Strain identifier
BacDive ID: 13804
Type strain:
Species: Thioclava pacifica
Strain Designation: TL 2
Strain history: <- D. Yu. Sorokin; TL 2
NCBI tax ID(s): 1353537 (strain), 285109 (species)
General
@ref: 3837
BacDive-ID: 13804
DSM-Number: 10166
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Thioclava pacifica TL 2 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sulfidic thermal sea water.
NCBI tax id
NCBI tax id | Matching level |
---|---|
285109 | species |
1353537 | strain |
strain history
- @ref: 3837
- history: <- D. Yu. Sorokin; TL 2
doi: 10.13145/bacdive13804.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Paracoccaceae
- genus: Thioclava
- species: Thioclava pacifica
- full scientific name: Thioclava pacifica Sorokin et al. 2005
@ref: 3837
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Thioclava
species: Thioclava pacifica
full scientific name: Thioclava pacifica Sorokin et al. 2005
strain designation: TL 2
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell shape | motility | confidence |
---|---|---|---|---|
31370 | negative | rod-shaped | yes | |
69480 | negative | 99.999 |
colony morphology
- @ref: 3837
- incubation period: 2-3 days
Culture and growth conditions
culture medium
- @ref: 3837
- name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
- growth: yes
- link: https://mediadive.dsmz.de/medium/514
- composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
3837 | positive | growth | 28 | mesophilic |
31370 | positive | growth | 15-47 | |
31370 | positive | optimum | 35 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
31370 | positive | growth | 6.5-8.5 | alkaliphile |
31370 | positive | optimum | 8 |
Physiology and metabolism
oxygen tolerance
- @ref: 31370
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.994 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31370 | 30089 | acetate | + | carbon source |
31370 | 16449 | alanine | + | carbon source |
31370 | 22653 | asparagine | + | carbon source |
31370 | 17057 | cellobiose | + | carbon source |
31370 | 17234 | glucose | + | carbon source |
31370 | 29987 | glutamate | + | carbon source |
31370 | 17754 | glycerol | + | carbon source |
31370 | 24996 | lactate | + | carbon source |
31370 | 25115 | malate | + | carbon source |
31370 | 15792 | malonate | + | carbon source |
31370 | 17306 | maltose | + | carbon source |
31370 | 29864 | mannitol | + | carbon source |
31370 | 26271 | proline | + | carbon source |
31370 | 17272 | propionate | + | carbon source |
31370 | 15361 | pyruvate | + | carbon source |
31370 | 30031 | succinate | + | carbon source |
31370 | 17992 | sucrose | + | carbon source |
68369 | 25115 | malate | + | assimilation |
68369 | 17128 | adipate | - | assimilation |
68369 | 27689 | decanoate | - | assimilation |
68369 | 24265 | gluconate | - | assimilation |
68369 | 17306 | maltose | + | assimilation |
68369 | 59640 | N-acetylglucosamine | - | assimilation |
68369 | 16899 | D-mannitol | + | assimilation |
68369 | 30849 | L-arabinose | - | assimilation |
68369 | 17634 | D-glucose | + | assimilation |
68369 | 5291 | gelatin | - | hydrolysis |
68369 | 4853 | esculin | + | hydrolysis |
68369 | 16199 | urea | - | hydrolysis |
68369 | 29016 | arginine | - | hydrolysis |
68369 | 17634 | D-glucose | - | fermentation |
68369 | 27897 | tryptophan | - | energy source |
68369 | 17632 | nitrate | - | reduction |
metabolite production
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
3837 | catalase | + | 1.11.1.6 |
3837 | cytochrome-c oxidase | + | 1.9.3.1 |
68369 | cytochrome oxidase | + | 1.9.3.1 |
68369 | gelatinase | - | |
68369 | beta-glucosidase | + | 3.2.1.21 |
68369 | urease | - | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
API 20NE
@ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
3837 | - | - | - | - | - | + | - | +/- | + | - | +/- | + | - | + | - | - | - | + | + | - | + |
Isolation, sampling and environmental information
isolation
- @ref: 3837
- sample type: sulfidic thermal sea water
- geographic location: New Britain, Matupi Harbour
- country: Papua New Guinea
- origin.country: PNG
- continent: Australia and Oceania
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Marine |
#Condition | #Sulfuric |
taxonmaps
- @ref: 69479
- File name: preview.99_2967.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_849;97_991;98_1170;99_2967&stattab=map
- Last taxonomy: Thioclava pacifica
- 16S sequence: AY656719
- Sequence Identity:
- Total samples: 304
- soil counts: 63
- aquatic counts: 159
- animal counts: 75
- plant counts: 7
Safety information
risk assessment
- @ref: 3837
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 3837
- description: Thioclava pacifica strain TL 2 16S ribosomal RNA gene, partial sequence
- accession: AY656719
- length: 1371
- database: ena
- NCBI tax ID: 1353537
