Strain identifier
BacDive ID: 11634
Type strain: 
Species: Paenibacillus castaneae
Strain Designation: Ch-32
Strain history: <- Angel Valverde Portal; Ch-32
NCBI tax ID(s): 474957 (species)
version 8.1 (current version)
General
@ref: 8095
BacDive-ID: 11634
DSM-Number: 19417
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-variable, motile, rod-shaped
description: Paenibacillus castaneae Ch-32 is an aerobe, spore-forming, mesophilic bacterium that was isolated from phyllosphere of sweet chestnut tree .
NCBI tax id
- NCBI tax id: 474957
- Matching level: species
strain history
- @ref: 8095
- history: <- Angel Valverde Portal; Ch-32
doi: 10.13145/bacdive11634.20230509.8.1
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 castaneae
- full scientific name: Paenibacillus castaneae Valverde et al. 2008
@ref: 8095
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Paenibacillaceae
genus: Paenibacillus
species: Paenibacillus castaneae
full scientific name: Paenibacillus castaneae Valverde et al. 2008
strain designation: Ch-32
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell shape | motility | confidence |
|---|---|---|---|---|
| 32544 | variable | rod-shaped | yes | |
| 69480 | yes | 98.373 | ||
| 69480 | positive | 100 |
pigmentation
- @ref: 32544
- production: yes
Culture and growth conditions
culture medium
- @ref: 8095
- name: NUTRIENT AGAR (DSMZ Medium 1)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1
- composition: Name: NUTRIENT AGAR (DSMZ Medium 1; with strain-specific modifications) Composition: Soil extract 500.0 g/l Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 8095 | positive | growth | 25-30 | mesophilic |
| 32544 | positive | growth | 30 | mesophilic |
| 32544 | positive | optimum | 30 | mesophilic |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 32544 | positive | growth | 5.7-7 |
| 32544 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 32544
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 32544 | yes | |
| 69481 | yes | 100 |
| 69480 | yes | 100 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 32544 | NaCl | positive | growth | 2 % |
| 32544 | NaCl | positive | optimum | 2 % |
observation
- @ref: 32544
- observation: aggregates in chains
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 32544 | 22599 | arabinose | + | carbon source |
| 32544 | 24265 | gluconate | + | carbon source |
| 32544 | 17234 | glucose | + | carbon source |
| 32544 | 17306 | maltose | + | carbon source |
| 32544 | 29864 | mannitol | + | carbon source |
| 32544 | 37684 | mannose | + | carbon source |
| 32544 | 4853 | esculin | + | hydrolysis |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 32544 | catalase | + | 1.11.1.6 |
| 32544 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
- @ref: 8095
- sample type: phyllosphere of sweet chestnut tree (Castanea sativa Miller)
- host species: Castanea sativa
- geographic location: Salamanca province, Sierra de Francia region
- country: Spain
- origin.country: ESP
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Plants | #Tree |
| #Host Body-Site | #Plant | #Leaf (Phyllosphere) |
Safety information
risk assessment
- @ref: 8095
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 8095
- description: Paenibacillus castaneae strain Ch-32 16S ribosomal RNA gene, complete sequence
- accession: EU099594
- length: 1549
- database: ena
- NCBI tax ID: 474957
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Paenibacillus castaneae DSM 19417 | GCA_002884445 | scaffold | ncbi | 474957 |
| 66792 | Paenibacillus castaneae CECT 7279 | GCA_011761405 | scaffold | ncbi | 474957 |
| 66792 | Paenibacillus castaneae strain CECT 7279 | 474957.4 | wgs | patric | 474957 |
| 66792 | Paenibacillus castaneae strain DSM 19417 | 474957.3 | wgs | patric | 474957 |
| 66792 | Paenibacillus castaneae DSM 19417 | 2916384205 | draft | img | 474957 |
| 66792 | Paenibacillus castaneae CECT 7279 | 2824397579 | draft | img | 474957 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 8095 | 46 | thermal denaturation, midpoint method (Tm) |
| 32544 | 46 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| flagellated | yes | 87.16 | no |
| gram-positive | yes | 78.289 | yes |
| anaerobic | no | 98.958 | yes |
| aerobic | yes | 88.542 | yes |
| halophile | no | 93.51 | no |
| spore-forming | yes | 93.704 | yes |
| glucose-util | yes | 90.314 | yes |
| thermophile | no | 99.694 | yes |
| motile | yes | 92.003 | yes |
