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. |
