Strain identifier

BacDive ID: 1673

Type strain: Yes

Species: Methylovirgula ligni

Strain Designation: BW863

Strain history: <- S. N. Dedysh, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; BW863 <- W. de Boer

NCBI tax ID(s): 569860 (species)

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General

@ref: 8284

BacDive-ID: 1673

DSM-Number: 19998

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

description: Methylovirgula ligni BW863 is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from beechwood blocks on acidic forest soil during decay by the white-rot fungus Hypholoma fasciculare.

NCBI tax id

  • NCBI tax id: 569860
  • Matching level: species

strain history

  • @ref: 8284
  • history: <- S. N. Dedysh, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; BW863 <- W. de Boer

doi: 10.13145/bacdive1673.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Beijerinckiaceae
  • genus: Methylovirgula
  • species: Methylovirgula ligni
  • full scientific name: Methylovirgula ligni Vorob'ev et al. 2009

@ref: 8284

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Beijerinckiaceae

genus: Methylovirgula

species: Methylovirgula ligni

full scientific name: Methylovirgula ligni Vorob'ev et al. 2009

strain designation: BW863

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
23152negative1.2-2.5 µm0.3-0.65 µmrod-shapedno
69480negative99.964

pigmentation

  • @ref: 23152
  • production: no
  • name: no pigments

Culture and growth conditions

culture medium

  • @ref: 8284
  • name: METHYLOVIRGULA LIGNI MEDIUM (DSMZ Medium 1219)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1219
  • composition: Name: METHYLOVIRGULA LIGNI MEDIUM (DSMZ Medium 1219) Composition: Agar 15.0 g/l Methanol 0.792 g/l Yeast extract 0.1 g/l KH2PO4 0.1 g/l (NH4)2SO4 0.1 g/l MgSO4 x 7 H2O 0.05 g/l CaCl2 x 2 H2O 0.01 g/l EDTA 0.005 g/l FeSO4 x 7 H2O 0.002 g/l CoCl2 x 6 H2O 0.0002 g/l CuCl2 x 5 H2O 0.0001 g/l ZnSO4 x 7 H2O 0.0001 g/l Na2MoO4 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
8284positivegrowth25mesophilic
23152positivegrowth4-30
23152positiveoptimum20-24psychrophilic

culture pH

@refabilitytypepHPH range
23152positivegrowth3.1-6.5acidophile
23152positiveoptimum4.5-5.0

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.978

halophily

  • @ref: 23152
  • salt: NaCl
  • growth: no
  • tested relation: growth
  • concentration: >0.7 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2315216236ethanol+carbon source
2315225115malate+carbon source
2315217790methanol+carbon source
2315215361pyruvate+carbon source
2315228938ammonium+nitrogen source
2315217632nitrate+nitrogen source
23152yeast extract+nitrogen source

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
8284beechwood blocks on acidic forest soil during decay by the white-rot fungus Hypholoma fasciculareHypholoma fasciculareVeluweNetherlandsNLDEurope
23152from decaying beechwood blocks incubated on an acidic forest soil

isolation source categories

Cat1Cat2Cat3
#Host#Fungi
#Host#Plants#Decomposing plant
#Environmental#Terrestrial#Forest
#Environmental#Terrestrial#Soil
#Condition#Acidic

Safety information

risk assessment

  • @ref: 8284
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 8284
  • description: Methylovirgula ligni partial 16S rRNA gene, type strain BW863T
  • accession: FM252034
  • length: 1402
  • database: ena
  • NCBI tax ID: 569860

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Methylovirgula ligni BW863GCA_004135935completencbi569860
66792Methylovirgula ligni BW863GCA_003387225scaffoldncbi569860
66792Methylovirgula ligni strain BW863569860.6completepatric569860
66792Methylovirgula ligni DSM 199982770939601draftimg569860

GC content

  • @ref: 23152
  • GC-content: 61.8-62.8
  • method: Thermal denaturation, fluorometry

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes77.531no
flagellatedno91.076yes
gram-positiveno96.315yes
anaerobicno96.064no
aerobicyes85.904no
halophileno92.64no
spore-formingno92.709no
glucose-utilyes64.08no
thermophileno95.635yes
glucose-fermentno92.641no

External links

@ref: 8284

culture collection no.: DSM 19998, NCIMB 14408

straininfo link

  • @ref: 71320
  • straininfo: 397492

literature

  • topic: Phylogeny
  • Pubmed-ID: 19622650
  • title: Methylovirgula ligni gen. nov., sp. nov., an obligately acidophilic, facultatively methylotrophic bacterium with a highly divergent mxaF gene.
  • authors: Vorob'ev AV, de Boer W, Folman LB, Bodelier PL, Doronina NV, Suzina NE, Trotsenko YA, Dedysh SN
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.010074-0
  • year: 2009
  • mesh: Acids/*metabolism, Alcohol Oxidoreductases/*genetics, Autotrophic Processes, Bacterial Proteins/*genetics, Beijerinckiaceae/classification/*genetics/isolation & purification/*metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Evolution, Molecular, Methanol/*metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8284Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19998)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19998
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
23152Alexey V. Vorob'ev, Wietse de Boer, Larissa B. Folman, Paul L. E. Bodelier, Nina V. Doronina, Natalia E. Suzina, Yuri A. Trotsenko, Svetlana N. Dedysh10.1099/ijs.0.010074-0Methylovirgula ligni gen. nov., sp. nov., an obligately acidophilic, facultatively methylotrophic bacterium with a highly divergent mxaF geneIJSEM 59: 2538-2545 200919622650
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
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
71320Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID397492.1StrainInfo: A central database for resolving microbial strain identifiers