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Thioclava pacifica DSM 10166 | GCA_000714535 | contig | ncbi | 1353537 |
66792 | Thioclava pacifica DSM 10166 | 1353537.7 | wgs | patric | 1353537 |
66792 | Thioclava pacifica DSM 10166 | 2585427686 | draft | img | 1353537 |
GC content
- @ref: 3837
- GC-content: 63.1
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 57.494 | yes |
gram-positive | no | 98.791 | yes |
anaerobic | no | 91.853 | yes |
halophile | yes | 50.711 | no |
spore-forming | no | 96.152 | no |
thermophile | no | 96.56 | yes |
glucose-util | yes | 82.917 | no |
flagellated | no | 78.211 | no |
aerobic | yes | 65.722 | yes |
glucose-ferment | no | 89.2 | yes |
External links
@ref: 3837
culture collection no.: DSM 10166, UNIQEM 229
straininfo link
- @ref: 82982
- straininfo: 139011
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 15879235 | Thioclava pacifica gen. nov., sp. nov., a novel facultatively autotrophic, marine, sulfur-oxidizing bacterium from a near-shore sulfidic hydrothermal area. | Sorokin DY, Tourova TP, Spiridonova EM, Rainey FA, Muyzer G | Int J Syst Evol Microbiol | 10.1099/ijs.0.63415-0 | 2005 | Aerobiosis, Carbohydrate Metabolism, Carbon/metabolism, Carboxylic Acids/metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, Bacterial, Genes, rRNA, Growth Inhibitors/pharmacology, Hot Springs/*microbiology, Hydrogen-Ion Concentration, Molecular Sequence Data, Oxidation-Reduction, Papua New Guinea, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/cytology/*isolation & purification/physiology, Ribulose-Bisphosphate Carboxylase/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sodium Chloride/pharmacology, Sulfides/metabolism, Temperature, Thiosulfates/*metabolism, Water Microbiology | Metabolism |
Phylogeny | 19196783 | Tropicimonas isoalkanivorans gen. nov., sp. nov., a branched-alkane-degrading bacterium isolated from Semarang Port in Indonesia. | Harwati TU, Kasai Y, Kodama Y, Susilaningsih D, Watanabe K | Int J Syst Evol Microbiol | 10.1099/ijs.0.65822-0 | 2009 | Alkanes/*metabolism, Microscopy, Electron, Transmission, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/metabolism/ultrastructure, Seawater/*microbiology, Species Specificity | Metabolism |
Phylogeny | 23378112 | Thioclava dalianensis sp. nov., isolated from surface seawater. | Zhang R, Lai Q, Wang W, Li S, Shao Z | Int J Syst Evol Microbiol | 10.1099/ijs.0.046094-0 | 2013 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/analysis, Water Microbiology | Genetics |
Phylogeny | 25173854 | Thioclava atlantica sp. nov., isolated from deep sea sediment of the Atlantic Ocean. | Lai Q, Li S, Xu H, Jiang L, Zhang R, Shao Z | Antonie Van Leeuwenhoek | 10.1007/s10482-014-0261-x | 2014 | Atlantic Ocean, Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Salinity, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature | Genetics |
Phylogeny | 25361528 | Thioclava indica sp. nov., isolated from surface seawater of the Indian Ocean. | Liu Y, Lai Q, Du J, Xu H, Jiang L, Shao Z | Antonie Van Leeuwenhoek | 10.1007/s10482-014-0320-3 | 2014 | Alkanes/metabolism, Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Enzymes/analysis, Fatty Acids/analysis, Genome, Bacterial, Glycolipids/analysis, Hydrogen-Ion Concentration, Indian Ocean, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Salinity, Seawater/*microbiology, Sequence Analysis, DNA, Temperature | Genetics |
Phylogeny | 28598317 | Thioclava nitratireducens sp. nov., isolated from surface seawater. | Liu Y, Lai Q, Shao Z | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001844 | 2017 | Arctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry | Transcriptome |
Phylogeny | 29570444 | Thioclava electrotropha sp. nov., a versatile electrode and sulfur-oxidizing bacterium from marine sediments. | Chang R, Bird L, Barr C, Osburn M, Wilbanks E, Nealson K, Rowe A | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002723 | 2018 | Autotrophic Processes, Bacterial Typing Techniques, Base Composition, California, DNA, Bacterial/genetics, Electrodes, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Salinity, Seawater/*microbiology, Sequence Analysis, DNA | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
3837 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10166) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-10166 | |||
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 | |||
31370 | 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 | 27683 | 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) | |||
68369 | Automatically annotated from API 20NE | |||||
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) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
82982 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID139011.1 | StrainInfo: A central database for resolving microbial strain identifiers |