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Updated: Apr 12, 2026
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Identification of Rare Bacterial Pathogens by 16S rRNA Gene Sequencing and MALDI-TOF MS
Published on: July 11, 2016
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Sphingomonas flavescens sp. nov., isolated from soil
Hyosun Lee1, Dhiraj Kumar Chaudhary2, Dong-Uk Kim3
1Department of Biological Science, College of Science and Engineering, Sangji University, Wonju, 26339, Republic of Korea.
Archives of Microbiology
|February 24, 2024
Summary
A novel aerobic bacterium, Sphingomonas flavescens strain PT-12T, was isolated from agricultural soil. Polyphasic taxonomic analysis confirms it represents a new species within the Sphingomonas genus.
Area of Science:
- Microbiology
- Bacteriology
- Taxonomy
Background:
- Soil harbors diverse microbial communities crucial for ecosystem health.
- Accurate bacterial classification is essential for understanding microbial roles and interactions.
- The genus Sphingomonas is known for its metabolic versatility and presence in various environments.
Purpose of the Study:
- To isolate and characterize a novel aerobic bacterium from agricultural soil.
- To determine the taxonomic position of the isolated strain using a polyphasic approach.
- To propose a new species within the Sphingomonas genus.
Main Methods:
- Isolation and cultivation of aerobic bacteria from agricultural soil.
- Gram staining, motility tests, and biochemical assays (catalase, oxidase).
- Physiological tests for growth conditions (temperature, salinity, pH).
- 16S rRNA gene sequencing and phylogenetic analysis.
- Genome sequencing to determine genome size and DNA G+C content.
- Average Nucleotide Identity (ANI) and digital DNA-DNA hybridization (dDDH) calculations.
- Chemotaxonomic analyses including fatty acid profiling and polar lipid analysis.
Main Results:
- Strain PT-12T is a Gram-negative, non-motile, rod-shaped, aerobic bacterium.
- Optimal growth observed between 18-37°C, 0-1.0% NaCl, and pH 6.0-8.0.
- Phylogenetic analysis placed strain PT-12T within the genus Sphingomonas, with highest 16S rRNA similarity to S. limnosediminicola (98.4%).
- Genome size is 2,656,862 bp with a DNA G+C content of 63.5%.
- ANI and dDDH values indicated distinctness from related species, with highest values to S. segetis YJ09T (76.2% ANI, 20.2% dDDH).
- Chemotaxonomic data (Q-10, homospermidine, specific fatty acids, and polar lipids) supported its classification.
Conclusions:
- The polyphasic data strongly support the classification of strain PT-12T as a novel species.
- The proposed name for this new species is Sphingomonas flavescens sp. nov.
- The type strain is PT-12T (KCTC 92114T = NBRC 115717T).
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