Strain identifier
BacDive ID: 11924
Type strain: 
Species: Thiomicrorhabdus frisia
Strain Designation: JB-A2
Strain history: <- J. Küver, Max-Planck-Inst. Marine Microbiology, Bremen, Germany; JB-A2 <- T. Brinkhoff {1997}
NCBI tax ID(s): 63655 (species)
version 8.1 (current version)
General
@ref: 4710
BacDive-ID: 11924
DSM-Number: 12351
keywords: 16S sequence, Bacteria, chemolithoautotroph, mesophilic, Gram-negative, motile, rod-shaped
description: Thiomicrorhabdus frisia JB-A2 is a chemolithoautotroph, mesophilic, Gram-negative bacterium that was isolated from marine sediment.
NCBI tax id
- NCBI tax id: 63655
- Matching level: species
strain history
- @ref: 4710
- history: <- J. Küver, Max-Planck-Inst. Marine Microbiology, Bremen, Germany; JB-A2 <- T. Brinkhoff {1997}
doi: 10.13145/bacdive11924.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Beggiatoales
- family: Piscirickettsiaceae
- genus: Thiomicrorhabdus
- species: Thiomicrorhabdus frisia
- full scientific name: Thiomicrorhabdus frisia (Brinkhoff et al. 1999) Boden et al. 2017
synonyms
- @ref: 20215
- synonym: Thiomicrospira frisia
@ref: 4710
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Thiotrichales
family: Piscirickettsiaceae
genus: Thiomicrorhabdus
species: Thiomicrorhabdus frisia
full scientific name: Thiomicrorhabdus frisia (Brinkhoff et al. 1999) Boden et al. 2017
strain designation: JB-A2
type strain: yes
Morphology
cell morphology
- @ref: 43182
- gram stain: negative
- cell length: 1.0-2.7 µm
- cell width: 0.3-0.5 µm
- cell shape: rod-shaped
- motility: yes
- flagellum arrangement: monotrichous
colony morphology
| @ref | colony color | medium used |
|---|---|---|
| 43182 | White | Triosulfate agar |
| 43182 | yellow | Triosulfate agar |
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 4710 | THIOMICROSPIRA PELOPHILA MEDIUM (DSMZ Medium 142) | yes | https://mediadive.dsmz.de/medium/142 | Name: THIOMICROSPIRA PELOPHILA MEDIUM (DSMZ Medium 142) Composition: NaCl 24.8756 g/l Na2S2O3 x 5 H2O 4.97512 g/l MgSO4 x 7 H2O 1.49254 g/l (NH4)2SO4 0.995025 g/l K2HPO4 0.497512 g/l Na2-EDTA 0.00995025 g/l ZnSO4 x 7 H2O 0.00437811 g/l Bromothymol blue 0.0039801 g/l CaCl2 x 2 H2O 0.00110249 g/l MnCl2 x 4 H2O 0.00100697 g/l FeSO4 x 7 H2O 0.000995025 g/l CoCl2 x 6 H2O 0.000320398 g/l CuSO4 x 5 H2O 0.000312438 g/l Pyridoxine hydrochloride 0.000298507 g/l (NH4)6Mo7O24 x 4 H2O 0.000218905 g/l Nicotinic acid 0.000199005 g/l Thiamine-HCl x 2 H2O 0.000199005 g/l Vitamin B12 9.95025e-05 g/l Calcium pantothenate 9.95025e-05 g/l p-Aminobenzoic acid 7.9602e-05 g/l D-(+)-biotin 1.99005e-05 g/l Distilled water |
| 43182 | Triosulfate agar | yes |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 4710 | positive | growth | 30 | mesophilic |
| 43182 | positive | maximum | 39 | mesophilic |
| 43182 | positive | minimum | 3.5 | psychrophilic |
| 43182 | positive | optimum | 32-35 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 43182 | positive | optimum | 6.5 | |
| 43182 | positive | minimum | 4.2 | |
| 43182 | positive | maximum | 8.5 | alkaliphile |
Physiology and metabolism
nutrition type
- @ref: 43182
- type: chemolithoautotroph
spore formation
| @ref | type of spore | spore formation |
|---|---|---|
| 43182 | endospore | no |
| 43182 | exospore (microbial cyst) | no |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 43182 | NaCl | positive | optimum | 0.47 M |
| 43182 | NaCl | positive | minimum | 0.1 M |
| 43182 | NaCl | positive | maximum | 1.24 M |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 43182 | 15226 | tetrathionate | + | electron donor |
| 43182 | 15379 | dioxygen | + | electron acceptor |
| 43182 | 16094 | thiosulfate | + | electron donor |
| 43182 | 15138 | sulfide | + | electron donor |
| 43182 | 18276 | dihydrogen | - | electron donor |
| 43182 | 18022 | thiocyanate | - | electron donor |
| 43182 | 17359 | sulfite | - | electron donor |
| 43182 | 18248 | iron | - | electron donor |
| 43182 | 18291 | manganese | - | electron donor |
| 43182 | 28938 | ammonium | + | nitrogen source |
| 43182 | 17632 | nitrate | - | reduction |
metabolite production
| @ref | Chebi-ID | metabolite | production |
|---|---|---|---|
