Strain identifier

BacDive ID: 17068

Type strain: Yes

Species: Thermotoga petrophila

Strain Designation: RKU-1

Strain history: T. Maruyama RKU-1.

NCBI tax ID(s): 93929 (species)

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General

@ref: 5208

BacDive-ID: 17068

DSM-Number: 13995

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, heterotroph, hyperthermophilic, rod-shaped

description: Thermotoga petrophila RKU-1 is an anaerobe, heterotroph, hyperthermophilic bacterium that was isolated from production fluid of an oil reservoir storage tank.

NCBI tax id

  • NCBI tax id: 93929
  • Matching level: species

strain history

@refhistory
5208<- T. Maruyama, Marine Biotechnology Institute, Kamaishi, Iwate, Japan; RKU-1 <- Y. Takahata {1996}
67770T. Maruyama RKU-1.

doi: 10.13145/bacdive17068.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/thermotogota
  • domain: Bacteria
  • phylum: Thermotogota
  • class: Thermotogae
  • order: Thermotogales
  • family: Thermotogaceae
  • genus: Thermotoga
  • species: Thermotoga petrophila
  • full scientific name: Thermotoga petrophila Takahata et al. 2001

  • synonyms

    • @ref: 20215
    • synonym: Thermotoga naphthophila

@ref: 5208

domain: Bacteria

phylum: Thermotogae

class: Thermotogae

order: Thermotogales

family: Thermotogaceae

genus: Thermotoga

species: Thermotoga petrophila

full scientific name: Thermotoga petrophila Takahata et al. 2001

strain designation: RKU-1

type strain: yes

Morphology

cell morphology

  • @ref: 43376
  • cell length: 2-7 µm
  • cell width: 0.7-1 µm
  • cell shape: rod-shaped

Culture and growth conditions

culture medium

  • @ref: 5208
  • name: THERMOTOGA PETROPHILA MEDIUM (DSMZ Medium 913)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/913
  • composition: Name: THERMOTOGA PETROPHILA MEDIUM (DSMZ Medium 913) Composition: MOPS 4.99501 g/l MgCl2 x 6 H2O 4.12088 g/l Yeast extract 1.998 g/l (NH4)2SO4 0.999001 g/l KH2PO4 0.499501 g/l KCl 0.487013 g/l Na2S x 9 H2O 0.2997 g/l NaBr 0.0749251 g/l MgSO4 x 7 H2O 0.02997 g/l Nitrilotriacetic acid 0.014985 g/l SrCl2 x 6 H2O 0.0112388 g/l NaCl 0.00999001 g/l Citric acid 0.00749251 g/l MnSO4 x H2O 0.00499501 g/l CoSO4 x 7 H2O 0.0017982 g/l ZnSO4 x 7 H2O 0.0017982 g/l CaCl2 x 2 H2O 0.000999001 g/l FeSO4 x 7 H2O 0.000999001 g/l Sodium resazurin 0.0004995 g/l NiCl2 x 6 H2O 0.0002997 g/l AlK(SO4)2 x 12 H2O 0.0001998 g/l H3BO3 9.99001e-05 g/l CuSO4 x 5 H2O 9.99001e-05 g/l Na2MoO4 x 2 H2O 9.99001e-05 g/l Pyridoxine hydrochloride 9.99001e-05 g/l Calcium D-(+)-pantothenate 4.995e-05 g/l p-Aminobenzoic acid 4.995e-05 g/l Nicotinic acid 4.995e-05 g/l Riboflavin 4.995e-05 g/l Thiamine HCl 4.995e-05 g/l (DL)-alpha-Lipoic acid 4.995e-05 g/l KI 3.74625e-05 g/l Folic acid 1.998e-05 g/l Biotin 1.998e-05 g/l Na2WO4 x 2 H2O 3.996e-06 g/l Na2SeO3 x 5 H2O 2.997e-06 g/l Vitamin B12 9.99001e-07 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
5208positivegrowth80hyperthermophilic
43376positivegrowth47-88hyperthermophilic
43376nogrowth89hyperthermophilic
43376nogrowth46thermophilic
43376positiveoptimum80hyperthermophilic
67770positivegrowth80hyperthermophilic

culture pH

@refabilitytypepHPH range
43376positivegrowth5.2-9alkaliphile
43376positiveoptimum7
43376nogrowth5
43376nogrowth9.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
5208anaerobe
43376obligate anaerobe

