Strain identifier
BacDive ID: 2899
Type strain:
Species: Acidovorax valerianellae
Strain history: CIP <- 2003, M. Le Saux, INRA, Beaucouze, France
NCBI tax ID(s): 187868 (species)
General
@ref: 6527
BacDive-ID: 2899
DSM-Number: 16619
keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, motile, plant pathogen
description: Acidovorax valerianellae DSM 16619 is an obligate aerobe, mesophilic, motile plant pathogen that was isolated from lamb's lettuce .
NCBI tax id
- NCBI tax id: 187868
- Matching level: species
strain history
@ref | history |
---|---|
6527 | <- CFBP <- L. Gardan |
36674 | 2003, M. Le Saux, Beaucouze, France |
123786 | CIP <- 2003, M. Le Saux, INRA, Beaucouze, France |
doi: 10.13145/bacdive2899.20230509.8.1
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 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
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | yes | 96.625 | ||
69480 | 99.996 | negative | ||
123786 | yes | negative | rod-shaped |
pigmentation
- @ref: 123786
- production: no
- name: Pyocyanin
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
6527 | 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 |
36674 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
123786 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 | |
123786 | CIP Medium 568 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=568 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
6527 | positive | growth | 28 | mesophilic |
36674 | positive | growth | 25 | mesophilic |
123786 | positive | growth | 10-30 | |
123786 | no | growth | 5 | psychrophilic |
123786 | no | growth | 37 | mesophilic |
123786 | no | growth | 41 | thermophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 123786
- oxygen tolerance: obligate aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.998 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
123786 | NaCl | positive | growth | 0-2 % |
123786 | NaCl | no | growth | 4 % |
123786 | NaCl | no | growth | 6 % |
123786 | NaCl | no | growth | 8 % |
123786 | 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 |
123786 | 16947 | citrate | - | carbon source |
123786 | 4853 | esculin | - | hydrolysis |
123786 | 17632 | nitrate | - | reduction |
123786 | 16301 | nitrite | - | reduction |
123786 | 17632 | nitrate | - | respiration |
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
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68369 | 35581 | indole | no |
123786 | 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 |
123786 | oxidase | + | |
123786 | beta-galactosidase | - | 3.2.1.23 |
123786 | alcohol dehydrogenase | + | 1.1.1.1 |
123786 | gelatinase | - | |
123786 | amylase | + | |
123786 | DNase | - | |
123786 | caseinase | + | 3.4.21.50 |
123786 | catalase | + | 1.11.1.6 |
123786 | tween esterase | + | |
123786 | lecithinase | - | |
123786 | lipase | - | |
123786 | lysine decarboxylase | - | 4.1.1.18 |
123786 | ornithine decarboxylase | - | 4.1.1.17 |
123786 | protease | + | |
123786 | tryptophan deaminase | - | |
123786 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
123786 | - | + | + | + | - | + | - | - | - | - | - | + | - | - | - | - | - | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
6527 | - | - | - | - | + | - | - | - | - | - | - | - | - | - | + | - | + | + | - | - | + |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
123786 | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | + | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | + | + | + | + | - | - | - | - | - | - | + | + | + | + | - | - | + | - | - | + | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | country | origin.country | continent | isolation date |
---|---|---|---|---|---|---|
6527 | lamb's lettuce (Valerianella locusta) | Valerianella locusta | France | FRA | Europe | |
123786 | Valerianella locusta | France | FRA | Europe | 1993 |
isolation source categories
- Cat1: #Host
- Cat2: #Plants
- Cat3: #Herbaceous plants (Grass,Crops)
Safety information
risk assessment
@ref | pathogenicity plant | biosafety level | biosafety level comment |
---|---|---|---|
6527 | yes | 1 | Risk group (German classification) |
123786 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Acidovorax valerianellae strain DSM 16619 16S ribosomal RNA gene, partial sequence | KF931150 | 1520 | ena | 187868 |
20218 | Acidovorax valerianellae strain DSM 16619 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence | KF931155 | 691 | ena | 187868 |
6527 | Acidovorax valerianelle partial 16S rRNA gene, strain CFBP 4730 | AJ431731 | 1492 | ena | 187868 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Paracidovorax valerianellae DSM 16619 | GCA_900102625 | scaffold | ncbi | 187868 |
66792 | Acidovorax valerianellae strain DSM 16619 | 187868.3 | wgs | patric | 187868 |
66792 | Acidovorax valerianellae DSM 16619 | 2615840716 | draft | img | 187868 |
GC content
- @ref: 6527
- GC-content: 64.5
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 85.785 | no |
flagellated | yes | 64.382 | no |
gram-positive | no | 98.791 | no |
anaerobic | no | 98.258 | no |
aerobic | yes | 95.494 | no |
halophile | no | 96.894 | no |
spore-forming | no | 92.659 | no |
glucose-ferment | no | 91.37 | no |
thermophile | no | 98.54 | yes |
glucose-util | yes | 55.417 | yes |
External links
@ref: 6527
culture collection no.: DSM 16619, CFBP 4730, NCPPB 4283, CIP 107997
straininfo link
- @ref: 72422
- straininfo: 87882
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 12807202 | Acidovorax valerianellae sp. nov., a novel pathogen of lamb's lettuce [Valerianella locusta (L.) Laterr]. | Gardan L, Stead DE, Dauga C, Gillis M | Int J Syst Evol Microbiol | 10.1099/ijs.0.02404-0 | 2003 | Bacterial 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, Virulence | Genetics |
Phylogeny | 29627890 | Acidovorax monticola sp. nov., isolated from soil. | Chaudhary DK, Kim J | Antonie Van Leeuwenhoek | 10.1007/s10482-018-1083-z | 2018 | Base Composition, Betaproteobacteria/*classification/genetics/isolation & purification, Forests, Metabolomics/methods, Molecular Typing, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Soil Microbiology | Phenotype |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
6527 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16619) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-16619 | |||
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 | |
36674 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/5569 | ||||
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) | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
68369 | Automatically annotated from API 20NE | |||||
68382 | Automatically annotated from API zym | |||||
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 | |||
72422 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID87882.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
123786 | Curators of the CIP | Collection of Institut Pasteur (CIP 107997) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107997 |