| 43182 | 33403 | elemental sulfur | yes |
| 43182 | 30411 | cobalamin | yes |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 43182 | nitrogenase | - | |
| 43182 | hydrogenase | - | 1.12.99.6 |
| 43182 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 4710 | marine sediment | Jadebusen | Germany | DEU | Europe |
| 43182 | Frisia, coastal region of north-western Germany and north-eastern Netherlands | Germany | DEU | Europe |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Marine |
| #Environmental | #Aquatic | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_3038.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_118;96_339;97_378;98_2338;99_3038&stattab=map
- Last taxonomy: Thiomicrorhabdus frisia
- 16S sequence: AF013974
- Sequence Identity:
- Total samples: 594
- soil counts: 44
- aquatic counts: 534
- animal counts: 10
- plant counts: 6
Safety information
risk assessment
- @ref: 4710
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 4710
- description: Thiomicrospira sp. JB-A2 16S ribosomal RNA gene, partial sequence
- accession: AF013974
- length: 1464
- database: ena
- NCBI tax ID: 63655
GC content
| @ref | GC-content | method |
|---|---|---|
| 4710 | 39.6 | high performance liquid chromatography (HPLC) |
| 43182 | 39.6 |
External links
@ref: 4710
culture collection no.: DSM 12351, ATCC 700878
straininfo link
- @ref: 81138
- straininfo: 44191
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 10319459 | Thiomicrospira kuenenii sp. nov. and Thiomicrospira frisia sp. nov., two mesophilic obligately chemolithoautotrophic sulfur-oxidizing bacteria isolated from an intertidal mud flat. | Brinkhoff T, Muyzer G, Wirsen CO, Kuever J | Int J Syst Bacteriol | 10.1099/00207713-49-2-385 | 1999 | Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Geologic Sediments/*microbiology, Gram-Negative Chemolithotrophic Bacteria/*classification/genetics/isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidation-Reduction, Phylogeny, RNA, Ribosomal, 16S/genetics, Ribulose-Bisphosphate Carboxylase/metabolism, Seawater, Sulfur/*metabolism, *Water Microbiology | Genetics |
| Phylogeny | 27334912 | Thiomicrospira hydrogeniphila sp. nov., an aerobic, hydrogen- and sulfur-oxidizing chemolithoautotroph isolated from a seawater tank containing a block of beef tallow. | Watsuji TO, Hada E, Miyazaki M, Ichimura M, Takai K | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001250 | 2016 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Fats, Fatty Acids/chemistry, Hydrogen/metabolism, Oxidation-Reduction, *Phylogeny, Piscirickettsiaceae/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sulfur/metabolism, Thiosulfates/metabolism, Tokyo | Metabolism |
| Phylogeny | 28920830 | Reclassification of Thiomicrospira hydrogeniphila (Watsuji et al. 2016) to Thiomicrorhabdus hydrogeniphila comb. nov., with emended description of Thiomicrorhabdus (Boden et al., 2017). | Boden R, Scott KM, Rae AW, Hutt LP | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002279 | 2017 | Bacterial Typing Techniques, DNA, Bacterial/genetics, Hydrogen/metabolism, Oxidation-Reduction, *Phylogeny, Piscirickettsiaceae/*classification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sulfur/metabolism, Thiosulfates/metabolism | Metabolism |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 4710 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12351) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-12351 | |||
| 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 | |||
| 43182 | Rich Boden, Kathleen M. Scott, John Williams, Sydney Russel, Kirsten Antonen, Alex W. Rae and Lee P. Hutt | 10.1099/ijsem.0.001855 | An evaluation of Thiomicrospira, Hydrogenovibrio and Thioalkalimicrobium: reclassification of four species of Thiomicrospira to each Thiomicrorhabdus gen. nov. and Hydrogenovibrio, and reclassification of all four species of Thioalkalimicrobium to Thiomicrospira | IJSEM 67: 1140-1151 2017 | 28581925 | |
| 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 | |||
| 81138 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID44191.1 | StrainInfo: A central database for resolving microbial strain identifiers |