Strain identifier

BacDive ID: 11649

Type strain: Yes

Species: Paenibacillus prosopidis

Strain Designation: PW21

Strain history: CIP <- 2011, DSMZ

NCBI tax ID(s): 630520 (species)

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General

@ref: 16319

BacDive-ID: 11649

DSM-Number: 22405

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, Gram-variable, motile, rod-shaped

description: Paenibacillus prosopidis PW21 is an aerobe, spore-forming, Gram-variable bacterium that was isolated from root nodules of Prosopis farcta.

NCBI tax id

  • NCBI tax id: 630520
  • Matching level: species

strain history

@refhistory
409082011, DSMZ
16319<- A. Valverde Portal, IRNASA-CSIC, Salamanca, Spain; PW21 <- A. Fterich
121966CIP <- 2011, DSMZ

doi: 10.13145/bacdive11649.20240916.9.1

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 prosopidis
  • full scientific name: Paenibacillus prosopidis Valverde et al. 2010

@ref: 16319

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Paenibacillus

species: Paenibacillus prosopidis

full scientific name: Paenibacillus prosopidis Valverde et al. 2010

strain designation: PW21

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
29495variablerod-shapedyes
121966positiverod-shapedyes

pigmentation

  • @ref: 29495
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16319R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830; with strain-specific modifications) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l MnSO4 0.01 g/l Distilled water
40908MEDIUM 328- for nutrient agaryesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
121966CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperature
16319positivegrowth28
29495positivegrowth05-40
29495positiveoptimum30
40908positivegrowth30

culture pH

@refabilitytypepH
29495positivegrowth6.5-8
29495positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 29495
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
29495yes
69480yes92.696
69481yes100

halophily

@refsaltgrowthtested relationconcentration
29495NaClpositivegrowth0-2 %
29495NaClpositiveoptimum0-2 %

observation

  • @ref: 29495
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2949522599arabinose+carbon source
2949524265gluconate+carbon source
2949517234glucose+carbon source
2949525115malate+carbon source
2949517306maltose+carbon source
2949529864mannitol+carbon source
294954853esculin+hydrolysis
68371Potassium 5-ketogluconate+builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate+builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose+builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose+builds acid from
6837128066gentiobiose+builds acid from
6837117151xylitol-builds acid from
6837128087glycogen+builds acid from
6837128017starch+builds acid from
6837116634raffinose+builds acid from
683716731melezitose-builds acid from
6837115443inulin+builds acid from
6837127082trehalose+builds acid from
6837117992sucrose+builds acid from
6837128053melibiose+builds acid from
6837117716lactose+builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837118305arbutin+builds acid from
6837127613amygdalin+builds acid from
6837159640N-acetylglucosamine+builds acid from
68371320061methyl alpha-D-glucopyranoside+builds acid from
6837143943methyl alpha-D-mannoside+builds acid from
6837117924D-sorbitol+builds acid from
6837116899D-mannitol+builds acid from
6837117268myo-inositol+builds acid from
6837116813galactitol-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837174863methyl beta-D-xylopyranoside+builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose+builds acid from
6837116988D-ribose+builds acid from
6837130849L-arabinose+builds acid from
6837117113erythritol-builds acid from
12196617632nitrate-reduction
12196616301nitrite-reduction

metabolite production

  • @ref: 121966
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
29495catalase+1.11.1.6
29495cytochrome oxidase+1.9.3.1
121966oxidase+
121966catalase+1.11.1.6
121966urease-3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase-3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121966--+--+-----+-+------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121966+/--+/-+++--+++++-+/--+++++++++++++++++-+++-++---+--+-+

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
16319root nodules of Prosopis farctaProsopis farctasouth of TunisiaTunisiaTUNAfrica
121966Plant, Root nodules, Prosopis farctaTunisiaTUNAfrica

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Tree
#Host Body-Site#Plant#Root nodule

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
163191Risk group (German classification)
1219661Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
16319Paenibacillus prosopidis strain PW21 16S ribosomal RNA gene, partial sequenceFJ8209951493nuccore630520
124043Paenibacillus prosopidis partial 16S rRNA gene, strain DSM 22405 type, clone 1LT9001891544nuccore630520
124043Paenibacillus prosopidis partial 16S rRNA gene, strain DSM 22405 type, clone 2LT9001901544nuccore630520
124043Paenibacillus prosopidis partial 16S rRNA gene, strain DSM 22405 type, clone 3LT9001911544nuccore630520
124043Paenibacillus prosopidis partial 16S rRNA gene, strain DSM 22405 type, clone 4LT9001921544nuccore630520
124043Paenibacillus prosopidis partial 16S rRNA gene, strain DSM 22405 type, clone 5LT9001931544nuccore630520
124043Paenibacillus prosopidis partial 16S rRNA gene, strain DSM 22405 type, clone 6LT9001941533nuccore630520
124043Paenibacillus prosopidis partial 16S rRNA gene, strain DSM 22405 type, clone 7LT9001951544nuccore630520
124043Paenibacillus prosopidis partial 16S rRNA gene, strain DSM 22405 type, clone 8LT9001961544nuccore630520
124043Paenibacillus prosopidis partial 16S rRNA gene, strain DSM 22405 type, clone 9LT9001971544nuccore630520

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paenibacillus prosopidis CECT 7506GCA_003337375scaffoldncbi630520
66792Paenibacillus prosopidis strain CECT 7506630520.3wgspatric630520
66792Paenibacillus prosopidis CECT 75062770939585draftimg630520

GC content

@refGC-contentmethod
1631952.9thermal denaturation, midpoint method (Tm)
2949552.9

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesyes100no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes59.57yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.841yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes76.789no
69480spore-formingspore-formingAbility to form endo- or exosporesyes92.696yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno92.516yes
69480flagellatedmotile2+Ability to perform flagellated movementyes86.988no

External links

@ref: 16319

culture collection no.: DSM 22405, CECT 7506, LMG 25259, CIP 110273

straininfo link

  • @ref: 80873
  • straininfo: 2625

literature

  • topic: Phylogeny
  • Pubmed-ID: 19897617
  • title: Paenibacillus prosopidis sp. nov., isolated from the nodules of Prosopis farcta.
  • authors: Valverde A, Fterich A, Mahdhi M, Ramirez-Bahena MH, Caviedes MA, Mars M, Velazquez E, Rodriguez-Llorente ID
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.014241-0
  • year: 2009
  • mesh: 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
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
16319Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22405)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22405
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
29495Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2589528776041
40908Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8114
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
80873Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID2625.1StrainInfo: A central database for resolving microbial strain identifiers
121966Curators of the CIPCollection of Institut Pasteur (CIP 110273)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110273
124043Dr. Isabel Schober, Dr. Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy