Because the solid components are mostly silica-bearing minerals and silica is known to effectively bind DNA from solution at neutral pH (Melzak et al., 1996; Nguyen & Elimelech, 2007), we assumed that DNA extraction from consolidated sediments with pH-buffering silicate and carbonate minerals could be hindered by the binding of DNA onto silica minerals after
the disruption of cells (Onstott et al., 2010). In case of unconsolidated marine sediments, polyadenylic acid (PolyA) has been applied to improve the recovery of DNA by blocking DNA binding sites prior to disrupting cells (Webster et al., 2003; Sørensen et al., 2004). In addition, electroelution has been used to separate extracted DNA from humic substances that inhibit PCR amplification (Kallmeyer & Smith, 2009). The method for DNA extraction developed in this study was extended from the one previously developed for DNA extraction BKM120 solubility dmso from single cells (e.g. radiolarians)
encapsulated within amorphous silica (opal-A) (Kouduka et al., 2006). This previous AZD1208 clinical trial method is based on the alkaline incubation of a silica-bearing cell to solubilize silica biominerals and cell membranes. For consolidated marine sediments, opal-A from diatoms and radiolarians is generally transformed into crystalline silica minerals such as opal-CT and quartz. It is necessary to raise the incubation temperature to accelerate the dissolution of the silica minerals (Williams et al., 1985). This study was conducted to establish a protocol for DNA extraction from a consolidated sediment sample by optimizing incubation and neutralization conditions for molecular phylogenetic analysis. In addition, efficacy of the developed method was determined by extracting DNA from cultured cells
under a variety of extraction conditions tested for the sediment sample. A consolidated marine sediment sample was obtained from the terrestrial deep subsurface at a depth of 351 m by an aseptic drilling procedure (Suzuki et al., 2009). The drilling site was located in a sedimentary basin of central Japan. This consolidated sediment sample was selected not because of the high level of biomass estimated by PLFA (mainly 16 : 0, 18 : 1ω9c and 18 : 0) content, cultivable heterotrophic prokaryotes and the high content of silicate minerals such as quartz and opal-CT (cristobalite). The deep subsurface sediment sample used in this study was deposited in the hemi-pelagic environment and buried. This burial diagenesis resulted in the opal-A of diatoms being transformed into opal-CT. In addition, DNA was not extracted by physical and chemical disruption of cells using an UltraClean Soil DNA Isolation kit (MoBio Laboratories, Carlsbad, CA), which has been successfully used to study unconsolidated marine sediments (Inagaki et al., 2006).