Strain identifier

BacDive ID: 130259

Type strain: Yes

Species: Diaphorobacter nitroreducens

Strain Designation: SL-205

Strain history: T. Qiu; Beijing Agro-Biotechnol. Res. Center, China; SL-205.

NCBI tax ID(s): 164759 (species)

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General

@ref: 21576

BacDive-ID: 130259

DSM-Number: 29460

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile

description: Diaphorobacter nitroreducens SL-205 is a mesophilic, motile bacterium that was isolated from biofilm of a denitrifying reactor using PHBV as carbon source.

NCBI tax id

  • NCBI tax id: 164759
  • Matching level: species

strain history

@refhistory
21576<- T. Qiu, Beijing Academy of Agriculture and Forestry Science; SL-205 <- L. Iili, Beijing Academy of Agriculture and Forestry Science
67770T. Qiu; Beijing Agro-Biotechnol. Res. Center, China; SL-205.

doi: 10.13145/bacdive130259.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Comamonadaceae
  • genus: Diaphorobacter
  • species: Diaphorobacter nitroreducens
  • full scientific name: Diaphorobacter nitroreducens Khan and Hiraishi 2003

  • synonyms

    • @ref: 20215
    • synonym: Diaphorobacter polyhydroxybutyrativorans

@ref: 21576

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Diaphorobacter

species: Diaphorobacter nitroreducens

full scientific name: Diaphorobacter nitroreducens Khan and Hiraishi 2003

strain designation: SL-205

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes98.66
69480100negative

multimedia

  • @ref: 21576
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_29460.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
21576LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium381.pdf
21576NUTRIENT AGAR (DSMZ Medium 1)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1.pdf
21576TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
21576positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.999

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate+assimilation
6836927689decanoate-assimilation
6836924265gluconate+assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-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
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
21576+-------------+-++--+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
21576biofilm of a denitrifying reactor using PHBV as carbon sourceBeijing, Fangshan DistrictChinaCHNAsia
67770Biofilms of a denitrifying reactor

isolation source categories

Cat1Cat2Cat3
#Engineered#Industrial#Machines and devices
#Engineered#Laboratory#Lab enrichment
#Environmental#Biofilm

taxonmaps

  • @ref: 69479
  • File name: preview.99_1320.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_491;97_892;98_1045;99_1320&stattab=map
  • Last taxonomy: Diaphorobacter nitroreducens
  • 16S sequence: JX974341
  • Sequence Identity:
  • Total samples: 21200
  • soil counts: 4505
  • aquatic counts: 6609
  • animal counts: 8073
  • plant counts: 2013

Safety information

risk assessment

  • @ref: 21576
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 21576
  • description: Diaphorobacter polyhydroxybutyrativorans strain SL-205 16S ribosomal RNA gene, partial sequence
  • accession: JX974341
  • length: 1428
  • database: ena
  • NCBI tax ID: 1546149

Genome sequences

  • @ref: 67770
  • description: Diaphorobacter nitroreducens SL-205
  • accession: GCA_002214645
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 164759

GC content

  • @ref: 21576
  • GC-content: 66.8
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedyes63.575no
gram-positiveno99.041no
anaerobicno97.73no
aerobicyes93.5no
halophileno94.559no
spore-formingno94.814no
glucose-utilno81.87yes
thermophileno98.537yes
motileyes89.118no
glucose-fermentno90.87yes

External links

@ref: 21576

culture collection no.: DSM 29460, ACCC 19739, JCM 30411

straininfo link

  • @ref: 88798
  • straininfo: 399216

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny26012582Diaphorobacter polyhydroxybutyrativorans sp. nov., a novel poly(3-hydroxybutyrate-co-3-hydroxyvalerate)-degrading bacterium isolated from biofilms.Qiu T, Zuo Z, Gao J, Gao M, Han M, Sun L, Zhang L, Wang XInt J Syst Evol Microbiol10.1099/ijs.0.0003532015Animals, Bacterial Typing Techniques, Base Composition, Beijing, *Biofilms, Bioreactors/*microbiology, Comamonadaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Manure, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Polyesters/*metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/microbiology, Swine, Ubiquinone/chemistryGenetics
28601768Heterotrophic nitrification and aerobic denitrification by Diaphorobacter polyhydroxybutyrativorans SL-205 using poly(3-hydroxybutyrate-co-3-hydroxyvalerate) as the sole carbon source.Zhang S, Sun X, Fan Y, Qiu T, Gao M, Wang XBioresour Technol10.1016/j.biortech.2017.05.1852017*3-Hydroxybutyric Acid, Aerobiosis, *Carbon, *Denitrification, Heterotrophic Processes, Nitrification, Pentanoic Acids
29775906Bioaugmentation with Diaphorobacter polyhydroxybutyrativorans to enhance nitrate removal in a poly (3-hydroxybutyrate-co-3-hydroxyvalerate)-supported denitrification reactor.Zhang S, Sun X, Wang X, Qiu T, Gao M, Sun Y, Cheng S, Zhang QBioresour Technol10.1016/j.biortech.2018.04.11520183-Hydroxybutyric Acid, *Bioreactors, *Comamonadaceae, *Denitrification, Nitrates, Pentanoic Acids, Polyesters
Phylogeny31046896Pulveribacter suum gen. nov., sp. nov., isolated from a pig farm dust collector.Heo J, Cho HY, Heo I, Hong SB, Kim JS, Kwon SW, Kim SJInt J Syst Evol Microbiol10.1099/ijsem.0.0030822019Animals, Bacterial Typing Techniques, Base Composition, Comamonadaceae/*classification/isolation & purification, DNA, Bacterial/genetics, *Dust, *Farms, Fatty Acids/chemistry, Genes, Bacterial, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Swine, Ubiquinone/chemistryTranscriptome
Phylogeny31282854Diaphorobacter polyhydroxybutyrativorans Qiu et al. 2015 is a later heterotypic synonym of Diaphorobacter nitroreducens Khan and Hiraishi 2003.Liu Y, Zhu HHInt J Syst Evol Microbiol10.1099/ijsem.0.0035822019Animals, Bacterial Typing Techniques, Base Composition, Bioreactors/microbiology, Comamonadaceae/*classification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, SwineTranscriptome

Reference

@idauthorstitledoi/urlcatalogue
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
21576Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29460Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29460)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
88798Reimer, 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-ID399216.1