eDNA metabarcoding as a biomonitoring tool for marine protected areas

Monitoring of marine protected areas (MPAs) is critical for marine
ecosystem management, yet current protocols rely on SCUBA-based visual
surveys that are costly and time consuming, limiting their scope and
effectiveness. Environmental DNA (eDNA) metabarcoding is a promising
alternative for marine ecosystem monitoring, but more direct comparisons
to visual surveys are needed to understand the strengths and limitations
of each approach. This study compares fish communities inside and outside
the Scorpion State Marine Reserve off Santa Cruz Island, CA using eDNA
metabarcoding and underwater visual census surveys. Results from eDNA
captured 76% (19/25) of fish species and 95% (19/20) of fish genera
observed during pairwise underwater visual census. Species missed by eDNA
were due to the inability of MiFish 12S barcodes to differentiate species
of rockfishes (Sebastes, n=4) or low site occupancy rates of
crevice-dwelling Lythrypnus gobies. However, eDNA detected an additional
23 fish species not recorded in paired visual surveys, but previously
reported from prior visual surveys, highlighting the sensitivity of eDNA.
Significant variation in eDNA signatures by location (50 m) and site
(~1000 m) demonstrates the sensitivity of eDNA to address key questions
such as community composition inside and outside MPAs. Results demonstrate
the utility of eDNA metabarcoding for monitoring marine ecosystems,
providing an important complementary tool to visual methods.