The extracellular metaproteome of soils under semiarid climate: A methodological comparison of extraction buffers

We compare the protein extraction efficiencies, as well as the phylogenetic and functional information provided, of two extraction protocols in soils that differ mainly in their organic matter and clay contents, the main factors limiting protein extraction in semiarid soils. These protocols utilise extractants commonly used for the assay of extracellular enzyme activities. The first method was based on the utilisation of the modified universal buffer (MUB). The second was based on the extraction of humic substances with sodium pyrophosphate. When compared to the total amount of proteins in soil, the results indicate a very-low extraction efficiency for both protocols. Analysis in an Orbitrap Fusion mass spectrometer and further searching against an "ad hoc" metagenome evidenced that the phylogenetic and functional information retrieved from the extracellular soil metaproteome can be biased by the extraction buffer.