Strain identifier

BacDive ID: 133065

Type strain: Yes

Species: Arthrobacter ginkgonis

Strain Designation: SYP-A7299

Strain history: Y.-X. Zhang; Shenyang Pharm. Univ., China; SYP-A7299.

NCBI tax ID(s): 1630594 (species)

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General

@ref: 24853

BacDive-ID: 133065

DSM-Number: 100491

keywords: 16S sequence, Bacteria, aerobe, Gram-positive, colony-forming

description: Arthrobacter ginkgonis SYP-A7299 is an aerobe, Gram-positive bacterium that forms circular colonies and was isolated from rhizosphere soil from Ginkgo biloba L..

NCBI tax id

  • NCBI tax id: 1630594
  • Matching level: species

strain history

@refhistory
24853<- Y. Zhang, Shenyang Pharmaceutical Univ., China; SYP-A7299 <- H. Xu
67770Y.-X. Zhang; Shenyang Pharm. Univ., China; SYP-A7299.

doi: 10.13145/bacdive133065.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Micrococcaceae
  • genus: Arthrobacter
  • species: Arthrobacter ginkgonis
  • full scientific name: Arthrobacter ginkgonis Cheng et al. 2017

@ref: 24853

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Arthrobacter

species: Arthrobacter ginkgonis

full scientific name: Arthrobacter ginkgonis Cheng et al. 2017

strain designation: SYP-A7299

type strain: yes

Morphology

cell morphology

  • @ref: 25173
  • gram stain: positive
  • motility: no

colony morphology

  • @ref: 25173
  • colony color: yellow
  • colony shape: circular
  • medium used: R2A medium

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
25173R2A mediumyes
24853TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
25173positivegrowth20.0-35.0
25173positiveoptimum28mesophilic
24853positivegrowth28mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
25173positivegrowth6.0-10.0alkaliphile
25173positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 25173
  • oxygen tolerance: aerobe

spore formation

  • @ref: 25173
  • spore formation: no

halophily

@refsalttested relationconcentrationgrowth
25173NaCloptimum0 %
25173NaClgrowth0.0-4.0 %(w/v)positive

murein

  • @ref: 24853
  • murein short key: A11.35
  • type: A4alpha L-Lys-L-Ala-L-Glu

observation

  • @ref: 67770
  • observation: quinones: MK-8(H2), MK-9(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2517317128adipate-carbon source
2517336219alpha-lactose-carbon source
2517373706bromosuccinate-carbon source
2517317057cellobiose-carbon source
2517362968cellulose-fermentation
2517318333D-arabitol-carbon source
2517316899D-mannitol-carbon source
2517316024D-mannose-carbon source
2517316523D-serine-carbon source
251734853esculin-fermentation
251735291gelatin-fermentation
2517330849L-arabinose-carbon source
25173506227N-acetylglucosamine-carbon source
2517317632nitrate-reduction
2517316634raffinose-carbon source
2517317164stachyose-carbon source
2517327897tryptophan-energy source
2517353424tween 20-fermentation
2517353423tween 40-fermentation
2517353425tween 60-fermentation
2517353426tween 80-fermentation
2517316199urea-fermentation
2517317521(-)-quinic acid+carbon source
2517315588D-malate+carbon source
2517316651(S)-lactate+carbon source
2517315589L-malate+carbon source
25173645522-hydroxybutyrate+carbon source
25173167632-oxobutanoate+carbon source
25173309162-oxoglutarate+carbon source
25173370543-hydroxybutyrate+carbon source
25173739183-O-methyl-D-glucose+carbon source
25173181014-hydroxyphenylacetic acid+carbon source
2517330089acetate+carbon source
2517313705acetoacetate+carbon source
2517317925alpha-D-glucose+carbon source
2517316947citrate+carbon source
2517329990D-aspartate+carbon source
2517315824D-fructose+carbon source
2517378697D-fructose 6-phosphate+carbon source
2517328847D-fucose+carbon source
2517315895D-galactonic acid lactone+carbon source
2517312936D-galactose+carbon source
2517318024D-galacturonic acid+carbon source
2517330612D-glucarate+carbon source
251738391D-gluconate+carbon source
2517314314D-glucose 6-phosphate+carbon source
2517315748D-glucuronate+carbon source
2517315740formate+carbon source
2517316537galactarate+carbon source
2517316865gamma-aminobutyric acid+carbon source
2517328066gentiobiose+carbon source
2517332323glucuronamide+carbon source
2517317754glycerol+carbon source
2517370744glycine-proline+carbon source
2517316977L-alanine+carbon source
2517329991L-aspartate+carbon source
2517318287L-fucose+carbon source
2517329985L-glutamate+carbon source
2517318183L-pyroglutamic acid+carbon source
2517362345L-rhamnose+carbon source
2517390603L-serine 2-naphthylamide+carbon source
2517317306maltose+carbon source
2517374611methyl (R)-lactate+carbon source
2517328037N-acetylgalactosamine+carbon source
2517317309pectin+carbon source
2517332032potassium gluconate+carbon source
2517317272propionate+carbon source
2517317992sucrose+carbon source
2517327082trehalose+carbon source
2517332528turanose+carbon source

