Agrobacterium bohemicum


Citation

Formal styling
Agrobacterium bohemicum Zahradník et al., 2018 (priority 2025)
Effective publication
Zahradník et al., 2018
SeqCode status
Valid (SeqCode)
Register List
seqco.de/r:t5yzyhi5 (validated)
Canonical URL
https://seqco.de/i:49626

Nomenclature

Rank
Species
Syllabication
bo.he'mi.cum
Etymology
N.L. neut. adj. bohemicum, from Bohemia, named in honor of the Garden of Bohemia, a location in the Czech Republic, where the strains were isolated
Nomenclatural type
NCBI Assembly: GCF_002896715.1
Reference strain
Strain sc|0039564: R90 = CCM 8736 = DSM 104667 Lookup StrainInfo
Nomenclatural status
Validly published under the SeqCode

Taxonomy

Description
Cells of A. bohemicum are Gram-negative, rod shaped (0.5–0.7 × 1.5–2.5 μm), forming single cells or ragged aggregates, strictly aerobic and motile. Good growth was monitored on LB, King’s B medium and YMA with or without tellurite (K2TeO3; 70 μg ml−1). Colonies on LB medium have a diameter of 1 mm after 48 h of growth at 28 °C and are white–yellowish, circular, convex and glistening. Strains produce colonies with blue central coloration on aniline blue medium. The growth on Litmus milk medium is accompanied by alkaline reaction. Cells grow between 10 and 35 °C (28–30 °C temperature optimum) in broad pH range (6–11.0) with optimum at pH 7.5. Cells do not grow in the presence of 2% NaCl or higher and are susceptible to all tested antibiotics: ampicillin, kanamycin, gentamicin sulfate, streptomycin, spectinomycin, tetracycline and chloramphenicol. Resistance was observed for acriflavine with MIC 20 μg ml−1. Codeine metabolism seems to be an important characteristic of this Agrobacterium species. This ability has not been published for other Agrobacterium species. The strains do not produce 3-ketolactose from lactose. Other negative tests are: ferric ammonium citrate coloration, citrate utilization and production acid from inositol, meso-erythritol and d-(+)-melezitose. Cells are not able to use nitrate or nitrite as a sole nitrogen source for growth. Good nitrogen sources are ammonium sulfate, ammonium nitrate and l-amino acids asparagine, glutamine, serine, proline, hydroxyproline, threonine and methionine. The strains utilize: adonitol, alanine, d-arabinose, l-arabinose, d-arabitol, l-asparagine, l-aspartate, d-cellobiose, cysteine, d-fructose, galactose, gentibiose, glucosamine, α-d-glucose, l-glutamate, l-glutamine, glycerol, hydroxyproline, inositol, lactose, lyxose, mannose, methyl-α and β-d-glukopyranoside, proline, raffinose, rhamnose, ribose, saccharose, serine, sorbitol, threonine, trehalose, d-mannitol and d-xylose. Weak or limited growth was recorded on valine, glycine, methionine, xylitol, 2-deoxy-d-glucose and methyl α-d-mannopyranoside. Strains are not able to utilize: arginine, tyrosine, histidine, acetamide, malonate, gelatin, starch, Tween 40, Tween 80, casein, lecithin, ornithine, Na-d-salicylate, d-sorbose, N-acetyl neuraminic acid, 3-methyl-glucose, p-OH-phenylacetic acid, α-OH-butyric acid and α-keto-butyric acid. The MLSA and whole-genome analysis confirmed that strains R89-1 and R90 were genetically different from other Agrobacterium species and formed a cluster with A. rubi and A. skierniewicense. The ANI value between strain R90 and Agrobacterium rubi W2/73, the most closely related type strain in the genus Agrobacterium, is only 82%.The type strain R90T was isolated from P. somniferum L. composted material in 2016.
Classification
Bacteria » Pseudomonadota » Alphaproteobacteria » Hyphomicrobiales » Rhizobiaceae » Agrobacterium » Agrobacterium bohemicum
Parent
Agrobacterium ncbigtdb

Genomics

Accession
NCBI Assembly:GCF_002896715.1
Cultures
Strain sc|0039564
Type
Isolate Genome
Estimated Quality Metrics
  • Completeness: 97.2%
  • Contamination: -0.1%
  • Quality: 97.7
Ribosomal and transfer RNA genes
  • 1 16S rRNA (up to 100.0%)
  • 0 23S rRNAs
  • tRNAs for 20 amino acids
Sequencing depth
85.0 ×
Source
Other features
  • G+C Content: 56.2%
  • Coding Density: 88.59%
  • Codon Table: 11
  • N50: 344,460 bp
  • Contigs: 30
  • Largest Contig: 835,148 bp
  • Assembly Length: 4,713,153 bp
  • Ambiguous Assembly Fraction: 0.16%
Submitter comments
Estimated contamination and completeness determined using CheckM, all other analyses performed on MiGA Gateway.
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 04:57 AM (UTC)

Publications
1

Citation Title
Zahradník et al., 2018, Systematic and Applied Microbiology Agrobacterium bohemicum sp. nov. isolated from poppy seed wastes in central Bohemia
Effective publication



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