Strain identifier
BacDive ID: 132572
Type strain:
Species: Paenibacillus cucumis
Strain Designation: AP-115
Strain history: <- P. Kämpfer, Justus-Liebig-Universität, Giessen, Germany <- J. A. McInroy, Department of Entomology and Plant Pathology, Auburn University, Alabama, USA; AP-115
NCBI tax ID(s): 1776858 (species)
General
@ref: 24361
BacDive-ID: 132572
DSM-Number: 101601
keywords: 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive, rod-shaped, colony-forming
description: Paenibacillus cucumis AP-115 is an aerobe, spore-forming, mesophilic bacterium that forms circular colonies and was isolated from field-grown cucumber plant.
NCBI tax id
- NCBI tax id: 1776858
- Matching level: species
strain history
- @ref: 24361
- history: <- P. Kämpfer, Justus-Liebig-Universität, Giessen, Germany <- J. A. McInroy, Department of Entomology and Plant Pathology, Auburn University, Alabama, USA; AP-115
doi: 10.13145/bacdive132572.20230509.8.1
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 cucumis
- full scientific name: Paenibacillus cucumis Kämpfer et al. 2016
@ref: 24361
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Paenibacillaceae
genus: Paenibacillus
species: Paenibacillus cucumis
full scientific name: Paenibacillus cucumis Kämpfer et al. 2016
strain designation: AP-115
type strain: yes
Morphology
cell morphology
- @ref: 43616
- gram stain: positive
- cell length: 2-3 µm
- cell width: 0.8-1 µm
- cell shape: rod-shaped
- motility: no
colony morphology
- @ref: 43616
- colony size: 2-3 mm
- colony color: Beige
- colony shape: circular
- incubation period: 2 days
- medium used: TSA agar
Culture and growth conditions
culture medium
@ref | name | growth | composition | link |
---|---|---|---|---|
41952 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
43616 | Trypticase Soy Agar (TSA) | yes | ||
24361 | CASO AGAR (MERCK 105458) (DSMZ Medium 220) | yes | 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 | https://mediadive.dsmz.de/medium/220 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
41952 | positive | growth | 30 | mesophilic |
43616 | positive | growth | 10-45 | |
43616 | positive | optimum | 28-30 | mesophilic |
24361 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
43616 | positive | growth | 5.5-9.5 | alkaliphile |
43616 | positive | optimum | 7-8 |
Physiology and metabolism
oxygen tolerance
- @ref: 43616
- oxygen tolerance: aerobe
spore formation
- @ref: 43616
- spore description: oval endospores are formed in a central position
- type of spore: endospore
- spore formation: yes
halophily
- @ref: 43616
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 1-5 %
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
43616 | 16947 | citrate | - | assimilation |
43616 | 17057 | cellobiose | - | builds acid from |
43616 | 15963 | ribitol | - | builds acid from |
43616 | 18333 | D-arabitol | - | builds acid from |
43616 | 17634 | D-glucose | - | builds acid from |
43616 | 16899 | D-mannitol | - | builds acid from |
43616 | 16024 | D-mannose | - | builds acid from |
43616 | 17924 | D-sorbitol | - | builds acid from |
43616 | 65327 | D-xylose | - | builds acid from |
43616 | 16813 | galactitol | - | builds acid from |
43616 | 17113 | erythritol | - | builds acid from |
43616 | 30849 | L-arabinose | - | builds acid from |
43616 | 62345 | L-rhamnose | - | builds acid from |
43616 | 17716 | lactose | - | builds acid from |
43616 | maltose hydrate | - | builds acid from | |
43616 | 28053 | melibiose | - | builds acid from |
43616 | 16634 | raffinose | - | builds acid from |
43616 | 17814 | salicin | - | builds acid from |
43616 | 17992 | sucrose | - | builds acid from |
43616 | 27082 | trehalose | - | builds acid from |
43616 | 30916 | 2-oxoglutarate | - | carbon source |
43616 | 16865 | gamma-aminobutyric acid | - | carbon source |
43616 | 30089 | acetate | - | carbon source |
43616 | 17128 | adipate | - | carbon source |
43616 | 78208 | azelaate | - | carbon source |
43616 | 16383 | cis-aconitate | - | carbon source |
43616 | 16947 | citrate | - | carbon source |
43616 | 15963 | ribitol | - | carbon source |
43616 | 17240 | itaconate | - | carbon source |
43616 | 28053 | melibiose | - | carbon source |
43616 | 36986 | mesaconate | - | carbon source |
43616 | 17272 | propionate | - | carbon source |
43616 | 17148 | putrescine | - | carbon source |
43616 | 33942 | ribose | - | carbon source |
43616 | 15708 | trans-aconitate | - | carbon source |
43616 | casein | - | hydrolysis | |
43616 | 5291 | gelatin | - | hydrolysis |
43616 | 28017 | starch | - | hydrolysis |
43616 | 18305 | arbutin | + | carbon source |
43616 | 17057 | cellobiose | + | carbon source |
43616 | 15824 | D-fructose | + | carbon source |
43616 | 12936 | D-galactose | + | carbon source |
43616 | 17634 | D-glucose | + | carbon source |
43616 | 16899 | D-mannitol | + | carbon source |
43616 | 16024 | D-mannose | + | carbon source |
