eDNA metabarcoding as a biomonitoring tool for marine protected areas

Abstract

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.

Short-lived detection of an introduced vertebrate eDNA signal in a nearshore rocky reef environment

“…If marine fish eDNA was patchy in this experiment, filtering a larger volume of water may reduce variation among the replicates. However, we chose one liter as our sampling volume since this is the standard sampling volume for marine eDNA studies [ 14 , 15 , 17 , 19 , 26 , 48 ], and passing more than one liter of water through a filter can be difficult in productive coastal ecosystems like kelp forests.…”

“…Temporal variation of eDNA in marine ecosystems is becoming increasingly important to understand, as eDNA is being viewed as a potential alternative to traditional visual survey methods used in marine ecosystems monitoring [ 2 , 5 ]. While eDNA has fewer logistical difficulties compared to visual surveys [ 19 ], the primary advantage is eDNA’s ability to efficiently detect larger numbers of taxa [ 3 , 4 , 15 ]. For example, at least 178 fish species inhabit Southern California kelp forest [ 20 ].…”

Characterizing Industrial and Artisanal Fishing Vessel Catch Composition Using Environmental DNA and Satellite-Based Tracking Data

“…eDNA was extracted and purified from sampled meltwater using a Qiagen DNeasy blood and tissue kit with modifications ([ 45 ], see Supplemental Materials S1 for protocol details). Preparation of sequencing libraries for eDNA analysis consisted of a two-step polymerase chain reaction protocol [ 46 ]. All reactions were conducted in PCR tubes using commercially available reagents (see Supplemental Materials S2 for product and protocol details).…”

“…These files were then processed through the Toolkit ’s Anacapa Classifier module to assign taxonomy, where ASVs were queried against the CRUX-generated 12S reference database. Taxonomic identity was assigned probabilistically using the Toolkit ’s modified Bayesian Least Common Ancestor method using a cutoff level of 60, following [ 46 ]. Furthermore, given uneven sequencing depth across samples, taxa with less than 1% of the proportion of reads were excluded from the analysis.…”

Environmental DNA reveals the fine-grained and hierarchical spatial structure of kelp forest fish communities

“…For instance, a rockfish-specific primer set has been developed and successfully discriminated 28 out of 44 commercially harvested species 58 . Further improvements could be also be made through development and curation of more comprehensive DNA reference libraries 59 , or using multiple primers to target different groups.…”