Strain identifier
BacDive ID: 12591
Type strain: 
Species: Promicromonospora citrea
Strain history: KCC A-0051 <-- RIA 562 <-- INMI 18.
NCBI tax ID(s): 43677 (species)
version 8.1 (current version)
General
@ref: 10773
BacDive-ID: 12591
DSM-Number: 43110
keywords: genome sequence, 16S sequence, Bacteria, mesophilic
description: Promicromonospora citrea DSM 43110 is a mesophilic bacterium that was isolated from garden soil.
NCBI tax id
- NCBI tax id: 43677
- Matching level: species
strain history
| @ref | history |
|---|---|
| 10773 | <- IMET <- V.D. Kuznetsov, RIA <- L.V. Kalakoutskii, INMI |
| 67770 | KCC A-0051 <-- RIA 562 <-- INMI 18. |
doi: 10.13145/bacdive12591.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micrococcales
- family: Promicromonosporaceae
- genus: Promicromonospora
- species: Promicromonospora citrea
- full scientific name: Promicromonospora citrea Krassilnikov et al. 1961 (Approved Lists 1980)
@ref: 10773
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Promicromonosporaceae
genus: Promicromonospora
species: Promicromonospora citrea
full scientific name: Promicromonospora citrea Krassilnikov et al. 1961
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | no | 93.85 | |
| 69480 | 100 | positive |
colony morphology
| @ref | colony color | incubation period | medium used |
|---|---|---|---|
| 19938 | Lemon yellow (1012) | 10-14 days | ISP 2 |
| 19938 | Lemon yellow (1012) | 10-14 days | ISP 3 |
| 19938 | Lemon yellow (1012) | 10-14 days | ISP 4 |
| 19938 | Lemon yellow (1012) | 10-14 days | ISP 5 |
| 19938 | Lemon yellow (1012) | 10-14 days | ISP 6 |
| 19938 | Lemon yellow (1012) | 10-14 days | ISP 7 |
multicellular morphology
| @ref | forms multicellular complex | medium name |
|---|---|---|
| 19938 | no | ISP 2 |
| 19938 | no | ISP 3 |
| 19938 | no | ISP 4 |
| 19938 | no | ISP 5 |
| 19938 | no | ISP 6 |
| 19938 | no | ISP 7 |
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 10773 | R2A MEDIUM (DSMZ Medium 830) | yes | https://mediadive.dsmz.de/medium/830 | Name: 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 |
| 10773 | 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 |
| 19938 | 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 | |
| 19938 | 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: | |
| 19938 | 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 | |
| 19938 | 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 | |
| 19938 | 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 | |
| 19938 | 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 |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 19938 | positive | optimum | 30 | mesophilic |
| 10773 | positive | growth | 28 | mesophilic |
| 67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.163
halophily
- @ref: 19938
- salt: NaCl
- growth: positive
- tested relation: maximum
- concentration: 2.5 %
murein
- @ref: 10773
- murein short key: A11.59
- type: A4alpha L-Lys-L-Ala-D-Glu
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 19938 | 62968 | cellulose | + | |
| 19938 | 16634 | raffinose | + | |
| 19938 | 26546 | rhamnose | + | |
| 19938 | 28757 | fructose | - | |
| 19938 | 29864 | mannitol | + | |
| 19938 | 17268 | myo-inositol | +/- | |
| 19938 | 18222 | xylose | + | |
| 19938 | 17992 | sucrose | + | |
| 19938 | 22599 | arabinose | + | |
| 19938 | 17234 | glucose | +/- | |
| 68368 | 5291 | gelatin | + | hydrolysis |
| 68368 | 27897 | tryptophan | - | energy source |
| 68368 | 16199 | urea | + | hydrolysis |
| 68368 | 16947 | citrate | - | assimilation |
| 68368 | 18257 | ornithine | + | degradation |
| 68368 | 25094 | lysine | + | degradation |
| 68368 | 29016 | arginine | + | hydrolysis |
metabolite production
| @ref | Chebi-ID | metabolite | production |
|---|---|---|---|
| 68368 | 15688 | acetoin | no |
| 68368 | 35581 | indole | no |
| 68368 | 16136 | hydrogen sulfide | no |
metabolite tests
| @ref | Chebi-ID | metabolite | voges-proskauer-test | indole test |
|---|---|---|---|---|
| 68368 | 15688 | acetoin | - | |
| 68368 | 35581 | indole | - |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 68368 | gelatinase | + | |
| 68368 | tryptophan deaminase | - | 4.1.99.1 |
| 68368 | urease | + | 3.5.1.5 |
| 68368 | ornithine decarboxylase | + | 4.1.1.17 |
| 68368 | lysine decarboxylase | + | 4.1.1.18 |
| 68368 | arginine dihydrolase | + | 3.5.3.6 |
| 68368 | beta-galactosidase | - | 3.2.1.23 |
API 20E
| @ref | ONPG | ADH Arg | LDC Lys | ODC | CIT | H2S | URE | TDA Trp | IND | VP | GEL |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 19938 | - | + | + | + | - | - | + | - | - | - | + |
Isolation, sampling and environmental information
isolation
| @ref | sample type |
|---|---|
| 10773 | garden soil |
