Strain identifier

BacDive ID: 23098

Type strain: Yes

Species: Pleomorphomonas diazotrophica

Strain Designation: R5-392

Strain history: <- M. Munusamy, National University of Singapore, Temasek Life Scs. Lab.; R5-392

NCBI tax ID(s): 1166257 (species)

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General

@ref: 19368

BacDive-ID: 23098

DSM-Number: 25022

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped

description: Pleomorphomonas diazotrophica R5-392 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from surface-sterilized root tissue of Jatropha curcas cv B1-2.

NCBI tax id

  • NCBI tax id: 1166257
  • Matching level: species

strain history

  • @ref: 19368
  • history: <- M. Munusamy, National University of Singapore, Temasek Life Scs. Lab.; R5-392

doi: 10.13145/bacdive23098.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Pleomorphomonadaceae
  • genus: Pleomorphomonas
  • species: Pleomorphomonas diazotrophica
  • full scientific name: Pleomorphomonas diazotrophica Madhaiyan et al. 2013

@ref: 19368

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Pleomorphomonadaceae

genus: Pleomorphomonas

species: Pleomorphomonas diazotrophica

full scientific name: Pleomorphomonas diazotrophica Madhaiyan et al. 2013

strain designation: R5-392

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30794negative2 µm0.45 µmrod-shapedno
69480yes97.651
69480negative99.977

multimedia

  • @ref: 19368
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_25022.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
19368R2A 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
19368NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
19368positivegrowth28mesophilic
30794positivegrowth20-37
30794positiveoptimum30mesophilic

culture pH

@refabilitytypepH
30794positivegrowth6.0-8.0
30794positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 30794
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.965

halophily

@refsaltgrowthtested relationconcentration
30794NaClpositivegrowth0-1 %
30794NaClpositiveoptimum1 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3079422599arabinose+carbon source
3079417234glucose+carbon source
3079417306maltose+carbon source
3079429864mannitol+carbon source
3079437684mannose+carbon source
307944853esculin+hydrolysis
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

@refChebi-IDmetaboliteproduction
3079435581indoleyes
6836935581indoleyes

metabolite tests

@refChebi-IDmetaboliteindole test
3079435581indole+
6836935581indole+

enzymes

@refvalueactivityec
30794acid phosphatase+3.1.3.2
30794alkaline phosphatase+3.1.3.1
30794alpha-galactosidase+3.2.1.22
30794catalase+1.11.1.6
30794cytochrome oxidase+1.9.3.1
30794urease+3.5.1.5
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
19368-+---+-++++-+++--+--+

Isolation, sampling and environmental information

isolation

  • @ref: 19368
  • sample type: surface-sterilized root tissue of Jatropha curcas cv B1-2
  • host species: Jatropha curcas
  • geographic location: Lim Chu Kang, Agrotechnology experimental station, Jatropha farm
  • country: Singapore
  • origin.country: SGP
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Shrub (Scrub)
#Host Body-Site#Plant#Root (Rhizome)
#Host Body-Site#Plant#Sterilized plant part

taxonmaps

  • @ref: 69479
  • File name: preview.99_144103.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_1902;97_2285;98_2811;99_144103&stattab=map
  • Last taxonomy: Pleomorphomonas
  • 16S sequence: JQ346801
  • Sequence Identity:
  • Total samples: 15
  • soil counts: 3
  • aquatic counts: 2
  • animal counts: 5
  • plant counts: 5

Safety information

risk assessment

  • @ref: 19368
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 19368
  • description: Pleomorphomonas diazotrophica strain R5-392 16S ribosomal RNA gene, partial sequence
  • accession: JQ346801
  • length: 1443
  • database: ena
  • NCBI tax ID: 1166257

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pleomorphomonas diazotrophica R5-392GCA_900114935scaffoldncbi1166257
66792Pleomorphomonas diazotrophica R5-392GCA_002844595contigncbi1166257
66792Pleomorphomonas diazotrophica R5-3922651870105draftimg1166257
66792Pleomorphomonas diazotrophica R5-3922839387131draftimg1166257

GC content

@refGC-contentmethod
1936863.2high performance liquid chromatography (HPLC)
3079463.2

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes88.525no
flagellatedno84.269yes
gram-positiveno98.164yes
anaerobicno94.87yes
aerobicno73.144no
halophileno96.259yes
spore-formingno93.26no
glucose-fermentno84.063yes
thermophileno98.289yes
glucose-utilyes93.421no

External links

@ref: 19368

culture collection no.: DSM 25022, KACC 16233

straininfo link

  • @ref: 87336
  • straininfo: 399306

literature

  • topic: Phylogeny
  • Pubmed-ID: 23223815
  • title: Pleomorphomonas diazotrophica sp. nov., an endophytic N-fixing bacterium isolated from root tissue of Jatropha curcas L.
  • authors: Madhaiyan M, Jin TY, Roy JJ, Kim SJ, Weon HY, Kwon SW, Ji L
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.044461-0
  • year: 2012
  • mesh: Alphaproteobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Jatropha/*microbiology, Molecular Sequence Data, Nitrogen Fixation, Nitrogenase/analysis, *Phylogeny, Plant Roots/microbiology, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
19368Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25022)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25022
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
30794Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2712528776041
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
68369Automatically annotated from API 20NE
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
87336Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID399306.1StrainInfo: A central database for resolving microbial strain identifiers