Strain identifier
BacDive ID: 13096
Type strain:
Species: Pseudomonas rhizosphaerae
Strain Designation: IH5
Strain history: CIP <- 2004, CECT <- A. Peix, CSIC, Salamanca, Spain: strain IH5
NCBI tax ID(s): 216142 (species)
General
@ref: 6349
BacDive-ID: 13096
DSM-Number: 16299
keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, motile
description: Pseudomonas rhizosphaerae IH5 is an obligate aerobe, mesophilic, motile bacterium that was isolated from rhizosphere of grasses.
NCBI tax id
- NCBI tax id: 216142
- Matching level: species
strain history
@ref | history |
---|---|
6349 | <- E. Velázquez; IH5 <- A. Peix |
122211 | CIP <- 2004, CECT <- A. Peix, CSIC, Salamanca, Spain: strain IH5 |
doi: 10.13145/bacdive13096.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Pseudomonadales
- family: Pseudomonadaceae
- genus: Pseudomonas
- species: Pseudomonas rhizosphaerae
- full scientific name: Pseudomonas rhizosphaerae Peix et al. 2003
@ref: 6349
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Pseudomonadales
family: Pseudomonadaceae
genus: Pseudomonas
species: Pseudomonas rhizosphaerae
full scientific name: Pseudomonas rhizosphaerae Peix et al. 2003
strain designation: IH5
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | yes | 96.374 | ||
69480 | 99.995 | negative | ||
122211 | yes | negative | rod-shaped |
pigmentation
- @ref: 122211
- production: no
- name: Pyocyanin
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
6349 | NUTRIENT AGAR (DSMZ Medium 1) | yes | https://mediadive.dsmz.de/medium/1 | Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water |
32908 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
122211 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 | |
122211 | CIP Medium 328 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
6349 | positive | growth | 25 | mesophilic |
32908 | positive | growth | 30 | mesophilic |
122211 | positive | growth | 5-30 | |
122211 | no | growth | 37 | mesophilic |
122211 | no | growth | 41 | thermophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 122211
- oxygen tolerance: obligate aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.997 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
122211 | NaCl | positive | growth | 0-6 % |
122211 | NaCl | no | growth | 8 % |
122211 | 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 |
122211 | 16947 | citrate | - | carbon source |
122211 | 4853 | esculin | - | hydrolysis |
122211 | 17632 | nitrate | - | reduction |
122211 | 16301 | nitrite | - | reduction |
122211 | 17632 | nitrate | - | respiration |
antibiotic resistance
- @ref: 122211
- 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 |
122211 | 35581 | indole | 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 |
122211 | oxidase | - | |
122211 | beta-galactosidase | - | 3.2.1.23 |
122211 | alcohol dehydrogenase | - | 1.1.1.1 |
122211 | gelatinase | - | |
122211 | amylase | + | |
122211 | DNase | - | |
122211 | caseinase | - | 3.4.21.50 |
122211 | catalase | + | 1.11.1.6 |
122211 | tween esterase | - | |
122211 | lecithinase | - | |
122211 | lipase | - | |
122211 | lysine decarboxylase | - | 4.1.1.18 |
122211 | ornithine decarboxylase | - | 4.1.1.17 |
122211 | protease | - | |
122211 | tryptophan deaminase | - | |
122211 | urease | - | 3.5.1.5 |
68382 | alkaline phosphatase | - | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | + | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
122211 | - | - | + | + | - | + | + | - | - | - | + | + | - | - | - | - | - | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
6349 | - | - | - | - | - | - | - | - | + | + | + | + | - | - | + | + | - | + | + | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
122211 | + | + | + | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | + | - | - | - | - | - | + | - | - | - | - | + | - | + | - | - | + | - | - | - | - | - | - | + | + | - | - | + | + | + | + | + | - | + | + | + | + | - | - | - | + | - | + | + | + | - | - | - | - | - | + | + | - | + | - | + | + | + | - | + | + | + | - | + | - | - | - | + | - | + | + | + | + | + | + | - | + | - | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | sampling date | isolation date |
