Strain identifier
BacDive ID: 132756
Type strain: 
Species: Massilia sp.
Strain Designation: Root335
Strain history: <- P. Schulze-Lefert, Max Planck Institute for Plant Breeding Research, Cologne, Germany; Root335 <- Y. Bai
NCBI tax ID(s): 1882437 (species)
version 8.1 (current version)
General
@ref: 24546
BacDive-ID: 132756
DSM-Number: 102448
keywords: genome sequence, Bacteria, mesophilic
description: Massilia sp. Root335 is a mesophilic bacterium that was isolated from roots of Arabidopsis thaliana ecotype Shakdara .
NCBI tax id
- NCBI tax id: 1882437
- Matching level: species
strain history
- @ref: 24546
- history: <- P. Schulze-Lefert, Max Planck Institute for Plant Breeding Research, Cologne, Germany; Root335 <- Y. Bai
doi: 10.13145/bacdive132756.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Oxalobacteraceae
- genus: Massilia
- species: Massilia sp.
- full scientific name: Massilia La Scola et al. 2000
synonyms
@ref synonym 20215 Naxibacter 20215 Mokoshia
@ref: 24546
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Oxalobacteraceae
genus: Massilia
species: Massilia sp.
full scientific name: Massilia sp.
strain designation: Root335
type strain: no
Culture and growth conditions
culture medium
- @ref: 24546
- 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: 24546
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Physiology and metabolism
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 | 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 24546 | - | - | - | - | - | + | + | + | + | + | + | - | - | + | +/- | - | - | + | - | + | + |
Isolation, sampling and environmental information
isolation
- @ref: 24546
- sample type: roots of Arabidopsis thaliana ecotype Shakdara (Sha)
- host species: Arabidopsis thaliana
- geographic location: Cologne (50.958N 6.856E)
- country: Germany
- origin.country: DEU
- continent: Europe
- latitude: 50.958
- longitude: 6.856
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
| #Host Body-Site | #Plant | #Root (Rhizome) |
Sequence information
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Massilia sp. Root335 | GCA_001425685 | scaffold | ncbi | 1736517 |
| 66792 | Massilia sp. Root335 | 1736517.3 | wgs | patric | 1736517 |
| 66792 | Massilia sp. Root335 | 2713896890 | draft | img | 1736517 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| flagellated | yes | 69.291 | no |
| gram-positive | no | 98.644 | no |
| anaerobic | no | 99.155 | no |
| aerobic | yes | 91.245 | no |
| halophile | no | 95.493 | no |
| spore-forming | no | 92.661 | no |
| thermophile | no | 99.402 | yes |
| glucose-util | yes | 89.977 | no |
| motile | yes | 87.72 | no |
| glucose-ferment | no | 87.965 | no |
External links
@ref: 24546
culture collection no.: DSM 102448
straininfo link
- @ref: 91057
- straininfo: 406783
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |
| 24546 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-102448 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 102448) | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
| 68369 | Automatically annotated from API 20NE | |||
| 91057 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID406783.1 |