Exploring and utilizing soil Microbiota: From dark to light

Soil, one of earth's most complex and underexplored ecosystems, serves as a critical reservoir of biological and chemical diversity essential for life. However, a substantial portion of its microbial communities remains uncultivated and uncharacterized, often referred to as soil microbial "dark matter." Recent advancements have significantly enhanced our understanding, transforming this microbial "dark matter" into valuable biological knowledge. This review highlights the historical progression of microbial research, focusing on the shift from studying soil microbiota to the broader concept of the soil microbiome. It further discusses the impact of technologies such as high-throughput sequencing, metagenomics, and artificial intelligence, which revolutionize soil microbial research by enabling the analysis of uncultured microbes and their genetic resources. The review also explores the vast diversity and functional potential of uncultured soil microbes, which offer a rich source of novel genes, including those involved in nutrient cycling, biogeochemical processes, and the potential development of new genetic tools. Lastly, it summarizes the current applications of microbial dark matter analysis and outlines future opportunities to leverage the immense potential of soil microbiomes to address global challenges. • Soil harbors a vast and largely unexplored diversity of microorganisms, many of which remain uncultivated and uncharacterized. • Soil microbiomes represent a valuable reservoir of functional genes and genetic resources, offering untapped potential for various biotechnological applications. • Significant advancements in technologies such as high-throughput sequencing, metagenomics, and artificial intelligence have enabled the transformation of previously unknown microbial communities into valuable, actionable knowledge.