Quantification of tree fine roots by real-time PCR

Abstract

AimsTree roots contribute large quantities of biomass in forests and are important drivers of different ecosystem processes. However, estimation of root biomass remains a challenge. We have developed a method to quantify fine root biomass of trees, tested on Pinus sylvestris L. and Betula sp. in soils in natural environment, by applying specific qPCR primers to soil DNA extracts.MethodsWe first validated the molecular probes in the laboratory by constructing regression equations among known root biomass in soil and the number of gene copies obtained by qPCR. Then, to test the applicability of the method in an ecosystem setting and because Pinus and Betula are important components of boreal forests after wildfire, we quantified fine root biomass from these trees in soils from forests with different degrees of tree mortality after wildfire.ResultsThe new primers specifically amplified ITS (Internal Transcribed Spacer) markers from DNA extracted from fine roots of Pinus and Betula, and regression equations allowed us to calculate root biomass in soil from the number of gene copies obtained by qPCR. Root biomass of Pinus correlated positively with fire-induced canopy mortality, confirming the adequacy of the method. The biomass of Betula roots in soil did not differ across the fire severity gradient due to an overall low and stochastic presence of birch, and did not relate to the establishment of new birch seedlings.ConclusionsThis study shows that DNA-based qPCR methods can be used for rapid, quantitative and species-specific analysis of tree root biomass in natural forest ecosystems.