43616 | 17924 | D-sorbitol | + | carbon source |
43616 | 65327 | D-xylose | + | carbon source |
43616 | 25115 | malate | + | carbon source |
43616 | 24265 | gluconate | + | carbon source |
43616 | 30849 | L-arabinose | + | carbon source |
43616 | 62345 | L-rhamnose | + | carbon source |
43616 | 68428 | maltitol | + | carbon source |
43616 | 17306 | maltose | + | carbon source |
43616 | 17268 | myo-inositol | + | carbon source |
43616 | 506227 | N-acetylglucosamine | + | carbon source |
43616 | 15361 | pyruvate | + | carbon source |
43616 | 17814 | salicin | + | carbon source |
43616 | 17992 | sucrose | + | carbon source |
43616 | 27082 | trehalose | + | carbon source |
43616 | 90146 | 4-nitrophenyl beta-D-glucuronide | + | hydrolysis |
43616 | L-alanine 4-nitroanilide | + | hydrolysis |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
43616 | 35581 | indole | no |
43616 | 15138 | sulfide | no |
enzymes
@ref | value | activity | ec |
---|---|---|---|
43616 | catalase | + | 1.11.1.6 |
43616 | cytochrome oxidase | + | 1.9.3.1 |
43616 | gelatinase | - | |
43616 | beta-galactosidase | - | 3.2.1.23 |
43616 | arginine dihydrolase | - | 3.5.3.6 |
43616 | lysine decarboxylase | - | 4.1.1.18 |
43616 | ornithine decarboxylase | - | 4.1.1.17 |
43616 | tryptophan deaminase | - | 4.1.99.1 |
43616 | urease | +/- | 3.5.1.5 |
fatty acid profile
fatty acids
@ref fatty acid percentage 43616 C10:0 3OH 3.5 43616 C12:0 7.3 43616 C12:0 2OH 1 43616 C12:0 3OH 3.4 43616 C14:0 4.8 43616 C16:0 27.8 43616 C16:1ω7c / C16:1ω6c 28 43616 C17:0 1.3 43616 C17:1ω6c 1.5 43616 C18:1ω7c / C18:1ω6c 18.4 - type of FA analysis: whole cell analysis
- incubation medium: TSA
- agar/liquid: agar
- incubation temperature: 28
- incubation time: 3
- incubation_oxygen: aerobic
- software version: Sherlock 2.11
- library/peak naming table: TSBA40
- system: MIS MIDI
- cutoff value:
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
24361 | field-grown cucumber plant | Alabama, Auburn | USA | USA | North America |
43616 | field-grown cucumber plant | Auburn, AL | USA | USA | North America |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Agriculture | #Field |
#Host | #Plants | #Herbaceous plants (Grass,Crops) |
taxonmaps
- @ref: 69479
- File name: preview.99_24721.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15358;96_141;97_15017;98_18591;99_24721&stattab=map
- Last taxonomy: Paenibacillus
- 16S sequence: KU201962
- Sequence Identity:
- Total samples: 879
- soil counts: 93
- aquatic counts: 18
- animal counts: 40
- plant counts: 728
Safety information
risk assessment
- @ref: 24361
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 24361
- description: Paenibacillus cucumis Kampfer et al. 2016 strain AP-115 16S ribosomal RNA gene, partial sequence
- accession: KU201962
- length: 1480
- database: ena
- NCBI tax ID: 1776858
GC content
@ref | GC-content | method |
---|---|---|
43616 | 51.4 | thermal denaturation, midpoint method (Tm) |
24361 | 51.4 | fluorimetric |
External links
@ref: 24361
culture collection no.: DSM 101601, CCM 8653, LMG 29222, CCM 8655
straininfo link
- @ref: 90889
- straininfo: 402596
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 27089462 | Paenibacillus cucumis sp. nov., isolated from a cucumber plant. | Kampfer P, Busse HJ, Kloepper JW, Hu CH, McInroy JA, Glaeser SP | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001087 | 2016 | Alabama, Bacterial Typing Techniques, Base Composition, Cucumis sativus/*microbiology, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Paenibacillus/*classification/genetics/isolation & purification, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spermidine/chemistry, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Phylogeny | 27902310 | Paenibacillus silvae sp. nov., isolated from a tropical rainforest soil. | Huang H, Zhang F, Liu M, Cui Y, Sun Q, Zhu J, Zou X, Bao S | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001608 | 2017 | Bacterial Typing Techniques, Base Composition, 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, RNA, Ribosomal, 16S/genetics, *Rainforest, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
@id | authors | title | doi/url | catalogue | journal | pubmed |
---|---|---|---|---|---|---|
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 | |||
24361 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-101601 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 101601) | |||
41952 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/34586 | ||||
43616 | Peter Kämpfer, Hans-Jürgen Busse, Joseph W. Kloepper, Chia-Hui Hu, John A. McInroy, Stefanie P. Glaeser | Paenibacillus cucumis sp. nov., isolated from a cucumber plant | 10.1099/ijsem.0.001087 | IJSEM 66: 2599-2603 2016 | 27089462 | |
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/ | |||
90889 | 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-ID402596.1 |