Strain identifier

BacDive ID: 159755

Type strain: Yes

Species: Pseudothauera hydrothermalis

Strain Designation: GD-2

NCBI tax ID(s): 2184083 (species)

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General

@ref: 66685

BacDive-ID: 159755

keywords: genome sequence, 16S sequence, Bacteria, Gram-negative, rod-shaped, colony-forming

description: Pseudothauera hydrothermalis GD-2 is a Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from sediment sample from a hot spring .

NCBI tax id

  • NCBI tax id: 2184083
  • Matching level: species

doi: 10.13145/bacdive159755.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Rhodocyclales
  • family: Zoogloeaceae
  • genus: Pseudothauera
  • species: Pseudothauera hydrothermalis
  • full scientific name: Pseudothauera hydrothermalis (Yang et al. 2018) Huang et al. 2022

  • synonyms

    • @ref: 20215
    • synonym: Thauera hydrothermalis

@ref: 66685

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Rhodocyclales

family: Zoogloeaceae

genus: Thauera

species: Thauera hydrothermalis

strain designation: GD-2

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
66685negative1-2.5 µm0.3-0.5 µmrod-shaped
69480yes97.151
69480negative99.999

colony morphology

  • @ref: 66685
  • colony color: white
  • colony shape: circular
  • incubation period: 2 days
  • medium used: Y7 agar

Culture and growth conditions

culture medium

  • @ref: 66685
  • name: Y7 agar
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
66685positivegrowth37-55
66685positiveoptimum45-50thermophilic

culture pH

@refabilitytypepHPH range
66685positivegrowth5.5-11alkaliphile
66685positiveoptimum7-7.5

Physiology and metabolism

spore formation

@refspore formationconfidence
66685no
69480no99.956
69481no100

halophily

@refsaltgrowthtested relationconcentration
66685NaClpositivegrowth0-4 %(w/v)
66685NaClpositiveoptimum0 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6668517108D-arabinose+builds acid from
6668517268myo-inositol+builds acid from
6668529864mannitol+builds acid from
6668530911sorbitol+builds acid from
6668515361pyruvate-carbon source
6668515824D-fructose-carbon source
6668516449alanine-carbon source
6668516988D-ribose-carbon source
6668517634D-glucose-carbon source
6668517754glycerol-carbon source
6668517790methanol-carbon source
6668525115malate-carbon source
6668528831propanol-carbon source
6668565327D-xylose-carbon source
66685butanol-carbon source
66685casamino acids-carbon source
6668515740formate+carbon source
6668516024D-mannose+carbon source
6668516150benzoate+carbon source
6668516236ethanol+carbon source
6668516411acetic acid+carbon source
6668516899D-mannitol+carbon source
6668517295L-phenylalanine+carbon source
6668517859glutaric acid+carbon source
6668522653asparagine+carbon source
6668524996lactate+carbon source
6668528260galactose+carbon source
6668529987glutamate+carbon source
6668530031succinate+carbon source
6668531011valerate+carbon source
6668535391aspartate+carbon source
6668527897tryptophan+energy source
6668516199urea-hydrolysis
6668527689decanoate-hydrolysis
666854853esculin+hydrolysis
666855291gelatin+hydrolysis
6668518401phenylacetate+hydrolysis
6668528017starch+hydrolysis
6668517632nitrate+reduction

metabolite production

  • @ref: 66685
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

  • @ref: 66685
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
66685alpha-galactosidase+3.2.1.22
66685alpha-glucosidase+3.2.1.20
66685beta-glucosidase+3.2.1.21
66685catalase+1.11.1.6
66685chymotrypsin+3.4.4.5
66685cytochrome oxidase+1.9.3.1
66685esterase Lipase (C 8)+
66685tryptophan deaminase+4.1.99.1

