The Effect of Spatio‐Temporal Sampling and Biological Replication on the Detection of Kelp Forest Fish Communities Using eDNA Metabarcoding

• Published in: Environmental DNA (Hoboken, N.J.) N.J.), 2024-09, Vol.6 (5), p.n/a
• Main Authors: Courtaillac, Kira‐Lee, Landschoff, Jannes, Hull, Kelvin, von der Heyden, Sophie
• Format: Article
• Language: English
• Subjects: Biodiversity; Biological effects; biological replication; Biomonitoring; Coastal management; Conserved sequence; Design optimization; DNA barcoding; DNA biosynthesis; Ecosystems; eDNA; Environmental DNA; Fish; Forests; Genetic testing; Heterogeneity; Investigations; Kelp beds; metabarcoding; pooling; Project design; Replication; Sampling; sampling design; Sampling designs; Sequences; Shoreline protection; spatio‐temporal distribution; Surveys
• ISSN: 2637-4943; 2637-4943
• DOI: 10.1002/edn3.70023

ABSTRACT Environmental DNA (eDNA) metabarcoding surveys can support the acquisition of extensive biodiversity data to support ecosystem monitoring and conservation actions. However, the optimization of eDNA metabarcoding project design is essential to capture spatio‐temporal heterogeneity of eDNA signals and maximize diversity detection. In this study, we developed a system‐specific approach to detect fish communities in kelp forests, by analyzing fine‐scale spatio‐temporal patterns in eDNA signals at two sites along the South African coastline, as well as testing the effect of biological replication and pooling of replicates on species detection. At each site, samples were collected at two stations along the shoreline at two depth zones, and this was repeated at two time points (24 h apart). We detected 113 operational taxonomic units (OTUs) across 32 families, but fewer than 20% of OTUs could be assigned to species, indicating that barcode reference libraries need to be drastically improved. We detected significant differences in communities across small spatial scales (