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.