Strain identifier

BacDive ID: 130630

Type strain: Yes

Species: Thioclava dalianensis

Strain Designation: DLFJ1-1

Strain history: <- LMG <- Q. Lai, Third Inst. Oceanography, State Oceanic Administration, Xiamen, China

NCBI tax ID(s): 1185766 (species)

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General

@ref: 21842

BacDive-ID: 130630

DSM-Number: 29618

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped

description: Thioclava dalianensis DLFJ1-1 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from oil-degrading bacterial consortium, enriched by surface seawater.

NCBI tax id

  • NCBI tax id: 1185766
  • Matching level: species

strain history

  • @ref: 21842
  • history: <- LMG <- Q. Lai, Third Inst. Oceanography, State Oceanic Administration, Xiamen, China

doi: 10.13145/bacdive130630.20230509.8.1

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 dalianensis
  • full scientific name: Thioclava dalianensis Zhang et al. 2013

@ref: 21842

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Thioclava

species: Thioclava dalianensis

full scientific name: Thioclava dalianensis Zhang et al. 2013

strain designation: DLFJ1-1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30859negative1.15 µm0.75 µmrod-shapedno
69480negative99.997

colony morphology

  • @ref: 21842
  • incubation period: 1-2 days

pigmentation

  • @ref: 30859
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 21842
  • 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
21842positivegrowth30mesophilic
30859positivegrowth04-37
30859positiveoptimum28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 30859
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.995

halophily

@refsaltgrowthtested relationconcentration
30859NaClpositivegrowth0.5-15 %
30859NaClpositiveoptimum3 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3085930089acetate+carbon source
3085915963ribitol+carbon source
3085921217L-alaninamide+carbon source
3085916449alanine+carbon source
3085922653asparagine+carbon source
3085935391aspartate+carbon source
3085917057cellobiose+carbon source
3085916947citrate+carbon source
3085923652dextrin+carbon source
3085928757fructose+carbon source
3085933984fucose+carbon source
3085924148galactonate+carbon source
3085924265gluconate+carbon source
3085917234glucose+carbon source
3085932323glucuronamide+carbon source
3085929987glutamate+carbon source
3085917754glycerol+carbon source
3085917596inosine+carbon source
3085917240itaconate+carbon source
3085924996lactate+carbon source
3085917716lactose+carbon source
3085925017leucine+carbon source
3085915792malonate+carbon source
3085917306maltose+carbon source
3085937684mannose+carbon source
3085928053melibiose+carbon source
3085951850methyl pyruvate+carbon source
3085928044phenylalanine+carbon source
3085926271proline+carbon source
3085926490quinate+carbon source
3085916634raffinose+carbon source
3085926546rhamnose+carbon source
3085917822serine+carbon source
3085930911sorbitol+carbon source
3085930031succinate+carbon source
3085926986threonine+carbon source
3085917748thymidine+carbon source
3085927082trehalose+carbon source
3085916704uridine+carbon source
6836925115malate+assimilation
6836927689decanoate-assimilation
6836924265gluconate+assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol+assimilation
6836930849L-arabinose+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
21842catalase+1.11.1.6
21842cytochrome-c oxidase+1.9.3.1
30859acid phosphatase+3.1.3.2
30859alkaline phosphatase+3.1.3.1
30859catalase+1.11.1.6
30859cytochrome oxidase+1.9.3.1
30859urease+3.5.1.5
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
21842-----+-++++/-++++-+/-++++
21842-----+-++/-++/-++++-+/-+++

Isolation, sampling and environmental information

isolation

  • @ref: 21842
  • sample type: oil-degrading bacterial consortium, enriched by surface seawater
  • geographic location: Dalian Port
  • country: China
  • origin.country: CHN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Engineered#Laboratory#Lab enrichment
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Surface water
#Host#Microbial#Bacteria

taxonmaps

  • @ref: 69479
  • File name: preview.99_5045.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_2464;97_3007;98_3770;99_5045&stattab=map
  • Last taxonomy: Thioclava dalianensis subclade
  • 16S sequence: JQ844756
  • Sequence Identity:
  • Total samples: 464
  • soil counts: 27
  • aquatic counts: 416
  • animal counts: 15
  • plant counts: 6

Safety information

risk assessment

  • @ref: 21842
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 21842
  • description: Thioclava dalianensis strain DLFJ1-1 16S ribosomal RNA gene, partial sequence
  • accession: JQ844756
  • length: 1435
  • database: ena
  • NCBI tax ID: 1185766

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Thioclava dalianensis CGMCC 1.12325GCA_900115035scaffoldncbi1185766
66792Thioclava dalianensis DLFJ1-1GCA_000715505contigncbi1185766
66792Thioclava dalianensis strain CGMCC 1.123251185766.6wgspatric1185766
66792Thioclava dalianensis CGMCC 1.123252663762756draftimg1185766
66792Thioclava dalianensis DLFJ1-12585427678draftimg1185766

GC content

  • @ref: 30859
  • GC-content: 62.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes59.058yes
flagellatedno74.523no
gram-positiveno98.577no
anaerobicno95.867yes
aerobicyes79.066no
halophileno52.613no
spore-formingno96.442no
glucose-fermentno92.449yes
thermophileno97.19yes
glucose-utilyes90.681yes

External links

@ref: 21842

culture collection no.: DSM 29618, CGMCC 1.12325, LMG 27290, MCCC 1A03957

straininfo link

  • @ref: 89142
  • straininfo: 382321

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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

@idauthorstitledoi/urlcatalogueID_cross_referencepubmedjournal
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
21842Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29618Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29618)
30859Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172718928776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa102533211880Nucleic Acids Res. 49: D498-D508 2020
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
89142Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID382321.1