ABSTRACT The conservation of biodiversity is fundamental for the persistence of ecosystems, particularly under climate change. The South African marine environment is characterized by high levels of biodiversity as well as endemism, but species distribution patterns are generally not well characterized. Environmental DNA (eDNA) metabarcoding is a promising tool to help plug the biodiversity information gap, but evidence from previous studies has shown highly variable eDNA signals, even at small temporal–spatial scales (< 300 m, 24 h). Passive samplers, deployed over several hours may circumvent some of the challenges of high eDNA variation by accumulating DNA over time. Using multiple markers (mtDNA 12S rRNA, mtDNA COI), we test both active (using Sterivex) and passive sampling (gauze filled metaprobe) in the detection of kelp forest‐associated biodiversity, focussing on fishes and invertebrates. We conducted our experiment across different time periods (6, 12, 24 h) and hypothesized that metaprobes at 24 h would harbor the greatest species richness. We detected 33 ESVs, assigned to 18 different fish families, with 12S rRNA, where active sampling retrieved a larger proportion of diversity (94% vs. 64%, p < 0.001). For COI, we detected 1481 ESVs assigned to 17 different phyla, 99 families, and 55 species, with passive sampling detecting more ESVs (82% vs. 67%, p < 0.001). COI metabarcoding detected an additional four families of fishes, highlighting the importance of multi‐marker approaches. For passive sampling only, there was a trend of significant accumulation of numbers of reads and ESVs over time. We found that active samples were more consistent across all statistics: variation in the number of reads, ESVs, and taxa retrieved, which was less in active than passive replicates. Overall, we highlight the need for region‐specific approaches and careful project planning before implementing eDNA metabarcoding as a biomonitoring tool.
Estévez‐Barcia et al. (Thu,) studied this question.