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Use of a Filter Cartridge for Filtration of Water Samples and Extraction of Environmental DNA

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Detecting kelp-forest associated metazoan biodiversity with eDNA metabarcoding.

Emma I Rossouw¹, Jannes Landschoff^1,2, Andrew Ndhlovu^1,3

¹Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa.

Npj Biodiversity

|September 6, 2024

Summary

This summary is machine-generated.

Aquatic environmental DNA (eDNA) metabarcoding detected 880 operational taxonomic units (OTUs) in a South African kelp forest, revealing high biodiversity. Further database development is crucial for eDNA to become a powerful marine biomonitoring tool.

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Area of Science:

Marine ecology
Molecular ecology
Biodiversity monitoring

Background:

Environmental DNA (eDNA) metabarcoding offers a novel approach to assess marine biodiversity.
Its application in Africa, particularly in sensitive ecosystems like kelp forests, remains limited.
South African kelp forests host high, endemic biodiversity vulnerable to environmental changes.

Purpose of the Study:

To evaluate aquatic eDNA metabarcoding for biodiversity detection in a South African kelp forest.
To assess the spatial and temporal variability of eDNA signals.
To highlight the potential of eDNA for future biomonitoring in the region.

Main Methods:

Fine-scale spatial (1m, 8m) and temporal (4-hourly for 24h) sampling of aquatic eDNA.
Targeted sequencing of two mitochondrial gene regions: cytochrome c oxidase subunit I (COI) and 12S ribosomal RNA (12S rRNA).
Analysis of detected operational taxonomic units (OTUs) and community composition.

Main Results:

Detected 880 OTUs across 75 metazoan families, including 44 fish OTUs from 24 families.
Observed significant spatial and temporal variability in eDNA signals, but no distinct spatio-temporal community structure.
Identified diverse taxa, including Placozoa, previously unreported in South Africa; species-level identification was limited (<3%).

Conclusions:

Aquatic eDNA metabarcoding successfully detected a wide array of biodiversity in a South African kelp forest.
The study underscores the understudied nature of this ecosystem's biodiversity.
Optimized sampling strategies, enhanced barcoding efforts, and regional database development are essential for robust eDNA biomonitoring.