nutrition type

  • @ref: 43376
  • type: heterotroph

halophily

@refsaltgrowthtested relationconcentration
43376NaClpositivegrowth0.1-5.5 %
43376NaClpositiveoptimum1 %
43376NaClnogrowth0 %
43376NaClnogrowth6 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4337622599arabinose+carbon source
4337622599arabinose+energy source
4337662968cellulose+carbon source
4337662968cellulose+energy source
4337633403elemental sulfur+reduction
4337628757fructose+carbon source
4337628757fructose+energy source
4337628757fructose+/-growth
4337628260galactose+carbon source
4337628260galactose+energy source
4337628260galactose+/-growth
4337617234glucose+carbon source
4337617234glucose+energy source
4337617234glucose+fermentation
4337617234glucose+/-growth
4337617716lactose+growth
4337617716lactose+carbon source
4337617716lactose+energy source
4337617306maltose+growth
4337617306maltose+carbon source
4337617306maltose+energy source
4337629864mannitol-growth
43376peptone+carbon source
43376peptone+energy source
4337633942ribose+growth
4337633942ribose+carbon source
4337633942ribose+energy source
4337628017starch+growth
4337628017starch+carbon source
4337628017starch+energy source
4337617992sucrose+carbon source
4337617992sucrose+energy source
4337617992sucrose+/-growth
4337616094thiosulfate+reduction
4337618222xylose-growth
43376yeast extract+carbon source
43376yeast extract+energy source

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.
4337617698chloramphenicolyesyes100 µg/mL
4337628077rifampicinyesyes100 µg/mL
4337617076streptomycinyesyes100 µg/mL
4337628001vancomycinyesyes100 µg/mL

metabolite production

@refChebi-IDmetaboliteproduction
4337630089acetateyes
4337616526carbon dioxideyes
4337618276dihydrogenyes
4337624996DL-lactateyes

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
5208production fluid of an oil reservoir storage tankNiigata, Kubiki oil reservoirJapanJPNAsia
67770Oil reservoir near the coast of the Sea of JapanNiigataJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Industrial#Oil reservoir
#Environmental#Aquatic

taxonmaps

  • @ref: 69479
  • File name: preview.99_1632.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_177;96_929;97_1081;98_1290;99_1632&stattab=map
  • Last taxonomy: Thermotoga
  • 16S sequence: AB027016
  • Sequence Identity:
  • Total samples: 777
  • soil counts: 93
  • aquatic counts: 246
  • animal counts: 428
  • plant counts: 10

Safety information

risk assessment

  • @ref: 5208
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 5208
  • description: Thermotoga sp. RKU-1 gene for 16S rRNA, partial sequence
  • accession: AB027016
  • length: 1482
  • database: ena
  • NCBI tax ID: 390874

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Thermotoga petrophila RKU-1GCA_000016785completencbi390874
66792Thermotoga petrophila RKU-1390874.12completepatric390874
66792Thermotoga petrophila RKU-1640427150completeimg390874

GC content

@refGC-contentmethod
520846.6high performance liquid chromatography (HPLC)
6777046.8high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes85.716no
flagellatedno88.667no
gram-positiveno92.834no
anaerobicyes99.014yes
halophileno87.451yes
spore-formingno91.323no
glucose-utilyes88.486yes
aerobicno97.772yes
thermophileyes100no
glucose-fermentyes53.831no

