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Strain identifier

BacDive ID: 7269

Type strain: Yes

Species: Agromyces aurantiacus

Strain history: AS 4.1717 <-- C.-L. Jiang YIM 21741.

NCBI tax ID(s): 165814 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 5401

BacDive-ID: 7269

DSM-Number: 14598

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

description: Agromyces aurantiacus DSM 14598 is a mesophilic bacterium that was isolated from primeval forest soil.

NCBI tax id

  • NCBI tax id: 165814
  • Matching level: species

strain history

doi: 10.13145/bacdive7269.20221219.7.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Agromyces
  • species: Agromyces aurantiacus
  • full scientific name: Agromyces aurantiacus Li et al. 2003

@ref: 5401

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Agromyces

species: Agromyces aurantiacus

full scientific name: Agromyces aurantiacus Li et al. 2003

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 98.657

colony morphology

@refcolony colorincubation periodmedium used
18388Saffron yellow (1017)10-14 daysISP 2
18388Saffron yellow (1017)10-14 daysISP 3
18388Saffron yellow (1017)10-14 daysISP 4
18388Saffron yellow (1017)10-14 daysISP 5
18388Saffron yellow (1017)10-14 daysISP 6
18388Saffron yellow (1017)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18388noISP 2
18388noISP 3
18388noISP 4
18388noISP 5
18388noISP 6
18388noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5401ISP MEDIUM 2 WITH 5% NaCl (DSMZ Medium 636)yeshttps://mediadive.dsmz.de/medium/636Name: ISP MEDIUM 2 WITH 5% NaCl (DSMZ Medium 636; with strain-specific modifications) Composition: NaCl 50.0 g/l Agar 20.0 g/l Malt extract 10.0 g/l Dextrose 4.0 g/l Yeast extract 4.0 g/l Distilled water
18388ISP 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
18388ISP 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:
18388ISP 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
18388ISP 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
18388ISP 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
18388ISP 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
38247MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)

culture temp

@refgrowthtypetemperaturerange
18388positiveoptimum28mesophilic
5401positivegrowth28mesophilic
38247positivegrowth30mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 98.083

halophily

  • @ref: 69480
  • halophily level: non-halophilic
  • confidence: 94.68

observation

  • @ref: 67770
  • observation: quinones: MK-12, MK-13

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1838817234glucose+
1838822599arabinose+
1838817992sucrose+
1838818222xylose+/-
1838817268myo-inositol+/-
1838829864mannitol+
1838828757fructose+
1838826546rhamnose+
1838816634raffinose+
1838862968cellulose+
6837928087glycogen-fermentation
6837917992sucrose-fermentation
6837917716lactose-fermentation
6837917306maltose-fermentation
6837916899D-mannitol-fermentation
6837965327D-xylose-fermentation
6837916988D-ribose-fermentation
6837917634D-glucose-fermentation
683795291gelatin-hydrolysis
6837916199urea-hydrolysis
683794853esculin+hydrolysis
6837917632nitrate-reduction

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase+3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
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

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18388--+--++-+----------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18388-+--++++-++-+-++---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
5401primeval forest soilYunnan Province, XishuangbannaChinaCHNAsia
67770Soil from a primeval forestXishuangbanna, Yunnan ProvinceChinaCHNAsia

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
54011Risk group (German classification)
183881

Sequence information

16S sequences

  • @ref: 5401
  • description: Agromyces aurantiacus 16S ribosomal RNA gene, partial sequence
  • accession: AF389342
  • length: 1464
  • database: ena
  • NCBI tax ID: 165814

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Agromyces aurantiacus DSM 14598GCA_016907355contigncbi165814
66792Agromyces aurantiacus strain DSM 14598165814.3wgspatric165814
66792Agromyces aurantiacus DSM 145982893554490draftimg165814

GC content

@refGC-contentmethod
540172.8
6777072.8thermal denaturation, midpoint method (Tm)

External links

@ref: 5401

culture collection no.: DSM 14598, AS 4.1717, CCTCC 001012, YIM 21741, JCM 12113, BCRC 16310, CCTCC AA 001012, CGMCC 4.1717, CIP 107976, IAM 15154, KCTC 9967

straininfo link

@refpassport
20218http://www.straininfo.net/strains/301836
20218http://www.straininfo.net/strains/301834
20218http://www.straininfo.net/strains/301835
20218http://www.straininfo.net/strains/301837

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12656188Agromyces aurantiacus sp. nov., isolated from a Chinese primeval forest.Li WJ, Zhang LP, Xu P, Cui XL, Xu LH, Zhang Z, Schumann P, Stackebrandt E, Jiang CLInt J Syst Evol Microbiol10.1099/ijs.0.02350-02003Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Base Composition, China, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Microscopy, Electron, Scanning, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Soil MicrobiologyGenetics
Phylogeny20435752Agromyces tropicus sp. nov., isolated from soil.Thawai C, Tanasupawat S, Suwanborirux K, Kudo TInt J Syst Evol Microbiol10.1099/ijs.0.021774-02010Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, ThailandGenetics
Phylogeny20639226Agromyces soli sp. nov., isolated from farm soil.Lee M, Ten LN, Woo SG, Park JInt J Syst Evol Microbiol10.1099/ijs.0.021568-02010Actinomycetales/*classification/genetics/*isolation & purification/physiology, Aerobiosis, Amino Acids/analysis, Base Composition, Carbohydrates/analysis, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analysisGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5401Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14598)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14598
18388Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM14598.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
38247Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5546
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
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)