---|---|---|---|---|---|---|---|
6349 | rhizosphere of grasses | Salamanca | Spain | ESP | Europe | ||
59228 | Rhizosphere of grasses | Salamanca | Spain | ESP | Europe | 1997 | |
122211 | Environment, Soil | Salamanca | Spain | ESP | Europe | 1997 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Plants | #Herbaceous plants (Grass,Crops) |
#Host Body-Site | #Plant | #Rhizosphere |
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
6349 | 1 | Risk group (German classification) |
122211 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 6349
- description: Pseudomonas rhizosphaerae 16S ribosomal RNA gene, complete sequence
- accession: AY152673
- length: 1531
- database: ena
- NCBI tax ID: 216142
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Pseudomonas rhizosphaerae DSM 16299 | GCA_000761155 | complete | ncbi | 216142 |
66792 | Pseudomonas rhizosphaerae DSM 16299 | 216142.3 | complete | patric | 216142 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 90.055 | no |
flagellated | yes | 68.466 | no |
gram-positive | no | 98.12 | no |
anaerobic | no | 98.206 | no |
aerobic | yes | 94.125 | no |
halophile | no | 89.775 | no |
spore-forming | no | 95.092 | no |
glucose-util | yes | 91.576 | no |
glucose-ferment | no | 90.193 | yes |
thermophile | no | 99.551 | yes |
External links
@ref: 6349
culture collection no.: CCUG 51518, CIP 108243, DSM 16299, CECT 5726, LMG 21640
straininfo link
- @ref: 82306
- straininfo: 87494
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 14657147 | Pseudomonas rhizosphaerae sp. nov., a novel species that actively solubilizes phosphate in vitro. | Peix A, Rivas R, Mateos PF, Martinez-Molina E, Rodriguez-Barrueco C, Velazquez E | Int J Syst Evol Microbiol | 10.1099/ijs.0.02703-0 | 2003 | Base Composition, Burkholderia/classification, Catalase/metabolism, Molecular Sequence Data, Phosphates/*metabolism, *Phylogeny, Pseudomonas/*classification/genetics/isolation & purification/metabolism, RNA, Bacterial/chemistry/genetics, RNA, Ribosomal, 16S/genetics | Metabolism |
Phylogeny | 15143034 | Pseudomonas lutea sp. nov., a novel phosphate-solubilizing bacterium isolated from the rhizosphere of grasses. | Peix A, Rivas R, Santa-Regina I, Mateos PF, Martinez-Molina E, Rodriguez-Barrueco C, Velazquez E | Int J Syst Evol Microbiol | 10.1099/ijs.0.02966-0 | 2004 | Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Molecular Sequence Data, Phenotype, Phosphates/metabolism, Phylogeny, Poaceae/microbiology, Pseudomonas/*classification/genetics/*isolation & purification/metabolism, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Solubility, Spain | Genetics |
Genetics | 25483321 | Complete genome sequence of Pseudomonas rhizosphaerae IH5T (=DSM 16299T), a phosphate-solubilizing rhizobacterium for bacterial biofertilizer. | Kwak Y, Jung BK, Shin JH | J Biotechnol | 10.1016/j.jbiotec.2014.11.031 | 2014 | *Biofuels, Bioreactors/microbiology, Genome, Bacterial/*genetics, Hydrolysis, Molecular Sequence Data, Phosphates, Pseudomonas/*genetics/*metabolism, Sequence Analysis, DNA, Sewage | Transcriptome |
Phylogeny | 33620302 | Pseudomonas kielensis sp. nov. and Pseudomonas baltica sp. nov., isolated from raw milk in Germany. | Gieschler S, Fiedler G, Bohnlein C, Grimmler C, Franz CMAP, Kabisch J | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004717 | 2021 |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
6349 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16299) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-16299 | |||
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 | |||
32908 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/5844 | ||||
59228 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 51518) | https://www.ccug.se/strain?id=51518 | |||
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 | |||
82306 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID87494.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
122211 | Curators of the CIP | Collection of Institut Pasteur (CIP 108243) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108243 |