Strain identifier

BacDive ID: 141156

Type strain: Yes

Species: Paenibacillus azotifigens

Strain Designation: NF2-4-5

Strain history: <- W.-T. Im, Hankyong National University, Anseong-si, Republic of Korea; NF2-4-5

NCBI tax ID(s): 2047734 (species)

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General

@ref: 64983

BacDive-ID: 141156

DSM-Number: 104138

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

description: Paenibacillus azotifigens NF2-4-5 is an aerobe, spore-forming, mesophilic bacterium that forms circular colonies and was isolated from paddy soil.

NCBI tax id

  • NCBI tax id: 2047734
  • Matching level: species

strain history

  • @ref: 64983
  • history: <- W.-T. Im, Hankyong National University, Anseong-si, Republic of Korea; NF2-4-5

doi: 10.13145/bacdive141156.20230509.8.1

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 azotifigens
  • full scientific name: Paenibacillus azotifigens Siddiqi et al. 2017

@ref: 64983

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Paenibacillus

species: Paenibacillus azotifigens

full scientific name: Paenibacillus azotifigens Siddiqi et al. 2017

strain designation: NF2-4-5

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
44077positive1.5-3 µm0.5-1.2 µmrod-shapedyes
69480yes96.332
69480positive99.999

colony morphology

  • @ref: 44077
  • colony size: 1.5-2.4 mm
  • colony color: milky-coloured
  • colony shape: circular
  • incubation period: 2 days
  • medium used: R2A agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
44077Dnase agarno
44077LB (Luria-Bertani) MEDIUMno
44077MacConkeyno
44077NA agaryes
44077Reasoner's 2A agar (R2A)yes
44077Trypticase Soy Agar (TSA)yes
64983R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) 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 Distilled water

culture temp

@refgrowthtypetemperaturerange
44077positiveoptimum30mesophilic
44077positivegrowth18-37
44077nogrowth15psychrophilic
44077nogrowth40thermophilic
64983positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
44077positiveoptimum6.5-7.0
44077positivegrowth6.0-8.5alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 44077
  • oxygen tolerance: aerobe

spore formation

@refspore descriptiontype of sporespore formationconfidence
44077ellipsoidal spores located subterminally in swollen sporangiaendosporeyes
69481yes100
69480yes100

halophily

@refsaltgrowthtested relationconcentration
44077NaClpositivegrowth0.5-2.0 %
44077NaClnogrowth3 %

observation

  • @ref: 44077
  • observation: nitrogen fixation

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
44077161933-hydroxybenzoate-assimilation
44077370543-hydroxybutyrate-assimilation
44077178794-hydroxybenzoate-assimilation
44077581435-dehydro-D-gluconate-assimilation
4407730089acetate-assimilation
4407717128adipate-assimilation
4407727689decanoate-assimilation
4407716947citrate-assimilation
4407717924D-sorbitol-assimilation
4407717268myo-inositol-assimilation
4407717240itaconate-assimilation
4407716977L-alanine-assimilation
4407718287L-fucose-assimilation
4407715971L-histidine-assimilation
4407717203L-proline-assimilation
4407762345L-rhamnose-assimilation
4407717115L-serine-assimilation
4407724996lactate-assimilation
4407725115malate-assimilation
4407715792malonate-assimilation
44077506227N-acetylglucosamine-assimilation
4407718401phenylacetate-assimilation
4407717272propionate-assimilation
440779300suberic acid-assimilation
4407731011valerate-assimilation
4407717234glucose-builds acid from
440775291gelatin-hydrolysis
440772-oxogluconate+assimilation
4407717634D-glucose+assimilation
4407716899D-mannitol+assimilation
4407716024D-mannose+assimilation
4407716988D-ribose+assimilation
4407724265gluconate+assimilation
4407728087glycogen+assimilation
4407730849L-arabinose+assimilation
4407717306maltose+assimilation
4407728053melibiose+assimilation
4407717814salicin+assimilation
4407717992sucrose+assimilation
440774853esculin+hydrolysis
4407717632nitrate+reduction

metabolite production

  • @ref: 44077
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
44077cytochrome oxidase+1.9.3.1
44077catalase+1.11.1.6
44077esterase Lipase (C 8)+
44077leucine arylamidase+3.4.11.1
44077alpha-galactosidase+3.2.1.22
44077beta-glucosidase+3.2.1.21
44077alkaline phosphatase+3.1.3.1
44077acid phosphatase+3.1.3.2
44077naphthol-AS-BI-phosphohydrolase+
44077beta-galactosidase+3.2.1.23
44077alpha-glucosidase+3.2.1.20
44077alpha-mannosidase+3.2.1.24
44077alpha-fucosidase+3.2.1.51
44077esterase+
44077lipase-
44077trypsin-3.4.21.4
44077beta-glucuronidase-3.2.1.31
44077arginine dihydrolase-3.5.3.6
44077urease-3.5.1.5
44077valine arylamidase-
44077cystine arylamidase-3.4.11.3
44077alpha-chymotrypsin-3.4.21.1

