Strain identifier

BacDive ID: 133089

Type strain: Yes

Species: Paenibacillus rhizoplanae

Strain Designation: JJ-64

Strain history: CIP <- 2016, P. Kämpfer, Giessen Univ., Giessen, Germany: strain JJ-64

NCBI tax ID(s): 1917181 (species)

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General

@ref: 24877

BacDive-ID: 133089

DSM-Number: 103963

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive, colony-forming

description: Paenibacillus rhizoplanae JJ-64 is an aerobe, spore-forming, mesophilic bacterium that forms circular colonies and was isolated from root surface of a field-grown corn plant .

NCBI tax id

  • NCBI tax id: 1917181
  • Matching level: species

strain history

@refhistory
24877<- P. Kämpfer, Univ. Giessen, Germany <- J. A. McInroy, Auburn University, USA; JJ-64
122206CIP <- 2016, P. Kämpfer, Giessen Univ., Giessen, Germany: strain JJ-64

doi: 10.13145/bacdive133089.20230509.8.1

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 rhizoplanae
  • full scientific name: Paenibacillus rhizoplanae Kämpfer et al. 2017

@ref: 24877

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Paenibacillus

species: Paenibacillus rhizoplanae

full scientific name: Paenibacillus rhizoplanae Kämpfer et al. 2017

strain designation: JJ-64

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthmotilityconfidencecell shape
25250positive2.0-3.0 µm0.8-1.0 µmno
69480yes97.197
69480positive100
122206positiveyesrod-shaped

colony morphology

  • @ref: 25250
  • colony size: 2.0-3.0 mm
  • colony color: beige
  • colony shape: circular
  • incubation period: 2 days
  • medium used: tryptic soy agar (TSA)

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
25250tryptic soy agar (TSA)yes
25250MacConkey agaryes
24877CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: 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
122206CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
25250positiveoptimum28-30mesophilic
25250positivegrowth10-36
25250nogrowth4psychrophilic
25250nogrowth45thermophilic
24877positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
25250positivegrowth6.0-9.5alkaliphile
25250positiveoptimum7.0-8.0

Physiology and metabolism

oxygen tolerance

  • @ref: 25250
  • oxygen tolerance: aerobe

spore formation

@refspore descriptiontype of sporespore formationconfidence
25250oval endospores in central positionendosporeyes
69481yes100
69480yes100

halophily

@refsaltgrowthtested relationconcentration
25250NaClpositivegrowth1.0-3.0 %(w/v)
25250NaClnogrowth4 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
25250309162-oxoglutarate-carbon source
2525016865gamma-aminobutyric acid-carbon source
2525030089acetate-carbon source
2525017128adipate-carbon source
2525078208azelaate-carbon source
25250casein-hydrolysis
2525017057cellobiose-builds acid from
2525016383cis-aconitate-carbon source
2525016947citrate-assimilation
2525016947citrate-carbon source
2525015963ribitol-builds acid from
2525015963ribitol-carbon source
2525018333D-arabitol-builds acid from
2525017634D-glucose-builds acid from
2525016899D-mannitol-builds acid from
2525016024D-mannose-builds acid from
2525017924D-sorbitol-builds acid from
2525065327D-xylose-builds acid from
2525017113erythritol-builds acid from
2525016813galactitol-builds acid from
252505291gelatin-hydrolysis
2525017240itaconate-carbon source
2525030849L-arabinose-builds acid from
2525062345L-rhamnose-builds acid from
2525062345L-rhamnose-carbon source
2525017716lactose-builds acid from
2525025115malate-carbon source
2525017306maltose-builds acid from
2525028053melibiose-builds acid from
2525036986mesaconate-carbon source
252508006N-acetyl-D-glucosamine-carbon source
2525017272propionate-carbon source
2525017148putrescine-carbon source
2525015361pyruvate-carbon source
2525016634raffinose-builds acid from
2525017814salicin-builds acid from
2525028017starch-hydrolysis
2525017992sucrose-builds acid from
2525015708trans-aconitate-carbon source
2525027082trehalose-builds acid from
25250288162-deoxy-d-ribose+carbon source
2525018305arbutin+carbon source
2525017057cellobiose+carbon source
2525015824D-fructose+carbon source
2525012936D-galactose+carbon source
2525018391D-gluconate+carbon source
2525016899D-mannitol+carbon source
2525016024D-mannose+carbon source
2525017924D-sorbitol+carbon source
2525065327D-xylose+carbon source
2525017234glucose+carbon source
2525017268myo-inositol+carbon source
2525030849L-arabinose+carbon source
2525068428maltitol+carbon source
2525017306maltose+carbon source
2525028053melibiose+carbon source
2525017814salicin+carbon source
2525017992sucrose+carbon source
2525027082trehalose+carbon source

