Strain identifier
BacDive ID: 141144
Type strain:
Species: Novosphingobium oryzae
Strain Designation: ZYY112
Strain history: X. Zhang; ACCC, China; ZYY112.
NCBI tax ID(s): 1522744 (species)
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
@ref | name | growth |
---|---|---|
44064 | Reasoner's 2A agar (R2A) | yes |
44064 | TSB | yes |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
44064 | positive | growth | 20-40 | |
67770 | positive | growth | 30 | mesophilic |
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
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
44064 | 17057 | cellobiose | - | assimilation |
44064 | 15824 | D-fructose | - | assimilation |
44064 | 15971 | L-histidine | - | assimilation |
44064 | 15603 | L-leucine | - | assimilation |
44064 | 17295 | L-phenylalanine | - | assimilation |
44064 | 62345 | L-rhamnose | - | assimilation |
44064 | 25115 | malate | - | assimilation |
44064 | 28053 | melibiose | - | assimilation |
44064 | 17992 | sucrose | - | assimilation |
44064 | 29016 | arginine | - | hydrolysis |
44064 | casein | - | hydrolysis | |
44064 | 16947 | citrate | - | hydrolysis |
44064 | 5291 | gelatin | - | hydrolysis |
44064 | 28017 | starch | - | hydrolysis |
44064 | 16199 | urea | - | hydrolysis |
44064 | 30916 | 2-oxoglutarate | + | assimilation |
44064 | 18333 | D-arabitol | + | assimilation |
44064 | 24996 | lactate | + | assimilation |
44064 | 30849 | L-arabinose | + | assimilation |
44064 | 18287 | L-fucose | + | assimilation |
44064 | 75146 | monomethyl succinate | + | assimilation |
44064 | 30031 | succinate | + | assimilation |
44064 | 27082 | trehalose | + | assimilation |
44064 | 27248 | urocanic acid | + | assimilation |
44064 | 17151 | xylitol | + | assimilation |
44064 | 4853 | esculin | + | hydrolysis |
44064 | 17632 | nitrate | + | reduction |
44064 | 16763 | 2-oxobutanoate | +/- | assimilation |
44064 | 17925 | alpha-D-glucose | +/- | assimilation |
44064 | 8295 | beta-hydroxybutyrate | +/- | assimilation |
44064 | 12936 | D-galactose | +/- | assimilation |
44064 | 16024 | D-mannose | +/- | assimilation |
44064 | 17924 | D-sorbitol | +/- | assimilation |
44064 | 16724 | 4-hydroxybutyrate | +/- | assimilation |
44064 | 17203 | L-proline | +/- | assimilation |
44064 | 51850 | methyl pyruvate | +/- | assimilation |
44064 | 143136 | succinamate | +/- | assimilation |
metabolite production
- @ref: 44064
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
44064 | catalase | + | 1.11.1.6 |
44064 | cytochrome oxidase | + | 1.9.3.1 |
44064 | beta-galactosidase | + | 3.2.1.23 |
fatty acid profile
fatty acids
@ref fatty acid percentage 44064 C14:0 2OH 13.2 44064 C16:0 12.9 44064 C16:1ω7c / C16:1ω6c 14.5 44064 C18:1ω7c / C18:1ω6c 50.7 44064 cyclo-C17:0 2.6 44064 cyclo-C19:0ω8c 2.4 - 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
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
44064 | rice roots at tillering | Qiyang County, Hunan Province | China | CHN | Asia |
67770 | Rice roots in Hunan Province | China | CHN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@id | authors | title | doi/url | journal | pubmed |
---|---|---|---|---|---|
20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | ||
44064 | Lei Zhang, Ju-Sheng Gao, Song-Gun Kim, Cai-Wen Zhang, Ju-Quan Jiang, Xiao-Tong Ma, Jun Zhang and Xiao-Xia Zhang | Novosphingobium oryzae sp. nov., a potential plant-promoting endophytic bacterium isolated from rice roots | 10.1099/ijsem.0.000718 | IJSEM 66: 302-307 2016 | 26514117 |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||
69479 | João 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 beta | https://microbeatlas.org/ |