Strain identifier
BacDive ID: 11296
Type strain: 
Species: Amphritea atlantica
Strain Designation: M41
Strain history: J. Wiese M41.
NCBI tax ID(s): 355243 (species)
version 8.1 (current version)
General
@ref: 7758
BacDive-ID: 11296
DSM-Number: 18887
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Amphritea atlantica M41 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from Bathymodiolus sp. specimen from hydrothermal sediment at 3000 m depth.
NCBI tax id
- NCBI tax id: 355243
- Matching level: species
strain history
| @ref | history |
|---|---|
| 7758 | <- J. Wiese, IFM-GEOMAR, Kiel, Germany; M41 |
| 67770 | J. Wiese M41. |
doi: 10.13145/bacdive11296.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Oceanospirillales
- family: Oceanospirillaceae
- genus: Amphritea
- species: Amphritea atlantica
- full scientific name: Amphritea atlantica Gärtner et al. 2008
@ref: 7758
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Oceanospirillales
family: Oceanospirillaceae
genus: Amphritea
species: Amphritea atlantica
full scientific name: Amphritea atlantica Gärtner et al. 2008 emend. Jang et al. 2015
strain designation: M41
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 32270 | negative | 1.25 µm | 0.5 µm | rod-shaped | yes | |
| 69480 | yes | 98.299 | ||||
| 69480 | negative | 99.999 |
Culture and growth conditions
culture medium
- @ref: 7758
- name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
- growth: yes
- link: https://mediadive.dsmz.de/medium/514
- composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 7758 | positive | growth | 28 | mesophilic |
| 32270 | positive | growth | 04-40 | |
| 32270 | positive | optimum | 32.5 | mesophilic |
| 67770 | positive | growth | 30 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 32270 | positive | growth | 4.6-9.5 | alkaliphile |
| 32270 | positive | optimum | 8 |
Physiology and metabolism
oxygen tolerance
- @ref: 32270
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.992 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 32270 | NaCl | positive | growth | 0.3-9 % |
| 32270 | NaCl | positive | optimum | 3 % |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 32270 | 21217 | L-alaninamide | + | carbon source |
| 32270 | 16449 | alanine | + | carbon source |
| 32270 | 22653 | asparagine | + | carbon source |
| 32270 | 35391 | aspartate | + | carbon source |
| 32270 | 28757 | fructose | + | carbon source |
| 32270 | 17234 | glucose | + | carbon source |
| 32270 | 29987 | glutamate | + | carbon source |
| 32270 | 27570 | histidine | + | carbon source |
| 32270 | 51850 | methyl pyruvate | + | carbon source |
| 32270 | 28044 | phenylalanine | + | carbon source |
| 32270 | 26271 | proline | + | carbon source |
| 32270 | 17992 | sucrose | + | carbon source |
| 32270 | 53423 | tween 40 | + | carbon source |
| 32270 | 53426 | tween 80 | + | carbon source |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 32270 | catalase | + | 1.11.1.6 |
| 32270 | cytochrome oxidase | + | 1.9.3.1 |
| 32270 | urease | + | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | host species | geographic location | latitude | longitude |
|---|---|---|---|---|---|
| 7758 | Bathymodiolus sp. specimen from hydrothermal sediment at 3000 m depth | Bathymodiolus | Logatchev hydrothermal vent field at the Mid-Atlantic Ridge | ||
| 67770 | Bathymodiolus sp. mussel sample at the Logatchev hydrothermal vent field at the Mid-Atlantic Ridge (14° 45.199' N 44° 58.759' W) at a depth of about 3,000 m | Bathymodiolus sp. | 14.7533 | -44.9793 |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Sediment |
| #Environmental | #Aquatic | #Thermal spring |
| #Host | #Invertebrates (Other) | #Mollusca |
| #Condition | #Thermophilic (>45°C) |
taxonmaps
- @ref: 69479
- File name: preview.99_34758.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_240;96_11715;97_14167;98_25649;99_34758&stattab=map
- Last taxonomy: Amphritea atlantica subclade
- 16S sequence: AM156910
- Sequence Identity:
- Total samples: 3154
- soil counts: 148
- aquatic counts: 2869
- animal counts: 109
- plant counts: 28
Safety information
risk assessment
- @ref: 7758
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 7758
- description: Amphritea atlantica partial 16S rRNA gene, type strain M41T
- accession: AM156910
- length: 1427
- database: ena
- NCBI tax ID: 355243
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Amphritea atlantica strain DSM 18887 | 355243.5 | wgs | patric | 355243 |
| 66792 | Amphritea atlantica DSM 18887 | 2599185211 | draft | img | 355243 |
| 67770 | Amphritea atlantica DSM 18887 | GCA_900111095 | scaffold | ncbi | 355243 |
| 66792 | Amphritea atlantica JCM 14776 | GCA_024347255 | complete | ncbi | 355243 |
GC content
- @ref: 7758
- GC-content: 52.2
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| flagellated | yes | 86.487 | no |
| gram-positive | no | 99.068 | yes |
| anaerobic | no | 98.568 | yes |
| aerobic | yes | 58.08 | no |
| halophile | yes | 71.737 | no |
| spore-forming | no | 96.052 | no |
| motile | yes | 92.422 | yes |
| glucose-ferment | no | 82.25 | no |
| thermophile | no | 99.227 | yes |
| glucose-util | yes | 86.897 | yes |
External links
@ref: 7758
culture collection no.: DSM 18887, LMG 24143, JCM 14776
straininfo link
- @ref: 80529
- straininfo: 308714
literature
- topic: Phylogeny
- Pubmed-ID: 18175678
- title: Amphritea atlantica gen. nov., sp. nov., a gammaproteobacterium from the Logatchev hydrothermal vent field.
- authors: Gartner A, Wiese J, Imhoff JF
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.65234-0
- year: 2008
- mesh: Animals, Atlantic Ocean, Bacterial Typing Techniques, Base Composition, Bivalvia/*microbiology, DNA, Bacterial/analysis, Gammaproteobacteria/*classification/genetics/isolation & purification/physiology, Genes, rRNA, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Species Specificity, Temperature
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 7758 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18887) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18887 | |||
| 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 | |||
| 32270 | 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 | 28510 | 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) | |||
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 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 | |||
| 80529 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID308714.1 | StrainInfo: A central database for resolving microbial strain identifiers |