Strain identifier

BacDive ID: 159875

Type strain: Yes

Species: Paraburkholderia fynbosensis

NCBI tax ID(s): 1200993 (species)

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General

@ref: 66624

BacDive-ID: 159875

keywords: genome sequence, 16S sequence, Bacteria, psychrophilic, Gram-negative, motile, rod-shaped, colony-forming

description: Paraburkholderia fynbosensis LMG 27177 is a psychrophilic, Gram-negative, motile bacterium that forms circular colonies and was isolated from root nodules of Lebeckia ambigua.

NCBI tax id

  • NCBI tax id: 1200993
  • Matching level: species

doi: 10.13145/bacdive159875.20230509.8.1

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 fynbosensis
  • full scientific name: Paraburkholderia fynbosensis De Meyer et al. 2018

@ref: 66624

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Paraburkholderia

species: Paraburkholderia fynbosensis

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
66624negative2.0-2.5 µm0.9 µmrod-shapedyes
69480negative99.98

colony morphology

  • @ref: 66624
  • colony size: 2.2-4 mm
  • colony color: white
  • colony shape: circular
  • medium used: 1/2 lupin agar medium

Culture and growth conditions

culture medium

  • @ref: 66624
  • name: 1/2 lupin agar medium
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
66624nogrowth4psychrophilic
66624nogrowth40thermophilic
66624positivegrowth10-37

culture pH

  • @ref: 66624
  • ability: positive
  • type: growth
  • pH: 5-9
  • PH range: alkaliphile

Physiology and metabolism

spore formation

@refspore formationconfidence
69480no99.997
69481no97

halophily

  • @ref: 66624
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6662417306maltose-assimilation
6662416024D-mannose+assimilation
6662416899D-mannitol+assimilation
6662417128adipate+assimilation
6662417634D-glucose+assimilation
6662418401phenylacetate+assimilation
6662425115malate+assimilation
6662430849L-arabinose+assimilation
6662432032potassium gluconate+assimilation
6662453258citric acid+assimilation
6662459640N-acetylglucosamine+assimilation
6662416899D-mannitol-oxidation
6662417268myo-inositol-oxidation
6662417634D-glucose-oxidation
6662417924D-sorbitol-oxidation
6662417992sucrose-oxidation
6662427613amygdalin-oxidation
6662428053melibiose-oxidation
6662430849L-arabinose-oxidation
6662462345L-rhamnose+oxidation
6662417632nitrate-reduction

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
6662417698chloramphenicolyesyes30 µg (disc)
6662418208penicillin gyesyes10 µg (disc)
6662428971ampicillinyesyes10 µg (disc)
6662417833gentamicinyesyes10 µg (disc)
666246104kanamycinyesyes30 µg (disc)
6662417076streptomycinyesyes10 µg (disc)
6662427902tetracyclineyesyes30 µg (disc)

metabolite production

@refChebi-IDmetaboliteproduction
6662415688acetoinyes
6662416136hydrogen sulfideno
6662435581indoleno

enzymes

@refvalueactivityec
66624gelatinase-
66624lysine decarboxylase-4.1.1.18
66624ornithine decarboxylase-4.1.1.17
66624protease-
66624urease-3.5.1.5
66624arginine dihydrolase+3.5.3.6
66624beta-galactosidase+3.2.1.23
66624beta-glucosidase+3.2.1.21
66624catalase+1.11.1.6
66624cytochrome oxidase+1.9.3.1
66624tryptophan deaminase+/-4.1.99.1

Isolation, sampling and environmental information

isolation

  • @ref: 66624
  • sample type: root nodules of Lebeckia ambigua
  • host species: Lebeckia ambigua
  • sampling date: 2002-2007
  • geographic location: Western Cape
  • country: South Africa
  • origin.country: ZAF
  • continent: Africa
  • latitude: -31.4464
  • longitude: 19.1447

isolation source categories

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

Sequence information

16S sequences

  • @ref: 66624
  • description: Burkholderia sp. WSM4178 16S rRNA gene, strain WSM4178
  • accession: HE862279
  • length: 1495
  • database: ena
  • NCBI tax ID: 1200993

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paraburkholderia fynbosensis LMG 27177GCA_902859935contigncbi1200993
66792Paraburkholderia fynbosensis strain LMG 271771200993.3wgspatric1200993
66792Paraburkholderia fynbosensis LMG 271772921684003draftimg1200993

GC content

  • @ref: 66624
  • GC-content: 62.40
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno97no
motileyes91.556yes
gram-positiveno97.851no
anaerobicno98.645no
halophileno93.733no
spore-formingno93.003no
thermophileno99.573no
glucose-utilyes92.575yes
flagellatedno84.829no
aerobicyes88.772no
glucose-fermentno90.545no

External links

@ref: 66624

culture collection no.: LMG 27177, HAMBI 3356, WSM 4178

literature

  • topic: Phylogeny
  • Pubmed-ID: 29957169
  • title: Symbiotic and non-symbiotic Paraburkholderia isolated from South African Lebeckia ambigua root nodules and the description of Paraburkholderia fynbosensis sp. nov.
  • authors: De Meyer SE, Cnockaert M, Moulin L, Howieson JG, Vandamme P
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002884
  • year: 2018
  • mesh: Bacterial Typing Techniques, Base Composition, Burkholderiaceae/*classification/isolation & purification, DNA, Bacterial/genetics, Fabaceae/*microbiology, Fatty Acids/chemistry, Nucleic Acid Hybridization, *Phylogeny, Quinones/chemistry, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiology, Sequence Analysis, DNA, South Africa, Symbiosis
  • topic2: Transcriptome

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
66624Sofie E. De Meyer, Margo Cnockaert, Lionel Moulin, John G. Howieson and Peter VandammeSymbiotic and non-symbiotic Paraburkholderia isolated from South African Lebeckia ambigua root nodules and the description of Paraburkholderia fynbosensis sp. nov.10.1099/ijsem.0.002884IJSEM 68: 2607-2614 201829957169
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