Strain identifier

BacDive ID: 11088

Type strain: Yes

Species: Nocardioides scoriae

Strain Designation: Sco-D01

Strain history: S. D. Lee Sco-D01.

NCBI tax ID(s): 642780 (species)

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

@ref: 16147

BacDive-ID: 11088

DSM-Number: 22127

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

description: Nocardioides scoriae Sco-D01 is a mesophilic, Gram-positive bacterium that was isolated from volcanic ash.

NCBI tax id

  • NCBI tax id: 642780
  • Matching level: species

strain history

@refhistory
16147<- S. D. Lee, Jeju National Univ., Rep. of Korea; Sco-D01
67770S. D. Lee Sco-D01.

doi: 10.13145/bacdive11088.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Nocardioidaceae
  • genus: Nocardioides
  • species: Nocardioides scoriae
  • full scientific name: Nocardioides scoriae (Lee and Lee 2010) Wang et al. 2023
  • synonyms

    • @ref: 20215
    • synonym: Marmoricola scoriae

@ref: 16147

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Marmoricola

species: Marmoricola scoriae

full scientific name: Marmoricola scoriae Lee and Lee 2010 emend. Nouioui et al. 2018

strain designation: Sco-D01

type strain: yes

Morphology

cell morphology

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

colony morphology

@refcolony colorincubation periodmedium used
19799Maize yellow10-14 daysISP 2
19799Beige10-14 daysISP 3
19799Beige10-14 daysISP 4
19799Light ivory10-14 daysISP 5
19799Sand yellow10-14 daysISP 6
19799Oxide red10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19799noISP 2
19799noISP 3
19799noISP 4
19799noISP 5
19799noISP 6
19799noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16147GYM 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
19799ISP 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
19799ISP 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:
19799ISP 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
19799ISP 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
19799ISP 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
19799ISP 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
16147TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
16147positivegrowth28mesophilic
19799positiveoptimum28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 98.029

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activity
1979962968cellulose+/-
1979916634raffinose+/-
1979926546rhamnose+/-
1979928757fructose+/-
1979929864mannitol+/-
1979917268myo-inositol+/-
1979918222xylose+/-
1979917992sucrose+/-
1979922599arabinose+/-
1979917234glucose+/-

enzymes

@refvalueactivityec
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 zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19799+-++++++-++---++---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
16147volcanic ashJeju Island, Oreum (a parasitic volcano)Republic of KoreaKORAsia
67770Volcanic ashJejuRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Dust
#Environmental#Terrestrial#Volcanic

Safety information

risk assessment

  • @ref: 16147
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16147
  • description: Marmoricola scoriae partial 16S rRNA gene, type strain Sco-D01T
  • accession: FN386750
  • length: 1425
  • database: ena
  • NCBI tax ID: 642780

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Marmoricola scoriae DSM 22127GCA_900104965chromosomencbi642780
66792Marmoricola scoriae strain DSM 22127642780.3completepatric642780
66792Marmoricola scoriae DSM 221272634166904draftimg642780

GC content

@refGC-contentmethod
1614772.0high performance liquid chromatography (HPLC)
6777072high performance liquid chromatography (HPLC)
6777073.5genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno53no
gram-positiveyes92.425no
anaerobicno98.882no
halophileno95.648no
spore-formingno83.578no
glucose-utilyes90.129no
thermophileno98.088no
flagellatedno95.353no
aerobicyes93.71no
motileno74.121no
glucose-fermentno89.668no

External links

@ref: 16147

culture collection no.: DSM 22127, KCTC 19597, JCM 17444

straininfo link

  • @ref: 80337
  • straininfo: 396522

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19880634Marmoricola scoriae sp. nov., isolated from volcanic ash.Lee DW, Lee SDInt J Syst Evol Microbiol10.1099/ijs.0.018242-02009Actinomycetales/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Geologic Sediments/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Volcanic Eruptions/*analysisMetabolism
Phylogeny20693360Marmoricola korecus sp. nov.Lee SD, Lee DW, Ko YHInt J Syst Evol Microbiol10.1099/ijs.0.025460-02010Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Lipids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry, *Volcanic EruptionsGenetics
Phylogeny25754550Marmoricola solisilvae sp. nov. and Marmoricola terrae sp. nov., isolated from soil and emended description of the genus Marmoricola.Kim SJ, Lim JM, Hamada M, Ahn JH, Weon HY, Suzuki KI, Ahn TY, Kwon SWInt J Syst Evol Microbiol10.1099/ijs.0.0001842015Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Forests, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Soil, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny25805631Nocardioides echinoideorum sp. nov., isolated from sea urchins (Tripneustes gratilla).Lin SY, Wen CZ, Hameed A, Liu YC, Hsu YH, Shen FT, Lai WA, Young CCInt J Syst Evol Microbiol10.1099/ijs.0.0002062015Actinomycetales/*classification/genetics/isolation & purification, Animals, Bacteria, Aerobic/classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sea Urchins/*microbiology, Seafood/*microbiology, Sequence Analysis, DNA, Taiwan, Vitamin K 2/analogs & derivatives/chemistryEnzymology

Reference

@idauthorscataloguedoi/urltitle
16147Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22127)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22127
19799Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM22127.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
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/
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)
80337Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID396522.1StrainInfo: A central database for resolving microbial strain identifiers