Strain identifier

BacDive ID: 133221

Type strain: Yes

Species: Piscinibacter defluvii

Strain Designation: SH-1

Strain history: C. O. Jeon; Chung-Ang Univ., South Korea; SH-1.

NCBI tax ID(s): 1796922 (species)

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General

@ref: 25008

BacDive-ID: 133221

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

description: Piscinibacter defluvii SH-1 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from sewage treatment plant.

NCBI tax id

  • NCBI tax id: 1796922
  • Matching level: species

strain history

  • @ref: 67770
  • history: C. O. Jeon; Chung-Ang Univ., South Korea; SH-1.

doi: 10.13145/bacdive133221.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Sphaerotilaceae
  • genus: Piscinibacter
  • species: Piscinibacter defluvii
  • full scientific name: Piscinibacter defluvii Cho et al. 2016

@ref: 25008

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiales, not assigned to family

genus: Piscinibacter

species: Piscinibacter defluvii

strain designation: SH-1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
25008negative1.8-2.1 µm0.7-0.8 µmrod-shapedyespolar
125439negative98.1

colony morphology

  • @ref: 25008
  • colony color: Creamwhite to yellowish
  • colony shape: circular
  • medium used: R2A

Culture and growth conditions

culture medium

  • @ref: 25008
  • name: Reasoner's 2A agar (R2A)
  • growth: yes

culture temp

@refgrowthtypetemperature
25008positivegrowth25-40
25008positiveoptimum7
67770positivegrowth30

culture pH

@refabilitytypepHPH range
25008positivegrowth6.0-9.5alkaliphile
25008positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
25008aerobe
125439obligate aerobe99.8

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 97.3

halophily

@refsalttested relationconcentrationgrowth
25008NaCloptimum0 %
25008NaClgrowth0-0.5 %(w/v)positive

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2500817128adipate-assimilation
250082509agar-hydrolysis
25008casein-hydrolysis
2500817634D-glucose-assimilation
2500816899D-mannitol-assimilation
2500816024D-mannose-assimilation
2500827689decanoate-assimilation
2500817234glucose-fermentation
2500830849L-arabinose-assimilation
2500825115malate-assimilation
25008506227N-acetylglucosamine-assimilation
2500818401phenylacetate-assimilation
2500853258sodium citrate-assimilation
2500827897tryptophan-energy source
2500853423tween 40-respiration
2500853426tween 80-respiration
25008309162-oxoglutarate+respiration
25008167244-hydroxybutyrate+respiration
2500830089acetate+respiration
2500840585alpha-cyclodextrin+respiration
2500817925alpha-D-glucose+respiration
2500823652dextrin+respiration
250084853esculin+hydrolysis
2500828087glycogen+respiration
2500817196L-asparagine+respiration
2500817306maltose+assimilation
2500817632nitrate+reduction
2500832032potassium gluconate+assimilation
2500828017starch+hydrolysis
25008143136succinamate+respiration
2500853424tween 20+hydrolysis
2500853426tween 80+hydrolysis
2500818186tyrosine+hydrolysis

metabolite production

  • @ref: 25008
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitemethylred-testindole test
2500817234glucose-
2500835581indole-

enzymes

@refvalueactivityec
25008acid phosphatase+3.1.3.2
25008alkaline phosphatase+3.1.3.1
25008alpha-chymotrypsin-3.4.21.1
25008alpha-fucosidase-3.2.1.51
25008alpha-galactosidase-3.2.1.22
25008alpha-glucosidase+3.2.1.20
25008alpha-mannosidase-3.2.1.24
25008beta-galactosidase+3.2.1.23
25008beta-glucosidase+3.2.1.21
25008beta-glucuronidase-3.2.1.31
25008catalase-1.11.1.6
25008cystine arylamidase-3.4.11.3
25008cytochrome oxidase+1.9.3.1
25008esterase (C 4)+
25008esterase lipase (C 8)+
25008leucine arylamidase+3.4.11.1
25008lipase (C 14)-
25008N-acetyl-beta-glucosaminidase-3.2.1.52
25008naphthol-AS-BI-phosphohydrolase+
25008trypsin-3.4.21.4
25008tryptophan deaminase-4.1.99.1
25008urease+3.5.1.5
25008valine arylamidase-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentenrichment culture durationenrichment culture temperature
25008sewage treatment plantRepublic of KoreaKORAsia3 days37
67770Activated sludge in Korea

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Waste
  • Cat3: #Water treatment plant

Sequence information

16S sequences

  • @ref: 25008
  • description: Piscinibacter defluvii strain SH-1 16S ribosomal RNA gene, partial sequence
  • accession: KU667249
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Piscinibacter defluvii SH-12881658920draftimg1796922
67770Piscinibacter defluvii SH-1GCA_004011805scaffoldncbi1796922

GC content

@refGC-contentmethod
2500869.9Thermal denaturation, fluorometry
6777069.9thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidence
125439BacteriaNetspore_formationAbility to form endo- or exosporesno97.3
125439BacteriaNetmotilityAbility to perform movementyes77.5
125439BacteriaNetgram_stainReaction to gram-stainingnegative98.1
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe99.8

External links

@ref: 25008

culture collection no.: KACC 18594, JCM 31230

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27550187Piscinibacter defluvii sp. nov., isolated from a sewage treatment plant, and emended description of the genus Piscinibacter Stackebrandt et al. 2009.Cho SH, Lee HJ, Jeon COInt J Syst Evol Microbiol10.1099/ijsem.0.0014382016Bacterial Typing Techniques, Base Composition, Burkholderiaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Putrescine/analogs & derivatives/chemistry, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Sewage/*microbiology, Ubiquinone/chemistryTranscriptome
Phylogeny29957173Piscinibacter caeni sp. nov., isolated from activated sludge.Chen DZ, Yu NN, Chu QY, Chen J, Ye JX, Cheng ZW, Zhang SH, Chen JMInt J Syst Evol Microbiol10.1099/ijsem.0.0028912018Bacteria/genetics, Bacterial Typing Techniques, Base Composition, Burkholderiales/*classification/genetics/isolation & purification, Cadaverine/chemistry, China, DNA, Bacterial/genetics, Drug Industry, Fatty Acids/chemistry, Industrial Waste, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, Putrescine/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Ubiquinone/chemistryTranscriptome
Phylogeny30648940Calidifontimicrobium sediminis gen. nov., sp. nov., a new member of the family Comamonadaceae.Ding YP, Khan IU, Li MM, Xian WD, Liu L, Zhou EM, Salam N, Li WJInt J Syst Evol Microbiol10.1099/ijsem.0.0031672019Bacterial Typing Techniques, Base Composition, Comamonadaceae/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Hot Springs/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, TibetTranscriptome

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
25008S. H. L. Cho, H. J.,Jeon, C. O.Piscinibacter defluvii sp. nov., isolated from a sewage treatment plant, and emended description of the genus Piscinibacter Stackebrandt et al. 200910.1099/ijsem.0.001438IJSEM 66: 4839-4843 201627550187
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG