Rhizobium oryzihabitans


Citation

Formal styling
Rhizobium oryzihabitans Zhao et al., 2020 (priority 2025)
Effective publication
Zhao et al., 2020
SeqCode status
Valid (SeqCode)
Register List
seqco.de/r:nojfpkk5 (validated)
Canonical URL
https://seqco.de/i:38934

Nomenclature

Rank
Species
Syllabication
o.ry.zi.ha.bi'tans
Etymology
L. fem. n. oryza, rice; L. pres. part. habitans, inhabiting, dwelling; N.L. neut. part. adj. oryzihabitans, rice inhabiting
Nomenclatural type
NCBI Assembly: GCF_010669145.1
Reference strain
Strain sc|0039559: M15 = ACCC 60121 = JCM 32903 Lookup StrainInfo
Nomenclatural status
Validly published under the SeqCode

Taxonomy

Description
Cells are Gram-negative, aerobic, flagellate and rods. Colonies are circular and cream-white on YMA at 30 ℃. Growth occurs from 15 ℃ to 50 ℃ and the pH range for growth is 5.0–12.0. The tolerant of NaCl concentrations is up to 7.0% (w/v). Positive reactions for nitrate reduction, aesculin hydrolysis, urease and nitro-D-methyl galactose activities, and assimilation of glucose, arabinose, mannose, mannitol, N-acetyl-glucosamine, maltose, gluconate, malic acid, citric acid, phenylacetic acid are positive. Catalase and oxidase positive. The following compounds utilize as carbon sources: N-acetyl-D-galactosamine, N-acetyl-D-glucosamine, adonitol, L-arabinose, D-arabitol, D-cellobiose, D-fructose, L-fucose, D-galactose, gentiobiose, α-D-glucose, m-inositol, α-D-lactose, lactulose, maltose, D-mannitol, D-mannose, D-melibiose, β-methyl-D-glucoside, D-raffinose, L-rhamnose, D-sorbitol, sucrose, D-trehalose, turanose, xylitol, acetic Acid, D-galactonic acid lactone, D-gluconic Acid, α-keto glutaric acid, DL-lactic acid, propionic acid, quinic acid, succinic acid, D-alanine, L-alanine, L-alanyl-glycine, L-asparagine, L-aspartic acid, L-glutamic acid, L-histidine, hydroxy-L-proline, L-ornithine, L-proline, L-pyroglutamic acid, L-serine, inosine, uridine, glycerol, glucose-1-phosphate, glucose-6-phosphate. The DNA G+C content of type strain is 59.28 mol %. Major cellular fatty acids are summed feature 8 (C18:1 ω7c and/or C18:1ω6c) and Summed feature 2 (aldehyde-C12:0 and/or unknown equivalent chain length).
The type strain, M15T (= JCM 32903T = ACCC 60121T), was isolated from the root of rice.
The GenBank/The European Bioinformatics Institute EMBL-EBI (EMBL))/DNA Data Bank of Japan (DDBJ) accession numbers for the 16S rRNA, recA, ropB and atpD gene sequences of strain M15T are MT023790, MT028481, MT028482 and MT028483, respectively. The complete genome has been deposited in GenBank under the accession numbers of SAMN14048699.
Classification
Bacteria » Pseudomonadota » Alphaproteobacteria » Hyphomicrobiales » Rhizobiaceae » Rhizobium » Rhizobium oryzihabitans
Parent
Rhizobium ncbi
Alternative placements

Genomics

Accession
NCBI Assembly:GCF_010669145.1
Cultures
Strain sc|0039559
Type
Isolate Genome
Estimated Quality Metrics
  • Completeness: 99.1%
  • Contamination: 1.9%
  • Quality: 89.6
Ribosomal and transfer RNA genes
  • 4 16S rRNAs (up to 100.0%)
  • 6 23S rRNAs (up to 100.0%)
  • tRNAs for 20 amino acids
Sequencing depth
150.0 ×
Source
Other features
  • G+C Content: 59.3%
  • Coding Density: 87.21%
  • Codon Table: 11
  • N50: 3,195,345 bp
  • Contigs: 9
  • Largest Contig: 3,195,345 bp
  • Assembly Length: 5,858,741 bp
  • Ambiguous Assembly Fraction: 0.0%
Automated checks
Complete

Last modified 6 months ago

Metadata

Outside links and data sources
Search sequences
Local history
Registered
Almost 2 years ago and claimed 9 months ago by Van Lill, Melandre
Submitted
9 months ago by Van Lill, Melandre
Curators
Validated
6 months ago by St. John, Emily
Date of priority
2025-03-20 07:49 PM (UTC)

Publications
2

Citation Title
Ma et al., 2023, Frontiers in Microbiology Phylogenomic reappraisal of the family Rhizobiaceae at the genus and species levels, including the description of Ectorhizobium quercum gen. nov., sp. nov
Zhao et al., 2020, Microorganisms Isolation, Identification and Characterization of Endophytic Bacterium Rhizobium oryzihabitans sp. nov., from Rice Root with Biotechnological Potential in Agriculture
Effective publication



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