Belowground DNA-based techniques: untangling the network of plant root interactions

Abstract

Plant roots are a central driver of ecosystem productivity, as plant investments belowground often comprise more than half of total plant biomass (Jackson et al. 1996). Despite this general observation, almost nothing is known about the distribution of roots in ecosystems; generally because roots of different species are morphologically indistinguishable, restricting species identification. This is in strict contrast to plant identification aboveground, which is straightforward after initial taxonomic training. Although in species poor systems containing roots of two species morphological identification has been possible in a few cases (Genney et al. 2002; Janecek et al. 2004; Mommer et al. 2011), disentangling and identifying roots from species-rich systems is impossible. To overcome problems of species identification, pioneering DNA-based techniques have been applied to plant roots (Jackson et al. 1999; Linder et al. 2000) and are now being used in experimental and observational studies of species-rich plant communities (e.g. Mommer et al. 2010; Kesanakurti et al. 2011; Dumbrell et al. 2011). In this paper, we discuss the current state of molecular techniques for plant species identification and quantification from mixed root samples. We focus on crucial aspects in the methodology regarding primer choice, DNA extraction and PCR inhibition, showing the potential caveats and their solutions. Finally we briefly discuss a few questions in the field of root ecology that will be advanced significantly by the appropriate use of these molecular tools.