| glucose-ferment | no | 87.197 | no |
External links
@ref: 8095
culture collection no.: DSM 19417, CECT 7279
straininfo link
- @ref: 80859
- straininfo: 308720
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 18984693 | Paenibacillus castaneae sp. nov., isolated from the phyllosphere of Castanea sativa Miller. | Valverde A, Peix A, Rivas R, Velazquez E, Salazar S, Santa-Regina I, Rodriguez-Barrueco C, Igual JM | Int J Syst Evol Microbiol | 10.1099/ijs.0.65663-0 | 2008 | Bacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis/genetics, DNA, Ribosomal/genetics, Fagaceae/*microbiology, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Plant Leaves/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spain, Species Specificity | Genetics |
| Phylogeny | 19897617 | Paenibacillus prosopidis sp. nov., isolated from the nodules of Prosopis farcta. | Valverde A, Fterich A, Mahdhi M, Ramirez-Bahena MH, Caviedes MA, Mars M, Velazquez E, Rodriguez-Llorente ID | Int J Syst Evol Microbiol | 10.1099/ijs.0.014241-0 | 2009 | DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Paenibacillus/*classification/genetics/*isolation & purification/metabolism, Phylogeny, Prosopis/*microbiology, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiology | Metabolism |
| Phylogeny | 20889764 | Paenibacillus algorifonticola sp. nov., isolated from a cold spring. | Tang QY, Yang N, Wang J, Xie YQ, Ren B, Zhou YG, Gu MY, Mao J, Li WJ, Shi YH, Zhang LX | Int J Syst Evol Microbiol | 10.1099/ijs.0.025346-0 | 2010 | Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Fresh Water/*microbiology, Hydrogen-Ion Concentration, Molecular Sequence Data, Paenibacillus/*classification/genetics/*isolation & purification/physiology, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spores, Bacterial/cytology, Temperature | Genetics |
| Phylogeny | 22941303 | Paenibacillus catalpae sp. nov., isolated from the rhizosphere soil of Catalpa speciosa. | Zhang J, Wang ZT, Yu HM, Ma Y | Int J Syst Evol Microbiol | 10.1099/ijs.0.040659-0 | 2012 | 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 | Genetics |
| Phylogeny | 23852155 | Paenibacillus endophyticus sp. nov., isolated from nodules of Cicer arietinum. | Carro L, Flores-Felix JD, Cerda-Castillo E, Ramirez-Bahena MH, Igual JM, Tejedor C, Velazquez E, Peix A | Int J Syst Evol Microbiol | 10.1099/ijs.0.050310-0 | 2013 | Base Composition, Cicer/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Paenibacillus/*classification/genetics/isolation & purification, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiology, Sequence Analysis, DNA, Spain, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
| Phylogeny | 27565539 | Paenibacillus sinopodophylli sp. nov., a siderophore-producing endophytic bacterium isolated from roots of Sinopodophyllum hexandrum (Royle) Ying. | Chen C, Xin K, Li M, Li X, Cheng J, Zhang L, Shen X | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001458 | 2016 | Bacterial Typing Techniques, Base Composition, Berberidaceae/*microbiology, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Paenibacillus/*classification/genetics/isolation & purification, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Siderophores/*biosynthesis, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
| Phylogeny | 31967956 | Paenibacillus paridis sp. nov., an endophytic bacterial species isolated from the root of Paris polyphylla Smith var. yunnanensis. | Wang M, Jiang XW, Tang SK, Zhi XY, Yang LL | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003997 | 2020 | Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Endophytes/classification/isolation & purification, Fatty Acids/chemistry, Melanthiaceae/*microbiology, Nucleic Acid Hybridization, Paenibacillus/*classification/isolation & purification, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Enzymology |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 8095 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19417) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19417 | |||
| 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 | |||
| 32544 | 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 | 28762 | 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) | |||
| 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 | |||
| 80859 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID308720.1 | StrainInfo: A central database for resolving microbial strain identifiers |