Preservation of ancient eukaryotic DNA in methane hydrate-associated marine sediments.

Sampling

Ancient eukaryotic DNA in marine sediment can provide valuable information on the paleo-environment. However, labile nucleic acids are generally considered to be microbially degraded in water and sediment columns. Previously, ancient eukaryotic DNA has been retrieved from sediments associated with anoxic water column in lake and semi-closed sea, due to the minimized effect of oxic biodegradation. Cold seep sediment is characterized by high upward flux of methane, where there is the possibility that the excess energy source might suppress the degradation of deposited organic matter including nucleic acids by microbial activity. We investigated the preservation of ancient eukaryotic DNA in marine sediments associated with and without methane hydrate in the eastern Japan Sea, between which the dominant prokaryotic populations are clearly distinct. Marine sediments were retrieved from the eastern Japan Sea during a cruise onboard R/V Marion Dufresne in June 2010. Two-step alkaline DNA extractions were conducted with 0.1 g of marine sediments. DNA from living organisms such as fungi was removed by the first extraction under mildly heated conditions at 65 degrees Celsius, which was followed by the second extraction at 95 degrees Celsius. Triplicate DNA extraction and subsequent clone library analysis were more reproducible for marine sediments associated with methane hydrate. Based on highly variable18S rRNA gene sequences, terrestrial and marine organisms were taxonomically identified at the species level. The diversity of ancient eukaryotic DNA represented by Alveolata, Fungi, Stramenopiles and Viridiplantae was comparable between this study and previous ones. As only 0.1g of g wet sediment is required, the overall methodology developed in this study has great potential to reconstruct terrestrial and marine ecology at high time resolution. In addition, methane hydrate-associated sediments, which are globally distributed along the continental margin, have great potential to reconstruct the past terrestrial and marine ecology around the world over geological timescales.

Method steps

1. Pipeline used: https://www.ebi.ac.uk/metagenomics/pipelines/4.1