Strain identifier

BacDive ID: 40

Type strain: Yes

Species: Gluconacetobacter diazotrophicus

Strain Designation: PA 5

Strain history: CIP <- 1992, LMG <- J. Döbereiner, Algoas, Brazil

NCBI tax ID(s): 272568 (strain), 33996 (species)

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General

@ref: 2248

BacDive-ID: 40

DSM-Number: 5601

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

description: Gluconacetobacter diazotrophicus PA 5 is a mesophilic, motile bacterium that was isolated from sugarcane roots.

NCBI tax id

NCBI tax idMatching level
33996species
272568strain

strain history

@refhistory
2248<- LMG <- J. Döbereiner, PA 5
118928CIP <- 1992, LMG <- J. Döbereiner, Algoas, Brazil

doi: 10.13145/bacdive40.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodospirillales
  • family: Acetobacteraceae
  • genus: Gluconacetobacter
  • species: Gluconacetobacter diazotrophicus
  • full scientific name: Gluconacetobacter diazotrophicus corrig. (Gillis et al. 1989) Yamada et al. 1998

  • synonyms

    @refsynonym
    20215Acetobacter diazotrophicus
    20215Gluconoacetobacter diazotrophicus

@ref: 2248

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Acetobacteraceae

genus: Gluconacetobacter

species: Gluconacetobacter diazotrophicus

full scientific name: Gluconacetobacter diazotrophicus (Gillis et al. 1989) Yamada et al. 1998

strain designation: PA 5

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes94.264
6948099.993negative

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2248SABOURAND GLUCOSE MEDIUM (DSMZ Medium 1429)yeshttps://mediadive.dsmz.de/medium/1429Name: SABOURAUD GLUCOSE MEDIUM (DSMZ Medium 1429) Composition: SABOURAUD- Glucose-Bouillon 30.0 g/l Agar 15.0 g/l Distilled water
40703MEDIUM 1 - for Acetobacter, Azotobacter, Gluconobacter, Gluconacetobacter, Mesorhizodium ciceri and Pseudomonas doudoroffiiyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Yeast extract (5.000 g);Peptone (3.000 g);Mannitol (25.000 g)
118928CIP Medium 1yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=1

culture temp

@refgrowthtypetemperaturerange
2248positivegrowth28mesophilic
40703positivegrowth30mesophilic

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.999

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2291928885butanol-growth
2291917108D-arabinose+growth
2291912936D-galactose+growth
2291917634D-glucose+growth
2291917716lactose-growth
2291916899D-mannitol+growth
2291916634raffinose+growth
2291917924D-sorbitol+growth
2291965327D-xylose+/-growth
2291916813galactitol-growth
2291916236ethanol+/-growth
2291928260galactose+growth
2291924265gluconate+growth
2291917754glycerol+growth
2291915428glycine-growth
2291928120L-fructose+growth
2291915603L-leucine+/-growth
2291918019L-lysine+/-growth
2291916643L-methionine-growth
2291962345L-rhamnose-growth
2291916857L-threonine-growth
2291925115malate-growth
2291917306maltose+/-growth
2291937684mannose+/-growth
2291928053melibiose+/-growth
2291917268myo-inositol-growth
2291917790methanol-growth
2291928017starch-growth
2291917992sucrose+growth
2291917632nitrate-reduction
2291927518acetylene+reduction
2291930911sorbitol+carbon source
2291916977L-alanine+nitrogen source
2291929991L-aspartate+nitrogen source
2291917561L-cysteine+nitrogen source
2291929985L-glutamate+nitrogen source
2291917203L-proline+nitrogen source
2291916828L-tryptophan+nitrogen source

enzymes

@refvalueactivityec
22919catalase+1.11.1.6
22919cytochrome oxidase-1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
2248sugarcane rootsAlagoasBrazilBRAMiddle and South America
53588Root,Saccharum officinarumAlagoasBrazilBRAMiddle and South America
118928Plant, Roots of Saccharum officinarum, sugarcaneBrazilBRAMiddle and South America1987

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_4759.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_29;96_64;97_2865;98_3566;99_4759&stattab=map
  • Last taxonomy: Gluconacetobacter diazotrophicus
  • 16S sequence: X75618
  • Sequence Identity:
  • Total samples: 3665
  • soil counts: 473
  • aquatic counts: 234
  • animal counts: 677
  • plant counts: 2281

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
22481Risk group (German classification)
1189281Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218A.diazotrophicus gene for 16S ribosomal RNAX756181485ena272568
20218Gluconacetobacter diazotrophicus strain DSM 5601 16S ribosomal RNA gene, partial sequenceJF7939771356ena33996
20218Gluconacetobacter diazotrophicus strain LMG 7603 16S ribosomal RNA gene, partial sequenceJF7939761356ena33996
20218Mutant Gluconacetobacter diazotrophicus PAL5 substrain B5 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Ile (trnI) gene, complete sequenceEF999412230ena272568
20218Mutant Gluconacetobacter diazotrophicus PAL5 substrain B9 16S-23S ribosomal RNA intergenic spacer, partial sequenceEF999413319ena272568

