REGULAR ARTICLE Field application of a DNA-based assay to the measurement of roots of perennial grasses Rebecca E. Haling & Richard J. Simpson & Richard A. Culvenor & Hans Lambers & Alan E. Richardson Received: 14 March 2012 / Accepted: 30 July 2012 / Published online: 19 August 2012 # Springer Science+Business Media B.V. 2012 Abstract Background and aims DNA-based methods present new opportunities for overcoming the difficulties of accurately identifying and quantifying roots of differ- ent plant species in field soils. In order to quantify species-specific root biomass from measurements of DNA, consideration needs to be given to replication and ability to recover roots for calibration purposes in order to account for spatial, temporal and inter- and intra-species variation in DNA content of roots and distribution of roots within the soil profile. Methods This paper develops the field application of a DNA-based technique for direct quantification of roots in soils. The method was applied to a field experiment to investigate differences in root growth of acid-soil resistant and sensitive genotypes of peren- nial pasture grasses in an acid soil. DNA was extracted directly from soil and species-specific DNA was quan- tified using quantitative real-time PCR prior to esti- mation of root biomass. Results Root growth of the perennial grasses was quantified using the DNA-based technique, although separate calibration procedures were needed to convert DNA content to root mass for each species, soil layer and sampling date. Compared to acid-soil resistant genotypes, lesser root growth in acid soil layers and reduced above-ground dry matter production was ob- served for acid-soil sensitive genotypes. Conclusions The DNA-based method allowed geno- typic differences in root growth to be assessed directly in soil and was advantageous for rapid processing of a large number of samples. However, high replication was still required to overcome spatial variability and separate calibrations were required for different species and soil depths across sampling times. The technique demon- strated greater root growth of acid-soil resistant peren- nial grasses which was beneficial for their establishment and persistence. Keywords Soil acidity . Aluminium toxicity . Acid tolerance . Tall wheatgrass . Weeping grass . Phalaris aquatica . Thinopyrum ponticum . Microlaena stipoides . Grasslands . Below ground species abundance . Taqman® . ITS region . qPCR Plant Soil (2012) 358:183–199 DOI 10.1007/s11104-012-1405-2 Responsible Editor: Peter J. Gregory. R. E. Haling : R. J. Simpson : R. A. Culvenor : A. E. Richardson (*) CSIRO Sustainable Agriculture National Research Flagship/CSIRO Plant Industry, GPO Box 1600, Canberra ACT 2601, Australia e-mail: alan.richardson@csiro.au R. E. Haling : R. J. Simpson : H. Lambers : A. E. Richardson School of Plant Biology and Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Australia Present Address: R. E. Haling School of Environmental and Rural Science, University of New England, Armidale NSW 2351, Australia