Rhizobium glycinendophyticum


Citation

Formal styling
Rhizobium glycinendophyticum Wang et al., 2020 (priority 2025)
Effective publication
Wang et al., 2020
SeqCode status
Valid (SeqCode)
Register List
seqco.de/r:aic8iu0f (validated)
Canonical URL
https://seqco.de/i:39360

Nomenclature

Rank
Species
Syllabication
gly.cin.en.do.phy'ti.cum
Etymology
N.L. fem. n. Glycine, the botanical genus name of the soy bean; Gr. pref. endo-, within; Gr. neut. n. phyton, plant; L. neut. adj. suff. -icum, used with the sense of belonging to; N.L. neut. adj. glycinendophyticum, an endophyte of soybean
Nomenclatural type
NCBI Assembly: GCF_006443685.1
Reference strain
Strain sc|0039552: CL12 = GDMCC 1.1597 = KACC 21281 Lookup StrainInfo
Nomenclatural status
Validly published under the SeqCode

Taxonomy

Description
Grow well on NA, BHI and 272 agar, but not on MacConkey and TSA agar. After 2 days of incubation at 30 °C on R2A agar, colonies are cream and circular, and cells are Gram-stain-negative, oxidase-positive, catalase-positive, aerobic, motile, rod-shaped and approximately 1.4–2.9 μm long and 0.6–0.8 μm wide (Fig. S4). The temperature range for growth is 10–42 °C (optimum, 30 °C). The pH range for growth is pH 5.0–9.5 (optimum, pH 7.0). Growth occurs at a NaCl concentration of 0–4.5% (optimum, 2.0%). It could not hydrolyse starch, CM-cellulose, casein, chitin, Tween 20, 40 and 80. It does not contain the nodulation genes (nodC and nodA) and nitrogenase reductase gene (nifH). The predominant fatty acids (> 5% of the total amounts) include Summed Feature 8 (C18:1ω7c and/or C18:1ω6c, 72.9%), Summed Feature 2 (iso-C16:1 I and/or C14:0 3-OH, 6.3%) and C18:0 (5.7%).

The type strain, CL12T (=GDMCC 1.1597T = KACC 21281T), was isolated from roots of G. max (Linn. Merr.). The genome size is 4.84 Mbp, with a high genomic DNA G+C content of 61.1 mol%. The GenBank accession numbers of 16S rRNA, recA, atpD, rpoB, glnA gene sequences and the whole genome sequence of strain CL12T are MF383489, MN087401, MN087402, MN087403, MN087404, and VFYP00000000, respectively.

Classification
Bacteria » Pseudomonadota » Alphaproteobacteria » Hyphomicrobiales » Rhizobiaceae » Rhizobium » Rhizobium glycinendophyticum
Parent
Rhizobium ncbi
Alternative placements

Genomics

Accession
NCBI Assembly:GCF_006443685.1
Cultures
Strain sc|0039552
Type
Isolate Genome
Estimated Quality Metrics
  • Completeness: 99.1%
  • Contamination: 0.9%
  • Quality: 94.6
Ribosomal and transfer RNA genes
  • 1 16S rRNA (up to 100.0%)
  • 1 23S rRNA (up to 100.0%)
  • tRNAs for 20 amino acids
Sequencing depth
206.0 ×
Source
Other features
  • G+C Content: 61.1%
  • Coding Density: 88.89%
  • Codon Table: 11
  • N50: 2,995,531 bp
  • Contigs: 16
  • Largest Contig: 2,995,531 bp
  • Assembly Length: 4,843,317 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 07:08 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
Wang et al., 2020, Antonie van Leeuwenhoek Rhizobium glycinendophyticum sp. nov., isolated from roots of Glycine max (Linn. Merr.)
Effective publication



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