Abstract: 

Sediment has the extraordinary ability to retain taxonomic information from micro- and macro-organisms in the form of DNA. This archive provides long-term ecological insights into community changes across time and space, allowing researchers to identify crucial tipping points in ecosystems. However, environmental DNA (eDNA) extraction from marine sediment is challenging; the presence of organic PCR inhibitors and the strong physical adsorption of DNA to sediment particles can make it harder to recover than from other mediums. Additionally, unlike microorganisms, macro-organism detection can be sparse due to their inherent spatial heterogeneity. A consensus method has not yet been achieved for marine sediments, leaving a gap in our understanding of how different extraction protocols bias the quality and community composition of recovered DNA.

In this study we compare four different extraction methods that vary in their chemical and mechanical lysis, incubation temperatures, and contaminant removal strategies. We included a manual method that was originally optimized for extracting fish eDNA from freshwater habitats, as well as three commercial kits. Using frozen and freeze-dried surface sediments from coastal Hong Kong, we extracted eDNA and amplified marker genes with 515F-Y/926R (16S rRNA) and mlCOIintF/HCO2198 (mitochondrial COI) primers to analyze the effect that extraction method has on the microbial and metazoan community. The top-performing protocol was the manual extraction method; we detected 30% more metazoan phyla than the second best, while also effectively detecting the microbial diversity. These findings offer practical methodological guidance for optimizing sediment eDNA extraction, ultimately enabling the accurate reconstruction of past ecological community dynamics.