Strain identifier

BacDive ID: 13845

Type strain: Yes

Species: Tateyamaria pelophila

Strain history: <- H. Cypionka (deposited as Roseobacter pelophilus, a name that appears in sequence databases) <- S. Dröge; SAM4

NCBI tax ID(s): 328415 (species)

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General

@ref: 6863

BacDive-ID: 13845

DSM-Number: 17270

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, Gram-negative, motile, rod-shaped

description: Tateyamaria pelophila DSM 17270 is a facultative anaerobe, Gram-negative, motile bacterium that was isolated from tidal-flat sediment.

NCBI tax id

  • NCBI tax id: 328415
  • Matching level: species

strain history

  • @ref: 6863
  • history: <- H. Cypionka (deposited as Roseobacter pelophilus, a name that appears in sequence databases) <- S. Dröge; SAM4

doi: 10.13145/bacdive13845.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Tateyamaria
  • species: Tateyamaria pelophila
  • full scientific name: Tateyamaria pelophila Sass et al. 2010

  • synonyms

    • @ref: 20215
    • synonym: Roseobacter pelophilus

@ref: 6863

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Tateyamaria

species: Tateyamaria pelophila

full scientific name: Tateyamaria pelophila Sass et al. 2010

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29458negative2.25 µm1.05 µmrod-shapedyes
69480negative97.982

pigmentation

  • @ref: 29458
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 6863
  • 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

@refgrowthtypetemperature
6863positivegrowth20
29458positivegrowth04-35
29458positiveoptimum25

culture pH

  • @ref: 29458
  • ability: positive
  • type: growth
  • pH: 06-09
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 29458
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69480no92.327
69481no100

halophily

  • @ref: 29458
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0.3-10.2 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2945830089acetate+carbon source
2945817057cellobiose+carbon source
2945824265gluconate+carbon source
2945824996lactate+carbon source
2945817306maltose+carbon source
2945837684mannose+carbon source
2945818257ornithine+carbon source
2945827082trehalose+carbon source
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836930849L-arabinose-assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
29458acid phosphatase+3.1.3.2
29458alkaline phosphatase+3.1.3.1
29458catalase+1.11.1.6
29458cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
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
6863-+---+--+-++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
6863-----+-++/--+/----------

Isolation, sampling and environmental information

isolation

  • @ref: 6863
  • sample type: tidal-flat sediment
  • geographic location: North Sea coast close to Neuharlingersiel
  • country: Germany
  • origin.country: DEU
  • continent: Europe

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Sediment
#Environmental#Terrestrial#Tidal flat

taxonmaps

  • @ref: 69479
  • File name: preview.99_62611.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_2764;97_8001;98_44339;99_62611&stattab=map
  • Last taxonomy: Tateyamaria pelophila subclade
  • 16S sequence: AJ968651
  • Sequence Identity:
  • Total samples: 97
  • soil counts: 3
  • aquatic counts: 82
  • animal counts: 12

Safety information

risk assessment

  • @ref: 6863
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6863
  • description: Tateyamaria pelophila partial 16S rRNA gene, type strain SAM4T
  • accession: AJ968651
  • length: 1275
  • database: nuccore
  • NCBI tax ID: 328415

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Tateyamaria pelophila DSM 17270GCA_019966495scaffoldncbi328415
66792Tateyamaria pelophila strain DSM 17270328415.5wgspatric328415

GC content

@refGC-contentmethod
686356.4high performance liquid chromatography (HPLC)
2945856.4

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno97.982no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no94.594yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes79.037yes
69480spore-formingspore-formingAbility to form endo- or exosporesno92.327no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno96.547no
69480flagellatedmotile2+Ability to perform flagellated movementno50.352no

External links

@ref: 6863

culture collection no.: DSM 17270, LMG 23018, SAM 4

straininfo link

  • @ref: 83021
  • straininfo: 138169

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19749035Tateyamaria pelophila sp. nov., a facultatively anaerobic alphaproteobacterium isolated from tidal-flat sediment, and emended descriptions of the genus Tateyamaria and of Tateyamaria omphalii.Sass H, Kopke B, Rutters H, Feuerlein T, Droge S, Cypionka H, Engelen BInt J Syst Evol Microbiol10.1099/ijs.0.013524-02009Bacteria, Anaerobic/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Geologic Sediments/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/metabolism, Seawater/*microbiologyMetabolism
Phylogeny31437270Isolation and polyphasic identification of Tateyamaria armeniaca sp. nov.Yoon JFEMS Microbiol Lett10.1093/femsle/fnz1822019Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Nucleic Acid Hybridization, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/*isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/analysisTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6863Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17270)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17270
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
29458Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2586228776041
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)
68369Automatically annotated from API 20NE
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
83021Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID138169.1StrainInfo: A central database for resolving microbial strain identifiers