Strain identifier
BacDive ID: 133659
Type strain: 
Species: Methylorubrum populi
Strain Designation: BJ001
NCBI tax ID(s): 223967 (species)
version 8.1 (current version)
General
@ref: 29990
BacDive-ID: 133659
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, motile, rod-shaped
description: Methylorubrum populi BJ001 is an aerobe, Gram-negative, motile bacterium that was isolated from plant endophyte.
NCBI tax id
- NCBI tax id: 223967
- Matching level: species
doi: 10.13145/bacdive133659.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Methylobacteriaceae
- genus: Methylorubrum
- species: Methylorubrum populi
- full scientific name: Methylorubrum populi (Van Aken et al. 2004) Green and Ardley 2018
synonyms
- @ref: 20215
- synonym: Methylobacterium populi
@ref: 29990
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Hyphomicrobiales
family: Methylobacteriaceae
genus: Methylorubrum
species: Methylorubrum populi
strain designation: BJ001
type strain: yes
Morphology
cell morphology
- @ref: 29990
- gram stain: negative
- cell length: 5.5 µm
- cell width: 0.9 µm
- cell shape: rod-shaped
- motility: yes
pigmentation
- @ref: 29990
- production: yes
Culture and growth conditions
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 29990 | positive | growth | 15-40 | |
| 29990 | positive | optimum | 25 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 29990 | positive | growth | 4.0-9.0 | alkaliphile |
| 29990 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 29990
- oxygen tolerance: aerobe
spore formation
- @ref: 29990
- spore formation: no
observation
- @ref: 29990
- observation: aggregates in clumps
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 29990 | 30089 | acetate | + | carbon source |
| 29990 | 16236 | ethanol | + | carbon source |
| 29990 | 15740 | formate | + | carbon source |
| 29990 | 28757 | fructose | + | carbon source |
| 29990 | 17754 | glycerol | + | carbon source |
| 29990 | 24996 | lactate | + | carbon source |
| 29990 | 15361 | pyruvate | + | carbon source |
| 29990 | 30031 | succinate | + | carbon source |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 29990 | acid phosphatase | + | 3.1.3.2 |
| 29990 | alkaline phosphatase | + | 3.1.3.1 |
| 29990 | catalase | + | 1.11.1.6 |
| 29990 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
- @ref: 29990
- sample type: plant endophyte
isolation source categories
| Cat1 | Cat2 |
|---|---|
| #Host | #Other |
| #Host | #Plants |
taxonmaps
- @ref: 69479
- File name: preview.99_253.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15368;96_177;97_192;98_215;99_253&stattab=map
- Last taxonomy: Methylorubrum
- 16S sequence: AY251818
- Sequence Identity:
- Total samples: 110728
- soil counts: 23280
- aquatic counts: 23711
- animal counts: 47578
- plant counts: 16159
Sequence information
16S sequences
- @ref: 29990
- description: Methylobacterium sp. BJ001 16S ribosomal RNA gene and 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence
- accession: AY251818
- length: 2243
- database: nuccore
- NCBI tax ID: 441620
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Methylorubrum populi BJ001 | GCA_000019945 | complete | ncbi | 441620 |
| 66792 | Methylorubrum populi BJ001 | 642555139 | complete | img | 441620 |
GC content
- @ref: 29990
- GC-content: 70.4
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | yes | 89.16 | yes |
| flagellated | no | 72.488 | no |
| gram-positive | no | 97.562 | yes |
| anaerobic | no | 97.424 | no |
| aerobic | yes | 85.648 | yes |
| halophile | no | 94.272 | no |
| spore-forming | no | 92.084 | yes |
| thermophile | no | 98.881 | no |
| glucose-util | yes | 90.359 | no |
| glucose-ferment | no | 88.684 | no |
External links
@ref: 29990
culture collection no.: ATCC BAA 705, NCIM B13946
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 15280290 | Methylobacterium populi sp. nov., a novel aerobic, pink-pigmented, facultatively methylotrophic, methane-utilizing bacterium isolated from poplar trees (Populus deltoides x nigra DN34). | Van Aken B, Peres CM, Doty SL, Yoon JM, Schnoor JL | Int J Syst Evol Microbiol | 10.1099/ijs.0.02796-0 | 2004 | Aerobiosis, Bacterial Typing Techniques, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry, Genes, rRNA, Methane/*metabolism, Methylobacterium/*classification/cytology/*isolation & purification/physiology, Molecular Sequence Data, Phylogeny, Pigments, Biological/biosynthesis, Populus/*microbiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology | Enzymology |
| Metabolism | 26965726 | Mixed regiospecificity compromises alkene synthesis by a cytochrome P450 peroxygenase from Methylobacterium populi. | Amaya JA, Rutland CD, Makris TM | J Inorg Biochem | 10.1016/j.jinorgbio.2016.02.031 | 2016 | Alkenes/*chemistry/*metabolism, Cytochrome P-450 Enzyme System/*metabolism, Methylobacterium/*enzymology, Oxidation-Reduction, Peroxidases/*metabolism, Stereoisomerism | Enzymology |
| Phylogeny | 30024371 | Review of the genus Methylobacterium and closely related organisms: a proposal that some Methylobacterium species be reclassified into a new genus, Methylorubrum gen. nov. | Green PN, Ardley JK | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002856 | 2018 | Bacterial Typing Techniques, DNA, Bacterial/genetics, Methylobacterium/*classification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Transcriptome |
Reference
| @id | authors | title | doi/url | ID_cross_reference | pubmed |
|---|---|---|---|---|---|
| 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 | ||
| 29990 | 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 | 26357 | 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 | ||
| 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/ |