolism | 32448506 | Functional 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 H | Biochem Biophys Res Commun | 10.1016/j.bbrc.2020.05.094 | 2020 | Calorimetry, 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 Relationship | Enzymology |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
3062 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7227) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-7227 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
39547 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/18637 | ||||
46359 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 15838) | https://www.ccug.se/strain?id=15838 | |||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68369 | Automatically annotated from API 20NE | |||||
68382 | Automatically annotated from API zym | |||||
69479 | João 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 | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
72414 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID97.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
116660 | Curators of the CIP | Collection of Institut Pasteur (CIP 106500) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106500 |