Strain identifier
BacDive ID: 140983
Type strain:
Species: Pseudomonas reidholzensis
Strain Designation: ID3
Strain history: CIP <- 2017, CCOS <- M. Opoku, ZHAW, Wädenswil, Switzerland: strain ID3
NCBI tax ID(s): 1785162 (species)
General
@ref: 43871
BacDive-ID: 140983
keywords: genome sequence, 16S sequence, Bacteria, aerobe, chemoorganotroph, Gram-negative, motile, rod-shaped
description: Pseudomonas reidholzensis ID3 is an aerobe, chemoorganotroph, Gram-negative bacterium that was isolated from soil sample of Reidholz forest between the cities Wädenswil and Richterswil, Switzerland.
NCBI tax id
- NCBI tax id: 1785162
- Matching level: species
strain history
- @ref: 122151
- history: CIP <- 2017, CCOS <- M. Opoku, ZHAW, Wädenswil, Switzerland: strain ID3
doi: 10.13145/bacdive140983.20230509.8.1
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 reidholzensis
- full scientific name: Pseudomonas reidholzensis Frasson et al. 2017
@ref: 43871
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Pseudomonadales
family: Pseudomonadaceae
genus: Pseudomonas
species: Pseudomonas reidholzensis
strain designation: ID3
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
43871 | negative | 1.0-2.2 µm | 0.5-0.9 µm | rod-shaped | yes | |
69480 | yes | 95.887 | ||||
69480 | negative | 99.99 | ||||
122151 | negative | rod-shaped |
pigmentation
- @ref: 43871
- production: yes
- name: Fluorescent pigment
Culture and growth conditions
culture medium
@ref | name | growth | link |
---|---|---|---|
43871 | King's medium B | yes | |
43871 | LB (Luria-Bertani) MEDIUM | yes | |
43871 | Reasoner's 2A agar (R2A) | yes | |
122151 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
43871 | positive | growth | 4-37 | |
43871 | positive | optimum | 25-30 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 43871
- oxygen tolerance: aerobe
nutrition type
- @ref: 43871
- type: chemoorganotroph
spore formation
@ref | spore formation | confidence |
---|---|---|
43871 | no | |
69481 | no | 100 |
69480 | no | 99.963 |
halophily
- @ref: 43871
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-6 %(w/v)
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
43871 | 18401 | phenylacetate | - | assimilation |
43871 | 18101 | 4-hydroxyphenylacetic acid | - | carbon source |
43871 | 18333 | D-arabitol | - | carbon source |
43871 | 18024 | D-galacturonic acid | - | carbon source |
43871 | 15748 | D-glucuronate | - | carbon source |
43871 | 16899 | D-mannitol | - | carbon source |
43871 | 16523 | D-serine | - | carbon source |
43871 | 17596 | inosine | - | carbon source |
43871 | 30849 | L-arabinose | - | carbon source |
43871 | 18183 | L-pyroglutamic acid | - | carbon source |
43871 | 30860 | methylmalonic acid | - | carbon source |
43871 | 506227 | N-acetylglucosamine | - | carbon source |
43871 | 17992 | sucrose | - | carbon source |
43871 | 18101 | 4-hydroxyphenylacetic acid | - | growth |
43871 | 18183 | L-pyroglutamic acid | - | growth |
43871 | skimmed milk | - | hydrolysis | |
43871 | 17632 | nitrate | - | reduction |
43871 | 30916 | 2-oxoglutarate | + | carbon source |
43871 | 18240 | 4-hydroxy-L-proline | + | carbon source |
43871 | 17925 | alpha-D-glucose | + | carbon source |
43871 | 8295 | beta-hydroxybutyrate | + | carbon source |
43871 | 73706 | bromosuccinate | + | carbon source |
43871 | 27689 | decanoate | + | carbon source |
43871 | 16383 | cis-aconitate | + | carbon source |
43871 | 16947 | citrate | + | carbon source |
43871 | 15570 | D-alanine | + | carbon source |
43871 | 8391 | D-gluconate | + | carbon source |
43871 | 33801 | D-saccharate | + | carbon source |
43871 | 17126 | DL-carnitine | + | carbon source |
43871 | 24996 | lactate | + | carbon source |
43871 | 16000 | ethanolamine | + | carbon source |
43871 | 16865 | gamma-aminobutyric acid | + | carbon source |
43871 | 17234 | glucose | + | carbon source |
43871 | 32323 | glucuronamide | + | carbon source |
43871 | 17754 | glycerol | + | carbon source |
43871 | 21217 | L-alaninamide | + | carbon source |
43871 | L-alanine 4-nitroanilide | + | carbon source | |
43871 | 29991 | L-aspartate | + | carbon source |
43871 | 29985 | L-glutamate | + | carbon source |
43871 | 15971 | L-histidine | + | carbon source |
43871 | 15603 | L-leucine | + | carbon source |
43871 | 17203 | L-proline | + | carbon source |
43871 | 17115 | L-serine | + | carbon source |
43871 | 25115 | malate | + | carbon source |
43871 | 51850 | methyl pyruvate | + | carbon source |
43871 | 32032 | potassium gluconate | + | carbon source |
43871 | 17272 | propionate | + | carbon source |
43871 | 17148 | putrescine | + | carbon source |
43871 | 26490 | quinate | + | carbon source |
43871 | 53258 | sodium citrate | + | carbon source |
43871 | 30031 | succinate | + | carbon source |
