Rhizobium indicum


Citation

Formal styling
Rhizobium indicum Rahi et al., 2020 (priority 2025)
Effective publication
Rahi et al., 2020
SeqCode status
Valid (SeqCode)
Register List
seqco.de/r:6pz9wau1 (validated)
Canonical URL
https://seqco.de/i:49630

Nomenclature

Rank
Species
Syllabication
in.di'cum
Etymology
L. neut. adj. indicum, of or belonging to India, where the type strain was isolated from the root nodules of pea cultivated in the trans-Himalayan region of India
Nomenclatural type
NCBI Assembly: GCA_005862305.2
Reference strain
Strain sc|0039555: JKLM 12A2 = JCM 33658 = KACC 21380 = MCC 3961 Lookup StrainInfo
Nomenclatural status
Validly published under the SeqCode

Taxonomy

Description
Cells are Gram-negative, aerobic, rod-shaped, motile, and 0.3–0.6 × 2–3 μm in size. Colonies are translucent, cream-white and circular convex, and grow 0.1 to 0.2 cm in diameter after three days of growth on YMA medium at 28 °C. Optimum growth observed at a pH of 7.0, a temperature of 28 °C, and a NaCl concentration of 0.25% (w/v). Strains do not grow at temperatures 4 °C and below 4 °C or at 40 °C and above 40 °C, at pH values of 4.0 or above 9.0, or at NaCl concentrations above 0.8% (w/v).
The genome consisted of 7,533,049 bp, with a circular chromosome of 5030 kb and five large circular plasmids ranging between 292 and 1125 kb.
The major fatty acids detected were C18:1 ω7c, C18:0, C14:0 3OH/C16:1 iso I, C16:0, C19:0 cyclo ω8c, C18:0 3OH, C18:1 ω7c 11-methyl, and C16:0 3OH, with a higher proportion of C18:0 in comparison to the type strains of other species. MALDI-TOF MS mean spectra profile has eight unique peaks in contrast to the type strains closely related to Rhizobium species.
Positive for catalase and oxidase. d-trehalose, sucrose, d-turanose, d-fructose, L-fucose, d-fructose-6-phosphate, pectin, d-galacturonic acid, d-glucuronic acid, glucuronamide, and acetic acid were assimilated on Biolog GENIII plates. The assimilation of dextrin, d-maltose, d-cellobiose, gentiobiose, stachyose, d-raffinose, α-d-lactose, d-melibiose, β-methyl-d-glucoside, d-salicin, N-acetyl-d-glucosamine, N-acetyl-β-d-mannosamine, N-acetyl-d-galactosamine, N-acetyl neuraminic acid, α-d-glucose, d-mannose, d-furctose, d-galactose, 3-methyl glucose, d-fucose, l-rhamnose, inosine, d-sorbitol, d-mannitol, d-arabitol, myo-inositol, glycerol, d-glucose-6-PO4, d-aspartic acid, d-serine, gelatin, glycyl-l-proline, l-alanine, l-arginine, l-asparatic acid, l-Glutamic acid, l-histidine, l-pyroglutamic acid, l-serine, mucic acid, quinic acid, d-saccharic acid, p-hydroxy-phenylacetic acid, methyl pyruvate, d-lactic acid methyl easter, l-lactic acid, citric acid, α-keto-glutaric acid, d-malic acid, l-malic acid, bromo-succinic acid, tween 40, γ-amino-butyric acid, α-hydroxy-butyric acid, α-hydroxy-D,L butyric acid, α-keto-butyric acid, acetoacetic acid, propionic acid and formic acid is negative. Sensitive to sodium lactate 1%, fusidic acid, d-serine, troleandomycin, rifamycin sv, minocycline, lincomycin, guanidine HCl, niaproof 4, vancomycin, tetrazolium violet, tetrazolium blue, nalidixic acid, lithium chloride, potassium tellurite, aztreonam, sodium butyrate and sodium bromate on Biolog GENIII plates.
Positive for nitrates to nitrogen conversion, aesculin hydrolysis, and β-galactosidase activity, and negative for nitrate reduction to nitrites, indole production from tryptophane, glucose acidification, arginine dihydrolase, urease, gelatine hydrolysis, and assimilation of glucose, arabinose, mannose, mannitol, N-acetyl-glucosamine, maltose, gluconate, caprate, adipate, malate, citrate and phenyl-acetate on API 20NE test strips. Positive for alkaline phosphatase, napthol phosphohydrolyase, α-glucosidase, esterase (C4), esterase lipase (C8), leucine arylamidase, acid phosphatase, valine arylamidase, cysteine arylamidase, trypsin, β-galactosidase, β-glucosidase, α-mannosidase and N-acetyl-β-glusaminidase, and negative for lipase, α-chymotrypsin, α-galactosidase, β-glucournidase and α-fucosidase on the API-Zym test strips.
Classification
Bacteria » Pseudomonadota » Alphaproteobacteria » Hyphomicrobiales » Rhizobiaceae » Rhizobium » Rhizobium indicum
Parent
Rhizobium ncbigtdb

Genomics

Accession
NCBI Assembly:GCA_005862305.2
Cultures
Strain sc|0039555
Type
Isolate Genome
Estimated Quality Metrics
  • Completeness: 99.1%
  • Contamination: 3.8%
  • Quality: 80.1
Ribosomal and transfer RNA genes
  • 3 16S rRNAs (up to 100.0%)
  • 3 23S rRNAs (up to 100.0%)
  • tRNAs for 20 amino acids
Sequencing depth
91.0 ×
Source
Other features
  • G+C Content: 60.8%
  • Coding Density: 86.91%
  • Codon Table: 11
  • N50: 5,030,384 bp
  • Contigs: 6
  • Largest Contig: 5,030,384 bp
  • Assembly Length: 7,533,049 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
12 months 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 07:25 PM (UTC)

Publications
1

Citation Title
Rahi et al., 2020, Systematic and Applied Microbiology Rhizobium indicum sp. nov., isolated from root nodules of pea (Pisum sativum) cultivated in the Indian trans-Himalayas
Effective publication



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