Performance of extraction methods for extracellular DNA from sediments across marine habitats

Abstract Background Using environmental DNA (eDNA) to detect taxa is quickly becoming an important technique to determine the distribution and diversity of macroorganisms. Assessing differences in communities based on eDNA extracted from sediment could enhance our understanding of marine communities among the many different marine habitats both from the present and from the past using sediment cores. Although the effect of extraction methods on metabarcoding results has been tested for both water and sediment samples, less is known about how sediment types may affect the extraction and sequencing of eDNA. Methods and Results We used two extraction methods to assess if the amount of extracted DNA was different among three marine habitats: coral reefs, mangrove forests, and seagrass meadows. First, an equal amount of DNA was added to sterilized sediment and there was no difference in the DNA extracted from the different habitats. Second, an equal amount of DNA from a species that did not occur naturally was added to the sediment and the number of sequenced reads of this species was not different among habitats. A concomitant test found that a commercial extraction kit, the MO BIO PowerSoil DNA isolation kit, and published extraction protocol from Lever et al. (2015, Frontiers in Microbiology, 6, 476) had similar results. Conclusions Although different environmental conditions within the habitats will likely affect the degradation of eDNA, these findings suggest that diverse characteristic of the sediments from different habitats does not affect the extraction of DNA. This is an important step in determining whether eDNA within sediment can be utilized to compare the communities from different marine habitats.