Strain identifier

BacDive ID: 24173

Type strain: Yes

Species: Methylobacterium tarhaniae

Strain Designation: N4211

Strain history: <- N. Sahin, Ondokuz Mayis Univ., Dept. of Biology, Samsun, Turkey; N4211 <- M. Camas

NCBI tax ID(s): 1187852 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 9.3 (current version):
version 9.2:
version 9.1:
version 9:
version 8.1:
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 9.3 (current version)

General

@ref: 20648

BacDive-ID: 24173

DSM-Number: 25844

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

description: Methylobacterium tarhaniae N4211 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from arid soil.

NCBI tax id

  • NCBI tax id: 1187852
  • Matching level: species

strain history

  • @ref: 20648
  • history: <- N. Sahin, Ondokuz Mayis Univ., Dept. of Biology, Samsun, Turkey; N4211 <- M. Camas

doi: 10.13145/bacdive24173.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Methylobacteriaceae
  • genus: Methylobacterium
  • species: Methylobacterium tarhaniae
  • full scientific name: Methylobacterium tarhaniae Veyisoglu et al. 2013

@ref: 20648

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Methylobacteriaceae

genus: Methylobacterium

species: Methylobacterium tarhaniae

full scientific name: Methylobacterium tarhaniae Veyisoglu et al. 2013

strain designation: N4211

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31003negative4.1 µm1.3 µmrod-shapedyes
125438negative98.469

colony morphology

  • @ref: 20648
  • incubation period: 3-7 days

pigmentation

  • @ref: 31003
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 20648
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: Name: 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

culture temp

@refgrowthtypetemperature
20648positivegrowth28
31003positivegrowth10-37
31003positiveoptimum26.5

culture pH

@refabilitytypepHPH range
31003positivegrowth4.0-9.0alkaliphile
31003positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
31003aerobe
125438aerobe90.567

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 90.2

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3100315963ribitol+carbon source
3100316449alanine+carbon source
3100322599arabinose+carbon source
3100329016arginine+carbon source
3100317057cellobiose+carbon source
3100323652dextrin+carbon source
3100328260galactose+carbon source
3100317234glucose+carbon source
3100317716lactose+carbon source
3100317306maltose+carbon source
3100329864mannitol+carbon source
3100337684mannose+carbon source
3100328044phenylalanine+carbon source
3100326271proline+carbon source
3100326546rhamnose+carbon source
3100317822serine+carbon source
3100330911sorbitol+carbon source
3100317992sucrose+carbon source
3100326986threonine+carbon source
3100317632nitrate+reduction

enzymes

@refvalueactivityec
31003acid phosphatase+3.1.3.2
31003alkaline phosphatase+3.1.3.1
31003catalase+1.11.1.6
31003urease+3.5.1.5

Isolation, sampling and environmental information

isolation

  • @ref: 20648
  • sample type: arid soil
  • geographic location: Abuja
  • country: Nigeria
  • origin.country: NGA
  • continent: Africa

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Condition#Xerophilic

taxonmaps

  • @ref: 69479
  • File name: preview.99_5594.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15368;96_262;97_289;98_1400;99_5594&stattab=map
  • Last taxonomy: Methylobacterium aquaticum
  • 16S sequence: JQ864432
  • Sequence Identity:
  • Total samples: 3074
  • soil counts: 319
  • aquatic counts: 656
  • animal counts: 1502
  • plant counts: 597

Safety information

risk assessment

  • @ref: 20648
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20648
  • description: Methylobacterium tarhaniae strain N4211 16S ribosomal RNA gene, partial sequence
  • accession: JQ864432
  • length: 1417
  • database: nuccore
  • NCBI tax ID: 1187852

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Methylobacterium tarhaniae DSM 25844GCA_001043955contigncbi1187852
66792Methylobacterium tarhaniae strain DSM 258441187852.3wgspatric1187852
66792Methylobacterium tarhaniae DSM 258442636415909draftimg1187852

GC content

@refGC-contentmethod
2064867.3fluorimetric
3100367.3

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthaerobe81.8
125439BacteriaNetgram_stainReaction to gram-stainingnegative81.3
125439BacteriaNetmotilityAbility to perform movementyes58.8
125439BacteriaNetspore_formationAbility to form endo- or exosporesno90.2
125438gram-positivegram-positivePositive reaction to Gram-stainingno98.469yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no94.32yes
125438spore-formingspore-formingAbility to form endo- or exosporesno85.278no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes90.567yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno95.599no
125438motile2+flagellatedAbility to perform flagellated movementyes75.843no

External links

@ref: 20648

culture collection no.: DSM 25844, KCTC 23615

straininfo link

  • @ref: 88128
  • straininfo: 404054

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23315404Methylobacterium tarhaniae sp. nov., isolated from arid soil.Veyisoglu A, Camas M, Tatar D, Guven K, Sazak A, Sahin NInt J Syst Evol Microbiol10.1099/ijs.0.049551-02013Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Methylobacterium/*classification/genetics/isolation & purification, Molecular Sequence Data, Nigeria, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/analogs & derivatives/analysisGenetics
Phylogeny29160200Methylobacterium frigidaeris sp. nov., isolated from an air conditioning system.Lee Y, Jeon COInt J Syst Evol Microbiol10.1099/ijsem.0.0025002017*Air Conditioning, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Methylobacterium/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome
Phylogeny31463788Methylobacterium terrae sp. nov., a radiation-resistant bacterium isolated from gamma ray-irradiated soil.Kim J, Chhetri G, Kim I, Kim H, Kim MK, Seo TJ Microbiol10.1007/s12275-019-9007-92019Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Gamma Rays, Genotype, Lipids/chemistry, Methylobacterium/*classification/genetics/*isolation & purification/radiation effects, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Radiation Tolerance, Republic of Korea, Sequence Analysis, DNA, Soil, *Soil Microbiology, Ubiquinone/analogs & derivatives/chemistry, Whole Genome SequencingGenetics

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmedjournal
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
20648Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-25844Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25844)
31003Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172733328776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa102533211880Nucleic Acids Res. 49: D498-D508 2020
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
88128Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID404054.1
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG