Strain identifier

BacDive ID: 13395

Type strain: Yes

Species: Pseudonocardia tetrahydrofuranoxydans

Strain Designation: K1

Strain history: CIP <- 2005, P. Kämpfer, Giessen Univ., Giessen, Germany <- J.R. Sudreesen: strain K1

NCBI tax ID(s): 1303679 (strain), 102884 (species)

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General

@ref: 11614

BacDive-ID: 13395

DSM-Number: 44239

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

description: Pseudonocardia tetrahydrofuranoxydans K1 is an aerobe, mesophilic, Gram-positive bacterium that builds an aerial mycelium and was isolated from water of a waste water treatment plant.

NCBI tax id

NCBI tax idMatching level
102884species
1303679strain

strain history

@refhistory
11614<- U. Kohlweyer and J. R. Andreesen, Univ. Halle; K1
67770CIP 109050 <-- P. Kämpfer <-- J. R. Sudreesen K1.
123490CIP <- 2005, P. Kämpfer, Giessen Univ., Giessen, Germany <- J.R. Sudreesen: strain K1

doi: 10.13145/bacdive13395.20230509.8.1

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 tetrahydrofuranoxydans
  • full scientific name: Pseudonocardia tetrahydrofuranoxydans Kämpfer et al. 2006

@ref: 11614

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Pseudonocardia

species: Pseudonocardia tetrahydrofuranoxydans

full scientific name: Pseudonocardia tetrahydrofuranoxydans Kämpfer et al. 2006

strain designation: K1

type strain: yes

Morphology

cell morphology

@refgram staincell widthcell shapemotilityconfidence
31757positive1.3 µmrod-shapedno
69480positive99.719
123490positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
19854Saffron yellow10-14 daysISP 2
19854Beige10-14 daysISP 3
19854Beige10-14 daysISP 4
19854Beige10-14 daysISP 5
19854Signal yellow10-14 daysISP 6
19854Beige10-14 daysISP 7
594322 days
123490

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19854yesAerial MyceliumCreamISP 2
19854yesAerial MyceliumCreamISP 3
19854noISP 4
19854yesAerial MyceliumCreamISP 5
19854noISP 6
19854yesAerial MyceliumISP 7

pigmentation

  • @ref: 31757
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11614GPHF-MEDIUM (DSMZ Medium 553)yeshttps://mediadive.dsmz.de/medium/553Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water
11614GYM 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
19854ISP 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
19854ISP 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:
19854ISP 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
19854ISP 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
19854ISP 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
19854ISP 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
40109MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulumyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g);Calcium carbonate (2.000 g)
123490CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
11614positivegrowth28mesophilic
19854positiveoptimum28mesophilic
31757positivegrowth11-36
31757positiveoptimum25-30mesophilic
40109positivegrowth30mesophilic
59432positivegrowth30mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepH
31757positivegrowth7
31757positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31757aerobe
59432aerobe
123490obligate aerobe

spore formation

@refspore formationconfidence
31757no
69480no100

halophily

@refsaltgrowthtested relationconcentration
31757NaClpositivegrowth4 %
31757NaClpositiveoptimum4 %

observation

@refobservation
31757aggregates in chains
67770quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
31757161933-hydroxybenzoate+carbon source
31757178794-hydroxybenzoate+carbon source
3175724996lactate+carbon source
3175725115malate+carbon source
3175737684mannose+carbon source
3175733942ribose+carbon source
3175717822serine+carbon source
3175717992sucrose+carbon source
3175727082trehalose+carbon source
3175718222xylose+carbon source
12349017632nitrate+reduction
12349016301nitrite-reduction

metabolite production

  • @ref: 123490
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31757catalase+1.11.1.6
31757cytochrome oxidase+1.9.3.1
123490oxidase-
123490alcohol dehydrogenase-1.1.1.1
123490catalase+1.11.1.6
123490lysine decarboxylase-4.1.1.18
123490ornithine decarboxylase-4.1.1.17
123490urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
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- FucosidaseControl
19854+-+-+++--++---+----
123490+++-++---++---+-----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11614water of a waste water treatment plantGöttingenGermanyDEUEurope
59432Sludge,waist water,enrichment with tetrahydrofuranGöttingenGermanyDEUEurope
67770Sludge from a wastewater treatment plantGöttingenGermanyDEUEurope
123490Environment, Wash waterGöttingenGermanyDEUEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Waste#Water treatment plant
#Environmental#Aquatic

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
116141Risk group (German classification)
1234902Risk group (French classification)

Sequence information

16S sequences

  • @ref: 11614
  • description: Pseudonocardia tetrahydrofuranoxydans 16S rRNA gene, type strain K1T
  • accession: AJ249200
  • length: 1440
  • database: ena
  • NCBI tax ID: 102884

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudonocardia tetrahydrofuranoxydans JCM 14745GCA_001313405contigncbi1303679
66792Pseudonocardia tetrahydrofuranoxydans JCM 147451303679.3wgspatric1303679
66792Pseudonocardia tetrahydrofuranoxydans JCM 147452734481945draftimg1303679

GC content

@refGC-contentmethod
3175771.3
6777071.3high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes70no
motileno90.121no
gram-positiveyes87.799yes
anaerobicno97.407yes
halophileno94.073no
spore-formingno91.726yes
thermophileno96.908yes
glucose-utilyes83.138no
aerobicyes95.838yes
flagellatedno98.445no
glucose-fermentno88.657no

External links

@ref: 11614

culture collection no.: DSM 44239, CIP 109050, CCUG 52126, JCM 14745

straininfo link

  • @ref: 82592
  • straininfo: 113658

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16825626Pseudonocardia tetrahydrofuranoxydans sp. nov.Kampfer P, Kohlweyer U, Thiemer B, Andreesen JRInt J Syst Evol Microbiol10.1099/ijs.0.64199-02006Actinomycetales/*classification/cytology/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/chemistry, Furans/*metabolism, Genes, rRNA, Gentian Violet, Molecular Sequence Data, Nucleic Acid Hybridization, Phenazines, Phylogeny, Quinones/analysis/chemistry, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Spores, Bacterial, *Water MicrobiologyGenetics
Phylogeny24198055Pseudonocardia sediminis sp. nov., isolated from marine sediment.Zhang DF, Jiang Z, Li L, Liu BB, Zhang XM, Tian XP, Zhang S, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.057844-02013Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Oceans and Seas, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
11614Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44239)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44239
19854Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44239.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
31757Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2803028776041
40109Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6748
59432Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 52126)https://www.ccug.se/strain?id=52126
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)
82592Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID113658.1StrainInfo: A central database for resolving microbial strain identifiers
123490Curators of the CIPCollection of Institut Pasteur (CIP 109050)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109050