Strain identifier

BacDive ID: 12688

Type strain: Yes

Species: Pseudoalteromonas tunicata

Strain Designation: D2

Strain history: CIP <- 1999, CCUG <- C. Holmström, Univ. Göteborg, Sweden: strain D2

NCBI tax ID(s): 314281 (species)

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General

@ref: 5147

BacDive-ID: 12688

DSM-Number: 14096

keywords: genome sequence, 16S sequence, Bacteria, psychrophilic, motile

description: Pseudoalteromonas tunicata D2 is a psychrophilic, motile bacterium that was isolated from adult tunicate Ciona intestinalis.

NCBI tax id

  • NCBI tax id: 314281
  • Matching level: species

strain history

@refhistory
5147<- C. Holmström; D2
123689CIP <- 1999, CCUG <- C. Holmström, Univ. Göteborg, Sweden: strain D2

doi: 10.13145/bacdive12688.20230509.8.1

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 tunicata
  • full scientific name: Pseudoalteromonas tunicata Holmström et al. 1998

@ref: 5147

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Pseudoalteromonadaceae

genus: Pseudoalteromonas

species: Pseudoalteromonas tunicata

full scientific name: Pseudoalteromonas tunicata Holmström et al. 1998

strain designation: D2

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes95.536
6948099.817negative
123689yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5147BACTO 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
42038MEDIUM 480 - for Pseudomonas tunicatayesSodium hydrogen carbonate (0.080 g);Distilled water make up to (1000.000 ml);Sodium chloride (17.600 g);Potassium chloride (0.250 g);Iron (II) sulphate heptahydrate(0.010 g);Boric acid (0.008 g);Magnesium chloride hexahydrate (1.870 g);Calcium chloridedih
123689CIP Medium 480yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=480

culture temp

@refgrowthtypetemperaturerange
5147positivegrowth20psychrophilic
42038positivegrowth20psychrophilic
123689positivegrowth5-30
123689nogrowth37mesophilic
123689nogrowth41thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no98.922

halophily

@refsaltgrowthtested relationconcentration
123689NaClpositivegrowth2-4 %
123689NaClnogrowth0 %
123689NaClnogrowth6 %
123689NaClnogrowth8 %
123689NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1236894853esculin-hydrolysis
12368917632nitrate-reduction
12368916301nitrite-reduction

antibiotic resistance

  • @ref: 123689
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 123689
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
123689oxidase-
123689beta-galactosidase-3.2.1.23
123689alcohol dehydrogenase-1.1.1.1
123689gelatinase+
123689amylase+
123689DNase+
123689caseinase-3.4.21.50
123689catalase+1.11.1.6
123689tween esterase+
123689lecithinase+
123689lipase-
123689lysine decarboxylase-4.1.1.18
123689ornithine decarboxylase-4.1.1.17
123689protease-
123689tryptophan deaminase-
123689urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)-
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123689-+-+-+----++-----+--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123689---+---+---------------------------------------------------+-------------------------------------+-

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
5147adult tunicate Ciona intestinalisCiona intestinaliswestern coastSwedenSWEEurope
123689Environment, Water surface, adult tunicate, Ciona intestinalisGöteborgSwedenSWEEurope1990

isolation source categories

  • Cat1: #Host
  • Cat2: #Invertebrates (Other)
  • Cat3: #Tunicata

taxonmaps

  • @ref: 69479
  • File name: preview.99_37457.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_57;96_17808;97_21947;98_27554;99_37457&stattab=map
  • Last taxonomy: Pseudoalteromonas
  • 16S sequence: Z25522
  • Sequence Identity:
  • Total samples: 31
  • aquatic counts: 15
  • animal counts: 16

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
51471Risk group (German classification)
1236891Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5147
  • description: Pseudoalteromonas tunicata 16S RNA gene, partial, strain D2
  • accession: Z25522
  • length: 1365
  • database: ena
  • NCBI tax ID: 87626

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudoalteromonas tunicata D2GCA_003568825completencbi314281
66792Pseudoalteromonas tunicata D2GCA_002310815completencbi314281
66792Pseudoalteromonas tunicata D2GCA_000153245scaffoldncbi87626
66792Pseudoalteromonas tunicata D287626.5wgspatric87626
66792Pseudoalteromonas tunicata strain D2314281.3completepatric314281
66792Pseudoalteromonas tunicata D2638341157draftimg87626
66792Pseudoalteromonas tunicata D22847754586completeimg87626

GC content

  • @ref: 5147
  • GC-content: 42

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes91.453no
flagellatedyes92.608no
gram-positiveno99.168no
anaerobicno96.206no
aerobicyes83.434no
halophileno58.177no
spore-formingno92.57no
glucose-utilyes92.194no
thermophileno99.376yes
glucose-fermentno74.085no

External links

@ref: 5147

culture collection no.: DSM 14096, CCUG 26757, CIP 105928, CCUG 44952

straininfo link

  • @ref: 81900
  • straininfo: 58170

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9828422Pseudoalteromonas tunicata sp. nov., a bacterium that produces antifouling agents.Holmstrom C, James S, Neilan BA, White DC, Kjelleberg SInt J Syst Bacteriol10.1099/00207713-48-4-12051998Animals, Anti-Bacterial Agents/*biosynthesis, Base Composition, Ciona intestinalis/microbiology, DNA, Bacterial/chemistry, Fatty Acids/analysis, Genotype, Gram-Negative Facultatively Anaerobic Rods/*classification/*isolation & purification/*metabolism, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Terminology as TopicGenetics
Phylogeny28699865Phaeobacter porticola sp. nov., an antibiotic-producing bacterium isolated from a sea harbour.Breider S, Freese HM, Sproer C, Simon M, Overmann J, Brinkhoff TInt J Syst Evol Microbiol10.1099/ijsem.0.0018792017Anti-Bacterial Agents/biosynthesis, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Heterotrophic Processes, North Sea, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome
36336812ChrII-encoded DNA helicase: A preliminary study.Tang B, Chen Z, Xia H, Wang R, Song XProtein Pept Lett10.2174/09298665306662211041122102022

Reference

@idauthorscataloguedoi/urltitle
5147Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14096)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14096
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
42038Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18002
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)
68382Automatically annotated from API zym
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
81900Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID58170.1StrainInfo: A central database for resolving microbial strain identifiers
123689Curators of the CIPCollection of Institut Pasteur (CIP 105928)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105928