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Strain identifier

BacDive ID: 1960

Type strain: Yes

Species: Paraburkholderia phymatum

Strain history: <- CCUG <- P. Vandamme, Ghent <- C. Boivin, Montpellier

NCBI tax ID(s): 148447 (species)

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

@ref: 6802

BacDive-ID: 1960

DSM-Number: 17167

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic

description: Paraburkholderia phymatum DSM 17167 is an aerobe, mesophilic bacterium that was isolated from root nodule of Machaerium lunatum.

NCBI tax id

  • NCBI tax id: 148447
  • Matching level: species

strain history: <- CCUG <- P. Vandamme, Ghent <- C. Boivin, Montpellier

doi: 10.13145/bacdive1960.20221219.7.1

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 phymatum
  • full scientific name: Paraburkholderia phymatum (Vandamme et al. 2003) Sawana et al. 2015
  • synonyms

    • @ref: 20215
    • synonym: Burkholderia phymatum

@ref: 6802

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Paraburkholderia

species: Paraburkholderia phymatum

full scientific name: Paraburkholderia phymatum (Vandamme et al. 2003) Sawana et al. 2015

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 98.456

colony morphology

  • @ref: 6802
  • incubation period: 1-2 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6802R2A 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
6802CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
41976MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)

culture temp

@refgrowthtypetemperaturerange
6802positivegrowth28mesophilic
41976positivegrowth30mesophilic
57560positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 57560
  • oxygen tolerance: aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 96.662

halophily

  • @ref: 69480
  • halophily level: non-halophilic
  • confidence: 98.762

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate+assimilation
6836924265gluconate+assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol+assimilation
6836916024D-mannose+assimilation
6836930849L-arabinose+assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
6802catalase+1.11.1.6
6802cytochrome-c oxidase+1.9.3.1
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382alkaline phosphatase+3.1.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
6802-++/-+/--+----++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6802+------++++++-++-+++-
6802+------++++++-++-++/-++
6802+------++++++-++-++++
6802+------++++++-++-+++-

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinent
6802root nodule of Machaerium lunatumMachaerium lunatumFrench GuianaFRAMiddle and South America
57560Root nodule of Machaerium lunatumFrench GuianaFRAMiddle and South America

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Shrub (Scrub)
#Host Body-Site#Plant#Root nodule

Safety information

risk assessment

  • @ref: 6802
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6802
  • description: Burkholderia sp. STM815 partial 16S rRNA gene, strain STM815
  • accession: AJ302312
  • length: 1435
  • database: ena
  • NCBI tax ID: 391038

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paraburkholderia phymatum STM815 LMG 21445GCA_902833665scaffoldncbi391038
66792Paraburkholderia phymatum STM815 strain LMG 21445391038.42wgspatric391038
66792Salmonella enterica HZ322GCA_002808925scaffoldpatric28901

GC content

  • @ref: 6802
  • GC-content: 62.1

External links

@ref: 6802

culture collection no.: DSM 17167, CCUG 47179, CIP 108236, LMG 21445, STM 815

straininfo link

@refpassport
20218http://www.straininfo.net/strains/386397
20218http://www.straininfo.net/strains/302138
20218http://www.straininfo.net/strains/531485
20218http://www.straininfo.net/strains/292597