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperatureisolation proceduregeographic location
44077paddy soilRepublic of KoreaKORAsianitrogen-free medium (Cavalcante and Doëbereiner, 1988)composition g per litre of water: 2g sucrose, 5g dextrose, 3g mannitol, 1g malic acid, 1g citric acid, 1g sodium acetate, 0.2g K2HPO4, 0.6g KH2PO4 , 0.2g MgSO4 . 7H2O, 0.02g CaCl2 2H2O, 0.002g Na2 MoO4 and 1ml vitamin solution7 days30One gram of soil was placed in 10ml (0.85% NaCl) sterile saline and stirred for 10min. An aqueous volume of 100µl of the mixture was spread on nitrogen-free medium
64983paddy soilRepublic of KoreaKORAsiaAnseoung city

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Engineered#Agriculture#Field
#Host#Plants#Herbaceous plants (Grass,Crops)
#Condition#Anoxic (anaerobic)
#Condition#Humid

Safety information

risk assessment

  • @ref: 64983
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 64983
  • description: Paenibacillus azotifigens strain NF2-4-5 16S ribosomal RNA gene, partial sequence
  • accession: KX510118
  • length: 1481
  • database: ena
  • NCBI tax ID: 2047734

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paenibacillus azotifigens LMG 29963GCA_008635805scaffoldncbi2047734
66792Paenibacillus azotifigens strain LMG 299632047734.3wgspatric2047734
66792Paenibacillus azotifigens LMG 299632904120120draftimg2047734

GC content

  • @ref: 64983
  • GC-content: 56.3
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes87.426yes
flagellatedyes81.249no
gram-positiveyes88.222no
anaerobicno95.49no
aerobicyes86.402yes
halophileno94.994no
spore-formingyes95.748yes
thermophileno99.91no
glucose-utilyes91.03yes
glucose-fermentno80.937no

External links

@ref: 64983

culture collection no.: KACC 18967, LMG 29963, DSM 104138

straininfo link

  • @ref: 96871
  • straininfo: 403211

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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
Phylogeny30073429Paenibacillus helianthi sp. nov., a nitrogen fixing species isolated from the rhizosphere of Helianthus annuus L.Ambrosini A, Sant'Anna FH, Heinzmann J, de Carvalho Fernandes G, Bach E, Passaglia LMPAntonie Van Leeuwenhoek10.1007/s10482-018-1135-42018Anaerobiosis/physiology, Bacterial Typing Techniques, Base Composition, Brazil, DNA, Bacterial/*genetics, Fatty Acids/biosynthesis, Genotype, Helianthus/*microbiology, Nitrogen/metabolism, Nitrogen Fixation/*physiology, Paenibacillus/classification/*genetics/isolation & purification/metabolism, Phenotype, *Phylogeny, RNA, Ribosomal, 16S/*genetics, Rhizosphere, Spores, Bacterial/physiologyGenetics
Phylogeny31985395Description of Paenibacillus tepidiphilus sp. nov., isolated from a tepid spring.Narsing Rao MP, Dong ZY, Kan Y, Dong L, Li S, Xiao M, Kang YQ, Zhang K, Li WJInt J Syst Evol Microbiol10.1099/ijsem.0.0040042020Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Hot Springs/*microbiology, Nucleic Acid Hybridization, Paenibacillus/*classification/isolation & purification, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, *Water MicrobiologyTranscriptome
Phylogeny32535648Description of Paenibacillus yunnanensis sp. nov., Isolated from a Tepid Spring.Narsing Rao MP, Dong ZY, Amoolya S, Neelavar S, Liu BB, Guo SX, Hozzein W, Li WJCurr Microbiol10.1007/s00284-020-02087-z2020Bacterial Typing Techniques, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Nucleic Acid Hybridization, *Paenibacillus/genetics, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorstitledoi/urljournalpubmedcatalogue
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
44077Muhammad Zubair Siddiqi, Gyu-Min Choi, Kang Duk Choi and Wan-Taek ImPaenibacillus azotifigens sp. nov., a novel nitrogen-fixing bacterium isolated from paddy soil10.1099/ijsem.0.002269IJSEM 67: 4917-4922 201729039306
64983Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-104138Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104138)
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
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
96871Reimer, 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-ID403211.1