Identification of the Park Grass Experiment soil metaproteome

Abstract

AbstractThe Park Grass Experiment, is an international reference soil with an impressive repository of temperate grassland (meta)data, however, it still lacks documentation of its soil metaproteome. The identification of these proteins is crucial to our understanding of soil ecology and their role in major biogeochemical processes. However, protein extraction can be fraught with technical difficulties including co-extraction of humic material and lack of a compatible databases to identify proteins. To address these issues, we used two compatible soil protein extraction techniques on Park Grass soil, one that removed humic material, namely a modified freeze-dry, heat/thaw/phenol/chloroform (HTPC) method and another which co-extracted humic material, namely an established surfactant method. Proteins were identified by matching mass spectra against a tailored Park Grass metagenome database. We identified a broad range of proteins from Park Grass soil, mainly in “protein metabolism”, “membrane transport”, “carbohydrate metabolism”, “respiration” and “ribosome associated” categories, enabling reconstitution of specific processes active in grassland soil. The soil microbiome was dominated by Proteobacteria, Actinobacteria, Acidobacteria and Firmicutes at phyla level and Bradyrhizobium, Rhizobium, Acidobacteria, Streptomyces and Pseudolabrys at genus level. Further functional enrichment analysis enabled us to identify many proteins in regulatory and signalling networks of key biogeochemical cycles such as the nitrogen cycle. The combined extraction methods connected previous Park Grass metadata with the metaproteome, biogeochemistry and soil ecology. This could provide a base on which future targeted studies of important soil processes and their regulation can be built.HighlightsParallel protein extraction methods identified 1266 proteins from Park Grass soilProteome was enriched in ribosomal and respiration proteins for the surfactant extraction method and nitrogen associated proteins for the modified phenol/chloroform methodIdentification of regulatory and signalling proteins in key biogeochemical cyclesLinks metaproteome to microbiome, biogeochemical cycles and Park Grass metadataProvides baseline for future targeted studies