Highly sensitive detection and quantification of dissolved free extracellular DNA using colloid adsorption and foam concentration

Abstract

Dissolved free extracellular DNA (exDNA), DNA released outside the cell, is present in aquatic environments at very low concentrations. Additionally, exDNA passes through a 0.22 μm filter, making it difficult to capture for analysis. Thus, information on exDNA is scarce, and the composition of genes present in exDNA is unknown. In this study, we developed a process for highly concentrating exDNA adsorbed on colloids and then dissolving the colloids with an acid using colloidal adsorption and foam concentration. After applying this strategy, 66.3% ± 3.3% of the uidA gene and 39.4% ± 2.4% of the tetA gene were recovered from genomic DNA carrying the uidA gene and plasmids carrying the tetA gene (n = 3), respectively. Using the developed method, 1000 mL of effluent of a wastewater treatment plant was concentrated to 400 μL, and exDNA was rapidly recovered at a high concentration (concentration ratio: 2500×). Furthermore, metagenomic analysis revealed the function of some exDNA genes, such as those encoding antibiotic resistance proteins. The information revealed in this study contributes to the elucidation of the mechanisms of horizontal gene transfer in aquatic environments.