Strain identifier

BacDive ID: 11150

Type strain: Yes

Species: Nocardioides caricicola

Strain Designation: YC6903

Strain history: KACC 13778 <-- G. C. Song et al. YC6903.

NCBI tax ID(s): 634770 (species)

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General

@ref: 16132

BacDive-ID: 11150

DSM-Number: 22177

keywords: 16S sequence, Bacteria, mesophilic, Gram-positive, ovoid-shaped

description: Nocardioides caricicola YC6903 is a mesophilic, Gram-positive, ovoid-shaped bacterium that was isolated from root of Carex scabrifolia Steud., a halophytic plant.

NCBI tax id

  • NCBI tax id: 634770
  • Matching level: species

strain history

@refhistory
16132<- Y. R. Chung, Gyeongsang Natl. Univ. (GNU), Jinju, Korea; YC6903 <- Fehmida
67770KACC 13778 <-- G. C. Song et al. YC6903.

doi: 10.13145/bacdive11150.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Nocardioidaceae
  • genus: Nocardioides
  • species: Nocardioides caricicola
  • full scientific name: Nocardioides caricicola Song et al. 2011

@ref: 16132

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides caricicola

full scientific name: Nocardioides caricicola Song et al. 2011

strain designation: YC6903

type strain: yes

Morphology

cell morphology

  • @ref: 29743
  • gram stain: positive
  • cell length: 3.5 µm
  • cell width: 0.5 µm
  • cell shape: ovoid-shaped
  • motility: no

colony morphology

@refincubation periodmedium usedcolony color
161323-7 days
2136710-14 daysISP 2
2136710-14 daysISP 3Light ivory (1015)
2136710-14 daysISP 4
2136710-14 daysISP 5None - light ivory (1015)
2136710-14 daysISP 7None - light ivory (1015)
21367suter without tyrosineNone - light ivory (1015)

multicellular morphology

@refforms multicellular complexmedium name
21367noISP 2
21367noISP 3
21367noISP 4
21367noISP 5
21367noISP 7
21367noSuter with tyrosine
21367noSuter without tyrosine

pigmentation

  • @ref: 29743
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16132R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: 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
21367ISP 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
21367ISP 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:
21367ISP 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
21367ISP 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
21367ISP 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
21367suter without tyrosineyesName: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes

culture temp

@refgrowthtypetemperaturerange
16132positivegrowth28mesophilic
29743positivegrowth10-45
29743positiveoptimum30mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
29743positivegrowth7.0-9.0alkaliphile
29743positiveoptimum8

Physiology and metabolism

spore formation

  • @ref: 29743
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
21367NaClpositivemaximum2.5 %
29743NaClpositivegrowth0-0.5 %

observation

@refobservation
29743aggregates in clumps
67770quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2136717234glucose-
2136722599arabinose-
2136717992sucrose-
2136718222xylose-
2136717268myo-inositol-
2136737684mannose-
2136728757fructose-
2136726546rhamnose-
2136716634raffinose-
2136762968cellulose+
297434853esculin+hydrolysis
6837917632nitrate-reduction
683794853esculin-hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
29743acid phosphatase+3.1.3.2
29743alkaline phosphatase+3.1.3.1
29743catalase+1.11.1.6
68379gelatinase-
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase-3.1.3.1
68379pyrazinamidase-3.5.1.B15
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase-3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
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
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
21367--+/----+/---+/----------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
21367+/-++------+/-+-----+/---

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
16132root of Carex scabrifolia Steud., a halophytic plantCarex scabrifoliaNamhea IslandRepublic of KoreaKORAsia
67770Halophyte, Carex scabrifolia Steud., growing on sand dunesCarex scabrifoliaNamhae IslandRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Aquatic plant
#Host Body-Site#Plant#Root (Rhizome)
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_104225.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_10636;97_12863;98_15823;99_104225&stattab=map
  • Last taxonomy: Nocardioides
  • 16S sequence: FJ750845
  • Sequence Identity:
  • Total samples: 1201
  • soil counts: 787
  • aquatic counts: 150
  • animal counts: 194
  • plant counts: 70

Safety information

risk assessment

  • @ref: 16132
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16132
  • description: Nocardioides caricicola 16S ribosomal RNA gene, partial sequence
  • accession: FJ750845
  • length: 1401
  • database: ena
  • NCBI tax ID: 634770

GC content

@refGC-contentmethod
1613271.7
6777071.7high performance liquid chromatography (HPLC)

External links

@ref: 16132

culture collection no.: DSM 22177, KACC 13778, JCM 17686

straininfo link

  • @ref: 80399
  • straininfo: 401120

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20173009Nocardioides caricicola sp. nov., an endophytic bacterium isolated from a halophyte, Carex scabrifolia Steud.Song GC, Yasir M, Bibi F, Chung EJ, Jeon CO, Chung YRInt J Syst Evol Microbiol10.1099/ijs.0.019919-02010Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, Cluster Analysis, Cyperaceae/*microbiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Hydrogen-Ion Concentration, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Salt-Tolerant Plants/microbiology, Sequence Analysis, DNA, TemperatureGenetics
Phylogeny23667145Nocardioides salsibiostraticola sp. nov., isolated from biofilm formed in coastal seawater.Cho Y, Jang GI, Hwang CY, Kim EH, Cho BCInt J Syst Evol Microbiol10.1099/ijs.0.051037-02013Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, *Biofilms, DNA, Bacterial/genetics, Diaminopimelic Acid/*analysis, Fatty Acids/analysis, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Svalbard, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny27381405Nocardioides intraradicalis sp. nov., isolated from the roots of Psammosilene tunicoides W. C. Wu et C. Y. Wu.Huang MJ, Huang HQ, Salam N, Xiao M, Duan YQ, Kim CJ, Li QQ, Chen W, Li WJInt J Syst Evol Microbiol10.1099/ijsem.0.0012742016Actinomycetales/*classification/genetics/isolation & purification, Base Composition, Caryophyllaceae/*microbiology, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16132Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22177)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22177
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
21367Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM22177.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
29743Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2612528776041
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68379Automatically annotated from API Coryne
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
80399Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID401120.1StrainInfo: A central database for resolving microbial strain identifiers