Metaproteomics of soils from semiarid environment: functional and phylogenetic information obtained with different protein extraction methods

Abstract

Microbial populations fulfil a critical role in the soil sustainability and their functionality can be ascertained by proteomics based on high-performance mass spectrometry (MS) measurements. However, soil proteomics is compromised by methodological issues, among which extraction is a limiting factor, and still has not been adequately applied in semiarid soils, which usually are nutrient limited. We aim to evaluate the functional and phylogenetic information retrieved from three semiarid soils with distinct edaphic properties and degradation levels. Three extraction methods with different physico-chemical bases were tested [1-3]. The HPLC-amino acid quantification of the extracted protein pellets revealed a tremendous inefficiency of the extraction methods, with a maximally 6.8% of the proteinaceous material being extracted in comparison with the protein content in the bulk soil. The composition of the proteomes extracted was analysed after SDS-PAGE and liquid chromatography coupled with electrospray-MS/MS. Chourey's method, based on boiling and DTT, yielded a high diversity of bacterial proteins and revealed differences in the community composition at the phylum level among the three soils. The overall metabolic information obtained by both extraction methods was similar, but Chourey's method provided additionally valuable bio-geochemical insights which suggest an ecological adaptation of microbial communities from semiarid soils for carbon and nitrogen fixation.

Biological significance: Microbial communities inhabiting the soil perform critical reactions for the sustainability of the planet. At biochemical level, soil proteomics is starting to provide incipient insights into the microbial functionality of soils. However, methodological comparisons are needed to assess which methods are more suitable. Precisely, such information under arid and semiarid environments is missing. By using amino acid quantification of extracted proteomes and LC-MS/MS based proteomics, we provide a novel methodological evaluation of the functional, phylogenetic and bio-geochemical information obtained by three extraction methods in semiarid soils with distinct edaphic properties.

Keywords: Carbon cycling; Degradation; Metaproteomics; Microbial community; Organic matter; Semiarid soil.