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Gluconacetobacter diazotrophicus LMG 7603GCA_014174315contigncbi33996
66792Gluconacetobacter diazotrophicus PA1 5 strain PAl 5272568.38plasmidpatric272568
66792Gluconacetobacter diazotrophicus PA1 5 strain PAl 5272568.37plasmidpatric272568
66792Gluconacetobacter diazotrophicus PA1 5 strain PAl 5 strain PAl 5; ATCC 49037272568.39plasmidpatric272568
66792Gluconacetobacter diazotrophicus PAl 5272568.12completepatric272568
66792Gluconacetobacter diazotrophicus PAl 5 (Prj:21071)272568.11completepatric272568
66792Gluconacetobacter diazotrophicus strain LMG 760333996.48wgspatric33996

GC content

  • @ref: 2248
  • GC-content: 61.0

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno78no
motileyes84.804no
gram-positiveno97.882no
anaerobicno98.934no
halophileno92.682no
spore-formingno95.1no
glucose-utilyes95.13yes
aerobicyes89.89no
thermophileno89.535yes
flagellatedno85.004no
glucose-fermentno89.516no

External links

@ref: 2248

culture collection no.: DSM 5601, ATCC 49037, LMG 7603, CCUG 37298, CIP 103539

straininfo link

  • @ref: 69725
  • straininfo: 14550

literature

Pubmed-IDtitleauthorsjournalDOIyearmeshtopictopic2
11413211Further observations on the interaction between sugar cane and Gluconacetobacter diazotrophicus under laboratory and greenhouse conditions.James EK, Olivares FL, de Oliveira AL, dos Reis FB Jr, da Silva LG, Reis VMJ Exp Bot10.1093/jexbot/52.357.7472001Acetobacteraceae/*physiology/ultrastructure, Microscopy, Electron, Plant Leaves/microbiology, Poaceae/*microbiology
15281930A putative new endophytic nitrogen-fixing bacterium Pantoea sp. from sugarcane.Loiret FG, Ortega E, Kleiner D, Ortega-Rodes P, Rodes R, Dong ZJ Appl Microbiol10.1111/j.1365-2672.2004.02329.x2004Cuba, Culture Media, DNA, Bacterial/genetics, Gluconacetobacter/genetics/growth & development/*isolation & purification, Hydrogen/metabolism, Hydrogen-Ion Concentration, Nitrogen Fixation/*physiology, Nitrogenase/metabolism, Pantoea/genetics/growth & development/*isolation & purification, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, RNA, Ribosomal, 23S/genetics, Saccharum/*microbiology, Soil Microbiology, TemperaturePhylogenyCultivation
17406771Effects of the inoculation of Burkholderia vietnamensis and related endophytic diazotrophic bacteria on grain yield of rice.Govindarajan M, Balandreau J, Kwon SW, Weon HY, Lakshminarasimhan CMicrob Ecol10.1007/s00248-007-9247-92007Burkholderia/classification/genetics/*growth & development/isolation & purification, Colony Count, Microbial, Crops, Agricultural, Culture Media, Genes, rRNA, Gram-Negative Bacteria/classification/genetics/*growth & development/isolation & purification, India, Molecular Sequence Data, *Nitrogen Fixation, Oryza/*growth & development/*microbiology, Phylogeny, Plant Roots/microbiology, Plant Shoots/microbiology, Polymerase Chain Reaction, RNA, Ribosomal, 16S, Sequence Analysis, DNAPhylogenyEnzymology
21304715Two genome sequences of the same bacterial strain, Gluconacetobacter diazotrophicus PAl 5, suggest a new standard in genome sequence submission.Giongo A, Tyler HL, Zipperer UN, Triplett EWStand Genomic Sci10.4056/sigs.9722212010Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2248Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5601)https://www.dsmz.de/collection/catalogue/details/culture/DSM-5601
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
22919L E Fuentes-Ramírez, R Bustillos-Cristales, A Tapia-Hernández, T Jiménez-Salgado, E T Wang, E Martínez-Romero, J Caballero-Mellado10.1099/00207713-51-4-1305Novel nitrogen-fixing acetic acid bacteria, Gluconacetobacter johannae sp. nov. and Gluconacetobacter azotocaptans sp. nov., associated with coffee plants.IJSEM 51: 1305-1314 200111491326
40703Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15348
53588Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 37298)https://www.ccug.se/strain?id=37298
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 updatesNucleic Acids Res. 49: D498-D508 202033211880
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)
69725Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID14550.1StrainInfo: A central database for resolving microbial strain identifiers
118928Curators of the CIPCollection of Institut Pasteur (CIP 103539)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103539