Crude Soil Samples Research Articles

The validation of forensic DNA extraction systems to utilize soil contaminated biological evidence.

The production of full DNA profiles from biological evidence found in soil has a high failure rate due largely to the inhibitory substance humic acid (HA). Abundant in various natural soils, HA co-extracts with DNA during extraction and inhibits DNA profiling by binding to the molecular components of the genotyping assay. To successfully utilize traces of soil contaminated evidence, such as that found at many murder and rape crime scenes in South Africa, a reliable HA removal extraction system would often be selected based on previous validation studies. However, for many standard forensic DNA extraction systems, peer-reviewed publications detailing the efficacy on soil evidence is either lacking or is incomplete. Consequently, these sample types are often not collected or fail to yield suitable DNA material due to the use of unsuitable methodology. The aim of this study was to validate the common forensic DNA collection and extraction systems used in South Africa, namely DNA IQ, FTA elute and Nucleosave for processing blood and saliva contaminated with HA. A forensic appropriate volume of biological evidence was spiked with HA (0, 0.5, 1.5 and 2.5 mg/ml) and processed through each extraction protocol for the evaluation of HA removal using QPCR and STR-genotyping. The DNA IQ magnetic bead system effectively removed HA from highly contaminated blood and saliva, and generated consistently acceptable STR profiles from both artificially spiked samples and crude soil samples. This system is highly recommended for use on soil-contaminated evidence over the cellulose card-based systems currently being preferentially used for DNA sample collection.

Mutants of Taq DNA polymerase resistant to PCR inhibitors allow DNA amplification from whole blood and crude soil samples

Potent PCR inhibitors in blood and soil samples can cause false negative results from PCR-based clinical and forensic tests. We show that the effect of these inhibitors is primarily upon Taq DNA polymerase, since mutational alteration of the polymerase can overcome the inhibition to the extent that no DNA purification is now required. An N-terminal deletion (Klentaq1) is some 10–100-fold inhibition resistant to whole blood compared to full-length, wild-type (w.t.) Taq, which is strongly inhibited by 0.1–1% blood. Further mutations at codon 708, both in Klentaq 1 and Taq, confer enhanced resistance to various inhibitors of PCR reactions, including whole blood, plasma, hemoglobin, lactoferrin, serum IgG, soil extracts and humic acid, as well as high concentrations of intercalating dyes. Blood PCR inhibitors can predominantly reduce the DNA extension speed of the w.t. Taq polymerase as compared to the mutant enzymes. Single-copy human genomic targets are readily amplified from whole blood or crude soil extract, without pretreatment to purify the template DNA, and the allowed increase in dye concentration overcomes fluorescence background and quenching in real-time PCR of blood.

Differentiation of the contribution of local resuspension from that of regional and remote sources on trace elements content in the atmospheric aerosol in the Mediterranean area

For the determination of effects of contaminated crude soil on the content of trace elements in the atmospheric aerosol, trace elements in crude soil samples from within the area of influence of local resuspension were analysed. The obtained results were used for determining the contribution of local resuspension on contents of trace elements in the atmospheric aerosol using the enrichment factors (EF) method. The content of trace elements in a crude soil could arise from the geochemical background of the soil or from anthropogenic contributions. Analysis of the quantile showed that Cd, Se and Ni originate from local emission sources. PCA showed that four groups of sources contributed to the content of trace elements in PM in part of the receptor. Using EF, it was ascertained that local resuspension of crude soil particles had a dominant influence on the content of Fe, Mn and Ti in the atmospheric aerosol, and that local resuspension had no influence on the content of Se in the atmospheric aerosol. Dust originating from deserts of North Africa and Middle East, through long-range transport and through resuspension of settled dust particles, significantly contributes to the content of Fe, Mn and Ti in the atmospheric aerosol. Cd originated from contaminated crude soil. The other investigated elements originated partly from crude soil but also from some other emission sources in the region.

Surface analysis of soil material by X‐ray photoelectron spectroscopy

SummaryThe surface composition of particles present in the fine earth (< 2 mm) of 50 soil horizons differing in composition and pedogenetic origin (13 soil profiles) was analysed by X‐ray photoelectron spectroscopy (XPS) to assess the capability and limitations of this technique and to gain better knowledge of the soil samples. The surfaces were systematically enriched in carbon, sometimes up to 1000 times, indicating that the soil particle surfaces are coated with organic substances, even in horizons where the bulk organic content is less than 0.1 g kg−1. The distribution of carbon in the various oxidation states was 0.569 ± 0.008 C[0], 0.275 ± 0.004 C[+1], 0.089 ± 0.003 C[+2] and 0.066 ± 0.002 C[+3] for most horizons (mean ± standard error, 69 data). Only Andosol surface horizons systematically had surface organic matter in a more oxidized state. After correcting the results for the presence of organic coatings, we found that Si was generally depleted and Al enriched at the surface of soil particles, while Fe was either depleted or enriched depending on the sample considered. However, the coating of the coarser soil particles by the finer ones and their differential composition explained this observation and limits the interest of XPS for characterizing the surface enrichment of inorganic elements in crude soil samples. These limitations should be considered when interpreting XPS results in future work. Nevertheless, XPS can analyse the adsorbed organic matter and its functional composition of carbon without the need for any chemical or physical extraction that might alter the structure and composition of the organic molecules.

Carbon source of humic substances in some Japanese volcanic ash soils determined by carbon stable isotopic ratio, δ 13C

Volcanic ash soils (including Andisols) have been known to accumulate extremely large amounts of humic acids in their thick surface horizons, and their accumulation mechanism is of interest. Two mechanisms have been proposed: (1) active metals like Al and Fe, supplied from weathered volcanic materials, stabilize humic acids through complexation reactions; (2) cultivated Japanese pampas grasses ( Miscanthus sinensis A.) and its charred materials are the major carbon source of humic acids. In the present study, contribution ratio of the pampas grass (C4-plant) on the carbons of the humic acids was determined by measuring their stable isotopic ratio of carbon (δ 13C). In Japanese volcanic ash soils, humic acids were originated from both C3- and C4-plants, and the contribution ratio of C4-plants (mostly pampas grass) ranged from 18% to 52%. Highly humified (dark-colored) humic acids tended to show higher contribution ratio of C4-plants among volcanic ash soils, although the major part of the carbon had originated from C3-plants. It was also clarified that the δ 13C values of crude soil samples correlated well with those of humic and fulvic acids. Therefore, reported δ 13C values of crude soil samples in the literature would be useful for estimating the carbon source of soil humic substances. Literature survey of the δ 13C values of crude soil samples also indicated that a large part of the carbon in humic substances has originated from C3-plants rather than C4-plants, implying the importance of the active metals (such as Al and Fe) on the formation and accumulation of the humic acids in volcanic ash soils.