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).