Strain identifier

BacDive ID: 158593

Type strain: Yes

Species: Paraburkholderia azotifigens

Strain Designation: NF2-5-3

NCBI tax ID(s): 2057004 (species)

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

@ref: 65306

BacDive-ID: 158593

keywords: 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped, colony-forming

description: Paraburkholderia azotifigens NF2-5-3 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from paddy soil.

NCBI tax id

  • NCBI tax id: 2057004
  • Matching level: species

doi: 10.13145/bacdive158593.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Burkholderiaceae
  • genus: Paraburkholderia
  • species: Paraburkholderia azotifigens
  • full scientific name: Paraburkholderia azotifigens Choi and Im 2018

@ref: 65306

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Paraburkholderia

species: Paraburkholderia azotifigens

strain designation: NF2-5-3

type strain: yes

Morphology

cell morphology

  • @ref: 65306
  • gram stain: negative
  • cell length: 2.4-3 µm
  • cell width: 0.8-1.2 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 65306
  • colony size: 1-1.5 mm
  • colony color: cream
  • colony shape: circular
  • medium used: R2A

Culture and growth conditions

culture medium

@refnamegrowth
65306Reasoner's 2A agar (R2A)yes
65306nutreint agaryes
65306tryptic soy agaryes
65306LB (Luria-Bertani) MEDIUMyes
65306MacConkey agaryes

culture temp

@refgrowthtypetemperaturerange
65306positivegrowth15-37
65306nogrowth10psychrophilic
65306nogrowth40thermophilic
65306positiveoptimum25-30mesophilic

culture pH

@refabilitytypepH
65306positivegrowth6-8
65306positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 65306
  • oxygen tolerance: aerobe

spore formation

  • @ref: 65306
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
65306NaClpositivegrowth0 %(w/v)
65306NaClpositivegrowth2 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
65306309162-oxoglutarate+assimilation
65306161933-hydroxybenzoate+assimilation
65306370543-hydroxybutyrate+assimilation
65306178794-hydroxybenzoate-assimilation
65306581435-dehydro-D-gluconate-assimilation
6530630089acetate+assimilation
6530617128adipate-assimilation
6530627689decanoate+assimilation
6530685146carboxymethylcellulose-hydrolysis
65306casein-hydrolysis
6530616947citrate-assimilation
6530617634D-glucose+assimilation
6530616899D-mannitol+assimilation
6530616024D-mannose+assimilation
6530616988D-ribose+assimilation
6530617924D-sorbitol+assimilation
6530616991dna-hydrolysis
653064853esculin+assimilation
6530624265gluconate+assimilation
6530617234glucose+builds acid from
6530628087glycogen-assimilation
6530617268myo-inositol+assimilation
6530617240itaconate-assimilation
6530616977L-alanine+assimilation
6530630849L-arabinose+assimilation
6530618287L-fucose+assimilation
6530615971L-histidine+assimilation
6530617203L-proline+assimilation
6530662345L-rhamnose+assimilation
6530617115L-serine+assimilation
6530624996lactate+assimilation
6530625115malate+assimilation
6530615792malonate-assimilation
6530617306maltose-assimilation
6530628053melibiose-assimilation
6530617632nitrate+assimilation
6530617632nitrate+reduction
6530618401phenylacetate+assimilation
6530617272propionate+assimilation
6530617814salicin-assimilation
6530628017starch-hydrolysis
653069300suberic acid-assimilation
6530617992sucrose+assimilation
6530631011valerate+assimilation

metabolite production

  • @ref: 65306
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
65306cytochrome oxidase+1.9.3.1
65306catalase+1.11.1.6
65306N-acetyl-beta-glucosaminidase+3.2.1.52
65306acid phosphatase+3.1.3.2
65306alkaline phosphatase+3.1.3.1
65306arginine dihydrolase+3.5.3.6
65306cystine arylamidase+3.4.11.3
65306esterase (C 4)+
65306esterase Lipase (C 8)+
65306beta-galactosidase+3.2.1.23
65306beta-glucosidase+3.2.1.21
65306leucine arylamidase+3.4.11.1
65306naphthol-AS-BI-phosphohydrolase+
65306urease+3.5.1.5
65306valine arylamidase+
65306N-acetyl-beta-glucosaminidase-3.2.1.52
65306trypsin-3.4.21.4
65306alpha-chymotrypsin-3.4.21.1
65306alpha-fucosidase-3.2.1.51
65306alpha-galactosidase-3.2.1.22
65306alpha-glucosidase-3.2.1.20
65306beta-glucuronidase-3.2.1.31
65306lipase (C 14)-
65306alpha-mannosidase-3.2.1.24
65306protease-

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    65306C12:01.1
    65306C14:05.3
    65306C16:025.8
    65306C18:01.8
    65306C19:0 iso1.4
    65306C16:0 2OH2.2
    65306C16:0 3OH5.4
    65306C16:1 2OH1.6
    65306C17:0 cyclo10.5
    65306C19:0 cyclo ω8c6.7
    65306iso-C16:1 I/C14:0 3-OH7.9
    65306C16:1ω7c/C16:1ω6c6.2
    65306C18:1ω7c/C18:1ω6c22.9
    65306C18:1ω7c 11-methyl1.2
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A
  • agar/liquid: agar
  • incubation temperature: 30
  • incubation time: 2
  • software version: Sherlock 6.0
  • library/peak naming table: TSBA60
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

  • @ref: 65306
  • sample type: paddy soil
  • geographic location: anseong city
  • country: Republic of Korea
  • origin.country: KOR
  • continent: Asia
  • enrichment culture: nitrogen-free medium
  • enrichment culture composition: (per litre water): 2 g sucrose, 5 g glucose, 3 g mannitol, 1 g malic acid, 1 g citric acid, 1 g sodium acetate, 0.2 g K2HPO4, 0.6 g KH2PO4, 0.2 g MgSO4 x 7H2O, 0.02 g CaCl2 x 2H2O and 0.002 g Na2MoO4
  • enrichment culture duration: 7 days
  • enrichment culture temperature: 30
  • isolation procedure: One gram of soil was placed in 10 ml (0.85 % NaCl) sterile saline and stirred for 10 min. An aqueous volume of 100 µl of the mixture was spread on nitrogen-free medium in triplicate and incubated at 30°C for 7 days

isolation source categories

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

Sequence information

16S sequences

  • @ref: 65306
  • description: 16S rRNA gene sequence
  • accession: KX510119
  • database: nuccore

GC content

  • @ref: 65306
  • GC-content: 64.2
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 65306

culture collection no.: KACC 18968, LMG 29961

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny29185955Paraburkholderia azotifigens sp. nov., a nitrogen-fixing bacterium isolated from paddy soil.Choi GM, Im WTInt J Syst Evol Microbiol10.1099/ijsem.0.0025052017Bacterial Typing Techniques, Base Composition, Burkholderiaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nitrogen Fixation, Nucleic Acid Hybridization, Oryza, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryTranscriptome
Phylogeny32101513Paraburkholderia flava sp. nov., isolated from cool temperate forest soil.Trinh NH, Kim JInt J Syst Evol Microbiol10.1099/ijsem.0.0040632020Bacterial Typing Techniques, Base Composition, Burkholderiaceae/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryTranscriptome

Reference

@idauthorstitledoi/urljournalpubmed
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
65306Gyu-Min Choi, Wan-Taek ImParaburkholderia azotifigens sp. nov., a nitrogen-fixing bacterium isolated from paddy soil10.1099/ijsem.0.002505IJSEM 68: 310-316 201829185955