Strain identifier
BacDive ID: 23182
Type strain: 
Species: Paenibacillus catalpae
Strain Designation: D75
Strain history: <- Y. Ma, Beijing Forestry Univ., College Biological Scs. and Biotechnol.; D75 <- Y. Ma and J. Zhang
NCBI tax ID(s): 1045775 (species)
version 9.1 (current version)
General
@ref: 19323
BacDive-ID: 23182
DSM-Number: 24714
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, Gram-positive, motile, rod-shaped
description: Paenibacillus catalpae D75 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from rhizosphere soil of Catalpa speciosa.
NCBI tax id
- NCBI tax id: 1045775
- Matching level: species
strain history
- @ref: 19323
- history: <- Y. Ma, Beijing Forestry Univ., College Biological Scs. and Biotechnol.; D75 <- Y. Ma and J. Zhang
doi: 10.13145/bacdive23182.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Paenibacillaceae
- genus: Paenibacillus
- species: Paenibacillus catalpae
- full scientific name: Paenibacillus catalpae Zhang et al. 2013
@ref: 19323
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Paenibacillaceae
genus: Paenibacillus
species: Paenibacillus catalpae
full scientific name: Paenibacillus catalpae Zhang et al. 2013
strain designation: D75
type strain: yes
Morphology
cell morphology
- @ref: 30629
- gram stain: positive
- cell length: 1.8 µm
- cell width: 0.65 µm
- cell shape: rod-shaped
- motility: yes
pigmentation
- @ref: 30629
- production: no
Culture and growth conditions
culture medium
- @ref: 19323
- name: CASO AGAR (MERCK 105458) (DSMZ Medium 220)
- growth: yes
- link: https://mediadive.dsmz.de/medium/220
- composition: Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 19323 | positive | growth | 30 |
| 30629 | positive | growth | 15-40 |
| 30629 | positive | optimum | 26.5 |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 30629 | positive | growth | 06-08 |
| 30629 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 30629
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 30629 | yes | |
| 69480 | yes | 92.95 |
| 69481 | yes | 99 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 30629 | NaCl | positive | growth | 0-2 % |
| 30629 | NaCl | positive | optimum | 0.75 % |
observation
- @ref: 30629
- observation: aggregates in clumps
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30629 | 17057 | cellobiose | + | carbon source |
| 30629 | 23652 | dextrin | + | carbon source |
| 30629 | 28260 | galactose | + | carbon source |
| 30629 | 24265 | gluconate | + | carbon source |
| 30629 | 17234 | glucose | + | carbon source |
| 30629 | 17754 | glycerol | + | carbon source |
| 30629 | 17716 | lactose | + | carbon source |
| 30629 | 25115 | malate | + | carbon source |
| 30629 | 17306 | maltose | + | carbon source |
| 30629 | 29864 | mannitol | + | carbon source |
| 30629 | 37684 | mannose | + | carbon source |
| 30629 | 28053 | melibiose | + | carbon source |
| 30629 | 37657 | methyl D-glucoside | + | carbon source |
| 30629 | 506227 | N-acetylglucosamine | + | carbon source |
| 30629 | 16634 | raffinose | + | carbon source |
| 30629 | 17992 | sucrose | + | carbon source |
| 30629 | 27082 | trehalose | + | carbon source |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 30629 | acid phosphatase | + | 3.1.3.2 |
| 30629 | alpha-galactosidase | + | 3.2.1.22 |
| 30629 | catalase | + | 1.11.1.6 |
| 30629 | urease | + | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
- @ref: 19323
- sample type: rhizosphere soil of Catalpa speciosa
- host species: Catalpa speciosa
- geographic location: Sichuan province, Mianyang
- country: China
- origin.country: CHN
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Soil |
| #Host | #Plants | #Tree |
| #Host Body-Site | #Plant | #Rhizosphere |
taxonmaps
- @ref: 69479
- File name: preview.99_1224.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15358;96_713;97_833;98_969;99_1224&stattab=map
- Last taxonomy: Paenibacillus
- 16S sequence: HQ657320
- Sequence Identity:
- Total samples: 7725
- soil counts: 4491
- aquatic counts: 439
- animal counts: 434
- plant counts: 2361
Safety information
risk assessment
- @ref: 19323
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 19323
- description: Paenibacillus catalpae strain D75 16S ribosomal RNA gene, partial sequence
- accession: HQ657320
- length: 1509
- database: nuccore
- NCBI tax ID: 1045775
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Paenibacillus catalpae CGMCC 1.10784 | GCA_900112695 | scaffold | ncbi | 1045775 |
| 66792 | Paenibacillus catalpae strain CGMCC 1.10784 | 1045775.4 | wgs | patric | 1045775 |
| 66792 | Paenibacillus catalpae CGMCC 1.10784 | 2675903006 | draft | img | 1045775 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 19323 | 51.0 | high performance liquid chromatography (HPLC) |
| 30629 | 51 |
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 99 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 66.735 | yes |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 96.731 | yes |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 77.683 | yes |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 92.95 | yes |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 92.38 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 84.188 | no |
External links
@ref: 19323
culture collection no.: DSM 24714, CGMCC 1.10784
straininfo link
- @ref: 87414
- straininfo: 404930
literature
- topic: Phylogeny
- Pubmed-ID: 22941303
- title: Paenibacillus catalpae sp. nov., isolated from the rhizosphere soil of Catalpa speciosa.
- authors: Zhang J, Wang ZT, Yu HM, Ma Y
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.040659-0
- year: 2012
- mesh: Bacterial Typing Techniques, Base Composition, Bignoniaceae/*microbiology, China, DNA, Bacterial/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Paenibacillus/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/analysis
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 19323 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24714) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-24714 | |||
| 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 | |||
| 30629 | 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 | 26960 | 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) | |||
| 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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
| 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 | |||
| 87414 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID404930.1 | StrainInfo: A central database for resolving microbial strain identifiers |