Strain identifier
BacDive ID: 1657
Type strain: 
Species: Methylocapsa aurea
Strain Designation: KYG
Strain history: <- S. N. Dedysh, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; KYG <- P. F. Dunfield
NCBI tax ID(s): 663610 (species)
version 8.1 (current version)
General
@ref: 16192
BacDive-ID: 1657
DSM-Number: 22158
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative, rod-shaped
description: Methylocapsa aurea KYG is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from sediment of an ephemeral brook in a forest.
NCBI tax id
- NCBI tax id: 663610
- Matching level: species
strain history
- @ref: 16192
- history: <- S. N. Dedysh, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; KYG <- P. F. Dunfield
doi: 10.13145/bacdive1657.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Beijerinckiaceae
- genus: Methylocapsa
- species: Methylocapsa aurea
- full scientific name: Methylocapsa aurea Dunfield et al. 2010
@ref: 16192
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Beijerinckiaceae
genus: Methylocapsa
species: Methylocapsa aurea
full scientific name: Methylocapsa aurea Dunfield et al. 2010
strain designation: KYG
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 23148 | negative | 1.8-3.1 µm | 0.7-1.2 µm | rod-shaped | no | |
| 69480 | negative | 99.993 |
colony morphology
- @ref: 23148
- colony color: yellow
Culture and growth conditions
culture medium
- @ref: 16192
- name: METHYLOCAPSA AUREA (DSMZ Medium 1323)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1323
- composition: Name: METHYLOCAPSA AUREA MEDIUM (DSMZ Medium 1323) Composition: NaNO3 0.2 g/l MgSO4 x 6 H2O 0.2 g/l KH2PO4 0.1258 g/l CaCl2 x 2 H2O 0.04 g/l K2HPO4 x 3 H2O 0.0171 g/l Na2-EDTA 0.00618 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 Na2MoO4 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 16192 | positive | growth | 28 | mesophilic |
| 23148 | positive | growth | 2-33 | |
| 23148 | positive | optimum | 25-30 | mesophilic |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 23148 | positive | growth | 5.2-7.2 |
| 23148 | positive | optimum | 6.0-6.2 |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.995 |
halophily
- @ref: 23148
- salt: NaCl
- growth: no
- tested relation: growth
- concentration: 0.3 %(w/v)
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 23148 | 30089 | acetate | + | carbon source |
| 23148 | 15740 | formate | + | carbon source |
| 23148 | 16183 | methane | + | carbon source |
| 23148 | 17790 | methanol | + | carbon source |
| 23148 | 28938 | ammonium | + | nitrogen source |
| 23148 | 16977 | L-alanine | + | nitrogen source |
| 23148 | 17196 | L-asparagine | + | nitrogen source |
| 23148 | 17203 | L-proline | + | nitrogen source |
| 23148 | 17632 | nitrate | + | nitrogen source |
| 23148 | peptone | + | nitrogen source | |
| 23148 | 16199 | urea | + | nitrogen source |
| 23148 | yeast extract | + | nitrogen source |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | sampling date |
|---|---|---|---|---|---|---|
| 16192 | sediment of an ephemeral brook in a forest | near Marburg | Germany | DEU | Europe | |
| 23148 | March 2003 |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Sediment |
| #Environmental | #Terrestrial | #Forest |
taxonmaps
- @ref: 69479
- File name: preview.99_2614.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_86;96_841;97_1665;98_2024;99_2614&stattab=map
- Last taxonomy: Methylocapsa aurea
- 16S sequence: FN433469
- Sequence Identity:
- Total samples: 998
- soil counts: 366
- aquatic counts: 567
- animal counts: 41
- plant counts: 24
Safety information
risk assessment
- @ref: 16192
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 16192
- description: Methylocapsa aurea partial 16S rRNA gene, type strain KYGT
- accession: FN433469
- length: 1409
- database: ena
- NCBI tax ID: 663610
Genome sequences
- @ref: 66792
- description: Methylocapsa aurea KYG
- accession: GCA_000746085
- assembly level: scaffold
- database: ncbi
- NCBI tax ID: 663610
GC content
| @ref | GC-content | method |
|---|---|---|
| 16192 | 61.4 | thermal denaturation, midpoint method (Tm) |
| 23148 | 61.4 | Thermal denaturation, fluorometry |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 62.989 | yes |
| flagellated | no | 80.078 | no |
| gram-positive | no | 98.159 | yes |
| anaerobic | no | 97.144 | no |
| aerobic | yes | 83.961 | no |
| halophile | no | 95.807 | no |
| spore-forming | no | 90.749 | no |
| glucose-util | yes | 81.347 | no |
| thermophile | no | 94.281 | yes |
| glucose-ferment | no | 91.98 | no |
External links
@ref: 16192
culture collection no.: DSM 22158, VKM B-2544
straininfo link
- @ref: 71304
- straininfo: 402674
literature
- topic: Phylogeny
- Pubmed-ID: 20061505
- title: Methylocapsa aurea sp. nov., a facultative methanotroph possessing a particulate methane monooxygenase, and emended description of the genus Methylocapsa.
- authors: Dunfield PF, Belova SE, Vorob'ev AV, Cornish SL, Dedysh SN
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.020149-0
- year: 2010
- mesh: Autotrophic Processes, Bacterial Proteins/genetics/*metabolism, Base Composition, Beijerinckiaceae/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, Methane/*metabolism, Molecular Sequence Data, Oxygenases/genetics/*metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology
- topic2: Metabolism
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 16192 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22158) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-22158 | |||
| 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 | |||
| 23148 | Peter F. Dunfield, Svetlana E. Belova, Alexey V. Vorob'ev, Sabrina L. Cornish, Svetlana N. Dedysh | 10.1099/ijs.0.020149-0 | Methylocapsa aurea sp. nov., a facultative methanotroph possessing a particulate methane monooxygenase, and emended description of the genus Methylocapsa | IJSEM 60: 2659-2664 2010 | 20061505 | |
| 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) | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
| 71304 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID402674.1 | StrainInfo: A central database for resolving microbial strain identifiers |