Strain identifier

BacDive ID: 140784

Type strain: Yes

Species: Nocardioides agrisoli

Strain Designation: djl-8

Strain history: <- Qing Hong, Nanjing Agricultural Univ.

NCBI tax ID(s): 1882242 (species)

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General

@ref: 43562

BacDive-ID: 140784

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

description: Nocardioides agrisoli djl-8 is an aerobe, mesophilic, Gram-positive bacterium that forms circular colonies and was isolated from pesticide-contaminated farmland soil.

NCBI tax id

  • NCBI tax id: 1882242
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- Qing Hong, Nanjing Agricultural Univ.

doi: 10.13145/bacdive140784.20230509.8.1

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 agrisoli
  • full scientific name: Nocardioides agrisoli Wang et al. 2017

@ref: 43562

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Propionibacteriales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides agrisoli

strain designation: djl-8

type strain: yes

Morphology

cell morphology

  • @ref: 43562
  • gram stain: positive
  • cell length: 0.9-1.3 µm
  • cell width: 0.4-0.6 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 43562
  • colony size: 0.5-1 mm
  • colony color: milky white
  • colony shape: circular
  • incubation period: 5 days
  • medium used: Luria Bertani agar

Culture and growth conditions

culture medium

  • @ref: 43562
  • name: LB (Luria-Bertani) MEDIUM
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
43562positivegrowth25-37mesophilic
43562positiveoptimum30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepH
43562positivegrowth5.5-8
43562positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
43562aerobe
67771aerobe

spore formation

  • @ref: 43562
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
43562NaClpositivegrowth0.5-4 %(w/v)
43562NaClpositiveoptimum1.5 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
43562168082-dehydro-D-gluconate-assimilation
43562581435-dehydro-D-gluconate-assimilation
4356227613amygdalin-assimilation
4356218305arbutin-assimilation
4356227689decanoate-assimilation
4356216947citrate-assimilation
4356215824D-fructose-assimilation
4356212936D-galactose-assimilation
4356262318D-lyxose-assimilation
4356216988D-ribose-assimilation
4356216443D-tagatose-assimilation
4356265327D-xylose-assimilation
4356217113erythritol-assimilation
435624853esculin-assimilation
4356228066gentiobiose-assimilation
4356217754glycerol-assimilation
4356217268myo-inositol-assimilation
4356215443inulin-assimilation
4356230849L-arabinose-assimilation
4356217266L-sorbose-assimilation
4356265328L-xylose-assimilation
4356229864mannitol-assimilation
4356228053melibiose-assimilation
4356274863methyl beta-D-xylopyranoside-assimilation
4356218401phenylacetate-assimilation
4356216634raffinose-assimilation
4356217814salicin-assimilation
4356232528turanose-assimilation
435624853esculin-hydrolysis
4356217368hypoxanthine-hydrolysis
4356216199urea-hydrolysis
4356215318xanthine-hydrolysis
4356217632nitrate-reduction
4356217128adipate+assimilation
4356217057cellobiose+assimilation
4356215963ribitol+assimilation
4356217108D-arabinose+assimilation
4356218333D-arabitol+assimilation
4356228847D-fucose+assimilation
4356217634D-glucose+assimilation
4356216024D-mannose+assimilation
4356225115malate+assimilation
4356216813galactitol+assimilation
4356224265gluconate+assimilation
4356228087glycogen+assimilation
4356218403L-arabitol+assimilation
4356218287L-fucose+assimilation
4356262345L-rhamnose+assimilation
4356217716lactose+assimilation
4356217306maltose+assimilation
435626731melezitose+assimilation
4356243943methyl alpha-D-mannoside+assimilation
4356237657methyl D-glucoside+assimilation
4356230911sorbitol+assimilation
4356217992sucrose+assimilation
4356227082trehalose+assimilation
4356217151xylitol+assimilation
43562casein+hydrolysis
435625291gelatin+hydrolysis
4356228017starch+hydrolysis
4356253426tween 80+hydrolysis

metabolite production

  • @ref: 43562
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
43562cytochrome oxidase+1.9.3.1
43562alpha-glucosidase-3.2.1.20
43562alkaline phosphatase-3.1.3.1
43562esterase Lipase (C 8)-
43562leucine arylamidase-3.4.11.1
43562valine aminopeptidase-
43562naphthol-AS-BI-phosphohydrolase+/-
43562catalase+1.11.1.6
43562urease-3.5.1.5
43562esterase (C 4)-
43562lipase (C 14)-
43562valine arylamidase-
43562trypsin-3.4.21.4
43562alpha-chymotrypsin-3.4.21.1
43562acid phosphatase-3.1.3.2
43562alpha-galactosidase-3.2.1.22
43562beta-galactosidase-3.2.1.23
43562beta-glucosidase-3.2.1.21
43562beta-glucuronidase-3.2.1.31
43562N-acetyl-beta-glucosaminidase-3.2.1.52
43562alpha-mannosidase-3.2.1.24
43562alpha-fucosidase-3.2.1.51
43562cystine arylamidase+3.4.11.3

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
43562pesticide-contaminated farmland soilNanjing, Jiangsu ProvinceChinaCHNAsia32.033119.283
67771From soilNanjing, Jiangsu ProvinceChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture
#Engineered#Contamination
#Environmental#Terrestrial#Soil

Sequence information

16S sequences

  • @ref: 43562
  • description: 16S rRNA gene sequence
  • accession: KX380192
  • database: nuccore

GC content

  • @ref: 43562
  • GC-content: 69.3
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 43562

culture collection no.: KCTC 39844, CCTCC AB 2017058

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny28875902Nocardioides agrisoli sp. nov., isolated from farmland soil.Wang X, Jiang WK, Cui MD, Yang ZG, Yu X, Hu G, Zhang H, Hong QInt J Syst Evol Microbiol10.1099/ijsem.0.0021582017Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny35333153Nocardioides mangrovi sp. nov., a novel endophytic actinobacterium isolated from root of Kandelia candel.Chen MS, Chen F, Chen XH, Zheng ZQ, Ma X, Tuo LInt J Syst Evol Microbiol10.1099/ijsem.0.0052952022Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nocardioides, Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizophoraceae/microbiology, Sequence Analysis, DNATranscriptome

Reference

@idauthorstitledoi/urljournalpubmed
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
43562Xiang Wang, Wan-Kui Jiang, Meng-Di Cui, Zhan-Gong Yang, Xing Yu, Gang Hu, Hao Zhang, Qing HongNocardioides agrisoli sp. nov., isolated from farmland soil10.1099/ijsem.0.002158IJSEM 67: 3722-3727 201728875902
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc