PNNL

Abstract

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. While analyzing the complex soil metaproteome is challenging, it shows promise in revealing specific functions performed by soil microorganisms. Here, we propose an approach to explore deep soil metaproteomes, which will improve our understanding of the metabolic potential within the soil microbiome. As a proof of concept, we generated high-quality deep-metaproteomes from native prairie soil using high-resolution tandem mass spectrometry. Peptides were identified using paired metagenomes. The lowest common ancestor method was used for conservative taxonomic assignment, revealing 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. By combining taxonomic and functional analyses, we disentangled the relative contributions of individual soil microbes to community metabolic functions. This study highlights the importance of taxon-specific functional analysis enabled by deep 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.