Fungal, bacterial and plant dsDNA contributions to soil total DNA extracted from silty soils under different farming practices: Relationships with chloroform-labile carbon

Abstract

Twelve differently-managed silty soils from North-Western France were chosen to compare two common methods of quantifying soil microbial biomass: Chloroform fumigation and extraction-labile carbon (CL_C) and microbial double stranded DNA (dsDNA). We also determined the contributions of each of the fungal, bacterial, and plant kingdoms to the total community dsDNA using real-time Polymerase Chain Reaction with kingdom-specific ribosomal primer sets. Regardless of the method, the highest microbial biomasses were associated with long-term untilled plots. Site (locations) specificities could also be detected, especially in conventionally cultivated lands. Regardless of site, a strong linear relationship could be drawn between CL_C and dsDNA in tilled lands (r = 0.91, n = 15, P = 0.01) and in grasslands (r = 0.78, n = 21, P = 0.01). Moreover, we propose a logarithmic model describing all of our silty soils, irrespective of management. In order to explain the non-linearity (log) of this relationship, we tested the hypothesis of a weak plant dsDNA contribution in total dsDNA in comparison with the well-documented root cell contribution to CL_C quantifications. Plant dsDNA never exceeded 2.6% of total dsDNA content for all of the soils studied. Among groups examined, the bacterial dsDNA contribution to the community dsDNA pool was the most site- and/or pedoclimatic-dependent. Fungi constituted a major component of total microbial biomass in grassland or in land with permanent plant cover where their proportion reached almost 50% of total dsDNA. More precisely, fungal dsDNA concentration was highly related to tillage. Our study demonstrated the expediency of the total microbial dsDNA quantification in agricultural silty soils rather than the time-consuming quantification of CL_C. Quantifying the relative contribution of bacterial or fungal biomass in total dsDNA by real-time PCR allows to access to a new level of knowledge of the soil microbial biomass and to reveal the balances between those two kingdoms according to soils or farming practices