A comparison of DNA extraction methods for biodiversity studies of eukaryotes in marine sediments

There is increasing interest in understanding the diversity of eukaryotic microorganisms living in marine sediments, particularly to assess the effects of anthropogenic activities. Sequencing technologies generate high-resolution data for biodiversity studies that are useful for environmental monitoring. However, there are challenges in coupling classical monitoring with new sequencing technology and, consequently, there is a requirement for stringent optimization and standardization of any new protocol. Sample preparation is a critical factor because errors introduced during this step will severely affect further analyses and conclusions. This is particularly important in studies where biodiversity between different samples is compared, such as in environmental monitoring programs. Several protocols for extracting genomic DNA from soil and sediment samples have been developed, but most are optimized for prokaryotes in terrestrial soils and may therefore not be optimally adapted for investigating benthic marine eukaryotes. In this study, we compared existing and modified genomic DNA extraction methods on 2 different marine sediments with the aim to find an optimal protocol for processing a high number of sediment samples for further sequencing analysis. The protocols were evaluated based on quantity and quality of genomic DNA and recovered biodiversity. Results indicated significant variations in overall genomic DNA yield and purity among protocols. Further, our data suggest an effect of genomic DNA extraction procedure on eukaryotic diversity profiles, particularly for sediments with a high content of silt and clay.