Strain identifier
BacDive ID: 158593
Type strain:
Species: Paraburkholderia azotifigens
Strain Designation: NF2-5-3
NCBI tax ID(s): 2057004 (species)
version 8.1 (current version)
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
@ref | name | growth |
---|---|---|
65306 | Reasoner's 2A agar (R2A) | yes |
65306 | nutreint agar | yes |
65306 | tryptic soy agar | yes |
65306 | LB (Luria-Bertani) MEDIUM | yes |
65306 | MacConkey agar | yes |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
65306 | positive | growth | 15-37 | |
65306 | no | growth | 10 | psychrophilic |
65306 | no | growth | 40 | thermophilic |
65306 | positive | optimum | 25-30 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
65306 | positive | growth | 6-8 |
65306 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 65306
- oxygen tolerance: aerobe
spore formation
- @ref: 65306
- spore formation: no
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
65306 | NaCl | positive | growth | 0 %(w/v) |
65306 | NaCl | positive | growth | 2 %(w/v) |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
65306 | 30916 | 2-oxoglutarate | + | assimilation |
65306 | 16193 | 3-hydroxybenzoate | + | assimilation |
65306 | 37054 | 3-hydroxybutyrate | + | assimilation |
65306 | 17879 | 4-hydroxybenzoate | - | assimilation |
65306 | 58143 | 5-dehydro-D-gluconate | - | assimilation |
65306 | 30089 | acetate | + | assimilation |
65306 | 17128 | adipate | - | assimilation |
65306 | 27689 | decanoate | + | assimilation |
65306 | 85146 | carboxymethylcellulose | - | hydrolysis |
65306 | casein | - | hydrolysis | |
65306 | 16947 | citrate | - | assimilation |
65306 | 17634 | D-glucose | + | assimilation |
65306 | 16899 | D-mannitol | + | assimilation |
65306 | 16024 | D-mannose | + | assimilation |
65306 | 16988 | D-ribose | + | assimilation |
65306 | 17924 | D-sorbitol | + | assimilation |
65306 | 16991 | dna | - | hydrolysis |
65306 | 4853 | esculin | + | assimilation |
65306 | 24265 | gluconate | + | assimilation |
65306 | 17234 | glucose | + | builds acid from |
65306 | 28087 | glycogen | - | assimilation |
65306 | 17268 | myo-inositol | + | assimilation |
65306 | 17240 | itaconate | - | assimilation |
65306 | 16977 | L-alanine | + | assimilation |
65306 | 30849 | L-arabinose | + | assimilation |
65306 | 18287 | L-fucose | + | assimilation |
65306 | 15971 | L-histidine | + | assimilation |
65306 | 17203 | L-proline | + | assimilation |
65306 | 62345 | L-rhamnose | + | assimilation |
65306 | 17115 | L-serine | + | assimilation |
65306 | 24996 | lactate | + | assimilation |
65306 | 25115 | malate | + | assimilation |
65306 | 15792 | malonate | - | assimilation |
65306 | 17306 | maltose | - | assimilation |
65306 | 28053 | melibiose | - | assimilation |
65306 | 17632 | nitrate | + | assimilation |
65306 | 17632 | nitrate | + | reduction |
65306 | 18401 | phenylacetate | + | assimilation |
65306 | 17272 | propionate | + | assimilation |
65306 | 17814 | salicin | - | assimilation |
65306 | 28017 | starch | - | hydrolysis |
65306 | 9300 | suberic acid | - | assimilation |
65306 | 17992 | sucrose | + | assimilation |
65306 | 31011 | valerate | + | assimilation |
metabolite production
- @ref: 65306
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
65306 | cytochrome oxidase | + | 1.9.3.1 |
65306 | catalase | + | 1.11.1.6 |
65306 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
65306 | acid phosphatase | + | 3.1.3.2 |
65306 | alkaline phosphatase | + | 3.1.3.1 |
65306 | arginine dihydrolase | + | 3.5.3.6 |
65306 | cystine arylamidase | + | 3.4.11.3 |
65306 | esterase (C 4) | + | |
65306 | esterase Lipase (C 8) | + | |
65306 | beta-galactosidase | + | 3.2.1.23 |
65306 | beta-glucosidase | + | 3.2.1.21 |
65306 | leucine arylamidase | + | 3.4.11.1 |
65306 | naphthol-AS-BI-phosphohydrolase | + | |
65306 | urease | + | 3.5.1.5 |
65306 | valine arylamidase | + | |
65306 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
65306 | trypsin | - | 3.4.21.4 |
65306 | alpha-chymotrypsin | - | 3.4.21.1 |
65306 | alpha-fucosidase | - | 3.2.1.51 |
65306 | alpha-galactosidase | - | 3.2.1.22 |
65306 | alpha-glucosidase | - | 3.2.1.20 |
65306 | beta-glucuronidase | - | 3.2.1.31 |
65306 | lipase (C 14) | - | |
65306 | alpha-mannosidase | - | 3.2.1.24 |
65306 | protease | - |
fatty acid profile
fatty acids
@ref fatty acid percentage 65306 C12:0 1.1 65306 C14:0 5.3 65306 C16:0 25.8 65306 C18:0 1.8 65306 C19:0 iso 1.4 65306 C16:0 2OH 2.2 65306 C16:0 3OH 5.4 65306 C16:1 2OH 1.6 65306 C17:0 cyclo 10.5 65306 C19:0 cyclo ω8c 6.7 65306 iso-C16:1 I/C14:0 3-OH 7.9 65306 C16:1ω7c/C16:1ω6c 6.2 65306 C18:1ω7c/C18:1ω6c 22.9 65306 C18:1ω7c 11-methyl 1.2 - 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
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 29185955 | Paraburkholderia azotifigens sp. nov., a nitrogen-fixing bacterium isolated from paddy soil. | Choi GM, Im WT | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002505 | 2017 | Bacterial 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/chemistry | Transcriptome |
Phylogeny | 32101513 | Paraburkholderia flava sp. nov., isolated from cool temperate forest soil. | Trinh NH, Kim J | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004063 | 2020 | Bacterial 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/chemistry | Transcriptome |
Reference
@id | authors | title | doi/url | journal | pubmed |
---|---|---|---|---|---|
20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | ||
65306 | Gyu-Min Choi, Wan-Taek Im | Paraburkholderia azotifigens sp. nov., a nitrogen-fixing bacterium isolated from paddy soil | 10.1099/ijsem.0.002505 | IJSEM 68: 310-316 2018 | 29185955 |