Where and when to sample: Investigating spatio-temporal variation of community assemblages in kelp forest systems with eDNA metabarcoding

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Abstract Environmental DNA metabarcoding is a powerful tool for monitoring marine biodiversity, yet several outstanding questions remain regarding the persistence of eDNA. In this study, we use fine-scale spatial (1 m, 8 m) and temporal sampling (every four hours for 24 hours), in combination with metabarcoding to test the effect of depth and time on community assemblages in a dynamic kelp forest ecosystem, specifically to enhance our understanding of sampling regimes. Using mtDNA COI and 12S rRNA, metabarcoding detected 880 OTUs representing 75 families in the broader eukaryotic community and 44 OTUs representing 24 fish families. Only a few OTUs (COI = 19, 12S = 11) could be assigned to species. No significant depth or time partitioning of OTU assemblages was found, likely reflecting high levels of eDNA transport, with community composition and OTU richness not significantly different across depth over the 24 hour sampling period. Together with incomplete barcoding reference databases, results indicate that understanding the fine-scale spatio-temporal dynamics of eDNA signatures is crucial for informing sampling strategies and interpreting the dynamics of aquatic communities. Finally, our study emphasizes how understudied South African kelp forest systems are, and the potential eDNA metabarcoding holds for documenting their high levels of biodiversity.

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