Strain identifier

BacDive ID: 133344

Type strain: Yes

Species: Aliidongia dinghuensis

Strain Designation: 7M-Z19

Strain history: <- J.-S. Lee, KCTC; KCTC 52134 <- L. Qiu, State Key Lab. for Biocontrol, Sun Yat-sen Univ., Guangzhou, People's Republic of China; 7M-Z19

NCBI tax ID(s): 1867774 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 8.1 (current version)

General

@ref: 64841

BacDive-ID: 133344

DSM-Number: 107831

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

description: Aliidongia dinghuensis 7M-Z19 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from forest soil.

NCBI tax id

  • NCBI tax id: 1867774
  • Matching level: species

strain history

  • @ref: 64841
  • history: <- J.-S. Lee, KCTC; KCTC 52134 <- L. Qiu, State Key Lab. for Biocontrol, Sun Yat-sen Univ., Guangzhou, People's Republic of China; 7M-Z19

doi: 10.13145/bacdive133344.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodospirillales
  • family: Rhodospirillaceae
  • genus: Aliidongia
  • species: Aliidongia dinghuensis
  • full scientific name: Aliidongia dinghuensis Chen et al. 2017

@ref: 64841

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodospirillales

family: Rhodospirillaceae

genus: Aliidongia

species: Aliidongia dinghuensis

full scientific name: Aliidongia dinghuensis Chen et al. 2017

strain designation: 7M-Z19

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
25168negative1.0-2.5 µm0.3-0.7 µmrod-shapedyesmonotrichous, polar
69480negative99.982
69480yes95.624

colony morphology

  • @ref: 25168
  • colony size: 1.0-3.0 mm
  • colony color: white
  • colony shape: circular
  • incubation period: 5 days
  • medium used: MM1F agar medium

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
25168MM1F agar mediumyes0.04 g MgSO4.7H2O l-1, 0.5 g fructose l-1, 0.02 g CaCl.2H2O l-1, 0.05 g yeast extract l-1, 15.0 g agar l-1, pH 7.0
25168Reasoner's 2A agar (R2A)yes
25168YP agaryes
25168tryptic soy agar (TSA)no
25168nutrient agar (NA)no
25168MacConkey agarno
64841R2A MEDIUM (DSMZ Medium 830)yesName: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled waterhttps://mediadive.dsmz.de/medium/830

culture temp

@refgrowthtypetemperaturerange
25168positivegrowth10.0-37.0
25168positiveoptimum28mesophilic
64841positivegrowth28mesophilic

culture pH

@refabilitytypepH
25168positivegrowth4.5-7.5
25168positiveoptimum6.0-6.5

Physiology and metabolism

oxygen tolerance

  • @ref: 25168
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
25168no
69481no100
69480no99.944

halophily

@refsalttested relationconcentration
25168NaClmaximum2 %(w/v)
25168NaCloptimum0 %(w/v)

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
25168casein-hydrolysis
25168esculin-hydrolysis4853
25168gelatin-hydrolysis5291
25168glucose-fermentation17234
25168nitrate-reduction17632
25168starch-hydrolysis28017
25168tryptophan-energy source27897
25168tween 80-hydrolysis53426
68369malate-assimilation25115
68369adipate-assimilation17128
68369decanoate-assimilation27689
68369gluconate-assimilation24265
68369maltose-assimilation17306
68369N-acetylglucosamine-assimilation59640
68369D-mannitol-assimilation16899
68369D-mannose-assimilation16024
68369L-arabinose-assimilation30849
68369D-glucose-assimilation17634
68369gelatin-hydrolysis5291
68369esculin-hydrolysis4853
68369urea+hydrolysis16199
68369arginine-hydrolysis29016
68369D-glucose-fermentation17634
68369tryptophan-energy source27897
68369nitrate+reduction17632

metabolite production

@refChebi-IDmetaboliteproduction
2516830033bacteriochlorophyll alphano
2516816136hydrogen sulfideno
2516835581indoleno
2516853388polyhydroxybutyrateyes
6836935581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
2516835581indole-
6836935581indole-

