Extraction of microbial proteome from soil: potential and limitations assessed through a model study

Proteomics is the study of functions and regulation of biological systems based on the analysis of the
protein expression profile, and there is a general agreement that soil proteomics may be a tool for better
soil management. Because of the ability of soils to stabilize extracellular proteins by various mechanisms,
development of soil proteomics needs an assessment of the efficiency of protein extraction from various
soil types. We evaluated the possibility of extraction of soil microbial proteome by inoculating Cupriavidus
metallidurans CH34, which has a known proteome, into sterile sand, kaolinite, montmorillonite and a mixture
of sand, kaolinite, montmorillonite, goethite and humic acids. One hour after inoculation, the viability of
C. metallidurans was determined by the colony-forming units method (CFU), the amount of extracted proteins
was determined by the Bradford method and the bacterial proteome was analysed by the two-dimensional gel
electrophoresis technique (2D-GE). The bacterial number was 2.5 × 106 CFU g−1 of soil in all microcosms,
whereas the total extracted protein content varied from 98.1 to 1268 μg g−1 in the various microcosms, but
was undetectable in the inoculated montmorillonite. The number of protein spots from the bacterial culture
and the inoculated microcosms varied between 317 and 591, with 54 variable spots among the pure culture
and the microcosms. No protein spots were detected in the 2D-GE from the montmorillonite microcosm. The
2D-GE of artificial soil microcosms showed a protein pattern that was different from those of pure culture
and sand and kaolinite microcosms. The results confirm the importance of clay-specific surface area and CEC
in protein adsorption as montmorillonite alone had the largest sorptive capacity, and show that the artificial
soil used also had a large sorptive capacity for microbial proteins. Globally, the results indicate that the
extraction of proteins from soils is strongly influenced by the clay type and organic matter content, and that
poor protein extraction efficiency may reduce the potential of soil proteomics