Strain identifier
BacDive ID: 13352
Type strain:
Species: Pseudonocardia hydrocarbonoxydans
Strain history: DSM 43281 <-- Schering Corp.; 228 <-- ATCC 15104 <-- P. Hirsch 70.
NCBI tax ID(s): 76726 (species)
General
@ref: 10924
BacDive-ID: 13352
DSM-Number: 43281
keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic, Gram-positive
description: Pseudonocardia hydrocarbonoxydans DSM 43281 is a spore-forming, mesophilic, Gram-positive bacterium that builds an aerial mycelium and was isolated from air contaminant.
NCBI tax id
- NCBI tax id: 76726
- Matching level: species
strain history
@ref | history |
---|---|
10924 | <- K. Kieslich, Schering 228 <- ATCC <- P. Hirsch, 70 |
67770 | DSM 43281 <-- Schering Corp.; 228 <-- ATCC 15104 <-- P. Hirsch 70. |
doi: 10.13145/bacdive13352.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Pseudonocardiales
- family: Pseudonocardiaceae
- genus: Pseudonocardia
- species: Pseudonocardia hydrocarbonoxydans
- full scientific name: Pseudonocardia hydrocarbonoxydans (Nolof and Hirsch 1962) Warwick et al. 1994
synonyms
@ref synonym 20215 Nocardia hydrocarbonoxydans 20215 Amycolata hydrocarbonoxydans
@ref: 10924
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Pseudonocardiaceae
genus: Pseudonocardia
species: Pseudonocardia hydrocarbonoxydans
full scientific name: Pseudonocardia hydrocarbonoxydans (Nolof and Hirsch 1962) Warwick et al. 1994
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 100
colony morphology
@ref | colony color | incubation period | medium used |
---|---|---|---|
19564 | Signal yellow | 10-14 days | ISP 2 |
19564 | Signal yellow | 10-14 days | ISP 3 |
19564 | Yellow | 10-14 days | ISP 4 |
19564 | Yellow | 10-14 days | ISP 5 |
19564 | Yellow | 10-14 days | ISP 6 |
19564 | Yellow | 10-14 days | ISP 7 |
multicellular morphology
@ref | forms multicellular complex | complex name | complex color | medium name |
---|---|---|---|---|
19564 | yes | Aerial Mycelium | White | ISP 2 |
19564 | yes | Aerial Mycelium | White | ISP 3 |
19564 | yes | Aerial Mycelium | White | ISP 4 |
19564 | yes | Aerial Mycelium | White | ISP 5 |
19564 | no | ISP 6 | ||
19564 | no | ISP 7 |
Culture and growth conditions
culture medium
@ref | name | growth | composition | link |
---|---|---|---|---|
19564 | 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 | |
19564 | 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: | |
19564 | 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 | |
19564 | 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 | |
19564 | 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 | |
19564 | 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 | |
10924 | GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) | yes | 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 | https://mediadive.dsmz.de/medium/65 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
19564 | positive | optimum | 30 | mesophilic |
10924 | positive | growth | 28 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
spore formation
- @ref: 19564
- spore description: Formation of spores, spore surface smooth, fragmentation
- type of spore: spore
- spore formation: yes
observation
- @ref: 67770
- observation: quinones: MK-8(H4), MK-8(H2), MK-8(H4)
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
19564 | 17234 | glucose | + | |
19564 | 22599 | arabinose | + | |
19564 | 17992 | sucrose | + | |
19564 | 18222 | xylose | +/- | |
19564 | 17268 | myo-inositol | - | |
19564 | 29864 | mannitol | - | |
19564 | 28757 | fructose | - | |
19564 | 26546 | rhamnose | +/- | |
19564 | 16634 | raffinose | +/- | |
19564 | 62968 | cellulose | +/- | |
68369 | 27689 | decanoate | - | assimilation |
68369 | 17306 | maltose | - | assimilation |
68369 | 59640 | N-acetylglucosamine | - | assimilation |
68369 | 16024 | D-mannose | - | assimilation |
68369 | 5291 | gelatin | - | hydrolysis |
68369 | 4853 | esculin | + | hydrolysis |
68369 | 16199 | urea | - | hydrolysis |
68369 | 29016 | arginine | - | hydrolysis |
68369 | 17634 | D-glucose | - | fermentation |
68369 | 27897 | tryptophan | - | energy source |
68369 | 17632 | nitrate | + | reduction |
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 |
---|---|---|---|
68369 | 35581 | indole | no |
68368 | 15688 | acetoin | yes |
68368 | 35581 | indole | no |
68368 | 16136 | hydrogen sulfide | no |
metabolite tests