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12583710Burkholderia tuberum sp. nov. and Burkholderia phymatum sp. nov., nodulate the roots of tropical legumes.Vandamme P, Goris J, Chen WM, de Vos P, Willems ASyst Appl Microbiol10.1078/072320202605176342002Base Sequence, Burkholderia/*classification/cytology/genetics/isolation & purification, Fabaceae/*microbiology, Fatty Acids/analysis, Molecular Sequence Data, Phylogeny, Plant Roots/metabolism/microbiology, RNA, Ribosomal, 16S, Soil Microbiology, Tropical ClimateGenetics
Phylogeny16269788Proof that Burkholderia strains form effective symbioses with legumes: a study of novel Mimosa-nodulating strains from South America.Chen WM, de Faria SM, Straliotto R, Pitard RM, Simoes-Araujo JL, Chou JH, Chou YJ, Barrios E, Prescott AR, Elliott GN, Sprent JI, Young JP, James EKAppl Environ Microbiol10.1128/AEM.71.11.7461-7471.20052005Acyltransferases/genetics, Bacterial Proteins/genetics, Base Sequence, Brazil, Burkholderia/*classification/growth & development, Mimosa/*microbiology, Molecular Sequence Data, *Nitrogen Fixation, Oxidoreductases/genetics, Phylogeny, RNA, Ribosomal, 16S/genetics, Restriction Mapping, Sequence Analysis, DNA, South America, *Symbiosis, VenezuelaGenetics
Phylogeny16449457Burkholderia terrae sp. nov., isolated from a forest soil.Yang HC, Im WT, Kim KK, An DS, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.63968-02006Bacterial Typing Techniques, Burkholderia/chemistry/*classification/genetics/isolation & purification, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Trees/*microbiologyGenetics
Phylogeny17176403Burkholderia phymatum is a highly effective nitrogen-fixing symbiont of Mimosa spp. and fixes nitrogen ex planta.Elliott GN, Chen WM, Chou JH, Wang HC, Sheu SY, Perin L, Reis VM, Moulin L, Simon MF, Bontemps C, Sutherland JM, Bessi R, de Faria SM, Trinick MJ, Prescott AR, Sprent JI, James EKNew Phytol10.1111/j.1469-8137.2006.01894.x2007Bacterial Proteins/classification/genetics, Bacteriological Techniques, Burkholderia/genetics/isolation & purification/*metabolism, Cupriavidus/genetics/isolation & purification/metabolism, DNA, Ribosomal/chemistry/classification, Fabaceae/microbiology, Green Fluorescent Proteins/analysis, Mimosa/*microbiology, Nitrogenase/metabolism, Phylogeny, Root Nodules, Plant/growth & development/metabolism/microbiology, Species Specificity, *SymbiosisMetabolism
Phylogeny19841903Mixotrophic metabolism in Burkholderia kururiensis subsp. thiooxydans subsp. nov., a facultative chemolithoautotrophic thiosulfate oxidizing bacterium isolated from rhizosphere soil and proposal for classification of the type strain of Burkholderia kururiensis as Burkholderia kururiensis subsp. kururiensis subsp. nov.Anandham R, Indira Gandhi P, Kwon SW, Sa TM, Kim YK, Jee HJArch Microbiol10.1007/s00203-009-0517-42009Burkholderia/*classification/genetics/growth & development/*metabolism, Chemoautotrophic Growth/*physiology, DNA, Bacterial/chemistry/genetics, Nucleic Acid Hybridization, Oxidation-Reduction, Phenotype, Phylogeny, Soil Microbiology, Thiosulfates/*metabolismMetabolism
Metabolism20456044Nodulation and nitrogen fixation by Mimosa spp. in the Cerrado and Caatinga biomes of Brazil.Dos Reis FB Jr, Simon MF, Gross E, Boddey RM, Elliott GN, Neto NE, de Fatima Loureiro M, de Queiroz LP, Scotti MR, Chen WM, Noren A, Rubio MC, de Faria SM, Bontemps C, Goi SR, Young JPW, Sprent JI, James EKNew Phytol10.1111/j.1469-8137.2010.03267.x2010Acetylene/metabolism, Blotting, Western, Brazil, *Ecosystem, Geography, Mimosa/cytology/microbiology/*physiology/ultrastructure, Nitrogen Fixation/*physiology, Nitrogen Isotopes, Oxidation-Reduction, Oxidoreductases/metabolism, Plant Root Nodulation/*physiology, Rhizobium/physiology, Root Nodules, Plant/cytology/enzymology/microbiology/ultrastructure, SymbiosisEnzymology
