Strain identifier
BacDive ID: 479
Type strain: 
Species: Marinobacter sediminum
Strain Designation: R 65
Strain history: <- L. A. Romanenko; R 65
NCBI tax ID(s): 256323 (species)
version 8.1 (current version)
General
@ref: 5895
BacDive-ID: 479
DSM-Number: 15400
keywords: genome sequence, 16S sequence, Bacteria, aerobe, heterotroph, mesophilic, Gram-negative, motile, rod-shaped
description: Marinobacter sediminum R 65 is an aerobe, heterotroph, mesophilic bacterium that was isolated from marine coastal sediments.
NCBI tax id
- NCBI tax id: 256323
- Matching level: species
strain history
- @ref: 5895
- history: <- L. A. Romanenko; R 65
doi: 10.13145/bacdive479.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Alteromonadales
- family: Alteromonadaceae
- genus: Marinobacter
- species: Marinobacter sediminum
- full scientific name: Marinobacter sediminum Romanenko et al. 2005
@ref: 5895
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Alteromonadales
family: Alteromonadaceae
genus: Marinobacter
species: Marinobacter sediminum
full scientific name: Marinobacter sediminum Romanenko et al. 2005
strain designation: R 65
type strain: yes
Morphology
cell morphology
- @ref: 23297
- gram stain: negative
- cell length: 1.8-2.5 µm
- cell width: 0.3-0.4 µm
- cell shape: rod-shaped
- motility: yes
Culture and growth conditions
culture medium
- @ref: 5895
- 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 |
|---|---|---|---|---|
| 5895 | positive | growth | 28 | mesophilic |
| 23297 | positive | growth | 4-42 | |
| 23297 | no | growth | 43 | thermophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 23297
- oxygen tolerance: aerobe
nutrition type
- @ref: 23297
- type: heterotroph
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 23297 | NaCl | positive | growth | 0.5-18.0 % |
| 23297 | NaCl | no | growth | 18.5 % |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 23297 | 17128 | adipate | - | assimilation |
| 23297 | 15963 | ribitol | - | assimilation |
| 23297 | 36219 | alpha-lactose | - | assimilation |
| 23297 | 27689 | decanoate | - | assimilation |
| 23297 | 17057 | cellobiose | - | assimilation |
| 23297 | 16947 | citrate | - | assimilation |
| 23297 | 18333 | D-arabitol | - | assimilation |
| 23297 | 15824 | D-fructose | - | assimilation |
| 23297 | 12936 | D-galactose | - | assimilation |
| 23297 | 8391 | D-gluconate | - | assimilation |
| 23297 | 16899 | D-mannitol | - | assimilation |
| 23297 | 16024 | D-mannose | - | assimilation |
| 23297 | 28053 | melibiose | - | assimilation |
| 23297 | 16634 | raffinose | - | assimilation |
| 23297 | 17924 | D-sorbitol | - | assimilation |
| 23297 | 16551 | D-trehalose | - | assimilation |
| 23297 | 17113 | erythritol | - | assimilation |
| 23297 | 28066 | gentiobiose | - | assimilation |
| 23297 | 30849 | L-arabinose | - | assimilation |
| 23297 | 18287 | L-fucose | - | assimilation |
| 23297 | 15589 | L-malate | - | assimilation |
| 23297 | 62345 | L-rhamnose | - | assimilation |
| 23297 | 6359 | lactulose | - | assimilation |
| 23297 | 17306 | maltose | - | assimilation |
| 23297 | 320055 | methyl beta-D-glucopyranoside | - | assimilation |
| 23297 | 17268 | myo-inositol | - | assimilation |
| 23297 | 28037 | N-acetylgalactosamine | - | assimilation |
| 23297 | 506227 | N-acetylglucosamine | - | assimilation |
| 23297 | 18401 | phenylacetate | - | assimilation |
| 23297 | 33951 | psicose | - | assimilation |
| 23297 | 17992 | sucrose | - | assimilation |
| 23297 | 32528 | turanose | - | assimilation |
| 23297 | 17151 | xylitol | - | assimilation |
| 23297 | 22599 | arabinose | - | builds acid from |
| 23297 | 28260 | galactose | - | builds acid from |
| 23297 | 17234 | glucose | - | builds acid from |
| 23297 | 17754 | glycerol | - | builds acid from |
| 23297 | 17716 | lactose | - | builds acid from |
