Assessment of rice root-associated bacteria

Despite their importance, little is known about the putative interactions between rice plants and their associated bacteria. On the basis of plant-extracted DNA, molecular tools such as bacterium-specific PCR have been employed to assess the occurrence and prevalence of rice-associated bacteria. Here, we examine the coverage and usefulness of a well-consolidated primer (799f) used in these efforts. In addition, we discuss a recent study (Hardoim PR, Andreote FD, Reinhold-Hurek B, Sessitsch A, van Overbeek LS, van Elsas JD. Rice root-associated bacteria: insights into community structures across 10 cultivars. FEMS Microbiol Ecol 2011;77:154-164) that addressed the influence of the factors plant genotype, soil type, and nutrient use efficiency on the bacterial communities at the rice roots. In particular, total bacteria, Alpha- and Betaproteobacteria, Pseudomonas, and Actinobacteria communities were targeted. In silico analyses revealed that the great majority of plant-associated bacterial taxa are covered by primer 799f. Thus, a test for bacterial detection on the basis of primer pair 799f-1492r revealed true bacterial PCR-based denaturing gradient gel electrophoresis (PCR-DGGE) profiles, avoiding contamination with plastid DNA. In agreement with data presented in Chapter 18, we observed many conspicuous bands that occurred as commonalities across 10 rice cultivars. In contrast, the prevalence of cultivar-specific bands was limited. The bacterial communities associated with the rice roots were largely influenced by rice genotype, with Oryza sativa subspecies indica tending to select similar bacterial communities, whereas subspecies japonica and aromatica selected divergent community structures. The study demonstrated the essentiality of primer 799f, used in combination with primer 1492r, for the investigation of the rice-associated bacterial community.