Identification of roots from grass swards using PCR-RFLP and FFLP of the plastid trnL (UAA) intron

BACKGROUND: The specific associations between plant roots and the soil microbial community are key to understanding nutrient cycling in grasslands, but grass roots can be difficult to identify using morphology alone. A molecular technique to identify plant species from root DNA would greatly facilitate investigations of the root rhizosphere. RESULTS: We show that trnL PCR product length heterogeneity and a maximum of two restriction digests can separate 14 common grassland species. The RFLP key was used to identify root fragments at least to genus level in a field study of upland grassland community diversity. Roots which could not be matched to known types were putatively identified by comparison of the nuclear ribosomal ITS sequence to the GenBank database. Ten taxa were identified among almost 600 root fragments. Additionally, we have employed capillary electrophoresis of fluorescent trnL PCR products (fluorescent fragment length polymorphism, FFLP) to discriminate all taxa identified at the field site. CONCLUSION: We have developed a molecular database for the identification of some common grassland species based on PCR-RFLP of the plastid transfer RNA leucine (trnL) UAA gene intron. This technique will allow fine-scale studies of the rhizosphere, where root identification by morphology is unrealistic and high throughput is desirable.