INFLUENCE OF SOIL SAMPLE PREPARATION ON BIOINDICATORS RESPONSE TO ASSESS SOIL MICROBIAL QUALITY
Résumé
A key step in assessing microbial community in soil is sample preparation. Soil samples amounts that are needed are usually small (in the mg-level in case of molecular techniques up to few g for enzymatic analysis) and frequently stored before microbial analysis. Furthermore for several analyses, soil cannot be incorporated in the test and microbial community should be extracted from the soil in an aqueous solution. The objective of this work was thus to study the influence of soil preparation on microbial bioindicators response. For this, a set of bioindicators (biomass, biodiversity (SSCP), denitrifier abundance (quantification of napA and narG genes), carbon mineralization (Biolog), protein synthesis (3H-leucine incorporation activity) was tested to three agricultural soils.
The response of molecular bioindicators based on DNA extraction (16 S RNA for bacterial biomass assessment and napA and narG for denitrifier abundance) was reproducible (n = 3) even if the extraction was done on 0.5 g of soil only, and the microbial diversity, genes abundance and biomass obtained for separated extractions were similar. On the opposite, soil microbial extraction needed for the analysis of some bioindicators (such as Biolog) resulted in a microbial community structure significantly different from that of the corresponding soil, which has to be taken into account during results analysis since the extraction modify the environmental variable effect reported on the community structure and gene abundance. This work thus underlined the great importance of considering the soil sample preparation methods when interpreting bioindicators outcomes.