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Strain identifier

BacDive ID: 12503

Type strain: Yes

Species: Petrimonas sulfuriphila

Strain Designation: BN3

Strain history: B. Denis BN3.

NCBI tax ID(s): 285070 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 6502

BacDive-ID: 12503

DSM-Number: 16547

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

description: Petrimonas sulfuriphila BN3 is an anaerobe, thermophilic, Gram-negative bacterium that was isolated from biodegraded oil reservoir.

NCBI tax id

  • NCBI tax id: 285070
  • Matching level: species

strain history

doi: 10.13145/bacdive12503.20221219.7.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Dysgonomonadaceae
  • genus: Petrimonas
  • species: Petrimonas sulfuriphila
  • full scientific name: Petrimonas sulfuriphila Grabowski et al. 2005

@ref: 6502

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Dysgonomonadaceae

genus: Petrimonas

species: Petrimonas sulfuriphila

full scientific name: Petrimonas sulfuriphila Grabowski et al. 2005

strain designation: BN3

type strain: yes

Morphology

cell morphology

  • @ref: 31375
  • gram stain: negative
  • cell length: 1.75 µm
  • cell width: 0.85 µm
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6502PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yeshttps://mediadive.dsmz.de/medium/104Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water
6502THERMOANAEROBACTER SULFUROPHILUS MEDIUM (DSMZ Medium 827)yeshttps://mediadive.dsmz.de/medium/827Name: THERMOANAEROBACTER SULFUROPHILUS MEDIUM (DSMZ Medium 827; with strain-specific modifications) Composition: Sulfur 9.98004 g/l D-Glucose 4.99002 g/l Trypticase peptone 2.99401 g/l Na2CO3 0.998004 g/l Yeast extract 0.499002 g/l Na2S x 9 H2O 0.499002 g/l KH2PO4 0.329341 g/l CaCl2 x 2 H2O 0.329341 g/l NH4Cl 0.329341 g/l KCl 0.329341 g/l MgCl2 x 6 H2O 0.329341 g/l HCl 0.00249501 g/l FeCl2 x 4 H2O 0.00149701 g/l Sodium resazurin 0.000499002 g/l CoCl2 x 6 H2O 0.000189621 g/l MnCl2 x 4 H2O 9.98004e-05 g/l Pyridoxine hydrochloride 9.98004e-05 g/l ZnCl2 6.98603e-05 g/l (DL)-alpha-Lipoic acid 4.99002e-05 g/l p-Aminobenzoic acid 4.99002e-05 g/l Calcium D-(+)-pantothenate 4.99002e-05 g/l Riboflavin 4.99002e-05 g/l Thiamine HCl 4.99002e-05 g/l Nicotinic acid 4.99002e-05 g/l Na2MoO4 x 2 H2O 3.59281e-05 g/l NiCl2 x 6 H2O 2.39521e-05 g/l Folic acid 1.99601e-05 g/l Biotin 1.99601e-05 g/l H3BO3 5.98802e-06 g/l CuCl2 x 2 H2O 1.99601e-06 g/l Vitamin B12 9.98004e-07 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
6502positivegrowth40thermophilic
31375positivegrowth15-40
31375positiveoptimum38.5mesophilic
67770positivegrowth40thermophilic

culture pH

  • @ref: 31375
  • ability: positive
  • type: optimum
  • pH: 7.2

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
6502anaerobe
31375anaerobe

spore formation

  • @ref: 31375
  • spore formation: no

halophily

  • @ref: 31375
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-4 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3137530089acetate+carbon source
3137522599arabinose+carbon source
3137517057cellobiose+carbon source
3137528757fructose+carbon source
3137528260galactose+carbon source
3137517234glucose+carbon source
3137517754glycerol+carbon source
3137524996lactate+carbon source
3137517716lactose+carbon source
3137517306maltose+carbon source
3137529864mannitol+carbon source
3137537684mannose+carbon source
3137526546rhamnose+carbon source
3137533942ribose+carbon source
3137517992sucrose+carbon source
3137517632nitrate+reduction

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
6502biodegraded oil reservoirCanadaCANNorth America
67770Oilfield well head in the Western Canadian Sedimentary Basin

isolation source categories

Cat1Cat2Cat3
#Engineered#Biodegradation
#Engineered#Industrial#Oil reservoir

taxonmaps

  • @ref: 69479
  • File name: preview.99_22975.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_103;96_283;97_11464;98_14091;99_22975&stattab=map
  • Last taxonomy: Petrimonas sulfuriphila subclade
  • 16S sequence: AY570690
  • Sequence Identity:
  • Total samples: 8360
  • soil counts: 1433
  • aquatic counts: 5527
  • animal counts: 1144
  • plant counts: 256

Safety information

risk assessment

  • @ref: 6502
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6502
  • description: Petrimonas sulfuriphila strain BN3 16S ribosomal RNA gene, partial sequence
  • accession: AY570690
  • length: 1411
  • database: ena
  • NCBI tax ID: 285070

Genome sequences

  • @ref: 66792
  • description: Petrimonas sulfuriphila DSM 16547
  • accession: 2828614168
  • assembly level: draft
  • database: img
  • NCBI tax ID: 285070

GC content

@refGC-contentmethod
650240.8high performance liquid chromatography (HPLC)
3137540.8

External links

@ref: 6502

culture collection no.: DSM 16547, JCM 12565, CIP 108780

straininfo link

@refpassport
20218http://www.straininfo.net/strains/387840
20218http://www.straininfo.net/strains/387841

literature

  • topic: Phylogeny
  • Pubmed-ID: 15879242
  • title: Petrimonas sulfuriphila gen. nov., sp. nov., a mesophilic fermentative bacterium isolated from a biodegraded oil reservoir.
  • authors: Grabowski A, Tindall BJ, Bardin V, Blanchet D, Jeanthon C
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63426-0
  • year: 2005
  • mesh: Acetic Acid/metabolism, Anaerobiosis, Bacteroidetes/*classification/cytology/*isolation & purification/metabolism, Base Composition, Canada, Carbohydrate Metabolism, Carbon Dioxide/metabolism, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/isolation & purification, Fermentation, Genes, rRNA, Gentian Violet, Glycerol/metabolism, Growth Inhibitors/pharmacology, Hydrogen/metabolism, Lactic Acid/metabolism, Molecular Sequence Data, Movement, Nitrates/metabolism, Peptones/metabolism, Phenazines, Phospholipids/analysis/isolation & purification, Phylogeny, Quinones/analysis/isolation & purification, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/pharmacology, *Soil Microbiology, Sulfur/metabolism, Temperature
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
6502Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16547)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16547
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
2768810.1099/ijs.0.63426-015879242
31375Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127688
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