Strain identifier
BacDive ID: 17932
Type strain: 
Species: Roseateles toxinivorans
Strain Designation: 2C20
Strain history: <- C. Lyra <- K. Lahti, Finnish Environment Institute; 2C20
NCBI tax ID(s): 270368 (species)
version 9.3 (current version)
General
@ref: 6681
BacDive-ID: 17932
DSM-Number: 16998
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Roseateles toxinivorans 2C20 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sediment of eutrophic lake.
NCBI tax id
- NCBI tax id: 270368
- Matching level: species
strain history
- @ref: 6681
- history: <- C. Lyra <- K. Lahti, Finnish Environment Institute; 2C20
doi: 10.13145/bacdive17932.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Sphaerotilaceae
- genus: Roseateles
- species: Roseateles toxinivorans
- full scientific name: Roseateles toxinivorans (Rapala et al. 2005) Liu et al. 2023
synonyms
- @ref: 20215
- synonym: Paucibacter toxinivorans
@ref: 6681
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Comamonadaceae
genus: Paucibacter
species: Paucibacter toxinivorans
full scientific name: Paucibacter toxinivorans Rapala et al. 2005
strain designation: 2C20
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 31455 | negative | 3.15 µm | 0.6 µm | rod-shaped | yes | |
| 125439 | negative | 99.2 | ||||
| 125438 | negative | 98.5 |
pigmentation
- @ref: 31455
- production: no
Culture and growth conditions
culture medium
- @ref: 6681
- 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 | growth | type | temperature |
|---|---|---|---|
| 6681 | positive | growth | 28 |
| 31455 | positive | growth | 20-30 |
| 31455 | positive | optimum | 25 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 31455 | aerobe | |
| 125439 | obligate aerobe | 94.4 |
spore formation
- @ref: 125439
- spore formation: no
- confidence: 98.9
observation
- @ref: 31455
- observation: aggregates in clumps
metabolite utilization
- @ref: 31455
- Chebi-ID: 53423
- metabolite: tween 40
- utilization activity: +
- kind of utilization tested: carbon source
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 31455 | acid phosphatase | + | 3.1.3.2 |
| 31455 | alkaline phosphatase | + | 3.1.3.1 |
| 31455 | catalase | + | 1.11.1.6 |
| 31455 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
- @ref: 6681
- sample type: sediment of eutrophic lake
- geographic location: Helsinki
- country: Finland
- origin.country: FIN
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Lake (large) |
| #Environmental | #Aquatic | #Sediment |
Safety information
risk assessment
- @ref: 6681
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 6681
- description: Paucibacter toxinivorans strain 2C20 16S ribosomal RNA gene, partial sequence
- accession: AY515390
- length: 1429
- database: nuccore
- NCBI tax ID: 270368
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Paucibacter toxinivorans DSM 16998 | GCA_004362525 | scaffold | ncbi | 270368 |
| 66792 | Paucibacter toxinivorans strain DSM 16998 | 270368.3 | wgs | patric | 270368 |
| 66792 | Paucibacter toxinivorans DSM 16998 | 2770939507 | draft | img | 270368 |
GC content
| @ref | GC-content |
|---|---|
| 6681 | 66.9 |
| 31455 | 66.1 |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 98.5 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 95.749 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 88.206 | yes |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 86.632 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 97.87 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 81.512 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 98.9 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 84.2 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 99.2 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 94.4 |
External links
@ref: 6681
culture collection no.: DSM 16998, HAMBI 2767, KCTC 42569, VYH 193597
straininfo link
- @ref: 86921
- straininfo: 265401
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 16014482 | Paucibacter toxinivorans gen. nov., sp. nov., a bacterium that degrades cyclic cyanobacterial hepatotoxins microcystins and nodularin. | Rapala J, Berg KA, Lyra C, Niemi RM, Manz W, Suomalainen S, Paulin L, Lahti K | Int J Syst Evol Microbiol | 10.1099/ijs.0.63599-0 | 2005 | Bacterial Toxins/*metabolism, Betaproteobacteria/chemistry/*classification/*genetics/metabolism, Biodegradation, Environmental, Cyanobacteria/metabolism/pathogenicity, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fresh Water/microbiology, Genes, rRNA, Geologic Sediments/microbiology, Microcystins, Molecular Sequence Data, Peptides, Cyclic/*metabolism, Phenotype, Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNA, Species Specificity | Metabolism |
| Phylogeny | 28671521 | Paucibacter oligotrophus sp. nov., isolated from fresh water, and emended description of the genus Paucibacter. | Pheng S, Lee JJ, Eom MK, Lee KH, Kim SG | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001931 | 2017 | Bacterial Typing Techniques, Base Composition, Burkholderiaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone/chemistry | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
|---|---|---|---|---|---|---|---|
| 6681 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16998) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-16998 | ||||
| 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 | ||||
| 31455 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 27757 | 28776041 | ||
| 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 | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
| 86921 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID265401.1 | StrainInfo: A central database for resolving microbial strain identifiers | ||||
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | 10.1101/2024.08.12.607695 | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | ||||
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | https://github.com/GenomeNet/deepG | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 |