A TbPO4-based capturer for environmental extracellular antibiotic genes by interrogating lanthanide phosphates nanoneedles

Accurate determination of antibiotic resistance genes (ARGs) in environmental DNA molecules (eDNA) is challenging owing to its low abundance in the aquatic environment. Here we report a facile and cost-efficient approach to extract trace amount of eDNAs in the aquatic environment using LnPO4 nanomaterials. Among the nanomaterials, less crystalline TbPO4 nanoneedles was identified as the most prominent candidate for long stranded DNA and short stranded DNA with adsorption efficiency above 97%. The adsorbed DNA was washed off from TbPO4 nanoneedles by optimized eluant (85% PBS, 15% EtOH, 4 g/L glycine, pH 10.0) with an optimal DNA recovery of 78.83%. Our approach showed a comparable or better eDNA extraction efficiency than a commercial extraction method for different environmental samples, but 89% less cost. The high purity of the extracted eDNA was demonstrated by a high A260/280 ratio. Using qPCR experiment, the occurrence of six common ARGs in the eDNA were detected with abundance ranging from 4.06 × 103 to 3.51 × 109 copies/L in river samples. This specific DNA capturer is valuable for the evaluation of spatial and temporal dynamic of ARGs pollution to provide insight into the potential risk with regard to the human health. [Display omitted] •A facile approach for extraction of trace amount of eDNA using LnPO4 nanoneedles was developed.•Less crystalline LnPO4 nanoneedles had a higher eDNA adsorption capacity compared to highly crystalline materials.•The developed approach showed a comparable eDNA extraction efficiency to a commercial extraction method, but less cost.•Occurrence of ARGs in the eDNA that extracted by TbPO4 nanomaterial from West River sample were detected.