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    66685C10:0 3OH7
    66685C14:03.5
    66685C18:1 w6c and/or C18:1 w7c3.6
    66685C16:1 w6c and/or C16:1 w7c33.6
    66685C16:047.9
    66685C12:07.4
  • type of FA analysis: whole cell analysis
  • incubation medium: Y7 medium
  • incubation temperature: 45
  • incubation time: 3
  • software version: Sherlock 6.0B
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

  • @ref: 66685
  • sample type: sediment sample from a hot spring (pH 7.0)
  • geographic location: Tibet Autonomous Region
  • country: China
  • origin.country: CHN
  • continent: Asia
  • enrichment culture: Y7 agar
  • enrichment culture composition: (1 g YE, 1 g glucose, 0.3 g sodium pyruvate, 0.3 g succinic acid, 0.5 g casamino acid, 0.5 g tryptone, 1.3 g (NH4)2SO4, 0.5 g KH2PO4, 0.5 g K2HPO4, 0.5 g MgSO4 x 7H2O, 0.07 g CaCl2 x 2H2O, 0.02 g FeCl3 x 6H2O)
  • enrichment culture duration: 3 days
  • enrichment culture temperature: 45
  • isolation procedure: 1 g sediment sample were incubated at 45°C in 100 ml Allen medium, supplemented with 1 g l-1 yeast extract (YE) for bacteria enrichment. After cultivation of 5 days, the enriched culture was serially diluted (10-fold) in tubes containing 0.9 ml Allen broth. Dilutions of 0.2 ml were spread on Y7 agar plates to cultivate separated colonies. The plates were incubated at 45°C for 3 days.

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Sediment
#Environmental#Aquatic#Thermal spring

taxonmaps

  • @ref: 69479
  • File name: preview.99_47666.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_129;96_8760;97_10537;98_12925;99_47666&stattab=map
  • Last taxonomy: Thauera hydrothermalis subclade
  • 16S sequence: MF033446
  • Sequence Identity:
  • Total samples: 273
  • soil counts: 38
  • aquatic counts: 210
  • animal counts: 22
  • plant counts: 3

Sequence information

16S sequences

  • @ref: 66685
  • description: Thauera sp. strain GD-2 16S ribosomal RNA gene, partial sequence
  • accession: MF033446
  • length: 1495
  • database: ena
  • NCBI tax ID: 2184083

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudothauera hydrothermalis GD-2GCA_003345255completencbi2184083
66792Thauera hydrothermalis GD-22841165597completeimg2184083

GC content

  • @ref: 66685
  • GC-content: 63.6
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes93.372no
flagellatedyes85.504no
gram-positiveno99.178yes
anaerobicno81.698no
aerobicno74.409no
halophileno92.571yes
spore-formingno93.842yes
glucose-utilno79.193no
thermophileno55.461no
glucose-fermentno87.968no

External links

@ref: 66685

culture collection no.: NBRC 112472, CGMCC 1.15527

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny30113299Thauera hydrothermalis sp. nov., a thermophilic bacterium isolated from hot spring.Yang L, Muhadesi JB, Wang MM, Wang BJ, Liu SJ, Jiang CYInt J Syst Evol Microbiol10.1099/ijsem.0.0029602018Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hot Springs/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Thauera/*classification/genetics/isolation & purification, Tibet, Ubiquinone/chemistryTranscriptome
Phylogeny35596013Thauera sedimentorum sp. nov., Isolated from Coastal Sediment.Baek J, Jaikwang N, Kim JH, Yoon JH, Lee JS, Sukhoom A, Kim WCurr Microbiol10.1007/s00284-022-02890-w2022Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, *Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Thauera/geneticsTranscriptome

Reference

@idauthorstitledoi/urljournalpubmed
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
66685Lan Yang, Jiang-Baota Muhadesi, Meng-Meng Wang, Bao-Jun Wang, Shuang-Jiang Liu, Cheng-Ying JiangThauera hydrothermalis sp. nov., a thermophilic bacterium isolated from hot spring10.1099/ijsem.0.002960IJSEM 68: 3163-3168 201830113299
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
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