Optimising environmental DNA biomonitoring for Kakadu National Park's freshwater fish communities

Aquatic ecosystems are in peril. World Heritage estates such as Kakadu
National Park are not immune to anthropogenic pressures. To better protect
freshwater fish communities and obtain relevant ecological data, there has
been a shift towards environmental (e)DNA metabarcoding. In tropical
lentic environments, seasonal variation drives significant environmental
change, particularly the resuspension of particulate matter and
phytoplankton productivity. These factors constrain the volume of water
that can be sampled, potentially affecting the detection capacity of eDNA
metabarcoding. Hence, information about the volume of samples required to
robustly detect fish is critical prior to developing metabarcoding
biomonitoring programs. In Kakadu, we sampled two contrasting systems with
distinct fish communities. Employing two mt-rRNA primers (12S and 16S), we
examined the detection of fish sampled from 1, 2, 5, and 10 L. Leveraging
MinION sequencing, 15 fish taxa were confidently assigned to the
species-level. Despite both systems containing unique fish communities
(perMANOVA: F = 5.73, P < 0.001), the most salient finding was that
fish richness and community structure were not influenced by sample
volume. In tropical systems where volume is inhibited, sampling a
consistently lower volume may still be suitable for fish detection.
Several species rarely observed using traditional monitoring approaches
were detected, including Porochilus rendahli and Oxyeleotris lineolata.
Our findings emphasise the need for multiple primers to capture a wider
diversity of fish. This study provides the foundations for a routine eDNA
monitoring program optimised for Australian tropical lentic freshwaters,
which may assist in the management of tropical fish communities.