Strain identifier
BacDive ID: 16570
Type strain: 
Species: Nonomuraea rhizophila
Strain history: DSM 45382 <-- S.-K. Tang; Yunnan Inst. of Microbiol., Yunnan Univ., China; YIM 67092.
NCBI tax ID(s): 870477 (species)
version 8.1 (current version)
General
@ref: 16546
BacDive-ID: 16570
DSM-Number: 45382
keywords: 16S sequence, Bacteria, mesophilic
description: Nonomuraea rhizophila DSM 45382 is a mesophilic bacterium that was isolated from rhizosphere soil of the perennial vine Tripterygium wilfordii Hook. f..
NCBI tax id
- NCBI tax id: 870477
- Matching level: species
strain history
| @ref | history |
|---|---|
| 16546 | <- S.-K. Tang, Yunnan Univ., Kunming, Yunnan Inst. Microbiol. (YIM), China; YIM 67092 <- J. Li |
| 67770 | DSM 45382 <-- S.-K. Tang; Yunnan Inst. of Microbiol., Yunnan Univ., China; YIM 67092. |
doi: 10.13145/bacdive16570.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Streptosporangiales
- family: Streptosporangiaceae
- genus: Nonomuraea
- species: Nonomuraea rhizophila
- full scientific name: Nonomuraea rhizophila Zhao et al. 2011
@ref: 16546
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Streptosporangiaceae
genus: Nonomuraea
species: Nonomuraea rhizophila
full scientific name: Nonomuraea rhizophila Zhao et al. 2011
type strain: yes
Morphology
colony morphology
| @ref | colony color | incubation period | medium used |
|---|---|---|---|
| 21429 | Sand yellow (1002) | 10-14 days | ISP 2 |
| 21429 | Ivory (1014) | 10-14 days | ISP 3 |
| 21429 | Ivory (1014) | 10-14 days | ISP 4 |
| 21429 | Honey yellow (1005) | 10-14 days | ISP 5 |
| 21429 | Sand yellow (1002) | 10-14 days | ISP 6 |
| 21429 | Ochre yellow (1024) | 10-14 days | ISP 7 |
| 21429 | Honey yellow (1005) | 10-14 days | Suter with tyrosine |
| 21429 | Honey yellow (1005) | 10-14 days | Suter without tyrosine |
multimedia
- @ref: 16546
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45382.jpg
- caption: Medium 65 28°C
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 16546 | 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 |
| 16546 | ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium84.pdf | |
| 21429 | 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 | |
| 21429 | 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: | |
| 21429 | 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 | |
| 21429 | 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 | |
| 21429 | 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 | |
| 21429 | 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 | |
| 21429 | Suter with tyrosine | yes | Name: 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 | |
| 21429 | Suter without tyrosine | yes | Name: 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 |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 16546 | positive | growth | 28 | mesophilic |
| 67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
halophily
- @ref: 21429
- salt: NaCl
- growth: positive
- tested relation: maximum
- concentration: 2.5 %
observation
- @ref: 67770
- observation: quinones: MK-9(H4), MK-9(H6), MK-9(H2)
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 21429 | 17234 | glucose | + | |
| 21429 | 22599 | arabinose | + | |
| 21429 | 17992 | sucrose | + | |
| 21429 | 18222 | xylose | + | |
| 21429 | 17268 | myo-inositol | + | |
| 21429 | 37684 | mannose | + | |
| 21429 | 28757 | fructose | + | |
| 21429 | 26546 | rhamnose | + | |
| 21429 | 16634 | raffinose | + | |
| 21429 | 62968 | cellulose | - | |
| 68379 | 17632 | nitrate | - | reduction |
| 68379 | 4853 | esculin | + | hydrolysis |
| 68379 | 5291 | gelatin | + | hydrolysis |
| 68379 | 17634 | D-glucose | - | fermentation |
| 68379 | 16988 | D-ribose | - | fermentation |
| 68379 | 65327 | D-xylose | - | fermentation |
| 68379 | 16899 | D-mannitol | - | fermentation |
| 68379 | 17306 | maltose | - | fermentation |
| 68379 | 17716 | lactose | - | fermentation |
| 68379 | 17992 | sucrose | - | fermentation |
| 68379 | 28087 | glycogen | - | fermentation |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 68379 | gelatinase | + | |
| 68379 | beta-glucosidase | + | 3.2.1.21 |
| 68379 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
| 68379 | alpha-glucosidase | + | 3.2.1.20 |
| 68379 | beta-galactosidase | + | 3.2.1.23 |
| 68379 | beta-glucuronidase | - | 3.2.1.31 |
| 68379 | alkaline phosphatase | + | 3.1.3.1 |
| 68379 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
| 68379 | pyrazinamidase | - | 3.5.1.B15 |
| 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 | trypsin | + | 3.4.21.4 |
| 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 coryne
| @ref | NIT | PYZ | PYRA | PAL | beta GUR | beta GAL | alpha GLU | beta NAG | ESC | URE | GEL | GLU | RIB | XYL | MAN | MAL | LAC | SAC | GLYG |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 21429 | - | - | - | + | - | + | + | + | + | +/- | + | - | - | - | - | - | - | - | - |
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 21429 | + | + | + | - | + | + | +/- | + | +/- | + | + | + | + | - | + | + | + | + | - |
Isolation, sampling and environmental information
isolation
| @ref | sample type | host species | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|---|
