Strain identifier

BacDive ID: 132515

Type strain: Yes

Species: Nocardioides pocheonensis

Strain history: KACC 14275 <-- W.-T. Im; Hankyoung Natl. Univ., South Korea; Gsoil 818.

NCBI tax ID(s): 661485 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 24304

BacDive-ID: 132515

DSM-Number: 22773

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

description: Nocardioides pocheonensis DSM 22773 is an aerobe, Gram-positive, rod-shaped bacterium that forms circular colonies and was isolated from soil from a ginseng field.

NCBI tax id

  • NCBI tax id: 661485
  • Matching level: species

strain history

@refhistory
24304<- S.-T. Lee, KAIST <- W.-T. Im; Gsoil 818
67770KACC 14275 <-- W.-T. Im; Hankyoung Natl. Univ., South Korea; Gsoil 818.

doi: 10.13145/bacdive132515.20230509.8.1

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 pocheonensis
  • full scientific name: Nocardioides pocheonensis (Lee et al. 2016) Wang et al. 2023
  • synonyms

    • @ref: 20215
    • synonym: Marmoricola pocheonensis

@ref: 24304

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Marmoricola

species: Marmoricola pocheonensis

full scientific name: Marmoricola pocheonensis Lee et al. 2016

type strain: yes

Morphology

cell morphology

  • @ref: 43654
  • gram stain: positive
  • cell length: 1-2 µm
  • cell width: 0.3-0.4 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 43654
  • colony size: 0.5-1 mm
  • colony color: Ivory
  • colony shape: circular
  • incubation period: 3 days
  • medium used: R2A agar plates

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43654Reasoner's 2A agar (R2A)yes
24304R2A 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

culture temp

@refgrowthtypetemperaturerange
43654positivegrowth10-40
43654positiveoptimum30mesophilic
24304positivegrowth28mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepH
43654positivegrowth6-8
43654positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 43654
  • oxygen tolerance: aerobe

spore formation

  • @ref: 43654
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentrationhalophily level
43654NaClpositivegrowth0-2 %(w/v)
43654NaClpositiveoptimum0 %(w/v)non-halophilic

observation

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

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
436542-oxogluconate-assimilation
436543-hydroxybenzoate-assimilation16193
436545-dehydro-D-gluconate-assimilation58143
43654acetate-assimilation30089
43654decanoate-assimilation27689
43654citrate-assimilation16947
43654D-mannitol-assimilation16899
43654D-mannose-assimilation16024
43654D-ribose-assimilation16988
43654D-sorbitol-assimilation17924
43654lactate-assimilation24996
43654malate-assimilation25115
43654itaconate-assimilation17240
43654L-alanine 4-nitroanilide-assimilation
43654L-fucose-assimilation18287
43654L-rhamnose-assimilation62345
43654L-serine-assimilation17115
43654malonate-assimilation15792
43654maltose-assimilation17306
43654melibiose-assimilation28053
43654phenylacetate-assimilation18401
43654propionate-assimilation17272
43654salicin-assimilation17814
43654suberic acid-assimilation9300
43654sucrose-assimilation17992
43654glucose-fermentation17234
43654cellulose-hydrolysis62968
43654dna-hydrolysis16991
43654gelatin-hydrolysis5291
43654starch-hydrolysis28017
436543-hydroxybutyrate+assimilation37054
436544-hydroxybenzoate+assimilation17879
43654adipate+assimilation17128
43654D-glucose+assimilation17634
43654gluconate+assimilation24265
43654glycogen+assimilation28087
43654myo-inositol+assimilation17268
43654L-arabinose+assimilation30849
43654L-histidine+assimilation15971
43654L-proline+assimilation17203
43654N-acetylglucosamine+assimilation506227
43654valerate+assimilation31011
43654esculin+hydrolysis4853
43654skimmed milk+hydrolysis
43654nitrate+reduction17632

