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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/bacdive158593.20221219.7.1

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

@refgram staincell lengthcell widthcell shapemotilityconfidence
65306negative2.4-3 µm0.8-1.2 µmrod-shapedno
69480negative98.66

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

@refspore formationconfidence
65306no
69480no96.342

halophily

@refsaltgrowthtested relationconcentrationhalophily levelconfidence
65306NaClpositivegrowth0 %(w/v)
65306NaClpositivegrowth2 %(w/v)
69480non-halophilic99.045

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
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