metabolite production

@refChebi-IDmetaboliteproduction
2525035581indoleno
2525015138sulfideno

enzymes

@refvalueactivityec
25250arginine dihydrolase-3.5.3.6
25250beta-galactosidase-3.2.1.23
25250catalase+1.11.1.6
25250cytochrome oxidase+1.9.3.1
25250gelatinase-
25250lysine decarboxylase-4.1.1.18
25250ornithine decarboxylase-4.1.1.17
25250tryptophan deaminase-4.1.99.1
25250urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    25250C15:0 anteiso46.9
    25250C17:0 anteiso2.5
    25250C14:011.2
    25250C16:021.5
    25250C14:0 iso4.3
    25250C15:0 iso6.9
    25250C16:0 iso6.7
  • type of FA analysis: whole cell analysis
  • incubation medium: Tryptic soy agar (TSA)
  • agar/liquid: agar
  • incubation temperature: 28
  • incubation time: 3
  • software version: Sherlock 2.11
  • library/peak naming table: TSBA 40
  • system: MIS MIDI
  • method/protocol: Kämpfer & Kroppenstedt 1996

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentenrichment culture compositionisolation procedureisolation date
24877root surface of a field-grown corn plant (Zea mays)Zea maysNebraska, DunbarUSAUSANorth America
25250nutritient agar (NA, Sigma-Aldrich)dilution method
122206Environment, Maize, zea mugs, rootsDunbar, NebraskaUnited States of AmericaUSANorth America1990-01-02

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root (Rhizome)

taxonmaps

  • @ref: 69479
  • File name: preview.99_5647.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15358;96_335;97_1860;98_4209;99_5647&stattab=map
  • Last taxonomy: Paenibacillus
  • 16S sequence: KY114946
  • Sequence Identity:
  • Total samples: 1496
  • soil counts: 546
  • aquatic counts: 286
  • animal counts: 395
  • plant counts: 269

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
248771Risk group (German classification)
1222061Risk group (French classification)

Sequence information

16S sequences

  • @ref: 24877
  • description: Paenibacillus rhizoplanae strain JJ-64 16S ribosomal RNA gene, partial sequence
  • accession: KY114946
  • length: 1484
  • database: ena
  • NCBI tax ID: 1917181

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paenibacillus rhizoplanae strain DSM 1039631917181.3wgspatric1917181
66792Paenibacillus rhizoplanae DSM 1039632913577593draftimg1917181

GC content

@refGC-contentmethod
2525052.9Thermal denaturation, fluorometry
2487752.9fluorimetric

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes84.521yes
gram-positiveyes85.547yes
anaerobicno97.139yes
aerobicyes74.17no
halophileno96.349no
spore-formingyes96.163no
glucose-utilyes90.299no
flagellatedyes80.628yes
thermophileno99.906no
glucose-fermentno78.822no

External links

@ref: 24877

culture collection no.: DSM 103963, CCM 8725, LMG 29875, CIP 111186

straininfo link

  • @ref: 91354
  • straininfo: 400265

literature

  • topic: Phylogeny
  • Pubmed-ID: 28068214
  • title: Paenibacillus rhizoplanae sp. nov., isolated from the rhizosphere of Zea mays.
  • authors: Kampfer P, Busse HJ, McInroy JA, Hu CH, Kloepper JW, Glaeser SP
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001779
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Paenibacillus/*classification/genetics/isolation & purification, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, Spermidine/chemistry, Vitamin K 2/analogs & derivatives/chemistry, Zea mays/*microbiology
  • topic2: Transcriptome

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
24877Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-103963Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103963)
25250P. B. Kämpfer, H. J.,McInroy, J. A.,Hu, C. H.,Kloepper, J. W.,Glaeser, S. P.Paenibacillus rhizoplanae sp. nov., isolated from the rhizosphere of Zea mays10.1099/ijsem.0.001779IJSEM 67: 1058-1063 201728068214
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
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/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions 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
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
91354Reimer, 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-ID400265.1
122206Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20111186Collection of Institut Pasteur (CIP 111186)