Phylogenetic fingerprinting of microbial communities in metal polluted soils using ribosomal intergenic spacer analysis (RISA)

Abstract

Aims. The aim of this study was to demonstrate the benefits of culture-independent PCR-based fingerprinting technique called ribosomal intergenic spacer analysis (RISA) in the examination of the effects of a polycyclic aromatic hydrocarbon (pyrene) and selected toxic metal (copper) on fungal communities in soil microcosms. Methods. Shifts in soil fungal communities in response to pyrene and copper contamination were studied by ribosomal intergenic spacer analysis (RISA). Results. It was found that CoPa1 band was present at the same position in control and pyrene lanes, but it showed very weak intensity or disappeared in all Cu-added soils. This band of microbial community member susceptible to copper toxicity was identified as Cryptococcus pseudolongus. Conclusions. RISA is a useful culture-independent approach for phylogenetic fingerprinting of dynamic microbial, fungal communities in polluted soils. The members of communities responding certain way to organic and inorganic contaminants in soil can be visualised by RISA and phylogenetically identified with the perspective of their use as bioindicators of specific contaminants.

Key words: RISA, soil, copper, pyrene, fungi, communities.