enzymes

@refvalueactivityec
25168acid phosphatase+3.1.3.2
25168alkaline phosphatase+3.1.3.1
25168alpha-chymotrypsin-3.4.21.1
25168alpha-fucosidase-3.2.1.51
25168alpha-galactosidase-3.2.1.22
25168alpha-glucosidase-3.2.1.20
25168alpha-mannosidase-3.2.1.24
25168beta-galactosidase-3.2.1.23
25168beta-glucosidase-3.2.1.21
25168beta-glucuronidase-3.2.1.31
25168catalase+1.11.1.6
25168cystine arylamidase-3.4.11.3
25168cytochrome oxidase+1.9.3.1
25168esterase (C 4)+
25168esterase Lipase (C 8)+
25168leucine arylamidase+3.4.11.1
25168lipase (C 14)-
25168N-acetyl-beta-glucosaminidase-3.2.1.52
25168naphthol-AS-BI-phosphohydrolase+
25168trypsin-3.4.21.4
25168tryptophan deaminase-4.1.99.1
25168valine arylamidase+
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease+3.5.1.5
68369arginine dihydrolase-3.5.3.6
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    25168C16:09.2
    25168C18:1ω7c27.2
    25168Cyclo C19:0ω8c36.2
  • type of FA analysis: whole cell analysis
  • incubation medium: YP
  • agar/liquid: agar
  • incubation temperature: 30
  • incubation time: 3
  • incubation pH: 6.00
  • system: MIS MIDI
  • method/protocol: Miller 1982

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
64841-+/-+/-+/--++/----++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
64841+---+---------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperature
25168forest soilDinghushan Biosphere Reserve, Guangdong ProvinceChinaCHNAsia23112MM1F0.04 g MgSO4.7H2O l-1, 0.5 g fructose l-1, 0.02 g CaCl.2H2O l-1, 0.05 g yeast extract l-1, 15.0 g agar l-1, pH 7.07 days28
64841forest soil samplesGuangdong Province, Dinghushan Biosphere Reserve (23° 10' N, 112° 31' E)ChinaCHNAsia23.1667112.517

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Forest
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_150926.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_634;96_57292;97_74089;98_99722;99_150926&stattab=map
  • Last taxonomy: Aliidongia dinghuensis subclade
  • 16S sequence: KX426600
  • Sequence Identity:
  • Total samples: 6677
  • soil counts: 5239
  • aquatic counts: 466
  • animal counts: 245
  • plant counts: 727

Safety information

risk assessment

  • @ref: 64841
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 25168
  • description: Rhodospirillum sp. 7M-Z19 16S ribosomal RNA gene, partial sequence
  • accession: KX426600
  • length: 1447
  • database: nuccore
  • NCBI tax ID: 1867774

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Aliidongia dinghuensis CGMCC 1.15725GCA_014643535contigncbi1867774
66792Aliidongia dinghuensis strain CGMCC 1.157251867774.3wgspatric1867774

GC content

  • @ref: 25168
  • GC-content: 65.8
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes88.923yes
gram-positiveno98.237yes
anaerobicno99.118no
aerobicyes92.055yes
halophileno93.381no
spore-formingno90.361yes
glucose-utilyes92.523no
flagellatedno76.11no
thermophileno98.503yes
glucose-fermentno88.304no

External links

@ref: 64841

culture collection no.: NBRC 112240, KCTC 52134, CGMCC 1.15725, DSM 107831

straininfo link

  • @ref: 91415
  • straininfo: 400487

literature

  • topic: Phylogeny
  • Pubmed-ID: 27902218
  • title: Aliidongia dinghuensis gen. nov., sp. nov., a poly-beta-hydroxybutyrate-producing bacterium isolated from Pinus massoniana forest soil.
  • authors: Chen MH, Zhou XY, Ou FH, Xia F, Lv YY, Qiu LH
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001588
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Hydroxybutyrates/*metabolism, Phospholipids/chemistry, *Phylogeny, Pinus, Polyesters/*metabolism, RNA, Ribosomal, 16S/genetics, Rhodospirillaceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry
  • topic2: Metabolism

Reference

@idauthorstitledoi/urljournalpubmedcatalogue
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
25168M. H. Z. Chen, X. Y.,Ou, F. H.,Xia, F.,Lv, Y. Y.,Qiu, L. H.Aliidongia dinghuensis gen. nov., sp. nov., a poly-beta-hydroxybutyrate-producing bacterium isolated from Pinus massoniana forest soil10.1099/ijsem.0.001588IJSEM 67: 212-217 201727902218
64841Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-107831Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 107831)
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
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
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
91415Reimer, 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-ID400487.1