Next-generation sequencing approaches for soil microbiome research

DNA sequencing technologies play a key role in modern soil microbiome research, providing a deep understanding of its structure and functional role in ecosystems. 16S rRNA gene, region of 18S-ITS-28S sequencing and shotgun sequencing using modern sequencing technologies (Illumina, Pacific Biosciences (PacBio), Oxford Nanopore Technologies (ONT)) allow us to identify the diversity and dynamics of microbial communities with high accuracy and resolution, which significantly expands our knowledge of biological processes and interactions between microorganisms in the soil. Soil microbiome analysis using sequencing contributes to the development of innovative methods for sustainable agricultural land management, improved fertility, plant disease management, and increased crop yields. Despite its significant potential, each sequencing technology has its own advantages and limitations related to accuracy, depth of coverage, cost, and data analysis complexity. Understanding these characteristics is crucial for selecting the optimal methods depending on the research objectives and available resources. This review systematizes modern sequencing methods, their technical capabilities and limitations, bioinformatics tools for sequencing data analysis, considers examples of successful applications in the study of soil microbiome in various ecosystems, and emphasizes new trends in metagenomics. In-depth study and development of soil microbiome sequencing technologies contributes to more sustainable and resource-efficient agriculture, emphasizing the need for a comprehensive and informed approach to the analysis of microbial communities.