Strain identifier

BacDive ID: 13804

Type strain: Yes

Species: Thioclava pacifica

Strain Designation: TL 2

Strain history: <- D. Yu. Sorokin; TL 2

For citation purpose refer to the digital object identifier (doi) of the current version.
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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 idMatching level
285109species
1353537strain

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

@refgram staincell shapemotilityconfidence
31370negativerod-shapedyes
69480negative99.999

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

@refgrowthtypetemperaturerange
3837positivegrowth28mesophilic
31370positivegrowth15-47
31370positiveoptimum35mesophilic

culture pH

@refabilitytypepHPH range
31370positivegrowth6.5-8.5alkaliphile
31370positiveoptimum8

Physiology and metabolism

oxygen tolerance

  • @ref: 31370
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.994

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3137030089acetate+carbon source
3137016449alanine+carbon source
3137022653asparagine+carbon source
3137017057cellobiose+carbon source
3137017234glucose+carbon source
3137029987glutamate+carbon source
3137017754glycerol+carbon source
3137024996lactate+carbon source
3137025115malate+carbon source
3137015792malonate+carbon source
3137017306maltose+carbon source
3137029864mannitol+carbon source
3137026271proline+carbon source
3137017272propionate+carbon source
3137015361pyruvate+carbon source
3137030031succinate+carbon source
3137017992sucrose+carbon source
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol+assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
3837catalase+1.11.1.6
3837cytochrome-c oxidase+1.9.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
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

Cat1Cat2Cat3
#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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Thioclava pacifica DSM 10166GCA_000714535contigncbi1353537
66792Thioclava pacifica DSM 101661353537.7wgspatric1353537
66792Thioclava pacifica DSM 101662585427686draftimg1353537

GC content

  • @ref: 3837
  • GC-content: 63.1

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes57.494yes
gram-positiveno98.791yes
anaerobicno91.853yes
halophileyes50.711no
spore-formingno96.152no
thermophileno96.56yes
glucose-utilyes82.917no
flagellatedno78.211no
aerobicyes65.722yes
glucose-fermentno89.2yes

External links

@ref: 3837

culture collection no.: DSM 10166, UNIQEM 229

straininfo link

  • @ref: 82982
  • straininfo: 139011

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15879235Thioclava 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 GInt J Syst Evol Microbiol10.1099/ijs.0.63415-02005Aerobiosis, 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 MicrobiologyMetabolism
Phylogeny19196783Tropicimonas 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 KInt J Syst Evol Microbiol10.1099/ijs.0.65822-02009Alkanes/*metabolism, Microscopy, Electron, Transmission, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/metabolism/ultrastructure, Seawater/*microbiology, Species SpecificityMetabolism
Phylogeny23378112Thioclava dalianensis sp. nov., isolated from surface seawater.Zhang R, Lai Q, Wang W, Li S, Shao ZInt J Syst Evol Microbiol10.1099/ijs.0.046094-02013Bacterial 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 MicrobiologyGenetics
Phylogeny25173854Thioclava atlantica sp. nov., isolated from deep sea sediment of the Atlantic Ocean.Lai Q, Li S, Xu H, Jiang L, Zhang R, Shao ZAntonie Van Leeuwenhoek10.1007/s10482-014-0261-x2014Atlantic 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, TemperatureGenetics
Phylogeny25361528Thioclava indica sp. nov., isolated from surface seawater of the Indian Ocean.Liu Y, Lai Q, Du J, Xu H, Jiang L, Shao ZAntonie Van Leeuwenhoek10.1007/s10482-014-0320-32014Alkanes/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, TemperatureGenetics
Phylogeny28598317Thioclava nitratireducens sp. nov., isolated from surface seawater.Liu Y, Lai Q, Shao ZInt J Syst Evol Microbiol10.1099/ijsem.0.0018442017Arctic 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/chemistryTranscriptome
Phylogeny29570444Thioclava 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 AInt J Syst Evol Microbiol10.1099/ijsem.0.0027232018Autotrophic 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, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
3837Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10166)https://www.dsmz.de/collection/catalogue/details/culture/DSM-10166
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
31370Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2768328776041
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)
68369Automatically annotated from API 20NE
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
82982Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID139011.1StrainInfo: A central database for resolving microbial strain identifiers