| 16546 | rhizosphere soil of the perennial vine Tripterygium wilfordii Hook. f. | Tripterygium wilfordii | Yunnan Province | China | CHN | Asia |
| 67770 | Rhizosphere soil of the perennial vine Tripterygium wilfordii Hook. f. from Yunnan Province | Tripterygium wilfordii | China | CHN | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Soil |
| #Host | #Plants | #Shrub (Scrub) |
| #Host Body-Site | #Plant | #Rhizosphere |
Safety information
risk assessment
| @ref | biosafety level | biosafety level comment |
|---|---|---|
| 16546 | 1 | Risk group (German classification) |
| 21429 | L1 | German classification |
Sequence information
16S sequences
- @ref: 16546
- description: Nonomuraea rhizophila strain YIM 67092 16S ribosomal RNA gene, partial sequence
- accession: HM755723
- length: 1521
- database: ena
- NCBI tax ID: 870477
GC content
| @ref | GC-content | method |
|---|---|---|
| 16546 | 69.3 | |
| 67770 | 69.3 | high performance liquid chromatography (HPLC) |
External links
@ref: 16546
culture collection no.: DSM 45382, CCTCC AA 209044, JCM 31212, YIM 67092
straininfo link
- @ref: 85597
- straininfo: 402908
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 20889768 | Nonomuraea rhizophila sp. nov., an actinomycete isolated from rhizosphere soil. | Zhao GZ, Li J, Huang HY, Zhu WY, Xu LH, Li WJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.028050-0 | 2010 | Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhizosphere, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, Tripterygium/microbiology | Genetics |
| Phylogeny | 21890732 | Nonomuraea soli sp. nov., an actinomycete isolated from soil. | Cao YR, Jin RX, Jiang Y, He WX, Jiang CL | Int J Syst Evol Microbiol | 10.1099/ijs.0.034751-0 | 2011 | Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Carbohydrates/analysis, Cell Wall/chemistry, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Hydrogen-Ion Concentration, Microscopy, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, Spores, Bacterial/cytology, Temperature | Genetics |
| Phylogeny | 22307516 | Nonomuraea monospora sp. nov., an actinomycete isolated from cave soil in Thailand, and emended description of the genus Nonomuraea. | Nakaew N, Sungthong R, Yokota A, Lumyong S | Int J Syst Evol Microbiol | 10.1099/ijs.0.035220-0 | 2012 | Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Caves/*microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Thailand, Vitamin K 2/analogs & derivatives/analysis | Genetics |
| Phylogeny | 23203622 | Nonomuraea solani sp. nov., an actinomycete isolated from eggplant root (Solanum melongena L.). | Wang X, Zhao J, Liu C, Wang J, Shen Y, Jia F, Wang L, Zhang J, Yu C, Xiang W | Int J Syst Evol Microbiol | 10.1099/ijs.0.045617-0 | 2012 | Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, *Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Solanum melongena/*microbiology | Genetics |
| Phylogeny | 24126467 | Nonomuraea shaanxiensis sp. nov., a novel actinomycete isolated from a soil sample. | Zhang Y, Zhao J, Liu C, Shen Y, Jia F, Wang X, Xiang W | Antonie Van Leeuwenhoek | 10.1007/s10482-013-0052-9 | 2013 | Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology | Metabolism |
| Phylogeny | 26971302 | Nonomuraea zeae sp. nov., isolated from the rhizosphere of corn (Zea mays L.). | Shen Y, Jia F, Liu C, Li J, Guo S, Zhou S, Wang X, Xiang W | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001019 | 2016 | Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry, Zea mays/*microbiology | Transcriptome |
| Phylogeny | 27561257 | Nonomuraea purpurea sp. nov., an actinomycete isolated from mangrove sediment. | Suksaard P, Mingma R, Srisuk N, Matsumoto A, Takahashi Y, Duangmal K | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001457 | 2016 | Actinobacteria/*classification/genetics/isolation & purification, Avicennia/*microbiology, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/microbiology, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Thailand, Vitamin K 2/analogs & derivatives/chemistry, *Wetlands | Transcriptome |
| Phylogeny | 29767331 | Nonomuraea insulae sp. nov., isolated from forest soil. | Saricaoglu S, Nouioui I, Ay H, Saygin H, Bektas KI, Guven K, Cetin D, Klenk HP, Isik K, Sahin N | Antonie Van Leeuwenhoek | 10.1007/s10482-018-1097-6 | 2018 | Actinomycetales/classification/genetics/*isolation & purification/metabolism, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry/metabolism, Forests, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Turkey | Metabolism |
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 16546 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45382) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45382 | |
| 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 | |
| 21429 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM45382.pdf | Compendium of Actinobacteria . HZI-Helmholtz-Centre for Infection Research, Braunschweig | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
| 68379 | Automatically annotated from API Coryne | |||
| 68382 | Automatically annotated from API zym | |||
| 85597 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID402908.1 | StrainInfo: A central database for resolving microbial strain identifiers |