| 67770 | Garden soil |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Soil |
| #Engineered | #Agriculture | #Garden |
taxonmaps
- @ref: 69479
- File name: preview.99_3773.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_1939;97_2331;98_2876;99_3773&stattab=map
- Last taxonomy: Promicromonospora
- 16S sequence: X83808
- Sequence Identity:
- Total samples: 1696
- soil counts: 474
- aquatic counts: 57
- animal counts: 703
- plant counts: 462
Safety information
risk assessment
| @ref | biosafety level | biosafety level comment |
|---|---|---|
| 10773 | 1 | Risk group (German classification) |
| 19938 | 1 |
Sequence information
16S sequences
- @ref: 20218
- description: P.citrea 16S rRNA gene
- accession: X83808
- length: 1453
- database: ena
- NCBI tax ID: 43677
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Promicromonospora citrea JCM 3051 | GCA_014647735 | contig | ncbi | 43677 |
| 66792 | Promicromonospora citrea strain ATCC 15908 | 43677.3 | wgs | patric | 43677 |
| 66792 | Promicromonospora citrea strain JCM 3051 | 43677.4 | wgs | patric | 43677 |
| 67770 | Promicromonospora citrea ATCC 15908 | GCA_013004695 | contig | ncbi | 43677 |
GC content
- @ref: 67770
- GC-content: 73.5
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 82 | no |
| gram-positive | yes | 88.474 | no |
| anaerobic | no | 99.657 | no |
| halophile | no | 83.199 | no |
| spore-forming | no | 53.309 | no |
| glucose-util | yes | 85.835 | no |
| aerobic | yes | 95.056 | no |
| flagellated | no | 97.74 | no |
| thermophile | no | 99.073 | yes |
| motile | no | 91.661 | no |
| glucose-ferment | no | 83.189 | no |
External links
@ref: 10773
culture collection no.: DSM 43110, ATCC 15908, IMET 7267, INMI 18, JCM 3051, KCC A-0051, RIA 562, CGMCC 4.1485, IFM 1286, IFO 12397, IMSNU 20110, KCTC 9069, LMG 4076, MTCC 271, NBIMCC 1485, NBRC 12397, NCIMB 12149, NRRL B-3485, VKM Ac-665
straininfo link
- @ref: 81805
- straininfo: 13746
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 13130039 | Promicromonospora vindobonensis sp. nov. and Promicromonospora aerolata sp. nov., isolated from the air in the medieval 'Virgilkapelle' in Vienna. | Busse HJ, Zlamala C, Buczolits S, Lubitz W, Kampfer P, Takeuchi M | Int J Syst Evol Microbiol | 10.1099/ijs.0.02522-0 | 2003 | Actinobacteria/*classification/genetics/*isolation & purification/metabolism, Air Microbiology, Austria, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species Specificity | Genetics |
| Phylogeny | 18523198 | Promicromonospora kroppenstedtii sp. nov., isolated from sandy soil. | Alonso-Vega P, Santamaria RI, Martinez-Molina E, Trujillo ME | Int J Syst Evol Microbiol | 10.1099/ijs.0.65458-0 | 2008 | Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Silicon Dioxide, *Soil Microbiology, Spain, Species Specificity | Genetics |
| Phylogeny | 19654362 | Promicromonospora umidemergens sp. nov., isolated from moisture from indoor wall material. | Martin K, Schafer J, Kampfer P | Int J Syst Evol Microbiol | 10.1099/ijs.0.014142-0 | 2009 | Actinomycetales/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, *Household Articles, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics | Metabolism |
| Phylogeny | 22058317 | Promicromonospora thailandica sp. nov., isolated from marine sediment. | Thawai C, Kudo T | Int J Syst Evol Microbiol | 10.1099/ijs.0.035972-0 | 2011 | Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Carbohydrates/analysis, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments, Molecular Sequence Data, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Thailand, *Water Microbiology | Genetics |
| Phylogeny | 29779147 | Promicromonospora viridis sp. nov., a novel actinomycete isolated from soil. | Jin L, Zhao J, Jiang S, Zhao Y, Han X, Guo X, Wang X, Xiang W | Antonie Van Leeuwenhoek | 10.1007/s10482-018-1099-4 | 2018 | Actinobacteria/*genetics, Phospholipids/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Soil Microbiology | Metabolism |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 10773 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43110) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-43110 | |||
| 19938 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM43110.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 | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 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/ | ||||
| 68368 | Automatically annotated from API 20E | |||||
| 69479 | João 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 | |||
| 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) | |||
| 81805 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID13746.1 | StrainInfo: A central database for resolving microbial strain identifiers |