Strain identifier
BacDive ID: 11088
Type strain:
Species: Nocardioides scoriae
Strain Designation: Sco-D01
Strain history: S. D. Lee Sco-D01.
NCBI tax ID(s): 642780 (species)
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
@ref | history |
---|---|
16147 | <- S. D. Lee, Jeju National Univ., Rep. of Korea; Sco-D01 |
67770 | S. 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
@ref | colony color | incubation period | medium used |
---|---|---|---|
19799 | Maize yellow | 10-14 days | ISP 2 |
19799 | Beige | 10-14 days | ISP 3 |
19799 | Beige | 10-14 days | ISP 4 |
19799 | Light ivory | 10-14 days | ISP 5 |
19799 | Sand yellow | 10-14 days | ISP 6 |
19799 | Oxide red | 10-14 days | ISP 7 |
multicellular morphology
@ref | forms multicellular complex | medium name |
---|---|---|
19799 | no | ISP 2 |
19799 | no | ISP 3 |
19799 | no | ISP 4 |
19799 | no | ISP 5 |
19799 | no | ISP 6 |
19799 | no | ISP 7 |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
16147 | GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) | yes | https://mediadive.dsmz.de/medium/65 | Name: 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 |
19799 | ISP 2 | yes | Name: 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 | |
19799 | ISP 3 | yes | Name: 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: | |
19799 | ISP 4 | yes | Name: 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 | |
19799 | ISP 5 | yes | Name: 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 | |
19799 | ISP 6 | yes | Name: 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 | |
19799 | ISP 7 | yes | Name: 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 | |
16147 | TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) | yes | https://mediadive.dsmz.de/medium/535 | Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
16147 | positive | growth | 28 | mesophilic |
19799 | positive | optimum | 28 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
spore formation
- @ref: 69480
- spore formation: no
- confidence: 98.029
observation
- @ref: 67770
- observation: quinones: MK-8(H4)
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity |
---|---|---|---|
19799 | 62968 | cellulose | +/- |
19799 | 16634 | raffinose | +/- |
19799 | 26546 | rhamnose | +/- |
19799 | 28757 | fructose | +/- |
19799 | 29864 | mannitol | +/- |
19799 | 17268 | myo-inositol | +/- |
19799 | 18222 | xylose | +/- |
19799 | 17992 | sucrose | +/- |
19799 | 22599 | arabinose | +/- |
19799 | 17234 | glucose | +/- |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | - | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | + | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | + | |
68382 | cystine arylamidase | + | 3.4.11.3 |
68382 | trypsin | + | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
19799 | + | - | + | + | + | + | + | + | - | + | + | - | - | - | + | + | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
16147 | volcanic ash | Jeju Island, Oreum (a parasitic volcano) | Republic of Korea | KOR | Asia |
67770 | Volcanic ash | Jeju | Republic of Korea | KOR | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Marmoricola scoriae DSM 22127 | GCA_900104965 | chromosome | ncbi | 642780 |
66792 | Marmoricola scoriae strain DSM 22127 | 642780.3 | complete | patric | 642780 |
66792 | Marmoricola scoriae DSM 22127 | 2634166904 | draft | img | 642780 |
GC content
@ref | GC-content | method |
---|---|---|
16147 | 72.0 | high performance liquid chromatography (HPLC) |
67770 | 72 | high performance liquid chromatography (HPLC) |
67770 | 73.5 | genome sequence analysis |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 53 | no |
gram-positive | yes | 92.425 | no |
anaerobic | no | 98.882 | no |
halophile | no | 95.648 | no |
spore-forming | no | 83.578 | no |
glucose-util | yes | 90.129 | no |
thermophile | no | 98.088 | no |
flagellated | no | 95.353 | no |
aerobic | yes | 93.71 | no |
motile | no | 74.121 | no |
glucose-ferment | no | 89.668 | no |
External links
@ref: 16147
culture collection no.: DSM 22127, KCTC 19597, JCM 17444
straininfo link
- @ref: 80337
- straininfo: 396522
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 19880634 | Marmoricola scoriae sp. nov., isolated from volcanic ash. | Lee DW, Lee SD | Int J Syst Evol Microbiol | 10.1099/ijs.0.018242-0 | 2009 | Actinomycetales/*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/*analysis | Metabolism |
Phylogeny | 20693360 | Marmoricola korecus sp. nov. | Lee SD, Lee DW, Ko YH | Int J Syst Evol Microbiol | 10.1099/ijs.0.025460-0 | 2010 | Actinomycetales/*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 Eruptions | Genetics |
Phylogeny | 25754550 | Marmoricola 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 SW | Int J Syst Evol Microbiol | 10.1099/ijs.0.000184 | 2015 | Actinomycetales/*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/chemistry | Genetics |
Phylogeny | 25805631 | Nocardioides echinoideorum sp. nov., isolated from sea urchins (Tripneustes gratilla). | Lin SY, Wen CZ, Hameed A, Liu YC, Hsu YH, Shen FT, Lai WA, Young CC | Int J Syst Evol Microbiol | 10.1099/ijs.0.000206 | 2015 | Actinomycetales/*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/chemistry | Enzymology |
Reference
@id | authors | catalogue | doi/url | title |
---|---|---|---|---|
16147 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22127) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-22127 | |
19799 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM22127.pdf | Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig | |
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
68382 | Automatically annotated from API zym | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |
80337 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID396522.1 | StrainInfo: A central database for resolving microbial strain identifiers |