Strain identifier
BacDive ID: 17792
Type strain: 
Species: Rhodothermus marinus
Strain Designation: R-10
Strain history: <- G.A. Alfredsson, Univ. of Iceland, R-10
NCBI tax ID(s): 518766 (strain), 29549 (species)
version 8.1 (current version)
General
@ref: 1632
BacDive-ID: 17792
DSM-Number: 4252
keywords: genome sequence, 16S sequence, Bacteria, thermophilic, Gram-negative
description: Rhodothermus marinus R-10 is a thermophilic, Gram-negative bacterium that was isolated from submarine hot spring.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 29549 | species |
| 518766 | strain |
strain history
- @ref: 1632
- history: <- G.A. Alfredsson, Univ. of Iceland, R-10
doi: 10.13145/bacdive17792.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/rhodothermota
- domain: Bacteria
- phylum: Rhodothermota
- class: Rhodothermia
- order: Rhodothermales
- family: Rhodothermaceae
- genus: Rhodothermus
- species: Rhodothermus marinus
- full scientific name: Rhodothermus marinus Alfredsson et al. 1995
synonyms
- @ref: 20215
- synonym: Rhodothermus obamensis
@ref: 1632
domain: Bacteria
phylum: Rhodothermaeota
class: Rhodothermia
order: Cytophagales
family: Rhodothermaceae
genus: Rhodothermus
species: Rhodothermus marinus
full scientific name: Rhodothermus marinus Alfredsson et al. 1995 emend. Park et al. 2019
strain designation: R-10
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.912
multimedia
- @ref: 66793
- multimedia content: EM_DSM_4252_1.jpg
- caption: electron microscopic image
- intellectual property rights: © HZI/Manfred Rohde
Culture and growth conditions
culture medium
- @ref: 1632
- name: MODIFIED THERMUS 162 MEDIUM (DSMZ Medium 630)
- growth: yes
- link: https://mediadive.dsmz.de/medium/630
- composition: Name: MODIFIED THERMUS 162 MEDIUM (DSMZ Medium 630; with strain-specific modifications) Composition: Agar 28.0 g/l NaCl 10.0 g/l Na2HPO4 x 12 H2O 4.3 g/l Yeast extract 2.5 g/l Tryptone 2.5 g/l KH2PO4 0.544 g/l MgCl2 x 6 H2O 0.2 g/l CaSO4 x 2 H2O 0.04 g/l Nitrilotriacetic acid 0.0064 g/l Fe(III) citrate 0.00122472 g/l FeCl2 x 4 H2O 0.0005 g/l MnCl2 x 4 H2O 0.00025 g/l CoCl2 x 4 H2O 0.00015 g/l CuCl2 x 2 H2O 2.5e-05 g/l Na2MoO4 x 2 H2O 2.5e-05 g/l H3BO3 1e-05 g/l NiCl2 x 6 H2O 1e-05 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range | confidence |
|---|---|---|---|---|---|
| 1632 | positive | growth | 65 | thermophilic | |
| 69480 | thermophilic | 97.208 |
Physiology and metabolism
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.95
Isolation, sampling and environmental information
isolation
- @ref: 1632
- sample type: submarine hot spring
- country: Iceland
- origin.country: ISL
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Marine |
| #Environmental | #Aquatic | #Thermal spring |
| #Condition | #Thermophilic (>45°C) |
taxonmaps
- @ref: 69479
- File name: preview.99_7548.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_302;96_1200;97_1415;98_1722;99_7548&stattab=map
- Last taxonomy: Rhodothermus marinus
- 16S sequence: X80994
- Sequence Identity:
- Total samples: 601
- soil counts: 193
- aquatic counts: 243
- animal counts: 134
- plant counts: 31
Safety information
risk assessment
- @ref: 1632
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | R.marinus 16S rRNA, tRNA-Ile and tRNA-Ala genes | X80994 | 2117 | ena | 518766 |
| 1632 | Rhodothermus marinus strain DSM 4252T 16S ribosomal RNA gene, partial sequence | AF217494 | 1471 | ena | 518766 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Rhodothermus marinus DSM 4252 | GCA_000024845 | complete | ncbi | 518766 |
| 66792 | Rhodothermus marinus DSM 4252 | 518766.26 | plasmid | patric | 518766 |