43871 | 53426 | tween 80 | + | carbon source |
43871 | 17992 | sucrose | + | growth |
43871 | 4853 | esculin | + | hydrolysis |
43871 | 17234 | glucose | + | oxidation |
43871 | 28053 | melibiose | + | oxidation |
enzymes
@ref | value | activity | ec |
---|---|---|---|
43871 | cytochrome oxidase | + | 1.9.3.1 |
43871 | catalase | + | 1.11.1.6 |
43871 | arginine dihydrolase | + | 3.5.3.6 |
43871 | tryptophan deaminase | + | 4.1.99.1 |
43871 | gelatinase | + | |
43871 | esterase (C 4) | + | |
43871 | leucine arylamidase | + | 3.4.11.1 |
43871 | acid phosphatase | + | 3.1.3.2 |
43871 | naphthol-AS-BI-phosphohydrolase | + |
fatty acid profile
fatty acids
@ref fatty acid percentage 43871 C10:0 3OH 0.62 43871 C12:0 2OH 0.3 43871 C14:0 0.6 43871 C16:0 34.23 43871 C16:1ω7c / C16:1ω6c 36.64 43871 C17:0 0.52 43871 C17:0 cyclo 5.11 43871 C17:1ω8c 0.35 43871 C18:0 0.59 43871 C18:1ω7c 16.87 43871 C17:0 iso - type of FA analysis: whole cell analysis
- incubation medium: Tryptic soy agar
- agar/liquid: agar
- incubation temperature: 28
- incubation time: 2
- software version: Sherlock 6.1
- library/peak naming table: ITSA1 1.10
- system: MIS MIDI
- instrument: Hewlett Packard HP 6890 gas chromatograph
- method/protocol: Sasser, 1990
- cutoff value:
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | latitude | longitude | enrichment culture | isolation date |
---|---|---|---|---|---|---|---|---|---|
43871 | soil sample of Reidholz forest between the cities Wädenswil and Richterswil, Switzerland | Reidholz forest | Switzerland | CHE | Europe | 47.2167 | 8.68333 | King's B medium | |
122151 | Environment, Forest soil | Reidholz Forest, Wädenswil | Switzerland | CHE | Europe | 2014-06-30 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Forest |
#Environmental | #Terrestrial | #Soil |
taxonmaps
- @ref: 69479
- File name: preview.99_239.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_61;97_89;98_203;99_239&stattab=map
- Last taxonomy: Pseudomonas
- 16S sequence: LT009707
- Sequence Identity:
- Total samples: 2133
- soil counts: 368
- aquatic counts: 543
- animal counts: 799
- plant counts: 423
Safety information
risk assessment
- @ref: 122151
- biosafety level: 1
- biosafety level comment: Risk group (French classification)
Sequence information
16S sequences
- @ref: 43871
- description: 16S rRNA gene sequence
- accession: LT009707
- database: nuccore
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Pseudomonas reidholzensis CCOS 865 | GCA_900536025 | contig | ncbi | 1785162 |
66792 | Pseudomonas reidholzensis strain CCOS 865 | 1785162.3 | wgs | patric | 1785162 |
GC content
- @ref: 43871
- GC-content: 63.8
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 92.821 | yes |
gram-positive | no | 98.602 | yes |
anaerobic | no | 97.994 | yes |
aerobic | yes | 92.276 | no |
halophile | no | 87.133 | no |
spore-forming | no | 95.541 | yes |
thermophile | no | 99.896 | yes |
glucose-util | yes | 90.798 | no |
flagellated | yes | 84.064 | no |
glucose-ferment | no | 87.02 | no |
External links
@ref: 43871
culture collection no.: LMG 29328, CCOS 865, CIP 111525
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 28820109 | Pseudomonas wadenswilerensis sp. nov. and Pseudomonas reidholzensis sp. nov., two novel species within the Pseudomonas putida group isolated from forest soil. | Frasson D, Opoku M, Picozzi T, Torossi T, Balada S, Smits THM, Hilber U | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002035 | 2017 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Multilocus Sequence Typing, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, Pseudomonas/*classification/genetics/isolation & purification, Pseudomonas putida, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Switzerland, Ubiquinone/chemistry | Transcriptome |
Genetics | 30687835 | High-Quality Draft Genome Sequence of Pseudomonas reidholzensis Strain CCOS 865(T). | Rutz D, Frasson D, Sievers M, Blom J, Rezzonico F, Pothier JF, Smits THM | Microbiol Resour Announc | 10.1128/MRA.01502-18 | 2019 |
Reference
@id | authors | title | doi/url | journal | pubmed | 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 | |||
43871 | David Frasson, Michael Opoku, Tara Picozzi, Tanja Torossi, Stefanie Balada, Theo H. M. Smits, Urs Hilber | Pseudomonas wadenswilerensis sp. nov. and Pseudomonas reidholzensis sp. nov., two novel species within the Pseudomonas putida group isolated from forest soil | 10.1099/ijsem.0.002035 | IJSEM 67: 2853-2861 2017 | 28820109 | |
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 | |||
69479 | João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |||
122151 | Curators of the CIP | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20111525 | Collection of Institut Pasteur (CIP 111525) |