Detection of shifts in microbial community structure and diversity in soil caused by copper contamination using amplified ribosomal DNA restriction analysis

Abstract

Amplified ribosomal DNA restriction analysis (ARDRA) was used for assessing the effect of copper contamination on the microbial community in soil. ARDRA is a DNA fingerprinting technique based on PCR amplification of 16S ribosomal DNA using primers for conserved regions, followed by restriction enzyme digestions and agarose gel electrophoresis. This results in distinguishable fingerprints for different bacterial species. Microbial community structure in soil was investigated by studying ARDRA patterns of the whole community, and by comparing ARDRA patterns of cloned 16S RNA gene sequences from soil and isolates obtained from soil by cultivation. Distinct differences in microbial community structure and a lower diversity were found in a soil contaminated with copper compared with non-contaminated soil. Diversity of ARDRA patterns from the clones was higher than that from isolates, supporting the general idea that the culturable population represents only a part of the total (amplifiable) population in soil. To compare microbial communities from various soils a method is described for the construction of a dendrogram representing the relatedness of the populations. ARDRA appears to be suitable for analysing microbial communities in soil and gives interesting information with respect to microbial ecology.