Strain identifier
BacDive ID: 8186
Type strain:
Species: Psychrobacter submarinus
Strain history: CIP <- 2002, DSMZ <- P. Schumann <- L.A. Romanenko, KMM
NCBI tax ID(s): 154108 (species)
General
@ref: 5237
BacDive-ID: 8186
DSM-Number: 14161
keywords: genome sequence, 16S sequence, Bacteria, mesophilic
description: Psychrobacter submarinus DSM 14161 is a mesophilic bacterium that was isolated from seawater at a depth of 300 m.
NCBI tax id
- NCBI tax id: 154108
- Matching level: species
strain history
@ref | history |
---|---|
5237 | <- P. Schumann <- L. A. Romanenko, KMM |
123347 | CIP <- 2002, DSMZ <- P. Schumann <- L.A. Romanenko, KMM |
doi: 10.13145/bacdive8186.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Pseudomonadales
- family: Moraxellaceae
- genus: Psychrobacter
- species: Psychrobacter submarinus
- full scientific name: Psychrobacter submarinus Romanenko et al. 2002
@ref: 5237
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Pseudomonadales
family: Moraxellaceae
genus: Psychrobacter
species: Psychrobacter submarinus
full scientific name: Psychrobacter submarinus Romanenko et al. 2002
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | no | 93.051 | ||
69480 | 99.998 | negative | ||
123347 | no | negative | oval-shaped |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
5237 | BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) | yes | https://mediadive.dsmz.de/medium/514 | Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514; with strain-specific modifications) Composition: NaCl 30.0 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 |
33154 | Marine agar (MA) | yes | Distilled water make up to (1000.000 ml);Marine agar (55.100 g) | |
123347 | CIP Medium 13 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
5237 | positive | growth | 25 | mesophilic |
33154 | positive | growth | 25 | mesophilic |
123347 | positive | growth | 15-25 | psychrophilic |
123347 | no | growth | 5 | psychrophilic |
123347 | no | growth | 30 | mesophilic |
123347 | no | growth | 37 | mesophilic |
123347 | no | growth | 41 | thermophilic |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.998 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
123347 | NaCl | positive | growth | 2-8 % |
123347 | NaCl | no | growth | 0 % |
123347 | NaCl | no | growth | 10 % |
metabolite utilization
@ref | metabolite | utilization activity | kind of utilization tested | Chebi-ID |
---|---|---|---|---|
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | gluconate | - | builds acid from | 24265 |
68371 | L-arabitol | - | builds acid from | 18403 |
68371 | D-arabitol | - | builds acid from | 18333 |
68371 | L-fucose | - | builds acid from | 18287 |
68371 | D-fucose | - | builds acid from | 28847 |
68371 | D-tagatose | - | builds acid from | 16443 |
68371 | D-lyxose | - | builds acid from | 62318 |
68371 | turanose | - | builds acid from | 32528 |
68371 | gentiobiose | - | builds acid from | 28066 |
68371 | xylitol | - | builds acid from | 17151 |
68371 | glycogen | - | builds acid from | 28087 |
68371 | starch | - | builds acid from | 28017 |
68371 | raffinose | - | builds acid from | 16634 |
68371 | melezitose | - | builds acid from | 6731 |
68371 | inulin | - | builds acid from | 15443 |
68371 | trehalose | - | builds acid from | 27082 |
68371 | sucrose | - | builds acid from | 17992 |
68371 | melibiose | - | builds acid from | 28053 |
68371 | lactose | - | builds acid from | 17716 |
68371 | cellobiose | - | builds acid from | 17057 |
68371 | salicin | - | builds acid from | 17814 |
68371 | esculin | - | builds acid from | 4853 |
68371 | arbutin | - | builds acid from | 18305 |
68371 | amygdalin | - | builds acid from | 27613 |
68371 | N-acetylglucosamine | - | builds acid from | 59640 |
68371 | methyl alpha-D-glucopyranoside | - | builds acid from | 320061 |
68371 | methyl alpha-D-mannoside | - | builds acid from | 43943 |
68371 | D-sorbitol | - | builds acid from | 17924 |
68371 | D-mannitol | - | builds acid from | 16899 |
68371 | myo-inositol | - | builds acid from | 17268 |
68371 | galactitol | - | builds acid from | 16813 |
68371 | L-rhamnose | - | builds acid from | 62345 |
68371 | L-sorbose | - | builds acid from | 17266 |
68371 | D-mannose | - | builds acid from | 16024 |
68371 | D-fructose | - | builds acid from | 15824 |
68371 | D-glucose | - | builds acid from | 17634 |
68371 | D-galactose | - | builds acid from | 12936 |
68371 | methyl beta-D-xylopyranoside | - | builds acid from | 74863 |
68371 | ribitol | - | builds acid from | 15963 |
68371 | L-xylose | - | builds acid from | 65328 |
68371 | D-xylose | - | builds acid from | 65327 |
68371 | D-ribose | - | builds acid from | 16988 |
68371 | L-arabinose | - | builds acid from | 30849 |
68371 | D-arabinose | - | builds acid from | 17108 |
68371 | erythritol | - | builds acid from | 17113 |
68371 | glycerol | - | builds acid from | 17754 |
123347 | citrate | - | carbon source | 16947 |
123347 | esculin | - | hydrolysis | 4853 |
123347 | nitrate | - | reduction | 17632 |
123347 | nitrite | - | reduction | 16301 |
123347 | nitrate | - | respiration | 17632 |
