Strain identifier

BacDive ID: 11202

Type strain: Yes

Species: Nocardiopsis tropica

Strain history: CIP <- 2000, DSM <- E.B. Shirling, ISP, Streptomyces viridis <- E. Baldacci: strain IPV 398

NCBI tax ID(s): 163605 (species)

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General

@ref: 11502

BacDive-ID: 11202

DSM-Number: 44381

keywords: 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-negative, rod-shaped

description: Nocardiopsis tropica DSM 44381 is an obligate aerobe, mesophilic, Gram-negative bacterium that builds an aerial mycelium and was isolated from Soil in the rhizosphere of Casuarina sp..

NCBI tax id

  • NCBI tax id: 163605
  • Matching level: species

strain history

@refhistory
11502<- L. Evtushenko, VKM
67770VKM Ac-1457 <-- PIBCh 11-647.
123589CIP <- 2000, DSM <- E.B. Shirling, ISP, Streptomyces viridis <- E. Baldacci: strain IPV 398

doi: 10.13145/bacdive11202.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Streptosporangiales
  • family: Nocardiopsidaceae
  • genus: Nocardiopsis
  • species: Nocardiopsis tropica
  • full scientific name: Nocardiopsis tropica Evtushenko et al. 2000

@ref: 11502

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiopsaceae

genus: Nocardiopsis

species: Nocardiopsis tropica

type strain: yes

Morphology

cell morphology

  • @ref: 123589
  • gram stain: negative
  • cell shape: rod-shaped

colony morphology

@refcolony colorincubation periodmedium used
19859Mahagony brown10-14 daysISP 2
19859Orange brown10-14 daysISP 3
19859Beige10-14 daysISP 4
19859Beige10-14 daysISP 5
19859Black brown10-14 daysISP 6
19859Beige10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19859yesAerial MyceliumIvoryISP 2
19859yesAerial MyceliumIvoryISP 3
19859yesAerial MyceliumIvoryISP 4
19859noISP 5
19859yesAerial MyceliumBeigeISP 6
19859yesAerial MyceliumISP 7

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
19859ISP 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
19859ISP 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:
19859ISP 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
19859ISP 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
19859ISP 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
19859ISP 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
37244MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123589CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
19859positiveoptimum28mesophilic
37244positivegrowth30mesophilic
67770positivegrowth28mesophilic
123589positivegrowth25-37mesophilic
123589nogrowth10psychrophilic
123589nogrowth41thermophilic
123589nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 123589
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
123589NaClpositivegrowth0-4 %
123589NaClnogrowth6 %
123589NaClnogrowth8 %
123589NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-10(H6), MK-10(H8)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1985917234glucose+
1985922599arabinose-
1985917992sucrose-
1985918222xylose-
1985917268myo-inositol-
1985929864mannitol+
1985928757fructose+
1985926546rhamnose+
1985916634raffinose+
1985962968cellulose+
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
6837132528turanose-builds acid from
6837128066gentiobiose+builds acid from
6837117151xylitol-builds acid from
6837128087glycogen+builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-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
6837116024D-mannose-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
6837165327D-xylose-builds acid from
6837116988D-ribose+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
12358916947citrate-carbon source
1235894853esculin-hydrolysis
123589606565hippurate+hydrolysis
12358917632nitrate+reduction
12358916301nitrite-reduction
12358917632nitrate-respiration

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideyes
12358935581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin-
6836835581indole-
12358915688acetoin-
12358917234glucose-

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
123589oxidase+
123589beta-galactosidase-3.2.1.23
123589alcohol dehydrogenase-1.1.1.1
123589gelatinase-
123589amylase-
123589caseinase-3.4.21.50
123589catalase+1.11.1.6
123589tween esterase-
123589gamma-glutamyltransferase-2.3.2.2
123589lecithinase-
123589lipase-
123589lysine decarboxylase-4.1.1.18
123589ornithine decarboxylase-4.1.1.17
123589protease-
123589tryptophan deaminase-
123589urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase+3.4.11.3
68382alpha-chymotrypsin+3.4.21.1
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
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
19859+---+++++++-+-+++--
123589+++-+++-+-+---+++---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19859+++++++----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123589+---+----++----------++-+-+/-----+/-----+-+-------+--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123589+-+++----+++---++-++-+----+----+-++--------------+---+-----++-----------+--+-++++---+-+-++++-++-++-

Isolation, sampling and environmental information

isolation

  • @ref: 67770
  • sample type: Soil in the rhizosphere of Casuarina sp.
  • host species: Casuarina sp.
  • country: Seychelles
  • origin.country: SYC
  • continent: Africa

taxonmaps

  • @ref: 69479
  • File name: preview.99_17053.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_152;96_659;97_762;98_12916;99_17053&stattab=map
  • Last taxonomy: Nocardiopsis
  • 16S sequence: LC214995
  • Sequence Identity:
  • Total samples: 22
  • soil counts: 9
  • aquatic counts: 3
  • animal counts: 7
  • plant counts: 3

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
115021Risk group (German classification)
198591Risk group (German classification)
1235891Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardiopsis tropica 16S ribosomal RNA gene, partial sequenceAF1059711452ena109330
67770Nocardiopsis tropica gene for 16S ribosomal RNA, partial sequence, culture_collection: JCM:10877LC2149951470ena109330

External links

@ref: 11502

culture collection no.: DSM 44381, CIP 106426, VKM Ac-1457, JCM 10877, CGMCC 4.2092, ATCC 15732, CBS 674.72, IFO 13373, RIA 1334, ISP 5381, IPV 398

literature

  • topic: Phylogeny
  • Pubmed-ID: 10826789
  • title: Nocardiopsis tropica sp. nov., Nocardiopsis trehalosi sp. nov., nom. rev. and Nocardiopsis dassonvillei subsp. albirubida subsp. nov., comb. nov.
  • authors: Evtushenko LI, Taran VV, Akimov VN, Kroppenstedt RM, Tiedje JM, Stackebrandt E
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/00207713-50-1-73
  • year: 2000
  • mesh: Actinomycetales/chemistry/*classification/cytology/physiology, DNA, Bacterial/analysis/genetics, DNA, Ribosomal/analysis/genetics, Fatty Acids/analysis, Mathematics, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11502Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44381)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44381
19859Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44381.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
37244Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18555
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
123589Curators of the CIPCollection of Institut Pasteur (CIP 106426)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106426