Metaproteomics uncovers the functional capacity of a soil microbiome

The soil microbiome plays a vital role in key ecosystem processes, but its functional capacity remains poorly understood. Microbial activities underpin many applications in environmental biotechnology, such as nutrient cycling, contaminant degradation, and the recovery and transformation of minerals and elements. However, analyzing the complex soil metaproteome is challenging. Here, we propose an approach to explore soil metaproteomes, which will improve our understanding of the metabolic potential within the soil microbiome. As a proof of concept, we generated high-quality metaproteomes from native prairie soil using high-resolution tandem mass spectrometry. Over 15,000 peptides were identified using paired metagenomes. By using lowest common ancestor method, the peptides were conservatively assigned to 21 bacterial, fungal, and archaeal phyla or superphyla, including rare soil bacterial phyla such as Candidatus Tectomicrobia, as well as viruses. Functional analysis at the pathway level was performed using complementary KEGG and MetaCyc databases, revealing essential biogeochemical cycles, such as carbon and sulfur cycling. By combining taxonomic and functional analyses, we disentangled the relative contributions of individual soil microbial phylum-level taxon to community metabolic functions. This study highlights the importance of taxon-resolved functional analysis enabled by soil metaproteomics, surpassing the capabilities of other single-omics methods. It offers new insights into how individual microbes function within complex soil microbiomes, paving the way for more targeted microbial strategies to improve system performance in bioeconomy applications.