Strain identifier

BacDive ID: 1658

Type strain: Yes

Species: Methylocella silvestris

Strain Designation: BL2

Strain history: CIP <- 2003, NCIMB <- Max Planck Inst., Marburg, Germany: strain BL2

NCBI tax ID(s): 199596 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 5968

BacDive-ID: 1658

DSM-Number: 15510

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

description: Methylocella silvestris BL2 is a psychrophilic, Gram-negative, rod-shaped bacterium that was isolated from acidic cambisol under a beech-dominated forest.

NCBI tax id

  • NCBI tax id: 199596
  • Matching level: species

strain history

@refhistory
5968<- P. F. Dunfield, MPI Terrestrische Mikrobiol., Marburg; BL2
122610CIP <- 2003, NCIMB <- Max Planck Inst., Marburg, Germany: strain BL2

doi: 10.13145/bacdive1658.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Beijerinckiaceae
  • genus: Methylocella
  • species: Methylocella silvestris
  • full scientific name: Methylocella silvestris Dunfield et al. 2003

@ref: 5968

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Beijerinckiaceae

genus: Methylocella

species: Methylocella silvestris

full scientific name: Methylocella silvestris Dunfield et al. 2003

strain designation: BL2

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
23149negative1.2-1.5 µm0.6-0.8 µmrod-shapedno
69480yes91.765
69480negative99.999
122610negativerod-shapedno

pigmentation

  • @ref: 23149
  • production: no
  • name: no pigments

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5968METHYLOCELLA SILVERSTRIS MEDIUM (DSMZ Medium 1181)yeshttps://mediadive.dsmz.de/medium/1181Name: METHYLOCELLA SILVERSTRIS MEDIUM (DSMZ Medium 1181) Composition: Na2HPO4 x 12 H2O 0.717 g/l KH2PO4 0.272 g/l MgSO4 x 7 H2O 0.2 g/l NaNO3 0.2 g/l NaH2PO4 x 2 H2O 0.14355 g/l CaCl2 x 6 H2O 0.006 g/l Fe(III)NH4-EDTA 0.004 g/l H3BO3 1.5e-05 g/l CaCl2 x 2 H2O 1e-05 g/l ZnSO4 x 7 H2O 5e-06 g/l MnCl2 x 4 H2O 1.5e-06 g/l Na2MoO4 x 2 H2O 1.5e-06 g/l CuCl2 x 6 H2O 5e-07 g/l Distilled water
36692MEDIUM 579 - for Methylocella silvestrisyesDistilled water make up to (1000.000 ml);Sodium nitrate (0.200 g);Magnesium sulphate heptahydrate (0.200 g);Calcium chloride dihydrate (0.060 g);Agar (15.000 g);E.D.T.A (0.004 g);Trace elements solution - M01002 (0.500 ml);Solution 3 - M01004 (10.000 ml)
122610CIP Medium 579yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=579

culture temp

@refgrowthtypetemperaturerange
5968positivegrowth20psychrophilic
23149positivegrowth4-30
23149positiveoptimum15-25
36692positivegrowth25mesophilic
122610positivegrowth15-30
122610nogrowth5psychrophilic
122610nogrowth37mesophilic
122610nogrowth41thermophilic

culture pH

@refabilitytypepH
23149positivegrowth4.5-7.0
23149positiveoptimum5.5

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.999

halophily

  • @ref: 23149
  • salt: NaCl
  • growth: no
  • tested relation: growth
  • concentration: >0.8 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2314916183methane+carbon source
2314917790methanol+carbon source
2314916830methylamine+carbon source
12261017632nitrate-reduction
12261016301nitrite-reduction

metabolite production

  • @ref: 122610
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
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)-
68382esterase lipase (C 8)-
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
122610oxidase+
122610beta-galactosidase-3.2.1.23
122610gelatinase-
122610catalase+1.11.1.6
122610gamma-glutamyltransferase-2.3.2.2
122610phenylalanine ammonia-lyase-4.3.1.24
122610tryptophan deaminase-
122610urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122610--+--+-----+--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
5968acidic cambisol under a beech-dominated forestMarburgGermanyDEUEurope
23149December 1999
122610Environment, Acid forest cambisolMarburgGermanyDEUEurope

isolation source categories

  • Cat1: #Condition
  • Cat2: #Acidic

taxonmaps

  • @ref: 69479
  • File name: preview.99_1472.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_86;96_841;97_983;98_1161;99_1472&stattab=map
  • Last taxonomy: Methylocella silvestris
  • 16S sequence: AJ491847
  • Sequence Identity:
  • Total samples: 2837
  • soil counts: 1894
  • aquatic counts: 513
  • animal counts: 308
  • plant counts: 122

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
59681Risk group (German classification)
1226101Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5968
  • description: Methylocella silvestris partial 16S rRNA gene, strain BL2
  • accession: AJ491847
  • length: 1409
  • database: ena
  • NCBI tax ID: 395965

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Methylocella silvestris BL2GCA_000021745completencbi395965
66792Methylocella silvestris BL2395965.5completepatric395965
66792Methylocella silvestris BL2, DSM 15510643348565completeimg395965

GC content

@refGC-contentmethod
596860
2314960.0high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes58.064yes
flagellatedno81.885no
gram-positiveno97.755no
anaerobicno96.352no
aerobicyes87.207no
halophileno90.473no
spore-formingno94.686no
thermophileno98.173yes
glucose-utilyes84.475no
glucose-fermentno91.648no

External links

@ref: 5968

culture collection no.: DSM 15510, NCIMB 13906, CIP 108128

straininfo link

  • @ref: 71305
  • straininfo: 128001

literature

  • topic: Phylogeny
  • Pubmed-ID: 13130000
  • title: Methylocella silvestris sp. nov., a novel methanotroph isolated from an acidic forest cambisol.
  • authors: Dunfield PF, Khmelenina VN, Suzina NE, Trotsenko YA, Dedysh SN
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.02481-0
  • year: 2003
  • mesh: Beijerinckiaceae/classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Genes, Bacterial, Germany, Methane/metabolism, Microscopy, Electron, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Soil Microbiology
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5968Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15510)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15510
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
23149Peter F. Dunfield, Valentina N. Khmelenina, Natalia E. Suzina, Yuri A. Trotsenko, Svetlana N. Dedysh10.1099/ijs.0.02481-0Methylocella silvestris sp. nov., a novel methanotroph isolated from an acidic forest cambisolIJSEM 53: 1231-1239 200313130000
36692Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5716
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)
68382Automatically annotated from API zym
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
71305Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID128001.1StrainInfo: A central database for resolving microbial strain identifiers
122610Curators of the CIPCollection of Institut Pasteur (CIP 108128)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108128