Detecting Useful RAPD Markers for DNA Virus Diversity Analysis in Soil Samples

Abstract

Viruses, including bacteriophages, influence bacterial life and contribute to soil structure modification. Their genomes primarily exist in DNA form. Therefore, it is essential to understand the diversity of DNA viruses in agricultural soils, which serve as habitats for beneficial bacteria such as Rhizobium and Azotobacter species. These viruses play a significant role in microbial dynamics by regulating bacterial populations, facilitating gene transfer, and impacting nutrient cycling within the soil ecosystem. This study aims to identify useful random amplified polymorphic DNA (RAPD) markers for detecting DNA virus diversity in soil. Twenty-five primers were tested using the PCR method with 50 soil samples collected from 44 locations where bean cultivation is prevalent in six geographical regions of Turkey. The soil samples were meticulously filtered using a 0.22-µm filter and the filtered samples were checked for eukaryotic and prokaryotic contamination markers. All primers' PCR amplification efficiency and the useful primers' polymorphism information content values were calculated.

Binary data were obtained using Phoretix1D software and a dendrogram illustrating the DNA virus diversity of the soil samples was created. Principal coordinates analysis of the samples was performed using GenAlEx software. PCR and dendrogram analysis revealed the primers that effectively distinguished and compared DNA virus diversity in soils.