Digging deeper into soil metagenomics: Opportunities and limitations for studying the genomic potential of soil bacteria and archaea

Abstract Soil microbial ecology has been transformed by recent progress in sequencing and metagenomics, reshaping our understanding of soil microbial functions. This article examines how metagenomics can be used to study the functional potential of soil microbiomes. We highlight opportunities and limitations of current tools and workflows utilized for the analyses of metagenomic sequencing data, providing guidance for methodological thoroughness and transparency, and emphasizing the need for standardized metadata, data availability and workflow reproducibility in metagenomic studies. We encourage authors to connect microbial functional potential to genomic context, functional redundancy and taxonomic diversity. By following these practices, the scientific community can ensure that soil metagenomics delivers robust, reproducible, and ecologically meaningful insights into the ‘living engine’ of fertile soils.