Strain identifier
BacDive ID: 24173
Type strain:
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)
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/bacdive24173.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: 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
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
31003 | negative | 4.1 µm | 1.3 µm | rod-shaped | yes | |
69480 | yes | 93.921 | ||||
69480 | negative | 99.999 |
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
@ref | growth | type | temperature | range |
---|---|---|---|---|
20648 | positive | growth | 28 | mesophilic |
31003 | positive | growth | 10-37 | |
31003 | positive | optimum | 26.5 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
31003 | positive | growth | 4.0-9.0 | alkaliphile |
31003 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 31003
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.991 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31003 | 15963 | ribitol | + | carbon source |
31003 | 16449 | alanine | + | carbon source |
31003 | 22599 | arabinose | + | carbon source |
31003 | 29016 | arginine | + | carbon source |
31003 | 17057 | cellobiose | + | carbon source |
31003 | 23652 | dextrin | + | carbon source |
31003 | 28260 | galactose | + | carbon source |
31003 | 17234 | glucose | + | carbon source |
31003 | 17716 | lactose | + | carbon source |
31003 | 17306 | maltose | + | carbon source |
31003 | 29864 | mannitol | + | carbon source |
31003 | 37684 | mannose | + | carbon source |
31003 | 28044 | phenylalanine | + | carbon source |
31003 | 26271 | proline | + | carbon source |
31003 | 26546 | rhamnose | + | carbon source |
31003 | 17822 | serine | + | carbon source |
31003 | 30911 | sorbitol | + | carbon source |
31003 | 17992 | sucrose | + | carbon source |
31003 | 26986 | threonine | + | carbon source |
31003 | 17632 | nitrate | + | reduction |
enzymes
@ref | value | activity | ec |
---|---|---|---|
31003 | acid phosphatase | + | 3.1.3.2 |
31003 | alkaline phosphatase | + | 3.1.3.1 |
31003 | catalase | + | 1.11.1.6 |
31003 | urease | + | 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
Cat1 | Cat2 | Cat3 |
---|---|---|
#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: ena
- NCBI tax ID: 1187852
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Methylobacterium tarhaniae DSM 25844 | GCA_001043955 | contig | ncbi | 1187852 |
66792 | Methylobacterium tarhaniae strain DSM 25844 | 1187852.3 | wgs | patric | 1187852 |
66792 | Methylobacterium tarhaniae DSM 25844 | 2636415909 | draft | img | 1187852 |
GC content
@ref | GC-content | method |
---|---|---|
20648 | 67.3 | fluorimetric |
31003 | 67.3 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 89.408 | yes |
gram-positive | no | 97.295 | yes |
anaerobic | no | 97.537 | no |
aerobic | yes | 94.074 | no |
halophile | no | 91.397 | no |
spore-forming | no | 91.259 | no |
flagellated | no | 71.713 | no |
glucose-util | yes | 90.88 | yes |
thermophile | no | 98.833 | no |
glucose-ferment | no | 89.027 | no |
External links
@ref: 20648
culture collection no.: DSM 25844, KCTC 23615
straininfo link
- @ref: 88128
- straininfo: 404054
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 23315404 | Methylobacterium tarhaniae sp. nov., isolated from arid soil. | Veyisoglu A, Camas M, Tatar D, Guven K, Sazak A, Sahin N | Int J Syst Evol Microbiol | 10.1099/ijs.0.049551-0 | 2013 | Bacterial 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/analysis | Genetics |
Phylogeny | 29160200 | Methylobacterium frigidaeris sp. nov., isolated from an air conditioning system. | Lee Y, Jeon CO | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002500 | 2017 | *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/chemistry | Transcriptome |
Phylogeny | 31463788 | Methylobacterium terrae sp. nov., a radiation-resistant bacterium isolated from gamma ray-irradiated soil. | Kim J, Chhetri G, Kim I, Kim H, Kim MK, Seo T | J Microbiol | 10.1007/s12275-019-9007-9 | 2019 | Bacterial 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 Sequencing | Genetics |
Reference
@id | authors | title | doi/url | catalogue | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | ||||
20648 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-25844 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25844) | ||||
31003 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 27333 | 28776041 | ||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | ||||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
69479 | João 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 beta | https://microbeatlas.org/ | ||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | ||||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | ||||
88128 | Reimer, 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 identifiers | 10.60712/SI-ID404054.1 |