Metabolism22282515Effect of phosphoglycerate mutase and fructose 1,6-bisphosphatase deficiency on symbiotic Burkholderia phymatum.Chen WM, Prell J, James EK, Sheu DS, Sheu SYMicrobiology (Reading)10.1099/mic.0.055095-02012Bacterial Proteins/genetics/metabolism, Burkholderia/*enzymology/genetics, Carbohydrate Metabolism, Cloning, Molecular, Fructose-Bisphosphatase/genetics/*metabolism, Genetic Complementation Test, Mimosa/*microbiology, Mutagenesis, Nitrogen Fixation, Phosphoglycerate Mutase/genetics/*metabolism, Plant Root Nodulation, Plant Roots/microbiology, *SymbiosisEnzymology
Phylogeny22467155Burkholderia diazotrophica sp. nov., isolated from root nodules of Mimosa spp.Sheu SY, Chou JH, Bontemps C, Elliott GN, Gross E, Dos Reis Junior FB, Melkonian R, Moulin L, James EK, Sprent JI, Young JPW, Chen WMInt J Syst Evol Microbiol10.1099/ijs.0.039859-02012Bacterial Typing Techniques, Base Composition, Brazil, Burkholderia/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/analysis, Genes, Bacterial, Mimosa/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiology, Sequence Analysis, DNAGenetics
Metabolism22556357Biosynthesis of branched-chain amino acids is essential for effective symbioses between betarhizobia and Mimosa pudica.Chen WM, Prell J, James EK, Sheu DS, Sheu SYMicrobiology (Reading)10.1099/mic.0.058370-02012Amino Acids, Branched-Chain/*biosynthesis, Burkholderia/genetics/growth & development/metabolism/*physiology, Culture Media/chemistry, Cupriavidus/genetics/growth & development/metabolism/*physiology, DNA Transposable Elements, Gene Deletion, Genes, Bacterial, Genetic Complementation Test, Mimosa/*microbiology/*physiology, Mutagenesis, Insertional, *SymbiosisCultivation
Metabolism23568428Enhanced degradation of haloacid by heterologous expression in related Burkholderia species.Su X, Deng L, Kong KF, Tsang JSBiotechnol Bioeng10.1002/bit.249172013Acetates/metabolism, Bacterial Proteins/genetics/*metabolism, Biodegradation, Environmental, *Burkholderia/enzymology/genetics/metabolism, Hydrolases/genetics/*metabolism, Metabolic Engineering/*methods, RNA, Messenger/analysis/genetics/metabolism, Substrate SpecificityEnzymology
Genetics23686262Regulon studies and in planta role of the BraI/R quorum-sensing system in the plant-beneficial Burkholderia cluster.Coutinho BG, Mitter B, Talbi C, Sessitsch A, Bedmar EJ, Halliday N, James EK, Camara M, Venturi VAppl Environ Microbiol10.1128/AEM.00635-132013Acyl-Butyrolactones/metabolism, Burkholderia/*genetics/physiology, Chromatography, Liquid, *Genome, Bacterial, Oligonucleotide Array Sequence Analysis, Quorum Sensing, *Regulon, Reverse Transcriptase Polymerase Chain Reaction, Species Specificity, Spectrometry, Mass, Electrospray Ionization, Tandem Mass SpectrometryPhylogeny
Genetics25197461Complete Genome sequence of Burkholderia phymatum STM815(T), a broad host range and efficient nitrogen-fixing symbiont of Mimosa species.Moulin L, Klonowska A, Caroline B, Booth K, Vriezen JA, Melkonian R, James EK, Young JP, Bena G, Hauser L, Land M, Kyrpides N, Bruce D, Chain P, Copeland A, Pitluck S, Woyke T, Lizotte-Waniewski M, Bristow J, Riley MStand Genomic Sci10.4056/sigs.48610212014Pathogenicity
Metabolism27060604Burkholderia genome mining for nonribosomal peptide synthetases reveals a great potential for novel siderophores and lipopeptides synthesis.Esmaeel Q, Pupin M, Kieu NP, Chataigne G, Bechet M, Deravel J, Krier F, Hofte M, Jacques P, Leclere VMicrobiologyopen10.1002/mbo3.3472016Antifungal Agents/metabolism, Bacterial Proteins/biosynthesis, Base Sequence, Burkholderia pseudomallei/*genetics/*metabolism, DNA, Bacterial/genetics, Gene Expression Profiling, Genome, Bacterial/*genetics, Lipopeptides/*biosynthesis/chemistry, Peptide Synthases/*metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Siderophores/*biosynthesis/chemistryGenetics
Metabolism29378510Transcriptomic profiling of Burkholderia phymatum STM815, Cupriavidus taiwanensis LMG19424 and Rhizobium mesoamericanum STM3625 in response to Mimosa pudica root exudates illuminates the molecular basis of their nodulation competitiveness and symbiotic evolutionary history.Klonowska A, Melkonian R, Miche L, Tisseyre P, Moulin LBMC Genomics10.1186/s12864-018-4487-22018Burkholderia/*genetics/metabolism, Cupriavidus/*genetics/metabolism, Gene Expression Profiling, Genome, Bacterial, Microbial Interactions, Mimosa/*microbiology, Plant Root Nodulation/*genetics, Plant Roots/physiology, Rhizobium/*genetics/metabolism, Symbiosis/geneticsGenetics
Metabolism29614780Metabolomics and Transcriptomics Identify Multiple Downstream Targets of Paraburkholderia phymatum sigma(54) During Symbiosis with Phaseolus vulgaris.Lardi M, Liu Y, Giudice G, Ahrens CH, Zamboni N, Pessi GInt J Mol Sci10.3390/ijms190410492018Gene Expression Regulation, Bacterial/genetics, Metabolomics/methods, Phaseolus/*metabolism/*microbiology, Promoter Regions, Genetic/genetics, Rhizobium/physiology, Root Nodules, Plant/metabolism/microbiology, Symbiosis/genetics/physiology, Transcriptome/*geneticsGenetics
Metabolism29781800Linkage of the Nit1C gene cluster to bacterial cyanide assimilation as a nitrogen source.Jones LB, Ghosh P, Lee JH, Chou CN, Kunz DAMicrobiology (Reading)10.1099/mic.0.0006682018Aminohydrolases/*genetics/metabolism, Bacteria/*genetics/growth & development/*metabolism, Bacterial Proteins/*genetics/metabolism, Conserved Sequence, Cyanides/*metabolism, Evolution, Molecular, Gene Deletion, Genetic Linkage, Multigene Family/*genetics, Transcription, Genetic
Metabolism33924023Paraburkholderia phymatum Homocitrate Synthase NifV Plays a Key Role for Nitrogenase Activity during Symbiosis with Papilionoids and in Free-Living Growth Conditions.Belles-Sancho P, Lardi M, Liu Y, Hug S, Pinto-Carbo MA, Zamboni N, Pessi GCells10.3390/cells100409522021Bacterial Proteins/*metabolism, Burkholderiaceae/*enzymology/genetics, Fabaceae/*microbiology, Genome, Bacterial, Green Fluorescent Proteins/metabolism, Host-Pathogen Interactions, Likelihood Functions, Metabolome, Nitrogenase/*metabolism, Oxo-Acid-Lyases/*metabolism, Phylogeny, Root Nodules, Plant/metabolism/microbiology, *SymbiosisGenetics
34357349Metabolomics and Dual RNA-Sequencing on Root Nodules Revealed New Cellular Functions Controlled by Paraburkholderia phymatum NifA.Belles-Sancho P, Lardi M, Liu Y, Eberl L, Zamboni N, Bailly A, Pessi GMetabolites10.3390/metabo110704552021
34394152Differential Expression of Paraburkholderia phymatum Type VI Secretion Systems (T6SS) Suggests a Role of T6SS-b in Early Symbiotic Interaction.Hug S, Liu Y, Heiniger B, Bailly A, Ahrens CH, Eberl L, Pessi GFront Plant Sci10.3389/fpls.2021.6995902021
36247538A novel function of the key nitrogen-fixation activator NifA in beta-rhizobia: Repression of bacterial auxin synthesis during symbiosis.Belles-Sancho P, Liu Y, Heiniger B, von Salis E, Eberl L, Ahrens CH, Zamboni N, Bailly A, Pessi GFront Plant Sci10.3389/fpls.2022.9915482022

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6802Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17167)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17167
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
41976Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5836
57560Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 47179)https://www.ccug.se/strain?id=47179
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)