Background: The soil microbiome consisting of bacteria, fungi, and archaea is essential for maintaining life and balancing ecosystems. Studying this microbiome is necessary in the aspect of threats such as weather change and soil degradation. Scope: Culture-independent methods, for example, 16S rRNA gene study, metagenomics, and metatranscriptomics, supplement traditional methods to provide detailed insights into microbial diversity and function. High-throughput sequencing, metatranscriptomics, and metaproteomics contribute to advancements in studying microbiome and microbial communities. Conclusion: Advancements in computer technology and bioinformatics tools like DADA2 and specialized pipelines are essential for processing biological data. Understanding soil microbiomes aids in developing sustainable practices for agriculture and forest ecosystems amid environmental challenges.