Strain identifier
BacDive ID: 17920
Type strain: 
Species: Plasticicumulans acidivorans
Strain Designation: TUD-YJ37
Strain history: <- G. Muyzer, Dept. Biotechnol., Delft Univ. Technol., Netherlands; TUD-YJ37 <- Y. Jiang, Dept. Biotechnol., Delft Univ. Technol., Netherlands
NCBI tax ID(s): 886464 (species)
version 8.1 (current version)
General
@ref: 17298
BacDive-ID: 17920
DSM-Number: 23606
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile
description: Plasticicumulans acidivorans TUD-YJ37 is a mesophilic, motile bacterium that was isolated from laboratory reactor inoculated with wastewater from a sewage treatment plant and fed with acetate.
NCBI tax id
- NCBI tax id: 886464
- Matching level: species
strain history
- @ref: 17298
- history: <- G. Muyzer, Dept. Biotechnol., Delft Univ. Technol., Netherlands; TUD-YJ37 <- Y. Jiang, Dept. Biotechnol., Delft Univ. Technol., Netherlands
doi: 10.13145/bacdive17920.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Gammaproteobacteria, not assigned to order
- family: Competibacteraceae
- genus: Plasticicumulans
- species: Plasticicumulans acidivorans
- full scientific name: Plasticicumulans acidivorans Jiang et al. 2011
@ref: 17298
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Oceanospirillales
family: Gammaproteobacteria, not assigned to family
genus: Plasticicumulans
species: Plasticicumulans acidivorans
full scientific name: Plasticicumulans acidivorans Jiang et al. 2011
strain designation: TUD-YJ37
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 97.454 | |
| 69480 | 100 | negative |
multimedia
- @ref: 17298
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_23606.jpg
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
- @ref: 17298
- name: R2A MEDIUM (DSMZ Medium 830)
- growth: yes
- link: https://mediadive.dsmz.de/medium/830
- composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
culture temp
- @ref: 17298
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.996 |
compound production
- @ref: 17298
- compound: PHB - poly(ß-hydroxybutyrate)
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 |
metabolite production
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 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 |
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 17298 | + | - | - | - | + | + | - | - | - | - | - | - | - | - | - | - | + | - | - | + | + |
Isolation, sampling and environmental information
isolation
- @ref: 17298
- sample type: laboratory reactor inoculated with wastewater from a sewage treatment plant and fed with acetate
- geographic location: Rotterdam, Dokhaven
- country: Netherlands
- origin.country: NLD
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Bioreactor | |
| #Engineered | #Laboratory | |
| #Engineered | #Waste | #Wastewater |
| #Engineered | #Waste | #Water treatment plant |
Safety information
risk assessment
- @ref: 17298
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 17298
- description: Plasticicumulans acidivorans strain TUD-YJ37 16S ribosomal RNA gene, partial sequence
- accession: GU206550
- length: 1491
- database: ena
- NCBI tax ID: 886464
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Plasticicumulans acidivorans DSM 23606 | GCA_003182095 | scaffold | ncbi | 886464 |
| 66792 | Plasticicumulans acidivorans strain DSM 23606 | 886464.6 | wgs | patric | 886464 |
| 66792 | Plasticicumulans acidivorans DSM 23606 | 2756170267 | draft | img | 886464 |
GC content
- @ref: 17298
- GC-content: 67.4
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| flagellated | yes | 74.632 | no |
| gram-positive | no | 99.281 | no |
| anaerobic | no | 79.702 | no |
| halophile | no | 90.217 | no |
| spore-forming | no | 95.51 | no |
| glucose-util | yes | 71.135 | no |
| aerobic | yes | 52.88 | no |
| thermophile | no | 97.423 | no |
| motile | yes | 87.412 | no |
| glucose-ferment | no | 87.852 | yes |
External links
@ref: 17298
culture collection no.: DSM 23606, CBS 122990
straininfo link
- @ref: 86909
- straininfo: 401519
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 20971833 | Plasticicumulans acidivorans gen. nov., sp. nov., a polyhydroxyalkanoate-accumulating gammaproteobacterium from a sequencing-batch bioreactor. | Jiang Y, Sorokin DY, Kleerebezem R, Muyzer G, van Loosdrecht M | Int J Syst Evol Microbiol | 10.1099/ijs.0.021410-0 | 2010 | Aerobiosis, Base Composition, Bioreactors/*microbiology, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Flagella/physiology, Gammaproteobacteria/*classification/genetics/*isolation & purification/physiology, Hydrogen-Ion Concentration, Locomotion, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Polyhydroxyalkanoates/*metabolism, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Temperature | Genetics |
| Phylogeny | 24002473 | Plasticicumulans lactativorans sp. nov., a polyhydroxybutyrate-accumulating gammaproteobacterium from a sequencing-batch bioreactor fed with lactate. | Jiang Y, Sorokin DY, Junicke H, Kleerebezem R, van Loosdrecht MCM | Int J Syst Evol Microbiol | 10.1099/ijs.0.051045-0 | 2013 | Bacterial Typing Techniques, Base Composition, Bioreactors/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gammaproteobacteria/*classification/genetics/isolation & purification, Hydroxybutyrates/*metabolism, Lactic Acid/*chemistry, Molecular Sequence Data, Netherlands, Phospholipids/chemistry, *Phylogeny, Polyesters/*metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/microbiology, Vitamin K 2/analogs & derivatives/chemistry | Metabolism |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 17298 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23606) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23606 | |||
| 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 | |||
| 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 | |||||
| 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 | |||
| 86909 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID401519.1 | StrainInfo: A central database for resolving microbial strain identifiers |