Strain identifier
BacDive ID: 7206
Type strain: 
Species: Methylotuvimicrobium alcaliphilum
Strain Designation: 20Z
Strain history: <- Y. A. Trotsenko, Inst. Biochem. Physiol. Microorg., RAS, Pushchino, Russia; 20Z <- V. N. Khmelenina
NCBI tax ID(s): 271065 (species)
version 9.2 (current version)
General
@ref: 8007
BacDive-ID: 7206
DSM-Number: 19304
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Methylotuvimicrobium alcaliphilum 20Z is an aerobe, mesophilic, Gram-negative bacterium that was isolated from surface sediment of the highly alkaline soda lake Shara-Nur.
NCBI tax id
- NCBI tax id: 271065
- Matching level: species
strain history
- @ref: 8007
- history: <- Y. A. Trotsenko, Inst. Biochem. Physiol. Microorg., RAS, Pushchino, Russia; 20Z <- V. N. Khmelenina
doi: 10.13145/bacdive7206.20241212.9.2
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Methylococcales
- family: Methylococcales, not assigned to family
- genus: Methylotuvimicrobium
- species: Methylotuvimicrobium alcaliphilum
- full scientific name: Methylotuvimicrobium alcaliphilum (Kalyuzhnaya et al. 2008) Orata et al. 2019
synonyms
@ref synonym 20215 Methylobacter alcaliphilus 20215 Methylomicrobium alcaliphilum
@ref: 8007
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Methylococcales
family: Methylococcales, not assigned to family
genus: Methylotuvimicrobium
species: Methylotuvimicrobium alcaliphilum
full scientific name: Methylotuvimicrobium alcaliphilum (Kalyuzhnaya et al. 2008) Orata et al. 2019
strain designation: 20Z
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 32326 | negative | 2.5 µm | 1.25 µm | rod-shaped | yes | |
| 69480 | negative | 99 |
Culture and growth conditions
culture medium
- @ref: 8007
- name: METHYLOMICROBIUM MEDIUM (DSMZ Medium 1180)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1180
- composition: Name: METHYLOMICROBIUM MEDIUM (DSMZ Medium 1180) Composition: NaCl 30.0 g/l NaHCO3 4.20035 g/l KNO3 1.0 g/l Na2HPO4 x 12 H2O 0.6 g/l Na2CO3 0.52994 g/l KH2PO4 0.28 g/l MgSO4 x 7 H2O 0.2 g/l CaCl2 x 2 H2O 0.02 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 MnCl2 x 4 H2O 3e-05 g/l H3BO3 3e-05 g/l Na2MoO4 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l Distilled water
culture temp
- @ref: 8007
- growth: positive
- type: growth
- temperature: 28
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 32326 | positive | growth | 7.2-9.5 | alkaliphile |
| 32326 | positive | optimum | 9 |
Physiology and metabolism
oxygen tolerance
- @ref: 32326
- oxygen tolerance: aerobe
halophily
- @ref: 32326
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: <8.7 %
Isolation, sampling and environmental information
isolation
- @ref: 8007
- sample type: surface sediment of the highly alkaline soda lake Shara-Nur
- geographic location: Siberia, Tuva
- country: Russia
- origin.country: RUS
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Lake (large) |
| #Environmental | #Aquatic | #Sediment |
| #Condition | #Alkaline | |
| #Condition | #Saline |
taxonmaps
- @ref: 69479
- File name: preview.99_1207.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_194;96_706;97_824;98_956;99_1207&stattab=map
- Last taxonomy: Methylotuvimicrobium
- 16S sequence: EF495157
- Sequence Identity:
- Total samples: 855
- soil counts: 170
- aquatic counts: 562
- animal counts: 118
- plant counts: 5
Safety information
risk assessment
- @ref: 8007
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 8007
- description: Methylomicrobium alcaliphilum strain 20Z 16S ribosomal RNA gene, partial sequence
- accession: EF495157
- length: 1395
- database: nuccore
- NCBI tax ID: 1091494
Genome sequences
- @ref: 66792
- description: Methylotuvimicrobium alcaliphilum 20Z
- accession: GCA_000968535
- assembly level: complete
- database: ncbi
- NCBI tax ID: 1091494
GC content
| @ref | GC-content | method |
|---|---|---|
| 8007 | 47.9 | thermal denaturation, midpoint method (Tm) |
| 32326 | 47.9 |
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 99 | yes |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 90.308 | yes |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 76.913 | yes |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 85.923 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 95.331 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 70.053 | no |
External links
@ref: 8007
culture collection no.: DSM 19304, NCIMB 14124, VKM B-2133
straininfo link
- @ref: 76659
- straininfo: 343457
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 18319461 | Classification of halo(alkali)philic and halo(alkali)tolerant methanotrophs provisionally assigned to the genera Methylomicrobium and Methylobacter and emended description of the genus Methylomicrobium. | Kalyuzhnaya MG, Khmelenina V, Eshinimaev B, Sorokin D, Fuse H, Lidstrom M, Trotsenko Y | Int J Syst Evol Microbiol | 10.1099/ijs.0.65317-0 | 2008 | DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Hydrogen-Ion Concentration, Methane/metabolism, Methylococcaceae/*classification/genetics/growth & development/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride, Species Specificity | Genetics |
| Metabolism | 35134957 | Adaptive evolution of Methylotuvimicrobium alcaliphilum to grow in the presence of rhamnolipids improves fatty acid and rhamnolipid production from CH4. | Awasthi D, Tang YH, Amer B, Baidoo EEK, Gin J, Chen Y, Petzold CJ, Kalyuzhnaya M, Singer SW | J Ind Microbiol Biotechnol | 10.1093/jimb/kuac002 | 2022 | *Fatty Acids/metabolism, Glycolipids/metabolism, *Methylococcaceae/metabolism, Pseudomonas aeruginosa/genetics/metabolism | Biotechnology |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 8007 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19304) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19304 | |||
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
| 32326 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28560 | 28776041 | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 76659 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID343457.1 | StrainInfo: A central database for resolving microbial strain identifiers |