Strain identifier

BacDive ID: 3978

Type strain: Yes

Species: Desulfobacula phenolica

Strain Designation: PhO1

Strain history: <- F. Widdel, Universität Konstanz, Fakultät für Biologie, Konstanz, Germany; PhO1 <- F. Bak {1984}

NCBI tax ID(s): 90732 (species)

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General

@ref: 1370

BacDive-ID: 3978

DSM-Number: 3384

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, motile

description: Desulfobacula phenolica PhO1 is an anaerobe, mesophilic, motile bacterium that was isolated from marine mud.

NCBI tax id

  • NCBI tax id: 90732
  • Matching level: species

strain history

  • @ref: 1370
  • history: <- F. Widdel, Universität Konstanz, Fakultät für Biologie, Konstanz, Germany; PhO1 <- F. Bak {1984}

doi: 10.13145/bacdive3978.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Deltaproteobacteria
  • order: Desulfobacterales
  • family: Desulfobacteraceae
  • genus: Desulfobacula
  • species: Desulfobacula phenolica
  • full scientific name: Desulfobacula phenolica (Bak and Widdel 1988) Kuever et al. 2001
  • synonyms

    • @ref: 20215
    • synonym: Desulfobacterium phenolicum

@ref: 1370

domain: Bacteria

phylum: Proteobacteria

class: Deltaproteobacteria

order: Desulfobacterales

family: Desulfobacteraceae

genus: Desulfobacula

species: Desulfobacula phenolica

full scientific name: Desulfobacula phenolica (Bak and Widdel 1988) Kuever et al. 2001

strain designation: PhO1

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes95.953
6948099.999negative

colony morphology

  • @ref: 1370
  • incubation period: 8-14 days

Culture and growth conditions

culture medium

  • @ref: 1370
  • name: DESULFOBACTERIUM MEDIUM (DSMZ Medium 383)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/383
  • composition: Name: DESULFOBACTERIUM MEDIUM (DSMZ Medium 383; with strain-specific modifications) Composition: NaCl 20.9372 g/l Na2SO4 2.99103 g/l MgCl2 x 6 H2O 2.99103 g/l Na2CO3 0.997009 g/l KCl 0.498504 g/l Na-benzoate 0.398804 g/l Na2S x 9 H2O 0.398804 g/l NH4Cl 0.299103 g/l KH2PO4 0.199402 g/l CaCl2 x 2 H2O 0.149551 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l NaOH 0.000498504 g/l Sodium resazurin 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l Pyridoxine hydrochloride 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Folic acid 1.99402e-05 g/l Biotin 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Vitamin B12 9.97009e-07 g/l Distilled water

culture temp

  • @ref: 1370
  • growth: positive
  • type: growth
  • temperature: 28
  • range: mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
1370anaerobe
69480anaerobe98.65

spore formation

@refspore formationconfidence
69481no100
69480no99.896

Isolation, sampling and environmental information

isolation

  • @ref: 1370
  • sample type: marine mud
  • geographic location: Venice
  • country: Italy
  • origin.country: ITA
  • continent: Europe

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Terrestrial#Mud (Sludge)
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_56160.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_40;96_82;97_86;98_95;99_56160&stattab=map
  • Last taxonomy: Desulfobacula
  • 16S sequence: AJ237606
  • Sequence Identity:
  • Total samples: 257
  • soil counts: 5
  • aquatic counts: 251
  • plant counts: 1

Safety information

risk assessment

  • @ref: 1370
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 1370
  • description: Desulfobacterium phenolicum 16S rRNA gene, partial, strain DSM 3384
  • accession: AJ237606
  • length: 1508
  • database: ena
  • NCBI tax ID: 90732

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Desulfobacula phenolica DSM 3384GCA_900105645scaffoldncbi90732
66792Desulfobacula phenolica strain DSM 338490732.5wgspatric90732
66792Desulfobacula phenolica DSM 33842616644807draftimg90732

GC content

  • @ref: 1370
  • GC-content: 40.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
glucose-fermentno85.951no
flagellatedno61.598no
gram-positiveno98.978no
anaerobicyes97.961yes
aerobicno97.399no
halophileno64.194no
spore-formingno87.351no
thermophileno96.776yes
glucose-utilno58.174no
motileyes82.515no

External links

@ref: 1370

culture collection no.: DSM 3384, ATCC 43956

straininfo link

  • @ref: 73484
  • straininfo: 42148

literature

  • topic: Phylogeny
  • Pubmed-ID: 22659505
  • title: Desulfoconvexum algidum gen. nov., sp. nov., a psychrophilic sulfate-reducing bacterium isolated from a permanently cold marine sediment.
  • authors: Konneke M, Kuever J, Galushko A, Jorgensen BB
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.043703-0
  • year: 2012
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Deltaproteobacteria/*classification/genetics/isolation & purification, Fatty Acids/analysis, Geologic Sediments/*microbiology, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sulfur-Reducing Bacteria/*classification/genetics/isolation & purification, Svalbard
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitle
1370Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3384)https://www.dsmz.de/collection/catalogue/details/culture/DSM-3384
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
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)
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
73484Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42148.1StrainInfo: A central database for resolving microbial strain identifiers