Molecular Analyses of Soil Fungal Community – Methods and Applications

Fungi play important and diverse roles in soil ecosystems. They act as plant pathogens, mycorrhizal symbionts and most importantly, as the principal decomposers of organic materials (Christensen, 1989; Thorn, 1997). Fungi also represent a dominant component of the soil microflora in terms of biomass (Thorn, 1997). Compared with bacterial communities, however, knowledge regarding the diversity and functions of soil fungal communities remains limited. Culture-independent molecular techniques, comprising of direct DNA extraction from soil followed by PCR and electrophoresis or cloning, have been introduced to investigate soil fungal communities (Anderson & Cairney, 2004). These techniques facilitate the detection of fungi, including fastidious or non-culturable strains, and an understanding of the fungal community structures and dynamics in soil (Hoshino & Matsumoto, 2007; Vandenkoornhuyse et al., 2002). Molecular techniques have provided novel insights and significant advances in research on soil fungal ecology and have been applied to various soils in different ecosystems, such as forests (Perkiomaki et al., 2003), grasslands (Brodie et al., 2003), dunes (Kowalchuk et al., 1997), stream sediments (Nikolcheva et al., 2003) and agricultural fields (Gomes et al., 2003). For example, in agricultural soils, a fungal community is affected by plant growth (Gomes et al., 2003) and cultural practices, such as application of fertilizers and pesticides (Girvan et al., 2004). With the development of new technologies, accumulating molecular data has contributed to the establishment of database combined with other environmental data and facilitated metaanalysis on a large scale. In agricultural soils, fungal communities are directly and indirectly related to crop production. Technological advances in molecular methods would help elucidate such a complicated relationship. Here I present molecular techniques applied to soil fungal community analyses, particularly in agricultural soils and discuss their limitations and future applications.