Comparison of fish assemblages across monitoring methods
The three approaches (dDNA, deep survey, and the 2022 WFD campaign)
collectively revealed a total of 91 fish species. Dietary DNA detected
nearly as many species than the 10-day deep survey (68 and 70
respectively) and three times more species than the WFD campaign.
Biosampler dDNA provided a fish assemblage that was broadly consistent
to the deep inventory, with almost two third species shared (n=51
species) (Figure 2). However, it also detected 17 species not recorded
with traditional techniques despite the use of multiple fishing
techniques. Conversely, 19 species recorded in the deep inventory were
not detected in shrimp digestive contents. When excluding unique species
absent from the reference databases, fish not detected by dDNA
metabarcoding were significantly less abundant in field surveys, with an
average of 7.3 (± 8.7) catches, compared to 21.0 (± 12.5) catches for
detected species (Wilcoxon test, p = 1e-4). Additionnally, species
detected exclusively through metabarcoding (n = 16) generally showed
significantly lower frequencies of occurrence (mean FO = 3.27%, SD =
2.8%) compared to species detected through both metabarcoding and deep
survey (mean FO, 8.01%, SD = 6.81%) (Wilcoxon rank-sum test, p-value =
0.0052).
The Venn diagram revealed limited overlap between species identified by
the 2022 WFD survey and those detected through dDNA or during the deep
inventory, with only 15 and 17 species shared, respectively.
Additionally, fish detected during the 2022 WFD campaign were
significantly larger (201.4 ± 104.8 mm) than those capture by dDNA
metabarcoding (145.9 ± 129.3 mm, Wilcoxon test, p = 0.003 and exhibited
a more restricted size range (Figure 3). In contrast, no significant
difference in expected size distribution was observed between dDNA and
deep inventory fish assemblages (Wilcoxon test, p = 0.46)