| 66792 | Rhodothermus marinus DSM 4252 | 518766.7 | complete | patric | 518766 |
| 66792 | Rhodothermus marinus R-10, DSM 4252 | 646311949 | complete | img | 518766 |
GC content
- @ref: 1632
- GC-content: 65.0
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 85 | no |
| motile | yes | 61.083 | no |
| flagellated | no | 89.88 | no |
| gram-positive | no | 96.01 | no |
| anaerobic | no | 96.217 | no |
| aerobic | yes | 70.399 | no |
| halophile | no | 58.113 | no |
| spore-forming | no | 91.227 | no |
| thermophile | yes | 99.998 | yes |
| glucose-util | yes | 90.478 | no |
| glucose-ferment | no | 78.261 | no |
External links
@ref: 1632
culture collection no.: DSM 4252, ATCC 43812
straininfo link
- @ref: 86783
- straininfo: 45166
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Enzymology | 10919332 | A highly thermostable endo-(1,4)-beta-mannanase from the marine bacterium Rhodothermus marinus. | Politz O, Krah M, Thomsen KK, Borriss R | Appl Microbiol Biotechnol | 10.1007/s002530000351 | 2000 | Amino Acid Sequence, Cloning, Molecular, Enzyme Stability, Escherichia coli/genetics, Galactose/analogs & derivatives, Gram-Negative Aerobic Bacteria/*enzymology/genetics, Hot Temperature, Mannans/metabolism, Mannosidases/genetics/*metabolism, Molecular Sequence Data, Recombinant Proteins/metabolism, Seawater, Sequence Analysis, DNA, Water Microbiology, beta-Mannosidase | Metabolism |
| Phylogeny | 10939650 | Polyphasic evidence for the reclassification of Rhodothermus obamensis Sako et al. 1996 as a member of the species Rhodothermus marinus Alfredsson et al. 1988. | Silva Z, Horta C, da Costa MS, Chung AP, Rainey FA | Int J Syst Evol Microbiol | 10.1099/00207713-50-4-1457 | 2000 | Cloning, Molecular, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Gram-Negative Aerobic Bacteria/chemistry/*classification/genetics, RNA, Bacterial/analysis, RNA, Ribosomal, 16S/analysis, Temperature, *Water Microbiology | Enzymology |
| Phylogeny | 20061490 | Rhodothermus profundi sp. nov., a thermophilic bacterium isolated from a deep-sea hydrothermal vent in the Pacific Ocean. | Marteinsson VT, Bjornsdottir SH, Bienvenu N, Kristjansson JK, Birrien JL | Int J Syst Evol Microbiol | 10.1099/ijs.0.012724-0 | 2010 | Amplified Fragment Length Polymorphism Analysis, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hydrothermal Vents/*microbiology, Molecular Sequence Data, Nucleic Acid Amplification Techniques, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodothermus/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
| Genetics | 21304669 | Complete genome sequence of Rhodothermus marinus type strain (R-10). | Nolan M, Tindall BJ, Pomrenke H, Lapidus A, Copeland A, Glavina Del Rio T, Lucas S, Chen F, Tice H, Cheng JF, Saunders E, Han C, Bruce D, Goodwin L, Chain P, Pitluck S, Ovchinikova G, Pati A, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brettin T, Goker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Detter JC | Stand Genomic Sci | 10.4056/sigs.46736 | 2009 | ||
| Enzymology | 22056431 | Biochemical characterization of a thermophilic cellobiose 2-epimerase from a thermohalophilic bacterium, Rhodothermus marinus JCM9785. | Ojima T, Saburi W, Sato H, Yamamoto T, Mori H, Matsui H | Biosci Biotechnol Biochem | 10.1271/bbb.110456 | 2011 | Amino Acid Sequence, Cellobiose/*chemistry/genetics/isolation & purification, Cloning, Molecular, Disaccharides/metabolism, Enzyme Stability, Hydrogen-Ion Concentration, Molecular Sequence Data, Racemases and Epimerases/*chemistry/genetics/isolation & purification, Recombinant Proteins/chemistry, Rhodothermus/*enzymology, Substrate Specificity, Temperature | Phylogeny |
