2026/05/01 by Miriam I. Brandt, Anders Lanzén, S. Mugu +2 · 1 voice
Biochemistry, Genetics and Molecular Biology · Earth and Planetary Sciences · Environmental Science · #Environmental DNA in Biodiversity Studies #Marine Biology and Ecology Research #Protist diversity and phylogeny
paper · doi:10.1002/edn3.70324
openalex publication_date 2026/05/01 · openalex created_date 2026/06/13 · openalex updated_date 2026/07/23
ABSTRACT DNA metabarcoding offers prospects to assess benthic biodiversity in a more scalable and comprehensive way, but processing methods remain insufficiently standardized and calibrated against traditional morphology‐based approaches. Here, we evaluated four processing strategies for DNA extraction from North Sea sandy and muddy sediments. These included two bulk DNA approaches (sieving and elutriation) and two direct environmental DNA (eDNA) approaches (3 × 0.5 g with homogenizer and 10 g with vortex). Animal and microbial diversity were assessed using mitochondrial cytochrome c oxidase subunit I (cox1) and small subunit ribosomal RNA markers (16S and 18S). Bulk DNA methods recovered more macro‐ and meiofauna Operational Taxonomic Units (OTUs) than direct eDNA approaches. However, effect sizes were small (< 0.4), while sample processing times were substantially longer (3–6 times slower), highlighting trade‐offs between biodiversity recovery and scalability for monitoring programs. Notably, the performance of size‐class sorting through sieving (1 mm) varied significantly with sediment grain size, recovering more macrofauna OTUs in sandy sediments but performing worse than direct eDNA methods in muddy sediments, thereby decreasing comparability across geographic regions. Both bulk approaches also led to increased detection of nontarget planktonic protists and reduced recovery of benthic prokaryotes, limiting their suitability for holistic biomonitoring. Both direct eDNA methods recovered similar OTU numbers and phylum‐level community compositions across markers, confirming that sample homogenizers enable efficient diversity recovery from small sediment volumes, also for animals. Sample completeness curves indicated that ~80% animal biodiversity coverage can be achieved with eDNA when spatial replication is increased to ~20 stations. Morphotaxonomy and metabarcoding datasets showed poor concordance at family and genus levels, with better levels of overlap for cox1 (20%–30%) compared to 18S (18SV1V2: 12%–20%, 18SV4: 6%–15%). Consequently, correlations between morphotaxonomy‐ and metabarcoding‐derived biotic indices were weak across all extraction strategies, highlighting the need to adapt biotic indices to metabarcoding data.