Strain identifier

BacDive ID: 24281

Type strain: No

Species: Paenibacillus sonchi

Strain history: CIP <- 2010, CECT <- A. Beneduzi, Rio Grande Univ., Porto Algere, Brazil: strain SBR5

NCBI tax ID(s): 483937 (species)

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

@ref: 20705

BacDive-ID: 24281

DSM-Number: 28159

keywords: 16S sequence, Bacteria, facultative anaerobe, spore-forming, mesophilic, Gram-variable, motile, rod-shaped

description: Paenibacillus sonchi DSM 28159 is a facultative anaerobe, spore-forming, mesophilic bacterium that was isolated from rhizosphere of Triticum aestivum.

NCBI tax id

  • NCBI tax id: 483937
  • Matching level: species

strain history

@refhistory
20705<- CECT <- A. Beneduzi
122240CIP <- 2010, CECT <- A. Beneduzi, Rio Grande Univ., Porto Algere, Brazil: strain SBR5

doi: 10.13145/bacdive24281.20230509.8.1

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 sonchi
  • full scientific name: Paenibacillus sonchi Hong et al. 2009

  • synonyms

    • @ref: 20215
    • synonym: Paenibacillus riograndensis

@ref: 20705

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Paenibacillus

species: Paenibacillus sonchi

full scientific name: Paenibacillus sonchi Hong et al. 2009 emend. Sant'Anna et al. 2017

type strain: no

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
29382variable4.15 µm0.72 µmrod-shapedyes
122240negativerod-shapedyes

pigmentation

  • @ref: 29382
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
20705CASO 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
40372MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122240CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
20705positivegrowth30mesophilic
29382positiveoptimum28mesophilic
40372positivegrowth30mesophilic

culture pH

  • @ref: 29382
  • ability: positive
  • type: optimum
  • pH: 7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29382facultative anaerobe
122240facultative anaerobe

spore formation

@refspore formation
29382yes
122240yes

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2938222599arabinose+carbon source
2938228757fructose+carbon source
2938228260galactose+carbon source
2938217234glucose+carbon source
2938217754glycerol+carbon source
2938217716lactose+carbon source
2938217306maltose+carbon source
2938229864mannitol+carbon source
2938237684mannose+carbon source
2938216634raffinose+carbon source
2938217992sucrose+carbon source
2938227082trehalose+carbon source
2938218222xylose+carbon source
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
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose+builds acid from
6837128066gentiobiose+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
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
6837130849L-arabinose+builds acid from
6837117113erythritol-builds acid from
6837117754glycerol+builds acid from
12224017632nitrate+reduction
12224016301nitrite-reduction

metabolite production

  • @ref: 122240
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
122240oxidase+
122240catalase+1.11.1.6
122240urease-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
122240--++-+-----+++-++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122240+-+/-++/-+--+++++-+/---++/---+++++++++++++++++/-++---+/---++-

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
20705rhizosphere of Triticum aestivumTriticum aestivumSao BorjaBrazilBRAMiddle and South America
122240Environment, Triticum aestivum, rhizosphere2004

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Rhizosphere

taxonmaps

  • @ref: 69479
  • File name: preview.99_3149.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15358;96_335;97_1860;98_2285;99_3149&stattab=map
  • Last taxonomy: Paenibacillus
  • 16S sequence: EU257201
  • Sequence Identity:
  • Total samples: 202
  • soil counts: 152
  • aquatic counts: 22
  • animal counts: 13
  • plant counts: 15

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
207051Risk group (German classification)
1222401Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20705
  • description: Paenibacillus riograndensis strain SBR5 16S ribosomal RNA gene, partial sequence
  • accession: EU257201
  • length: 1506
  • database: ena
  • NCBI tax ID: 1073571

