Strain identifier

BacDive ID: 12683

Type strain: Yes

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)

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General

@ref: 2839

BacDive-ID: 12683

DSM-Number: 6820

keywords: genome sequence, 16S sequence, Bacteria, psychrophilic, Gram-negative

description: Pseudoalteromonas carrageenovora DSM 6820 is a psychrophilic, Gram-negative bacterium that was isolated from sample of sea water and marine algae.

NCBI tax id

NCBI tax idMatching level
227species
1314868strain

strain history

@refhistory
2839<- NCIMB <- W. Yaphe
67770M. Akagawa-Matsushita <-- IAM 12662 <-- IFO 12985 <-- NCMB 302 <-- W. Yaphe.
117195CIP <- 1993, M. Akagawa-Matsushita, Kitakyushu, Japan <- 1982, IFO: strain 12985, Pseudomonas carrageenovora <- W. Yaphe, Canada

doi: 10.13145/bacdive12683.20250331.9.3

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

@refgram stainconfidence
125438negative100
125439negative95.6

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2839BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: 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
2839SEA WATER AGAR (DSMZ Medium 246)yeshttps://mediadive.dsmz.de/medium/246Name: 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
42022Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
117195CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperature
2839positivegrowth20
42022positivegrowth22
67770positivegrowth25

Physiology and metabolism

oxygen tolerance

  • @ref: 125439
  • oxygen tolerance: obligate aerobe
  • confidence: 98.6

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 97.1

compound production

@refcompound
2839kappa carrageenase
2839lambda carrageenase
2839carrageenase
67770Carageenanase

observation

  • @ref: 67770
  • observation: quinones: Q-8

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
2839sample of sea water and marine algaeNova scotia, HalifaxCanadaCANNorth America
67770Red alga (Cow BayNova ScotiaCanadaCANNorth America
117195Other, Seaweed

isolation source categories

Cat1Cat2Cat3
#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

@refbiosafety levelbiosafety level comment
28391Risk group (German classification)
1171951Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pseudoalteromonas carrageenovora gene for 16S rRNA, partial sequence, strain: NBRC 12985AB6803591461nuccore227
2839Pseudoalteromonas carrageenovora 16S rRNA gene, type strain IAM 12662TX821361423nuccore227
124043Pseudoalteromonas carrageenovora strain NBRC 12985 16S ribosomal RNA gene, partial sequence.OQ4380701137nuccore227

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudoalteromonas carrageenovora IAM 12662 ATCC43555TGCA_900239935chromosomencbi1314868
66792Pseudoalteromonas carrageenovora IAM 12662GCA_014925295chromosomencbi1314868
66792Pseudoalteromonas carrageenovora IAM 126621314868.5wgspatric1314868
66792Pseudoalteromonas carrageenovora IAM 12662 strain ATCC 43555 strain ATCC43555T1314868.3completepatric1314868
66792Pseudoalteromonas carrageenovora strain NBRC 12985227.5wgspatric227
66792Pseudoalteromonas carrageenovora IAM 126622847759026completeimg1314868
67770Pseudoalteromonas carrageenovora NBRC 12985GCA_006539245contigncbi227

GC content

  • @ref: 67770
  • GC-content: 39.5
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno100no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.221no
125438spore-formingspore-formingAbility to form endo- or exosporesno87.66no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes76.065no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno97.5no
125438motile2+flagellatedAbility to perform flagellated movementyes84.908no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno97.1
125439BacteriaNetmotilityAbility to perform movementyes52.9
125439BacteriaNetgram_stainReaction to gram-stainingnegative95.6
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe98.6

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

@refstraininfo
81894264316
81895312172

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology8112578The gene encoding the kappa-carrageenase of Alteromonas carrageenovora is related to beta-1,3-1,4-glucanases.Barbeyron T, Henrissat B, Kloareg BGene10.1016/0378-1119(94)90531-21994Amino 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/geneticsGenetics
Phylogeny10826813Assignment 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 RInt J Syst Evol Microbiol10.1099/00207713-50-1-2652000Alteromonas/*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 MicrobiologyGenetics
Phylogeny15878450The 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 ACarbohydr Res10.1016/j.carres.2005.03.0122005Acylation, Carbohydrate Sequence, Lipopolysaccharides/*chemistry/isolation & purification, Magnetic Resonance Spectroscopy, Molecular Sequence Data, Pseudoalteromonas/*chemistry/*classification, Spectrometry, Mass, Matrix-Assisted Laser Desorption-IonizationGenetics
Genetics16198323The 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 MCarbohydr Res10.1016/j.carres.2005.09.0072005Carbohydrate Conformation, Carbohydrate Sequence, Lipopolysaccharides/*chemistry/isolation & purification, Magnetic Resonance Spectroscopy, Models, Molecular, Molecular Sequence Data, Pseudoalteromonas/*chemistryEnzymology
Enzymology29030427Structural 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 MJ Biol Chem10.1074/jbc.M117.8082792017*Carbohydrate Metabolism, Catalysis, Crystallography, X-Ray, Flavobacteriaceae/*enzymology, Glycoside Hydrolases/chemistry/classification/*metabolism, Kinetics, *Marine Biology, Phylogeny, Protein Conformation, Pseudoalteromonas/*enzymology, Substrate SpecificityMetabolism
Metabolism30524390Evolutionary 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 GFront Microbiol10.3389/fmicb.2018.027402018

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2839Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6820)https://www.dsmz.de/collection/catalogue/details/culture/DSM-6820
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
42022Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15497
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69479João 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
81894Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID264316.1StrainInfo: A central database for resolving microbial strain identifiers
81895Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID312172.1StrainInfo: A central database for resolving microbial strain identifiers
117195Curators of the CIPCollection of Institut Pasteur (CIP 103674)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103674
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1