Strain identifier

BacDive ID: 1776

Type strain: Yes

Species: Georgenia soli

Strain Designation: CC-NMPT-T3

Strain history: CCM 7658 <-- P. Kämpfer CC-NMPT-T3.

NCBI tax ID(s): 638953 (species)

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General

@ref: 15981

BacDive-ID: 1776

DSM-Number: 21838

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-positive, coccus-shaped

description: Georgenia soli CC-NMPT-T3 is an aerobe, Gram-positive, coccus-shaped bacterium that was isolated from iron-ore-contaminated soil.

NCBI tax id

  • NCBI tax id: 638953
  • Matching level: species

strain history

@refhistory
15981<- P. Kämpfer, Univ. Giessen, Germany; CC-NMPT-T3
67770CCM 7658 <-- P. Kämpfer CC-NMPT-T3.

doi: 10.13145/bacdive1776.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Bogoriellaceae
  • genus: Georgenia
  • species: Georgenia soli
  • full scientific name: Georgenia soli Kämpfer et al. 2010

@ref: 15981

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Bogoriellaceae

genus: Georgenia

species: Georgenia soli

full scientific name: Georgenia soli Kämpfer et al. 2010

strain designation: CC-NMPT-T3

type strain: yes

Morphology

cell morphology

@refgram staincell widthcell shapeconfidence
29525positive1.25 µmcoccus-shaped
69480positive93.196

colony morphology

@refcolony colorincubation periodmedium used
21362Lemon yellow (1012)10-14 daysISP 2
2136210-14 daysISP 3
2136210-14 daysISP 4
21362Ivory (1014)10-14 daysISP 5
21362Ivory (1014)10-14 daysISP 7
21362Ivory (1014)10-14 dayssuter with tyrosine
21362Green beige (1000)10-14 dayssuter without tyrosine
614332 days

multicellular morphology

@refforms multicellular complexmedium name
21362noISP 2
21362noISP 3
21362noISP 4
21362noISP 5
21362noISP 7
21362noSuter with tyrosine
21362noSuter without tyrosine

Culture and growth conditions

culture medium

@refnamegrowthcomposition
21362ISP 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
21362ISP 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
21362ISP 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
21362suter with tyrosineyesName: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes
21362suter without tyrosineyesName: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes
21362ISP 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
21362ISP 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:

culture temp

@refgrowthtypetemperature
29525positivegrowth25-30
61433positivegrowth30
67770positivegrowth28

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29525aerobe
61433aerobe

halophily

  • @ref: 21362
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 7.5 %

murein

  • @ref: 15981
  • murein short key: A11.54
  • type: A4alpha L-Lys-L-Glu

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2136217234glucose+
2136222599arabinose-
2136217992sucrose-
2136218222xylose-
2136217268myo-inositol-
2136237684mannose-
2136228757fructose-
2136226546rhamnose-
2136216634raffinose-
2136262968cellulose+
2952533942ribose+carbon source
2952517814salicin+carbon source
2952518222xylose+carbon source
6837917632nitrate+reduction
683794853esculin+hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose+fermentation
6837916988D-ribose+fermentation
6837916899D-mannitol-fermentation
6837917306maltose+fermentation
6837917716lactose+fermentation
6837917992sucrose+fermentation
6837928087glycogen+fermentation

enzymes

@refvalueactivityec
29525catalase+1.11.1.6
29525cytochrome oxidase+1.9.3.1
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+
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
21362++------++/-++++/--++++

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
21362+++-++---++-+++-+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15981iron-ore-contaminated soilKarnataka, New Mangalore PortIndiaINDAsia
61433Soil,ore contaminatedKarnataka,near New Mangalore PortIndiaINDAsia
67770Iron-ore-contaminated soil near New Mangalore PortKarnatakaIndiaINDAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_87962.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_948;97_1103;98_1314;99_87962&stattab=map
  • Last taxonomy: Georgenia soli
  • 16S sequence: FN356976
  • Sequence Identity:
  • Total samples: 862
  • soil counts: 625
  • aquatic counts: 70
  • animal counts: 112
  • plant counts: 55

Safety information

risk assessment

  • @ref: 15981
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15981
  • description: Georgenia soli partial 16S rRNA gene, type strain CC-NMPT-T3T
  • accession: FN356976
  • length: 1483
  • database: nuccore
  • NCBI tax ID: 638953

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Georgenia soli strain DSM 21838638953.3wgspatric638953
66792Georgenia soli DSM 218382627854285draftimg638953
67770Georgenia soli DSM 21838GCA_002563695contigncbi638953

GC content

  • @ref: 67770
  • GC-content: 72.7
  • method: genome sequence analysis

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno87no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes93.196yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no94.746yes
69480spore-formingspore-formingAbility to form endo- or exosporesno65.983no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes82.864yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno95.909yes
69480flagellatedmotile2+Ability to perform flagellated movementno84.5no

External links

@ref: 15981

culture collection no.: DSM 21838, CCM 7658, NBRC 107791, CCUG 57735, JCM 17968

straininfo link

  • @ref: 71423
  • straininfo: 411819

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19666812Georgenia soli sp. nov., isolated from iron-ore-contaminated soil in India.Kampfer P, Arun AB, Busse HJ, Langer S, Young CC, Chen WM, Schumann P, Syed AA, Rekha PDInt J Syst Evol Microbiol10.1099/ijs.0.014902-02009Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, India, *Iron, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Soil Pollutants, Species SpecificityGenetics
Phylogeny21930682Georgenia daeguensis sp. nov., isolated from 4-chlorophenol enrichment culture.Woo SG, Cui Y, Kang MS, Jin L, Kim KK, Lee ST, Lee M, Park JInt J Syst Evol Microbiol10.1099/ijs.0.033217-02011Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Bacterial Typing Techniques, Base Composition, Carbohydrates/analysis, Chlorophenols/*metabolism, Cluster Analysis, Culture Media/chemistry, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiologyMetabolism
Phylogeny26303654Georgenia subflava sp. nov., isolated from a deep-sea sediment.Wang S, Xu X, Wang L, Jiao K, Zhang GInt J Syst Evol Microbiol10.1099/ijsem.0.0005532015Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
15981Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21838)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21838
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
21362Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM21383.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
29525Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2592228776041
61433Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 57735)https://www.ccug.se/strain?id=57735
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
71423Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID411819.1StrainInfo: A central database for resolving microbial strain identifiers