Sedimentary ancient DNA
Sedimentary ancient DNA (sedaDNA) can be found both intracellularly in small pieces of tissue, and extracellularly, particularly adsorbed with negatively charged minerals and biomolecules (Massilani et al., 2022; Pedersen et al., 2015; Pedreira-Segade et al., 2018; Wnuk et al., 2020). Allophane from volcanic soils and montmorillonite clay mineral have a high affinity to nucleic acids (Huang et al., 2014) and while these molecular interactions can protect the DNA molecules over time (Blum, Lorenz, & Wackernagel, 1997), they may also impede the DNA extraction and in vitro amplification processes (Pedersen et al., 2015; Wnuk et al., 2020). For example, humic acids are known inhibitors of enzymes used to amplify DNA in vitro—using a standard molecular biology method called PCR, or polymerase chain reaction (Simmons & Cross, 2013, p. 276). The humic acids and metal ions commonly found in soils and sands have similar characteristics to DNA molecules and as such bind nucleotides and inhibit DNA isolation (Pedersen et al., 2015; Wnuk et al., 2020). Horizon-stabilising techniques have indicated that sediment samples impregnated with resin can yield high DNA content and limit these inhibiting factors, resulting in better DNA sequencing library preparation efficiency than when analysing loose sediments (Massilani et al., 2022).