Comparison of CE-SSCP and DGGE for monitoring a complex microbial community remediating mine drainage

Capillary electrophoresis single-strand conformation polymorphism (CE-SSCP) is a promising high-throughput tool for profiling complex bioremediation communities, but has not been well characterized with respect to other methods such as denaturing gradient gel electrophoresis (DGGE). The purpose of this study was to compare CE-SSCP with DGGE with respect to: 1) overall representation of the community in terms of the dominant species identified and corresponding Shannon diversity indices; 2) reproducibility and resolution; and 3) artifacts, using a complex sulfate-reducing community remediating mine drainage as a model system. Some of the dominant microorganisms were detected by both methods, but there were also differences in the reported community compositions, and more phylogenetic groups were detected by CE-SSCP. CE-SSCP Shannon diversity indices were slightly higher than those determined from DGGE data, and differed in terms of the time point at which the community was reported to have the highest diversity. Both methods had high reproducibility, but CE-SSCP resolution was higher in terms of the total number of peaks resolved, reduced co-migration of distinct DNA sequences, and length and legibility of the DNA sequencing data of clones used to identify peaks. Ten double bands in the same lane representing the same species were found by DGGE, whereas only one such artifact was observed by CE-SSCP. Finally, less overall sample preparation and analysis time was required for CE-SSCP than for DGGE. The results suggest that CE-SSCP offers several advantages over DGGE, especially for high-throughput monitoring.