Enhancing aquatic ecosystem environmental DNA capture, preservation and analysis with magnetic spiky silica nanoparticles

Abstract Environmental DNA analysis has transformed the way we monitor aquatic ecosystems, but its large-scale implementation is often limited by extraction methods that are costly, inefficient, and difficult to standardize across different environments. Here we present a solution based on engineered magnetic spiky silica nanoparticles that can overcome these challenges. The material features a high-surface-area, amine-modified spiky silica shell with tunable morphology and porosity, and a magnetic core, enabling efficient capture and purification of environmental DNA directly from water samples. Our optimized workflow outperforms commercial kits in environmental DNA yield, purity, and fragment recovery, while also preserving the DNA at room temperature for easy transport and storage. The method is compatible with standard sequencing approaches and offers a scalable, cost-effective solution for robust environmental DNA-based ecological monitoring in aquatic systems.