Analysis of Rhizosphere Fungal Communities Using rRNA and rDNA

Soils and soil-borne microbial communities are probably the greatest source of organismal diversity on Earth. In this soil matrix, plant roots and the soil impacted by those roots – the rhizosphere – host a great diversity of fungi. Fungal community composition in soil and rhizosphere has been assessed by growing fungi from environmental samples in different pure culture media. These studies have provided some impressive and comprehensive volumes of fungi (Domsch et al. 1980; Rambelli et al. 1983). However, such culture-based studies may suffer from some serious limitations because many soil-borne organisms can be difficult to bring into pure culture, or because the diversity is shadowed by few fast-growing organisms that hamper detection of others. The application of molecular techniques has resulted in great improvements in our understanding of the rhizosphere fungal ecology and revolutionized the tools available for exploring environmental fungal communities (Horton and Bruns 2001). A majority of these fungal community studies use PCR-based tools that specifically target the fungal ribosomal RNA (rRNA)-encoding genes (rDNA) or the non-coding regions of the rRNA gene repeats. The rDNA is a convenient target as the fungal rDNA is arranged in tandem repeats in multiple copies that contain both coding regions for primary rRNAs and non-coding regions with various levels of sequence conservation. The rRNA genes and their spacer regions are extremely useful for detecting and identifying the fungi in complex environmental samples. However, rDNA may persist in the environmental DNA pools for organisms that maintain no metabolic activity and are not necessarily participating in the ecosystem functions at the time of assessment. This results in a fundamental difficulty of interpreting rDNA assays: the environmental DNA pools can maintain a large component of organisms that