Abstract
DNA preserved in sedimentary materials can be used to study past ecosystem changes, such as species' colonization and extinction. It is believed that minerals, especially clay minerals, enhance the preservation of DNA. However, the role of minerals, as well as organic matter, on DNA sorption in heterogeneous sediments is still not clear. In this study, we examined the effect of mineral and organic matter on DNA binding in lake sediments. Bulk and size-fractionated sediments (0–4, 4–16, 16–64, and >64 μm), having different mineral and organic composition, were used to test DNA sorption; similar experiments were also run after the removal of sedimentary organic matter. Additionally, diffuse reflectance infrared spectroscopy (DRIFT) was used to determine the chemical changes caused by DNA sorption and subsequently produce a DNA-infrared (IR) fingerprint. Clay minerals were the main minerals to sorb DNA in the different samples. Moreover, mica promoted DNA sorption in all size fractions, while chlorite promoted DNA sorption in size fractions greater than 16 μm; clay-mineral and organo-mineral complexes caused a preference of certain clay minerals over others. Sedimentary organic matter affected DNA sorption by covering as well as by amplifying potential DNA binding sites, yet DNA sorption did not change significantly. DNA sorption showed IR spectral modifications mainly at ~1640, 1416, and 1231 cm−1. Interestingly, the DNA-IR fingerprint in the heterogeneous sediments was evident by those peaks after spectral subtraction. Finally, we proposed a simple model, based on sediment geochemistry, that can be used to determine potential DNA-hotspots in sediments.
Highlights
Sediments and soils can be seen as natural archives that store in formation about past ecosystem changes
As for the 165-cm sediment, it showed bigger aggregates than the other samples, as indicated by a relatively higher difference in percentiles before and after sonication (Fig. 1c). This difference points to possible Deoxyribonucleic acid (DNA) binding sites that can become exposed upon disaggregation
In the Hotagen sediments, mica was the main DNA sorbent, regardless of size fraction, while chlorite had prominent DNA binding roles in size fractions greater than 16 μm. This is possibly due to the heterogeneity of lake sediments and the presence of clay-mineral and organo-clay mineral complexes
Summary
Sediments and soils can be seen as natural archives that store in formation about past ecosystem changes. A key mechanism for DNA preser vation in sediments is absorption onto minerals in general and clay minerals in particular (Levy-Booth et al, 2007; Yu et al, 2013). The interaction between nucleotides or DNA and well-defined homo-ionic clay minerals has been studied as a function of pH, ionic strength, pressure, temperature, cation type, cation concentration, contact time, nucleotide length, and others (e.g., Cai et al, 2006a; Freeman et al, 2020; Levy-Booth et al, 2007; Pedreir a-Segade et al, 2018; Sheng et al, 2019; Xie et al, 2019; Xue and Feng, 2018; Yu et al, 2013). Cation bridges between clay mineral surfaces and phosphate moieties of DNA (or nucleotides) render DNA strands stable against enzymatic degradation (Cai et al, 2006c; Levy-Booth et al, 2007), partially explaining DNA preservation for extended periods
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