Microbial community analysis of 12 PCB contaminated field plots using 16S ribosomal DNAs

An understanding of the complete microbial community structure in PCB contaminated soils is essential for effective bioremediation. Two molecular methods: ARDRA (Amplified Ribosomal DNA Restriction Analysis) and T-RFLP (Terminally Labeled Restriction Fragment Length Polymorphism) were adopted to study this issue in 12 randomized experimental field plots including three controls. The working hypothesis of this study has been that molecular screening of the 16S rDNAs from total soil DNAs can be used to characterize community structures, using rDNA sequence and rDNA restriction fragment size analysis. Several significant observations were made such as (1) characterization of soils and dechlorination analysis show that PCB congeners having least chlorine are comparatively easier to dechlorinate. Plants significantly enhance more microbial population. (2) Eight operational taxonomic units (OTUs, A-H) were found from all 12 soil plots. The most prevalent was OTU-B identifying Rhodanohacter sp, Saccharothrix sp. and OTU-D identifying Bacillus. The Phylogenic studies of other OTUs identified mostly uncultured species. (3) When T-RFLP method was used, different rDNA fragment sizes identified four bacterial species namely, Mycoplasma sp., Bacillus sp., Leuconostoc pseudomesenteroides RO1., Uncultured--Pseudomonas., and several uncultivable species such as Clostridia sp. The T-RFLP method was much more powerful, effective and resulted in identifying more species from one plot compared to what could be obtained from all 12 plots using the ARDRA method. It was confirmed that several enzymes were needed to identify complete microbial community structure of field plots. (4) Tests for comparative capability of dechlorination by indigenous mixed vs. single cultures showed that the former was more effective for dechlorination. The abundance of uncultivable bacterial species by both molecular methods suggests that they have role in dechlorination of PCBs and have the capability to survive in the contaminated environment.