External links

@ref: 5208

culture collection no.: DSM 13995, JCM 10881, ATCC BAA 488

straininfo link

  • @ref: 86068
  • straininfo: 49543

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11594624Thermotoga petrophila sp. nov. and Thermotoga naphthophila sp. nov., two hyperthermophilic bacteria from the Kubiki oil reservoir in Niigata, Japan.Takahata Y, Nishijima M, Hoaki T, Maruyama TInt J Syst Evol Microbiol10.1099/00207713-51-5-19012001Anaerobiosis, Bacteria/*classification/genetics/*growth & development/isolation & purification/ultrastructure, DNA, Ribosomal/analysis, Genotype, Japan, Microscopy, Electron, Molecular Sequence Data, Petroleum/*microbiology, Phenotype, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *TemperatureGenetics
Enzymology20823531Cloning, expression, purification, crystallization and preliminary X-ray diffraction studies of the catalytic domain of a hyperthermostable endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1.Santos CR, Squina FM, Navarro AM, Ruller R, Prade R, Murakami MTActa Crystallogr Sect F Struct Biol Cryst Commun10.1107/S17443091100291312010*Catalytic Domain, Cloning, Molecular, Crystallization, Crystallography, X-Ray, Enzyme Stability, Gene Expression, Gram-Negative Anaerobic Straight, Curved, and Helical Rods/*enzymology, Mannosidases/*chemistry/genetics/isolation & purificationPhylogeny
Enzymology20872163Functional and biophysical characterization of a hyperthermostable GH51 alpha-L-arabinofuranosidase from Thermotoga petrophila.dos Santos CR, Squina FM, Navarro AM, Oldiges DP, Paes Leme AF, Ruller R, Mort AJ, Prade R, Murakami MTBiotechnol Lett10.1007/s10529-010-0409-32010Arabinose/metabolism, Bacteria/*enzymology, Circular Dichroism, Cloning, Molecular, Crystallization, DNA, Bacterial/chemistry/genetics, Enzyme Stability, Gene Expression, Glycoside Hydrolases/chemistry/*genetics/isolation & purification/*metabolism, Hot Temperature, Hydrogen-Ion Concentration, Molecular Sequence Data, Protein Conformation, Recombinant Proteins/chemistry/genetics/isolation & purification/metabolism, Sequence Analysis, DNA, Substrate SpecificityMetabolism
Enzymology21070746Thermal-induced conformational changes in the product release area drive the enzymatic activity of xylanases 10B: Crystal structure, conformational stability and functional characterization of the xylanase 10B from Thermotoga petrophila RKU-1.Santos CR, Meza AN, Hoffmam ZB, Silva JC, Alvarez TM, Ruller R, Giesel GM, Verli H, Squina FM, Prade RA, Murakami MTBiochem Biophys Res Commun10.1016/j.bbrc.2010.11.0102010Bacteria/*enzymology, Binding Sites, Crystallography, X-Ray, Disaccharides/biosynthesis, Endo-1,4-beta Xylanases/*chemistry/genetics/isolation & purification, Enzyme Stability, *Hot Temperature, Protein Conformation, Protein Structure, SecondaryStress
Enzymology21796714Structure of a novel thermostable GH51 alpha-L-arabinofuranosidase from Thermotoga petrophila RKU-1.Souza TA, Santos CR, Souza AR, Oldiges DP, Ruller R, Prade RA, Squina FM, Murakami MTProtein Sci10.1002/pro.6932011Bacteria/*enzymology, Bacterial Proteins/*chemistry/*metabolism, Enzyme Stability, Glycoside Hydrolases/*chemistry/*metabolism, Molecular Sequence Data, Protein Structure, Secondary, Protein Structure, Tertiary, Substrate Specificity, TemperatureMetabolism
Enzymology22714267Cloning, characterization and molecular docking of a highly thermostable beta-1,4-glucosidase from Thermotoga petrophila.Haq IU, Khan MA, Muneer B, Hussain Z, Afzal S, Majeed S, Rashid N, Javed MM, Ahmad IBiotechnol Lett10.1007/s10529-012-0953-02012Bacteria, Anaerobic/*enzymology/genetics, Cloning, Molecular, Electrophoresis, Polyacrylamide Gel, Escherichia coli/genetics, Glucan 1,4-beta-Glucosidase/chemistry/*genetics/isolation & purification/*metabolism, Glucosides/metabolism, Hydrolysis, Kinetics, Models, Molecular, Molecular Dynamics Simulation, Molecular Weight, Polymerase Chain Reaction, Recombinant Proteins/chemistry/genetics/isolation & purification/metabolism, Substrate SpecificityMetabolism
Metabolism25838236Overexpression and characterization of a Ca(2+) activated thermostable beta-glucosidase with high ginsenoside Rb1 to ginsenoside 20(S)-Rg3 bioconversion productivity.Xie J, Zhao D, Zhao L, Pei J, Xiao W, Ding G, Wang ZJ Ind Microbiol Biotechnol10.1007/s10295-015-1608-72015Biotransformation, Calcium/*metabolism/pharmacology, Enzyme Activation, Enzyme Stability/drug effects, Escherichia coli/genetics, Ginsenosides/*metabolism, Gram-Negative Anaerobic Straight, Curved, and Helical Rods/enzymology/genetics, Hydrogen-Ion Concentration, Molecular Weight, Temperature, beta-Glucosidase/chemistry/*genetics/isolation & purification/*metabolismEnzymology
