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BacDive ID 11061
Type strain
Culture col. no. DSM 17939 CCUG 52476 KCTC 19131 Gsoil 161 JCM 16926 JCM 15303 1 more
NCBI tax ID(s) 363861
Links
For citation purpose refer to the digital object identifier (doi) of the current version.

Archive

version 9.2 (current version):
version 9.2 (current version)

General

@ref: 7277

BacDive-ID: 11061

DSM-Number: 17939

keywords: 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, rod-shaped

description: Aeromicrobium panaciterrae DSM 17939 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil, ginseng field.

NCBI tax id

  • NCBI tax id: 363861
  • Matching level: species

strain history

@refhistory
7277<- Sung-Taik Lee <- Wan-Taek Im, Gsoil 161
67770W.-T. Im Gsoil 161.
67771<- ST Lee, KAIST

doi: 10.13145/bacdive11061.20241212.9.2

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Nocardioidaceae
  • genus: Aeromicrobium
  • species: Aeromicrobium panaciterrae
  • full scientific name: Aeromicrobium panaciterrae Cui et al. 2007

@ref: 7277

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Aeromicrobium

species: Aeromicrobium panaciterrae

full scientific name: Aeromicrobium panaciterrae Cui et al. 2007

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31948positive1-1.5 µm0.2-0.4 µmrod-shapedno
67771positive

colony morphology

@refcolony colorincubation periodmedium used
18408Daffodil yellow (1007)10-14 daysISP 2
18408Daffodil yellow (1007)10-14 daysISP 3
18408Daffodil yellow (1007)10-14 daysISP 4
18408Daffodil yellow (1007)10-14 daysISP 5
18408Daffodil yellow (1007)10-14 daysISP 6
18408Daffodil yellow (1007)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18408noISP 2
18408noISP 3
18408noISP 4
18408noISP 5
18408noISP 6
18408noISP 7

pigmentation

  • @ref: 31948
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7277R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: 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 water
7277GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
18408ISP 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
18408ISP 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:
18408ISP 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
18408ISP 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
18408ISP 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
18408ISP 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

culture temp

@refgrowthtypetemperature
7277positivegrowth28
18408positiveoptimum28
31948positivegrowth15-30
31948positiveoptimum22.5
67770positivegrowth28
67771positivegrowth30

culture pH

@refabilitytypepHPH range
31948positivegrowth5-8.5alkaliphile
31948positiveoptimum6.75

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31948aerobe
67771aerobe

spore formation

  • @ref: 31948
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31948NaClpositivegrowth0-3 %
31948NaClpositiveoptimum1.5 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3194830089acetate+carbon source
3194816449alanine+carbon source
3194817057cellobiose+carbon source
3194817234glucose+carbon source
3194817306maltose+carbon source
3194837684mannose+carbon source
3194817814salicin+carbon source
3194830031succinate+carbon source
3194817992sucrose+carbon source
6837928087glycogen-fermentation
6837917992sucrose-fermentation
6837917716lactose-fermentation
6837917306maltose-fermentation
6837916899D-mannitol-fermentation
6837965327D-xylose-fermentation
6837916988D-ribose-fermentation
6837917634D-glucose-fermentation
683795291gelatin-hydrolysis
683794853esculin-hydrolysis
6837917632nitrate-reduction

enzymes

@refvalueactivityec
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
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
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382valine arylamidase+
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
68379beta-glucosidase-3.2.1.21
68379pyrrolidonyl arylamidase-3.4.19.3
68382alpha-glucosidase-3.2.1.20
68382leucine arylamidase+3.4.11.1
68379gelatinase-
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
68379pyrazinamidase+3.5.1.B15

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18408-+-+-----+/----------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18408+++-++---+---------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7277soil, ginseng fieldPocheon ProvinceRepublic of KoreaKORAsia
67770Soil of a ginseng fieldPocheon ProvinceRepublic of KoreaKORAsia
67771From soil of the ginseng soilRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
184081German classification
72771Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7277
  • description: Aeromicrobium panaciterrae gene for 16S rRNA, partial sequence, strain: Gsoil 161
  • accession: AB245387
  • length: 1470
  • database: nuccore
  • NCBI tax ID: 363861

GC content

@refGC-contentmethod
727765.5
6777065.5high performance liquid chromatography (HPLC)

External links

@ref: 7277

culture collection no.: DSM 17939, CCUG 52476, KCTC 19131, Gsoil 161, JCM 16926, JCM 15303

straininfo link

  • @ref: 80310
  • straininfo: 302748

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17392187Aeromicrobium panaciterrae sp. nov., isolated from soil of a ginseng field in South Korea.Cui YS, Im WT, Yin CR, Lee JS, Lee KC, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.64697-02007Actinomycetales/*classification/genetics/*isolation & purification, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Korea, Molecular Sequence Data, Panax/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyGenetics
Phylogeny18676469Aeromicrobium flavum sp. nov., isolated from air.Tang Y, Zhou G, Zhang L, Mao J, Luo X, Wang M, Fang CInt J Syst Evol Microbiol10.1099/ijs.0.65443-02008Actinomycetales/*classification/genetics/isolation & purification/physiology, *Air Microbiology, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7277Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17939)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17939
18408Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM17939.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
31948Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2820428776041
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
80310Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID302748.1StrainInfo: A central database for resolving microbial strain identifiers

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