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitiveis resistant
25173161680aztreonamyesyes
251736472lincomycinyesyes
2517348607lithium chlorideyesyes
2517345735troleandomycinyesyes
2517371321fusidateyesyes
2517332735guanidinium chlorideyesyes
2517350694minocyclineyesyes
2517375273niaproofyesyes
2517328077rifampicinyesyes
2517316523d-serineyesyes
2517328001vancomycinyesyes
2517375229sodium bromateyesyes

metabolite production

@refChebi-IDmetaboliteproduction
2517335581indoleno
2517316136hydrogen sulfideyes

metabolite tests

  • @ref: 25173
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
25173acid phosphatase+3.1.3.2
25173alkaline phosphatase+3.1.3.1
25173alpha-chymotrypsin-3.4.21.1
25173alpha-fucosidase-3.2.1.51
25173alpha-galactosidase-3.2.1.22
25173alpha-glucosidase+3.2.1.20
25173alpha-mannosidase-3.2.1.24
25173arginine dihydrolase-3.5.3.6
25173beta-galactosidase-3.2.1.23
25173beta-glucosidase-3.2.1.21
25173beta-glucuronidase-3.2.1.31
25173catalase+1.11.1.6
25173cystine arylamidase+3.4.11.3
25173cytochrome oxidase-1.9.3.1
25173esterase (C 4)+
25173esterase Lipase (C 8)+
25173leucine arylamidase+3.4.11.1
25173lipase (C 14)+
25173N-acetyl-beta-glucosaminidase-3.2.1.52
25173naphthol-AS-BI-phosphohydrolase-
25173trypsin-3.4.21.4
25173tryptophan deaminase-4.1.99.1
25173valine arylamidase+

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    25173C15:0 anteiso59
    25173C17:0 anteiso9.5
    25173C16:03
    25173C15:0 iso13.2
    25173C16:0 iso7.8
    25173C17:0 iso3.4
  • type of FA analysis: whole cell analysis
  • incubation medium: tryptone soy agar (TSA; Difco)
  • agar/liquid: agar
  • incubation temperature: 28
  • incubation time: 3
  • software version: Sherlock 6.1
  • library/peak naming table: TSBA 6
  • system: MIS MIDI
  • method/protocol: Sasser 1990
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture compositionisolation procedure
24853rhizosphere soil from Ginkgo biloba L.Ginkgo bilobaLiaoning Province, Dandong (40° 41' 31.2'' N 124° 33' 46.1'' E)ChinaCHNAsia40.692124.563
25173root of Ginkgo biloba L.R2A mediumyeast extract 0.5 g, proteose peptone 0.5 g, Casamino acids 0.5 g, glucose 0.5 g, soluble starch 0.5 g, sodium pyruvate 0.3 g, K2HPO4 0.3 g, MgSO4.7H2O 0.05 g, agar 15 g, distilled water 1000 mlserial dilution plating
67770Rhizosphere of Ginkgo biloba L. from DandongGinkgo bilobaLiaoning ProvinceChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Host Body-Site#Plant#Rhizosphere
#Host#Plants#Tree

taxonmaps

  • @ref: 69479
  • File name: preview.99_151937.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_158;97_5075;98_20239;99_151937&stattab=map
  • Last taxonomy: Arthrobacter ginkgonis subclade
  • 16S sequence: KP128918
  • Sequence Identity:
  • Total samples: 2268
  • soil counts: 1548
  • aquatic counts: 111
  • animal counts: 185
  • plant counts: 424

Safety information

risk assessment

  • @ref: 24853
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24853
  • description: Arthrobacter ginkgonis strain SYP-A7299 16S ribosomal RNA gene, partial sequence
  • accession: KP128918
  • length: 1545
  • database: ena
  • NCBI tax ID: 1630594

GC content

  • @ref: 24853
  • GC-content: 68.9
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 24853

culture collection no.: DSM 100491, KCTC 39592, JCM 30742

straininfo link

  • @ref: 91330
  • straininfo: 399848

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27902303Arthrobacter ginkgonis sp. nov., an actinomycete isolated from rhizosphere of Ginkgo biloba L.Cheng J, Zhang MY, Zhao JC, Xu H, Zhang Y, Zhang TY, Wu YY, Zhang YXInt J Syst Evol Microbiol10.1099/ijsem.0.0016232017Arthrobacter/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Ginkgo biloba/*microbiology, Glycolipids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistryTranscriptome
Phylogeny29099354Arthrobacter paludis sp. nov., isolated from a marsh.Zhang Q, Oh M, Kim JH, Kanjanasuntree R, Konkit M, Sukhoom A, Kantachote D, Kim WInt J Syst Evol Microbiol10.1099/ijsem.0.0024262017Arthrobacter/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, *WetlandsTranscriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
24853Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100491Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100491)
25173J. Z. Cheng, M. Y.,Zhao, J. C.,Xu, H.,Zhang, Y.,Zhang, T. Y.,Wu, Y. Y.,Zhang, Y. X.Arthrobacter ginkgonis sp. nov., an actinomycete isolated from rhizosphere of Ginkgo biloba L10.1099/ijsem.0.001623IJSEM 67: 319-324 201727902303
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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/
91330Reimer, 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-ID399848.1