Enzymology26122986Thermodynamic and saccharification analysis of cloned GH12 endo-1,4-beta-glucanase from Thermotoga petrophila in a mesophilic host.Ul Haq I, Muneer B, Hussain Z, Khan MA, Afzal S, Majeed S, Akram F, Akmal SProtein Pept Lett10.2174/09298665226661506301050352015Amino Acid Sequence, Bacteria/enzymology/genetics, Bacterial Proteins/*chemistry/genetics/metabolism, Cellulase/*chemistry/genetics/metabolism, Enzyme Stability, Escherichia coli, Hydrogen-Ion Concentration, Molecular Sequence Data, Recombinant Proteins/*chemistry/genetics/metabolism, Sequence Alignment, Temperature, ThermodynamicsMetabolism
29460835[Construction and characterization of a recombinant mutant homolog of the CheW protein from Thermotoga petrophila RKU-1].Grishin DV, Zhdanov DD, Gladilina JA, Pokrovsky VS, Podobed OV, Pokrovskaya MV, Aleksandrova SS, Milyushkina AL, Vigovskiy MA, Sokolov NNBiomed Khim10.18097/PBMC201864010532018Bacterial Proteins, Escherichia coli, Escherichia coli Proteins, *Gram-Negative Anaerobic Straight, Curved, and Helical Rods, Recombinant Proteins
Metabolism29751706[Comparison of three different thermophilic beta-glucosidases for baicalin transformation].Wu T, Zhang SS, Pei JJ, Xiao W, Wang ZZ, Zhao LGZhongguo Zhong Yao Za Zhi10.19540/j.cnki.cjcmm.20180201.0022018Flavonoids, Hydrogen-Ion Concentration, beta-Glucosidase/*metabolism
Metabolism30121908Thermostable Recombinant Polypeptides as the Source of L-Amino Acids for Culture Media.Grishin DV, Zhdanov DD, Gladilina YA, Podobed OV, Pokrovsky VS, Pokrovskaya MV, Aleksandrova SS, Sokolov NNBull Exp Biol Med10.1007/s10517-018-4194-72018Amino Acids/*chemistry/*metabolism, Culture Media/*chemistry, Fibroblasts/metabolism, Humans, Hydrogen-Ion Concentration, Recombinant Proteins/*chemistry/*metabolism, TemperatureCultivation
Enzymology30465846Enhanced production, overexpression and characterization of a hyperthermophilic multimodular GH family 2 betaglucuronidase (TpGUS) cloned from Thermotoga petrophila RKU-1(T) in a mesophilic host.Haq IU, Akram FInt J Biol Macromol10.1016/j.ijbiomac.2018.11.1892018Amino Acid Sequence, Cations/pharmacology, Cloning, Molecular/*methods, Enzyme Stability/drug effects, Escherichia coli/*metabolism, Glucuronidase/*biosynthesis/chemistry/*metabolism, Gram-Negative Anaerobic Straight, Curved, and Helical Rods/*metabolism, Hydrogen-Ion Concentration, Kinetics, Models, Molecular, Recombinant Proteins/isolation & purification, Sequence Analysis, DNA, Substrate Specificity/drug effects, *TemperaturePathogenicity
Phylogeny33038732A novel Thermotoga strain TFO isolated from a Californian petroleum reservoir phylogenetically related to Thermotoga petrophila and T. naphthophila, two thermophilic anaerobic isolates from a Japanese reservoir: Taxonomic and genomic considerations.Summers ZM, Belahbib H, Pradel N, Bartoli M, Mishra P, Tamburini C, Dolla A, Ollivier B, Armougom FSyst Appl Microbiol10.1016/j.syapm.2020.1261322020Anaerobiosis, Bacterial Typing Techniques, California, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Nucleic Acid Hybridization, Petroleum/*microbiology, Phospholipids/chemistry, *Phylogeny, Sequence Analysis, DNA, Thermotoga/*classification/isolation & purificationTranscriptome
Biotechnology35398211Efficient production of inositol from glucose via a tri-enzymatic cascade pathway.Wang J, Cheng H, Zhao Z, Zhang YBioresour Technol10.1016/j.biortech.2022.1271252022*Glucose/metabolism, *InositolMetabolism
35800333Computer-Aided Design of alpha-L-Rhamnosidase to Increase the Synthesis Efficiency of Icariside I.Huang JJ, Hu HX, Lu YJ, Bao YD, Zhou JL, Huang MFront Bioeng Biotechnol10.3389/fbioe.2022.9268292022

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5208Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13995)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13995
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
43376Yoh Takahata, Miyuki Nishijima, Toshihiro Hoaki, Tadashi Maruyama10.1099/00207713-51-5-1901Thermotoga petrophila sp. nov. and Thermotoga naphthophila sp. nov., two hyperthermophilic bacteria from the Kubiki oil reservoir in Niigata, Japan.IJSEM 51: 1901-1909 200111594624
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
86068Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49543.1StrainInfo: A central database for resolving microbial strain identifiers