GC content

  • @ref: 20705
  • GC-content: 55.1

External links

@ref: 20705

culture collection no.: DSM 28159, CCGB 1313, CECT 7330, SBR 5, CIP 110206

straininfo link

  • @ref: 88219
  • straininfo: 365764

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19648317Paenibacillus riograndensis sp. nov., a nitrogen-fixing species isolated from the rhizosphere of Triticum aestivum.Beneduzi A, Costa PB, Parma M, Melo IS, Bodanese-Zanettini MH, Passaglia LMPInt J Syst Evol Microbiol10.1099/ijs.0.011973-02009Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, *Nitrogen Fixation, Paenibacillus/*classification/genetics/*isolation & purification/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Triticum/*microbiologyMetabolism
Phylogeny20601486Paenibacillus jilunlii sp. nov., a nitrogen-fixing species isolated from the rhizosphere of Begonia semperflorens.Jin HJ, Zhou YG, Liu HC, Chen SFInt J Syst Evol Microbiol10.1099/ijs.0.025056-02010Amino Acids/analysis, Base Composition, Begoniaceae/*microbiology, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Molecular Sequence Data, *Nitrogen Fixation, Nucleic Acid Hybridization, Oxidoreductases/genetics, Paenibacillus/*classification/*isolation & purification/physiology, Peptidoglycan/chemistry, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Genetics22038959Genome sequence of the diazotrophic Gram-positive rhizobacterium Paenibacillus riograndensis SBR5(T).Beneduzi A, Campos S, Ambrosini A, de Souza R, Granada C, Costa P, Arruda L, Moreira F, Vargas LK, Weiss V, Tieppo E, Faoro H, de Souza EM, Pedrosa FO, Passaglia LMJ Bacteriol10.1128/JB.06100-112011Base Sequence, *Genome, Bacterial, Molecular Sequence Data, *Nitrogen Fixation, Paenibacillus/*genetics/isolation & purification/metabolism, Triticum/growth & development/*microbiologyEnzymology
Metabolism24956360Alternative nitrogenase and pseudogenes: unique features of the Paenibacillus riograndensis nitrogen fixation system.Fernandes Gde C, Trarbach LJ, de Campos SB, Beneduzi A, Passaglia LMRes Microbiol10.1016/j.resmic.2014.06.0022014Gene Expression Regulation, Bacterial, Metabolic Networks and Pathways/genetics, Multigene Family, *Nitrogen Fixation, Nitrogenase/*genetics/*metabolism, Paenibacillus/*enzymology/genetics/*metabolism, *PseudogenesEnzymology
Genetics25959170Complete genome sequence of Paenibacillus riograndensis SBR5(T), a Gram-positive diazotrophic rhizobacterium.Brito LF, Bach E, Kalinowski J, Ruckert C, Wibberg D, Passaglia LM, Wendisch VFJ Biotechnol10.1016/j.jbiotec.2015.04.0252015*Genome, Bacterial, Molecular Sequence Annotation, Paenibacillus/*genetics, Plant Development, Sequence Analysis, DNA/*methods, Soil MicrobiologyTranscriptome
Metabolism27130283Iron deficiency resistance mechanisms enlightened by gene expression analysis in Paenibacillus riograndensis SBR5.Sperb ER, Tadra-Sfeir MZ, Sperotto RA, Fernandes Gde C, Pedrosa Fde O, de Souza EM, Passaglia LMRes Microbiol10.1016/j.resmic.2016.04.0072016*Gene Expression Regulation, Bacterial, High-Throughput Nucleotide Sequencing, Iron/*metabolism, Iron Deficiencies, Paenibacillus/genetics/*growth & development/*metabolism, Real-Time Polymerase Chain Reaction, Reverse Transcriptase Polymerase Chain Reaction
Cultivation27780731How to transform a recalcitrant Paenibacillus strain: From culture medium to restriction barrier.Bach E, de Carvalho Fernandes G, Passaglia LMPJ Microbiol Methods10.1016/j.mimet.2016.10.0122016Culture Media/*chemistry, DNA, Fungal, Electroporation/*methods, Escherichia coli/genetics, Gene Expression, Gene Transfer Techniques, Paenibacillus/*genetics, Plasmids/genetics, Rhizosphere, *Transformation, Genetic, Triticum/microbiology
