Strain identifier

BacDive ID: 132572

Type strain: Yes

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)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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

@refnamegrowthcompositionlink
41952MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
43616Trypticase Soy Agar (TSA)yes
24361CASO AGAR (MERCK 105458) (DSMZ Medium 220)yesName: 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 waterhttps://mediadive.dsmz.de/medium/220

culture temp

@refgrowthtypetemperaturerange
41952positivegrowth30mesophilic
43616positivegrowth10-45
43616positiveoptimum28-30mesophilic
24361positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
43616positivegrowth5.5-9.5alkaliphile
43616positiveoptimum7-8

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

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4361616947citrate-assimilation
4361617057cellobiose-builds acid from
4361615963ribitol-builds acid from
4361618333D-arabitol-builds acid from
4361617634D-glucose-builds acid from
4361616899D-mannitol-builds acid from
4361616024D-mannose-builds acid from
4361617924D-sorbitol-builds acid from
4361665327D-xylose-builds acid from
4361616813galactitol-builds acid from
4361617113erythritol-builds acid from
4361630849L-arabinose-builds acid from
4361662345L-rhamnose-builds acid from
4361617716lactose-builds acid from
43616maltose hydrate-builds acid from
4361628053melibiose-builds acid from
4361616634raffinose-builds acid from
4361617814salicin-builds acid from
4361617992sucrose-builds acid from
4361627082trehalose-builds acid from
43616309162-oxoglutarate-carbon source
4361616865gamma-aminobutyric acid-carbon source
4361630089acetate-carbon source
4361617128adipate-carbon source
4361678208azelaate-carbon source
4361616383cis-aconitate-carbon source
4361616947citrate-carbon source
4361615963ribitol-carbon source
4361617240itaconate-carbon source
4361628053melibiose-carbon source
4361636986mesaconate-carbon source
4361617272propionate-carbon source
4361617148putrescine-carbon source
4361633942ribose-carbon source
4361615708trans-aconitate-carbon source
43616casein-hydrolysis
436165291gelatin-hydrolysis
4361628017starch-hydrolysis
4361618305arbutin+carbon source
4361617057cellobiose+carbon source
4361615824D-fructose+carbon source
4361612936D-galactose+carbon source
4361617634D-glucose+carbon source
4361616899D-mannitol+carbon source
4361616024D-mannose+carbon source
4361617924D-sorbitol+carbon source
4361665327D-xylose+carbon source
4361625115malate+carbon source
4361624265gluconate+carbon source
4361630849L-arabinose+carbon source
4361662345L-rhamnose+carbon source
4361668428maltitol+carbon source
4361617306maltose+carbon source
4361617268myo-inositol+carbon source
43616506227N-acetylglucosamine+carbon source
4361615361pyruvate+carbon source
4361617814salicin+carbon source
4361617992sucrose+carbon source
4361627082trehalose+carbon source
43616901464-nitrophenyl beta-D-glucuronide+hydrolysis
43616L-alanine 4-nitroanilide+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
4361635581indoleno
4361615138sulfideno

enzymes

@refvalueactivityec
43616catalase+1.11.1.6
43616cytochrome oxidase+1.9.3.1
43616gelatinase-
43616beta-galactosidase-3.2.1.23
43616arginine dihydrolase-3.5.3.6
43616lysine decarboxylase-4.1.1.18
43616ornithine decarboxylase-4.1.1.17
43616tryptophan deaminase-4.1.99.1
43616urease+/-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43616C10:0 3OH3.5
    43616C12:07.3
    43616C12:0 2OH1
    43616C12:0 3OH3.4
    43616C14:04.8
    43616C16:027.8
    43616C16:1ω7c / C16:1ω6c28
    43616C17:01.3
    43616C17:1ω6c1.5
    43616C18:1ω7c / C18:1ω6c18.4
  • 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

@refsample typegeographic locationcountryorigin.countrycontinent
24361field-grown cucumber plantAlabama, AuburnUSAUSANorth America
43616field-grown cucumber plantAuburn, ALUSAUSANorth America

isolation source categories

Cat1Cat2Cat3
#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

@refGC-contentmethod
4361651.4thermal denaturation, midpoint method (Tm)
2436151.4fluorimetric

External links

@ref: 24361

culture collection no.: DSM 101601, CCM 8653, LMG 29222, CCM 8655

straininfo link

  • @ref: 90889
  • straininfo: 402596

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27089462Paenibacillus cucumis sp. nov., isolated from a cucumber plant.Kampfer P, Busse HJ, Kloepper JW, Hu CH, McInroy JA, Glaeser SPInt J Syst Evol Microbiol10.1099/ijsem.0.0010872016Alabama, 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/chemistryTranscriptome
Phylogeny27902310Paenibacillus silvae sp. nov., isolated from a tropical rainforest soil.Huang H, Zhang F, Liu M, Cui Y, Sun Q, Zhu J, Zou X, Bao SInt J Syst Evol Microbiol10.1099/ijsem.0.0016082017Bacterial 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/chemistryTranscriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
24361Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-101601Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 101601)
41952Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/34586
43616Peter Kämpfer, Hans-Jürgen Busse, Joseph W. Kloepper, Chia-Hui Hu, John A. McInroy, Stefanie P. GlaeserPaenibacillus cucumis sp. nov., isolated from a cucumber plant10.1099/ijsem.0.001087IJSEM 66: 2599-2603 201627089462
69479João 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 betahttps://microbeatlas.org/
90889Reimer, 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 identifiers10.60712/SI-ID402596.1