Strain identifier
BacDive ID: 12683
Type strain:
Species: Pseudoalteromonas carrageenovora
Strain history: CIP <- 1993, M. Akagawa-Matsushita, Kitakyushu, Japan <- 1982, IFO: strain 12985, Pseudomonas carrageenovora <- W. Yaphe, Canada
NCBI tax ID(s): 1314868 (strain), 227 (species)
General
@ref: 2839
BacDive-ID: 12683
DSM-Number: 6820
keywords: genome sequence, 16S sequence, Bacteria, psychrophilic, motile
description: Pseudoalteromonas carrageenovora DSM 6820 is a psychrophilic, motile bacterium that was isolated from sample of sea water and marine algae.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1314868 | strain |
227 | species |
strain history
@ref | history |
---|---|
2839 | <- NCIMB <- W. Yaphe |
67770 | M. Akagawa-Matsushita <-- IAM 12662 <-- IFO 12985 <-- NCMB 302 <-- W. Yaphe. |
117195 | CIP <- 1993, M. Akagawa-Matsushita, Kitakyushu, Japan <- 1982, IFO: strain 12985, Pseudomonas carrageenovora <- W. Yaphe, Canada |
doi: 10.13145/bacdive12683.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Alteromonadales
- family: Pseudoalteromonadaceae
- genus: Pseudoalteromonas
- species: Pseudoalteromonas carrageenovora
- full scientific name: Pseudoalteromonas carrageenovora (Akagawa-Matsushita et al. 1992) Gauthier et al. 1995
synonyms
- @ref: 20215
- synonym: Alteromonas carrageenovora
@ref: 2839
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Alteromonadales
family: Pseudoalteromonadaceae
genus: Pseudoalteromonas
species: Pseudoalteromonas carrageenovora
full scientific name: Pseudoalteromonas carrageenovora (Akagawa-Matsushita et al. 1992) Gauthier et al. 1995
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | yes | 98.184 | |
69480 | 99.997 | negative |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
2839 | BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) | yes | https://mediadive.dsmz.de/medium/514 | 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 |
2839 | SEA WATER AGAR (DSMZ Medium 246) | yes | https://mediadive.dsmz.de/medium/246 | Name: SEA WATER AGAR (DSMZ Medium 246) Composition: Agar 20.0 g/l Peptone 10.0 g/l Beef extract 10.0 g/l Tap water Sea water |
42022 | Marine agar (MA) | yes | Distilled water make up to (1000.000 ml);Marine agar (55.100 g) | |
117195 | CIP Medium 13 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
2839 | positive | growth | 20 | psychrophilic |
42022 | positive | growth | 22 | psychrophilic |
67770 | positive | growth | 25 | mesophilic |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.978 |
compound production
@ref | compound |
---|---|
2839 | kappa carrageenase |
2839 | lambda carrageenase |
2839 | carrageenase |
67770 | Carageenanase |
observation
- @ref: 67770
- observation: quinones: Q-8
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
2839 | sample of sea water and marine algae | Nova scotia, Halifax | Canada | CAN | North America |
67770 | Red alga (Cow Bay | Nova Scotia | Canada | CAN | North America |
117195 | Other, Seaweed |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Marine |
#Host | #Algae |
taxonmaps
- @ref: 69479
- File name: preview.99_1002.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_57;96_122;97_129;98_145;99_1002&stattab=map
- Last taxonomy: Pseudoalteromonas
- 16S sequence: X82136
- Sequence Identity:
- Total samples: 3222
- soil counts: 24
- aquatic counts: 2792
- animal counts: 384
- plant counts: 22
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
2839 | 1 | Risk group (German classification) |
117195 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Pseudoalteromonas carrageenovora gene for 16S rRNA, partial sequence, strain: NBRC 12985 | AB680359 | 1461 | ena | 227 |
2839 | Pseudoalteromonas carrageenovora 16S rRNA gene, type strain IAM 12662T | X82136 | 1423 | ena | 227 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Pseudoalteromonas carrageenovora IAM 12662 ATCC43555T | GCA_900239935 | chromosome | ncbi | 1314868 |
66792 | Pseudoalteromonas carrageenovora IAM 12662 | GCA_014925295 | chromosome | ncbi | 1314868 |
66792 | Pseudoalteromonas carrageenovora IAM 12662 | 1314868.5 | wgs | patric | 1314868 |
66792 | Pseudoalteromonas carrageenovora IAM 12662 strain ATCC 43555 strain ATCC43555T | 1314868.3 | complete | patric | 1314868 |
66792 | Pseudoalteromonas carrageenovora strain NBRC 12985 | 227.5 | wgs | patric | 227 |
66792 | Pseudoalteromonas carrageenovora IAM 12662 | 2847759026 | complete | img | 1314868 |
67770 | Pseudoalteromonas carrageenovora NBRC 12985 | GCA_006539245 | contig | ncbi | 227 |
GC content
- @ref: 67770
- GC-content: 39.5
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 92.424 | no |