Metabolism28109177Glutamine synthetase stabilizes the binding of GlnR to nitrogen fixation gene operators.Fernandes GC, Hauf K, Sant'Anna FH, Forchhammer K, Passaglia LMFEBS J10.1111/febs.140212017Bacterial Proteins/*genetics, Binding Sites, DNA-Binding Proteins/*genetics/metabolism, Gene Expression Regulation, Bacterial, Genome, Bacterial, Glutamate-Ammonia Ligase/*genetics/metabolism, Glutamine/metabolism, Multiprotein Complexes/genetics/metabolism, Nitrogen/*metabolism, Nitrogen Fixation/*genetics, Paenibacillus/genetics/metabolism, Promoter Regions, Genetic, Transcription Factors/*geneticsGenetics
Phylogeny29039306Paenibacillus azotifigens sp. nov., a novel nitrogen-fixing bacterium isolated from paddy soil.Siddiqi MZ, Choi GM, Choi KD, Im WTInt J Syst Evol Microbiol10.1099/ijsem.0.0022692017Bacterial Typing Techniques, Cell Wall/chemistry, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, *Nitrogen Fixation, Nucleic Acid Hybridization, Paenibacillus/*classification/genetics/isolation & purification, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny29046663Reclassification of Paenibacillus riograndensis as a Genomovar of Paenibacillus sonchi: Genome-Based Metrics Improve Bacterial Taxonomic Classification.Sant'Anna FH, Ambrosini A, de Souza R, de Carvalho Fernandes G, Bach E, Balsanelli E, Baura V, Brito LF, Wendisch VF, de Oliveira Pedrosa F, de Souza EM, Passaglia LMPFront Microbiol10.3389/fmicb.2017.018492017
Transcriptome29100491Detailed transcriptome analysis of the plant growth promoting Paenibacillus riograndensis SBR5 by using RNA-seq technology.Brito LF, Irla M, Kalinowski J, Wendisch VFBMC Genomics10.1186/s12864-017-4235-z20175' Untranslated Regions/genetics, *Gene Expression Profiling, Nucleotide Motifs, Paenibacillus/*genetics/*physiology, *Plant Development, Plants/*microbiology, Promoter Regions, Genetic/genetics, RNA, Bacterial/genetics, *Sequence Analysis, RNAGenetics
Enzymology32274563CRISPR interference-based gene repression in the plant growth promoter Paenibacillus sonchi genomovar Riograndensis SBR5.Brito LF, Schultenkamper K, Passaglia LMP, Wendisch VFAppl Microbiol Biotechnol10.1007/s00253-020-10571-62020Biofilms/growth & development, *CRISPR-Cas Systems, Chromosomes, *Gene Expression, L-Iditol 2-Dehydrogenase/metabolism, Paenibacillus/enzymology/*genetics, Promoter Regions, Genetic, RNA, Guide, Sorbitol/metabolismMetabolism
33424789Inorganic Phosphate Solubilization by Rhizosphere Bacterium Paenibacillus sonchi: Gene Expression and Physiological Functions.Brito LF, Lopez MG, Straube L, Passaglia LMP, Wendisch VFFront Microbiol10.3389/fmicb.2020.5886052020
Biotechnology35456781Metabolic Engineering of Corynebacterium glutamicum for Sustainable Production of the Aromatic Dicarboxylic Acid Dipicolinic Acid.Schwardmann LS, Dransfeld AK, Schaffer T, Wendisch VFMicroorganisms10.3390/microorganisms100407302022

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
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
20705Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-28159Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28159)
29382Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172579028776041
40372Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8040
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
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/
88219Reimer, 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-ID365764.1
122240Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110206Collection of Institut Pasteur (CIP 110206)