Strain identifier
BacDive ID: 7193
Type strain: 
Species: Methylobacterium marchantiae
Strain Designation: JT1
Strain history: <- P. Kämpfer, Univ. Giessen, Germany; JT1 <- S. Schauer
NCBI tax ID(s): 600331 (species)
version 8.1 (current version)
General
@ref: 15615
BacDive-ID: 7193
DSM-Number: 21328
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Methylobacterium marchantiae JT1 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from thallus of the liverwort Marchantia polymorpha L..
NCBI tax id
- NCBI tax id: 600331
- Matching level: species
strain history
- @ref: 15615
- history: <- P. Kämpfer, Univ. Giessen, Germany; JT1 <- S. Schauer
doi: 10.13145/bacdive7193.20230509.8.1
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 marchantiae
- full scientific name: Methylobacterium marchantiae Schauer et al. 2011
@ref: 15615
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Methylobacteriaceae
genus: Methylobacterium
species: Methylobacterium marchantiae
full scientific name: Methylobacterium marchantiae Schauer et al. 2011
strain designation: JT1
type strain: yes
Morphology
cell morphology
- @ref: 29827
- gram stain: negative
- cell length: 2.9 µm
- cell width: 1.15 µm
- cell shape: rod-shaped
- motility: yes
pigmentation
- @ref: 29827
- production: yes
Culture and growth conditions
culture medium
- @ref: 15615
- 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 |
|---|---|---|---|---|
| 15615 | positive | growth | 28 | mesophilic |
| 29827 | positive | growth | 4.0-32 | |
| 29827 | positive | optimum | 27.5 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 29827 | positive | growth | 6.0-9.0 | alkaliphile |
| 29827 | positive | optimum | 7.2 |
Physiology and metabolism
oxygen tolerance
- @ref: 29827
- oxygen tolerance: aerobe
halophily
- @ref: 29827
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0.0-2.0 %
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 29827 | 30089 | acetate | + | carbon source |
| 29827 | 35391 | aspartate | + | carbon source |
| 29827 | 16947 | citrate | + | carbon source |
| 29827 | 16236 | ethanol | + | carbon source |
| 29827 | 15740 | formate | + | carbon source |
| 29827 | 28757 | fructose | + | carbon source |
| 29827 | 29987 | glutamate | + | carbon source |
| 29827 | 17754 | glycerol | + | carbon source |
| 29827 | 30031 | succinate | + | carbon source |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 29827 | catalase | + | 1.11.1.6 |
| 29827 | cytochrome oxidase | + | 1.9.3.1 |
| 29827 | urease | + | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | host species | geographic location | country | origin.country | continent | latitude | longitude | sampling date |
|---|---|---|---|---|---|---|---|---|---|
| 15615 | thallus of the liverwort Marchantia polymorpha L. | Marchantia polymorpha | Bergpark Wilhelmshöhe near Kassel, about 500 m above sea level, 51° 19'N 9° 24' E | Germany | DEU | Europe | 51.3167 | 9.4167 | |
| 60862 | Phyllospere (thallus) (Marchantia polymorpha) | Kassel,Bergpark Wilhelmshöhe | Germany | DEU | Europe | 2003-10-01 |
isolation source categories
- Cat1: #Host
- Cat2: #Plants
taxonmaps
- @ref: 69479
- File name: preview.99_790.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15368;96_285;97_548;98_631;99_790&stattab=map
- Last taxonomy: Methylobacterium bullatum
- 16S sequence: FJ157976
- Sequence Identity:
- Total samples: 24347
- soil counts: 5760
- aquatic counts: 3552
- animal counts: 8689
- plant counts: 6346
Safety information
risk assessment
- @ref: 15615
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 15615
- description: Methylobacterium marchantiae strain JT1 collection-date 2003 from Germany 16S ribosomal RNA gene, partial sequence
- accession: FJ157976
- length: 1421
- database: ena
- NCBI tax ID: 600331
Genome sequences
- @ref: 66792
- description: Methylobacterium marchantiae DSM 21328
- accession: GCA_022179405
- assembly level: contig
- database: ncbi
- NCBI tax ID: 600331
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| flagellated | no | 74.884 | no |
| gram-positive | no | 97.897 | yes |
| anaerobic | no | 98.521 | yes |
| aerobic | yes | 93.909 | yes |
| halophile | no | 90.728 | no |
| spore-forming | no | 94.403 | no |
| motile | yes | 88.831 | yes |
| glucose-ferment | no | 89.387 | no |
| thermophile | no | 99.315 | no |
| glucose-util | yes | 87.191 | no |
External links
@ref: 15615
culture collection no.: DSM 21328, CCUG 56108
straininfo link
- @ref: 76646
- straininfo: 404897
literature
- topic: Phylogeny
- Pubmed-ID: 20495043
- title: Methylobacterium marchantiae sp. nov., a pink-pigmented, facultatively methylotrophic bacterium isolated from the thallus of a liverwort.
- authors: Schauer S, Kampfer P, Wellner S, Sproer C, Kutschera U
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.021915-0
- year: 2010
- mesh: Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Fimbriae, Bacterial/physiology, Hepatophyta/*microbiology, Locomotion, Methylobacterium/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Pigments, Biological/metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 15615 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21328) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21328 | |||
| 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 | |||
| 29827 | 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 | 26203 | 28776041 | |
| 60862 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 56108) | https://www.ccug.se/strain?id=56108 | |||
| 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 | |||
| 76646 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID404897.1 | StrainInfo: A central database for resolving microbial strain identifiers |