metabolite production

  • @ref: 43654
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
43654catalase+1.11.1.6
43654cytochrome oxidase-1.9.3.1
43654esterase Lipase (C 8)+
43654beta-galactosidase+3.2.1.23
43654alpha-glucosidase+3.2.1.20
43654beta-glucosidase+3.2.1.21
43654alkaline phosphatase-3.1.3.1
43654lipase (C 14)-
43654leucine arylamidase-3.4.11.1
43654valine arylamidase-
43654cystine arylamidase-3.4.11.3
43654trypsin-3.4.21.4
43654esterase (C 4)+
43654acid phosphatase+3.1.3.2
43654naphthol-AS-BI-phosphohydrolase+
43654arginine dihydrolase-3.5.3.6
43654urease-3.5.1.5
43654alpha-chymotrypsin-3.4.21.1
43654alpha-galactosidase-3.2.1.22
43654beta-glucuronidase-3.2.1.31
43654N-acetyl-beta-glucosaminidase-3.2.1.52
43654alpha-mannosidase-3.2.1.24
43654alpha-fucosidase-3.2.1.51

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
24304soil from a ginseng fieldPocheon ProvinceRepublic of KoreaKORAsia
43654Soil of a ginseng fieldPocheon ProvinceRepublic of KoreaKORAsia
67770Ginseng field in Pocheon ProvinceRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_56180.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_723;97_7475;98_40112;99_56180&stattab=map
  • Last taxonomy: Marmoricola pocheonensis
  • 16S sequence: GQ339906
  • Sequence Identity:
  • Total samples: 276
  • soil counts: 226
  • aquatic counts: 8
  • animal counts: 22
  • plant counts: 20

Safety information

risk assessment

  • @ref: 24304
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24304
  • description: Marmoricola pocheonensis strain Gsoil 818 16S ribosomal RNA gene, partial sequence
  • accession: GQ339906
  • length: 1457
  • database: ena
  • NCBI tax ID: 661485

Genome sequences

  • @ref: 67770
  • description: Marmoricola pocheonensis Gsoil 818
  • accession: GCA_003725535
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 661485

GC content

@refGC-contentmethod
4365470high performance liquid chromatography (HPLC)
2430470.0high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno76.265yes
flagellatedno93.844yes
gram-positiveyes88.278no
anaerobicno98.751yes
aerobicyes92.147yes
halophileno96.693yes
spore-formingno83.259yes
glucose-utilyes88no
thermophileno95.181yes
glucose-fermentno88.528yes

External links

@ref: 24304

culture collection no.: DSM 22773, KACC 14275, Gsoil 818, JCM 32749

straininfo link

  • @ref: 90841
  • straininfo: 406886

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny26883120Marmoricola ginsengisoli sp. nov. and Marmoricola pocheonensis sp. nov. isolated from a ginseng-cultivating field.Lee HY, Liu Q, Kang MS, Kim SK, Lee SY, Im WTInt J Syst Evol Microbiol10.1099/ijsem.0.0009772016Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Panax/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny30821673Marmoricola mangrovicus sp. nov., an endophytic actinobacterium isolated from Kandelia candel.Li FN, Jiang ZK, Liu SW, Tuo L, Lee SM, Sun CHInt J Syst Evol Microbiol10.1099/ijsem.0.0033262019Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Plant Bark/*microbiology, RNA, Ribosomal, 16S/genetics, Rhizophoraceae/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny31995462Marmoricola caldifontis sp. nov., a novel actinobacterium isolated from a hot spring.Habib N, Khan IU, Xiao M, Li S, Saqib M, Xian WD, Butt S, Li WJInt J Syst Evol Microbiol10.1099/ijsem.0.0040162020Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Hot Springs/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tibet, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
24304Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-22773Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22773)
43654Hye-Yeon Lee, Qingmei Liu, Myung-Suk Kang, Soo-Ki Kim, Soon-Youl Lee, Wan-Taek ImMarmoricola ginsengisoli sp. nov. and Marmoricola pocheonensis sp. nov. isolated from a ginseng-cultivating field10.1099/ijsem.0.000977IJSEM 66: 1996-2001 201626883120
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
90841Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID406886.1