**4. Summary**

High‐throughput sequencing is probably the fastest growing method used in the biology and biotechnology. To date emerged a series of modifications which resulted in the development

On the market, there is a large selection of sequencing systems introduced by many other companies, but this chapter focuses on Illumina sequencing system. It is the most common method in the study of metagenomes different environments. Due to the a very dynamic development of the technology described herein, performance data and bandwidth become

DNA prepared for sequencing must meet several requirements. First of all, it must be free from contamination and PCR inhibitors such as humic acids, ethanol, and phenol compounds. A very important and crucial step in the preparation of biological samples is appropriate for DNA extraction and its purification. Commercially available kits provide high‐performance elution of DNA, contain enzyme (such as DNase) inhibitors, and allow getting rid of impurities.

An important advantage is the ability to simultaneously sequencing of many samples at the same time. This is done by marking samples by attaching specific, short DNA fragments of known sequence treated as barcodes. The principle of the sequencing uses fluorescently la‐

of equipment relatively cheap and efficient.

96 Soil Contamination - Current Consequences and Further Solutions

**Figure 2.** Cluster formation in Illumina NGS sequencing.

outdated several times a year.

The better understanding of the link between bacterial diversity and their community structure and function is very important to study microbial diversity in contaminated soil. This is not only important for basic scientific research but also to study biodiversity in soil contaminated with PAHs. Significantly higher amounts of 16S rRNA have been found in all microbial groups analyzed in fields that have never been cultivated than agricultural fields and also in soil contaminated with PAHs. This suggests a decrease in bacterial biomass or activity in cultivated fields. However, it is unknown what these reductions in diversity mean to ecosystem func‐ tioning, and it is important for the sustainability of ecosystems to examine and better under‐ stand the link between diversity and function. There are some limitations associated with studying organisms in contaminated soil. There are some taxonomic and methodological limitations. The methods to study bacterial diversity (numerical, taxonomic, structural) are improving for some group of bacteria and fungi. It is generally thought that a diverse popu‐ lation of microorganisms will be more resilient to biotic and abiotic stress and more capable of adapting with environmental changes (contamination). The knowledge of plant–microbe– soil‐contaminant interactions is increasing, but the complexity of interacting biological, chemical, and physical factors means that much remains to be understood.

As new techniques are developed, our level of understanding increases and our knowledge expands.
