Introduction
Environmental DNA metabarcoding is a sensitive, non-invasive and broadly applicable tool for species detection, including biodiversity measurement and biosecurity surveillance (Taberlet et al. 2018, Deiner et al. 2017). Macro-organisms shed their DNA into the air, soil, and water, which can be sampled by collecting, extracting, amplifying, sequencing, and ultimately identified by comparing against a reference database of known DNA sequences (Taberlet et al. 2018, Thomsen et al. 2015). Diverse applications have been developed for eDNA metabarcoding and the field has grown rapidly in recent years (Koziol et al. 2019, Jarman et al. 2018). Nevertheless, a common limitation of eDNA studies is a lack of replication (Buxton et al. 2021, Derocles et al. 2018, Dickie et al. 2018, Zinger et al. 2017). For aquatic systems this is in part due to the logistical challenge of filtering sufficient water (Bessey et al. 2020).
Passive collection methods (Bessey et al, 2021, Kirtane et al. 2020), which involves direct submersion into a water body of materials that collect eDNA, facilitate increased replication because they are cheaper, simpler, and faster to apply than active filtration. This enables analyses that are generally not practical with water filtering as an eDNA collection method. Frequency of occurrence methods become more feasible, as well as mapping residence of species of interest. For studies investigating diversity, greater biological replication improves the reliability of both alpha and beta diversity estimates (Zinger et al. 2017, Prosser 2010). Furthermore, because passive eDNA requires minimal or no supporting technology it suits deployment to remote environments, and by non-experts.
Few studies investigate the mechanisms or optimal material properties needed for passive eDNA collection. Kirtane et al. (2020) used adsorbent-filled sachets of Montmorillonite clay and granular activated carbon to passively capture eDNA in freshwater laboratory, microcosm and field experiments. In the laboratory, they found that extracellular DNA adsorbed to these materials at different rates, depending on the water matrix. In their field experiments, granular activated carbon sachets captured significantly more eDNA than clay and detected as many fish species as a 1 L conventional grab sample. These materials were chosen for their high adsorption capacity to trap DNA but also for their low adsorption affinity to allow high yield during extraction. They suggest adsorption mechanisms for granular activated carbon are dependent on the water matrix, whereas that of clay is more dependent on adsorption kinetics and capacity. Bessey et al. (2021) compared the effectiveness of positively charged nylon and non-charged cellulose ester membrane materials for passive collection of fish eDNA at both a species-rich tropical and species-poor temperate marine site. They found that both materials detected fish as effectively as conventional active eDNA filtration methods in temperate systems and provided similar estimates of total fish biodiversity but differed in tropical waters. Their materials were chosen to investigate the possible role of electrostatic attraction and because both are commonly used in conventional aquatic eDNA studies using filtration methods. The observations that significant material effects exist, and may be system specific, indicates there is potential for improvements to passive eDNA collection through material selection that could create greater efficiencies for users.
The optimal submersion time for efficient passive eDNA collection is also unclear. Kirtane et al. (2020) found that, regardless of material used (clay or granular carbon) or water matrix (molecular grade water, microcosm tank water, or natural creek water), an equilibrium concentration of eDNA was absorbed in less than 24 hours. In field trials, they also found that fish species detection did not significantly increase with longer submersion duration (7 days compared to 21). In both tropical and marine waters, Bessey et al. (2021) likewise found that increased submersion time did not increase species richness (comparing 4, 8, 12, and 24 hours of submersion). Combined, these studies indicate that long-duration submersion (days or hours) may not be necessary and therefore, investigations into minimal submersion times are another potential avenue to increase passive eDNA collection efficiency.
Using a DNA metabarcoding approach, here we evaluate the effect of materials and submersion time on the efficiency with which fish eDNA could be collected passively from a large marine mesocosm. We also use scanning electron microscopy to visualise modes of eDNA adherence or entanglement to the different materials. We show that for most materials, passively collected eDNA consistently performs similarly to conventionally filtered eDNA samples, and that high collection efficiency can be achieved in as little as five minutes.