antibiotic resistance
- @ref: 123347
- metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
- is antibiotic: yes
- is sensitive: no
- is resistant: yes
metabolite production
- @ref: 123347
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | methylred-test |
---|---|---|---|---|
123347 | 15688 | acetoin | - | |
123347 | 17234 | glucose | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
123347 | oxidase | + | |
123347 | beta-galactosidase | - | 3.2.1.23 |
123347 | alcohol dehydrogenase | - | 1.1.1.1 |
123347 | gelatinase | - | |
123347 | amylase | - | |
123347 | DNase | - | |
123347 | caseinase | - | 3.4.21.50 |
123347 | catalase | + | 1.11.1.6 |
123347 | tween esterase | + | |
123347 | lecithinase | - | |
123347 | lipase | - | |
123347 | lysine decarboxylase | - | 4.1.1.18 |
123347 | ornithine decarboxylase | - | 4.1.1.17 |
123347 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
123347 | tryptophan deaminase | - | |
123347 | urease | - | 3.5.1.5 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
123347 | - | + | + | + | - | + | - | - | - | - | + | + | - | - | - | - | - | - | - | - |
API 50CHac
@ref | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
123347 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | +/- | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | latitude | longitude | country | isolation date |
---|---|---|---|---|---|---|
5237 | seawater at a depth of 300 m | Pacific Ocean 12°41'N, 132°38'W | 12.6833 | -132.633 | ||
123347 | Environment, Seawater at a depth of 300m | Pacific Ocean | 1985 |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Marine
taxonmaps
- @ref: 69479
- File name: preview.99_1920.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_80;96_193;97_209;98_1507;99_1920&stattab=map
- Last taxonomy: Psychrobacter
- 16S sequence: AJ309940
- Sequence Identity:
- Total samples: 1598
- soil counts: 91
- aquatic counts: 1139
- animal counts: 350
- plant counts: 18
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
5237 | 1 | Risk group (German classification) |
123347 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 5237
- description: Psychrobacter submarinus 16S rRNA gene, strain KMM 225
- accession: AJ309940
- length: 1428
- database: ena
- NCBI tax ID: 154108
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Psychrobacter submarinus KMM 225 | GCA_904846685 | contig | ncbi | 154108 |
66792 | Psychrobacter submarinus strain Psychrobacter submarinus KMM225 | 154108.8 | wgs | patric | 154108 |
GC content
- @ref: 5237
- GC-content: 46.7
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 89.225 | no |
gram-positive | no | 98.135 | no |
anaerobic | no | 98.476 | no |
aerobic | yes | 86.532 | no |
halophile | yes | 76.476 | no |
spore-forming | no | 96.421 | no |
thermophile | no | 99.255 | no |
glucose-util | no | 62.162 | no |
flagellated | no | 91.809 | no |
glucose-ferment | no | 93.896 | no |
External links
@ref: 5237
culture collection no.: DSM 14161, KMM 225, CIP 107641
straininfo link
- @ref: 77589
- straininfo: 88148
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 12148642 | Psychrobacter submarinus sp. nov. and Psychrobacter marincola sp. nov., psychrophilic halophiles from marine environments. | Romanenko LA, Schumann P, Rohde M, Lysenko AM, Mikhailov VV, Stackebrandt E | Int J Syst Evol Microbiol | 10.1099/00207713-52-4-1291 | 2002 | Animals, Bacterial Typing Techniques, *Cold Temperature, DNA, Ribosomal/analysis, Gammaproteobacteria/chemistry/*classification/genetics/physiology, Genotype, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sodium Chloride/*metabolism, Urochordata/*microbiology | Genetics |
Pathogenicity | 33838818 | Structure and in vitro antiproliferative activity of the acidic capsular polysaccharide from the deep-sea bacterium Psychrobacter submarinus KMM 225(T). | Kokoulin MS, Kuzmich AS, Romanenko LA, Chikalovets IV | Carbohydr Polym | 10.1016/j.carbpol.2021.117941 | 2021 | Aquatic Organisms/chemistry, Carbohydrate Sequence, Cell Proliferation/*drug effects, Cell Survival/drug effects, Humans, K562 Cells, Magnetic Resonance Spectroscopy/methods, Polysaccharides, Bacterial/*chemistry/isolation & purification/*pharmacology, Psychrobacter/*chemistry, Seawater/microbiology | Enzymology |
Reference
@id | authors | catalogue | doi/url | title |
---|---|---|---|---|
5237 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14161) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-14161 | |
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 | |
33154 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/5099 | ||
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) | |
68371 | Automatically annotated from API 50CH acid | |||
68382 | Automatically annotated from API zym | |||
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 | |
77589 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID88148.1 | StrainInfo: A central database for resolving microbial strain identifiers | |
123347 | Curators of the CIP | Collection of Institut Pasteur (CIP 107641) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107641 |