| 23297 | 17306 | maltose | - | builds acid from |
| 23297 | 29864 | mannitol | - | builds acid from |
| 23297 | 506227 | N-acetylglucosamine | - | builds acid from |
| 23297 | 26546 | rhamnose | - | builds acid from |
| 23297 | 17992 | sucrose | - | builds acid from |
| 23297 | 4853 | esculin | - | hydrolysis |
| 23297 | 5291 | gelatin | - | hydrolysis |
| 23297 | 53423 | tween 40 | + | hydrolysis |
| 23297 | 16763 | 2-oxobutanoate | +/- | assimilation |
| 23297 | 28644 | 2-oxopentanoate | +/- | assimilation |
| 23297 | 17634 | D-glucose | +/- | assimilation |
| 23297 | 53426 | tween 80 | +/- | hydrolysis |
metabolite production
- @ref: 23297
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 23297 | amylase | - | |
| 23297 | arginine dihydrolase | - | 3.5.3.6 |
| 23297 | beta-galactosidase | - | 3.2.1.23 |
| 23297 | caseinase | - | 3.4.21.50 |
| 23297 | catalase | + | 1.11.1.6 |
| 23297 | chitinase | - | 3.2.1.14 |
| 23297 | cytochrome oxidase | + | 1.9.3.1 |
| 23297 | gelatinase | - | |
| 23297 | urease | - | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 23297 | marine coastal sediments | Peter the Great Bay, Sea of Japan | Russia | RUS | Asia |
| 5895 | bottom sediments | Sea of Japan | Russia | RUS | Europe |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Marine |
| #Environmental | #Terrestrial | #Coast |
| #Environmental | #Terrestrial | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_34863.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_89;96_1317;97_1564;98_4746;99_34863&stattab=map
- Last taxonomy: Marinobacter
- 16S sequence: AJ609270
- Sequence Identity:
- Total samples: 227
- soil counts: 5
- aquatic counts: 218
- animal counts: 2
- plant counts: 2
Safety information
risk assessment
- @ref: 5895
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 5895
- description: Marinobacter sedimentalis 16S rRNA gene, type strain R65T
- accession: AJ609270
- length: 1512
- database: ena
- NCBI tax ID: 256323
Genome sequences
- @ref: 66792
- description: Marinobacter sediminum strain R65
- accession: 256323.4
- assembly level: wgs
- database: patric
- NCBI tax ID: 256323
GC content
- @ref: 23297
- GC-content: 56.5
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | yes | 92.098 | yes |
| gram-positive | no | 98.66 | yes |
| anaerobic | no | 98.071 | yes |
| aerobic | yes | 88.59 | yes |
| halophile | yes | 95.858 | no |
| spore-forming | no | 96.526 | no |
| glucose-util | no | 51.52 | no |
| thermophile | no | 98.923 | no |
| flagellated | yes | 92.46 | no |
| glucose-ferment | no | 90.537 | no |
External links
@ref: 5895
culture collection no.: DSM 15400, KMM 3657
straininfo link
- @ref: 70158
- straininfo: 127680
literature
- topic: Phylogeny
- Pubmed-ID: 15653867
- title: Marinobacter bryozoorum sp. nov. and Marinobacter sediminum sp. nov., novel bacteria from the marine environment.
- authors: Romanenko LA, Schumann P, Rohde M, Zhukova NV, Mikhailov VV, Stackebrandt E
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.63258-0
- year: 2005
- mesh: Alteromonadaceae/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 5895 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15400) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-15400 | |||
| 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 | |||
| 23297 | Lyudmila A. Romanenko, Peter Schumann, Manfred Rohde, Natalia V. Zhukova, Valery V. Mikhailov, Erko Stackebrandt | 10.1099/ijs.0.63258-0 | Marinobacter bryozoorum sp. nov. and Marinobacter sediminum sp. nov., novel bacteria from the marine environment | IJSEM 55: 143-148 2005 | 15653867 | |
| 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 | |||
| 70158 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID127680.1 | StrainInfo: A central database for resolving microbial strain identifiers |