@ref | Chebi-ID | metabolite | indole test | voges-proskauer-test |
---|---|---|---|---|
68369 | 35581 | indole | - | |
68368 | 15688 | acetoin | + | |
68368 | 35581 | indole | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68369 | gelatinase | - | |
68369 | beta-glucosidase | + | 3.2.1.21 |
68369 | urease | - | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
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 |
68382 | esterase (C 4) | - | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
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 | Control |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
19564 | + | - | + | - | + | + | + | + | + | + | + | + | + | - | + | + | - | - | - | |
10924 | - | - | +/- | - | + | +/- | - | +/- | - | +/- | - | - | - | - | + | + | - | - | - | - |
API 20E
@ref | ONPG | ADH Arg | LDC Lys | ODC | CIT | H2S | URE | TDA Trp | IND | VP | GEL |
---|---|---|---|---|---|---|---|---|---|---|---|
19564 | + | + | + | + | + | - | + | - | - | + | + |
API 20NE
@ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
10924 | + | - | - | - | - | + | - | + | +/- | +/- | - | +/- | - | - | +/- | - | +/- | +/- | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type |
---|---|
10924 | air contaminant |
67770 | Air contaminant |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Laboratory | #Contaminant |
#Environmental | #Air |
taxonmaps
- @ref: 69479
- File name: preview.99_17769.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_2672;97_3280;98_4128;99_17769&stattab=map
- Last taxonomy: Pseudonocardia
- 16S sequence: AJ252826
- Sequence Identity:
- Total samples: 1556
- soil counts: 920
- aquatic counts: 153
- animal counts: 418
- plant counts: 65
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
19564 | 1 | Risk group (German classification) |
10924 | 1 | Risk group (German classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | A.hydrocarbonoxydans (DSM 43281) 16S ribosomal RNA (partial) | X76955 | 1342 | ena | 76726 |
20218 | Pseudonocardia hydrocarbonoxydans 16S rRNA gene, strain IMSNU 22140T | AJ252826 | 1511 | ena | 76726 |
20218 | Pseudonocardia hydrocarbonoxydans 16S ribosomal RNA gene, partial sequence | GU083569 | 1398 | ena | 76726 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Pseudonocardia hydrocarbonoxydans strain NBRC 14498 | 76726.4 | wgs | patric | 76726 |
67770 | Pseudonocardia hydrocarbonoxydans NBRC 14498 | GCA_006539565 | contig | ncbi | 76726 |
GC content
- @ref: 67770
- GC-content: 69
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 63 | no |
motile | no | 92.163 | no |
flagellated | no | 98.314 | no |
gram-positive | yes | 89.017 | no |
anaerobic | no | 98.772 | no |
halophile | no | 89.319 | no |
spore-forming | yes | 73.59 | yes |
glucose-util | yes | 88.77 | yes |
aerobic | yes | 92.223 | no |
glucose-ferment | no | 91.505 | yes |
thermophile | no | 99.209 | yes |
External links
@ref: 10924
culture collection no.: DSM 43281, ATCC 15104, NCIB 9436, JCM 3392, BCRC 13740, CGMCC 4.1218, HUT 6554, IFO 14498, IMET 7645, IMSNU 22140, KCTC 9301, KCTC 9692, NBRC 14498, NCIMB 9436, NRRL B-16171, PCM 2249, VKM Ac-799, VTT E-073031
straininfo link
- @ref: 82550
- straininfo: 88653
literature
- topic: Phylogeny
- Pubmed-ID: 28151383
- title: Pseudonocardia profundimaris sp. nov., isolated from marine sediment.
- authors: Zhang G, Wang L, Li J, Zhou Y
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.001849
- year: 2017
- mesh: Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Glycolipids/chemistry, Nucleic Acid Hybridization, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry
- topic2: Transcriptome
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
10924 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43281) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-43281 | |||
19564 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM43281.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) | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68368 | Automatically annotated from API 20E | |||||
68369 | Automatically annotated from API 20NE | |||||
68382 | Automatically annotated from API zym | |||||
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) | |||
82550 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID88653.1 | StrainInfo: A central database for resolving microbial strain identifiers |