Comparing Metal–Organic Framework Encapsulation With Conventional Filtering for Environmental DNA Capture From Seawater

Abstract

Effective sample collection is a pivotal step in environmental DNA (eDNA) workflows. For aquatic eDNA applications, this typically requires water filtration and cold storage, which present logistical challenges in remote or resource-limited settings. Metal–organic frameworks (MOFs) are porous materials composed of metal ions coordinated with organic linkers that can form around biological molecules in solution. By directly encapsulating and preserving eDNA in situ within a collected water sample, MOFs may simplify field sampling without the need for specialized equipment. In this study, eDNA capture and preservation from seawater samples using the MOF Zeolitic Imidazolate Framework-8 (ZIF-8) was compared with the performance of conventional filtration through mixed cellulose ester (MCE) filters. ZIF-8 samples were stored at ambient temperature for 2 weeks, while MCE filters were either frozen or preserved in a lysis buffer for 5 days. The performance of each method was assessed by high-throughput DNA sequencing and a metabarcoding assay targeting the 16S rRNA gene of fish. The MCE filter method detected, at present, a greater number of fish amplicon sequence variants (ASVs) and taxa than our trial application of the MOF method. However, community composition analyses (PERMANOVA and NMDS ordination) revealed no significant differences between the methods, demonstrating that despite yielding lower DNA quantities, ZIF-8 collection effectively replicates the marine fish community structure. Analysis of taxon abundance showed that MOFs captured dominant taxa effectively but were less sensitive to rarer taxa. With further optimisation to enhance eDNA capture efficiency by MOFs beyond this trial application, MOFs could serve as a practical, field-friendly alternative for eDNA sampling, especially where filtration is difficult.