gram-positive | no | 99.08 | no |
anaerobic | no | 97.834 | no |
halophile | yes | 62.661 | no |
spore-forming | no | 96.459 | no |
glucose-util | yes | 91.536 | no |
flagellated | yes | 89.354 | no |
thermophile | no | 99.233 | yes |
aerobic | yes | 90.008 | no |
glucose-ferment | no | 77.721 | no |
External links
@ref: 2839
culture collection no.: DSM 6820, ATCC 43555, IAM 12662, IFO 12985, NBRC 12985, NCIMB 302, JCM 8851, CGMCC 1.2912, CGMCC 1.6485, CIP 103674
straininfo link
@ref | straininfo |
---|---|
81894 | 264316 |
81895 | 312172 |
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Enzymology | 8112578 | The gene encoding the kappa-carrageenase of Alteromonas carrageenovora is related to beta-1,3-1,4-glucanases. | Barbeyron T, Henrissat B, Kloareg B | Gene | 10.1016/0378-1119(94)90531-2 | 1994 | Amino Acid Sequence, *Bacterial Proteins, Base Sequence, Cloning, Molecular, Conserved Sequence, *Genes, Bacterial, Glycoside Hydrolases/*genetics, Gram-Negative Aerobic Bacteria/*enzymology/*genetics, Molecular Sequence Data, Restriction Mapping, Sequence Homology, Amino Acid, Streptomyces/enzymology/genetics | Genetics |
Phylogeny | 10826813 | Assignment of Alteromonas elyakovii KMM 162T and five strains isolated from spot-wounded fronds of Laminaria japonica to Pseudoalteromonas elyakovii comb. nov. and the extended description of the species. | Sawabe T, Tanaka R, Iqbal MM, Tajima K, Ezura Y, Ivanova EP, Christen R | Int J Syst Evol Microbiol | 10.1099/00207713-50-1-265 | 2000 | Alteromonas/*classification/cytology/genetics/physiology, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Gammaproteobacteria/*classification/cytology/genetics/physiology, Laminaria/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Water Microbiology | Genetics |
Phylogeny | 15878450 | The complete structure of the core carbohydrate backbone from the LPS of marine halophilic bacterium Pseudoalteromonas carrageenovora type strain IAM 12662T. | Silipo A, Lanzetta R, Parrilli M, Sturiale L, Garozzo D, Nazarenko EL, Gorshkova RP, Ivanova EP, Molinaro A | Carbohydr Res | 10.1016/j.carres.2005.03.012 | 2005 | Acylation, Carbohydrate Sequence, Lipopolysaccharides/*chemistry/isolation & purification, Magnetic Resonance Spectroscopy, Molecular Sequence Data, Pseudoalteromonas/*chemistry/*classification, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization | Genetics |
Genetics | 16198323 | The O-chain structure from the LPS of marine halophilic bacterium Pseudoalteromonas carrageenovora-type strain IAM 12662T. | Silipo A, Molinaro A, Nazarenko EL, Gorshkova RP, Ivanova EP, Lanzetta R, Parrilli M | Carbohydr Res | 10.1016/j.carres.2005.09.007 | 2005 | Carbohydrate Conformation, Carbohydrate Sequence, Lipopolysaccharides/*chemistry/isolation & purification, Magnetic Resonance Spectroscopy, Models, Molecular, Molecular Sequence Data, Pseudoalteromonas/*chemistry | Enzymology |
Enzymology | 29030427 | Structural insights into marine carbohydrate degradation by family GH16 kappa-carrageenases. | Matard-Mann M, Bernard T, Leroux C, Barbeyron T, Larocque R, Prechoux A, Jeudy A, Jam M, Nyvall Collen P, Michel G, Czjzek M | J Biol Chem | 10.1074/jbc.M117.808279 | 2017 | *Carbohydrate Metabolism, Catalysis, Crystallography, X-Ray, Flavobacteriaceae/*enzymology, Glycoside Hydrolases/chemistry/classification/*metabolism, Kinetics, *Marine Biology, Phylogeny, Protein Conformation, Pseudoalteromonas/*enzymology, Substrate Specificity | Metabolism |
Metabolism | 30524390 | Evolutionary Evidence of Algal Polysaccharide Degradation Acquisition by Pseudoalteromonas carrageenovora 9(T) to Adapt to Macroalgal Niches. | Gobet A, Barbeyron T, Matard-Mann M, Magdelenat G, Vallenet D, Duchaud E, Michel G | Front Microbiol | 10.3389/fmicb.2018.02740 | 2018 |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
2839 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6820) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-6820 | |||
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 | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
42022 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/15497 | ||||
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 | |||
81894 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID264316.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
81895 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID312172.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
117195 | Curators of the CIP | Collection of Institut Pasteur (CIP 103674) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103674 |