Strain identifier

BacDive ID: 7790

Type strain: Yes

Species: Sinomonas atrocyanea

Strain Designation: A 9.2, A9.2

Strain history: CIP <- 1986, DSM, Arthrobacter atrocyaneus <- ATCC <- M.P. Starr: strain A9.2

NCBI tax ID(s): 37927 (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 1:
version 8.1 (current version)

General

@ref: 8552

BacDive-ID: 7790

DSM-Number: 20127

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-positive

description: Sinomonas atrocyanea A 9.2 is a mesophilic, Gram-positive bacterium that was isolated from air.

NCBI tax id

  • NCBI tax id: 37927
  • Matching level: species

strain history

@refhistory
8552<- ATCC <- M.P. Starr, A 9.2
67770IAM 12339 <-- CCM 1645 <-- MRI.
116540CIP <- 1986, DSM, Arthrobacter atrocyaneus <- ATCC <- M.P. Starr: strain A9.2

doi: 10.13145/bacdive7790.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Micrococcaceae
  • genus: Sinomonas
  • species: Sinomonas atrocyanea
  • full scientific name: Sinomonas atrocyanea (Kuhn and Starr 1960) Zhou et al. 2009

  • synonyms

    • @ref: 20215
    • synonym: Arthrobacter atrocyaneus

@ref: 8552

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Sinomonas

species: Sinomonas atrocyanea

full scientific name: Sinomonas atrocyanea (Kuhn and Starr 1960) Zhou et al. 2009 emend. Nouioui et al. 2018

strain designation: A 9.2, A9.2

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 100

colony morphology

@refcolony colorincubation periodmedium used
19789Ivory (1014)10-14 daysISP 2
19789Sulfur white (1016)10-14 daysISP 3
19789Oyster white (1013)10-14 daysISP 4
19789Rapeseed yellow (1021)10-14 daysISP 5
19789Honey yellow (1005)10-14 daysISP 6
19789Colorless10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19789noISP 2
19789noISP 3
19789noISP 4
19789noISP 5
19789noISP 6
19789noISP 7

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
19789ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
19789ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
19789ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
19789ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
19789ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
19789ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
37385MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
8552CORYNEBACTERIUM AGAR (DSMZ Medium 53)yesName: CORYNEBACTERIUM AGAR (DSMZ Medium 53) Composition: Agar 15.0 g/l Casein peptone 10.0 g/l NaCl 5.0 g/l Glucose 5.0 g/l Yeast extract 5.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/53
116540CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
19789positiveoptimum28mesophilic
8552positivegrowth30mesophilic
37385positivegrowth30mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no96
69480no99.822

compound production

  • @ref: 19789
  • compound: Indigoidin

murein

  • @ref: 8552
  • murein short key: A11.22
  • type: A3alpha L-Lys-L-Ser-L-Ala2-3; alpha-carboxyl group of D-Glu substituted by glycine amide

observation

  • @ref: 67770
  • observation: quinones: MK-9(H2), MK-8(H2) (7:1)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1978962968cellulose-
1978916634raffinose-
1978926546rhamnose-
1978928757fructose-
1978929864mannitol-
1978917268myo-inositol-
1978918222xylose-
1978917992sucrose-
1978922599arabinose-
1978917234glucose-
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate+assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea+hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose+fermentation
6837916988D-ribose+fermentation
6837965327D-xylose+fermentation
6837916899D-mannitol+fermentation
6837917306maltose+fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-

enzymes

@refvalueactivityec
68379gelatinase+
68379urease+3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase+3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase+3.2.1.31
68379alkaline phosphatase-3.1.3.1
68379pyrrolidonyl arylamidase+3.4.19.3
68379pyrazinamidase-3.5.1.B15
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase-3.2.1.23
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)-
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
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

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19789--+-++++-+++++++---

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19789--+-++++-+++++++---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19789----+----+-

Isolation, sampling and environmental information

isolation

@refsample type
8552air
67770Air
116540Environment, Air contaminant of laboratory

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Air

taxonmaps

  • @ref: 69479
  • File name: preview.99_7227.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_3294;97_4040;98_5304;99_7227&stattab=map
  • Last taxonomy: Sinomonas
  • 16S sequence: X80746
  • Sequence Identity:
  • Total samples: 3115
  • soil counts: 1972
  • aquatic counts: 434
  • animal counts: 554
  • plant counts: 155

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
85521Risk group (German classification)
197891Hazard group
1165401Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218A.atrocyaneus 16S rDNAX807461472ena37927
8552Sinomonas atrocyanea strain DSM 20127 16S ribosomal RNA gene, partial sequenceEU6973881404ena37927

