- Metabarcoding offers a powerful approach for assessing benthic biodiversity in remote
and understudied deep-sea environments. However, the methodological performance
of different DNA extraction strategies remains insufficiently evaluated, especially for
benthic meiofaunal communities. In this study, we compared two extraction strategies—
community DNA (ComDNA) from isolated benthic metazoans and sedimentary
environmental DNA (SedDNA) from whole sediment—to assess benthic metazoan
diversity in the Clarion-Clipperton Fracture Zone (CCZ), an area targeted for future
polymetallic nodule mining. Using the 18S V1–V2 rRNA marker, we analyzed alpha
and beta diversity, taxonomic composition, and the number of metazoan operational
taxonomic units (OTUs) recovered by each strategy. ComDNA extractions yielded
substantially higher benthic metazoan OTU richness (2,145 OTUs) than SedDNA
(392 OTUs), with only 1.2% of OTUs shared between them. Community composition
also differed significantly, driven by strategy-specific detection biases. To evaluate
the effectiveness of SedDNA for biodiversity monitoring, we modeled the sediment
volume required to recover OTU richness comparable to ComDNA samples. Depending
on sequencing depth and statistical approach, we estimated that the processing of
27–82 mL of sediment is necessary to match ComDNA-derived richness. Our findings
underscore the superior taxonomic resolution of ComDNA extractions but also highlight
the potential of optimized SedDNA protocols for scalable biodiversity monitoring.
We recommend sediment homogenization, increased sample volume, and a higher
sequencing depth of at least 100,000 reads per sample for improving SedDNA-based
assessments, particularly in heterogeneous deep-sea environments. These results
provide critical methodological guidance for the development of standardized, efficient
monitoring strategies in the context of deep-sea mining impact assessments.