| Metabolism | 27842803 | Evaluation of the production of exopolysaccharides by two strains of the thermophilic bacterium Rhodothermus marinus. | Sardari RR, Kulcinskaja E, Ron EY, Bjornsdottir S, Friethjonsson OH, Hreggviethsson GO, Karlsson EN | Carbohydr Polym | 10.1016/j.carbpol.2016.08.062 | 2016 | Amino Sugars/chemistry, Arabinose/chemistry, Glucose/metabolism, Lactose/metabolism, Maltose/metabolism, Polysaccharides, Bacterial/*biosynthesis/chemistry/isolation & purification, Rhodothermus/chemistry/classification/*metabolism, Sucrose/metabolism, Uronic Acids/chemistry, Xylose/chemistry | Phylogeny |
| Metabolism | 29037779 | (13)C metabolic flux analysis of three divergent extremely thermophilic bacteria: Geobacillus sp. LC300, Thermus thermophilus HB8, and Rhodothermus marinus DSM 4252. | Cordova LT, Cipolla RM, Swarup A, Long CP, Antoniewicz MR | Metab Eng | 10.1016/j.ymben.2017.10.007 | 2017 | Carbon Isotopes/*metabolism, Geobacillus/*metabolism, *Hot Temperature, *Metabolome, *Models, Biological, Rhodothermus/*metabolism, Thermus thermophilus/*metabolism | Stress |
| 29045010 | Characterization of carotenoids in Rhodothermus marinus. | Ron EYC, Plaza M, Kristjansdottir T, Sardari RRR, Bjornsdottir SH, Gudmundsson S, Hreggvidsson GO, Turner C, van Niel EWJ, Nordberg-Karlsson E | Microbiologyopen | 10.1002/mbo3.536 | 2017 | Antioxidants/analysis/chemistry, Aquatic Organisms/chemistry/growth & development, Bioreactors/microbiology, Carotenoids/*analysis/chemistry, Chromatography, High Pressure Liquid, Mass Spectrometry, Rhodothermus/*chemistry/growth & development | ||
| Genetics | 31919149 | Complete Genome Sequences of Rhodothermus marinus Strains AA2-13 and AA3-38, Isolated from Arima Onsen Hot Spring in Japan. | Tomariguchi N, Miyazaki K | Microbiol Resour Announc | 10.1128/MRA.01475-19 | 2020 | Phylogeny | |
| Enzymology | 31992772 | Characterization and diversity of the complete set of GH family 3 enzymes from Rhodothermus marinus DSM 4253. | Ara KZG, Manberger A, Gabrisko M, Linares-Pasten JA, Jasilionis A, Friethjonsson OH, Hreggviethsson GO, Janecek S, Nordberg Karlsson E | Sci Rep | 10.1038/s41598-020-58015-5 | 2020 | Enzyme Activation, Gene Order, Genes, Bacterial, Genetic Loci, Glycoside Hydrolases/chemistry/classification/*genetics/*metabolism, Hydrogen-Ion Concentration, Hydrolysis, Kinetics, Models, Molecular, *Multigene Family, Protein Conformation, Rhodothermus/*enzymology/*genetics, Structure-Activity Relationship, Temperature | Phylogeny |
| Phylogeny | 35072600 | Rhodothermus bifroesti sp. nov., a thermophilic bacterium isolated from the basaltic subsurface of the volcanic island Surtsey. | Bergsten P, Vannier P, Mougeolle A, Rigaud L, Marteinsson VT | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005214 | 2022 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Iceland, Islands, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhodothermus/cytology/isolation & purification, Sequence Analysis, DNA | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 1632 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4252) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-4252 | |||
| 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 | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 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) | |||
| 66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | |
| 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 | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 86783 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID45166.1 | StrainInfo: A central database for resolving microbial strain identifiers |