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sinomonas atrocyanea KCTC 3377GCA_001577305completencbi37927
66792Sinomonas atrocyanea CGMCC 1.1891GCA_014644475scaffoldncbi37927
66792Sinomonas atrocyanea strain CGMCC 1.189137927.6wgspatric37927
66792Sinomonas atrocyanea strain KCTC 337737927.4plasmidpatric37927
66792Sinomonas atrocyanea strain NBRC 1295637927.5wgspatric37927
66792Sinomonas atrocyanea KCTC 33772684622557completeimg37927
67770Sinomonas atrocyanea NBRC 12956GCA_006539205contigncbi37927

GC content

@refGC-contentmethod
855270.3high performance liquid chromatography (HPLC)
855269.5
6777070.5Buoyant density centrifugation (BD)
6777069.5thermal denaturation, midpoint method (Tm)
6777071.4genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno96no
flagellatedno93.37no
gram-positiveyes90.062no
anaerobicno99.489no
aerobicyes95.073no
halophileno90.361no
spore-formingno84.583no
thermophileno98.58yes
glucose-utilyes75.482yes
motileno51.357no
glucose-fermentno78.934yes

External links

@ref: 8552

culture collection no.: DSM 20127, ATCC 13752, CCM 1645, CGMCC 1.1891, JCM 1329, NCIB 9220, BCRC 10953, CCUG 23838, CCUG 23884, CDA 852, CIP 102365, IAM 12339, IFO 12670, IFO 12956, IMET 10432, KCCM 41106, KCTC 3377, LMG 3814, NBIMCC 2007, NBRC 12670, NBRC 12956, NCAIM B.02134, NCIMB 9220, NRRL B-4200, VKM Ac-1104

straininfo link

  • @ref: 77233
  • straininfo: 92120

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism16347639Degradation of the Phosphonate Herbicide Glyphosate by Arthrobacter atrocyaneus ATCC 13752.Pipke R, Amrhein NAppl Environ Microbiol10.1128/aem.54.5.1293-1296.19881988
Phylogeny19196763Proposal of Sinomonas flava gen. nov., sp. nov., and description of Sinomonas atrocyanea comb. nov. to accommodate Arthrobacter atrocyaneus.Zhou Y, Wei W, Wang X, Lai RInt J Syst Evol Microbiol10.1099/ijs.0.000695-02009Arthrobacter/*classification/genetics/growth & development, Micrococcaceae/*classification/genetics/growth & development, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Species SpecificityGenetics
Phylogeny21571934Description of Sinomonas soli sp. nov., reclassification of Arthrobacter echigonensis and Arthrobacter albidus (Ding et al. 2009) as Sinomonas echigonensis comb. nov. and Sinomonas albida comb. nov., respectively, and emended description of the genus Sinomonas.Zhou Y, Chen X, Zhang Y, Wang W, Xu JInt J Syst Evol Microbiol10.1099/ijs.0.030361-02011Amino Acids/chemistry, Arthrobacter/classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Micrococcaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Polycyclic Aromatic Hydrocarbons, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants, Trees/microbiology, Vitamin K 2/analogs & derivatives/chemistryEnzymology
Phylogeny25563924Sinomonas humi sp. nov., an amylolytic actinobacterium isolated from mangrove forest soil.Lee LH, Azman AS, Zainal N, Yin WF, Mutalib NA, Chan KGInt J Syst Evol Microbiol10.1099/ijs.0.0000532015Avicennia/*microbiology, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Glycolipids/chemistry, Malaysia, Micrococcaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny25589734Sinomonas susongensis sp. nov., isolated from the surface of weathered biotite.Bao YY, Huang Z, Mao DM, Sheng XF, He LYInt J Syst Evol Microbiol10.1099/ijs.0.0000642015*Aluminum Silicates, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Ferrous Compounds, Glycolipids/chemistry, Micrococcaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny26205207Sinomonas halotolerans sp. nov., an actinobacterium isolated from a soil sample.Guo QQ, Ming H, Meng XL, Huang JR, Duan YY, Li SH, Li S, Zhang JX, Li WJ, Nie GXAntonie Van Leeuwenhoek10.1007/s10482-015-0543-y2015Aerobiosis, Bacterial Typing Techniques, Base Composition, Carbohydrates/analysis, Cell Wall/chemistry, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Glycolipids/analysis, Hydrogen-Ion Concentration, Micrococcaceae/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Peptidoglycan/analysis, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, Temperature, VietnamGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8552Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20127)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20127
19789Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM20127.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
37385Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14043
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
68379Automatically annotated from API Coryne
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
77233Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92120.1StrainInfo: A central database for resolving microbial strain identifiers
116540Curators of the CIPCollection of Institut Pasteur (CIP 102365)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20102365