Strain identifier
BacDive ID: 12503
Type strain:
Species: Petrimonas sulfuriphila
Strain Designation: BN3
Strain history: B. Denis BN3.
NCBI tax ID(s): 285070 (species)
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
@ref | history |
---|---|
6502 | <- D. Blanchet; BN3 |
67770 | B. Denis BN3. |
doi: 10.13145/bacdive12503.20230509.8.1
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
@ref | name | growth | link | composition |
---|---|---|---|---|
6502 | PYG MEDIUM (MODIFIED) (DSMZ Medium 104) | yes | https://mediadive.dsmz.de/medium/104 | Name: 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 |
6502 | THERMOANAEROBACTER SULFUROPHILUS MEDIUM (DSMZ Medium 827) | yes | https://mediadive.dsmz.de/medium/827 | Name: 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
@ref | growth | type | temperature | range |
---|---|---|---|---|
6502 | positive | growth | 40 | thermophilic |
31375 | positive | growth | 15-40 | |
31375 | positive | optimum | 38.5 | mesophilic |
67770 | positive | growth | 40 | thermophilic |
culture pH
- @ref: 31375
- ability: positive
- type: optimum
- pH: 7.2
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
6502 | anaerobe |
31375 | anaerobe |
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
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31375 | 30089 | acetate | + | carbon source |
31375 | 22599 | arabinose | + | carbon source |
31375 | 17057 | cellobiose | + | carbon source |
31375 | 28757 | fructose | + | carbon source |
31375 | 28260 | galactose | + | carbon source |
31375 | 17234 | glucose | + | carbon source |
31375 | 17754 | glycerol | + | carbon source |
31375 | 24996 | lactate | + | carbon source |
31375 | 17716 | lactose | + | carbon source |
31375 | 17306 | maltose | + | carbon source |
31375 | 29864 | mannitol | + | carbon source |
31375 | 37684 | mannose | + | carbon source |
31375 | 26546 | rhamnose | + | carbon source |
31375 | 33942 | ribose | + | carbon source |
31375 | 17992 | sucrose | + | carbon source |
31375 | 17632 | nitrate | + | reduction |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent |
---|---|---|---|---|
6502 | biodegraded oil reservoir | Canada | CAN | North America |
67770 | Oilfield well head in the Western Canadian Sedimentary Basin |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | GC-content | method |
---|---|---|
6502 | 40.8 | high performance liquid chromatography (HPLC) |
31375 | 40.8 |
External links
@ref: 6502
culture collection no.: DSM 16547, JCM 12565, CIP 108780
straininfo link
- @ref: 81722
- straininfo: 139006
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
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
6502 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16547) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-16547 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
31375 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 27688 | 28776041 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
69479 | João 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 | |||
81722 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID139006.1 | StrainInfo: A central database for resolving microbial strain identifiers |