Strain identifier

BacDive ID: 141144

Type strain: Yes

Species: Novosphingobium oryzae

Strain Designation: ZYY112

Strain history: X. Zhang; ACCC, China; ZYY112.

NCBI tax ID(s): 1522744 (species)

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

@ref: 44064

BacDive-ID: 141144

DSM-Number: 29082

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

description: Novosphingobium oryzae ZYY112 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from rice roots at tillering.

NCBI tax id

  • NCBI tax id: 1522744
  • Matching level: species

strain history

  • @ref: 67770
  • history: X. Zhang; ACCC, China; ZYY112.

doi: 10.13145/bacdive141144.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Erythrobacteraceae
  • genus: Novosphingobium
  • species: Novosphingobium oryzae
  • full scientific name: Novosphingobium oryzae Zhang et al. 2016

@ref: 44064

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Novosphingobium

species: Novosphingobium oryzae

strain designation: ZYY112

type strain: yes

Morphology

cell morphology

  • @ref: 44064
  • gram stain: negative
  • cell length: 1 µm
  • cell width: 0.7 µm
  • cell shape: rod-shaped

colony morphology

  • @ref: 44064
  • colony color: yellow
  • incubation period: 3-4 days
  • medium used: R2A agar

Culture and growth conditions

culture medium

@refnamegrowth
44064Reasoner's 2A agar (R2A)yes
44064TSByes

culture temp

@refgrowthtypetemperaturerange
44064positivegrowth20-40
67770positivegrowth30mesophilic

culture pH

  • @ref: 44064
  • ability: positive
  • type: growth
  • pH: 5.0-8.0

Physiology and metabolism

oxygen tolerance

  • @ref: 44064
  • oxygen tolerance: aerobe

halophily

  • @ref: 44064
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-0.8 %(w/v)

observation

  • @ref: 67770
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4406417057cellobiose-assimilation
4406415824D-fructose-assimilation
4406415971L-histidine-assimilation
4406415603L-leucine-assimilation
4406417295L-phenylalanine-assimilation
4406462345L-rhamnose-assimilation
4406425115malate-assimilation
4406428053melibiose-assimilation
4406417992sucrose-assimilation
4406429016arginine-hydrolysis
44064casein-hydrolysis
4406416947citrate-hydrolysis
440645291gelatin-hydrolysis
4406428017starch-hydrolysis
4406416199urea-hydrolysis
44064309162-oxoglutarate+assimilation
4406418333D-arabitol+assimilation
4406424996lactate+assimilation
4406430849L-arabinose+assimilation
4406418287L-fucose+assimilation
4406475146monomethyl succinate+assimilation
4406430031succinate+assimilation
4406427082trehalose+assimilation
4406427248urocanic acid+assimilation
4406417151xylitol+assimilation
440644853esculin+hydrolysis
4406417632nitrate+reduction
44064167632-oxobutanoate+/-assimilation
4406417925alpha-D-glucose+/-assimilation
440648295beta-hydroxybutyrate+/-assimilation
4406412936D-galactose+/-assimilation
4406416024D-mannose+/-assimilation
4406417924D-sorbitol+/-assimilation
44064167244-hydroxybutyrate+/-assimilation
4406417203L-proline+/-assimilation
4406451850methyl pyruvate+/-assimilation
44064143136succinamate+/-assimilation

metabolite production

  • @ref: 44064
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
44064catalase+1.11.1.6
44064cytochrome oxidase+1.9.3.1
44064beta-galactosidase+3.2.1.23

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    44064C14:0 2OH13.2
    44064C16:012.9
    44064C16:1ω7c / C16:1ω6c14.5
    44064C18:1ω7c / C18:1ω6c50.7
    44064cyclo-C17:02.6
    44064cyclo-C19:0ω8c2.4
  • type of FA analysis: whole cell analysis
  • incubation medium: TSA
  • library/peak naming table: TSBA 6.0
  • system: MIS MIDI
  • method/protocol: Sasser, 1990
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
44064rice roots at tilleringQiyang County, Hunan ProvinceChinaCHNAsia
67770Rice roots in Hunan ProvinceChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root (Rhizome)

taxonmaps

  • @ref: 69479
  • File name: preview.99_12650.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_323;97_359;98_9534;99_12650&stattab=map
  • Last taxonomy: Novosphingobium oryzae
  • 16S sequence: KJ940052
  • Sequence Identity:
  • Total samples: 696
  • soil counts: 301
  • aquatic counts: 257
  • animal counts: 81
  • plant counts: 57

Sequence information

16S sequences

  • @ref: 44064
  • description: 16S rRNA gene sequence
  • accession: KJ940052
  • database: nuccore

GC content

  • @ref: 44064
  • GC-content: 60.8
  • method: thermal denaturation, midpoint method (Tm)

External links

@ref: 44064

culture collection no.: ACCC 06131, JCM 30537, DSM 29082, BCRC 81083

literature

  • topic: Phylogeny
  • Pubmed-ID: 26514117
  • title: Novosphingobium oryzae sp. nov., a potential plant-promoting endophytic bacterium isolated from rice roots.
  • authors: Zhang L, Gao JS, Kim SG, Zhang CW, Jiang JQ, Ma XT, Zhang J, Zhang XX
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.000718
  • year: 2015
  • mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Oryza/*microbiology, Phospholipids/chemistry, *Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spermidine/chemistry, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/chemistry
  • topic2: Genetics

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
44064Lei Zhang, Ju-Sheng Gao, Song-Gun Kim, Cai-Wen Zhang, Ju-Quan Jiang, Xiao-Tong Ma, Jun Zhang and Xiao-Xia ZhangNovosphingobium oryzae sp. nov., a potential plant-promoting endophytic bacterium isolated from rice roots10.1099/ijsem.0.000718IJSEM 66: 302-307 201626514117
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/