Strain identifier

BacDive ID: 13370

Type strain: Yes

Species: Pseudonocardia sulfidoxydans

Strain Designation: 592

Strain history: CIP <- 1998, A. Lipski, Osnabrück Univ., Osnabrück, Germany: strain 592

NCBI tax ID(s): 1223511 (strain), 54011 (species)

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General

@ref: 11621

BacDive-ID: 13370

DSM-Number: 44248

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, spore-forming, mesophilic

description: Pseudonocardia sulfidoxydans 592 is an obligate aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from biofiltermaterial.

NCBI tax id

NCBI tax idMatching level
1223511strain
54011species

strain history

@refhistory
11621<- K. Reichert, 592
385721998, A. Lipski, Univ. Osnabrück, Germany: strain 592
67770A. Lipski 592.
123383CIP <- 1998, A. Lipski, Osnabrück Univ., Osnabrück, Germany: strain 592

doi: 10.13145/bacdive13370.20230509.8.1

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 sulfidoxydans
  • full scientific name: Pseudonocardia sulfidoxydans Reichert et al. 1998

@ref: 11621

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Pseudonocardia

species: Pseudonocardia sulfidoxydans

full scientific name: Pseudonocardia sulfidoxydans Reichert et al. 1998

strain designation: 592

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no90.954
69480100positive
123383nopositiverod-shaped

colony morphology

@refcolony colorincubation periodmedium used
20031Saffron yellow (1017)10-14 daysISP 2
20031Colorless10-14 daysISP 3
20031Colorless10-14 daysISP 4
20031Colorless10-14 daysISP 5
20031Saffron yellow (1017)10-14 daysISP 6
20031Colorless10-14 daysISP 7
123383

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
20031yesAerial MyceliumSaffron yellow (1017)ISP 2
20031yesAerial MyceliumWhiteISP 3
20031yesAerial MyceliumWhiteISP 4
20031yesAerial MyceliumWhiteISP 5
20031yesAerial MyceliumWhiteISP 6
20031yesAerial MyceliumWhiteISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11621TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
20031ISP 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
20031ISP 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
20031ISP 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
20031ISP 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
20031ISP 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
20031ISP 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:
38572MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123383CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
11621positivegrowth28mesophilic
20031positiveoptimum28mesophilic
38572positivegrowth30mesophilic
67770positivegrowth25mesophilic
123383positivegrowth25-37mesophilic
123383nogrowth10psychrophilic
123383nogrowth41thermophilic
123383nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 123383
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 69481
  • spore formation: yes
  • confidence: 99

halophily

@refsaltgrowthtested relationconcentration
20031NaClpositivemaximum5 %
123383NaClpositivegrowth0-2 %
123383NaClnogrowth4 %
123383NaClnogrowth6 %
123383NaClnogrowth8 %
123383NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2003117234glucose+
2003122599arabinose-
2003117992sucrose+
2003118222xylose+
2003117268myo-inositol+/-
2003129864mannitol-
2003128757fructose+
2003126546rhamnose+/-
2003116634raffinose+
2003162968cellulose-
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose+builds acid from
6837128053melibiose-builds acid from
6837117716lactose+builds acid from
6837117306maltose+builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol+builds acid from
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis
1233834853esculin-hydrolysis
123383606565hippurate+hydrolysis
12338317632nitrate+reduction
12338316301nitrite-reduction
12338317632nitrate-respiration

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
12338335581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin-
6836835581indole-
12338315688acetoin-
12338317234glucose-

enzymes

@refvalueactivityec
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase+4.1.1.17
68368lysine decarboxylase+4.1.1.18
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase-3.2.1.23
123383oxidase-
123383beta-galactosidase+3.2.1.23
123383alcohol dehydrogenase-1.1.1.1
123383gelatinase-
123383amylase-
123383DNase-
123383caseinase-3.4.21.50
123383catalase+1.11.1.6
123383tween esterase-
123383gamma-glutamyltransferase-2.3.2.2
123383lecithinase-
123383lipase-
123383lysine decarboxylase-4.1.1.18
123383ornithine decarboxylase-4.1.1.17
123383phenylalanine ammonia-lyase-4.3.1.24
123383protease-
123383tryptophan deaminase-
123383urease-3.5.1.5
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
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
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
20031+-+-++---+----+----
123383-++-+++--++--+------

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
20031-+++-------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123383+---+/-+/----++++/---------------++-+--+/------+/----------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123383+++--------------+++-+---------+--------++-----+++----+-------+---+--------+--+++-------+-+-----+++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
11621biofiltermaterial
67770Tree-bark compost from biofilters
123383Experimental biofilterBrögbern, LingenGermanyDEUEurope1995

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Bioremediation
  • Cat3: #Biofilter

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: Y08537
  • Sequence Identity:
  • Total samples: 1556
  • soil counts: 920
  • aquatic counts: 153
  • animal counts: 418
  • plant counts: 65

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
116211Risk group (German classification)
200311German classification
1233832Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: P.sulfidoxydans 16S rRNA gene
  • accession: Y08537
  • length: 1505
  • database: ena
  • NCBI tax ID: 54011

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudonocardia sulfidoxydans NBRC 16205GCA_007989085contigncbi1223511
66792Pseudonocardia sulfidoxydans NBRC 162051223511.3wgspatric1223511

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes99no
motileno88.543no
gram-positiveyes89.196no
anaerobicno98.914no
halophileno94.088no
spore-formingyes69.821no
thermophileno99.127no
glucose-utilyes87.27no
flagellatedno98.557no
aerobicyes92.258no
glucose-fermentno89.961no

External links

@ref: 11621

culture collection no.: DSM 44248, IFO 16205, NBRC 16205, JCM 10411, CGMCC 4.1533, CIP 105686, IMSNU 22143, NCIMB 13545, VTT E-073032

straininfo link

  • @ref: 82568
  • straininfo: 50533

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9731282Pseudonocardia asaccharolytica sp. nov. and Pseudonocardia sulfidoxydans sp. nov., two new dimethyl disulfide-degrading actinomycetes and emended description of the genus Pseudonocardia.Reichert K, Lipski A, Pradella S, Stackebrandt E, Altendorf KInt J Syst Bacteriol10.1099/00207713-48-2-4411998Actinomycetales/*classification/isolation & purification/metabolism/ultrastructure, Base Sequence, DNA, Bacterial, Disulfides/metabolism, Molecular Sequence Data, PhylogenyMetabolism
Phylogeny28151383Pseudonocardia profundimaris sp. nov., isolated from marine sediment.Zhang G, Wang L, Li J, Zhou YInt J Syst Evol Microbiol10.1099/ijsem.0.0018492017Actinomycetales/*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/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11621Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44248)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44248
20031Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44248.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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
38572Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17732
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/
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
69479João 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
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
82568Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID50533.1StrainInfo: A central database for resolving microbial strain identifiers
123383Curators of the CIPCollection of Institut Pasteur (CIP 105686)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105686